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Chapter 11. Community analysis-based methods  

Energy Technology Data Exchange (ETDEWEB)

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.

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

2010-05-01

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Microbial Community Analysis Using MEGAN.  

UK PubMed Central (United Kingdom)

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.

Huson DH; Weber N

2013-01-01

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Community detection algorithms: a comparative analysis  

CERN Document Server

Uncovering the community structure exhibited by real networks is a crucial step towards an understanding of complex systems that goes beyond the local organization of their constituents. Many algorithms have been proposed so far, but none of them has been subjected to strict tests to evaluate their performance. Most of the sporadic tests performed so far involved small networks with known community structure and/or artificial graphs with a simplified structure, which is very uncommon in real systems. Here we test several methods against a recently introduced class of benchmark graphs, with heterogeneous distributions of degree and community size. The methods are also tested against the benchmark by Girvan and Newman and on random graphs. As a result of our analysis, three recent algorithms introduced by Rosvall and Bergstrom, Blondel et al. and Ronhovde and Nussinov, respectively, have an excellent performance, with the additional advantage of low computational complexity, which enables one to analyze large s...

Lancichinetti, Andrea

2009-01-01

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Metaproteomic analysis of Chesapeake Bay microbial communities  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Natural microbial communities are extremely complex and dynamic systems in terms of their population structure and functions. However, little is known about the in situ functions of the microbial communities. Results This study describes the application of proteomic approaches (metaproteomics) to observe expressed protein profiles of natural microbial communities (metaproteomes). The technique was validated using a constructed community and subsequently used to analyze Chesapeake Bay microbial community (0.2 to 3.0 ?m) metaproteomes. Chesapeake Bay metaproteomes contained proteins from pI 4–8 with apparent molecular masses between 10–80 kDa. Replicated middle Bay metaproteomes shared ~92% of all detected spots, but only shared 30% and 70% of common protein spots with upper and lower Bay metaproteomes. MALDI-TOF analysis of highly expressed proteins produced no significant matches to known proteins. Three Chesapeake Bay proteins were tentatively identified by LC-MS/MS sequencing coupled with MS-BLAST searching. The proteins identified were of marine microbial origin and correlated with abundant Chesapeake Bay microbial lineages, Bacteroides and ?-proteobacteria. Conclusion Our results represent the first metaproteomic study of aquatic microbial assemblages and demonstrate the potential of metaproteomic approaches to link metagenomic data, taxonomic diversity, functional diversity and biological processes in natural environments.

Kan Jinjun; Hanson Thomas E; Ginter Joy M; Wang Kui; Chen Feng

2005-01-01

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Enhancing Sentiment Analysis on Twitter Using Community Detection  

Directory of Open Access Journals (Sweden)

Full Text Available The increasing popularity of social media in recent years has created new opportunities to study the interactions of different groups of people. Never before have so many data about such a large number of individuals been readily available for analysis. Two popular topics in the study of social networks are community detection and sentiment analysis. Community detection seeks to find groups of associated individuals within networks, and sentiment analysis attempts to determine how individuals are feeling. While these are generally treated as separate issues, this study takes an integrative approach and uses community detection output to enable community-level sentiment analysis. Community detection is performed using the Walktrap algorithm on a network of Twitter users associated with Microsoft Corporation’s @technet account. This Twitter account is one of several used by Microsoft Corporation primarily for communicating with information technology professionals. Once community detection is finished, sentiment in the tweets produced by each of the communities detected in this network is analyzed based on word sentiment scores from the well-known SentiWordNet lexicon. The combination of sentiment analysis with community detection permits multilevel exploration of sentiment information within the @technet network, and demonstrates the power of combining these two techniques.

William Deitrick; Benjamin Valyou; Wes Jones; Joshua Timian; Wei Hu

2013-01-01

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Vulnerability metrics and analysis for communities in complex networks  

International Nuclear Information System (INIS)

This paper applies the problem of community detection in complex networks to identify sets of network elements that are critical to the connectivity of the network and its communities. Specifically, the paper defines a vulnerability set and value for each of the communities in a complex network. Also, for each community it identifies a value of relative vulnerability in comparison with the remaining communities. The approach allows to visualize/identify the critical elements of a complex network. This is an important first step for many recent problems arising in social networks, critical infrastructures and homeland security. By identifying these elements one can prioritize resource allocation to protect, interdict or improve performance in these types of systems. The sets and metrics introduced are illustrated with numerous examples and discussions. Based on the analysis of the examples the manuscript provides an intuitive description of a community's presence in the interior or periphery of a network.

2011-01-01

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Density Analysis of Network Community Divisions  

CERN Multimedia

We present a compact matrix formulation of the modularity, a commonly used quality measure for the community division in a network. Using this formulation we calculate the density of modularities, a statistical measure of the probability of finding a particular modularity for a random but valid community division into $C$ communities. We present our results for some well--known and some artificial networks, and we conclude that the general features of the modularity density are quite similar for the different networks. From a simple model of the modularity we conclude that all nnected networks must show similar shapes of their modularity densities. The general features of this density may give valuable information in the search for good optimization schemes of the modularity.

Holmström, E; Brännlund, J; Holmstr\\"om, Erik; Bock, Nicolas; Br\\"{a}nnlund, Johan

2006-01-01

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Metagenomic analysis of soil microbial communities  

Directory of Open Access Journals (Sweden)

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. .

?oki? Lidija; Savi? M.; Naran?i? Tanja; Vasiljevi? Branka

2010-01-01

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Community flux balance analysis for microbial consortia at balanced growth.  

UK PubMed Central (United Kingdom)

A central focus in studies of microbial communities is the elucidation of the relationships between genotype, phenotype, and dynamic community structure. Here, we present a new computational method called community flux balance analysis (cFBA) to study the metabolic behavior of microbial communities. cFBA integrates the comprehensive metabolic capacities of individual microorganisms in terms of (genome-scale) stoichiometric models of metabolism, and the metabolic interactions between species in the community and abiotic processes. In addition, cFBA considers constraints deriving from reaction stoichiometry, reaction thermodynamics, and the ecosystem. cFBA predicts for communities at balanced growth the maximal community growth rate, the required rates of metabolic reactions within and between microbes and the relative species abundances. In order to predict species abundances and metabolic activities at the optimal community growth rate, a nonlinear optimization problem needs to be solved. We outline the methodology of cFBA and illustrate the approach with two examples of microbial communities. These examples illustrate two useful applications of cFBA. Firstly, cFBA can be used to study how specific biochemical limitations in reaction capacities cause different types of metabolic limitations that microbial consortia can encounter. In silico variations of those maximal capacities allow for a global view of the consortium responses to various metabolic and environmental constraints. Secondly, cFBA is very useful for comparing the performance of different metabolic cross-feeding strategies to either find one that agrees with experimental data or one that is most efficient for the community of microorganisms.

Khandelwal RA; Olivier BG; Röling WF; Teusink B; Bruggeman FJ

2013-01-01

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Analysis of medications returned to community pharmacies.  

UK PubMed Central (United Kingdom)

BACKGROUND: There are many causes of medication waste, including excess supply, treatment changes, and patient nonadherence to therapy. Investigating medication returns may indicate areas for targeting interventions to reduce waste. OBJECTIVE: To identify and quantify the types and amounts of medications returned to community pharmacies and, specifically, to quantify the percentage of medication returned from the original dispensing, its therapeutic category, and reasons for not being used. METHODS: Unsolicited medication returned for disposal to the 24 community pharmacies in the Taranaki region (approximately 37,000 households) of New Zealand over a 6-week period was analyzed. The results were entered into a database, recording medication, amount originally issued (if known), date of issue, Anatomical Therapeutic Chemical (ATC) classification, and reason for nonuse. Cross-tabulation of ATC category versus percentage returned as well as ATC category versus reason for returns was performed. Adjusted standardized residuals were investigated to determine specific cells that were in excess of the expected counts. RESULTS: Complete information was available for 2704 items. The majority (51%) of returns contained 75-100% of the original dispensed amount of medication. For the respiratory category, 77% of the returns were in the 75-100% group, significantly more than for any other therapeutic group. Reasons for returns were recorded as bereavement (22%), surplus to requirements (17%), expired (8%), medication change (11%), dose change (3%), and unknown (39%). The cardiovascular group and respiratory groups had a higher rate of returned drugs due to medication changes and surplus to requirements, respectively. CONCLUSIONS: The majority of returned medications contained greater than 75% of the original amount issued. Identification of therapeutic groups having higher rates of returns due to medication changes or surplus to requirements may suggest areas to target to reduce medication waste.

James TH; Helms ML; Braund R

2009-10-01

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ASAP, a systematic annotation package for community analysis of genomes  

Digital Repository Infrastructure Vision for European Research (DRIVER)

ASAP (a systematic annotation package for community analysis of genomes) is a relational database and web interface developed to store, update and distribute genome sequence data and functional characterization (https://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm). ASAP facilitates ongoing communit...

Glasner, Jeremy D.; Liss, Paul; Plunkett, Guy; Darling, Aaron; Prasad, Tejasvini; Rusch, Michael; Byrnes, Alexis

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[Analysis of parasitic communities in fishes from Lake Baikal].  

Science.gov (United States)

Analysis of infracommunities and component communities of fish parasites in Lake Baikal has been conducted for the first time. It has been revealed that parasite infracommunities for the majority of Baikal fishes are weakly balanced and impoverished (the Berger-Parker Index is > 0.5; Evension is Esox lucius, and Percafluviatilis). The component parasitic communities of Leuciscus leuciscus baicalensis, Rutilus rutilus, and Leocottus kesslerii are the most diverse in Lake Baikal since the Shennon index for L. leuciscus baicalensis, R. rutilus, and L. kesslerii is 2.4, for Paracotlus knerii--2.2, Limnocoitus godlewskii--2.3, Phoxinus phoxinus--2.1, Lota lota and Limnocuttus pallidus--1.9, P. fluviatilis--1.8, Leuciscus idus--1.8. The component parasitic communities of other fishes in Lake Baikal have low indices of biological diversity (H = 0.5-1.05, Smp is close to 1). A classification of mature and immature components of parasitic communities based on the ratio of specialist species and generalist species has been proposed. It is established that the component parasitic communities in sublitoral, profundal, and pseudoabyssal zones are mature, while in the littoral zone they are immature (impoverished and weakly balanced). The component parasitic communities in benthophagous fishes and predators are mature, in planktivorous fishes they are immature. The component parasitic communities are mature in the family Cyprinidae and immature in the families Coregonidae and Cottidae. The component parasitic communities of the Boreal Plain and Boreal Submountain faunal complexes are mature, but they are immature in Lake Baikal and Arctic freshwater complexes. PMID:16755724

Rusinek, O T

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SmashCommunity: A metagenomic annotation and analysis tool.  

DEFF Research Database (Denmark)

SUMMARY: SmashCommunity is a stand-alone metagenomic annotation and analysis pipeline suitable for data from Sanger and 454 sequencing technologies. It supports state-of-the-art software for essential metagenomic tasks such as assembly and gene prediction. It provides tools to estimate 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.

Arumugam, Manimozhiyan; Harrington, Eoghan D

2010-01-01

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SmashCommunity: a metagenomic annotation and analysis tool.  

UK PubMed Central (United Kingdom)

SUMMARY: SmashCommunity is a stand-alone metagenomic annotation and analysis pipeline suitable for data from Sanger and 454 sequencing technologies. It supports state-of-the-art software for essential metagenomic tasks such as assembly and gene prediction. It provides tools to estimate 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 source code and documentation are available at http://www.bork.embl.de/software/smash CONTACT: bork@embl.de SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Arumugam M; Harrington ED; Foerstner KU; Raes J; Bork P

2010-12-01

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Metaproteogenomic analysis of a community of sponge symbionts.  

UK PubMed Central (United Kingdom)

Sponges harbour complex communities of diverse microorganisms, which have been postulated to form intimate symbiotic relationships with their host. Here we unravel some of these interactions by characterising the functional features of the microbial community of the sponge Cymbastela concentrica through a combined metagenomic and metaproteomic approach. We discover the expression of specific transport functions for typical sponge metabolites (for example, halogenated aromatics, dipeptides), which indicates metabolic interactions between the community and the host. We also uncover the simultaneous performance of aerobic nitrification and anaerobic denitrification, which would aid to remove ammonium secreted by the sponge. Our analysis also highlights the requirement for the microbial community to respond to variable environmental conditions and hence express an array of stress protection proteins. Molecular interactions between symbionts and their host might also be mediated by a set of expressed eukaryotic-like proteins and cell-cell mediators. Finally, some sponge-associated bacteria (for example, a Phyllobacteriaceae phylotype) appear to undergo an evolutionary adaptation process to the sponge environment as evidenced by active mobile genetic elements. Our data clearly show that a combined metaproteogenomic approach can provide novel information on the activities, physiology and interactions of sponge-associated microbial communities.

Liu M; Fan L; Zhong L; Kjelleberg S; Thomas T

2012-08-01

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Molecular analysis of lichen-associated bacterial communities.  

UK PubMed Central (United Kingdom)

The bacterial communities associated with 11 different lichen samples (belonging to eight different species) from different habitats were investigated. The culturable aerobic-heterotrophic fraction of the bacterial communities was isolated from nine lichen samples on protein-rich and sugar-rich/N-free media. Thirty-four bacterial isolates were purified and pooled into groups (phylotypes) by analysis of the ribosomal internal transcribed spacer polymorphism. Twenty five phylotypes were identified, each comprising between one and three isolates. One isolate of each phylotype was partially sequenced and the resulting 16S rRNA gene sequences were compared in a phylogenetic analysis. Three genera of Firmicutes, four of Actinobacteria and three of Proteobacteria were identified. Two phylotypes, belonging to the phyla Actinobacteria and Proteobacteria, respectively, were not identified at genus level. Some bacterial taxa were retrieved frequently in different lichen species sampled in the same or different sites. Paenibacillus and Burkholderia phylotypes seem to be common in lichens. Luteibactor rhizovicina was found in three different lichens of two different regions. In a cultivation-independent approach, total DNA was extracted from 11 lichen samples. Molecular fingerprints of the bacterial communities were obtained by PCR-amplification of the internal transcribed spacer region, and sequencing of selected bands indicated the presence of additional bacteria.

Cardinale M; Puglia AM; Grube M

2006-09-01

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A Large-Scale Community Structure Analysis In Facebook  

CERN Multimedia

In this work we present a large-scale community structure detection and analysis applied to the largest Online Social Network actually existing, namely Facebook. This network gathers more than 500 millions users at 2011. The structure and the characteristics of this social network have been widely investigated during the last years. Although some related work focuses on analyzing clustering phenomena on a small scale, this is the first large-scale study which considers a significant sample of the network. The process of data mining from the social network platform is here described, in order to clarify how the required information has been acquired avoiding privacy related issues. Data have been collected adopting two different techniques of graph mining, and are here discussed accordingly to the structural properties of these samples which have been already investigated in previous works. To the purpose of discovering the community structure of the considered samples, we devised and described two efficient c...

Ferrara, Emilio

2012-01-01

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Analysis of community structure in networks of correlated data  

Energy Technology Data Exchange (ETDEWEB)

We present a reformulation of modularity that allows the analysis of the community structure in networks of correlated data. The new modularity preserves the probabilistic semantics of the original definition even when the network is directed, weighted, signed, and has self-loops. This is the most general condition one can find in the study of any network, in particular those defined from correlated data. We apply our results to a real network of correlated data between stores in the city of Lyon (France).

Gomez, S.; Jensen, P.; Arenas, A.

2008-12-25

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Teoria humanística: análise semântica do conceito de community Teoría humanística: análisis semántico del concepto de community Humanistic theory: semantic analysis of the community concept  

Directory of Open Access Journals (Sweden)

Full Text Available A teoria Humanística de Enfermagem apresenta a palavra community que pode ser interpretada como comunidade e comunhão. Este estudo objetivou refletir criticamente acerca da clareza semântica do conceito de community. Pesquisa bibliográfica realizada em dicionários, na literatura de lingüística, fenomenologia com a utilização do modelo de análise de teorias de Meleis. Após leitura compreensiva da Teoria Humanística recortamos trechos onde aparece a palavra community a qual foi substituída por comunhão e comunidade. Inferimos que community é usada de forma indistinta pelas autoras podendo significar comunidade e comunhão. Concluímos que embora as teóricas utilizem o termo comunidade para designar fenômenos que estariam mais bem representados pelo termo comunhão, este pode ser apreendido em sua plenitude como a perfeita união das palavras princípio EU-TU originando o NÓS.La teoría Humanística de Enfermería presenta la palabra community, que se puede interpretar como comunidad y comunión. Reflexionar de forma crítica sobre la exactitud semántica del concepto community fue el objetivo del estudio. Se realizó una investigación bibliográfica en diccionarios, en la literatura lingüística, en fenomenología, utilizando el modelo de análisis de teorías de Meleis. Tras una lectura comprensiva de la Teoría Humanística se recortaron fragmentos donde la palabra community se había sustituido por comunión y comunidad. Se infiere que community está utilizada de modo indistinto por las autoras, y así, puede significar tanto comunidad como comunión. Se concluye que, aunque las teóricas usen el término comunidad para designar fenómenos que estarían mejor representados por el término comunión, éste se puede tomar en su plenitud, como la perfecta unión de las palabras YO-TÚ que originan al NOSOTROS.The humanistic theory in Nursing introduces the word community, which can be understood as community and communion. The aim of this study is to critically analyze the true semantic meaning of community. This study was conducted through bibliographic research in dictionaries, Linguistics literature and Phenomenology by using Meleis' model of theory analysis. After carefully reading about Humanistic Theory, we have clipped some passages where communion and community replaced the word community. We then inferred that community is indistinctly used by authors and can be understood as community and communion, and we reached the conclusion that although theorists commonly use the term `community' to refer to phenomena which would be better characterized by the term `communion', `community' can be totally comprehended as a perfect union between the beginning-words ME-YOU giving rise to US.

Lorita Marlena Freitag Pagliuca; Antônia do Carmo Soares Campos Campos

2003-01-01

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Metaproteome analysis of the microbial communities in agricultural biogas plants.  

UK PubMed Central (United Kingdom)

In biogas plants agricultural waste and energy crops are converted by complex microbial communities to methane for the production of renewable energy. In Germany, this process is widely applied namely in context of agricultural production systems. However, process disturbances, are one of the major causes for economic losses. In addition, the conversion of biomass, in particular of cellulose, is in most cases incomplete and, hence, insufficient. Besides technical aspects, a more profound characterization concerning the functionality of the microbial communities involved would strongly support the improvement of yield and stability in biogas production. To monitor these communities on the functional level, metaproteome analysis was applied in this study to full-scale agricultural biogas plants. Proteins were extracted directly from sludge for separation by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and subsequent identification with mass spectrometry. Protein profiles obtained with SDS-PAGE were specific for different biogas plants and often stable for several months. Differences of protein profiles were visualized by clustering, which allowed not only the discrimination between mesophilic and thermophilic operated biogas plants but also the detection of process disturbances such as acidification. In particular, acidification of a biogas plant was detected in advance by disappearance of major bands in SDS-PAGE. Identification of proteins from SDS-PAGE gels revealed that methyl CoM reductase, which is responsible for the release of methane during methanogenesis, from the order Methanosarcinales was significantly decreased. Hence, it is assumed that this enzyme might be a promising candidate to serve as a predictive biomarker for acidification.

Heyer R; Kohrs F; Benndorf D; Rapp E; Kausmann R; Heiermann M; Klocke M; Reichl U

2013-09-01

 
 
 
 
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Metaproteome analysis of the microbial communities in agricultural biogas plants.  

Science.gov (United States)

In biogas plants agricultural waste and energy crops are converted by complex microbial communities to methane for the production of renewable energy. In Germany, this process is widely applied namely in context of agricultural production systems. However, process disturbances, are one of the major causes for economic losses. In addition, the conversion of biomass, in particular of cellulose, is in most cases incomplete and, hence, insufficient. Besides technical aspects, a more profound characterization concerning the functionality of the microbial communities involved would strongly support the improvement of yield and stability in biogas production. To monitor these communities on the functional level, metaproteome analysis was applied in this study to full-scale agricultural biogas plants. Proteins were extracted directly from sludge for separation by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and subsequent identification with mass spectrometry. Protein profiles obtained with SDS-PAGE were specific for different biogas plants and often stable for several months. Differences of protein profiles were visualized by clustering, which allowed not only the discrimination between mesophilic and thermophilic operated biogas plants but also the detection of process disturbances such as acidification. In particular, acidification of a biogas plant was detected in advance by disappearance of major bands in SDS-PAGE. Identification of proteins from SDS-PAGE gels revealed that methyl CoM reductase, which is responsible for the release of methane during methanogenesis, from the order Methanosarcinales was significantly decreased. Hence, it is assumed that this enzyme might be a promising candidate to serve as a predictive biomarker for acidification. PMID:23369865

Heyer, R; Kohrs, F; Benndorf, D; Rapp, E; Kausmann, R; Heiermann, M; Klocke, M; Reichl, U

2013-01-29

22

A Collaboration and Productiveness Analysis of the BPM Community  

Science.gov (United States)

The main scientific event for academics working in the field of Business Process Management is the International BPM Conference. In this paper, social network analysis techniques are used to unveil the co-authorship networks that can be derived from the papers presented at this conference. Links between two researchers are established by their co-authorship of a paper at one of the conference editions throughout the years 2003-2008. Beyond the relations between individual authors, aggregated analyses are presented of the interactions between the institutes that the authors are affiliated with as well as their country of residence. Additionally, the output of individual authors is measured. All analyses are carried out for the individual conference years and at cumulative levels. In this way, this paper identifies the hotbeds of BPM research and maps the progressive collaboration patterns within the BPM community.

Reijers, Hajo A.; Song, Minseok; Romero, Heidi; Dayal, Umeshwar; Eder, Johann; Koehler, Jana

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GeoChips for Analysis of Microbial Functional Communities  

Energy Technology Data Exchange (ETDEWEB)

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).

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

2008-09-30

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Analysis of the potential for community forestry in New Brunswick  

Energy Technology Data Exchange (ETDEWEB)

Community forestry is a form of forest practice and administration in which all forest management occurs within the bounds of sustainable forestry, the community is empowered to make major land use decisions collectively, and some form of community economic development occurs as a result. This thesis reviews the concept of community forestry as reflected in the literature and in practice across Canada. It then describes the methodology and results obtained in an evaluation of case studies of two existing community forest initiatives in New Brunswick, the Irishtown Reservoir Forest and the Eel Ground Forest. These initiatives are evaluated in terms of community empowerment, sustainable forestry, and community economic development. The thesis concludes with an assessment of the potential for community forestry in New Brunswick.

Betts, M.

1995-12-31

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Community  

Directory of Open Access Journals (Sweden)

Full Text Available The term community in the English language can be traced back to the 14th century and originates from the French word comuneté and the Latin word communitatem. In English the term initially came to denote five distinct senses. Community served as a distinction of the common people from those of rank (1), as a denotation of a state or organized society (2), the people of a district (3), as a designation for the community of shared interests (4) and as a sense of common identity and characteristics (5). In these early meanings of the term it is important to note the distinction between the designation of actual social groups on the one hand and the indication of a particular relational quality on the other.

Sichling, Florian

2008-01-01

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A meta-analysis of changes in bacterial and archaeal communities with time  

Science.gov (United States)

Ecologists have long studied the temporal dynamics of plant and animal communities with much less attention paid to the temporal dynamics exhibited by microbial communities. As a result, we do not know if overarching temporal trends exist for microbial communities or if changes in microbial communities are generally predictable with time. Using microbial time series assessed via high-throughput sequencing, we conducted a meta-analysis of temporal dynamics in microbial communities, including 76 sites representing air, aquatic, soil, brewery wastewater treatment, human- and plant-associated microbial biomes. We found that temporal variability in both within- and between-community diversity was consistent among microbial communities from similar environments. Community structure changed systematically with time in less than half of the cases, and the highest rates of change were observed within ranges of 1 day to 1 month for all communities examined. Microbial communities exhibited species–time relationships (STRs), which describe the accumulation of new taxa to a community, similar to those observed previously for plant and animal communities, suggesting that STRs are remarkably consistent across a broad range of taxa. These results highlight that a continued integration of microbial ecology into the broader field of ecology will provide new insight into the temporal patterns of microbial and ‘macro'-bial communities alike.

Shade, Ashley; Gregory Caporaso, J; Handelsman, Jo; Knight, Rob; Fierer, Noah

2013-01-01

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Analysis on Influencing Factors of Community Safety Culture Based on the Structural Equation Model  

Directory of Open Access Journals (Sweden)

Full Text Available The purpose of this study is to research community safety culture building train of thought through the analysis of the influence factors of community safety culture, This study employs a Likert scale method for the design of questionnaire, investigate community through questionnaire, obtain the relevant data, and by use of the structural equation model (SEM) of statistics, puts forward that the factors including economy, society, education, since and technology, and management form important influence factors on community safety culture. Thus we should take comprehensive measures from the above aspects in the community safety culture construction.

Zhixin LI; Jingzhen XU; Lihua ZHANG

2013-01-01

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An Analysis of Health Care Assessments Used for Sustaining Communities  

Directory of Open Access Journals (Sweden)

Full Text Available This research addresses the needs for creating realistic health care assessment methodologies. The informationacquired from health care assessments shape the policies which will ultimately sustain communities. Health careassessment tools and methods dictate the priorities of community health care. These priorities assist with thedevelopment of community health care research, the exploration of community based need initiatives and thedesign of pertinent policies which meet the demands of community health care. Community health assessmentinvolves people and allows them to express their views, which leads to more self esteem, particularly indisadvantaged communities. Participatory community health care research relates to the continuity of theeconomic, social, institutional and environmental aspects of human society, as well as the non-humanenvironment in which our communities thrive. This research will review the current literature pertinent toparticipatory action research. Additionally, this research will address the advantages, disadvantages and theethical issues of participatory action research methods. Selected case studies are used to explain communitybased models which have identified necessary strategies which have been utilized to articulate and assist currentcommunity health issues in specified populations.

Vereda Johnson Williams

2010-01-01

29

Analysis and Improvement of HITS Algorithm for Detecting Web Communities  

UK PubMed Central (United Kingdom)

In this paper, we discuss problems with HITS (HyperlinkInducedTopic Search) algorithm, which capitalizes on hyperlinksto extract topic-bound communities of web pages.Despite its theoretically sound foundations, we observedHITS algorithm failed in real applications. In order to understandthis problem, we developed a visualization toolLinkViewer, which graphically presents the extraction process.This tool helped reveal that a large and densely linkedset of unrelated Web pages in the base set impeded the extraction.These pages were obtained when the root set wasexpanded into the base set. As remedies for this topic driftproblem, prior studies applied textual analysis method. Onthe other hand, we propose two methods which utilize onlythe structural information of the Web: 1) The projectionmethod, which projects eigenvectors on the root subspace,so that most elements in the root set will be relevant tothe original topic, and 2) The base-set downsizing method,which filters out the pages without links to multiple pagesin the root set. These methods are shown to be robust forbroader types of topics and low in computation cost.

Saeko Nomura; Satoshi Oyama; Tetsuo Hayamizu; Toru Ishida

30

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

Directory of Open Access Journals (Sweden)

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.

Helene Amundsen

2012-01-01

31

Understanding bias in microbial community analysis techniques due to rrn operon copy number heterogeneity.  

UK PubMed Central (United Kingdom)

Molecular tools based on rRNA (rrn) genes are valuable techniques for the study of microbial communities. However, the presence of operon copy number heterogeneity represents a source of systematic error in community analysis. To understand the types and magnitude of such bias, four commonly used rrn-based techniques were used to perform an in silico analysis of a hypothetical community comprised organisms from the Comprehensive Microbial Resource database. Community profiles were generated, and diversity indices were calculated for length heterogeneity PCR, automated ribosomal integenic spacer analysis, denaturing gradient gel electrophoresis, and terminal RFLP (using RsaI, MspI, and HhaI). The results demonstrate that all techniques present a quantitative bias toward organisms with higher copy numbers. In addition, techniques may underestimate diversity by grouping similar ribotypes or overestimate diversity by allowing multiple signals for one organism. The results of this study suggest that caution should be used when interpreting rrn-based community analysis techniques.

Crosby LD; Criddle CS

2003-04-01

32

A Unified Community Detection, Visualization and Analysis method  

CERN Multimedia

Community detection in social graphs has attracted researchers' interest for a long time. With the widespread of social networks on the Internet it has recently become an important research domain. Most contributions focus upon the definition of algorithms for optimizing the so-called modularity function. In the first place interest was limited to unipartite graph inputs and partitioned community outputs. Recently bipartite graphs, directed graphs and overlapping communities have been investigated. Few contributions embrace at the same time the three types of nodes. In this paper we present a method which unifies commmunity detection for the three types of nodes and at the same time merges partitionned and overlapping communities. Moreover results are visualized in such a way that they can be analyzed and semantically interpreted. For validation we experiment this method on well known simple benchmarks. It is then applied to real data in three cases. In two examples of photos sets with tagged people we reveal...

Crampes, Michel

2013-01-01

33

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

Science.gov (United States)

|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,…

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

34

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

UK PubMed Central (United Kingdom)

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.

Smith RJ; Lehning AJ; Dunkle RE

2013-02-01

35

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

Science.gov (United States)

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. PMID:23350565

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

2013-02-01

36

University-Community Engagement: A grid-group analysis  

Directory of Open Access Journals (Sweden)

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 that the model offers a heuristic structure through which to view the diversity of university-community engagement and create shared understandings of the appropriateness of a wide range of possible engagement methods.

David Low

2008-01-01

37

Analysis of open innovation communities from the perspective of Social Network Analysis Analysis of open innovation communities from the perspective of Social Network Analysis Análisis de las comunidades de innovación abierta desde la perspectiva del Análisis de Redes Sociales  

Directory of Open Access Journals (Sweden)

Full Text Available Purpose: Open innovation represents an emergent paradigm by which organizations make use of internal and external resources to drive their innovation processes. The growth of information and communication technologies has facilitated the emergence of online open innovation communities which allow a direct contact with customers and users. The aim of this work consists of analyzing the behavior of open innovation community members from the perspective of social network analysis, in order to determine to what extent the activity of users is related to the interest that posted ideas are generating and to what extent the scoring systems based on collective intelligence are adequate for the identification of users posting ideas that can be potentially implemented by the organization.Design/methodology/approach: Open innovation communities can be represented as graphs, where the nodes represent the community members and the arcs between nodes represent the interactions among users according to the different ways of participation allowed within the community. Using social network analysis techniques, several variables representing different participation features of community members can be collected. The correlation coefficients among these variables provide information about the relationships among users' activity, the interest that their posted ideas arouse within the community and the score that posted ideas receive from the rest of the community.Findings and Originality/value: Obtained results show a positive correlation among the different participation possibilities offered by the studied community. That means that users which are active posting ideas are also active commenting or scoring other users' ideas. However, obtained results also show that those ideas generating more interest among community members are not always the ones that receive a better evaluation by other community members. With respect to those ideas which are finally implemented by the organization, obtained results point out that they are in general the ones that arouse more interest within the community rather that the ones that obtain a better evaluation.Research limitations/implications: This work analyzes the case study of IdeaStorm innovation community promoted by Dell. Despite of being a single case study, it is representative enough as IdeaStorm is one of the most popular innovation communities and one of the pioneers in the implementation of the open innovation paradigm.Practical implications: Putting into practice open innovation communities has the drawback of the huge volume of generated information, many times quite difficult to process by the innovation department of the organization. That is the reason why it is quite important for the organization to know the patterns of behavior of community members, how the community scoring system is working and to what extent posted ideas are aligned with the organization strategic innovation policies.Originality/value: This work deals with the issue of putting into practice the open innovation paradigm using social network analysis techniques for modeling the behavior and activity of users belonging to open innovation communities. Moreover, this study not only considers the activity of community members but also the implications for the organization in the form of ideas that have been finally implemented.Purpose: Open innovation represents an emergent paradigm by which organizations make use of internal and external resources to drive their innovation processes. The growth of information and communication technologies has facilitated the emergence of online open innovation communities which allow a direct contact with customers and users. The aim of this work consists of analyzing the behavior of open innovation community members from the perspective of social network analysis, in order to determine to what extent the activity of users is related to the interest that posted ideas are generating and to what extent the scoring systems based on collective intelligence are adequate

Rocio Martinez-Torres

2013-01-01

38

Cost-Benefit Analysis of the Community Patent  

Digital Repository Infrastructure Vision for European Research (DRIVER)

For more than 40 years, governments and professional associations have acted, voted or lobbied against the implementation of the Community Patent (COMPAT, officially called the EU Patent). The econometric results and simulations presented in this paper suggest that, thanks to its attractiveness in t...

Danguy, Jérôme; Van Pottelsberghe, Bruno

39

Pyrosequencing analysis of the bacterial community in drinking water wells.  

UK PubMed Central (United Kingdom)

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.

Navarro-Noya YE; Suárez-Arriaga MC; Rojas-Valdes A; Montoya-Ciriaco NM; Gómez-Acata S; Fernández-Luqueño F; Dendooven L

2013-07-01

40

Pyrosequencing analysis of the bacterial community in drinking water wells.  

Science.gov (United States)

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. PMID:23563631

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

2013-04-06

 
 
 
 
41

Defining Campus Violence: A Phenomenological Analysis of Community Stakeholder Perspectives  

Science.gov (United States)

|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…

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

2011-01-01

42

A comparative analysis of the community contributions and profits of Virginia's hospitals.  

UK PubMed Central (United Kingdom)

BACKGROUND: In return for receiving favorable treatment from the government, U.S. general hospitals are expected to provide contributions to their community consisting of charity care, bad debt, and taxes paid. Recently, the Government Accountability Office proposed that an analysis that compares what for-profit and nonprofit hospitals contribute be conducted. PURPOSE: For 72 Virginia hospitals, it is determined whether (a) for-profit hospitals' community contributions exceed their profits and (b) nonprofit hospitals' community contributions exceed the for-profits' contributions in addition to the nonprofits' forgone taxes. METHODOLOGY/APPROACH: Based on audited fiscal year 2004 financial statements, six null hypotheses were tested for significant differences between the two independent variables, namely, hospital charter and size, and the three dependent variables, including (a) operating income, (b) the ratio of community contributions to net patient revenues, and (c) the ratio of community contributions to operating income. FINDINGS: No significant differences were found to exist between (a) hospital charter and operating income, (b) hospital charter and the percentage of community contributions to net patient revenues, and (c) hospital charter and the percentage of community contributions to operating income. The community contributions of nonprofits exceeded their taxes forgone by a wide margin, but they fell short of exceeding the for-profits' community contributions plus the taxes forgone by a very slight margin. PRACTICE IMPLICATIONS: Hospital management, in conjunction with health care policy planners, needs to develop mutually acceptable standards regarding the required level of hospitals' community contributions. It is proposed that the most equitable standard is "quartile comparisons" for a given hospital's financial performance and its level of community contributions. Furthermore, to reduce charity care, it is imperative that high-cost hospital treatment of primary health care for indigent patients be shifted to lower cost delivery systems.

McDermott DR

2007-04-01

43

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

Science.gov (United States)

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. PMID:23859984

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

2013-06-29

44

Pyrosequencing-Based Analysis of the Bacterial Community in Korean Traditional Seafood, Ojingeo Jeotgal.  

UK PubMed Central (United Kingdom)

Jeotgal fermentation is dependent upon a diverse microbial community, although a detailed understanding of its microbial composition is limited to a relatively small number of jeotgal. Pyrosequencing-based bacterial community analysis was performed in fermented squid, ojingeo jeotgal. Leuconostoc was identified as the predominant bacterial genus, with Bacillus and Staphylococcus also accounting for a large proportion of the bacterial community. Phylogenetic analysis with 16S rRNA genes of Leuconostoc type species indicated that L. citreum- and L. holzapfelii-like strains could be the major Leuconostoc strains in jeotgal. High concentrations of NaCl were thought to be an important factor determining the makeup of the bacterial community in fermented squid; however, a genomic survey with osmotic stress-related genes suggests the existence of more complex factors selecting the dominant bacterial species in fermented squid.

Jung J; Choi S; Jeon CO; Park W

2013-07-01

45

[Dianchi Lake macroinvertebrate community succession trends and retrogressive analysis].  

UK PubMed Central (United Kingdom)

Historical records and data from yield surveys conducted in 2009 and 2010 were used to investigate macroinvertebrate community succession trends in Dianchi Lake. Species richness has declined from 57 in the 1980s to 32 in 2010, representing a species loss of 44%. Among the major benthic groups, the highest rate of loss was recorded for mollusks (75%) and aquatic insects (39%). Surveys in 2009 and 2010 across the lake revealed that the total density was 1776 ind/m2, comprising oligochaetes (1706 ind/m2) and chironomids (68 ind/m2). Over a nearly twenty-year span (1992-2010), the density and biomass of oligochaetes first increased sharply (1992-2002) and then declined gradually (2002-2010). Further, chironomids have decreased gradually while the proportion of abundant species has increased. Limnodrilus hoffmeisteri became the sole dominant species with an average relative abundance of 74.1%. Cosmopolitan species, such as Einfeldia sp., disappeared across the lake; instead, tolerant species such as Chironomus plumosus, Ch. attenuatus and Tanypus chinensis became the common. Mollusk community structure has become simpler and many native species have gone extinct. Species of concern include Margarya melanioides, M. mondi, M. mansugi and Cipangopaludina dianchiensis, all rated as critically endangered by the IUCN. We found that the Shannon-Wiener index declined in Dianchi Lake, particularly in Caohai Lake, from 2.70 in the 1950s to 0.30 in 2009 and 2010. Species richness and biodiversity was significantly negative correlated with total phosphorus and total nitrogen. Factors responsible for the benthic community retrogression described here include habitat destruction, lowering of water quality, outbreaks of blue-green algae, extinction of submerged plants and lack of germplasm resources.

Wang CM; Xie ZC; Song LR; Xiao BD; Li GB; Li L

2011-04-01

46

Temporal molecular and isotopic analysis of active bacterial communities in two New Zealand sponges.  

UK PubMed Central (United Kingdom)

The characterization of changes in microbial communities is an essential step towards a better understanding of host-microbe associations. It is well established that sponges (phylum Porifera) harbour a diverse and abundant microbial community, but it is not known whether these microbial communities change over time. Here, we followed two sponge species (Ancorina alata and Tethya stolonifera) over a 2-year sampling period using RNA (16S rRNA)-based amplicon pyrosequencing and bulk stable isotope analysis (?(13) C and ?(15)N). A total of 4468 unique operational taxonomic units (OTUs) was identified, which were affiliated with 26 bacterial phyla. Bacterial communities of both sponge species were remarkably stable throughout the monitoring period, driven by a small number of OTUs that dominated their respective communities. Variability of sponge-associated bacterial communities was driven by OTUs that were low in abundance or transient over time. Stable isotope analysis provided evidence of both bacteria- and host-derived nutrients and their variability throughout the season. While ?(15) N values were similar, significant differences were found in ?(13) C of sponge tissue, indicative of a varying reliance on particulate organic matter as a carbon source. Further temporal studies, such as those undertaken here, will be highly valuable to identify which members of a sponge bacterial community are truly symbiotic in nature.

Simister R; Taylor MW; Rogers KM; Schupp PJ; Deines P

2013-07-01

47

Why immunization coverage fails to catch up in India? A community-based analysis.  

UK PubMed Central (United Kingdom)

BACKGROUND: An effort has been made in this paper to examine the impact of community and household vis-à-vis individual-level variables on immunization coverage among Indian children. METHODS: National Family Health Survey-2 data set has been used for the analysis. Multilevel regression analyses have been used to explore the relative effects of community-, household- and individual-level factors on immunization coverage. Three community-level variables, i.e. availability of health facilities, availability of all-weather roads and information, education and communication (IEC) activities conducted during last year, are included in this analysis. RESULTS: Availability of health facility and information, education and communication activities plays a significant role in determining the level of immunization coverage among children. Even with community-level variables in the model, individual-level variables, i.e. parent's education, birth order of child and number of antenatal care visits, retain their predictive role for the potential immunization coverage. CONCLUSIONS: Universal immunization can be achieved by providing services at community level and information about the available services and their benefits to the community. There is a considerable, unexplained variation in the immunization coverage between different communities, even in the most complex model used in this study, which could explain the entire heterogeneity of immunization coverage among Indian states.

Sahu D; Pradhan J; Jayachandran V; Khan N

2010-05-01

48

Conceptualisation of community-based basic nursing education in South Africa: a grounded theory analysis.  

UK PubMed Central (United Kingdom)

Community-based education is about a decade old in basic nursing education in South Africa. An extensive review of literature revealed that although CBE was a familiar concept in South Africa, there was however, limited understanding of what this phenomenon means. The purpose of the study was to analyse the concept 'community-based education' with the aim of discovering shared understanding of this phenomenon in basic nursing education within the South African context. Strauss and Corbin's (1990) grounded theory approach was used to guide the research process. The South African Nursing Council's (SANC) education committee, the National Department of Health, human resources division representatives as well as seven nursing education institutions with well-established CBE programmes participated in the study. The data was collected by means of observations, interviews and document analysis. Purposive sampling and later theoretical sampling was used for selecting interviewees. This resulted in a total of 45 interviewees. The data collection and initial data analysis took place concurrently. Descriptive analysis followed by conceptual analysis was performed using Strauss and Corbin's model. The findings in this study revealed that community-based education is education that uses the community extensively, especially the under-developed and under-resourced settings, for learning purposes in order to enhance relevance of nursing education to the needs of the South African population. The core discriminatory characteristics of CBE were found to include; primacy of the community as a learning environment; the early exposure of students to community-based learning experiences; community-based learning experiences dominating the curriculum, exposure to community-based learning experiences throughout the curriculum, vertical sequencing of community-based learning experiences in a curriculum, starting from primary settings to secondary and later tertiary health care settings to facilitate the development of competencies required when serving in all these settings, and lastly, learning through providing service to the under-resourced communities. Community involvement and partnership, problem-centred learning, valid assessment of learning emanated as important characteristics of CBE but which were identified as gaps in the existing programmes. Recommendations focused on these gaps as well as to the problem of community-based learning experiences which were mainly concentrated in first and/or second year levels in most of the programmes.

Mtshali NG

2005-05-01

49

An Analysis of the Student Evaluation Form at Oakton Community College.  

Science.gov (United States)

This paper reports the results of an evaluative statistical analysis of the instrument employed for student evaluation of faculty at Oakton Community College (Illinois). The analysis was performed because the locally devised instrument had never been subjected to systematic study of reliability or validity, and because a review of pertinent…

Bers, Trudy

50

Integrated Microbial Survey Analysis of Prokaryotic Communities for the PhyloChip Microarray ? †  

Digital Repository Infrastructure Vision for European Research (DRIVER)

PhyloTrac is an integrated desktop application for analysis of PhyloChip microarray data. PhyloTrac combined with PhyloChip provides turnkey and comprehensive identification and analysis of bacterial and archaeal communities in complex environmental samples. PhyloTrac is free for noncommercial organ...

Schatz, Michael C.; Phillippy, Adam M.; Gajer, Pawel; DeSantis, Todd Z.; Andersen, Gary L.; Ravel, Jacques

51

Analysis of stomach bacterial communities in Australian feral horses.  

UK PubMed Central (United Kingdom)

We investigated the community structure of bacteria that populate the stomach of the Brumby, a breed of feral horses from the Australian outback. Using a 16S rRNA gene clone library, we identified 155 clones that were assigned to 26 OTUs based on a 99.0 % sequence identity cutoff. Two OTUs represented 73.5 % of clones, while 18 OTUs were each assigned only a single clone. Four major bacterial types were identified in the Brumby stomach: Lactobacillaceae, Streptococcaceae, Veillonellaceae and Pasteurellaceae. The first three groups, which represented 98.1 % of the Brumby stomach library clones, belonged to the bacterial phylum Firmicutes. We found that 49.7 % of clones were related to bacterial species previously identified in the equine hindgut, and that 44.5 % of clones were related to symbiotic bacterial species identified in the mouth or throat of either horses or other mammals. Our results indicated that the composition of mutualistic bacterial communities of feral horses was consistent with other studies on domestic horses. In addition to bacterial sequences, we also identified four plastid 16S rRNA gene sequences, which may help in further characterizing the type of vegetation consumed by Brumby horses in their natural environment.

St-Pierre B; de la Fuente G; O'Neill S; Wright AD; Al Jassim R

2013-01-01

52

Exploiting community behavior for enhanced link analysis and Web search  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Methods for Web link analysis and authority ranking such as PageRank are based on the assumption that a user endorses a Web page when creating a hyperlink to this page. There is a wealth of additional user-behavior information that could be considered for improving authority analysis, for example, t...

Luxenburger, J.; Weikum, G.

53

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

Science.gov (United States)

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...

54

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

UK PubMed Central (United Kingdom)

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.

Sharma M; Bhatia G

1996-12-01

55

Addressing cancer disparities via community network mobilization and intersectoral partnerships: a social network analysis.  

Science.gov (United States)

Community mobilization and collaboration among diverse partners are vital components of the effort to reduce and eliminate cancer disparities in the United States. We studied the development and impact of intersectoral connections among the members of the Massachusetts Community Network for Cancer Education, Research, and Training (MassCONECT). As one of the Community Network Program sites funded by the National Cancer Institute, this infrastructure-building initiative utilized principles of Community-based Participatory Research (CBPR) to unite community coalitions, researchers, policymakers, and other important stakeholders to address cancer disparities in three Massachusetts communities: Boston, Lawrence, and Worcester. We conducted a cross-sectional, sociometric network analysis four years after the network was formed. A total of 38 of 55 members participated in the study (69% response rate). Over four years of collaboration, the number of intersectoral connections reported by members (intersectoral out-degree) increased, as did the extent to which such connections were reported reciprocally (intersectoral reciprocity). We assessed relationships between these markers of intersectoral collaboration and three intermediate outcomes in the effort to reduce and eliminate cancer disparities: delivery of community activities, policy engagement, and grants/publications. We found a positive and statistically significant relationship between intersectoral out-degree and community activities and policy engagement (the relationship was borderline significant for grants/publications). We found a positive and statistically significant relationship between intersectoral reciprocity and community activities and grants/publications (the relationship was borderline significant for policy engagement). The study suggests that intersectoral connections may be important drivers of diverse intermediate outcomes in the effort to reduce and eliminate cancer disparities. The findings support investment in infrastructure-building and intersectoral mobilization in addressing disparities and highlight the benefits of using CBPR approaches for such work. PMID:22384156

Ramanadhan, Shoba; Salhi, Carmel; Achille, Erline; Baril, Nashira; D'Entremont, Kerrie; Grullon, Milagro; Judge, Christine; Oppenheimer, Sarah; Reeves, Chrasandra; Savage, Clara; Viswanath, Kasisomayajula

2012-02-23

56

Transcriptomic analysis of a marine bacterial community enriched with dimethylsulfoniopropionate.  

UK PubMed Central (United Kingdom)

Dimethylsulfoniopropionate (DMSP) is an important source of reduced sulfur and carbon for marine microbial communities, as well as the precursor of the climate-active gas dimethylsulfide (DMS). In this study, we used metatranscriptomic sequencing to analyze gene expression profiles of a bacterial assemblage from surface waters at the Bermuda Atlantic Time-series Study (BATS) station with and without a short-term enrichment of DMSP (25?nM for 30?min). An average of 303?143 reads were obtained per treatment using 454 pyrosequencing technology, of which 51% were potential protein-encoding sequences. Transcripts from Gammaproteobacteria and Bacteroidetes increased in relative abundance on DMSP addition, yet there was little change in the contribution of two bacterioplankton groups whose cultured members harbor known DMSP degradation genes, Roseobacter and SAR11. The DMSP addition led to an enrichment of transcripts supporting heterotrophic activity, and a depletion of those encoding light-related energy generation. Genes for the degradation of C3 compounds were significantly overrepresented after DMSP addition, likely reflecting the metabolism of the C3 component of DMSP. Mapping these transcripts to known biochemical pathways indicated that both acetyl-CoA and succinyl-CoA may be common entry points of this moiety into the tricarboxylic acid cycle. In a short time frame (30?min) in the extremely oligotrophic Sargasso Sea, different gene expression patterns suggest the use of DMSP by a diversity of marine bacterioplankton as both carbon and sulfur sources.

Vila-Costa M; Rinta-Kanto JM; Sun S; Sharma S; Poretsky R; Moran MA

2010-11-01

57

Investigating student communities with network analysis of interactions in a physics learning center  

Directory of Open Access Journals (Sweden)

Full Text Available 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. 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 that contribute to participation in the learning community. Results of the sequential multiple regression indicate that the PLC learning community is an equitable environment as we find that gender and ethnicity are not significant predictors of participation in the PLC. We find that providing students space for collaboration provides a vital element in the formation of a supportive learning community.

Eric Brewe1,2; Laird Kramer2; Vashti Sawtelle2; Eric Brewe1,2

2012-01-01

58

MetaMicrobesOnline: phylogenomic analysis of microbial communities.  

Science.gov (United States)

The metaMicrobesOnline database (freely available at http://meta.MicrobesOnline.org) offers phylogenetic analysis of genes from microbial genomes and metagenomes. Gene trees are constructed for canonical gene families such as COG and Pfam. Such gene trees allow for rapid homologue analysis and subfamily comparison of genes from multiple metagenomes and comparisons with genes from microbial isolates. Additionally, the genome browser permits genome context comparisons, which may be used to determine the closest sequenced genome or suggest functionally associated genes. Lastly, the domain browser permits rapid comparison of protein domain organization within genes of interest from metagenomes and complete microbial genomes. PMID:23203984

Chivian, Dylan; Dehal, Paramvir S; Keller, Keith; Arkin, Adam P

2012-11-30

59

MetaMicrobesOnline: phylogenomic analysis of microbial communities.  

UK PubMed Central (United Kingdom)

The metaMicrobesOnline database (freely available at http://meta.MicrobesOnline.org) offers phylogenetic analysis of genes from microbial genomes and metagenomes. Gene trees are constructed for canonical gene families such as COG and Pfam. Such gene trees allow for rapid homologue analysis and subfamily comparison of genes from multiple metagenomes and comparisons with genes from microbial isolates. Additionally, the genome browser permits genome context comparisons, which may be used to determine the closest sequenced genome or suggest functionally associated genes. Lastly, the domain browser permits rapid comparison of protein domain organization within genes of interest from metagenomes and complete microbial genomes.

Chivian D; Dehal PS; Keller K; Arkin AP

2013-01-01

60

Energy Engineering Analysis Program, Kaiserlautern Community, FRG: Executive Summary.  

Science.gov (United States)

This Summary outlines documents of the information compiled during Phase II of Contract DACA9O-83-C-0013, Energy Engineering Analysis Program. A complete schedule of services is included as Appendix A to this report. The purpose of the contract is to redu...

L. A. Daly H. Donges

1984-01-01

 
 
 
 
61

Inventory of activation analysis facilities available in the European Community to Industrial users  

International Nuclear Information System (INIS)

This inventory includes lists of activation equipment produced in the European Community, facilities available for industrial users and activation laboratories existing in the European companies. The aim of this inventory is to provide all information that may be useful, to companies interested in activation analysis, as well as to give an idea on existing routine applications and on the European market in facilities.

1975-01-01

62

Determination of seasonal phytoplankton communities, based on quantitative data using a mathematical analysis  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The definition of algal communities has always been a very discussed subject. We applied a principal component analysis on quantitative phytoplankton data. This ordination technique made it possible to distinguish the algal groups present. This technique is very often applied in the phytosociology ...

Caljon, A.

63

Energy Engineering Analysis Program, Kaiserlautern Community, FRG: Executive summary. Summary report  

Energy Technology Data Exchange (ETDEWEB)

This Summary outlines documents of the information compiled during Phase II of Contract DACA9O-83-C-0013, Energy Engineering Analysis Program. A complete schedule of services is included as Appendix A to this report. The purpose of the contract is to reduce energy consumption in the community by identifying actions and/or projects that will accomplish this end.

Daly, L.A.; Donges, H.

1984-05-01

64

Analysis of the Bacterial Communities in Lime Concretion Black Soil upon the Incorporation of Crop Residues  

Directory of Open Access Journals (Sweden)

Full Text Available To analyze the bacterial communities in lime concretion black soil upon the incorporation of crop residues for two years in wheat-maize system, total DNA was directly extracted and PCR-amplified with the F357GC and R518 primers targeting the 16S rRNA genes of V3 region. The amplified fragments were analyzed by perpendicular DGGE. Analyzing of species richness index S and Shannon diversity index H revealed that there was a high diversity of soil bacterial community compositions among all treatments after incorporation of crop residues and fertilizing under field conditions. Eleven DGGE bands recovered were re-amplified, sequenced. Phylogenetic analysis of the representative DGGE fingerprints identified four groups of the prokaryotic communities in the soil by returning wheat residues and fertilizing under field conditions. The bacterial communities belonged to gamma proteobacterium, Cupriavidus sp, halophilic eubacterium, Acidobacterium sp, Sorangium sp, delta proteobacterium, Streptococcus sp and Streptococcus agalactiae were main bacterial communities. Principal Component Analysis (PCA) showed that there were the differences in DNA profiles among the six treatments. It showed that wheat residue returning, maize residue returning and fertilizing all can improve bacterial diversity in varying degrees. As far as improvement of bacterial diversity was concerned, wheat residue returning was higher than fertilizing, and fertilizing higher than maize residue returning.

Shao-Qiang Tao; Qiang Xia; Lin Zhu; Jing-jing Chen; Ya- Nan Wang; Bing Qin

2012-01-01

65

Metagenomic Analysis of Fungal Communities Inhabiting the Fairy Ring Zone of Tricholoma matsutake.  

UK PubMed Central (United Kingdom)

Tricholoma matsutake, an ectomycorrhizae that has mutual relationships with the rootlet of Pinus denisflora, forms a fruiting body that serves as a valuable food in Asia. However, the artificial culture of this fungus has not been successful. Soil fungi, including T. matsutake, coexist with many other microorganisms and plants; therefore, complex microbial communities have an influence on the fruiting body formation of T. matsutake. Here, we report on the structures of fungal communities associated with the fairy ring of T. matsutake through the pyrosequencing method. Soil samples were collected inside the fairy ring zone, in the fairy ring zone, and outside the fairy ring zone. A total of 37,125 sequencing reads were obtained and 728 to 1,962 Operational Taxonomic Units (OTUs) were observed in the sampling zones. The fairy ring zone had the lowest OTUs and the lowest fungal diversity of all sampling zones. The number of OTUs and fungal taxa inside and outside the fairy ring zone was, respectively, about two times and 1.5 times higher than the fairy ring. Taxonomic analysis showed that each sampling zone has different fungal communities. In particular, out of 209 genera total, six genera, in the fairy ring zone, such as genus Hemimycena, were uniquely present and 31 genera, such as genus Mycena, Boletopsis, and Repetophragma, were specifically absent. The results of metagenomic analysis based on the pyrosequencing indicate a decrease of fungal communities in the fairy ring zone and changes of fungal communities depending on the fairy ring growth of T. matsutake.

Kim M; Yoon H; You YH; Kim YE; Woo JR; Seo Y; Lee GM; Kim YJ; Kong WS; Kim JG

2013-08-01

66

Occupational burnout and work factors in community and hospital midwives: a survey analysis.  

UK PubMed Central (United Kingdom)

BACKGROUND: community-based midwifery practice has been promoted in the UK maternity policy over the last decade as a means of increasing continuity of care. However, there have been growing concerns to suggest that the community-based continuity model may not be sustainable due to the high levels of occupational burnout in midwives resulted by increased on-call work. AIMS: this paper attempted to identify work factors associated with the levels of burnout in community midwives as compared to hospital midwives, aiming at contributing to the debate of organising sustainable midwifery care. METHODS: a statistical analysis was conducted drawing on data from a survey of all midwives working at one Hospital Trust in England (n=238). Occupational burnout was measured using the Maslach Burnout Inventory (MBI). RESULTS: the sample midwives (n=128, 54%) had significantly higher levels of burnout compared to the reference groups. Multiple regression analysis identified as follows: (1) high levels of occupational autonomy were a key protective factor of burnout, and more prevalent in the community, (2) working hours were positively associated with burnout, and community midwives were more likely to have higher levels of stress recognition, and (3) support for work-life-balance from the Trust had a significant protective effect on the levels of burnout. CONCLUSION: the results should be taken into account in the maternity policy in order to incorporate continuity of care and sustainable organisation of midwifery care.

Yoshida Y; Sandall J

2013-08-01

67

Analysis of the bacterial community within carrot wash water.  

UK PubMed Central (United Kingdom)

Vegetables are washed after harvest to remove unwanted organic and inorganic particles, but wash water contaminated with certain pathogenic microorganisms can potentially contaminate produce. In this study, the microbial diversity of wash water was analyzed in samples taken from a carrot-processing facility. A 16S rRNA gene library with 427 clones was constructed and analyzed by amplified rDNA restriction analysis. For taxonomic classification, the 16S rRNA gene nucleotide sequences of 94 amplified rDNA restriction analysis fingerprints were determined. Each fingerprint indicates a distinct group of microorganisms. The nucleotide sequences were assigned to corresponding reference species. The most prevalent genus was Tolumonas , with 26% of the clones, followed by Acinetobacter and Flacobacterium , with 11% each. The latter two genera contain species that are known to cause nosocomial infections. The fourth most common genus was Arcobacter , comprising 9% of all clones. Some species of Arcobacter are considered to be emerging food pathogens, mainly associated with the contamination of meat products. So far, they have not been considered as contaminants of fresh produce. Based on the sequence data, an Arcobacter-specific PCR assay was developed to facilitate the detection of vegetable-associated Arcobacter strains.

Hausdorf L; Fröhling A; Schlüter O; Klocke M

2011-05-01

68

Separation of the bacterial species, Escherichia coli, from mixed-species microbial communities for transcriptome analysis.  

UK PubMed Central (United Kingdom)

BACKGROUND: The study of bacterial species interactions in a mixed-species community can be facilitated by transcriptome analysis of one species in the community using cDNA microarray technology. However, current applications of microarrays are mostly limited to single species studies. The purpose of this study is to develop a method to separate one species, Escherichia coli as an example, from mixed-species communities for transcriptome analysis. RESULTS: E. coli cells were separated from a dual-species (E. coli and Stenotrophomonas maltophilia) community using immuno-magnetic separation (IMS). High recovery rates of E. coli were achieved. The purity of E. coli cells was as high as 95.0% separated from suspended mixtures consisting of 1.1 - 71.3% E. coli, and as high as 96.0% separated from biofilms with 8.1% E. coli cells. Biofilms were pre-dispersed into single-cell suspensions. The reagent RNAlater (Ambion, Austin, TX) was used during biofilm dispersion and IMS to preserve the transcriptome of E. coli. A microarray study and quantitative PCR confirmed that very few E. coli genes (only about eight out of 4,289 ORFs) exhibited a significant change in expression during dispersion and separation, indicating that transcriptional profiles of E. coli were well preserved. CONCLUSIONS: A method based on immuno-magnetic separation (IMS) and application of RNAlater was developed to separate a bacterial species, E. coli as an example, from mixed-species communities while preserving its transcriptome. The method combined with cDNA microarray analysis should be very useful to study species interactions in mixed-species communities.

Dai D; Holder D; Raskin L; Xi C

2011-01-01

69

Metagenomic analysis of the turkey gut RNA virus community  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Viral enteric disease is an ongoing economic burden to poultry producers worldwide, and despite considerable research, no single virus has emerged as a likely causative agent and target for prevention and control efforts. Historically, electron microscopy has been used to identify suspect viruses, with many small, round viruses eluding classification based solely on morphology. National and regional surveys using molecular diagnostics have revealed that suspect viruses continuously circulate in United States poultry, with many viruses appearing concomitantly and in healthy birds. High-throughput nucleic acid pyrosequencing is a powerful diagnostic technology capable of determining the full genomic repertoire present in a complex environmental sample. We utilized the Roche/454 Life Sciences GS-FLX platform to compile an RNA virus metagenome from turkey flocks experiencing enteric disease. This approach yielded numerous sequences homologous to viruses in the BLAST nr protein database, many of which have not been described in turkeys. Our analysis of this turkey gut RNA metagenome focuses in particular on the turkey-origin members of the Picornavirales, the Caliciviridae, and the turkey Picobirnaviruses.

Day J Michael; Ballard Linda L; Duke Mary V; Scheffler Brian E; Zsak Laszlo

2010-01-01

70

Attitudes towards Autonomous Data Collection and Analysis in the Planetary Science Community  

Directory of Open Access Journals (Sweden)

Full Text Available As missions are planned to targets further away from Earth, it becomes all but required to increase the role of autonomy in the mission. An investigation of what aspects of mission operations and decision making autonomy will be accepted in by the planetary science community is thus required to aid in development planning. This paper presents a data set collected regarding attitudes towards autonomous data collection and analysis in the planetary science community and initial analysis of this data. A survey, conducted at the 2013 Lunar and Planetary Science Conference, asked respondents to identify whether or not they would accept conclusions drawn by autonomous data collection techniques and what factors would impact this acceptance. It also looked at the acceptance of computers and computer software in the data collection and analysis process.

Jeremy Straub

2013-01-01

71

Service utilization in community health centers in China: a comparison analysis with local hospitals  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Being an important part of China's Urban Health Care Reform System, Community Health Centers (CHCs) have been established throughout the entire country and are presently undergoing substantial reconstruction. However, the services being delivered by the CHCs are far from reaching their performance targets. In order to assess the role of the CHCs, we examined their performance in six cities located in regions of South-East China. The purpose of this investigation was to identify the utilization and the efficiency of community health resources that are able to provide basic medical and public health services. Methods The study was approved by Peking University Health Science Center Institutional Reviewing Board (NO: IRB00001052-T1). Data were collected from all the local health bureaux and processed using SPSS software. Methods of analysis mainly included: descriptive analysis, paired T-test and one-way ANOVA. Results The six main functions of the CHCs were not fully exploited and the surveys that were collected on their efficiency and utilization of resources indicate that they have a low level of performance and lack the trust of local communities. Furthermore, the CHCs seriously lack funding support and operate under difficult circumstances, and residents have less positive attitudes towards them. Conclusion The community health service must be adjusted according to the requirements of urban medical and health reform, taking into account communities' health needs. More research is required on the living standards and health needs of residents living within the CHC's range, taking into consideration the users' needs in expanding the newly implemented service, and at the same time revising the old service system so as to make the development of CHCs realistic and capable of providing a better service to patients. Several suggestions are put forward for an attainable scheme for developing a community health service.

Pan Xilong; Dib Hassan H; Wang Xiaohang; Zhang Hong

2006-01-01

72

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

Directory of Open Access Journals (Sweden)

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.

M. Behangana; L. Luiselli

2008-01-01

73

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

DEFF Research Database (Denmark)

Microbial activity within the environment can have distinct geochemical effects, and so changes in a microbial community structure can result in geochemical change. We examined seasonal changes in both the microbial community and the geochemistry of an inter-tidal salt marsh in north-west England 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 and the Mahalanobis distance metric), and we show that the use of the Mahalanobis distance metric improves the statistical analysis by providing detailed information on the reasons samples cluster together and identifying the distinguishing features between the separate clusters. Five clusters of like samples were 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, in the warmer months. The conditions therefore remained most favourable for aerobic species throughout the year, explaining their continual dominance at this site. However, as the abundance of PLFA synthesised by anaerobes increased, increases in dissolved Mn concentrations were observed, which we suggest were due to anaerobic respiration of Mn(IV) to Mn(II). Overall, the geochemical conditions were consistent with the microbial community structure and changes within it.

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

2002-01-01

74

Beyond the genome: community-level analysis of the microbial world.  

UK PubMed Central (United Kingdom)

The development of culture-independent strategies to study microbial diversity and function has led to a revolution in microbial ecology, enabling us to address fundamental questions about the distribution of microbes and their influence on Earth's biogeochemical cycles. This article discusses some of the progress that scientists have made with the use of so-called "omic" techniques (metagenomics, metatranscriptomics, and metaproteomics) and the limitations and major challenges these approaches are currently facing. These 'omic methods have been used to describe the taxonomic structure of microbial communities in different environments and to discover new genes and enzymes of industrial and medical interest. However, microbial community structure varies in different spatial and temporal scales and none of the 'omic techniques are individually able to elucidate the complex aspects of microbial communities and ecosystems. In this article we highlight the importance of a spatiotemporal sampling design, together with a multilevel 'omic approach and a community analysis strategy (association networks and modeling) to examine and predict interacting microbial communities and their impact on the environment.

Zarraonaindia I; Smith DP; Gilbert JA

2013-03-01

75

Community-based care for the specialized management of heart failure: an evidence-based analysis.  

UK PubMed Central (United Kingdom)

UNLABELLED: In August 2008, the Medical Advisory Secretariat (MAS) presented a vignette to the Ontario Health Technology Advisory Committee (OHTAC) on a proposed targeted health care delivery model for chronic care. The proposed model was defined as multidisciplinary, ambulatory, community-based care that bridged the gap between primary and tertiary care, and was intended for individuals with a chronic disease who were at risk of a hospital admission or emergency department visit. The goals of this care model were thought to include: the prevention of emergency department visits, a reduction in hospital admissions and re-admissions, facilitation of earlier hospital discharge, a reduction or delay in long-term care admissions, and an improvement in mortality and other disease-specific patient outcomes.OHTAC approved the development of an evidence-based assessment to determine the effectiveness of specialized community based care for the management of heart failure, Type 2 diabetes and chronic wounds.PLEASE VISIT THE MEDICAL ADVISORY SECRETARIAT WEB SITE AT: www.health.gov.on.ca/ohtas to review the following reports associated with the Specialized Multidisciplinary Community-Based care series.Specialized multidisciplinary community-based care series: a summary of evidence-based analysesCommunity-based care for the specialized management of heart failure: an evidence-based analysisCommunity-based care for chronic wound management: an evidence-based analysisPlease note that the evidence-based analysis of specialized community-based care for the management of diabetes titled: "Community-based care for the management of type 2 diabetes: an evidence-based analysis" has been published as part of the Diabetes Strategy Evidence Platform at this URL: http://www.health.gov.on.ca/english/providers/program/mas/tech/ohtas/tech_diabetes_20091020.htmlPLEASE VISIT THE TORONTO HEALTH ECONOMICS AND TECHNOLOGY ASSESSMENT COLLABORATIVE WEB SITE AT: http://theta.utoronto.ca/papers/MAS_CHF_Clinics_Report.pdf to review the following economic project associated with this series:Community-based Care for the specialized management of heart failure: a cost-effectiveness and budget impact analysis. OBJECTIVE: The objective of this evidence-based analysis was to determine the effectiveness of specialized multidisciplinary care in the management of heart failure (HF). CLINICAL NEED: TARGET POPULATION AND CONDITION HF is a progressive, chronic condition in which the heart becomes unable to sufficiently pump blood throughout the body. There are several risk factors for developing the condition including hypertension, diabetes, obesity, previous myocardial infarction, and valvular heart disease.(1) Based on data from a 2005 study of the Canadian Community Health Survey (CCHS), the prevalence of congestive heart failure in Canada is approximately 1% of the population over the age of 12.(2) This figure rises sharply after the age of 45, with prevalence reports ranging from 2.2% to 12%.(3) Extrapolating this to the Ontario population, an estimated 98,000 residents in Ontario are believed to have HF. Disease management programs are multidisciplinary approaches to care for chronic disease that coordinate comprehensive care strategies along the disease continuum and across healthcare delivery systems.(4) Evidence for the effectiveness of disease management programs for HF has been provided by seven systematic reviews completed between 2004 and 2007 (Table 1) with consistency of effect demonstrated across four main outcomes measures: all cause mortality and hospitalization, and heart-failure specific mortality and hospitalization. (4-10) However, while disease management programs are multidisciplinary by definition, the published evidence lacks consistency and clarity as to the exact nature of each program and usual care comparators are generally ill defined. Consequently, the effectiveness of multidisciplinary care for the management of persons with HF is still uncertain. Therefore, MAS has completed a systematic review of specialized, multidisciplina

2009-01-01

76

Evaluation of molecular community analysis methods for discerning fecal sources and human waste.  

UK PubMed Central (United Kingdom)

Molecular microbial community analyses provide information on thousands of microorganisms simultaneously, and integrate biotic and abiotic perturbations caused by fecal contamination entering water bodies. A few studies have explored community methods as emerging approaches for microbial source tracking (MST), however, an evaluation of the current state of this approach is lacking. Here, we utilized three types of community-based methods with 64 blind, single- or dual-source, challenge samples generated from 12 sources, including: humans (feces), sewage, septage, dogs, pigs, deer, horses, cows, chickens, gulls, pigeons, and geese. Each source was a composite from multiple donors from four representative geographical regions in California. Methods evaluated included terminal restriction fragment polymorphism (TRFLP), phylogenetic microarray (PhyloChip), and next generation (Illumina) sequencing. These methods correctly identified dominant (or sole) sources in over 90% of the challenge samples, and exhibited excellent specificity regardless of source, rarely detecting a source that was not present in the challenge sample. Sensitivity, however, varied with source and community analysis method. All three methods distinguished septage from human feces and sewage, and identified deer and horse with 100% sensitivity and 100% specificity. Method performance improved if the composition of blind dual-source reference samples were defined by DNA contribution of each single source within the mixture, instead of by Enterococcus colony forming units. Data analysis approach also influenced method performance, indicating the need to standardize data interpretation. Overall, results of this study indicate that community analysis methods hold great promise as they may be used to identify any source, and they are particularly useful for sources that currently do not have, and may never have, a source-specific single marker gene.

Cao Y; Van De Werfhorst LC; Dubinsky EA; Badgley BD; Sadowsky MJ; Andersen GL; Griffith JF; Holden PA

2013-07-01

77

Community Structure Analysis of Gene Interaction Networks in Duchenne Muscular Dystrophy  

Science.gov (United States)

Duchenne Muscular Dystrophy (DMD) is an important pathology associated with the human skeletal muscle and has been studied extensively. Gene expression measurements on skeletal muscle of patients afflicted with DMD provides the opportunity to understand the underlying mechanisms that lead to the pathology. Community structure analysis is a useful computational technique for understanding and modeling genetic interaction networks. In this paper, we leverage this technique in combination with gene expression measurements from normal and DMD patient skeletal muscle tissue to study the structure of genetic interactions in the context of DMD. We define a novel framework for transforming a raw dataset of gene expression measurements into an interaction network, and subsequently apply algorithms for community structure analysis for the extraction of topological communities. The emergent communities are analyzed from a biological standpoint in terms of their constituent biological pathways, and an interpretation that draws correlations between functional and structural organization of the genetic interactions is presented. We also compare these communities and associated functions in pathology against those in normal human skeletal muscle. In particular, differential enhancements are observed in the following pathways between pathological and normal cases: Metabolic, Focal adhesion, Regulation of actin cytoskeleton and Cell adhesion, and implication of these mechanisms are supported by prior work. Furthermore, our study also includes a gene-level analysis to identify genes that are involved in the coupling between the pathways of interest. We believe that our results serve to highlight important distinguishing features in the structural/functional organization of constituent biological pathways, as it relates to normal and DMD cases, and provide the mechanistic basis for further biological investigations into specific pathways differently regulated between normal and DMD patients. These findings have the potential to serve as fertile ground for therapeutic applications involving targeted drug development for DMD.

Narayanan, Tejaswini; Subramaniam, Shankar

2013-01-01

78

Cost-benefit analysis of communities that care outcomes at eighth grade.  

UK PubMed Central (United Kingdom)

This paper presents a cost-benefit analysis of the Communities That Care (CTC) prevention system, a public health approach to reducing risk, enhancing protection, and reducing the prevalence of adolescent health and behavior problems community wide. The analysis is based on outcomes from a panel of students followed from Grade 5 through Grade 8 in a randomized controlled trial involving 24 communities in 7 states. Previous analyses have shown that CTC prevented the initiation of cigarette smoking, alcohol use, and delinquency by the end of 8th grade in CTC communities compared to controls. This paper estimates long-term monetary benefits associated with significant intervention effects on cigarette smoking and delinquency as compared to the cost of conducting the intervention. Under conservative cost assumptions, the net present benefit is $5,250 per youth, including $812 from the prevention of cigarette smoking and $4,438 from the prevention of delinquency. The benefit-cost ratio indicates a return of $5.30 per $1.00 invested. Under less conservative but still viable cost assumptions, the benefit-cost ratio due to prevention of cigarette smoking and delinquency increases to $10.23 per $1.00 invested. Benefits from CTC's reduction in alcohol initiation as well as broader inclusion of quality-of-life gains would further increase CTC's benefit-cost ratio. Results provide evidence that CTC is a cost-beneficial preventive intervention and a good investment of public dollars, even under very conservative cost and benefit assumptions.

Kuklinski MR; Briney JS; Hawkins JD; Catalano RF

2012-04-01

79

[Survey and clinical feature analysis of the aged subjective tinnitus in a community].  

UK PubMed Central (United Kingdom)

OBJECTIV: To investigate the basic incidence of subjective tinnitus in Xingui Community, Daliang, Shunde District, Guangdong Province, conduct preliminary analysis on its clinical feature, provide scientific evidence for subjective tinnitus prevention and cure in community. METHODS: Performed census in the entire population, totally 17253 people in Xingui Community, then gave tinnitus surveys for the people who have subjective tinnitus, and finally conducted analysis and evaluation. RESULTS: the morbidity of tinnitus in the investigated people is 28.7%. With the increases of age, the morbidity goes up graually, but it is not statistically significant(P>0.05) among different age group, and between different sex. There is an obvious correlation between tinnitus and hearing loss; Matching tone of tinnitus is related to the nature of hearing loss. The morbidity of decompensation tinnitus is 3.2%, it is not statistically significant among different age group(P>0.05). CONCLUSION: subjective tinnitus is common in aged people, so it is very important to strengthern the work of subjective tinnitus prevention and cure in Community.

Li YL; Tang Z; Yu XF

2013-08-01

80

ARISA analysis of ruminal bacterial community dynamics in lactating dairy cows during the feeding cycle.  

UK PubMed Central (United Kingdom)

The bovine rumen undergoes substantial changes in environmental conditions during the animal's feeding cycle, but the effects of these changes on microbial populations have not been examined systematically. Two dairy cows fed a mixed forage/concentrate ration at 12 h intervals over 4 feeding cycles displayed substantial changes in ruminal pH and volatile fatty acid (VFA) concentrations. Automated ribosomal intergenic spacer analysis (ARISA) of solid- and liquid-associated bacterial populations in samples collected at 2, 4, 6, 9, and 12 h after feeding revealed a high degree of bacterial diversity. A total of 155 different amplicon lengths (ALs) were detected across all 83 samples, and 11-74 detected per sample. A substantial proportion (11%) of the ALs was detected in one cow but not in the other. The proportions of ALs that were detected only in the liquid phase or the solid phase were 13.5% and 1.9%, respectively. Correspondence analysis indicated that bacterial community composition differed between cows and between solid or liquid phases, but overall the solid-associated population displayed less change in composition within and across feeding cycles. The data support the notion that cows fed the same diets can have substantial differences in bacterial community composition, and that the solids-associated (biofilm) communities display greater stability than do associated planktonic communities.

Welkie DG; Stevenson DM; Weimer PJ

2010-04-01

 
 
 
 
81

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

Directory of Open Access Journals (Sweden)

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.

Machida Ryuji J; Hashiguchi Yasuyuki; Nishida Mutsumi; Nishida Shuhei

2009-01-01

82

Cost-benefit analysis of communities that care outcomes at eighth grade.  

Science.gov (United States)

This paper presents a cost-benefit analysis of the Communities That Care (CTC) prevention system, a public health approach to reducing risk, enhancing protection, and reducing the prevalence of adolescent health and behavior problems community wide. The analysis is based on outcomes from a panel of students followed from Grade 5 through Grade 8 in a randomized controlled trial involving 24 communities in 7 states. Previous analyses have shown that CTC prevented the initiation of cigarette smoking, alcohol use, and delinquency by the end of 8th grade in CTC communities compared to controls. This paper estimates long-term monetary benefits associated with significant intervention effects on cigarette smoking and delinquency as compared to the cost of conducting the intervention. Under conservative cost assumptions, the net present benefit is $5,250 per youth, including $812 from the prevention of cigarette smoking and $4,438 from the prevention of delinquency. The benefit-cost ratio indicates a return of $5.30 per $1.00 invested. Under less conservative but still viable cost assumptions, the benefit-cost ratio due to prevention of cigarette smoking and delinquency increases to $10.23 per $1.00 invested. Benefits from CTC's reduction in alcohol initiation as well as broader inclusion of quality-of-life gains would further increase CTC's benefit-cost ratio. Results provide evidence that CTC is a cost-beneficial preventive intervention and a good investment of public dollars, even under very conservative cost and benefit assumptions. PMID:22108900

Kuklinski, Margaret R; Briney, John S; Hawkins, J David; Catalano, Richard F

2012-04-01

83

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

International Nuclear Information System (INIS)

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.

2006-02-01

84

Application of nonlinear analysis methods for identifying relationships between microbial community structure and groundwater geochemistry.  

UK PubMed Central (United Kingdom)

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.

Schryver JC; Brandt CC; Pfiffner SM; Palumbo AV; Peacock AD; White DC; McKinley JP; Long PE

2006-02-01

85

Application of nonlinear analysis methods for identifying relationships between microbial community structure and groundwater geochemistry.  

Science.gov (United States)

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. PMID:16435170

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

2006-01-31

86

A comparison of fungal communities from four salt marsh plants using automated ribosomal intergenic spacer analysis (ARISA).  

UK PubMed Central (United Kingdom)

Fungal decomposers are important contributors to the detritus-based food webs of salt marsh ecosystems. Knowing the composition of salt marsh fungal communities is essential in understanding how detritus processing is affected by changes in community dynamics. Automated ribosomal intergenic spacer analysis (ARISA) was used to examine the composition of fungal communities associated with four temperate salt marsh plants, Spartina alterniflora (short and tall forms), Juncus roemerianus, Distichlis spicata and Sarcocornia perennis. Plant tissues were homogenized and subjected to a particle-filtration protocol that yielded 106 microm particulate fractions, which were used as a source of fungal isolates and fungal DNA. Genera identified from sporulating cultures demonstrated that the 106 microm particles from each host plant were reliable sources of fungal DNA for ARISA. Analysis of ARISA data by principal component analysis (PCA), principal coordinate analysis (PCO) and species diversity comparisons indicated that the fungal communities from the two grasses, S. alterniflora and D. spicata were more similar to each other than they were to the distinct communities associated with J. roemerianus and S. perennis. Principal component analysis also showed no consistent, seasonal pattern in the composition of these fungal communities. Comparisons of ARISA fingerprints from the different fungal communities and those from pure cultures of selected Spartina ascomycetes supported the host/substrate specificity observed for the fungal communities.

Torzilli AP; Sikaroodi M; Chalkley D; Gillevet PM

2006-09-01

87

Molecular analysis of bacterial communities from a Canadian high Arctic polythermal glacier  

Science.gov (United States)

The goal of this study is to characterize the bacterial communities beneath, on, and adjacent to a high Arctic polythermal glacier, with a view to understanding the origins of the subglacial microbial population. The study site is John Evans Glacier (JEG), Ellesmere Island, Canada. JEG is a polythermal glacier consisting of a core of ice at the pressure melting point, surrounded by an outer layer of cold ice. Basal melting and seasonal inputs of meltwater from the glacier surface provide liquid water for subglacial microbial life. Samples were collected from the subglacial, supraglacial, and proglacial environments at JEG. Subglacial samples included basal ice and water that had been stored beneath the glacier. Dry snow, wet snow, and water from supraglacial streams were collected as representatives of the supraglacial environment, which changes in character through the melt season. Sediments and algal mats were collected from an area directly in front of the glacier terminus and along a transect adjacent to the glacier to reflect the developing proglacial environment. Hydrochemical analyses were conducted to assess the role of microbial activity in biogeochemical processes. To compare the bacterial communities, molecular techniques were applied to total community DNA that was released from the samples by a physical cell disruption technique. The polymerase chain reaction (PCR) was used with bacterial-specific primers, one of which was fluorescently labeled, to amplify community 16S rDNA genes. Single digestions with the restriction enzymes HaeIII and HhaI were performed to conduct inter- and intra-community comparisons of the terminal restriction fragment length polymorphisms (tRFLPs) of the fluorescently tagged amplified 16S rDNA genes. Preliminary results indicate that although some species are present throughout the different environments, several species are unique to each particular habitat. Further study of replicate tRFLP data and statistical analyses will allow analysis of community richness, diversity, and origin.

Bhatia, M.; Sharp, M.; Foght, J.

2003-04-01

88

Analysis of domestic tourism between the Spanish peninsular autonomous communities: specialization and competitive advantage  

Directory of Open Access Journals (Sweden)

Full Text Available This paper presents an implementation of shift share analysis ofnational tourism between the Spanish peninsular autonomous communities withovernight stays in hotels data. Thus, it achieves a more complete interpretation ofthe available statistical information. Among other things, it allows us to know theposition which each region has in terms of specialization and competitive advantageand, hence, the potential markets for development can be identified.

José J. Benítez Rochel; Susana Cabrera Yeto

2011-01-01

89

Comparative study of three analysis methods (TTGE, flow cytometry and HPLC) for xenobiotic impact assessment on phytoplankton communities  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The impacts of the fungicide Opus(A (R)) (epoxiconazole) on marine phytoplankton communities were assessed in a 12-day field experiment using in situ microcosms maintained underwater at 6 m depth. Three community analysis methods were compared for their sensitivity threshold in fungicide impact dete...

Stachowski-haberkorn, Sabine; Quiniou, Louis; Beker, Beatriz; Haberkorn, Hansy; Marie, Dominique; De La Broise, Denis

90

A directed network analysis of heterospecific pollen transfer in a biodiverse community.  

UK PubMed Central (United Kingdom)

Community studies have shown that plant species are often pollinated by multiple pollinators; however, networks of heterospecific pollen transfer (HPT) in natural communities remain largely unexplored. We analyzed pollen deposition on stigmas of 57 flowering species to build a picture of plant-plant interactions via HPT in a biodiverse alpine meadow in southwest China. Plant species were categorized as pollen donors or recipients by their link numbers and link qualities. We identified 3609 heterospecific pollen grains, representing 410 links among 69 pollen species. Each plant species received on average 7.2 pollen species and donated its pollen to 5.5 species; only a few species donated or received large amounts of pollen or pollen from a large number of species. Compared to specialized plants, generalized plants tended to receive more heterospecific pollen but exported no more pollen to other species. Plant position in the network was related to both floral traits (stigma position) and pollinator generalization level. When different species share the same pollinator, bidirectional HPT may occur, but this was rarely observed in the species-rich community, indicating that interspecific pollen interference was largely unidirectional. Our study highlights the importance of understanding how sympatric flowering plants reduce deleterious effects of HPT, for example via stigma position. This study is the first to present a pollen transfer network for an entire community and to unravel its properties using directed network analysis.

Fang Q; Huang SQ

2013-05-01

91

Leaving a spinal unit and returning to the wider community: an interpretative phenomenological analysis.  

UK PubMed Central (United Kingdom)

PURPOSE: The study investigated the experience of community (re)integration from the perspective of people with spinal cord injury (SCI) within 12 months of discharge from a specialist spinal injuries unit in New Zealand (NZ). METHOD: Nine participants were interviewed. The verbatim transcripts were analysed using Interpretive Phenomenological Analysis (IPA). RESULTS: Three main themes were: Leaving, Not Coping with a Capital C, and Power and Control. Leaving related to the process of planning for, and discharge from the spinal unit. Not Coping with a Capital C incorporated the coping and adjustment to life following a SCI, including the role of hope. Power and Control denoted the alteration in balance of power and control following SCI which was evident both in the rehabilitation facility and within the wider community setting. CONCLUSIONS: The results indicated that the spinal unit may not adequately equip the recovering person with SCI for life in the real world. Individuals with SCI returning to the community remained hopeful of recovery of function and or cure; this focus, particularly on physical rehabilitation, potentially reduced their availability for other forms of community reintegration such as work and leisure activities.

Nunnerley JL; Hay-Smith EJ; Dean SG

2013-07-01

92

Community participation in two vaccination trials in slums of Kolkata, India: a multi-level analysis.  

UK PubMed Central (United Kingdom)

This study aims at understanding the individual and community-level characteristics that influenced participation in two consecutive vaccine trials (typhoid and cholera) in urban slums of Kolkata, India. The study area was divided into 80 geographic clusters (communities), with 59,533 subjects aged > or = 2 years for analysis. A multi-level model was employed in which the individuals were seen nested within the cluster. Rates of participation in both the trials were nearly the same; those who participated in the initial trial were likely to participate in the subsequent cholera vaccine trial. Communities with predominantly Hindu population, lower percentage of households with an educated household head, or lower percentage of households owning a motorbike had higher participation than their counterparts. At individual scale, higher participation was observed among younger subjects, females, and individuals from households with a household head who had no or minimal education. Geographic patterns were also observed in participation in the trials. The results illustrated that participation in the trial was mostly influenced by various individual and community-level factors, which need to be addressed for a successful vaccination campaign.

Ali M; Sur D; Lopez AL; Kanungo S; Ochiai RL; Manna B; Kim DR; Deen J; Bhattacharya SK; Clemens JD

2010-10-01

93

Community participation in two vaccination trials in slums of Kolkata, India: a multi-level analysis.  

Science.gov (United States)

This study aims at understanding the individual and community-level characteristics that influenced participation in two consecutive vaccine trials (typhoid and cholera) in urban slums of Kolkata, India. The study area was divided into 80 geographic clusters (communities), with 59,533 subjects aged > or = 2 years for analysis. A multi-level model was employed in which the individuals were seen nested within the cluster. Rates of participation in both the trials were nearly the same; those who participated in the initial trial were likely to participate in the subsequent cholera vaccine trial. Communities with predominantly Hindu population, lower percentage of households with an educated household head, or lower percentage of households owning a motorbike had higher participation than their counterparts. At individual scale, higher participation was observed among younger subjects, females, and individuals from households with a household head who had no or minimal education. Geographic patterns were also observed in participation in the trials. The results illustrated that participation in the trial was mostly influenced by various individual and community-level factors, which need to be addressed for a successful vaccination campaign. PMID:20941896

Ali, Mohammad; Sur, Dipika; Lopez, Anna Lena; Kanungo, Suman; Ochiai, R Leon; Manna, Byomkesh; Kim, Deok Ryun; Deen, Jacqueline; Bhattacharya, Sujit K; Clemens, John D

2010-10-01

94

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

UK PubMed Central (United Kingdom)

It is increasingly recognised 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). In order 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.

Underwood M

2013-08-01

95

Microbial community analysis of swine wastewater anaerobic lagoons by next-generation DNA sequencing.  

UK PubMed Central (United Kingdom)

Anaerobic lagoons are a standard practice for the treatment of swine wastewater. This practice relies heavily on microbiological processes to reduce concentrated organic material and nutrients. Despite this reliance on microbiological processes, research has only recently begun to identify and enumerate the myriad and complex interactions that occur in this microbial ecosystem. To further this line of study, we utilized a next-generation sequencing (NGS) technology to gain a deeper insight into the microbial communities along the water column of four anaerobic swine wastewater lagoons. Analysis of roughly one million 16S rDNA sequences revealed a predominance of operational taxonomic units (OTUs) classified as belonging to the phyla Firmicutes (54.1%) and Proteobacteria (15.8%). At the family level, 33 bacterial families were found in all 12 lagoon sites and accounted for between 30% and 50% of each lagoon's OTUs. Analysis by nonmetric multidimensional scaling (NMS) revealed that TKN, COD, ORP, TSS, and DO were the major environmental variables in affecting microbial community structure. Overall, 839 individual genera were classified, with 223 found in all four lagoons. An additional 321 genera were identified in sole lagoons. The top 25 genera accounted for approximately 20% of the OTUs identified in the study, and the low abundances of most of the genera suggests that most OTUs are present at low levels. Overall, these results demonstrate that anaerobic lagoons have distinct microbial communities which are strongly controlled by the environmental conditions present in each individual lagoon.

Ducey TF; Hunt PG

2013-06-01

96

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

Directory of Open Access Journals (Sweden)

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.

Khadka C; Vacik H

2012-01-01

97

[Structural analysis of the new model of primary care in the community of Valencia  

UK PubMed Central (United Kingdom)

OBJECTIVES: To analyse the structure of the new model of primary care (NMPC) in the Community of Valencia, and to identify the strategic importance of its characteristic variables and the possibilities of intervention to affect these variables. DESIGN: A qualitative study through a method of structural analysis (crossed impact method-multiplication applied to a classification) of the relationships between 37 variables characterising the NMPC which were identified by prior qualitative research, with interpretation of the results using the Téniere-Buchot Model. SETTING: Community of Valencia. RESULTS: The structural variables identified were those relating to the political-legal framework and to the allocation of primary care resources; and the resultant variables, those relating to efficiency and primary care quality. Between these two categories, the intervention variables covered management, NMPC professionals, health needs and the community's use of services. CONCLUSIONS: The structural analysis gives the legal-political and economical framework a determining role in NMPC, which can hardly be influenced from within the system. Management and organisation are identified as key variables from which an intervention can be made in the short or medium term to achieve the aims of the system.

Compañ L; Portella E; Peiró S

1996-11-01

98

On the Analysis of a Label Propagation Algorithm for Community Detection  

CERN Multimedia

This paper initiates formal analysis of a simple, distributed algorithm for community detection on networks. We analyze an algorithm that we call \\textsc{Max-LPA}, both in terms of its convergence time and in terms of the "quality" of the communities detected. \\textsc{Max-LPA} is an instance of a class of community detection algorithms called \\textit{label propagation} algorithms. As far as we know, most analysis of label propagation algorithms thus far has been empirical in nature and in this paper we seek a theoretical understanding of label propagation algorithms. In our main result, we define a clustered version of \\er random graphs with clusters $V_1, V_2,..., V_k$ where the probability $p$, of an edge connecting nodes within a cluster $V_i$ is higher than $p'$, the probability of an edge connecting nodes in distinct clusters. We show that even with fairly general restrictions on $p$ and $p'$ ($p = \\Omega(\\frac{1}{n^{1/4-\\epsilon}})$ for any $\\epsilon > 0$, $p' = O(p^2)$, where $n$ is the number of nodes...

Kothapalli, Kishore; Sardeshmukh, Vivek

2012-01-01

99

Prospective policy analysis: how an epistemic community informed policymaking on intentional self poisoning in Sri Lanka  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Policy analysis is often retrospective and not well suited to helping policy makers decide what to do; in contrast prospective policy analysis seeks to assist in formulating responses to challenging public policy questions. Suicide in Sri Lanka is a major public health problem, with ingestion of pesticides being the primary method. Previous policy interventions have been associated with reduced mortality through restricting access to the most toxic pesticides. Additional means of reducing access are still needed. Methods The prospective policy analysis comprised two stages. The first used a consensus activity within a well defined policy community to generate and frame policy options. The second broadened the analysis to include other stakeholders. We report the consensus activity with seven actors from agriculture, health, and academia. Policy options were identified through two rounds of discussion along with ratings by each participant on their degree of support for each option. Data were analysed quantitatively and discussions analysed with Nvivo 8 to code prominent and recurrent themes. Results The main finding was the strong support and consensus for two proposals: further regulation of pesticides and the novel idea of repackaging pesticides into non-lethal doses. Participants identified several factors that were supportive of future policy change including a strong legislative framework, good links between agriculture, health and academia, and a collaborative relationship with industry. Identified barriers and potential threats to policy change included political interference, difficulties of intersectoral collaboration, acceptability of options to the community, difficulty of implementation in rural communities and the challenge of reducing mortality. Conclusions The development and consideration of policy options within this epistemic community reflected an appreciation and understanding of many of the factors that can facilitate or thwart policy change. The understanding of context, evidence and ideas, implementation and impact influenced how the participants considered and rated the options. Use of epistemic community actors identified the level of support for each option, helped elaborate the particularities of context, as well as the power and influence of ideas. Further examination of the potential barriers and opportunities for these options will determine if broader consensus, involving a wider range of stakeholders, can be achieved and policy change promoted.

Pearson Melissa; Anthony Zwi B; Buckley Nicholas A

2010-01-01

100

The use of robustness analysis for planning actions in a poor Brazilian community  

Directory of Open Access Journals (Sweden)

Full Text Available This paper reports on the use of Robustness Analysis for planning actions in a poor Brazilian community. The focus is on food and agricultural production and the project is based on a participatory approach incorporating both community-driven development and sustainability in food production. A comparison is made with other soft Operations Research (OR) methodologies and first actions and results are reported.Este artigo propõe o uso da Análise de Robustez para o planejamento de ações em uma comunidade de baixa renda no Brasil. O foco está na produção agrícola e de alimentos e o projeto fundamenta-se em uma abordagem participativa incorporando tanto o desenvolvimento voltado para a comunidade quanto a sustentabilidade na produção de alimentos. Apresenta-se uma comparação com outras metodologias de PO soft e relatam-se alguns resultados e ações.

Anderson Amendoeira Namen; Cláudio Thomás Bornstein; Jonathan Rosenhead

2010-01-01

 
 
 
 
101

An Analysis of Interactions Within and Between Extreme Right Communities in Social Media  

CERN Document Server

Many extreme right groups have had an online presence for some time through the use of dedicated websites. This has been accompanied by increased activity in social media websites in recent years, which may enable the dissemination of extreme right content to a wider audience. In this paper, we present exploratory analysis of the activity of a selection of such groups on Twitter, using network representations based on reciprocal follower and mentions interactions. We find that stable communities of related users are present within individual country networks, where these communities are usually associated with variants of extreme right ideology. Furthermore, we also identify the presence of international relationships between certain groups across geopolitical boundaries.

O'Callaghan, Derek; Conway, Maura; Carthy, Joe; Cunningham, Pádraig

2012-01-01

102

Comparison of primer sets for use in automated ribosomal intergenic spacer analysis of aquatic bacterial communities: an ecological perspective.  

UK PubMed Central (United Kingdom)

Two primer sets for automated ribosomal intergenic spacer analysis (ARISA) were used to assess the bacterial community composition (BCC) in Lake Mendota, Wisconsin, over 3 years. Correspondence analysis revealed differences in community profiles generated by different primer sets, but overall ecological patterns were conserved in each case. ARISA is a powerful tool for evaluating BCC change through space and time, regardless of the specific primer set used.

Jones SE; Shade AL; McMahon KD; Kent AD

2007-01-01

103

Cost-Benefit Analysis of Communities That Care Outcomes at Eighth Grade  

Science.gov (United States)

This paper presents a cost-benefit analysis of the Communities That Care (CTC) prevention system, a public health approach to reducing risk, enhancing protection, and reducing the prevalence of adolescent health and behavior problems community wide. The analysis is based on outcomes from a panel of students followed from Grade 5 through Grade 8 in a randomized controlled trial involving 24 communities in 7 states. Previous analyses have shown that CTC prevented the initiation of cigarette smoking, alcohol use, and delinquency by the end of 8th grade in CTC communities compared to controls. This paper estimates long-term monetary benefits associated with significant intervention effects on cigarette smoking and delinquency as compared to the cost of conducting the intervention. Under conservative cost assumptions, the net present benefit is $5,250 per youth, including $812 from the prevention of cigarette smoking and $4,438 from the prevention of delinquency. The benefit-cost ratio indicates a return of $5.30 per $1.00 invested. Under less conservative but still viable cost assumptions, the benefit-cost ratio due to prevention of cigarette smoking and delinquency increases to $10.23 per $1.00 invested. Benefits from CTC’s reduction in alcohol initiation as well as broader inclusion of quality-of-life gains would further increase CTC’s benefit-cost ratio. Results provide evidence that CTC is a cost-beneficial preventive intervention and a good investment of public dollars, even under very conservative cost and benefit assumptions.

Kuklinski, Margaret R.; Briney, John S.; Hawkins, J. David; Catalano, Richard F.

2011-01-01

104

Annual-cycle thermal energy storage for a community solar system: details of a sensitivity analysis  

Energy Technology Data Exchange (ETDEWEB)

This report presents results and conclusions of a simulation and sensitivity analysis of community-sized, annual-cycle thermal-energy-storage (ACTES) solar energy systems. The analysis which is based on an hourly simulation is used to (1) size systems in 10 locations, (2) identify critical design parameters, and (3) provide a basic conceptual approach for future studies and designs. This research is a forerunner to an economic analysis of this particular system (based on large constructed tanks) and a general analysis of the value of ACTES technologies for solar applications. A total of 440 systems were sized for 10 locations in the United States. Three different building types and four different community sizes were modeled. All designs used each of two collector types at each of two different tilt angles. Two linear relationships were derived which simplify system sizing. The average ambient temperature is used to determine average yearly collector efficiency. This parameter combined with estimates of space/DHW loads, storage/distribution losses, and total yearly insolation per square meter allows estimation of collector area. Storage size can be estimated from the winter net load which is based on space and DHW loads, storage and distribution losses, and collector solar heat gain for the winter months.

Baylin, F.; Monte, R.; Sillman, S.

1980-07-01

105

Energy engineering analysis program, Fulda Military Community Germany. Executive summary. Final report  

Energy Technology Data Exchange (ETDEWEB)

This Executive Summary outlines the results of all work for the Energy Engineering Analysis Program (EEAP), Fulda Military Community, Germany. This work was authorized under contract number DACA 90-82-C-0204 with the U.S. Army Corps of Engineers, Europe Division, Frankfurt AIM, Germany. The primary purpose of the Energy Engineering Analysis Program was to develop Energy Conservation investment Program (ECiP) projects that comply with the objectives set forth in the Army Facilities Energy Plan. The work was performed in three phases: Phase I consisted of data gathering and inspection of facilities culminating in a data report; Phase II included energy data analysis, evaluation of the technical and economic feasibility of energy conservation opportunities, and completion of the front pages of DD Forms 1391; Phase III included preparation and completion of DO Forms 1391, including detailed justifications and project development brochures (PDB-I`s).

NONE

1984-05-01

106

Energy Engineering Analysis Program. Bamberg Military Community Germany. Executive summary. Final report  

Energy Technology Data Exchange (ETDEWEB)

This Executive Summary outlines the results of all work for the Energy Engineering Analysis Program (EEAP), Bamberg Military Community, Germany. This work was authorized under contract number DACA 90-82-C-0204 with the U.S. Army Corps of Engineers, Europe Division, Frankfurt A/M, Germany. The primary purpose of the Energy Engineering Analysis Program was to develop Energy Conservation Investment Program (ECIP) projects that comply with the objectives set forth in the Army Facilities Energy Plan. The work was performed in three phases: Phase 1 consisted of data gathering and inspection of facilities culminating in a data report; Phase II included energy data analysis, evaluation of the technical and economic feasibility of energy conservation opportunities, and completion of the front pages of DD Forms 1391; Phase III included preparation and completion of DD Forms 1391, including detailed justifications and project development brochures (PDB-I`s).

NONE

1984-05-01

107

Bacterial community analysis of shallow groundwater undergoing sequential anaerobic and aerobic chloroethene biotransformation.  

Science.gov (United States)

At Department of Energy Site 300, beneficial hydrocarbon cocontaminants and favorable subsurface conditions facilitate sequential reductive dechlorination of trichloroethene (TCE) and rapid oxidation of the resultant cis-dichloroethene (cis-DCE) upon periodic oxygen influx. We assessed the geochemistry and microbial community of groundwater from across the site. Removal of cis-DCE was shown to coincide with oxygen influx in hydrocarbon-containing groundwater near the source area. Principal component analysis of contaminants and inorganic compounds showed that monitoring wells could be differentiated based upon concentrations of TCE, cis-DCE, and nitrate. Structurally similar communities were detected in groundwater from wells containing cis-DCE, high TCE, and low nitrate levels. Bacteria identified by sequencing 16S rRNA genes belonged to seven phylogenetic groups, including Alpha-, Beta-, Gamma- and Deltaproteobacteria, Nitrospira, Firmicutes and Cytophaga-Flexibacter-Bacteroidetes (CFB). Whereas members of the Burkholderiales and CFB group were abundant in all wells (10(4)-10(9) 16S rRNA gene copies L(-1)), quantitative PCR showed that Alphaproteobacteria were elevated (>10(6) L(-1)) only in wells containing hydrocarbon cocontaminants. The study shows that bacterial community structure is related to groundwater geochemistry and that Alphaproteobacteria are enriched in locales where cis-DCE removal occurs. PMID:17386036

Miller, Todd R; Franklin, Mark P; Halden, Rolf U

2007-03-26

108

Bacterial community analysis of shallow groundwater undergoing sequential anaerobic and aerobic chloroethene biotransformation.  

UK PubMed Central (United Kingdom)

At Department of Energy Site 300, beneficial hydrocarbon cocontaminants and favorable subsurface conditions facilitate sequential reductive dechlorination of trichloroethene (TCE) and rapid oxidation of the resultant cis-dichloroethene (cis-DCE) upon periodic oxygen influx. We assessed the geochemistry and microbial community of groundwater from across the site. Removal of cis-DCE was shown to coincide with oxygen influx in hydrocarbon-containing groundwater near the source area. Principal component analysis of contaminants and inorganic compounds showed that monitoring wells could be differentiated based upon concentrations of TCE, cis-DCE, and nitrate. Structurally similar communities were detected in groundwater from wells containing cis-DCE, high TCE, and low nitrate levels. Bacteria identified by sequencing 16S rRNA genes belonged to seven phylogenetic groups, including Alpha-, Beta-, Gamma- and Deltaproteobacteria, Nitrospira, Firmicutes and Cytophaga-Flexibacter-Bacteroidetes (CFB). Whereas members of the Burkholderiales and CFB group were abundant in all wells (10(4)-10(9) 16S rRNA gene copies L(-1)), quantitative PCR showed that Alphaproteobacteria were elevated (>10(6) L(-1)) only in wells containing hydrocarbon cocontaminants. The study shows that bacterial community structure is related to groundwater geochemistry and that Alphaproteobacteria are enriched in locales where cis-DCE removal occurs.

Miller TR; Franklin MP; Halden RU

2007-05-01

109

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

Directory of Open Access Journals (Sweden)

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.

Eppley John M; Tyson Gene W; Getz Wayne M; Banfield Jillian F

2007-01-01

110

Project management competence analysis in rural communities through territorial representation: application to Aymara women communities in Puno (Peru)  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The acquisition of technical, contextual and behavioral competences is a prerequisite for sustainable development and strengthening of rural communities. Territorial display of the status of these skills helps to design the necessary learning, so its inclusion in planning processes is useful for dec...

Sastre Merino, Susana; Ríos Carmenado, Ignacio de los

111

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

Directory of Open Access Journals (Sweden)

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 (? = .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 combined use of SPSS and GIS. The results from this study indicate a potential for OLAP-GIS decision support systems as a valuable tool for CHA data analysis.

Scotch Matthew; Parmanto Bambang; Monaco Valerie

2008-01-01

112

Using a SWOT analysis to inform healthy eating and physical activity strategies for a remote First Nations community in Canada.  

UK PubMed Central (United Kingdom)

PURPOSE: To plan community-driven health promotion strategies based on a strengths, weaknesses, opportunities, and threats (SWOT) analysis of the healthy eating and physical activity patterns of First Nation (FN) youth. DESIGN: Cross-sectional qualitative and quantitative data used to develop SWOT themes and strategies. SETTING: Remote, subarctic FN community of Fort Albany, Ontario, Canada. SUBJECTS: Adult (n ?=? 25) and youth (n ?=? 66, grades 6-11) community members. MEASURES: Qualitative data were collected using five focus groups with adults (two focus groups) and youth (three focus groups), seven individual interviews with adults, and an environmental scan of 13 direct observations of events/locations (e.g., the grocery store). Quantitative data on food/physical activity behaviors were collected using a validated Web-based survey with youth. ANALYSIS: Themes were identified from qualitative and quantitative data and were analyzed and interpreted within a SWOT matrix. RESULTS: Thirty-two SWOT themes were identified (e.g., accessibility of existing facilities, such as the gymnasium). The SWOT analysis showed how these themes could be combined and transformed into 12 strategies (e.g., expanding and enhancing the school snack/breakfast program) while integrating suggestions from the community. CONCLUSION: SWOT analysis was a beneficial tool that facilitated the combination of local data and community ideas in the development of targeted health promotion strategies for the FN community of Fort Albany.

Skinner K; Hanning RM; Sutherland C; Edwards-Wheesk R; Tsuji LJ

2012-07-01

113

Actinomycetal community structures in seawater and freshwater examined by DGGE analysis of 16S rRNA gene fragments.  

UK PubMed Central (United Kingdom)

The actinomycetal community structures in marine and freshwater environments (the Pacific Ocean, East China Sea, Tokyo Bay, and Arakawa River) were investigated by a culture-independent molecular method to clarify spatial and seasonal distributions. Deoxyribonucleic acid (DNA) was extracted from environmental water samples, and a community analysis was carried out on polymerase chain reaction-amplified 16S ribosomal DNA. The amplified DNA fragments were analyzed by denaturing gradient gel electrophoresis (DGGE) and nonmetric multidimensional scaling analysis, followed by sequencing analysis. The actinomycetal community structures were different at each station in the Pacific Ocean, the East China Sea, Tokyo Bay, and Arakawa River, and different populations predominated in each area. There were vertical variations in actinomycetal communities in the Pacific Ocean and East China Sea between the surface and 100-m depth, but communities were similar from 200- to 1,000-m depths. There were also distinct seasonal variations in communities in Tokyo Bay. Phylogenetic analysis of DNA fragments recovered from DGGE bands revealed that most of the predominant actinomycetal strains were uncultured and were quite different from well known culturable strains, such as the Streptomyces, Micromonospora, Microbispora, Salinispora, and Actinoplanes groups. These results suggest that the marine environment is an attractive target for discovering new actinomycetal populations producing bioactive compounds and that sampling depth and season are important considerations for isolating various populations effectively.

Yoshida A; Seo Y; Suzuki S; Nishino T; Kobayashi T; Hamada-Sato N; Kogure K; Imada C

2008-09-01

114

Actinomycetal community structures in seawater and freshwater examined by DGGE analysis of 16S rRNA gene fragments.  

Science.gov (United States)

The actinomycetal community structures in marine and freshwater environments (the Pacific Ocean, East China Sea, Tokyo Bay, and Arakawa River) were investigated by a culture-independent molecular method to clarify spatial and seasonal distributions. Deoxyribonucleic acid (DNA) was extracted from environmental water samples, and a community analysis was carried out on polymerase chain reaction-amplified 16S ribosomal DNA. The amplified DNA fragments were analyzed by denaturing gradient gel electrophoresis (DGGE) and nonmetric multidimensional scaling analysis, followed by sequencing analysis. The actinomycetal community structures were different at each station in the Pacific Ocean, the East China Sea, Tokyo Bay, and Arakawa River, and different populations predominated in each area. There were vertical variations in actinomycetal communities in the Pacific Ocean and East China Sea between the surface and 100-m depth, but communities were similar from 200- to 1,000-m depths. There were also distinct seasonal variations in communities in Tokyo Bay. Phylogenetic analysis of DNA fragments recovered from DGGE bands revealed that most of the predominant actinomycetal strains were uncultured and were quite different from well known culturable strains, such as the Streptomyces, Micromonospora, Microbispora, Salinispora, and Actinoplanes groups. These results suggest that the marine environment is an attractive target for discovering new actinomycetal populations producing bioactive compounds and that sampling depth and season are important considerations for isolating various populations effectively. PMID:18418650

Yoshida, Akihiro; Seo, Yuna; Suzuki, Shuhei; Nishino, Tomohiko; Kobayashi, Takeshi; Hamada-Sato, Naoko; Kogure, Kazuhiro; Imada, Chiaki

2008-04-17

115

Community-based care for the management of type 2 diabetes: an evidence-based analysis.  

UK PubMed Central (United Kingdom)

UNLABELLED: In June 2008, the Medical Advisory Secretariat began work on the Diabetes Strategy Evidence Project, an evidence-based review of the literature surrounding strategies for successful management and treatment of diabetes. This project came about when the Health System Strategy Division at the Ministry of Health and Long-Term Care subsequently asked the secretariat to provide an evidentiary platform for the Ministry's newly released Diabetes Strategy.After an initial review of the strategy and consultation with experts, the secretariat identified five key areas in which evidence was needed. Evidence-based analyses have been prepared for each of these five areas: insulin pumps, behavioural interventions, bariatric surgery, home telemonitoring, and community based care. For each area, an economic analysis was completed where appropriate and is described in a separate report.To review these titles within the Diabetes Strategy Evidence series, please visit the Medical Advisory Secretariat Web site, http://www.health.gov.on.ca/english/providers/program/mas/mas_about.html,DIABETES STRATEGY EVIDENCE PLATFORM: Summary of Evidence-Based AnalysesContinuous Subcutaneous Insulin Infusion Pumps for Type 1 and Type 2 Adult Diabetics: An Evidence-Based AnalysisBehavioural Interventions for Type 2 Diabetes: An Evidence-Based AnalysisBARIATRIC SURGERY FOR PEOPLE WITH DIABETES AND MORBID OBESITY: An Evidence-Based SummaryCommunity-Based Care for the Management of Type 2 Diabetes: An Evidence-Based AnalysisHome Telemonitoring for Type 2 Diabetes: An Evidence-Based AnalysisApplication of the Ontario Diabetes Economic Model (ODEM) to Determine the Cost-effectiveness and Budget Impact of Selected Type 2 Diabetes Interventions in Ontario OBJECTIVE: The objective of this report is to determine the efficacy of specialized multidisciplinary community care for the management of type 2 diabetes compared to usual care. CLINICAL NEED: TARGET POPULATION AND CONDITION Diabetes (i.e. diabetes mellitus) is a highly prevalent chronic metabolic disorder that interferes with the body's ability to produce or effectively use insulin. The majority (90%) of diabetes patients have type 2 diabetes. (1) Based on the United Kingdom Prospective Diabetes Study (UKPDS), intensive blood glucose and blood pressure control significantly reduce the risk of microvascular and macrovascular complications in type 2 diabetics. While many studies have documented that patients often do not meet the glycemic control targets specified by national and international guidelines, factors associated with glycemic control are less well studied, one of which is the provider(s) of care. Multidisciplinary approaches to care may be particularly important for diabetes management. According guidelines from the Canadian Diabetes Association (CDA), the diabetes health care team should be multi-and interdisciplinary. Presently in Ontario, the core diabetes health care team consists of at least a family physician and/or diabetes specialist, and diabetes educators (registered nurse and registered dietician). Increasing the role played by allied health care professionals in diabetes care and their collaboration with physicians may represent a more cost-effective option for diabetes management. Several systematic reviews and meta-analyses have examined multidisciplinary care programs, but these have either been limited to a specific component of multidisciplinary care (e.g. intensified education programs), or were conducted as part of a broader disease management program, of which not all were multidisciplinary in nature. Most reviews also do not clearly define the intervention(s) of interest, making the evaluation of such multidisciplinary community programs challenging. EVIDENCE-BASED ANALYSIS METHODS: RESEARCH QUESTIONS: What is the evidence of efficacy of specialized multidisciplinary community care provided by at least a registered nurse, registered dietician and physician (primary care and/or specialist) for the management of type 2 diabetes compared to usual care? [Henceforth referre

2009-01-01

116

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

UK PubMed Central (United Kingdom)

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 complex socio-economic and cultural determinants of health in multi-ethnic population groups. These lessons learned can improve future RHSP in Vietnam and are also of relevance for health promotion in other minority population groups in the region and globally.

Rheinländer T; Xuan le TT; Hoat LN; Dalsgaard A; Konradsen F

2012-10-01

117

?????????????????? Analysis of Bacterial Community Structure in Water Retting and Enzymatic Retting Liquid  

Directory of Open Access Journals (Sweden)

Full Text Available ????????????????????????DGGE??(Denaturing gradient gel electrophoresis)???????????????????DGGE???????????????8%?????????25%~65%???60??150 V?????7 h????DGGE????????PCR-DGGE??????????????????????????????????????????????????16S rDNA V3??PCR???DGGE??????????????Blast???????????????????????-????????????????????????????????????????????????????????????????????????????????????????? In order to investigate the bacterial community diversity of warm water retting liquid and enzymatic retting liquid, both of the retting liquid samples were studied by using Denaturing Gradient Gel Electrophoresis (DGGE). During using DGGE method to analyze the bacterial diversity, DGGE bands were separated obviously by the gel concentration of 8%, range of 25% - 65% denaturant gradient, temperature of 60?C and voltage of 150 V for electrophoresis time of about 7 h. Through analysis, the selected bands of DGGE profiles were cloned and sequenced. The obtained sequence results by Blast analysis were used to construct the phylogenetic tree. We found Pseudomonas of Gammaproteobacteria were the dominant bacteria both in warm water retting and enzymatic retting liquid samples. Bacillus of Firmicutes occurred along with the whole process of the two retting samples. However, in addition to share the dominant bacteria, the two samples also represented the differences in bacterial community structure.

???; ???

2012-01-01

118

Microbial community analysis involved in the aerobic/extended-idle process performing biological phosphorus removal.  

UK PubMed Central (United Kingdom)

Recently, it has been found that biological phosphorus removal can be achieved in an aerobic/extended-idle (AEI) process using both glucose and acetate as the sole substrate. However, the microbial consortiums involved in glucose-fed and acetate-fed systems have not yet been characterized. Thus the aims of this paper were to investigate the diversities and dynamics of bacterial communities during the acclimation period, and to quantify polyphosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs) in the systems. The phylogenetic analysis showed that the microbial communities were mainly composed of phylum Proteobacteria, Bacteroidetes, Chlorobi and another six kinds of unclassified bacteria. Fluorescence in-situ hybridization (FISH) analysis revealed that PAOs and GAOs accounted for 43 ± 7 and 16 ± 3% of all bacteria in the glucose-fed system, and 19 ± 4 and 35 ± 5% of total bacteria in the acetate-fed system, respectively. The results showed that the conventional PAOs could thrive in the AEI process, and a defined anaerobic zone was not necessarily required for putative PAOs growth.

Zeng TJ; Yang GJ; Wang DB; Li XM; Zheng W; Yang Q; Zeng GM

2013-01-01

119

Facebook in Higher Education Courses: An Analysis of Students’ Attitudes,Community of Practice, and Classroom Community  

Directory of Open Access Journals (Sweden)

Full Text Available Educators wanting to enhance their classroom learning environment are finding Facebook to be a beneficial supplement. This study aims to determine students’ attitudes and perceptions of courses into which Facebook has been incorporated. In a posttest only research design involving 106 students at two large public universities, it was found that students were favorably disposed toward the classroom use of Facebook. They perceived that it enhanced their senses of social learning and connectedness, with older students experiencing a stronger effect. Implications for how Facebook can enhance higher education courses and for the management of social media in the classroom are discussed. Key words: Facebook in higher education; Communities of practice; Classroom community; Social learning and effectiveness; Learner-centered activities

Casimir C. Barczyk; Doris G. Duncan

2013-01-01

120

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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 i...

Helene Amundsen

 
 
 
 
121

Microbial community analysis of shallow subsurface samples with PCR-DGGE  

International Nuclear Information System (INIS)

This work is part of the site investigations for the disposal of spent nuclear fuel in Olkiluoto bedrock. The purpose of the research was to study the suitability of PCR-DGGE (polymerase chain reaction - denaturing gradient gel electrophoresis) method for monitoring of hydrogeomicrobiology of Olkiluoto repository site. PCR-DGGE method has been applied for monitoring microbial processes in several applications. The benefit of the method is that microorganisms are not cultivated but the presence of microbial communities can be monitored by direct DNA extractions from the environmental samples. Partial 16SrDNA gene sequence is specifically amplified by PCR (polymerase chain reaction) which detect bacteria as a group. The gene sequences are separated in DGGE, and the nucleotide bands are then cut out, extracted, sequenced and identified by the genelibraries by e.g. Blast program. PCR-DGGE method can be used to detect microorganisms which are present abundantly in the microbial communities because small quantities of genes cannot be separated reliably. However, generally the microorganisms involved in several environmental processes are naturally enriched and present as major population. This makes it possible to utilize PCRDGGE as a monitoring method. In this study, we studied the structure of microbial communities in ten ground water samples originating from Olkiluoto. Two universal bacterial primer sets were compared which amplified two different regions of the 16SrDNA gene. The longer sequence amplified resulted in fewer bands in DGGE, in addition there were problems with purification of the sequences after DGGE. The shorter sequence gave more bands in DGGE and more clear results without any amplification problems. Comparison of the sequences from the gene-libraries resulted in the detection of the same species by both primer sets, in addition some different species were detected. Several species were anaerobic bacteria, such as acetogenic and sulphate reducing 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.)

2005-01-01

122

[Statistical methods for analysis of communities' species structure (with riverine macrozoobenthos as an example)].  

UK PubMed Central (United Kingdom)

Species turnover or coherence in species co-occurrence as well as boundary clumping and nestedness in structural composition of ecological communities reflect the extent of determinancy in their organization (Leibold, Mikkelson, 2002). These phenomena may be a consequence of either interactions between species or heterogeneity in spatial distribution of populations density. We have examined statistical patterns of species structure variability using benthic communities of riverine ecosystems as an example. The ecosystems studied are characterized by strongly pronounced linear gradient of landscape features and environmental factors. The results of a long-term hydrobiological survey being conducted at 22 observational stations on the Sok River along with its tributary, the Baytugan River (Lower Volga basin, total watercourse length is 375 km) are involved into the analysis. A spreadsheet for statistical processing of the data included 375 macrozoobenthic taxa contained in 147 samples. An assessment of species structure nestedness in benthic communities at separate sites and along the watercourse as a whole has been carried out using various metrics such as nestedness "temperature" (Patterson, Atmar, 2000), discrepancy measure (Brualdi, Sanderson, 1999), nestedness based on overlap and decreasing fill (NODE--Almeida-Neto et al., 2008) and others. Statistical significance of ecosystems structural determinancy has been tested by means of randomization procedures and standard null models (Gotelli, 2000). The conclusions seem to be ambiguous and dependent on a level and scale of an ecosystem resolution into separate blocks, also on configuration and completion of initial bio-geographical tables. A searching for reliable and representative criteria of nestedness, invariant to various non-ecological modifications of the matrices but sensitive to estimation of analyzed ecological processes and suitable for comparisons of communities, is clearly needed. A quantitative estimation of species turnover and coherence in species cooccurrence has been performed using different indices of unique combinations and checkerboard score (Stone, Roberts, 1992) as well as Schluter's variance test. By means of empirical Bayesian approach (Gotelli, Ulrich, 2010) records of species pairwise combinations are formed where the frequency of species co-occurrence cannot be interpreted as a random value. Positive and negative relationships between taxa in macrozoobenthic communities, which are found out to be statistically significant, in most cases can be explained as being not the consequence of competition for resources but of spatial heterogeneity of biotopical conditions along the whole length of the watercourse.

Shitikov VK; Zinchenko TD

2011-09-01

123

Microbial community analysis of shallow subsurface samples with PCR-DGGE  

Energy Technology Data Exchange (ETDEWEB)

This work is part of the site investigations for the disposal of spent nuclear fuel in Olkiluoto bedrock. The purpose of the research was to study the suitability of PCR-DGGE (polymerase chain reaction - denaturing gradient gel electrophoresis) method for monitoring of hydrogeomicrobiology of Olkiluoto repository site. PCR-DGGE method has been applied for monitoring microbial processes in several applications. The benefit of the method is that microorganisms are not cultivated but the presence of microbial communities can be monitored by direct DNA extractions from the environmental samples. Partial 16SrDNA gene sequence is specifically amplified by PCR (polymerase chain reaction) which detect bacteria as a group. The gene sequences are separated in DGGE, and the nucleotide bands are then cut out, extracted, sequenced and identified by the genelibraries by e.g. Blast program. PCR-DGGE method can be used to detect microorganisms which are present abundantly in the microbial communities because small quantities of genes cannot be separated reliably. However, generally the microorganisms involved in several environmental processes are naturally enriched and present as major population. This makes it possible to utilize PCRDGGE as a monitoring method. In this study, we studied the structure of microbial communities in ten ground water samples originating from Olkiluoto. Two universal bacterial primer sets were compared which amplified two different regions of the 16SrDNA gene. The longer sequence amplified resulted in fewer bands in DGGE, in addition there were problems with purification of the sequences after DGGE. The shorter sequence gave more bands in DGGE and more clear results without any amplification problems. Comparison of the sequences from the gene-libraries resulted in the detection of the same species by both primer sets, in addition some different species were detected. Several species were anaerobic bacteria, such as acetogenic and sulphate reducing 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.)

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

2005-11-15

124

Functional community analysis of brain: a new approach for EEG-based investigation of the brain pathology.  

UK PubMed Central (United Kingdom)

Analysis of structure of the brain functional connectivity (SBFC) is a fundamental issue for understanding of the brain cognition as well as the pathology of brain disorders. Analysis of communities among sub-parts of a system is increasingly used for social, ecological, and other networks. This paper presents a new methodology for investigation of the SBFC and understanding of the brain based on graph theory and community pattern analysis of functional connectivity graph of the brain obtained from encephalograms (EEGs). The methodology consists of three main parts: fuzzy synchronization likelihood (FSL), community partitioning, and decisions based on partitions. As an example application, the methodology is applied to analysis of brain of patients with attention deficit/hyperactivity disorder (ADHD) and the problem of discrimination of ADHD EEGs from healthy (non-ADHD) EEGs.

Ahmadlou M; Adeli H

2011-09-01

125

Design and evaluation of PCR primers for denaturing gradient gel electrophoresis analysis of plant parasitic and fungivorous nematode communities.  

UK PubMed Central (United Kingdom)

A PCR-DGGE primer pair, Tyl2F-Tyl4R, specific to plant parasitic and fungivorous nematodes was designed based on the 18S rRNA gene. The results of community analysis using the primers showed that they are specific to the order Tylenchida. This primer pair detected species belonging to Tylenchida with high sensitivity and high resolution. The number of detected species of plant parasitic and fungivorous nematodes and their band intensity were much improved compared with PCR-DGGE analysis using the SSU18A-SSU9R primer, which is commonly used for nematode community analysis. It was confirmed that using a group-specific primer was effective for nematode community analysis with PCR-DGGE.

Kushida A

2013-01-01

126

Sampling strategy in molecular microbial ecology: influence of soil sample size on DNA fingerprinting analysis of fungal and bacterial communities.  

UK PubMed Central (United Kingdom)

Assessing soil microbial community structure by the use of molecular techniques requires a satisfactory sampling strategy that takes into account the high microbial diversity and the heterogeneous distribution of microorganisms in the soil matrix. The influence of the sample size of three different soil types (sand, silt and clay soils) on the DNA yield and analysis of bacterial and fungal community structure were investigated. Six sample sizes from 0.125 g to 4 g were evaluated. The genetic community structure was assessed by automated ribosomal intergenic spacer analysis (A-RISA fingerprint). Variations between bacterial (B-ARISA) and fungal (F-ARISA) community structure were quantified by using principal component analysis (PCA). DNA yields were positively correlated with the sample size for the sandy and silty soils, suggesting an influence of the sample size on DNA recovery, whereas no correlation was observed in the clay soil. B-ARISA was shown to be consistent between the different sample sizes for each soil type indicating that the sampling procedure has no influence on the assessment of bacterial community structure. On the contrary for F-ARISA profiles, strong variations were observed between replicates of the smaller samples (<1 g). Principal component analysis analysis revealed that sampling aliquots of soil > or =1 g are required to obtain robust and reproducible fingerprinting analysis of the genetic structure of fungal communities. However, the smallest samples could be adequate for the detection of minor populations masked by dominant ones in larger samples. The sampling strategy should therefore be different according to the objectives: rather large soil samples (> or =1 g) for a global description of the genetic community structure, or a large number of small soil samples for a more complete inventory of microbial diversity.

Ranjard L; Lejon DP; Mougel C; Schehrer L; Merdinoglu D; Chaussod R

2003-11-01

127

Developing the national community health assistant strategy in Zambia: a policy analysis.  

UK PubMed Central (United Kingdom)

BACKGROUND: In 2010, the Ministry of Health in Zambia developed the National Community Health Assistant strategy, aiming to integrate community health workers (CHWs) into national health plans by creating a new group of workers, called community health assistants (CHAs). The aim of the paper is to analyse the CHA policy development process and the factors that influenced its evolution and content. A policy analysis approach was used to analyse the policy reform process. METHODOLOGY: Data were gathered through review of documents, participant observation and key informant interviews with CHA strategic team members in Lusaka district, and senior officials at the district level in Kapiri Mposhi district where some CHAs have been deployed. RESULTS: The strategy was developed in order to address the human resources for health shortage and the challenges facing the community-based health workforce in Zambia. However, some actors within the strategic team were more influential than others in informing the policy agenda, determining the process, and shaping the content. These actors negotiated with professional/statutory bodies and health unions on the need to develop the new cadre which resulted in compromises that enabled the policy process to move forward. International agencies also indirectly influenced the course as well as the content of the strategy. Some actors classified the process as both insufficiently consultative and rushed. Due to limited consultation, it was suggested that the policy content did not adequately address key policy content issues such as management of staff attrition, general professional development, and progression matters. Analysis of the process also showed that the strategy might create a new group of workers whose mandate is unclear to the existing group of health workers. CONCLUSIONS: This paper highlights the complex nature of policy-making processes for integrating CHWs into the health system. It reiterates the need for recognising the fact that actors' power or position in the political hierarchy may, more than their knowledge and understanding of the issue, play a disproportionate role in shaping the process as well as content of health policy reform.

Zulu JM; Kinsman J; Michelo C; Hurtig AK

2013-01-01

128

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

Science.gov (United States)

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 techniques basées sur les lipides dans l'étude de la microbiologie des eaux souterraines est intéressante parce qu'elle ne nécessite pas de mise en culture et qu'elle peut fournir des données quantitatives sur les communautés dans leur ensemble. Toutefois, les effets combinés de changements physiologiques et phylogénétiques sur la composition d'une communauté peuvent brouiller l'interprétation des données de nombreuses questions se posent sur la validité des différentes techniques lipidiques. Malgré ces oppositions, la recherche basée sur les lipides a commencéà montrer des tendances dans la composition des communautés dans les aquifères pollués et dans ceux non perturbés ces résultats contribuent ainsi à notre compréhension de l'écologie microbienne des eaux souterraines et montrent qu'il existe un potentiel pour leur utilisation en vue d'une optimisation de la dépollution biologique des eaux souterraines. Resumen Se revisan distintas técnicas bioquímicas que se basan en el análisis de lípidos para caracterizar las comunidades microbianas en hábitats subsuperficiales, incluyendo acuíferos. Estas técnicas, entre las que se incluye el análisis de ácidos grasos fosfolípidos (PLFA), pueden proporcionar información sobre toda una serie de características de las comunidades microbianas, como su biomasa, fisiología, identidad taxonómica y funcional y composición. Además, el análisis estadístico multivariado de los datos de lípidos permite relacionar los cambios espaciales o temporales en las comunidades microbianas con factores ambientales. Las técnicas basadas en lípidos son muy útiles para el estudio microbiológico de las aguas subterráneas, puesto que no requieren cultivos y además proporcionan datos cuantitativos de comunidades completas. Sin embargo, la acción combinada de los cambios fisiológicos y filogenéticos en la composición de lípidos en una comunidad pueden confundir la interpretación de los datos, por lo existen muchas cuestiones abiertas respecto a la validez de algunas de estas técnicas. A pesar de es

Green, Christopher T.; Scow, Kate M.

129

GeoChip-based analysis of the functional gene diversity and metabolic potential of soil microbial communities of mangroves.  

UK PubMed Central (United Kingdom)

Mangroves are unique and highly productive ecosystems and harbor very special microbial communities. Although the phylogenetic diversity of sediment microbial communities of mangrove habitats has been examined extensively, little is known regarding their functional gene diversity and metabolic potential. In this study, a high-throughput functional gene array (GeoChip 4.0) was used to analyze the functional diversity, composition, structure, and metabolic potential of microbial communities in mangrove habitats from mangrove national nature reserves in China. GeoChip data indicated that these microbial communities were functionally diverse as measured by the number of genes detected, unique genes, and various diversity indices. Almost all key functional gene categories targeted by GeoChip 4.0 were detected in the mangrove microbial communities, including carbon (C) fixation, C degradation, methane generation, nitrogen (N) fixation, nitrification, denitrification, ammonification, N reduction, sulfur (S) metabolism, metal resistance, antibiotic resistance, and organic contaminant degradation. Detrended correspondence analysis (DCA) of all detected genes showed that Spartina alterniflora (HH), an invasive species, did not harbor significantly different microbial communities from Aegiceras corniculatum (THY), a native species, but did differ from other species, Kenaelia candel (QQ), Aricennia marina (BGR), and mangrove-free mud flat (GT). Canonical correspondence analysis (CCA) results indicated the microbial community structure was largely shaped by surrounding environmental variables, such as total nitrogen (TN), total carbon (TC), pH, C/N ratio, and especially salinity. This study presents a comprehensive survey of functional gene diversity of soil microbial communities from different mangrove habitats/species and provides new insights into our understanding of the functional potential of microbial communities in mangrove ecosystems.

Bai S; Li J; He Z; Van Nostrand JD; Tian Y; Lin G; Zhou J; Zheng T

2013-08-01

130

Biofilm formation and microbial community analysis of the simulated river bioreactor for contaminated source water remediation.  

UK PubMed Central (United Kingdom)

BACKGROUND, AIM, AND SCOPE: The start-up pattern of biofilm remediation system affects the biofilm characteristics and operating performances. The objective of this study was to evaluate the performances of the contaminated source water remediation systems with different start-up patterns in view of the pollutants removal performances and microbial community succession. METHODS: The operating performances of four lab-scale simulated river biofilm reactors were examined which employed different start-up methods (natural enrichment and artificial enhancement via discharging sediment with influent velocity gradient increase) and different bio-fillers (Elastic filler and AquaMats® ecobase). At the same time, the microbial communities of the bioreactors in different phases were analyzed by polymerase chain reaction, denaturing gradient gel electrophoresis, and sequencing. RESULTS AND DISCUSSION: The pollutants removal performances became stable in the four reactors after 2 months' operation, with ammonia nitrogen and permanganate index (COD(Mn)) removal efficiencies of 84.41-94.21% and 69.66-76.60%, respectively. The biomass of mature biofilm was higher in the bioreactors by artificial enhancement than that by natural enrichment. Microbial community analysis indicated that elastic filler could enrich mature biofilm faster than AquaMats®. The heterotrophic bacteria diversity of biofilm decreased by artificial enhancement, which favored the ammonia-oxidizing bacteria (AOB) developing on the bio-fillers. Furthermore, Nitrosomonas- and Nitrosospira-like AOB coexisted in the biofilm, and Pseudomonas sp., Sphaerotilus sp., Janthinobacterium sp., Corynebacterium aurimucosum were dominant in the oligotrophic niche. CONCLUSION: Artificial enhancement via the combination of sediment discharging and influent velocity gradient increasing could enhance the biofilm formation and autotrophic AOB enrichment in oligotrophic niche.

Xu XY; Feng LJ; Zhu L; Xu J; Ding W; Qi HY

2012-06-01

131

Cambio: a file format translation and analysis application for the nuclear response emergency community  

International Nuclear Information System (INIS)

Cambio is an application intended to automatically read and display any spectrum file of any format in the world that the nuclear emergency response community might encounter. Cambio also provides an analysis capability suitable for HPGe spectra when detector response and scattering environment are not well known. Why is Cambio needed: (1) Cambio solves the following problem - With over 50 types of formats from instruments used in the field and new format variations appearing frequently, it is impractical for every responder to have current versions of the manufacturer's software from every instrument used in the field; (2) Cambio converts field spectra to any one of several common formats that are used for analysis, saving valuable time in an emergency situation; (3) Cambio provides basic tools for comparing spectra, calibrating spectra, and isotope identification with analysis suited especially for HPGe spectra; and (4) Cambio has a batch processing capability to automatically translate a large number of archival spectral files of any format to one of several common formats, such as the IAEA SPE or the DHS N42. Currently over 540 analysts and members of the nuclear emergency response community worldwide are on the distribution list for updates to Cambio. Cambio users come from all levels of government, university, and commercial partners around the world that support efforts to counter terrorist nuclear activities. Cambio is Unclassified Unlimited Release (UUR) and distributed by internet downloads with email notifications whenever a new build of Cambio provides for new formats, bug fixes, or new or improved capabilities. Cambio is also provided as a DLL to the Karlsruhe Institute for Transuranium Elements so that Cambio's automatic file-reading capability can be included at the Nucleonica web site.

2009-01-01

132

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

Directory of Open Access Journals (Sweden)

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.

Laura Lamb

2011-01-01

133

Metagenome Analysis of a Complex Community Reveals the Metabolic Blueprint of Anammox Bacterium "Candidatus Jettenia asiatica".  

UK PubMed Central (United Kingdom)

Anaerobic ammonium-oxidizing (anammox) bacteria are key players in the global nitrogen cycle and responsible for significant global nitrogen loss. Moreover, the anammox process is widely implemented for nitrogen removal from wastewaters as a cost-effective and environment-friendly alternative to conventional nitrification-denitrification systems. Currently, five genera of anammox bacteria have been identified, together forming a deep-branching order in the Planctomycetes-Verrucomicrobium-Chlamydiae superphylum. Members of all genera have been detected in wastewater treatment plants and have been enriched in lab-scale bioreactors, but genome information is not yet available for all genera. Here we report the metagenomic analysis of a granular sludge anammox reactor dominated (?50%) by "Candidatus Jettenia asiatica." The metagenome was sequenced using both Illumina and 454 pyrosequencing. After de novo assembly 37,432 contigs with an average length of 571?nt were obtained. The contigs were then analyzed by BLASTx searches against the protein sequences of "Candidatus Kuenenia stuttgartiensis" and a set of 25 genes essential in anammox metabolism were detected. Additionally all reads were mapped to the genome of an anammox strain KSU-1 and de novo assembly was performed again using the reads that could be mapped on KSU-1. Using this approach, a gene encoding copper-containing nitrite reductase NirK was identified in the genome, instead of cytochrome cd(1)-type nitrite reductase (NirS, present in "Ca. Kuenenia stuttgartiensis" and "Ca. Scalindua profunda"). Finally, the community composition was investigated through MetaCluster analysis, 16S rRNA gene analysis and read mapping, which showed the presence of other important community members such as aerobic ammonia-oxidizing bacteria, methanogens, and the denitrifying methanotroph "Ca. Methylomirabilis oxyfera", indicating a possible active methane and nitrogen cycle in the bioreactor under the prevailing operational conditions.

Hu Z; Speth DR; Francoijs KJ; Quan ZX; Jetten MS

2012-01-01

134

Community representatives: representing the "community"?  

UK PubMed Central (United Kingdom)

This paper takes as its starting point the apparent disjunction between the assumptions of the self-evidence of the meaning of community in major international declarations and strategies which promote community participation and the observation that meanings of "community" are a subject of extensive debate in literatures of social analysis and to some extent health. Given that the word's meaning is not agreed, those working to promote "community participation" in health are forced to adjudicate on competing meanings in order to operationalise the notion. This raises questions about how this is done and what are the implications of particular choices for what may be achieved by the participating "community". This paper presents the findings of an empirical study which examined the manner in which ideas of "community" are operationalised by people engaged in encouraging community participation in health promotion in the context of the selection of members for health for all steering groups in healthy cities projects in the United Kingdom. It argues that the demands of the role of the "community representative" are such that particular interpretations of "community" achieve ascendance. The paper explores the consequences of the interpretation of "community" as part of the "voluntary sector" and argues that this may compromise one of the stated desired outcomes of community participation i.e. extending democracy in health decision-making.

Jewkes R; Murcott A

1998-04-01

135

Using social network analysis to sketch the patterns of interaction among nursing students in a blog community.  

Science.gov (United States)

Web logs, or blogs have recently raised interest in the educational and research arena. However, the analysis of participants' behavioral patterns remains absent. The aim of this study was to use social network analysis to draw the patterns of 48 junior college nursing students' peer interactions in a blog community in Taiwan. The results showed that the density of interactions were different in terms of the participants with different grade-point-average background. The more active students in the blog community dominated discourse interaction. Nursing students with higher grade point average interacted mainly within their respective groups. The social network analysis helped to provide information on patterns of nursing students' interaction culture within a blog community. PMID:23851707

Lin, Kai-Yin

2013-08-01

136

Using social network analysis to sketch the patterns of interaction among nursing students in a blog community.  

UK PubMed Central (United Kingdom)

Web logs, or blogs have recently raised interest in the educational and research arena. However, the analysis of participants' behavioral patterns remains absent. The aim of this study was to use social network analysis to draw the patterns of 48 junior college nursing students' peer interactions in a blog community in Taiwan. The results showed that the density of interactions were different in terms of the participants with different grade-point-average background. The more active students in the blog community dominated discourse interaction. Nursing students with higher grade point average interacted mainly within their respective groups. The social network analysis helped to provide information on patterns of nursing students' interaction culture within a blog community.

Lin KY

2013-08-01

137

Comparison of DNA Extraction Methods in Analysis of Salivary Bacterial Communities  

Science.gov (United States)

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.

Girard, Myriam; Francois, Patrice; Schrenzel, Jacques

2013-01-01

138

Comparative community gene expression analysis of Aquificales-dominated geothermal springs.  

UK PubMed Central (United Kingdom)

Members of Sulfurihydrogenibium are often observed as visible filamentous biomass in circumneutral hot springs and play roles in sulfur-cycling, hydrogen oxidation and iron mineralization. To gain insight into the ecophysiology of Sulfurihydrogenibium populations, we conducted preliminary metatranscriptomic analysis of three distinct thermal springs; Calcite Springs (YNP-CS) and Mammoth Springs (YNP-MHS) in Yellowstone National Park, USA, and Furnas Springs (AZ) in Azores, Portugal. Genes to which transcripts were assigned revealed commonly expressed functions among the sites, while several differences were also observed. All three sites, Sulfurihydrogenibium spp. dominate and are obtaining energy via metabolism of sulfur compounds under microaerophilic conditions. Cell motility was one of the expressed functions in two sites (YNP-CS and AZ) with slower stream flow rates and thicker well-formed biofilms. The transcripts from YNP-CS and -MHS exhibited varying levels of sequence divergence from the reference genomes and corresponding metagenomes, suggesting the presence of microdiversity among Sulfurihydrogenibium populations in situ. Conversely, the majority of the AZ transcripts were identical to the S.?azorense genome. Our initial results show that the metatranscriptomes in these similar Aquificales-dominated communities can reveal community-level gene function in geochemically distinct thermal environments.

Hamamura N; Meneghin J; Reysenbach AL

2013-04-01

139

Comparative community gene expression analysis of Aquificales-dominated geothermal springs.  

Science.gov (United States)

Members of Sulfurihydrogenibium are often observed as visible filamentous biomass in circumneutral hot springs and play roles in sulfur-cycling, hydrogen oxidation and iron mineralization. To gain insight into the ecophysiology of Sulfurihydrogenibium populations, we conducted preliminary metatranscriptomic analysis of three distinct thermal springs; Calcite Springs (YNP-CS) and Mammoth Springs (YNP-MHS) in Yellowstone National Park, USA, and Furnas Springs (AZ) in Azores, Portugal. Genes to which transcripts were assigned revealed commonly expressed functions among the sites, while several differences were also observed. All three sites, Sulfurihydrogenibium spp. dominate and are obtaining energy via metabolism of sulfur compounds under microaerophilic conditions. Cell motility was one of the expressed functions in two sites (YNP-CS and AZ) with slower stream flow rates and thicker well-formed biofilms. The transcripts from YNP-CS and -MHS exhibited varying levels of sequence divergence from the reference genomes and corresponding metagenomes, suggesting the presence of microdiversity among Sulfurihydrogenibium populations in situ. Conversely, the majority of the AZ transcripts were identical to the S.?azorense genome. Our initial results show that the metatranscriptomes in these similar Aquificales-dominated communities can reveal community-level gene function in geochemically distinct thermal environments. PMID:23279131

Hamamura, Natsuko; Meneghin, Jennifer; Reysenbach, Anna-Louise

2013-01-01

140

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

UK PubMed Central (United Kingdom)

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.

Lazarevic V; Gaïa N; Girard M; François P; Schrenzel J

2013-01-01

 
 
 
 
141

[Removal of BTEX by a biotrickling filter and analysis of corresponding bacterial communities].  

Science.gov (United States)

The pre-acclimated microbial consortium and the activated sludge were used as start inoculums of a bench-scale biotrickling filter (BTF). The performance of the biotrickling filter on the removal of BTEX mixture was evaluated, and the changes in the bacterial community structure of the BTF were analyzed by PCR-DGGE technique. The results showed that the BTF could be acclimated within a short time, the biomass that adhered to the surface of packing materials increased rapidly from 5.7 mg x g(-1) at 10th day to 112 mg x g(-1) at 30th day. BTF could simultaneously remove all components of the BTEX mixture efficiently. The maximum removal capacity of the BTF was 216.6 g x (m3 x h)(-1), which was achieved with an inlet loading rate of 269.7 g x (m3 x h)(-1) and an empty bed retention time (EBRT) of 39 s. DGGE analysis indicated that the dominant microorganisms may be derived from the pre-acclimated microbial consortiums rather than the activated sludge. Although the bacterial community changed with run time, the spatial distribution was very uniform. PMID:24027982

Li, Jian-Jun; Liao, Dong-Qi; Xu, Mei-Ying; Sun, Guo-Ping

2013-07-01

142

[Removal of BTEX by a biotrickling filter and analysis of corresponding bacterial communities].  

UK PubMed Central (United Kingdom)

The pre-acclimated microbial consortium and the activated sludge were used as start inoculums of a bench-scale biotrickling filter (BTF). The performance of the biotrickling filter on the removal of BTEX mixture was evaluated, and the changes in the bacterial community structure of the BTF were analyzed by PCR-DGGE technique. The results showed that the BTF could be acclimated within a short time, the biomass that adhered to the surface of packing materials increased rapidly from 5.7 mg x g(-1) at 10th day to 112 mg x g(-1) at 30th day. BTF could simultaneously remove all components of the BTEX mixture efficiently. The maximum removal capacity of the BTF was 216.6 g x (m3 x h)(-1), which was achieved with an inlet loading rate of 269.7 g x (m3 x h)(-1) and an empty bed retention time (EBRT) of 39 s. DGGE analysis indicated that the dominant microorganisms may be derived from the pre-acclimated microbial consortiums rather than the activated sludge. Although the bacterial community changed with run time, the spatial distribution was very uniform.

Li JJ; Liao DQ; Xu MY; Sun GP

2013-07-01

143

Prokaryotic diversity, composition structure, and phylogenetic analysis of microbial communities in leachate sediment ecosystems.  

UK PubMed Central (United Kingdom)

In order to obtain insight into the prokaryotic diversity and community in leachate sediment, a culture-independent DNA-based molecular phylogenetic approach was performed with archaeal and bacterial 16S rRNA gene clone libraries derived from leachate sediment of an aged landfill. A total of 59 archaeal and 283 bacterial rDNA phylotypes were identified in 425 archaeal and 375 bacterial analyzed clones. All archaeal clones distributed within two archaeal phyla of the Euryarchaeota and Crenarchaeota, and well-defined methanogen lineages, especially Methanosaeta spp., are the most numerically dominant species of the archaeal community. Phylogenetic analysis of the bacterial library revealed a variety of pollutant-degrading and biotransforming microorganisms, including 18 distinct phyla. A substantial fraction of bacterial clones showed low levels of similarity with any previously documented sequences and thus might be taxonomically new. Chemical characteristics and phylogenetic inferences indicated that (1) ammonium-utilizing bacteria might form consortia to alleviate or avoid the negative influence of high ammonium concentration on other microorganisms, and (2) members of the Crenarchaeota found in the sediment might be involved in ammonium oxidation. This study is the first to report the composition of the microbial assemblages and phylogenetic characteristics of prokaryotic populations extant in leachate sediment. Additional work on microbial activity and contaminant biodegradation remains to be explored.

Liu J; Wu W; Chen C; Sun F; Chen Y

2011-09-01

144

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

UK PubMed Central (United Kingdom)

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.

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 JD; Reinhold-Hurek B

2012-01-01

145

Microbial community analysis of fresh and old microbial biofilms on Bayon temple sandstone of Angkor Thom, Cambodia.  

UK PubMed Central (United Kingdom)

The temples of Angkor monuments including Angkor Thom and Bayon in Cambodia and surrounding countries were exclusively constructed using sandstone. They are severely threatened by biodeterioration caused by active growth of different microorganisms on the sandstone surfaces, but knowledge on the microbial community and composition of the biofilms on the sandstone is not available from this region. This study investigated the microbial community diversity by examining the fresh and old biofilms of the biodeteriorated bas-relief wall surfaces of the Bayon Temple by analysis of 16S and 18S rRNA gene sequences. The results showed that the retrieved sequences were clustered in 11 bacterial, 11 eukaryotic and two archaeal divisions with disparate communities (Acidobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Proteobacteria; Alveolata, Fungi, Metazoa, Viridiplantae; Crenarchaeote, and Euyarchaeota). A comparison of the microbial communities between the fresh and old biofilms revealed that the bacterial community of old biofilm was very similar to the newly formed fresh biofilm in terms of bacterial composition, but the eukaryotic communities were distinctly different between these two. This information has important implications for understanding the formation process and development of the microbial diversity on the sandstone surfaces, and furthermore to the relationship between the extent of biodeterioration and succession of microbial communities on sandstone in tropic region.

Lan W; Li H; Wang WD; Katayama Y; Gu JD

2010-07-01

146

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

UK PubMed Central (United Kingdom)

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 associated closely with pathogenicity of S. epidermidis, ACME was more likely to be an indicator for colonization rather than a virulence factor.

Du X; Zhu Y; Song Y; Li T; Luo T; Sun G; Yang C; Cao C; Lu Y; Li M

2013-01-01

147

NESTED AUTOMATED RIBOSOMAL INTERGENIC SPACER ANALYSIS: A RAPID AND ACCURATE METHOD FOR COMPARISON OF BACTERIAL COMMUNITY COMPOSITION  

UK PubMed Central (United Kingdom)

Nested automated ribosomal intergenic spacer analysis (ARISA) was used to examine the community structure of epilithic biofilms in freshwater streams experiencing different levels of human impact. This molecular fingerprinting technique generated reproducible profiles of bacterial community structure that varied significantly between stream sites. Nested ARISA was determined to be a cost-effective, high-throughput approach to assess bacterial community composition from very small sample volumes, requiring little sampling effort and without the need for taxonomic identification of individual organisms. In combination with multidimensional scaling, nested ARISA provides a rapid and sensitive method to carry out complex analyses of bacterial community structure. Nested automated ribosomal intergenic spacer analysis (ARISA) provides a high-throughput molecular method with which to screen large numbers of environmental samples for differences in microbial community structure. This sensitive approach benefits assessments from small sample volumes or environments exhibiting reduced microbial biomass (both aquatic and terrestrial). Differences in bacterial community structure (obtained from ARISA profiles) could be used to characterize the impact of anthropogenic disturbance on freshwater systems, analogous to the current use of macroinvertebrate indicators of freshwater ecological health.

LEAR G; LEWIS GD

2009-06-01

148

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

DEFF Research Database (Denmark)

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 independent validation in all DNA extraction based studies.

Albertsen, Mads; Karst, SØren Michael

149

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

UK PubMed Central (United Kingdom)

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 < 0.001) in beta diversity were observed among the different matrices at the genus-species level, except for lichens and rocks which shared a more similar community structure, while at deep taxonomic resolution two distinct bacterial communities between lichens and rocks were found.

Esposito A; Ciccazzo S; Borruso L; Zerbe S; Daffonchio D; Brusetti L

2013-10-01

150

Smoking cessation in community pharmacy practice-a clinical information needs analysis.  

UK PubMed Central (United Kingdom)

BACKGROUND: With the emerging role of pharmacists in implementing smoking cessation services and the recent evidence about smoking cessation pharmacotherapies, a needs analysis to assess baseline knowledge about current smoking cessation practice is needed; hence, training and development in this area can target possible 'gaps'. OBJECTIVE: This study aimed at exploring pharmacy students' knowledge about and attitudes toward smoking cessation, as compared to practicing community pharmacists and smoking cessation educators. The overall objective was to uncover underlying 'gaps' in pharmacy-based smoking cessation practice, particularly clinical gaps. SETTING: Final-year pharmacy students at the University of Sydney, practicing community pharmacists and smoking cessation educators in Australia. METHOD: As no previous standard pharmacist-focused smoking cessation knowledge questionnaires exist, a review of the literature informed the development of such a questionnaire. The questionnaire was administered to a cohort of fourth-year pharmacy students at the University of Sydney, practicing pharmacists and smoking cessation educators. Data analysis was performed using Predictive Analytics SoftWare (PASW® Statistics 18). Mean total scores, independent t-tests, analysis of variances and exploratory factor analysis were performed. MAIN OUTCOME MEASURE: To determine areas of major clinical deficits about current evidence related to smoking cessation interventions at the pharmacy level. RESULTS: Responses from 250 students, 51 pharmacists and 20 educators were obtained. Smoking educators scored significantly higher than pharmacists and students (P??.05). All groups scored high on 'general' knowledge questions as compared to specialised pharmacologic and pharmacotherapeutic questions. All respondents demonstrated positive attitudes toward the implications of smoking cessation. Factor analysis of the 24-item knowledge section extracted 12 items loading on 5 factors accounting for 53% of the total variance. CONCLUSIONS: The results provide a valid indication of 'gaps' in the practice of up-to-date smoking cessation services among Australian pharmacy professionals, particularly in clinical expertise areas involving assessment of nicotine dependence and indications, dosages, adverse effects, contraindications, drug interactions and combinations of available pharmacotherapies. These gaps should be addressed, and the results should inform the design, implementation and evaluation of a pharmacy-based educational training program targeting current clinical issues in smoking cessation.

Saba M; Bittoun R; Kritikos V; Saini B

2013-01-01

151

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

Directory of Open Access Journals (Sweden)

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.

Reese Justin T; Childers Christopher P; Sundaram Jaideep P; Dickens C Michael; Childs Kevin L; Vile Donald C; Elsik Christine G

2010-01-01

152

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

UK PubMed Central (United Kingdom)

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 (alpha = .01) from SPSS-GIS for satisfaction and time (p < .002). Descriptive results indicated that participants had greater success in answering the tasks when using SOVAT as compared to SPSS-GIS. CONCLUSION: Using SOVAT, tasks were completed more efficiently, with a higher rate of success, and with greater satisfaction, than the combined use of SPSS and GIS. The results from this study indicate a potential for OLAP-GIS decision support systems as a valuable tool for CHA data analysis.

Scotch M; Parmanto B; Monaco V

2008-01-01

153

Beyond Streptococcus mutans: dental caries onset linked to multiple species by 16S rRNA community analysis.  

UK PubMed Central (United Kingdom)

Dental caries in very young children may be severe, result in serious infection, and require general anesthesia for treatment. Dental caries results from a shift within the biofilm community specific to the tooth surface, and acidogenic species are responsible for caries. Streptococcus mutans, the most common acid producer in caries, is not always present and occurs as part of a complex microbial community. Understanding the degree to which multiple acidogenic species provide functional redundancy and resilience to caries-associated communities will be important for developing biologic interventions. In addition, microbial community interactions in health and caries pathogenesis are not well understood. The purpose of this study was to investigate bacterial community profiles associated with the onset of caries in the primary dentition. In a combination cross-sectional and longitudinal design, bacterial community profiles at progressive stages of caries and over time were examined and compared to those of health. 16S rRNA gene sequencing was used for bacterial community analysis. Streptococcus mutans was the dominant species in many, but not all, subjects with caries. Elevated levels of S. salivarius, S. sobrinus, and S. parasanguinis were also associated with caries, especially in subjects with no or low levels of S. mutans, suggesting these species are alternative pathogens, and that multiple species may need to be targeted for interventions. Veillonella, which metabolizes lactate, was associated with caries and was highly correlated with total acid producing species. Among children without previous history of caries, Veillonella, but not S. mutans or other acid-producing species, predicted future caries. Bacterial community diversity was reduced in caries as compared to health, as many species appeared to occur at lower levels or be lost as caries advanced, including the Streptococcus mitis group, Neisseria, and Streptococcus sanguinis. This may have implications for bacterial community resilience and the restoration of oral health.

Gross EL; Beall CJ; Kutsch SR; Firestone ND; Leys EJ; Griffen AL

2012-01-01

154

A Statistical Analysis of the Community Structure of a Weighted Collaboration Network Among Rappers  

CERN Document Server

The social network formed by the collaboration between rappers is studied using standard statistical techniques for analyzing complex networks. In addition, the community structure of the rap music community is analyzed using a new method that uses weighted edges to determine which connections are most important and revealing among all the communities. The results of this method as well as possible reasons for the structure of the rap music community are discussed.

Smith, R D

2006-01-01

155

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

UK PubMed Central (United Kingdom)

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.

Lu L; Li J; Gisler P

2011-06-01

156

Modified therapeutic community for co-occurring disorders: single investigator meta analysis.  

Science.gov (United States)

This paper presents the results of a meta-analysis for a single investigator examining the effectiveness of the modified therapeutic community (MTC) for clients with co-occurring substance use and mental disorders (COD). The flexibility and utility of meta-analytic tools are described, although their application in this context is atypical. The analysis includes 4 comparisons from 3 studies (retrieved N = 569) for various groups of clients with COD (homeless persons, offenders, and outpatients) in substance abuse treatment, comparing clients assigned either to an MTC or a control condition of standard services. An additional study is included in a series of sensitivity tests. The overall findings increase the research base of support for the MTC program for clients with COD, as results of the meta-analysis indicate significant MTC treatment effects for 5 of the 6 outcome domains across the 4 comparisons. Limitations of the approach are discussed. Independent replications, clinical trials, multiple outcome domains, and additional meta-analyses should be emphasized in future research. Given the need for research-based approaches, program and policy planners should consider the MTC when designing programs for co-occurring disorders. PMID:20687003

Sacks, Stanley; McKendrick, Karen; Sacks, JoAnn Y; Cleland, Charles M

2010-07-01

157

Modified therapeutic community for co-occurring disorders: single investigator meta analysis.  

UK PubMed Central (United Kingdom)

This paper presents the results of a meta-analysis for a single investigator examining the effectiveness of the modified therapeutic community (MTC) for clients with co-occurring substance use and mental disorders (COD). The flexibility and utility of meta-analytic tools are described, although their application in this context is atypical. The analysis includes 4 comparisons from 3 studies (retrieved N = 569) for various groups of clients with COD (homeless persons, offenders, and outpatients) in substance abuse treatment, comparing clients assigned either to an MTC or a control condition of standard services. An additional study is included in a series of sensitivity tests. The overall findings increase the research base of support for the MTC program for clients with COD, as results of the meta-analysis indicate significant MTC treatment effects for 5 of the 6 outcome domains across the 4 comparisons. Limitations of the approach are discussed. Independent replications, clinical trials, multiple outcome domains, and additional meta-analyses should be emphasized in future research. Given the need for research-based approaches, program and policy planners should consider the MTC when designing programs for co-occurring disorders.

Sacks S; McKendrick K; Sacks JY; Cleland CM

2010-07-01

158

Formation and microbial community analysis of chloroanilines-degrading aerobic granules in the sequencing airlift bioreactor.  

UK PubMed Central (United Kingdom)

AIMS: This paper investigates a selection-based acclimation strategy for improving the performance and stability of aerobic granules at a high chloroanilines loading. METHODS AND RESULTS: The experiments were conducted in a sequencing airlift bioreactor (SABR) to develop aerobic granules fed with chloroanilines (ClA). The evolution of aerobic granulation was monitored using image analysis and scanning electron microscopy, and PCR-DGGE analysis of microbial community was performed. The sludge granulation was apparently developed by decreased settling time and gradual increased ClA loading to 0.8 kg m(-3) day(-1). A steady-state performance of the granular SABR was reached at last, as evidenced by biomass concentration of 6.3 g l(-1) and constant ClA removal efficiency of 99.9%. The mature granules had a mean size of 1.55 mm, minimal settling velocity of 68.4 m h(-1), specific ClA degradation rate of 0.181 g gVSS(-1) day(-1). Phylogenetic analysis of aerobic ClA-degrading granules confirmed the dominance of beta-, gamma-Proteobacteria and Flavobacteria. CONCLUSIONS: The chosen operating strategy involving step increase in ClA loading and enhancement of major selection pressures was successful in cultivating the aerobic ClA-degrading granules. SIGNIFICANCE AND IMPACT OF THE STUDY: This research could be helpful for improving the stability of aerobic granules via optimizing operating conditions and developing economic feasible full-scale granular bioreactor.

Zhu L; Xu X; Luo W; Cao D; Yang Y

2008-01-01

159

Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities.  

UK PubMed Central (United Kingdom)

An automated method of ribosomal intergenic spacer analysis (ARISA) was developed for the rapid estimation of microbial diversity and community composition in freshwater environments. Following isolation of total community DNA, PCR amplification of the 16S-23S intergenic spacer region in the rRNA operon was performed with a fluorescence-labeled forward primer. ARISA-PCR fragments ranging in size from 400 to 1,200 bp were next discriminated and measured by using an automated electrophoresis system. Database information on the 16S-23S intergenic spacer was also examined, to understand the potential biases in diversity estimates provided by ARISA. In the analysis of three natural freshwater bacterial communities, ARISA was rapid and sensitive and provided highly reproducible community-specific profiles at all levels of replication tested. The ARISA profiles of the freshwater communities were quantitatively compared in terms of both their relative diversity and similarity level. The three communities had distinctly different profiles but were similar in their total number of fragments (range, 34 to 41). In addition, the pattern of major amplification products in representative profiles was not significantly altered when the PCR cycle number was reduced from 30 to 15, but the number of minor products (near the limit of detection) was sensitive to changes in cycling parameters. Overall, the results suggest that ARISA is a rapid and effective community analysis technique that can be used in conjunction with more accurate but labor-intensive methods (e.g., 16S rRNA gene cloning and sequencing) when fine-scale spatial and temporal resolution is needed.

Fisher MM; Triplett EW

1999-10-01

160

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

UK PubMed Central (United Kingdom)

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 nigrolineatus.

McDonald R; Schreier HJ; Watts JE

2012-01-01

 
 
 
 
161

Succession and phylogenetic profile of eukaryotic communities in the composting process of rice straw estimated by PCR-DGGE analysis.  

UK PubMed Central (United Kingdom)

The succession and phylogenetic profile of eukaryotic communities during the composting process of rice straw (RS) were studied by applying polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis followed by sequencing of 18S rDNA. Principal component analysis and cluster analysis of the DGGE band patterns of eukaryotic communities resulted in exactly the same grouping as found with phospholipid fatty acid (PLFA) analysis (Cahyani et al. in Soil Sci Plant Nutr 48:735, 2002) and by the DGGE pattern analysis of the bacterial communities (Cahyani et al. in Soil Sci Plant Nutr 49:619, 2003) for the same samples, namely the communities characterizing the pre-composting stage (initial RS materials), and thermophilic, middle, and curing stages of the compost. Different eukaryotic members characterized the respective stages as follows: fungi (Ascomycota) for the initial RS materials, protozoans (Apicomplexa) as well as the fungi (Ascomycota) of the initial RS materials for the thermophilic stage, fungi (Ascomycota and Basidiomycota), protozoans (Opalozoa, Ciliophora and Leptomyxida), nematodes and stramenopiles for the middle stage, and fungi (Ascomycota, Zygomycota and Oomycota), algae (Haptophyceae and Chrysophyceae), and nematodes for the curing stage, respectively. Temperature, moisture content, and substrates available seemed to play a key role in determining the composition of eukaryotic members present at the respective stages of the composting process of RS.

Cahyani VR; Matsuya K; Asakawa S; Kimura M

2004-10-01

162

Changing perspectives on community identity and function: A remote sensing and artifactual re-analysis of Barton Ramie, Belize  

Science.gov (United States)

This dissertation presents the results of the remote sensing and artifact re-analysis of the archaeological site of Barton Ramie, Belize. The site was the focus of Dr. Gordon R. Willey's innovative archaeological program in the Belize River Valley to study ancient Maya settlement, environment, and population in 1954-1956. Through the use of artifact analysis combined with the examination of high-resolution Worldview-1 imagery and a Geographic Information System (GIS)-based spatial analysis, I consider how the inhabitants of Barton Ramie forged community functioning and identity. I focus on the range of intra-site diversity including differential access to labor, goods, land, and the activities evidenced in households and non-domestic structures. Using a community theory framework, emphasizing the many practices that tied the community together, I underscore the variability expressed in architectural elaboration, sumptuary goods, ritual, and specialization. That variability has profound implications for understanding community diversity and economic, social, and ritual functioning. High-resolution panchromatic Worldview-1 satellite imagery successfully detected the remains of Barton Ramie settlement. Surface archaeology has been largely destroyed due to extensive agricultural activities in recent decades. GIS analysis and ground-truthing determined that mound size is the primary factor enabling detection of ancient features. The confirmation of features in an intensively plowed environment has implications including settlement, survey, and population for other disturbed environments. I argue that the Barton Ramie community developed from a complex interaction of networks and practices. These include activities at the household level, articulation between households to form sub-communities (or neighborhoods), and a larger imagined community of the Barton Ramie polity. Individual households articulated to form seven discrete sub-communities, bounded by landscape features and indicated by interaction spheres in my GIS analysis. This analysis confirmed Dr. Willey's original observations on neighborhoods and settlement. Each subcommunity had a local ritual structure to integrate the households and mitigate the clear status differences. These differences are seen in high status households on prized land, using architectural elaboration, sumptuary goods, and ritual to maintain their status. Once Barton Ramie is understood as a heterogeneous polity connected to a wider economic network, it can be placed into the wider political interaction of the Belize Valley.

Weller, Errin Teresa

163

Radiological emergency response for community agencies with cognitive task analysis, risk analysis, and decision support framework.  

UK PubMed Central (United Kingdom)

Radiological nuclear emergency responders must be able to coordinate evacuation and relief efforts following the release of radioactive material into populated areas. In order to respond quickly and effectively to a nuclear emergency, high-level coordination is needed between a number of large, independent organizations, including police, military, hazmat, and transportation authorities. Given the complexity, scale, time-pressure, and potential negative consequences inherent in radiological emergency responses, tracking and communicating information that will assist decision makers during a crisis is crucial. The emergency response team at the Angra dos Reis nuclear power facility, located outside of Rio de Janeiro, Brazil, presently conducts emergency response simulations once every two years to prepare organizational leaders for real-life emergency situations. However, current exercises are conducted without the aid of electronic or software tools, resulting in possible cognitive overload and delays in decision-making. This paper describes the development of a decision support system employing systems methodologies, including cognitive task analysis and human-machine interface design. The decision support system can aid the coordination team by automating cognitive functions and improving information sharing. A prototype of the design will be evaluated by plant officials in Brazil and incorporated to a future trial run of a response simulation.

Meyer TS; Muething JZ; Lima GA; Torres BR; del Rosario TK; Gomes JO; Lambert JH

2012-01-01

164

[Pharmacoeconomic analysis of community-acquired pneumonia treatment with telithromycin or clarithromycin  

UK PubMed Central (United Kingdom)

A pharmacoeconomic analysis was carried out comparing the efficacy of two treatment options for community-acquired pneumonia (CAP): telithromycin and clarithromycin. It was a retrospective analysis using a decision tree model. The efficacy of the two treatment options was estimated from a randomized, double-blind clinical trial, in which 800 mg/day oral telithromycin for 10 days was compared to 1000 mg/day oral clarithromycin for 10 days in patients with CAP (162 and 156 respectively). The use of resources was estimated based on the clinical trial and Spanish sources, and the unit costs from a Spanish health costs database. Costs were evaluated for the acquisition of antibiotic treatments, change of antibiotic due to therapeutic failure, hospital admissions, adverse reactions to treatment, primary care visits, tests and indirect costs (working days lost). The model was validated by a panel of Spanish clinical experts. As the clinical trial was designed to show equivalence, there were no significant differences in efficacy between the treatment options (clinical cure rate 88.3% and 88.5%, respectively), and a cost minimization analysis was performed. In the base case, the average cost of the disease per patient was 308.29 euros with telithromycin and 331.5 euros with clarithromycin (a difference of 23.21 euros). The results were stable in the susceptibility analysis, with differences favorable to telithromycin ranging between 5.50 and 45.45 euros. Telithromycin results in a cost savings of up to 45.45 euros per CAP patient compared to clarithromycin.

Rubio-Terrés C; Cots JM; Domínguez-Gil A; Herreras A; Sánchez Gascón F; Chang J; Trilla A

2003-09-01

165

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

UK PubMed Central (United Kingdom)

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. These findings should be considered when designing online communities as well as designing and evaluating psychosocial and educational interventions for cancer patients.

Durant KT; McCray AT; Safran C

2012-01-01

166

Medicina comunitaria: introducción a un análisis crítico/ Community medicine: introduction to a critical analysis  

Scientific Electronic Library Online (English)

Full Text Available Abstract in spanish Este artículo de Jairnilson Silva Paim, publicado originalmente en 1976 en la revista Saúde em Debate del Centro Brasileiro de Estudos de Saúde (CEBES), realiza un análisis del concepto "comunidad", como así también de la utilización de las expresiones "salud comunitaria" y "medicina comunitaria" relacionadas a la propuesta de medicina integral y medicina preventiva. Su publicación en español en la sección Textos fundacionales, apunta a la reconstrucción histó (more) rica de un movimiento originado en América Latina como medicina social y/o salud colectiva hace más de cuatro décadas y que en el caso de Brasil tiene como claros antecedentes la obra de Sergio Arouca O Dilema preventivista: contribuição para a compreensão e crítica da medicina preventiva y las de Cecília Donnangelo Medicina e sociedade: o médico e seu mercado de trabalho y Medicina e estrutura social: o campo da emergência da medicina comunitária. Estos tres textos son producto de tesis de doctorado y libre docencia, escritos en el primer lustro de los años '70 al igual que este artículo que estamos publicando, y otros que el CEBES recupera en su número especial del año 2008, titulado Saúde em Debate: Fundamentos da Reforma Sanitária. Abstract in english This article by Jairnilson Silva Paim, originally published in 1976 in the journal Saúde em Debate belonging to the Centro Brasileiro de Estudos de Saúde (CEBES), makes an analysis of the concept of "community", together with the use of the expressions "community health" and "community medicine" related to the proposal of integral medicine and preventive medicine. Its publication in Spanish in the Founding Texts section points at the historical reconstruction of a movem (more) ent originated in Latin America as social and/or collective medicine more than four decades ago. In the case of Brazil, it has, as clear antecedents, the work of Sergio Arouca O Dilema preventivista: contribuição para a compreensão e crítica da medicina preventiva and Cecília Donnangelo's ones Medicina e sociedade: o médico e seu mercado de trabalho and Medicina e estrutura social: o campo da emergência da medicina comunitária. These three texts are the product of a PhD. thesis and free teaching, written in the early seventies as well as the articles we are publishing and others that the CEBES recovers in its 2008 special issue with the title Saúde em Debate: Fundamentos da Reforma Sanitária.

Paim, Jairnilson Silva

2009-04-01

167

Analysis of the evolution of microbial communities associated with different cultures of rotifer strains belonging to different cryptic species of the Brachionus plicatilis species complex  

UK PubMed Central (United Kingdom)

The evolution of the composition of microbial communities associated with cultures of 3 different strains belonging to different cryptic species of the rotifer Brachionus plicatilis was monitored during four subsequent cycles of batch cultivation using denaturing gradient gel electrophoresis, cluster analysis, multidimensional scaling and principal component analysis. The data suggest that the evolving microbial communities are different with different B. plicatilis strain cultures. Moreover, large changes in rotifer growth rate were found to be associated with large changes in the microbial community composition, suggesting that there might be a causal link. Finally, Lorenz curves and Gini-coefficient analysis revealed that good performing B. plicatilis cultures showed a more even microbial community structure.

Qi Zizhong; Dierckens Kristof; Defoirdt Tom; Sorgeloos Patrick; Boon Nico; Bao Zhenmin; Bossier Peter

2009-07-01

168

Taxonomic Profiling and Metagenome Analysis of a Microbial Community from a Habitat Contaminated with Industrial Discharges.  

UK PubMed Central (United Kingdom)

Industrial units, manufacturing dyes, chemicals, solvents, and xenobiotic compounds, produce liquid and solid wastes, which upon conventional treatment are released in the nearby environment and thus are the major cause of pollution. Soil collected from contaminated Kharicut Canal bank (N 22°57.878'; E 072°38.478'), Ahmedabad, Gujarat, India was used for metagenomic DNA preparation to study the capabilities of intrinsic microbial community in dealing with xenobiotics. Sequencing of metagenomic DNA on the Genome Sequencer FLX System using titanium chemistry resulted in 409,782 reads accounting for 133,529,997 bases of sequence information. Taxonomic analyses and gene annotations were carried out using the bioinformatics platform Sequence Analysis and Management System for Metagenomic Datasets. Taxonomic profiling was carried out by three different complementary approaches: (a) 16S rDNA, (b) environmental gene tags, and (c) lowest common ancestor. The most abundant phylum and genus were found to be "Proteobacteria" and "Pseudomonas," respectively. Metagenome reads were mapped on sequenced microbial genomes and the highest numbers of reads were allocated to Pseudomonas stutzeri A1501. Assignment of obtained metagenome reads to Gene Ontology terms, Clusters of Orthologous Groups of protein categories, protein family numbers, and Kyoto Encyclopedia of Genes and Genomes hits revealed genomic potential of indigenous microbial community. In total, 157,024 reads corresponded to 37,028 different KEGG hits, and amongst them, 11,574 reads corresponded to 131 different enzymes potentially involved in xenobiotic biodegradation. These enzymes were mapped on biodegradation pathways of xenobiotics to elucidate their roles in possible catalytic reactions. Consequently, information obtained from the present study will act as a baseline which, subsequently along with other "-omic" studies, will help in designing future bioremediation strategies in effluent treatment plants and environmental clean-up projects.

Shah V; Zakrzewski M; Wibberg D; Eikmeyer F; Schlüter A; Madamwar D

2013-06-01

169

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

Science.gov (United States)

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 seasonally active taxa in the surface waters of the lake are thus 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. PMID:23267353

Charvet, Sophie; Vincent, Warwick F; Comeau, André; Lovejoy, Connie

2012-12-20

170

Meta-analysis of antibiotics and the risk of community-associated Clostridium difficile infection.  

UK PubMed Central (United Kingdom)

The rising incidence of Clostridium difficile infection (CDI) could be reduced by lowering exposure to high-risk antibiotics. The objective of this study was to determine the association between antibiotic class and the risk of CDI in the community setting. The EMBASE and PubMed databases were queried without restriction to time period or language. Comparative observational studies and randomized controlled trials (RCTs) considering the impact of exposure to antibiotics on CDI risk among nonhospitalized populations were considered. We estimated pooled odds ratios (OR) for antibiotic classes using random-effect meta-analysis. Our search criteria identified 465 articles, of which 7 met inclusion criteria; all were observational studies. Five studies considered antibiotic risk relative to no antibiotic exposure: clindamycin (OR = 16.80; 95% confidence interval [95% CI], 7.48 to 37.76), fluoroquinolones (OR = 5.50; 95% CI, 4.26 to 7.11), and cephalosporins, monobactams, and carbapenems (CMCs) (OR = 5.68; 95% CI, 2.12 to 15.23) had the largest effects, while macrolides (OR = 2.65; 95% CI, 1.92 to 3.64), sulfonamides and trimethoprim (OR = 1.81; 95% CI, 1.34 to 2.43), and penicillins (OR = 2.71; 95% CI, 1.75 to 4.21) had lower associations with CDI. We noted no effect of tetracyclines on CDI risk (OR = 0.92; 95% CI, 0.61 to 1.40). In the community setting, there is substantial variation in the risk of CDI associated with different antimicrobial classes. Avoidance of high-risk antibiotics (such as clindamycin, CMCs, and fluoroquinolones) in favor of lower-risk antibiotics (such as penicillins, macrolides, and tetracyclines) may help reduce the incidence of CDI.

Brown KA; Khanafer N; Daneman N; Fisman DN

2013-05-01

171

Meta-analysis of antibiotics and the risk of community-associated Clostridium difficile infection.  

Science.gov (United States)

The rising incidence of Clostridium difficile infection (CDI) could be reduced by lowering exposure to high-risk antibiotics. The objective of this study was to determine the association between antibiotic class and the risk of CDI in the community setting. The EMBASE and PubMed databases were queried without restriction to time period or language. Comparative observational studies and randomized controlled trials (RCTs) considering the impact of exposure to antibiotics on CDI risk among nonhospitalized populations were considered. We estimated pooled odds ratios (OR) for antibiotic classes using random-effect meta-analysis. Our search criteria identified 465 articles, of which 7 met inclusion criteria; all were observational studies. Five studies considered antibiotic risk relative to no antibiotic exposure: clindamycin (OR = 16.80; 95% confidence interval [95% CI], 7.48 to 37.76), fluoroquinolones (OR = 5.50; 95% CI, 4.26 to 7.11), and cephalosporins, monobactams, and carbapenems (CMCs) (OR = 5.68; 95% CI, 2.12 to 15.23) had the largest effects, while macrolides (OR = 2.65; 95% CI, 1.92 to 3.64), sulfonamides and trimethoprim (OR = 1.81; 95% CI, 1.34 to 2.43), and penicillins (OR = 2.71; 95% CI, 1.75 to 4.21) had lower associations with CDI. We noted no effect of tetracyclines on CDI risk (OR = 0.92; 95% CI, 0.61 to 1.40). In the community setting, there is substantial variation in the risk of CDI associated with different antimicrobial classes. Avoidance of high-risk antibiotics (such as clindamycin, CMCs, and fluoroquinolones) in favor of lower-risk antibiotics (such as penicillins, macrolides, and tetracyclines) may help reduce the incidence of CDI. PMID:23478961

Brown, Kevin A; Khanafer, Nagham; Daneman, Nick; Fisman, David N

2013-03-11

172

Community-associated Clostridium difficile infection and antibiotics: a meta-analysis.  

UK PubMed Central (United Kingdom)

OBJECTIVES: Antibiotic exposure is the most important risk factor for Clostridium difficile infection (CDI). Most evaluations of antimicrobial risk factors have been conducted in healthcare settings. The objective of this meta-analysis was to evaluate the association between antibiotic exposure and community-associated CDI (CA-CDI) (i.e. symptom onset in the community with no healthcare facility admission within 12 weeks) and to determine the classes of antibiotics posing the greatest risk. METHODS: We searched four electronic databases for subject headings and text words related to CA-CDI and antibiotics. Studies that investigated the risk of CA-CDI associated with antibiotic usage were considered eligible. Data from the identified studies were combined using a random-effects model and ORs were calculated. RESULTS: Of 910 citations identified, eight studies (n?=?30?184 patients) met our inclusion criteria. Antibiotic exposure was associated with an increased risk of CA-CDI (OR 6.91, 95% CI 4.17-11.44, I(2)?=?95%). The risk was greatest with clindamycin (OR 20.43, 95% CI 8.50-49.09) followed by fluoroquinolones (OR 5.65, 95% CI 4.38-7.28), cephalosporins (OR 4.47, 95% CI 1.60-12.50), penicillins (OR 3.25, 95% CI 1.89-5.57), macrolides (OR 2.55, 95% CI 1.91-3.39) and sulphonamides/trimethoprim (OR 1.84, 95% CI 1.48-2.29). Tetracyclines were not associated with an increased CDI risk (OR 0.91, 95% CI 0.57-1.45). CONCLUSIONS: Antibiotic exposure was an important risk factor for CA-CDI, but the risk was different amongst different antibiotic classes. The risk was greatest with clindamycin followed by fluoroquinolones and cephalosporins, whereas tetracyclines were not associated with an increased risk.

Deshpande A; Pasupuleti V; Thota P; Pant C; Rolston DD; Sferra TJ; Hernandez AV; Donskey CJ

2013-09-01

173

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

Directory of Open Access Journals (Sweden)

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, Registry, minimal information standards

Ostraat ML; Mills KC; Guzan KA; Murry D

2013-01-01

174

Taxonomic profiling and metagenome analysis of a microbial community from a habitat contaminated with industrial discharges.  

UK PubMed Central (United Kingdom)

Industrial units, manufacturing dyes, chemicals,solvents, and xenobiotic compounds, produce liquid and solid wastes, which upon conventional treatment are released in the nearby environment and thus are the major cause of pollution. Soil collected from contaminated Kharicut Canalbank (N 22°57.878?; E 072°38.478?), Ahmeda bad, Gujarat,India was used for metagenomic DNA preparation to study the capabilities of intrinsic microbial community in dealing with xenobiotics. Sequencing of metagenomic DNA on the Genome Sequencer FLX System using titanium chemistry resulted in 409,782 reads accounting for 133,529,997 bases of sequence information. Taxonomic analyses and gene annotations were carried out using the bioinformatics platform Sequence Analysis and Management System for Metagenomic Datasets. Taxonomic profiling was carried out by three different complementary approaches: (a) 16S rDNA, (b) environmental gene tags, and (c) lowest common ancestor. The most abundant phylum and genus were found to be “Proteobacteria”and “Pseudomonas,” respectively. Metagenome reads were mapped on sequenced microbial genomes and the highest numbers of reads were allocated to Pseudomonas stutzeri A1501. Assignment of obtained metagenome reads to Gene Ontology terms, Clusters of Orthologous Groups of protein categories, protein family numbers, and Kyoto Encyclopedia of Genes and Genomes hits revealed genomic potential of indigenous microbial community. In total, 157,024 reads corresponded to 37,028 different KEGG hits, and amongst them, 11,574 reads corresponded to 131 different enzymes potentially involved in xenobiotic biodegradation. These enzymes were mapped on biodegradation pathways of xenobiotics to elucidate their roles in possible catalytic reactions. Consequently, information obtained from the present study will act as a baseline which, subsequently along with other“-omic” studies, will help in designing future bioremediation strategies in effluent treatment plants and environmental cleanup projects.

Shah V; Zakrzewski M; Wibberg D; Eikmeyer F; Schlüter A; Madamwar D

2013-10-01

175

Taxonomic profiling and metagenome analysis of a microbial community from a habitat contaminated with industrial discharges.  

Science.gov (United States)

Industrial units, manufacturing dyes, chemicals,solvents, and xenobiotic compounds, produce liquid and solid wastes, which upon conventional treatment are released in the nearby environment and thus are the major cause of pollution. Soil collected from contaminated Kharicut Canalbank (N 22°57.878?; E 072°38.478?), Ahmeda bad, Gujarat,India was used for metagenomic DNA preparation to study the capabilities of intrinsic microbial community in dealing with xenobiotics. Sequencing of metagenomic DNA on the Genome Sequencer FLX System using titanium chemistry resulted in 409,782 reads accounting for 133,529,997 bases of sequence information. Taxonomic analyses and gene annotations were carried out using the bioinformatics platform Sequence Analysis and Management System for Metagenomic Datasets. Taxonomic profiling was carried out by three different complementary approaches: (a) 16S rDNA, (b) environmental gene tags, and (c) lowest common ancestor. The most abundant phylum and genus were found to be “Proteobacteria”and “Pseudomonas,” respectively. Metagenome reads were mapped on sequenced microbial genomes and the highest numbers of reads were allocated to Pseudomonas stutzeri A1501. Assignment of obtained metagenome reads to Gene Ontology terms, Clusters of Orthologous Groups of protein categories, protein family numbers, and Kyoto Encyclopedia of Genes and Genomes hits revealed genomic potential of indigenous microbial community. In total, 157,024 reads corresponded to 37,028 different KEGG hits, and amongst them, 11,574 reads corresponded to 131 different enzymes potentially involved in xenobiotic biodegradation. These enzymes were mapped on biodegradation pathways of xenobiotics to elucidate their roles in possible catalytic reactions. Consequently, information obtained from the present study will act as a baseline which, subsequently along with other“-omic” studies, will help in designing future bioremediation strategies in effluent treatment plants and environmental cleanup projects. PMID:23728164

Shah, Varun; Zakrzewski, Martha; Wibberg, Daniel; Eikmeyer, Felix; Schlüter, Andreas; Madamwar, Datta

2013-10-01

176

Poverty dynamics : an analysis of the 1994 and 1995 waves of the European Community Household Panel Survey  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Recent poverty research internationally based on analysis of panel data has highlighted the importance of income dynamics. In this paper, we study mobility into and out of relative income poverty from one year to the next using data for twelve countries from the European Community Household Panel Su...

Whelan, Christopher T.; Layte, Richard; Maitre, Bertrand; Nolan, Brian

177

Three-year financial analysis of pharmacy services at an independent community pharmacy.  

UK PubMed Central (United Kingdom)

OBJECTIVE: To assess the financial performance of pharmacy services including vaccinations, cholesterol screenings, medication therapy management (MTM), adherence management services, employee health fairs, and compounding services provided by an independent community pharmacy. METHODS: Three years (2008-10) of pharmacy records were examined to determine the total revenue and costs of each service. Costs included products, materials, labor, marketing, overhead, equipment, reference materials, and fax/phone usage. Costs were allocated to each service using accepted principles (e.g., time for labor). Depending on the service, the total revenue was calculated by multiplying the frequency of the service by the revenue per patient or by adding the total revenue received. A sensitivity analysis was conducted for the adherence management services to account for average dispensing net profit. RESULTS: 7 of 11 pharmacy services showed a net profit each year. Those services include influenza and herpes zoster immunization services, MTM, two adherence management services, employee health fairs, and prescription compounding services. The services that realized a net loss included the pneumococcal immunization service, cholesterol screenings, and two adherence management services. The sensitivity analysis showed that all adherence services had a net gain when average dispensing net profit was included. CONCLUSION: Most of the pharmacist services had an annual positive net gain. It seems likely that these services can be sustained. Further cost management, such as reducing labor costs, could improve the viability of services with net losses. However, even with greater efficiency, external factors such as competition and reimbursement challenge the sustainability of these services.

Doucette WR; McDonough RP; Mormann MM; Vaschevici R; Urmie JM; Patterson BJ

2012-03-01

178

Microbial community analysis during continuous fermentation of thermally hydrolysed waste activated sludge.  

UK PubMed Central (United Kingdom)

Acidogenic fermentation of thermally hydrolysed waste activated sludge was carried out at laboratory scale in two reactors operated under different hydraulic retention times (HRT). Process performance was assessed in terms of volatile fatty acid (VFA) composition and yield. The diversity of the microbial population was investigated by constructing a 16S rRNA gene library and subsequent phylogenetic analysis of clones. Fluorescence in situ hybridization (FISH) was used to assess the relative abundance of different bacterial groups. Bacteroidetes and Firmicutes were the dominant taxonomic groups representing 93% of the total sequences obtained in the reactor with 4 d HRT. A similar VFA yield (0.4-0.5 g VFA(COD) g SCOD(-1)) was obtained for the HRTs tested (1-4 d), indicating that extended retention times were not useful. Within Firmicutes, Clostridia was the major group detected in the clone sequences. These had close affiliation to Sporanaerobacter acetigenes, suggesting organisms of this group were important for hydrolysis of the protein fraction of the substrate. However, FISH analysis failed to detect the major portion of the bacteria, and this is most likely due to the lack of appropriate probes. This work emphasizes the diversity of fermentative communities, and indicates that more work is needed to identify and detect the important members.

Cirne DG; Bond P; Pratt S; Lant P; Batstone DJ

2012-01-01

179

Phylogenetic microarray analysis of a microbial community performing reductive dechlorination at a TCE-contaminated site.  

UK PubMed Central (United Kingdom)

A high-density phylogenetic microarray (PhyloChip) was applied to track bacterial and archaeal populations through different phases of remediation at Ft. Lewis, WA, a trichloroethene (TCE)-contaminated groundwater site. Biostimulation with whey, and bioaugmentation with a Dehalococcoides-containing enrichment culture were strategies implemented to enhance dechlorination. As a measure of species richness, over 1300 operational taxonomic units (OTUs) were detected in DNA from groundwater samples extracted during different stages of treatment and in the bioaugmentation culture. In order to determine active members within the community, 16S rRNA from samples were analyzed by microarray and ?600 OTUs identified. A cDNA clone library of the expressed 16S rRNA corroborated the observed diversity and activity of some of the phyla. Principle component analysis of the treatment plot samples revealed that the microbial populations were constantly changing during the course of the study. Dynamic analysis of the archaeal population showed significant increases in methanogens at the later stages of treatment that correlated with increases in methane concentrations of over 2 orders of magnitude. Overall, the PhyloChip analyses in this study have provided insights into the microbial ecology and population dynamics at the TCE-contaminated field site useful for understanding the in situ reductive dechlorination processes.

Lee PK; Warnecke F; Brodie EL; Macbeth TW; Conrad ME; Andersen GL; Alvarez-Cohen L

2012-01-01

180

Characterization of bacterial and fungal soil communities by automated ribosomal intergenic spacer analysis fingerprints: biological and methodological variability.  

UK PubMed Central (United Kingdom)

Automated rRNA intergenic spacer analysis (ARISA) was used to characterise bacterial (B-ARISA) and fungal (F-ARISA) communities from different soil types. The 16S-23S intergenic spacer region from the bacterial rRNA operon was amplified from total soil community DNA for B-ARISA. Similarly, the two internal transcribed spacers and the 5.8S rRNA gene (ITS1-5.8S-ITS2) from the fungal rRNA operon were amplified from total soil community DNA for F-ARISA. Universal fluorescence-labeled primers were used for the PCRs, and fragments of between 200 and 1,200 bp were resolved on denaturing polyacrylamide gels by use of an automated sequencer with laser detection. Methodological (DNA extraction and PCR amplification) and biological (inter- and intrasite) variations were evaluated by comparing the number and intensity of peaks (bands) between electrophoregrams (profiles) and by multivariate analysis. Our results showed that ARISA is a high-resolution, highly reproducible technique and is a robust method for discriminating between microbial communities. To evaluate the potential biases in community description provided by ARISA, we also examined databases on length distribution of ribosomal intergenic spacers among bacteria (L. Ranjard, E. Brothier, and S. Nazaret, Appl. Environ. Microbiol. 66:5334-5339, 2000) and fungi.

Ranjard L; Poly F; Lata JC; Mougel C; Thioulouse J; Nazaret S

2001-10-01

 
 
 
 
181

Comparative study of three analysis methods (TTGE, flow cytometry and HPLC) for xenobiotic impact assessment on phytoplankton communities.  

Science.gov (United States)

The impacts of the fungicide Opus (epoxiconazole) on marine phytoplankton communities were assessed in a 12-day field experiment using in situ microcosms maintained underwater at 6 m depth. Three community analysis methods were compared for their sensitivity threshold in fungicide impact detection. When phytoplankton communities were exposed to 1 microg l(-1) of epoxiconazole, no effects could be demonstrated using TTGE (Temporal Temperature Gradient gel Electrophoresis), flow cytometry or HPLC. When exposed to 10 microg l(-1), TTGE fingerprints from PCR amplified 18S rDNA of communities exhibited significant differences compared with controls (ANOSIM, P = 0.028). Neither flow cytometry counts, nor HPLC pigment profiles allowed to show significant differences in microcosms exposed to 10 microg l(-1) of epoxiconazole. When exposed to 100 microg l(-1), all three methods allowed to detect significant differences in treated microcosms, as compared to controls. The TTGE analysis appears in this study as the most sensitive method for fungicide impact assessment on eukaryote microbial communities. PMID:19096934

Stachowski-Haberkorn, Sabine; Quiniou, Louis; Beker, Beatriz; Haberkorn, Hansy; Marie, Dominique; de la Broise, Denis

2008-12-19

182

Comparative study of three analysis methods (TTGE, flow cytometry and HPLC) for xenobiotic impact assessment on phytoplankton communities.  

UK PubMed Central (United Kingdom)

The impacts of the fungicide Opus (epoxiconazole) on marine phytoplankton communities were assessed in a 12-day field experiment using in situ microcosms maintained underwater at 6 m depth. Three community analysis methods were compared for their sensitivity threshold in fungicide impact detection. When phytoplankton communities were exposed to 1 microg l(-1) of epoxiconazole, no effects could be demonstrated using TTGE (Temporal Temperature Gradient gel Electrophoresis), flow cytometry or HPLC. When exposed to 10 microg l(-1), TTGE fingerprints from PCR amplified 18S rDNA of communities exhibited significant differences compared with controls (ANOSIM, P = 0.028). Neither flow cytometry counts, nor HPLC pigment profiles allowed to show significant differences in microcosms exposed to 10 microg l(-1) of epoxiconazole. When exposed to 100 microg l(-1), all three methods allowed to detect significant differences in treated microcosms, as compared to controls. The TTGE analysis appears in this study as the most sensitive method for fungicide impact assessment on eukaryote microbial communities.

Stachowski-Haberkorn S; Quiniou L; Beker B; Haberkorn H; Marie D; de la Broise D

2009-04-01

183

The Roles of Government Agency in Assisting CSR Project for Community Development: Analysis from the Recipients Perspectives  

Directory of Open Access Journals (Sweden)

Full Text Available Corporate Social responsibility (CSR) initiatives by the corporations are playing increasingly significant role in the effort of contributing to community development particularly in the developing country. The international prominence of the initiatives in this area can be traced to the objectives of Millenium Development Goals (MDGs) that established corporations as partners of development. However, realizing the corporate sectors constraints in playing the roles as agents of development, the CSR initiatives need to be implemented with the involvement of the government agency to assist community development. This paper will explore the roles played by government agency in CSR project through a case study of successful CSR initiative in Bukit Awang, PasirPuteh Kelantan in Malaysia. A qualitative research strategy that explores the perspective of social actors that involved in the project and thematic data analysis are undertaken for that purpose. The result from the analysis reveals two main roles played by the government agency in CSR project by the corporation to the community. The roles are as the supporting agency and as leader in the community. These roles have assisted in the implementation of the CSR project with the objectives to develop the community involved.

Sarmila M. S.; Zaimah R.; N. Lyndon; Azima A. M.; Suhana Saad; S. Selvadurai

2013-01-01

184

Achieving high cancer control trial enrollment in the community setting: an analysis of the Community Clinical Oncology Program.  

UK PubMed Central (United Kingdom)

Determining the factors that lead to successful enrollment of patients in cancer control clinical trials is essential as cancer patients are often burdened with side effects such as pain, nausea, and fatigue. One promising intervention for increasing enrollment in cancer control trials is the National Cancer Institute's Community Clinical Oncology Program (CCOP). In this article, we examined CCOP staffing, policies, and procedures associated with enrollment in control trials. Data were obtained from three sources: the online CCOP, MB-CCOP, and Research Base Management System, CCOP Annual Progress Reports, and a survey of CCOP Administrators conducted in 2011. We analyzed cancer control trial accrual in 2011 among 46 CCOPs using multivariate regression. Three factors were significant predictors of accrual. First, having a team of staff dedicated to enrolling patients in control and prevention trials, compared to having no dedicated staff, was associated on average with an additional 30 patients enrolled in control trials (p<0.05). Second, CCOPs that recognized physicians for enrolling a large number of patients compared to CCOPs that did not recognize high enrolling physicians enrolled on average an additional 25 patients in control trials (p<0.05). Lastly, the number of cancer control trials available was also associated with enrollment (?=5.50, p<0.00). Our results indicate that CCOPs looking to increase enrollment in control trials should consider dedicating a team of staff to enroll patients in these types of trials. In addition, CCOPs or other volunteer research systems looking to increase physician participation should consider recognizing high enrolling physicians.

Jacobs SR; Weiner BJ; Minasian LM; Good MJ

2013-03-01

185

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

UK PubMed Central (United Kingdom)

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.

Thiel DB; Platt T; Platt J; King SB; Kardia SL

2013-07-01

186

Word frequency and content analysis approach to identify demand patterns in a virtual community of carriers of hepatitis C.  

UK PubMed Central (United Kingdom)

BACKGROUND: Orkut, a Brazilian virtual social network, is responsible for popularization of the Internet among people of low income and educational level. It's observed that rapid growth of virtual communities can be reached by low cost Internet access in community local area network houses. Orkut poses an important social resource for Brazilian patients with chronic conditions like hepatitis C virus (HCV) carriers, who face several obstacles in adapting to everyday difficulties. OBJECTIVE: Identify Patterns of Recurring Demands (PRD) expressed in messages posted by members of virtual communities dedicated to HCV carriers. METHODS: Pre-selection: we identified terms commonly associated to HCV on generic Internet searches (primary Keywords - Kps); Kps were used to identify the most representative HCV communities in a virtual community site (Orkut); all messages published along 8 years on all topics of the community were collected and tabulated; the word frequency was used to construct a "word cloud" (graphic representation of the word frequency) on which was applied a content analysis technique. RESULTS: The most cited terms expressed: search for information about medications (prescribed and "forbidden"); emphasis on counting time, which were interpreted as surviving expectations; frequent mention of God, doctors, and "husbands" (female carriers were 68%). These elements provided material for further research - they will be useful in the construction of categories in discourse analysis. CONCLUSIONS: The present work is a disclosure of preliminary findings considered original and promising. The word frequency/content analysis approach expressed needs of social support and material assistance that may provide subsidies for further qualitative approach and public health policies aimed to HCV carriers. The study of PRD by word frequency may be useful in identifying demands underestimated by other means.

Vasconcellos-Silva PR; Carvalho D; Lucena C

2013-01-01

187

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

CERN Multimedia

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...

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

2010-01-01

188

Analysis of microbial community in Japanese vineyard soils by culture-independent molecular approach  

Directory of Open Access Journals (Sweden)

Full Text Available Keiko Fujita, Seiichi Furuya, Minako Kohno, Shunji Suzuki, Tsutomu TakayanagiInstitute of Enology and Viticulture, University of Yamanashi, Kofu, Yamanashi, JapanAbstract: Soil microbes play an important role in the management of soil environment. They form various microbial communities in response to environmental factors, including soil texture and chemical components. Because of this, it is difficult to determine the microbial community structure of soil. In vineyard soils, the overall microbial community structure has yet to be unraveled. To understand the microbial community in vineyard soil, we surveyed comprehensively microbial communities in Japanese vineyard soils by using a culture-independent molecular approach. We identified 681 fungal clone sequences and 1076 bacterial clone sequences in soil samples collected from nine independent Japanese vineyards, and the results suggested that Ascomycota is the dominant group in the fungal community, whereas Proteobacterium and Acidobacterium are the dominant groups in the bacterial community. DNA was directly extracted from the soil samples, and the fungal internal transcribed spacer 1 (ITS 1) region or the bacterial 16S ribosomal DNA (rDNA) region was amplified by polymerase chain reaction. The recovered fungal clones were sorted into 225 operational taxonomic units and the majority of the clone sequences were assigned to Ascomycota. Meanwhile, the recovered bacterial clones were sorted into 17 phyla, and the abundant phyla were Proteobacterium and Acidobacterium. These results differed from the reported fungal and bacterial community structures in forest and agricultural soils. Moreover, we preliminarily generated a catalog of Japanese vineyard soils. The microbial community structures in the vineyard soils were extremely complex, suggesting that the microbial community structure in each vineyard soil has individual characteristics. Our study comprehensively showed for the first time fungal and bacterial community structures in Japanese vineyard soils, and is most likely to provide a clue to understand the nature of Japanese vineyard soils.Keywords: Japanese vineyard, soil microbe, microbial community structure, 16S rDNA

Keiko Fujita; Seiichi Furuya; Minako Kohno; et al

2010-01-01

189

Phospholipid fatty acid profiles and carbon utilization patterns for analysis of microbial community structure under field and greenhouse conditions.  

UK PubMed Central (United Kingdom)

The description of soil microbial community structure by phospholipid fatty acid (PLFA) profiles is based on the relationship between the phylogeny of microorganisms and their PLFA profiles. Based on this relationship, two community based microbiological measurements, namely, potential C source utilization patterns in Biolog microtiter plates and PLFA profiles were used to examine metabolic fingerprints of soil microbial communities and changes in species composition between field and greenhouse soils. Field and greenhouse experiments were conducted using Palouse and Ritzville silt loams. Soil sampled under wheat (Triticum aestivum L.), barley (Hordeum vulgare L.), pea (Pisum sativa L.), jointed goatgrass (Aegilops cylindrica L.), downy brome (Bromus tectorum L.), and control soils (no plants) were used for these analyses. Principal component analysis (PCA) of PLFA profiles and C source utilization patterns were used to describe changes in microbial biomass and metabolic fingerprints from the two soil types under field and greenhouse conditions. Biomass measurements from extractable PLFA profiles per g dry weight ranged from 28.8 nmol in wheat soil in the greenhouse to 71.4 nmol in pea soil in the field. In general, biomass was higher in all the field samples than in greenhouse samples. Principal component analysis the two soils with different plants in the field and greenhouse showed clear separation. Principal component analysis C utilization patterns on the effects of environment on soil microbial community yielded similar results with PLFA measurements. However, higher variability observed among different plants with the Biolog data resulted in the low amounts variance for Biolog data explained by the first two dimensions of the PCA. This suggests that PLFA may be more sensitive community analysis than the Biolog technique.

Ibekwe AM; Kennedy AC

1998-06-01

190

[Costs-analysis of methadone program in the autonomous community La Rioja, Spain].  

UK PubMed Central (United Kingdom)

BACKGROUND: Methadone programs have been organized in each Spanish region in a specific way. In spite of the regional interests to manage those programs in a more efficient way, so far the costs of the programs are unknown. As a previous step, it would be desirable to understand the activities related to these programs as well as their respective costs. This article aims to calculate the cost of the Methadone program in the autonomous community of La Rioja, and to understand those parameters which generate a greater cost to this programme. METHODS: The study followed a similar structure as the research recently applied to the region of Murcia. The reference year for the study of the annual costs of the Methadone program was 2010. Data were obtained from different registries of several institutions involved in the regional program. Costs were classified according to different stages and dispensation centres which participated in this programme. RESULTS: Data analysis, for a concentration of 2 mg/ml of methadone, showed an approximate annual cost of 165.759 euros. Taking the total number of patients into consideration the individual cost was 412,34 euros. CONCLUSIONS: Dispensation is the stage which caused the largest cost to the programme, the highest per patient cost corresponded to the centre with less patients due to the fact that fixed costs are shared by a smaller group of persons; the biggest global cost of the programme came from Logroño's center but its average cost is lower.

Del Pozo Iribarría J; Soldevilla Iñiguez D; Murga García JA; Antoñanzas Villar F

2012-10-01

191

Molecular analysis of the microbial communities of Mars analog lakes in Western Australia.  

UK PubMed Central (United Kingdom)

Unique, shallow interdune lakes and groundwaters with extremely low pH and high salinity exist in Australia, along with nearby lakes that possess higher pH values. These acidic hypersaline environments are possibly the best modern terrestrial analogues for past martian environments. However, no previous microbiological analyses of these lakes have been conducted. During the Australian winter of 2005, water samples were taken from several hypersaline lakes located in southern Western Australia that possessed acidic to slightly alkaline pH. These samples were subjected to molecular analysis to identify bacterial communities. DNA extraction and polymerase chain reaction (PCR) amplification of the 16S rRNA gene sequences, by using universal bacterial primers, were also performed on the samples. Extracted DNA was amplified with 1070 forward and 1392 GC-clamped reverse primers and analyzed by using denaturant gradient gel electrophoresis (DGGE). In addition, libraries were developed from DNA retrieved from four lakes, including a marginal marine neutral lake, an inland neutral lake, and two inland acid lakes, and selected clones with distinct operational taxonomic units were sequenced. The DGGE profiles and clone sequence data indicate that there are distinct, abundant, and diverse microbial populations in these Australian hypersaline environments, especially the acidic ones. These results are significant for two reasons: (1) they provide the first microbiological survey of natural acid saline lakes and (2) they hint at the possibility that there could have been a diverse microbial population in acidic hypersaline environments on Mars.

Mormile MR; Hong BY; Benison KC

2009-12-01

192

Seasonal dynamics of bacterioplankton community structure in a eutrophic lake as determined by 5S rRNA analysis.  

Science.gov (United States)

Community structure of bacterioplankton was studied during the major growth season for phytoplankton (April to October) in the epilimnion of a temperate eutrophic lake (Lake Plusssee, northern Germany) by using comparative 5S rRNA analysis. Estimates of the relative abundances of single taxonomic groups were made on the basis of the amounts of single 5S rRNA bands obtained after high-resolution electrophoresis of RNA directly from the bacterioplankton. Full-sequence analysis of single environmental 5S rRNAs enabled the identification of single taxonomic groups of bacteria. Comparison of partial 5S rRNA sequences allowed the detection of changes of single taxa over time. Overall, the whole bacterioplankton community showed two to eight abundant (>4% of the total 5S rRNA) taxa. A distinctive seasonal succession was observed in the taxonomic structure of this pelagic community. A rather-stable community structure, with seven to eight different taxonomic units, was observed beginning in April during the spring phytoplankton bloom. A strong reduction in this diversity occurred at the beginning of the clear-water phase (early May), when only two to four abundant taxa were observed, with one taxon dominating (up to 72% of the total 5S rRNA). The community structure during summer stagnation (June and July) was characterized by frequent changes of different dominating taxa. During late summer, a dinoflagellate bloom (Ceratium hirudinella) occurred, with Comamonas acidovorans (beta-subclass of the class Proteobacteria) becoming the dominant bacterial species (average abundance of 43% of the total 5S rRNA). Finally, the seasonal dynamics of the community structure of bacterioplankton were compared with the abundances of other major groups of the aquatic food web, such as phyto- and zooplankton, revealing that strong grazing pressure by zooplankton can reduce microbial diversity substantially in pelagic environments. PMID:10388718

Höfle, M G; Haas, H; Dominik, K

1999-07-01

193

Seasonal dynamics of bacterioplankton community structure in a eutrophic lake as determined by 5S rRNA analysis.  

UK PubMed Central (United Kingdom)

Community structure of bacterioplankton was studied during the major growth season for phytoplankton (April to October) in the epilimnion of a temperate eutrophic lake (Lake Plusssee, northern Germany) by using comparative 5S rRNA analysis. Estimates of the relative abundances of single taxonomic groups were made on the basis of the amounts of single 5S rRNA bands obtained after high-resolution electrophoresis of RNA directly from the bacterioplankton. Full-sequence analysis of single environmental 5S rRNAs enabled the identification of single taxonomic groups of bacteria. Comparison of partial 5S rRNA sequences allowed the detection of changes of single taxa over time. Overall, the whole bacterioplankton community showed two to eight abundant (>4% of the total 5S rRNA) taxa. A distinctive seasonal succession was observed in the taxonomic structure of this pelagic community. A rather-stable community structure, with seven to eight different taxonomic units, was observed beginning in April during the spring phytoplankton bloom. A strong reduction in this diversity occurred at the beginning of the clear-water phase (early May), when only two to four abundant taxa were observed, with one taxon dominating (up to 72% of the total 5S rRNA). The community structure during summer stagnation (June and July) was characterized by frequent changes of different dominating taxa. During late summer, a dinoflagellate bloom (Ceratium hirudinella) occurred, with Comamonas acidovorans (beta-subclass of the class Proteobacteria) becoming the dominant bacterial species (average abundance of 43% of the total 5S rRNA). Finally, the seasonal dynamics of the community structure of bacterioplankton were compared with the abundances of other major groups of the aquatic food web, such as phyto- and zooplankton, revealing that strong grazing pressure by zooplankton can reduce microbial diversity substantially in pelagic environments.

Höfle MG; Haas H; Dominik K

1999-07-01

194

Microbial community analysis of thermophilic contact oxidation process by using ribosomal RNA approaches and the quinone profile method.  

UK PubMed Central (United Kingdom)

Microbial community structure of a lab scale thermophilic aerobic wastewater treatment reactor was analyzed by a combination of culture-independent methods. Quinone profile method provides for chemical analysis of respiratory quinone molecular species, which corresponds to bacterial groups. Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rDNA partial sequences (PCR-DGGE) clarifies community changes at species level, as DGGE can separate DNA fragments of different sequences. Certain phvlogenetic groups of bacterial cells can be labeled by fluorescence in situ hybridization (FISH). Quinone profile showed a predominant presence of MK-7. PCR-DGGE revealed that constituents of the community were unchanged during the stable phase. FISH demonstrated the existence of the relatives of Bacillus lentus and B. thermocloacae in considerable proportions. The community was mainly composed of Bacillaceae, and obligate thermophilic and mesophilic Bacillus appeared in spite of the temperature fluctuation from 35 degrees C to 60 degrees C. The combination of these culture-independent methods revealed the community precisely enough to evaluate the reactor performance.

Kurisu F; Satoh H; Mino T; Matsuo T

2002-01-01

195

Microbial community analysis of thermophilic contact oxidation process by using ribosomal RNA approaches and the quinone profile method.  

Science.gov (United States)

Microbial community structure of a lab scale thermophilic aerobic wastewater treatment reactor was analyzed by a combination of culture-independent methods. Quinone profile method provides for chemical analysis of respiratory quinone molecular species, which corresponds to bacterial groups. Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rDNA partial sequences (PCR-DGGE) clarifies community changes at species level, as DGGE can separate DNA fragments of different sequences. Certain phvlogenetic groups of bacterial cells can be labeled by fluorescence in situ hybridization (FISH). Quinone profile showed a predominant presence of MK-7. PCR-DGGE revealed that constituents of the community were unchanged during the stable phase. FISH demonstrated the existence of the relatives of Bacillus lentus and B. thermocloacae in considerable proportions. The community was mainly composed of Bacillaceae, and obligate thermophilic and mesophilic Bacillus appeared in spite of the temperature fluctuation from 35 degrees C to 60 degrees C. The combination of these culture-independent methods revealed the community precisely enough to evaluate the reactor performance. PMID:11827349

Kurisu, Futoshi; Satoh, Hiroyasu; Mino, Takashi; Matsuo, Tomonori

2002-01-01

196

Addressing Cancer Disparities via Community Network Mobilization and Intersectoral Partnerships: A Social Network Analysis  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Community mobilization and collaboration among diverse partners are vital components of the effort to reduce and eliminate cancer disparities in the United States. We studied the development and impact of intersectoral connections among the members of the Massachusetts Community Network for Cancer ...

Achille, Erline; Baril, Nashira; D'Entremont, Kerrie; Grullon, Milagro; Judge, Christine; Oppenheimer, Sarah; Reeves, Chrasandra

197

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

Science.gov (United States)

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…

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

2011-01-01

198

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

Science.gov (United States)

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…

Kitchen, Peter; Williams, Allison; Chowhan, James

2012-01-01

199

Perceptions of Underprepared Community College Students Regarding Their Educational Achievement: Preliminary Analysis of a Pilot Study  

Science.gov (United States)

This study serves as the preliminary analyses of a pilot study of community college students who persisted through their remedial classes and their programs of study and had attained the associate degree at a multicultural community college. This study is informed by Tinto's academic integration model, Astin's social involvement model and Freire's…

Barbatis, Peter

2008-01-01

200

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

UK PubMed Central (United Kingdom)

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.

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

2013-04-01

 
 
 
 
201

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

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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.

Claudia DURAN; Felisa CORDOVA

2012-01-01

202

A Multilevel Analysis of the Role of Parental and Community Variables on Young Children's Health.  

UK PubMed Central (United Kingdom)

OBJECTIVE: The purpose of this study was to examine the associations among community characteristics, family economic adversity, parents' health beliefs, and parents' and children's health using cross-level mediation analyses. METHODS: Survey data were collected from a nationally representative sample of 1,337 families with children between 3 and 6 years nested within 45 Trinidad and Tobago community clusters. RESULTS: At the individual level, parents' health belief of internality was a significant mediator between family economic adversity, adult health, and children's health. In the cross-level mediation analyses, health belief of internality was a significant mediator between community health problems and children's health. There were between-community variations in the relationship between adult health, health belief of powerful others, and children's health. CONCLUSIONS: There is strong evidence of the role of community and family influences on children's health. Findings indicate the need to use a multilevel analytical approach in studies of children's health.

Narine L; Krishnakumar A; Roopnarine JL; Logie C

2013-08-01

203

Análisis de la situación de salud en una comunidad especial Analysis of the health situation in a special community  

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Full Text Available El análisis de la situación de salud, por los servicios médicos, en una comunidad especial, incluye además de elementos curativos y preventivos, el entorno biológico y social del colectivo. El propósito del presente trabajo ha sido analizar los elementos teóricos que debe contener esta propuesta en un sistema primario de salud. Se abordan los aspectos que caracterizan actualmente este proceso en el nivel primario y se reflexiona acerca de sus perspectivas de desarrollo en función de mejorar la salud comunitaria. Se ofrecen aspectos conceptuales generales para la realización del análisis en las comunidades especiales bajo el liderazgo de los médicos, así como su metodología general para el desarrollo exitoso.The analysis of the health situation by medical services in a special community includes, besides healing and preventive elements, the biological and social environment of the community. The purpose of the present work has been to analyze theoretical elements of this proposal in a primary health system. The aspects characterizing this process at the moment in the primary care are approached and it is thought about its developmental perspectives with the purpose of improving community health. General conceptual aspects are provided for the analysis in special communities under the leadership of physicians, as well as its general methodology for the successful development

Alejandro Velázquez Pupo; Henry Rodríguez Reyes; Ernesto Sánchez Hernández; Marilaysis Duconger Danger; Edgar Benítez Sánchez

2010-01-01

204

Microbial community of salt crystals processed from Mediterranean seawater based on 16S rRNA analysis.  

UK PubMed Central (United Kingdom)

Phylogenetic analysis of 16S rRNA was used to investigate for the first time the structure of the microbial community that inhabits salt crystals retrieved from the bottom of a solar saltern, located in the coastal area of the Mediterranean Sea (Sfax, Tunisia). This community lives in an extremely salty environment of 250-310 g/L total dissolved salt. A total of 78 bacterial 16S rRNA clone sequences making up to 21 operational taxonomic units (OTUs), determined by the DOTUR program to 97% sequence similarity, was analyzed. These OTUs were affiliated to Bacteroidetes (71.4% of OTUs), and gamma-Proteobacteria and alpha-Proteobacteria (equally represented by 14.2% of the OTUs observed). The archaeal community composition appeared more diverse with 68 clones, resulting in 44 OTUs, all affiliated with the Euryarchaeota phylum. Of the bacterial and archaeal clones showing <97% 16S rRNA sequence identity with sequences in public databases, 47.6% and 84.1% respectively were novel clones. Both rarefaction curves and diversity measurements (Simpson, Shannon-Weaver, Chao) showed a more diverse archaeal than bacterial community at the Tunisian solar saltern pond. The analysis of an increasing clone's number may reveal additional local diversity.

Baati H; Guermazi S; Gharsallah N; Sghir A; Ammar E

2010-01-01

205

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

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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).

Muhammad Hanif; Yoichi Atsuta; Koichi Fujie; Hiroyuki Daimon

2012-01-01

206

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

UK PubMed Central (United Kingdom)

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).

Hanif M; Atsuta Y; Fujie K; Daimon H

2012-01-01

207

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

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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 ? in power low distribution (L(x)=x-?) increased as the decline of taxon level (from functional group to species) for the partial linear correlation constructed network. ? 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 interactions) in the partial linear correlation constructed network. And the addition of a taxon would result in an increase of 3 interactions (positive interactions) in the linear correlation constructed network. For partial linear correlation constructed network, the network connectance decreased as the number of taxa. The constant connectance hypothesis did not hold for our networks. It was found that network structure changed with season and location. The same taxon in the network would connect to different taxa as the change of season and location. A higher level of species aggregation may used to find a more stable network structure. Positive interactions were considered to be caused mainly by mutualism, predation/parasitism, etc. the number and portion of positive interactions may be the most important indices for community stability and functionality. Mutualism is the most significant trophic relationship, seconded by predation/parasitism, and competition is the worst for community stability.

WenJun Zhang

2011-01-01

208

Phylogenetic analysis of bacterial community composition in sediment contaminated with multiple heavy metals from the Xiangjiang River in China.  

UK PubMed Central (United Kingdom)

Understanding the ecology of sediments that are contaminated with heavy metals is critical for bioremediating these sediments, which has become a public concern over the course of the development of modern industry. To investigate the bacterial community composition of sediments that are contaminated with heavy metals in the Xiangjiang River, a total of four sediment samples contaminated with multiple heavy metals were obtained, and a culture-independent molecular analysis, polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), was performed. The results revealed that heavy metal pollution affected the sediment microbial community diversity, and the greatest species diversity appeared in the moderately polluted sediment X sample. The dominant family in these sediments includes ?-Proteobacteria, ?-Proteobacteria and Firmicutes. Moreover, ?-Proteobacteria was significantly increased with increases in heavy metal. A redundancy analysis (RDA) also confirmed this phenomenon.

Zhu J; Zhang J; Li Q; Han T; Xie J; Hu Y; Chai L

2013-05-01

209

Phylogenetic analysis of bacterial community composition in sediment contaminated with multiple heavy metals from the Xiangjiang River in China.  

Science.gov (United States)

Understanding the ecology of sediments that are contaminated with heavy metals is critical for bioremediating these sediments, which has become a public concern over the course of the development of modern industry. To investigate the bacterial community composition of sediments that are contaminated with heavy metals in the Xiangjiang River, a total of four sediment samples contaminated with multiple heavy metals were obtained, and a culture-independent molecular analysis, polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), was performed. The results revealed that heavy metal pollution affected the sediment microbial community diversity, and the greatest species diversity appeared in the moderately polluted sediment X sample. The dominant family in these sediments includes ?-Proteobacteria, ?-Proteobacteria and Firmicutes. Moreover, ?-Proteobacteria was significantly increased with increases in heavy metal. A redundancy analysis (RDA) also confirmed this phenomenon. PMID:23507235

Zhu, Jianyu; Zhang, Jingxia; Li, Qian; Han, Tao; Xie, Jianping; Hu, Yuehua; Chai, Liyuan

2013-03-15

210

Analysis of structures of permafrost wetland plant communities along environmental gradients in the Da Hinggan Mountains, China  

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Full Text Available Aims Changes in permafrost wetland plant communities were indicators of the retreat of permafrost in the Da Hinggan Mountains in China. Our objective was to understand the changes in species diversity and ecological characteristics of permafrost wetland plant communities along environmental gradients as the keys to predict changes in permafrost and permafrost wetlands in response to global warming.Methods We analyzed the distribution of 24 permafrost wetland plant communities in the Da Hinggan Mountains using detrended canonical correspondence analysis (DCCA). Species diversity, life forms and hydro- ecotypes of permafrost wetland plant communities were compared in three types of permafrost using multiple comparisons in ANOVA.Important findings The 24 permafrost wetland plant communities were classified into three groups according to three types of permafrost. From the predominantly continuous permafrost to the sparsely island permafrost to the predominantly continuous and island permafrost, shrub diversity decreased (p < 0.05), herbaceous diversity increased(p < 0.05), the percentage of mesophytes was 38.5%, 55.9% and 64.4%, respectively, the importance value decreased for helophytes (p < 0.05) and increased for mesophytes and xerophiles (p < 0.05), suggesting that the soil moisture tended to a moderate amount of moisture, and even drought. Hemicryptophytes were dominant and phanerophytes and geophytes were subdominant in the three types of permafrost, suggesting short summers and long, cold, wet winters in the areas. The species diversity and ecological characteristics of permafrost wetland plant communities in the predominantly continuous and island permafrost were similar to that in the sparsely island permafrost.

SUN Ju; LI Xiu-Zhen; WANG Xian-Wei; LÜ Jiu-Jun; LI Zong-Mei; HU Yuan-Man

2010-01-01

211

Outcomes of traditional cosmetic abdominoplasty in a community setting: a retrospective analysis of 1008 patients.  

UK PubMed Central (United Kingdom)

BACKGROUND: Abdominoplasty is one of the most commonly performed cosmetic operative procedures. Few large studies have examined outcomes of cosmetic abdominoplasty in a community setting. The authors explored postoperative outcome and the preoperative and intraoperative factors that may contribute to these complications. METHODS: A retrospective review of consecutive patients undergoing abdominoplasty over an 11-year period was performed. Baseline patient demographics, intraoperative technique, and postoperative outcomes were recorded. Preoperative and intraoperative characteristics were analyzed to determine characteristics that predispose patients to complications and undesirable outcomes. RESULTS: The 1008 study patients underwent either a full or modified abdominoplasty with a total complication rate of 32.6 percent. The most common complication was seroma (15.4 percent). Liposuction of the abdominal flap was performed in 469 patients (46.5 percent) and liposuction of the flanks was performed in 555 patients (55.1 percent). Chi-square analysis followed by logistic regression revealed that liposuction of the flanks and abdomen was independently associated with seroma formation in addition to major and minor complications (p < 0.05). CONCLUSIONS: Seroma formation following abdominoplasty is the most common complication. Concomitant liposuction of the flanks and abdomen with the addition of aggressive undermining leads to higher seroma rates. This association is likely multifactorial and may be secondary to increased resorptive demands placed on the abdominal lymphatics in the setting of greater dead space and larger fluid shifts as a result of liposuction. To reduce seroma rates, surgeons should avoid aggressive liposuction and undermining, particularly in high-risk patients.

Neaman KC; Armstrong SD; Baca ME; Albert M; Vander Woude DL; Renucci JD

2013-03-01

212

A comparative analysis of community acquired and hospital acquired methicillin resistant Staphylococcus aureus.  

UK PubMed Central (United Kingdom)

Purpose: Staphylococcus aureus has developed resistance against most of the therapeutic agents. The most notable example of this phenomenon was the emergence of Methicillin resistant Staphylococcus aureus (MRSA). We are reporting the prevalence and the antibiotic susceptibility pattern of the MRSA isolates from a tertiary care hospital. Methods: A total of 450 Staphylococcus aureus isolates from clinical samples were taken up for the study and they were screened for MRSA by using standard microbiological methods. An antibiotic assay was done for the confirmed MRSA isolates. The differentiation of the isolates into community acquired MRSA (CAMRSA) and hospital acquired MRSA (HAMRSA) was done according to the prescribed criteria. The double disc diffusion test was performed for both the groups, to identify the inducible clindamycin resistance. The HAMRSA and the CAMRSA isolates were subjected to a molecular analysis by PCR, to detect the presence of the Mec A gene and the PVL gene respectively. Results: Out of the 450 Staphylococcus aureus isolates, 121 were Methicillin Resistant Staphylococcus aureus (MRSA, 27%) and 329 were Methicillin Sensitive Staphylococcus aureus (MSSA, 73%). 91 MRSA isolates were grouped into HAMRSA and 30 were grouped into CAMRSA, with a prevalence of 20% and 7% respectively. All the MRSA strains were resistant to Penicillin (100%), Cefoxitin (100%) and Oxacillin (100%). 53.7% of the HAMRSA isolates showed inducible clindamycin resistance against that of 44.4% among the CAMRSA isolates. All the isolates were susceptible to Vancomycin and Linezolid. 64% of the HAMRSA isolates showed the presence of the Mec A gene and 48% of the CAMRSA isolates showed the presence of the PVL genes. Conclusion: The prevalence of the HAMRSA was higher than that of the CAMRSA and they showed a higher drug resistance.

P R V; M J

2013-07-01

213

A comparative analysis of community acquired and hospital acquired methicillin resistant Staphylococcus aureus.  

Science.gov (United States)

Purpose: Staphylococcus aureus has developed resistance against most of the therapeutic agents. The most notable example of this phenomenon was the emergence of Methicillin resistant Staphylococcus aureus (MRSA). We are reporting the prevalence and the antibiotic susceptibility pattern of the MRSA isolates from a tertiary care hospital. Methods: A total of 450 Staphylococcus aureus isolates from clinical samples were taken up for the study and they were screened for MRSA by using standard microbiological methods. An antibiotic assay was done for the confirmed MRSA isolates. The differentiation of the isolates into community acquired MRSA (CAMRSA) and hospital acquired MRSA (HAMRSA) was done according to the prescribed criteria. The double disc diffusion test was performed for both the groups, to identify the inducible clindamycin resistance. The HAMRSA and the CAMRSA isolates were subjected to a molecular analysis by PCR, to detect the presence of the Mec A gene and the PVL gene respectively. Results: Out of the 450 Staphylococcus aureus isolates, 121 were Methicillin Resistant Staphylococcus aureus (MRSA, 27%) and 329 were Methicillin Sensitive Staphylococcus aureus (MSSA, 73%). 91 MRSA isolates were grouped into HAMRSA and 30 were grouped into CAMRSA, with a prevalence of 20% and 7% respectively. All the MRSA strains were resistant to Penicillin (100%), Cefoxitin (100%) and Oxacillin (100%). 53.7% of the HAMRSA isolates showed inducible clindamycin resistance against that of 44.4% among the CAMRSA isolates. All the isolates were susceptible to Vancomycin and Linezolid. 64% of the HAMRSA isolates showed the presence of the Mec A gene and 48% of the CAMRSA isolates showed the presence of the PVL genes. Conclusion: The prevalence of the HAMRSA was higher than that of the CAMRSA and they showed a higher drug resistance. PMID:23998061

P R, Vysakh; M, Jeya

2013-07-01

214

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

UK PubMed Central (United Kingdom)

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.

Yu K; Zhang T

2012-01-01

215

Analysis of Spectral clustering approach for tracking community formation in social network  

Directory of Open Access Journals (Sweden)

Full Text Available The study of tracking community formation in social networks is an active area of research. A common pattern among the cohesive subgroup of people in a network is considered as a community which is a partition of the entire network structure. In recent years, spectral clustering has become one of the most popular modern clustering algorithms. It is simple to implement, can be solved efficiently by standard linear algebra method and very often outperforms traditional clustering algorithms such as the k-means algorithm. Existing method of community tracking methods is based on hierarchical clustering algorithm. This paper establishes that spectral clustering is an efficient way for tracking community formation in social network.

Sanjiv Sharma; G.N. Purohit

2012-01-01

216

[Analysis of endophytic fungi community of Ligusticum chuanxiong using PCR-DGGE].  

UK PubMed Central (United Kingdom)

OBJECTIVE: To research the diversity of endophytic fungal communities among Ligusticum chuanxiong growing at 5 areas in Sichuan province, and illuminate the developing mechanism of geoherbs from the microecological perspective. METHOD: The PCR-DGGE and DNA sequencing techniques were used to analyze the endophytic fungi community of L. chuanxiong. RESULT: The community of endophytic fungi present difference among different growing areas. Though minor difference were found among individuals at the same area, similarity among individuals from the same growing areas were higher significantly than those from different growing areas. Compared with the other 4 growing areas, L. chuanxiong from Shiyang town, Dujiangyan city had more abundant endophytic fungi and low similarity to others, and which probably had special types of fungi. CONCLUSION: The abundant and stable endophytic fungal community is an important factor for the development of geoherb L. chuanxiong at Shiyang town, Dujiangyan city.

Wang H; Yan ZY; He DM; Wang M

2013-06-01

217

The community succession of rice field weeds in Shanghai area and factor analysis  

UK PubMed Central (United Kingdom)

The investigation of the weed species, community structure and weed-caused damage to rice in Shanghai area showed that the main rice field weeds had 22 species under 11 families, and among them the main harmful weeds were Alternanthera philoxeroides, Sagittaria pygmea, Juncellus serotinus, Cyperus difformis, Eclipta prostrata, Ammannia baccifera, Echinochloa crusgalli, Leptochloa chinensis, Monochoria vaginalis and so on. The comparison between the investigation result and the data of 1982 and the model tests showed that the application of herbicides and the change of farming system played a leading role in the weed community succession in Shanghai area. Since 1980s the communities with eradicable annual weeds (such as Echinochloa crusgalli and Cyperus difformis) being predominant have been changing into perennial weed-dominated communities (such as Alternanthera philoxeroides and Sagittaria pygmaea).

Lu Zhengrong; Shen Jianying; Lu Yitong

2005-01-01

218

Comparative analysis of midgut bacterial communities of Aedes aegypti mosquito strains varying in vector competence to dengue virus.  

UK PubMed Central (United Kingdom)

Differences in midgut bacterial communities of Aedes aegypti, the primary mosquito vector of dengue viruses (DENV), might influence the susceptibility of these mosquitoes to infection by DENV. As a first step toward addressing this hypothesis, comparative analysis of bacterial communities from midguts of mosquito strains with differential genetic susceptibility to DENV was performed. 16S rRNA gene libraries and real-time PCR approaches were used to characterize midgut bacterial community composition and abundance in three Aedes aegypti strains: MOYO, MOYO-R, and MOYO-S. Although Pseudomonas spp.-related clones were predominant across all libraries, some interesting and potentially significant differences were found in midgut bacterial communities among the three strains. Pedobacter sp.- and Janthinobacterium sp.-related phylotypes were identified only in the MOYO-R strain libraries, while Bacillus sp. was detected only in the MOYO-S strain. Rahnella sp. was found in MOYO-R and MOYO strains libraries but was absent in MOYO-S libraries. Both 16S rRNA gene library and real-time PCR approaches confirmed the presence of Pedobacter sp. only in the MOYO-R strain. Further, real-time PCR-based quantification of 16S rRNA gene copies showed bacterial abundance in midguts of the MOYO-R strain mosquitoes to be at least 10-100-folds higher than in the MOYO-S and MOYO strain mosquitoes. Our study identified some putative bacteria with characteristic physiological properties that could affect the infectivity of dengue virus. This analysis represents the first report of comparisons of midgut bacterial communities with respect to refractoriness and susceptibility of Aedes aegypti mosquitoes to DENV and will guide future efforts to address the potential interactive role of midgut bacteria of Aedes aegypti mosquitoes in determining vectorial capacity for DENV.

Charan SS; Pawar KD; Severson DW; Patole MS; Shouche YS

2013-07-01

219

[16S rDNA-RFLP analysis of structure and diversity of an aerobic microbial community degrading hexachlorobenzene].  

UK PubMed Central (United Kingdom)

Hexachlorobenzene is a chlorinated aromatic hydrocarbon that was widely used as a seed dressing for prevention of fungal growth on crops, and is also a component of fireworks, ammunition, and synthetic rubbers. Because of the bioaccumulation and persistence of hexachlorobenzene as well as its potential toxicity, hexachlorobenzene must be removed from environment. The potential for aerobic dechlorination of hexachlorobenzene by a hexachlorobenzene-adapted mixed culture was investigated. An aerobic microbial community which was able to grow at the presence of hexachlorobenzene was enriched from sediment from contaminated site after incubating about 2 months. During the growth of the mixed microorganisms on hexachlorobenzene, the accumulating consumption of oxygen, the microbial population curve and the release of Cl- were investigated. The data suggest the rapid degradation of hexachlorobenzene to support microbial growth and the aerobic decholrination of hexachlorobenzene was observed. The result showed that the mixed microorganisms were able to utilize hexachlorobenzene as sole carbon and energy source. It was shown that up to 55% of HCB could be degraded during 18 days incubation at 30 degrees C in mineral salts medium (pH 7.0) with 4.5mg/L HCB. The calculated rate of hexachlorobenzene biodegradation was 137.5 microg/ (L x d). The 16S rDNA genes were amplified from community DNA by using primers specific to bacteria and were subsequently cloned. The cloned 16S rDNA fragments were reamplified, and restriction analysis was performed following separate digestion with enzymes Hae III and Rsa I. Application of restriction fragment length polymorphism screening approach revealed 9 clusters, and 3 major clusters were sequenced. Nearly complete 16S rDNA sequence analysis show that the microbial community was dominated by Alcaligenes and Azospirillum groups. This is the first report describing aerobic dechlorination of hexachlorobenzene via dehalorespiration by a microbial community which was enriched from contaminated site. The microbial community can be used to degrade highly recalcitrant chlorinated pollutants.

Liu T; Chen ZL; Cao L; Sun WM; Shen YF

2006-10-01

220

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

UK PubMed Central (United Kingdom)

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 response to increasing atmospheric CO2 concentrations or atmospheric nutrient deposition.

Cleveland CC; Reed SC; Keller AB; Nemergut DR; O'Neill SP; Ostertag R; Vitousek PM

2013-09-01

 
 
 
 
221

Community-acquired pneumonia in the childhood: analysis of the diagnostic methods  

Scientific Electronic Library Online (English)

Full Text Available Abstract in english Immunological assays such as CIE, LA, and Dot-ELISA were compared in order to diagnose community-acquired pneumonia. Serum, pleural fluid and urine samples were comparatively employed for bacterial antigen detection. Dot-ELISA proved to be an original and practical alternative procedure for detecting bacterial polysaccharide antigens from pleural fluid and/or concentrated urine samples, providing a rapid diagnosis for pediatric patients with community-acquired pneumonia.

Requejo, Henry I. Z.

2007-04-01

222

OOPS, Turning MIT Opencourseware into Chinese: An analysis of a community of practice of global translators  

Directory of Open Access Journals (Sweden)

Full Text Available An all-volunteer organization called the Opensource Opencourseware Prototype System (OOPS), headquartered in Taiwan, was initially designed to translate open source materials from MIT OpenCourseWare (OCW) site into Chinese. Given the recent plethora of open educational resources (OER), such as the OCW, the growing use of such resources by the world community, and the emergence of online global education communities to localize resources such as the OOPS, a key goal of this research was to understand how the OOPS members negotiate meanings and form a collective identity in this cross-continent online community. To help with our explorations and analyses within the OOPS translation community, several core principles from Etienne Wenger’s concept of Communities of Practice (COP) guided our analyses, including mutual engagement, joint enterprise, shared repertoire, reification, and overall identity of the community. In this paper, we detail how each of these key components was uniquely manifested within the OOPS. Three issues appeared central to the emergence, success, and challenges of the community such as OOPS: 1) strong, stable, and fairly democratic leadership; 2) participation incentives; and 3) online storytelling or opportunities to share one’s translation successes, struggles, and advice within an asynchronous discussion forum. While an extremely high level of enthusiasm among the OOPS members underpinned the success of the OOPS, discussion continues on issues related to quality control, purpose and scope, and forms of legitimate participation. This study, therefore, provides an initial window into the emergence and functioning of an online global education COP in the OER movement. Future research directions related to online global educational communities are discussed.

Mimi Miyoung Lee; Meng-Fen Grace Lin; Curtis J. Bonk

2007-01-01

223

Detection of spatial and temporal influences on bacterial communities in an urban stream by automated ribosomal intergenic ribosomal spacer analysis.  

UK PubMed Central (United Kingdom)

The Yarqon is the largest urban river in Israel, and is a slow-flowing stream whose water originates mostly from wastewater treatment plants. Thus, its microbial community is expected to be heavily impacted both by anthropogenic factors and by seasonal temporal variation. In order to identify the main factors that influence the bacterial community, and their spatial-temporal variation, 50 samples were collected representing five different time points and eleven locations. Samples were analyzed for biotic and a-biotic parameters and the bacterial populations were analyzed by Automated Ribosomal Intergenic Spacer Analysis (ARISA). Bacterial richness and diversity were calculated and compared across samples. Canonical Correspondence Analysis (CCA) showed that ARISA clustered the samples according to temporal variation. Molecular fingerprinting analysis provided a snapshot of the microbial community and showed good correlation with geochemical parameters, despite the rapid changes of the Mediterranean environment and the anthropogenic impact. Molecular fingerprinting methods based on natural fragment length polymorphisms may therefore represent a supplementary approach for stream monitoring, alongside physico-chemical measurements.

Or A; Gophna U

2011-01-01

224

Quantitative classification and analysis of relationships between plant communities and their groundwater environment in the Ejin Desert Oasis of China  

Directory of Open Access Journals (Sweden)

Full Text Available Aims Ejin Desert Oasis is a typical arid oasis in the Hexi corridor of northwestern and northern China. Water resources in the area have changed since 2000. Our objective was to classify the plant community types and determine the relationship between vegetation and environmental factors in order to evaluate the influence of waterregulation on vegetation in this region.Methods We obtained data on 29 plant species from 151 study plots of natural vegetation of the Ejin Desert Oasis and classified the plant communities by two-way indicators species analysis (TWINSPAN) and correlated them with six groundwater environmental variables using detrended correspondence analysis (DCA) and detrended canonical correspondence analysis (DCCA) ordinations.Important findings Six plant associations were identified. The main factor correlated to their distribution was groundwater depth, which had more influence on the distribution of plant species and vegetation than other variables because change of groundwater depth leads to changes in both salinity and mineralization. The first ordination axis was correlated with the gradient of groundwater depth, and the second axis was correlated with pH. Compared with other areas, the scarcity of plant species and the differentiation of plant communities were obvious.

ZHU Jun-Tao; YU Jing-Jie; WANG Ping; WANG Zhi-Yong

2011-01-01

225

Insights into the phylogeny and metabolic potential of a primary tropical peat swamp forest microbial community by metagenomic analysis.  

Science.gov (United States)

A primary tropical peat swamp forest is a unique ecosystem characterized by long-term accumulation of plant biomass under high humidity and acidic water-logged conditions, and is regarded as an important terrestrial carbon sink in the biosphere. In this study, the microbial community in the surface peat layer in Pru Toh Daeng, a primary tropical peat swamp forest, was studied for its phylogenetic diversity and metabolic potential using direct shotgun pyrosequencing of environmental DNA, together with analysis of 16S rRNA gene library and key metabolic genes. The community was dominated by aerobic microbes together with a significant number of facultative and anaerobic microbial taxa. Acidobacteria and diverse Proteobacteria (mainly Alphaproteobacteria) constituted the major phylogenetic groups, with minor representation of archaea and eukaryotic microbes. Based on comparative pyrosequencing dataset analysis, the microbial community showed high metabolic versatility of plant polysaccharide decomposition. A variety of glycosyl hydrolases targeting lignocellulosic and starch-based polysaccharides from diverse bacterial phyla were annotated, originating mostly from Proteobacteria, and Acidobacteria together with Firmicutes, Bacteroidetes, Chlamydiae/Verrucomicrobia, and Actinobacteria, suggesting the key role of these microbes in plant biomass degradation. Pyrosequencing dataset annotation and direct mcrA gene analysis indicated the presence of methanogenic archaea clustering in the order Methanomicrobiales, suggesting the potential on partial carbon flux from biomass degradation through methanogenesis. The insights on the peat swamp microbial assemblage thus provide a valuable approach for further study on biogeochemical processes in this unique ecosystem. PMID:21057783

Kanokratana, Pattanop; Uengwetwanit, Tanaporn; Rattanachomsri, Ukrit; Bunterngsook, Benjarat; Nimchua, Thidarat; Tangphatsornruang, Sithichoke; Plengvidhya, Vethachai; Champreda, Verawat; Eurwilaichitr, Lily

2010-11-06

226

Insights into the phylogeny and metabolic potential of a primary tropical peat swamp forest microbial community by metagenomic analysis.  

UK PubMed Central (United Kingdom)

A primary tropical peat swamp forest is a unique ecosystem characterized by long-term accumulation of plant biomass under high humidity and acidic water-logged conditions, and is regarded as an important terrestrial carbon sink in the biosphere. In this study, the microbial community in the surface peat layer in Pru Toh Daeng, a primary tropical peat swamp forest, was studied for its phylogenetic diversity and metabolic potential using direct shotgun pyrosequencing of environmental DNA, together with analysis of 16S rRNA gene library and key metabolic genes. The community was dominated by aerobic microbes together with a significant number of facultative and anaerobic microbial taxa. Acidobacteria and diverse Proteobacteria (mainly Alphaproteobacteria) constituted the major phylogenetic groups, with minor representation of archaea and eukaryotic microbes. Based on comparative pyrosequencing dataset analysis, the microbial community showed high metabolic versatility of plant polysaccharide decomposition. A variety of glycosyl hydrolases targeting lignocellulosic and starch-based polysaccharides from diverse bacterial phyla were annotated, originating mostly from Proteobacteria, and Acidobacteria together with Firmicutes, Bacteroidetes, Chlamydiae/Verrucomicrobia, and Actinobacteria, suggesting the key role of these microbes in plant biomass degradation. Pyrosequencing dataset annotation and direct mcrA gene analysis indicated the presence of methanogenic archaea clustering in the order Methanomicrobiales, suggesting the potential on partial carbon flux from biomass degradation through methanogenesis. The insights on the peat swamp microbial assemblage thus provide a valuable approach for further study on biogeochemical processes in this unique ecosystem.

Kanokratana P; Uengwetwanit T; Rattanachomsri U; Bunterngsook B; Nimchua T; Tangphatsornruang S; Plengvidhya V; Champreda V; Eurwilaichitr L

2011-04-01

227

Supportive Environments for Physical Activity, Community Action and Policy in Eight EU Member States : Comparative Analysis and Specificities of Context  

DEFF Research Database (Denmark)

BACKGROUND: A multi-level theoretical framework of physical activity (PA) promotion that addresses supportive environments, PA behavior, community action and PA promoting policies is related to research and development in an international comparative study. METHODS: Most-different and most-similar case selection was applied to data from eight EU Member States. Data from semi-structured key informant qualitative interviews, focus group interviews with experts and policy-makers, as well as document analysis were linked to corresponding Eurobarometer data. RESULTS AND DISCUSSION: The framework on the interplay of environment, PA behavior, community action and policies appears to be working across most different countries. Comprehensive systems of PA infrastructures are interlinked with relatively high levels of PA prevalence. These countries implement comprehensive national policies on PA promotion and show a positive perception of related local governments' engagement. Less comprehensive systems of infrastructures interplay with lower levels of PA prevalence, less community action and fewer policies. Differences between similar cases are linked to country-specific contexts. CONCLUSIONS: Framework application and comparative analysis indicates how to relate theory to empirical research and complex data sets. In-depth analysis of country-specific contexts and longitudinal observation on changes within and between countries might advise on how to integrate the framework into intervention research.

Ruetten, Alfred; Frahsa, Annika

2013-01-01

228

Supportive Environments for Physical Activity, Community Action and Policy in Eight EU Member States: Comparative Analysis and Specificities of Context.  

UK PubMed Central (United Kingdom)

BACKGROUND: A multi-level theoretical framework of physical activity (PA) promotion that addresses supportive environments, PA behavior, community action and PA promoting policies is related to research and development in an international comparative study. METHODS: Most-different and most-similar case selection was applied to data from eight EU Member States. Data from semi-structured key informant qualitative interviews, focus group interviews with experts and policy-makers, as well as document analysis were linked to corresponding Eurobarometer data. RESULTS AND DISCUSSION: The framework on the interplay of environment, PA behavior, community action and policies appears to be working across most different countries. Comprehensive systems of PA infrastructures are interlinked with relatively high levels of PA prevalence. These countries implement comprehensive national policies on PA promotion and show a positive perception of related local governments' engagement. Less comprehensive systems of infrastructures interplay with lower levels of PA prevalence, less community action and fewer policies. Differences between similar cases are linked to country-specific contexts. CONCLUSIONS: Framework application and comparative analysis indicates how to relate theory to empirical research and complex data sets. In-depth analysis of country-specific contexts and longitudinal observation on changes within and between countries might advise on how to integrate the framework into intervention research.

Ruetten A; Frahsa A; Engbers L; Gusi N; Mota J; Pacenka R; Troelsen J; Vasickova J; Vuillemin A

2013-05-01

229

'Supportive Environments for Physical Activity, Community Action and Policy in Eight EU Member States: Comparative Analysis and Specificities of Context'  

DEFF Research Database (Denmark)

BACKGROUND: A multi-level theoretical framework of physical activity (PA) promotion that addresses supportive environments, PA behavior, community action and PA promoting policies is related to research and development in an international comparative study. METHODS: Most-different and most-similar case selection was applied to data from eight EU Member States. Data from semi-structured key informant qualitative interviews, focus group interviews with experts and policy-makers, as well as document analysis were linked to corresponding Eurobarometer data. RESULTS AND DISCUSSION: The framework on the interplay of environment, PA behavior, community action and policies appears to be working across most different countries. Comprehensive systems of PA infrastructures are interlinked with relatively high levels of PA prevalence. These countries implement comprehensive national policies on PA promotion and show a positive perception of related local governments' engagement. Less comprehensive systems of infrastructures interplay with lower levels of PA prevalence, less community action and fewer policies. Differences between similar cases are linked to country-specific contexts. CONCLUSIONS: Framework application and comparative analysis indicates how to relate theory to empirical research and complex data sets. In-depth analysis of country-specific contexts and longitudinal observation on changes within and between countries might advise on how to integrate the framework into intervention research.

Rütten, Alfred; Frasha, A.

2013-01-01

230

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

Directory of Open Access Journals (Sweden)

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.

AK Gregg; M Hatay; AF Haas; NL Robinett; K Barott; MJA Vermeij; KL Marhaver; P Meirelles; F Thompson; F Rohwer

2013-01-01

231

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

UK PubMed Central (United Kingdom)

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.

Gregg A; Hatay M; Haas A; Robinett N; Barott K; Vermeij M; Marhaver K; Meirelles P; Thompson F; Rohwer F

2013-01-01

232

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

Directory of Open Access Journals (Sweden)

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 frail included women (OR?=?1.9), those who reported myocardial infarction (OR?=?3.8), urinary incontinence (OR?=?2.7), those who rated their oral health worse than others (OR?=?3.2), and those who did not use dental services (OR?=?2.1). For each additional year of age and each additional drug consumed, the probability of being frail increased 10% and 30%, respectively. Conclusions Utilization of dental services and self-perception of oral health were associated with a higher probability of being frail.

Castrejón-Pérez Roberto; Borges-Yáñez S; Gutiérrez-Robledo Luis M; Ávila-Funes J

2012-01-01

233

Analysis of the attached microbial community on mucilaginous cyanobacterial aggregates in the eutrophic Lake Taihu reveals the importance of Planctomycetes.  

UK PubMed Central (United Kingdom)

The phylogenetic diversity of the microbial community assemblage of the carpet-like mucilaginous cyanobacterial blooms in the eutrophic Lake Taihu was investigated. 16S ribosomal DNA clone libraries produced from the DNA of cyanobacterial assemblages that had been washed to remove unattached bacteria contained only cyanobacteria. However, a further treatment which included grinding the freeze-dried material to physically detach cells followed by the removal of larger cells by filtration allowed us to detect a large variety of bacteria within the cyanobacterial bloom community. Interestingly, the dominant members of the microbial community were Planctomycetes followed by Cytophaga-Flavobacterium-Bacteroides (CFB), Betaproteobacteria, and Gammaproteobacteria. The analysis of the 16S ribosomal DNA clone libraries made from enrichment culture revealed much higher phylogenetic diversity of bacteria. Dominant bacterial groups in the enrichment system were identified as members of the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria subdivisions, CFB group, and Planctomycetes. In addition, the clone libraries constructed from Planctomycetes-specific 16S ribosomal RNA primers also verified that the enrichment allowed a diversity of Planctomycetes to proliferate, although the community composition was altered after enrichment.

Cai HY; Yan ZS; Wang AJ; Krumholz LR; Jiang HL

2013-07-01

234

Analysis of the attached microbial community on mucilaginous cyanobacterial aggregates in the eutrophic Lake Taihu reveals the importance of Planctomycetes.  

Science.gov (United States)

The phylogenetic diversity of the microbial community assemblage of the carpet-like mucilaginous cyanobacterial blooms in the eutrophic Lake Taihu was investigated. 16S ribosomal DNA clone libraries produced from the DNA of cyanobacterial assemblages that had been washed to remove unattached bacteria contained only cyanobacteria. However, a further treatment which included grinding the freeze-dried material to physically detach cells followed by the removal of larger cells by filtration allowed us to detect a large variety of bacteria within the cyanobacterial bloom community. Interestingly, the dominant members of the microbial community were Planctomycetes followed by Cytophaga-Flavobacterium-Bacteroides (CFB), Betaproteobacteria, and Gammaproteobacteria. The analysis of the 16S ribosomal DNA clone libraries made from enrichment culture revealed much higher phylogenetic diversity of bacteria. Dominant bacterial groups in the enrichment system were identified as members of the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria subdivisions, CFB group, and Planctomycetes. In addition, the clone libraries constructed from Planctomycetes-specific 16S ribosomal RNA primers also verified that the enrichment allowed a diversity of Planctomycetes to proliferate, although the community composition was altered after enrichment. PMID:23571665

Cai, Hai-Yuan; Yan, Zai-sheng; Wang, Ai-Jie; Krumholz, Lee R; Jiang, He-Long

2013-04-10

235

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

Science.gov (United States)

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 < 0.001) in beta diversity were observed among the different matrices at the genus-species level, except for lichens and rocks which shared a more similar community structure, while at deep taxonomic resolution two distinct bacterial communities between lichens and rocks were found. PMID:23712376

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

2013-05-28

236

Home visitation program effectiveness and the influence of community behavioral norms: a propensity score matched analysis of prenatal smoking cessation  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background The influence of community context on the effectiveness of evidence-based maternal and child home visitation programs following implementation is poorly understood. This study compared prenatal smoking cessation between home visitation program recipients and local-area comparison women across 24 implementation sites within one state, while also estimating the independent effect of community smoking norms on smoking cessation behavior. Methods Retrospective cohort design using propensity score matching of Nurse-Family Partnership (NFP) clients and local-area matched comparison women who smoked cigarettes in the first trimester of pregnancy. Birth certificate data were used to classify smoking status. The main outcome measure was smoking cessation in the third trimester of pregnancy. Multivariable logistic regression analysis examined, over two time periods, the association of NFP exposure and the association of baseline county prenatal smoking rate on prenatal smoking cessation. Results The association of NFP participation and prenatal smoking cessation was stronger in a later implementation period (35.5% for NFP clients vs. 27.5% for comparison women, p? Conclusions Following a statewide implementation, program recipients of NFP demonstrated increased smoking cessation compared to comparison women, with a stronger program effect in later years. The significant association of county smoking rate with cessation suggests that community behavioral norms may present a challenge for evidence-based programs as models are translated into diverse communities.

Matone Meredith; O'Reilly Amanda LR; Luan Xianqun; Localio Russell; Rubin David M

2012-01-01

237

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

Science.gov (United States)

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. PMID:23622816

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

2013-04-10

238

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

Directory of Open Access Journals (Sweden)

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.

Malcolm J. Reid; Christopher Harman; Merete Grung; Kevin V. Thomas

2011-01-01

239

Metagenomics-based analysis of viral communities in dairy lagoon wastewater.  

Science.gov (United States)

Microbial populations, especially those of viruses, are poorly studied in dairy wastewater treatment operations. Here we report signature nucleic acid metagenomic sequences obtained by pyrosequencing viromes of virus-like particles that were extracted from two dairy waste treatment lagoons. The lagoons are operated in series, with Lagoon I being used as the primary stage and Lagoon II as the secondary stage of wastewater treatment. An average of 2000 sequences was obtained from each lagoon. More than 300 signatures from each lagoon matched sequences in the virus database of the National Center for Biotechnology Information (NCBI). We utilized a bioinformatics approach and transmission electron microscopy (TEM) to characterize the viral diversity and presence of potential viral pathogens within the lagoons. Our results showed differences in viral community compositions between Lagoon I and Lagoon II, suggesting that the viral community changes significantly in the transition of water between the two lagoons. Furthermore, the diverse viral community in the lagoon samples contained signature sequences of a variety of bacterial, plant, and animal viruses. Bacteriophage sequences dominated the viral community metagenomes in both lagoons. Ultimately these results can be used to identify viral bioindicators to rapidly assess wastewater treatment quality and the potential impacts of dairy operations on watersheds. Our viral metagenomic sequences have been submitted to GenBank (GPID 65805) and can provide insight into the composition and structure of viral communities within wastewaters of dairy lagoon systems. PMID:23220059

Alhamlan, F S; Ederer, M M; Brown, C J; Coats, E R; Crawford, R L

2012-12-04

240

Metagenomics-based analysis of viral communities in dairy lagoon wastewater.  

UK PubMed Central (United Kingdom)

Microbial populations, especially those of viruses, are poorly studied in dairy wastewater treatment operations. Here we report signature nucleic acid metagenomic sequences obtained by pyrosequencing viromes of virus-like particles that were extracted from two dairy waste treatment lagoons. The lagoons are operated in series, with Lagoon I being used as the primary stage and Lagoon II as the secondary stage of wastewater treatment. An average of 2000 sequences was obtained from each lagoon. More than 300 signatures from each lagoon matched sequences in the virus database of the National Center for Biotechnology Information (NCBI). We utilized a bioinformatics approach and transmission electron microscopy (TEM) to characterize the viral diversity and presence of potential viral pathogens within the lagoons. Our results showed differences in viral community compositions between Lagoon I and Lagoon II, suggesting that the viral community changes significantly in the transition of water between the two lagoons. Furthermore, the diverse viral community in the lagoon samples contained signature sequences of a variety of bacterial, plant, and animal viruses. Bacteriophage sequences dominated the viral community metagenomes in both lagoons. Ultimately these results can be used to identify viral bioindicators to rapidly assess wastewater treatment quality and the potential impacts of dairy operations on watersheds. Our viral metagenomic sequences have been submitted to GenBank (GPID 65805) and can provide insight into the composition and structure of viral communities within wastewaters of dairy lagoon systems.

Alhamlan FS; Ederer MM; Brown CJ; Coats ER; Crawford RL

2013-02-01

 
 
 
 
241

Isolation and analysis of mRNA from environmental microbial communities.  

UK PubMed Central (United Kingdom)

The advent of metagenomics has revealed that our planet harbors millions of previously undiscovered microbial species. However, functional insights into the activities of microbial communities cannot easily be obtained using metagenomics. Using transcriptional analyses to study microbial gene functions is currently problematic due to difficulties working with unstable microbial mRNA as a small fraction of total cellular RNA. Current techniques can be expensive and time consuming, and still result in significant levels of rRNA contamination. We have adapted techniques to rapidly isolate high high-quality RNA from environmental samples and developed a simple method for specific isolation of mRNA by size separation. This new technique was evaluated by constructing cDNA libraries directly from uncultured environmental microbial communities, including agricultural soil samples, aquatic flocculants, organic composts, mammalian oral and faecal samples, and wastewater sludge. The sequencing of a fraction of these cDNA clones revealed a high degree of novelty, demonstrating the potential of this approach to capture a large number of unique transcripts directly from the environment. To our knowledge, this is the first study that uses gel electrophoresis to isolate mRNA from microbial communities. We conclude that this method could be used to provide insights into the microbial 'metatranscriptome' of entire microbial communities. Coupled with high-throughput sequencing or the construction of cDNA microarrays, this approach will provide a useful tool to study the transcriptional activities of microorganisms, including those of entire microbial communities and of non-culturable microorganisms.

McGrath KC; Thomas-Hall SR; Cheng CT; Leo L; Alexa A; Schmidt S; Schenk PM

2008-10-01

242

Ichthyofauna of Cabuçu and Berlinque beaches: a comparative analysis of fish communities in Todos os Santos Bay, Bahia - Brazil  

Directory of Open Access Journals (Sweden)

Full Text Available This study presents the composition of the ichthyofauna and the spatial and seasonal analysis of fish community structure at Cabuçu (12º47´S - 38º46´W - Saubara) and Berlinque beaches (13º06´S - 38º45´W - Vera Cruz) in Todos os Santos Bay (13ºS - 38ºW), Bahia State, Brazil. Fish were collected between July 2002 and July 2003, during the lowest of the syzygial tides. Abiotic factors such as the pH, temperature and salinity of the water were measured. The similarity among the sampling sites was analyzed by cluster analysis based on a presence-absence data matrix of species using the Sorensen coefficient. A total of 719 fish (63 species) and 2,231.77g were captured at Cabuçu beach. At Berlinque beach, a total of 381 fish (40 species) and 2,605.64g were captured. Community indexes do not indicate seasonal changes in the fish communities of the two beaches. The ANOSIM and SIMPER routines of the Primer software demonstrate that the ichthyofaunal composition of the two beaches differs markedly.

Jailza Tavares de Oliveira-Silva; Marlene Campos Peso-Aguiar; Paulo Roberto Duarte Lopes

2008-01-01

243

[Clinical analysis of 22 cases community-acquired Pseudomonas aeruginosa urinary tract infection].  

UK PubMed Central (United Kingdom)

OBJECTIVE: To study the characteristics of community-acquired urinary tract infections (CAUTIs) in children, analyze the risk factors and the susceptibility of antibiotics, thus to provide references to the diagnosis and medication of Pseudomonas aeruginosa (PA)-CAUTIs. Mothod Totally 22 cases of PA-CAUTIs were selected in one hospital from Jan, 2006 to Jan, 2012, their clinical information, laboratory results and radiological images were collected, and were compared with the CAUTIs cased by E. coli of those randomly selected over the same period. RESULT: In those 22 cases with PA-CAUTIs, the mean value of protein level was (32.25 ± 13.81) mg/ml, 19 of them were hospitalized, 6 had urinary operation history, 7 of them had long-term usage of glucocorticoids or immunosuppressive agents, and 20 had underlying diseases. A total of 22 children with 26 PA-CAUTIs episodes were compared to E. coli-CAUTIs. Compared with E. coli-CAUTIs patients, children with PA-CAUTIs more often presented with a lower albumin (P = 0.017), a history of urinary operation(P = 0.03), more cases had a history of urinary operation (P = 0.03), a long-term usage of glucocorticoids or immunosuppressive medication (P = 0.044). Through multivariate logistic regression of variables that were significant in univariate analysis (with hospitalizations, long-term usage of glucocorticoids or immunosuppressive, albumin, underlying disease and urinary operation histories), and it turned out that underlying diseases (odds ratio 8.500, 95% CI 1.513 - 47.761, P = 0.037) and with urinary operation histories (odds ratio 6.196, 95% CI 1.120 - 34.273, P = 0.037) were proved as the independent risk factors for PA-CAUTIs. Those PA bacterial strains had a 36.36% resistance rate to piperacillin, aztreonam and gentamicin, a 31.82% resistance rate to cefepime and ceftazidime, while the resistance rate (4.55%) to carbapenem antibiotics was relatively low, only to bacillosporin all the strains were sensitive. CONCLUSION: Underlying diseases and the urinary operation histories are the independent risk factors of the occurrence of PA-CAUTIs, carbapenem antibiotics and bacillosporin can be considered as the drugs of choice for its treatment.

Fu XH; Zhou W; Zhang XM; Yin YB; Jing CM; Liu L; Zhao J

2013-04-01

244

Community analysis of bacteria colonizing intestinal tissue of neonates with necrotizing enterocolitis  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Necrotizing enterocolitis (NEC) is the most common gastrointestinal emergency in newborn neonates. Bacteria are believed to be important in the pathogenesis of NEC but bacterial characterization has only been done on human faecal samples and experimental animal studies. The aim of this study was to investigate the microbial composition and the relative number of bacteria in inflamed intestinal tissue surgically removed from neonates diagnosed with NEC (n = 24). The bacterial populations in the specimens were characterized by laser capture microdissection and subsequent sequencing combined with fluorescent in situ hybridization (FISH), using bacterial rRNA-targeting oligonucleotide probes. Results Bacteria were detected in 22 of the 24 specimens, 71% had moderate to high densities of bacteria. The phyla detected by 16S rRNA gene sequencing were: Proteobacteria (49.0%), Firmicutes (30.4%), Actinobacteria (17.1%) and Bacteroidetes (3.6%). A major detected class of the phylum Proteobacteria belonged to ?-proteobacteria. Surprisingly, Clostridium species were only detected in 4 of the specimens by FISH, but two of these specimens exhibited histological pneumatosis intestinalis and both specimens had a moderate to a high density of C. butyricum and C. parputrificum detected by using species specific FISH probes. A 16S rRNA gene sequence tag similar to Ralstonia species was detected in most of the neonatal tissues and members of this genus have been reported to be opportunistic pathogens but their role in NEC has still to be clarified. Conclusion In this study, in situ identification and community analysis of bacteria found in tissue specimens from neonates with NEC, were analysed for the first time. Although a large variability of bacteria was found in most of the analyzed specimens, no single or combination of known potential pathogenic bacteria species was dominating the samples suggestive NEC as non-infectious syndrome. However there was a significant correlation between the presence of C. butyricum &C. parputrificum and histological pneumatosis intestinalis. Finally this study emphasizes the possibility to examine the microbial composition directly on excised human tissues to avoid biases from faecal samples or culturing.

Smith Birgitte; Bodé Susan; Petersen Bodil L; Jensen Tim K; Pipper Christian; Kloppenborg Julie; Boyé Mette; Krogfelt Karen A; Mølbak Lars

2011-01-01

245

Analysis of GLBTQ youth community-based programs in the United States.  

UK PubMed Central (United Kingdom)

Gay, lesbian, bisexual, transgender, and queer/questioning (GLBTQ) youth face oppression despite some increases in cultural support for GLBTQ individuals. Research has revealed the psychological and social distress associated with oppression and the benefits of peer social support programs. This study was conducted to analyze the types and frequency of services, age of participants, and organizational structures of the 116 GLBTQ community-based programs operating in the United States. Using an Internet survey, information from 61 of the programs was secured. The results revealed the community-based youth programs provide critical and unique programs and services that can promote the mental and physical health of GLBTQ youth.

Allen KD; Hammack PL; Himes HL

2012-01-01

246

Hunting practices among the Awá-Guajá: towards a long-term analysis of sustainability in an Amazonian indigenous community  

Directory of Open Access Journals (Sweden)

Full Text Available Indigenous Reserves have played an indispensable role in maintaining forest areas in the Neotropics. In the Amazon there is a clear correlation between these reserves and the presence of forest cover; however, the simple presence of uninterrupted vegetation is no guarantee for the conservation of biodiversity, especially where hunting is practiced. This study describes hunting practices among the Awá-Guajá people from 1993 through 1994, also identifying sociocultural, technological, and demographic changes that have influenced their resource acquisition strategies over the last two decades. The data was obtained through ethnographic fieldwork, recording 78 days of foraging returns, with follow-up visits through 2010. This work provides useful information for an effective diachronic analysis of hunting in this community, by revealing foraging patterns of the early to mid-1990s, and describing community transformations over the last two decades in this locale.

Helbert Medeiros Prado; Louis Carlos Forline; Renato Kipnis

2012-01-01

247

Bacterial community analysis of the water surface layer from a rice-planted and an unplanted flooded field  

Scientific Electronic Library Online (English)

Full Text Available Abstract in english The bacterial communities in floodwater, from a rice-planted and an unplanted field were characterized at the beginning (flooding stage) and at the end (harvest stage) of the rice cropping cycle. Most probable number estimations and plate counts of aerobic and anaerobic heterotrophic bacteria and of several metabolic bacterial groups (methanogens, sulfate-reducers, anaerobic sulfur and nonsulfur phototrophs, denitrifiers and ammonifiers) were similar in rice and unplanted (more) floodwater at both sampling times. The analysis of denitrifiers and methanogens by fluorescent in situ hybridization revealed a shift in the phylogenetic affiliation only of the former group in the rice-planted floodwater. Terminal restriction fragment length polymorphism of 16S rRNA gene amplicons indicated that the bacterial communities of the rice-planted and unplanted soils were consistently diverse and strongly influenced by the season.

Scavino, Ana Fernández; Menes, Javier; Ferrando, Lucía; Tarlera, Silvana

2010-06-01

248

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

Science.gov (United States)

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 transfer and remote job execution on the grid network of machines. In addition, science support was needed to vet that the grid technology did not have any adverse affects of the science module outputs. Other open source, unproven technologies, such as a workflow package to manage jobs submitted by the user, were infused into the overall system with successful results. This presentation will discuss the basic capabilities of LC-ComPS, explain how the technology was infused, and provide lessons learned for using and integrating the various technologies while developing and operating the system, and finally outline plans moving forward (maintenance and operations decisions) based on the experience to date.

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

2008-12-01

249

Functional gene array-based analysis of microbial communities in heavy metals-contaminated lake sediments.  

Science.gov (United States)

Lake DePue (IL, USA) has been contaminated for > 80 years by an adjacent Zn-smelting facility. Previous work indicated that sulfate reduction increased and biomass declined as pore-water metal concentrations increased, while 16S rRNA gene profiles remained relatively stable. To better understand this phenomenon, the sediment microbial community structure and functional potential were investigated using a functional gene microarray (GeoChip) targeting > 10 000 functional genes. Nonmetric multidimensional scaling and clustering analyses showed that the overall community structure was similar across all sites based on the relative abundance of all detected genes, but some individual gene categories did show differences. A subset of sulfate reduction genes (dsr) and the most relevant metal resistance genes were more abundant than other categories and were highly correlated with metal contamination. The most significant correlations were between pore-water metal concentrations and dsr, with Zn, Cd, and Mn as the most predictive for the presence of dsr. These results suggest that metal contamination influences sediment microbial community structure and function by increasing the abundance of relevant metal-resistant and sulfate-reducing populations. These populations therefore appear to contribute significantly to the resistance and stability of the microbial communities throughout the gradient of metal contamination in Lake DePue. PMID:23710534

Kang, Sanghoon; Van Nostrand, Joy D; Gough, Heidi L; He, Zhili; Hazen, Terry C; Stahl, David A; Zhou, Jizhong

2013-07-09

250

Course Shopping in Urban Community Colleges: An Analysis of Student Drop and Add Activities  

Science.gov (United States)

|This study examined the course shopping behaviors among a sample of approximately 5,000 community college students enrolled across nine campuses of a large urban district. The sample was purposely designed as an analytic, rather than a random, sample that sought to obtain adequate numbers of students in course areas that were of theoretical and…

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

2007-01-01

251

A comparative analysis of pressure sore treatment modalities in community settings  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The management of pressure sores in community settings, poses a clinical problem which challenges the patient’s tolerance and the clinician’s diligence and ingenuity. Pressure sores can be painful, lead to infection and are associated with considerable morbidity and increased mortality (Patterson & ...

N. Small; M. Mulder; M.J. Mackenzie; M. Nel

252

An Analysis of Policies and Procedures for Obtaining New Course Approval at Oakton Community College.  

Science.gov (United States)

Procedures and policies by which a new course is introduced into the Oakton Community College curriculum were analyzed in order to discover appropriate procedures for attaining course approval from the internal college governance structure, to implement those procedures in obtaining final approval, and to make recommendations for improvement of…

Woloshin, Phyllis Lerman

253

The Effect of Therapeutic Community on Time to First Re-Arrest: A Survival Analysis  

Science.gov (United States)

|This research examines the effect of therapeutic community (TC) on time to first re-arrest after release from prison. The comparison groups of primary interest in this research are male inmates assessed by corrections personnel as needing TC and who successfully completed the program, and inmates assessed as needing the program but who did not…

Jensen, Eric L.; Kane, Stephanie L.

2010-01-01

254

Needs Analysis for the West Hills College at Lemoore, West Hills Community College District. Commission Report.  

Science.gov (United States)

This report reviews the proposal by the West Hills Community College District (WHCCD) (California) to transition its off-campus center to full college status. The proposal's objectives include: (1) establishing a new comprehensive college that will serve approximately 1,700 full-time-equivalent students by 2015; and (2) providing greater access to…

California State Postsecondary Education Commission, Sacramento.

255

Implementation of a 911 System: An Analysis of Community Response - Executive Summary and Final Report.  

Science.gov (United States)

This research evaluated the effect upon performance of the prehospital emergency care system that introduces the '911' single-number telephone access capacity in a community. The study employed a data system established in all rescue/fire departments in D...

E. G. Fine

1982-01-01

256

A Community Stakeholder Analysis of Drug Resistance Strategies of Rural Native Hawaiian Youth  

Science.gov (United States)

|This study examines and validates the drug resistance strategies identified by rural Hawaiian youth from prior research with a sample of community stakeholders on the Island of Hawai'i. One hundred thirty-eight stakeholders with a vested interest in reducing youth substance use (i.e., teachers, principals, social service agency providers, and…

Okamoto, Scott K.; Helm, Susana; Delp, Justin A.; Stone, Kristina; Dinson, Ay-Laina; Stetkiewicz, Jennifer

2011-01-01

257

The integration of Ukraine and Moldova into the Energy Community - a liberal intergovernmantal analysis  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The aim of the study is to analyse the integration of Ukraine and Moldova into the Energy Community using the theoretical framework of liberal intergovernmentalism. The main focus is on cooperation with regard to gas energy security and the theoretical framework of liberal intergovernmentalism is ap...

Petersen, Anne Hald

258

Community control and pricing patterns of nonprofit hospitals: An antitrust analysis.  

UK PubMed Central (United Kingdom)

Traditional control of nonprofit hospitals by the communities they serve has been offered as justification for restraining antitrust enforcement of mergers that involve nonprofit hospitals. The community is arguably a constraint on a nonprofit's inclination to exercise market power in the form of higher prices; however, community control is likely to be attenuated for hospitals that through merger or acquisition become members of hospital systems--particularly those that operate on a regional or multiregional basis. We report findings from a study in which we examined empirically the relationship between market concentration and pricing patterns for three types of nonprofit hospitals that are distinguishable based on degree of community control: an independent hospital, a member of a local hospital system, and a member of a nonlocal hospital system. Study results indicated that when conditions existed to create a more concentrated market, (1) all three types of nonprofit hospitals exercised market power in the form of higher prices, and (2) hospitals that were members of nonlocal systems were more aggressive in exercising market power than were either independent or local system hospitals. The results have important implications for antitrust enforcement policy.

Young GJ; Desai KR; Hellinger FJ

2000-12-01

259

A spatial analysis of community disadvantage and access to healthcare services in the U.S.  

UK PubMed Central (United Kingdom)

Ongoing socioeconomic and racial and ethnic gaps in access to healthcare make it vital to examine the relationship between characteristics of communities and their impact on the availability of healthcare services. This study investigates how community-based resource constraints influence the provision of healthcare services in the United States. Drawing on several theoretical frameworks including research in the spatial distribution of healthcare, we compile data on 3141 U.S. counties in order to investigate the argument that gaps in the provision of substance abuse treatment are a function of resource constraints experienced by disadvantaged communities. Our principal aim is to demonstrate that socioeconomic privation, racial and ethnic isolation and limited healthcare infrastructure constrain the provision of substance abuse treatment services. Since prior research shows spatial clustering of socioeconomic privation, racial and ethnic isolation, and healthcare resources, we explicitly model the spatial dimensions of community-based resource disadvantage. Central findings support our chief expectations: counties with greater socioeconomic privation and diminished healthcare infrastructure experienced limited access to substance abuse treatment. Moreover, treatment clusters themselves were significantly related to socioeconomic privation and diminished healthcare infrastructure. Counties with a higher proportion of racial and ethnic minority members, however, did not experience less access to substance abuse treatment, with one exception, although post hoc analyses showed poverty had a moderating effect on race and ethnicity. Study limitations and implications for the organization of treatment resources are discussed.

Archibald ME; Putnam Rankin C

2013-08-01

260

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

UK PubMed Central (United Kingdom)

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.

Beazley MJ; Martinez RJ; Rajan S; Powell J; Piceno YM; Tom LM; Andersen GL; Hazen TC; Van Nostrand JD; Zhou J; Mortazavi B; Sobecky PA

2012-01-01

 
 
 
 
261

Functional gene array-based analysis of microbial communities in heavy metals contaminated lake sediments.  

UK PubMed Central (United Kingdom)

Lake DePue (IL, USA) has been contaminated for >80 years by an adjacent Zn-smelting facility. Previous work indicated that sulfate reduction increased and biomass declined as pore water metal concentrations increased, while 16S rRNA gene profiles remained relatively stable. To better understand this phenomenon, the sediment microbial community structure and functional potential were investigated using a functional gene microarray (GeoChip) targeting >10,000 functional genes. Non-metric multidimensional scaling and clustering analyses showed that the overall community structure was similar across all sites based on the relative abundance of all detected genes, but some individual gene categories did show differences. A subset of sulfate reduction genes (dsr) and the most relevant metal resistance genes were more abundant than other categories and were highly correlated to metal contamination. The most significant correlations were between pore water metal concentrations and dsr, with Zn, Cd, and Mn as the most predictive for the presence of dsr. These results suggest that metal contamination influences sediment microbial community structure and function by increasing the abundance of relevant metal resistant and sulfate-reducing populations. These populations therefore appear to contribute significantly to the resistance and stability of the microbial communities throughout the gradient of metal contamination in Lake DePue. This article is protected by copyright. All rights reserved.

Kang S; Van Nostrand JD; Gough HL; He Z; Hazen TC; Stahl DA; Zhou J

2013-05-01

262

A comparative analysis of traditional and online lab science transfer courses in the rural community college  

Science.gov (United States)

Through distance learning, the community college system has moved beyond geographical boundaries to serve all students and provide educational opportunities at a distance to individuals previously out of reach of the college community. With the inception of the Mississippi Virtual Community College (MSVCC) in January 2000, Mississippi's public community colleges have experienced unprecedented growth in online enrollments and online course offerings to include the laboratory sciences; however, transfer of online lab science courses are problematic for individuals who wish to gain admittance to Medical, Dental, and Pharmacy schools in Mississippi. Currently online lab science courses are not accepted for transfer for students seeking admission to Mississippi Medical, Dental, or Pharmacy schools. The need for this study, the statement of the problem, and the purpose of the study address transfer issues related to the transfer of online lab science courses in Mississippi and the impact of such on the student and community college. The study also addresses existing doubts regarding online course delivery as a viable method of lab science delivery. The purpose of the study was to investigate differences between online instructional delivery as compared to traditional face-to-face delivery with the following research questions to: (1) Investigate the perception of quality of online courses as compared to traditional face-to-face courses. (2) Investigate the difference in student performance in online transfer lab science courses as compared to student performance in traditional face-to-face lab science courses. The results of this 13 semester study show significant differences in both perception of quality and student performance between online instructional delivery as compared to traditional face-to-face delivery. The findings demonstrate a need for Mississippi Dental, Medical, and Pharmacy schools to reexamine the articulation agreement between IHL and Community and Junior Colleges and consider accepting online lab sciences courses taken at the community college as transfer for admission to Medical, Dental, and Pharmacy schools. Conclusions are included in the study; however, additional studies are needed to address the issue of student performance in the online lab science classroom.

Scott, Andrea

263

Isolation and analysis of mRNA from environmental microbial communities.  

Science.gov (United States)

The advent of metagenomics has revealed that our planet harbors millions of previously undiscovered microbial species. However, functional insights into the activities of microbial communities cannot easily be obtained using metagenomics. Using transcriptional analyses to study microbial gene functions is currently problematic due to difficulties working with unstable microbial mRNA as a small fraction of total cellular RNA. Current techniques can be expensive and time consuming, and still result in significant levels of rRNA contamination. We have adapted techniques to rapidly isolate high high-quality RNA from environmental samples and developed a simple method for specific isolation of mRNA by size separation. This new technique was evaluated by constructing cDNA libraries directly from uncultured environmental microbial communities, including agricultural soil samples, aquatic flocculants, organic composts, mammalian oral and faecal samples, and wastewater sludge. The sequencing of a fraction of these cDNA clones revealed a high degree of novelty, demonstrating the potential of this approach to capture a large number of unique transcripts directly from the environment. To our knowledge, this is the first study that uses gel electrophoresis to isolate mRNA from microbial communities. We conclude that this method could be used to provide insights into the microbial 'metatranscriptome' of entire microbial communities. Coupled with high-throughput sequencing or the construction of cDNA microarrays, this approach will provide a useful tool to study the transcriptional activities of microorganisms, including those of entire microbial communities and of non-culturable microorganisms. PMID:18582973

McGrath, Ken C; Thomas-Hall, Skye R; Cheng, Chu Ting; Leo, Lesina; Alexa, Andrei; Schmidt, Susanne; Schenk, Peer M

2008-06-25

264

Needs Analysis for Educating Community Pharmacists to Interface with Prehospital Stroke Chain of Survival.  

UK PubMed Central (United Kingdom)

BACKGROUND: Awareness of the American Heart Association's Stroke Chain of Survival, and willingness to learn and share this information with the public, was assessed for community pharmacists practicing near a primary stroke center. METHODS: Twenty-three community pharmacies local to a primary stroke center were identified and surveyed. The surveyor showed each pharmacist a flier with a mnemonic for assessing stroke symptoms, briefly explained steps in the Stroke Chain of Survival, and noted if the pharmacist was available, listened to the entire presentation, read the information on the flier, agreed to post the flier, and if the pharmacist made any comments. The surveyor also assessed whether the Stroke Chain of Survival was new information to each pharmacist. RESULTS: All subjects read the information on the flier. Twenty-two (95.7%) listened to the entire presentation, and 23 (100%) were willing to post the flier. Two (11%) indicated that the parent company does not allow public posting of noncorporate information but agreed to post the flier internally. Twenty-one (91%) expressed appreciation for receiving the information. Seventeen (74%) indicated that the Stroke Chain of Survival was new information to them, 14 (61%) spontaneously remarked on the importance of the information, and 4 (17%) asked for additional information. CONCLUSIONS: Community pharmacists surveyed were willing to interface with the prehospital phase of the Stroke Chain of Survival; nearly 75% of them required education to do so. Community pharmacies are potentially a venue for educating the public on the Stroke Chain of Survival. It may be necessary to approach community pharmacy corporate leadership to partner with such efforts.

Denetclaw TH; Cefalu P; Manila LL; Panagotacos JJ

2012-12-01

265

Anaerobic treatment of municipal wastewater at ambient temperature: Analysis of archaeal community structure and recovery of dissolved methane.  

Science.gov (United States)

Anaerobic treatment is an attractive option for the biological treatment of municipal wastewater. In this study, municipal wastewater was anaerobically treated with a bench-scale upflow anaerobic sludge blanket (UASB) reactor at temperatures from 6 to 31 °C for 18 months to investigate total chemical oxygen demand (COD) removal efficiency, archaeal community structure, and dissolved methane (D-CH(4)) recovery efficiency. The COD removal efficiency was more than 50% in summer and below 40% in winter with no evolution of biogas. Analysis of the archaeal community structures of the granular sludge from the UASB using 16S rRNA gene-cloning indicated that after microorganisms had adapted to low temperatures, the archaeal community had a lower diversity and the relative abundance of acetoclastic methanogens decreased together with an increase in hydrogenotrophic methanogens. D-CH(4), which was detected in the UASB effluent throughout the operation, could be collected with a degassing membrane. The ratio of the collection to recovery rates was 60% in summer and 100% in winter. For anaerobic treatment of municipal wastewater at lower temperatures, hydrogenotrophic methanogens play an important role in COD removal and D-CH(4) can be collected to reduce greenhouse gas emissions and avoid wastage of energy resources. PMID:22921025

Bandara, Wasala M K R T W; Kindaichi, Tomonori; Satoh, Hisashi; Sasakawa, Manabu; Nakahara, Yoshihito; Takahashi, Masahiro; Okabe, Satoshi

2012-08-07

266

Anaerobic treatment of municipal wastewater at ambient temperature: Analysis of archaeal community structure and recovery of dissolved methane.  

UK PubMed Central (United Kingdom)

Anaerobic treatment is an attractive option for the biological treatment of municipal wastewater. In this study, municipal wastewater was anaerobically treated with a bench-scale upflow anaerobic sludge blanket (UASB) reactor at temperatures from 6 to 31 °C for 18 months to investigate total chemical oxygen demand (COD) removal efficiency, archaeal community structure, and dissolved methane (D-CH(4)) recovery efficiency. The COD removal efficiency was more than 50% in summer and below 40% in winter with no evolution of biogas. Analysis of the archaeal community structures of the granular sludge from the UASB using 16S rRNA gene-cloning indicated that after microorganisms had adapted to low temperatures, the archaeal community had a lower diversity and the relative abundance of acetoclastic methanogens decreased together with an increase in hydrogenotrophic methanogens. D-CH(4), which was detected in the UASB effluent throughout the operation, could be collected with a degassing membrane. The ratio of the collection to recovery rates was 60% in summer and 100% in winter. For anaerobic treatment of municipal wastewater at lower temperatures, hydrogenotrophic methanogens play an important role in COD removal and D-CH(4) can be collected to reduce greenhouse gas emissions and avoid wastage of energy resources.

Bandara WM; Kindaichi T; Satoh H; Sasakawa M; Nakahara Y; Takahashi M; Okabe S

2012-11-01

267

PhyloChip microarray analysis reveals altered gastrointestinal microbial communities in a rat model of colonic hypersensitivity  

Energy Technology Data Exchange (ETDEWEB)

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.

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

268

Metaproteome analysis to determine the metabolically active part of a thermophilic microbial community producing biogas from agricultural biomass.  

UK PubMed Central (United Kingdom)

Complex consortia of microorganisms are responsible for biogas production. A lot of information about the taxonomic structure and enzymatic potential of such communities has been collected by a variety of gene-based approaches, yet little is known about which of all the assumable metabolic pathways are active throughout the process of biogas formation. To tackle this problem, we established a protocol for the metaproteomic analysis of samples taken from biogas reactors fed with agricultural biomass. In contrast to previous studies where an anaerobic digester was fed with synthetic wastewater, the complex matrix in this study required the extraction of proteins with liquid phenol and the application of paper bridge loading for 2-dimensional gel electrophoresis. Proteins were subjected to nanoHPLC (high-performance liquid chromatography) coupled to tandem mass spectrometry for characterization. Several housekeeping proteins as well as methanogenesis-related enzymes were identified by a MASCOT search and de novo sequencing, which proved the feasibility of our approach. The establishment of such an approach is the basis for further metaproteomic studies of biogas-producing communities. In particular, the apparent status of metabolic activities within the communities can be monitored. The knowledge collected from such experiments could lead to further improvements of biogas production.

Hanreich A; Heyer R; Benndorf D; Rapp E; Pioch M; Reichl U; Klocke M

2012-07-01

269

Analysis and quantification of ammonia-oxidizing bacteria community with amoA gene in sewage treatment plants.  

Science.gov (United States)

The analysis and quantification of ammonia-oxidizing bacteria (AOB) is crucial, as they initiate the biological removal of ammonia-nitrogen from sewage. Previous methods for analyzing the microbial community structure, which involve the plating of samples or culture media over agar plates, have been inadequate because many microorganisms found in a sewage plant are unculturable. In this study, to exclusively detect AOB, the analysis was carried out via denaturing gradient gel electrophoresis using a primer specific to the amoA gene, which is one of the functional genes known as ammonia monooxygenase. An AOB consortium (S1 sample) that could oxidize an unprecedented 100% of ammonia in 24 h was obtained from sewage sludge. In addition, real-time PCR was used to quantify the AOB. Results of the microbial community analysis in terms of carbon utilization ability of samples showed that the aeration tank water sample (S2), influent water sample (S3), and effluent water sample (S4) used all the 31 substrates considered, whereas the AOB consortium (S1) used only Tween 80, D-galacturonic acid, itaconic acid, D-malic acid, and L-serine after 192 h. The largest concentration of AOB was detected in S1 (7.6 × 10(6) copies/microliter), followed by S2 (3.2 × 10(6) copies/microliter), S4 (2.8 × 10(6) copies/microliter), and S3 (2.4 × 10(6) copies/microliter). PMID:22814491

Hong, Sun Hwa; Jeong, Hyun Duck; Jung, Bongjin; Lee, Eun Young

2012-09-01

270

Analysis and quantification of ammonia-oxidizing bacteria community with amoA gene in sewage treatment plants.  

UK PubMed Central (United Kingdom)

The analysis and quantification of ammonia-oxidizing bacteria (AOB) is crucial, as they initiate the biological removal of ammonia-nitrogen from sewage. Previous methods for analyzing the microbial community structure, which involve the plating of samples or culture media over agar plates, have been inadequate because many microorganisms found in a sewage plant are unculturable. In this study, to exclusively detect AOB, the analysis was carried out via denaturing gradient gel electrophoresis using a primer specific to the amoA gene, which is one of the functional genes known as ammonia monooxygenase. An AOB consortium (S1 sample) that could oxidize an unprecedented 100% of ammonia in 24 h was obtained from sewage sludge. In addition, real-time PCR was used to quantify the AOB. Results of the microbial community analysis in terms of carbon utilization ability of samples showed that the aeration tank water sample (S2), influent water sample (S3), and effluent water sample (S4) used all the 31 substrates considered, whereas the AOB consortium (S1) used only Tween 80, D-galacturonic acid, itaconic acid, D-malic acid, and L-serine after 192 h. The largest concentration of AOB was detected in S1 (7.6 × 10(6) copies/microliter), followed by S2 (3.2 × 10(6) copies/microliter), S4 (2.8 × 10(6) copies/microliter), and S3 (2.4 × 10(6) copies/microliter).

Hong SH; Jeong HD; Jung B; Lee EY

2012-09-01

271

High-throughput analysis of ammonia oxidiser community composition via a novel, amoA-based functional gene array.  

Science.gov (United States)

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. PMID:23284709

Abell, Guy C J; Robert, Stan S; Frampton, Dion M F; Volkman, John K; Rizwi, Farhan; Csontos, József; Bodrossy, Levente

2012-12-19

272

High-throughput analysis of ammonia oxidiser community composition via a novel, amoA-based functional gene array.  

UK PubMed Central (United Kingdom)

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.

Abell GC; Robert SS; Frampton DM; Volkman JK; Rizwi F; Csontos J; Bodrossy L

2012-01-01

273

Recycling of carbon/energy taxes and the labor market. A general equilibrium analysis for the European Community  

International Nuclear Information System (INIS)

A quantitative assessment of a cost shift from labor to energy by means of a carbon/energy tax is provided. In the analysis a general equilibrium model for the European Community is utilized, focusing on the modelling of labor supply. The importance of the feedback from an induced increase in labor demand to wage formation is highlighted. (It is shown that the goals of C)2 reduction and improved employment are complementary, provided that the reduction in labor costs, financed by the carbon/energy tax, is not offset by increased wage claims. Under this condition reduced CO2 is consistent with an increase in GDP. 1 fig., 3 tabs., 17 refs.

1996-01-01

274

A for-profit venture marketing research and analysis study conducted for Action for Boston Community Development. [Home repair services  

Energy Technology Data Exchange (ETDEWEB)

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.

1987-04-27

275

SYNCSA--R tool for analysis of metacommunities based on functional traits and phylogeny of the community components.  

UK PubMed Central (United Kingdom)

SUMMARY: SYNCSA is an R package for the analysis of metacommunities based on functional traits and phylogeny of the community components. It offers tools to calculate several matrix correlations that express trait-convergence assembly patterns, trait-divergence assembly patterns and phylogenetic signal in functional traits at the species pool level and at the metacommunity level. AVAILABILITY AND IMPLEMENTATION: SYNCSA is a package for the R environment, under a GPL-2 open-source license and freely available on CRAN official web server for R (http://cran.r-project.org). CONTACT: vanderleidebastiani@yahoo.com.br.

Debastiani VJ; Pillar VD

2012-08-01

276

A comparative analysis of two community stressors' long-term mental health effects.  

UK PubMed Central (United Kingdom)

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.

Dew MA; Bromet EJ; Schulberg HC

1987-04-01

277

Comparative analysis of two community stressors' long-term mental health effects  

International Nuclear Information System (INIS)

[en] 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

1987-01-01

278

Analysis: Economic Impacts of Wind Applications in Rural Communities; June 18, 2004 -- January 31, 2005  

Energy Technology Data Exchange (ETDEWEB)

The purpose of this report is to compile completed studies on the economic impact of wind farms in rural communities and then to compare these studies. By summarizing the studies in an Excel spreadsheet, the raw data from a study is easily compared with the data from other studies. In this way, graphs can be made and conclusions drawn. Additionally, the creation of a database in which economic impact studies are summarized allows a greater understanding of the type of information gathered in an economic impact study, the type of information that is most helpful in using these studies to promote wind energy development in rural communities, and the limitations on collecting data for these studies.

Pedden, M.

2006-01-01

279

Soil microbial community analysis of between no-till and tillage in a controlled horticultural field.  

UK PubMed Central (United Kingdom)

The present study evaluated the changes of soil microbial communities that were subjected to no-till and compared the results to those subject to tillage for organic farming in a controlled horticultural field by fatty acid methyl ester. Fungi (P < 0.001), gram-positive bacteria (P < 0.001), arbuscular mycorrhizal fungi (P < 0.01), and actinomycetes (P < 0.01) in the no-till soils were significantly larger than those in the tillage soils. The no-till in the subsoil had a significantly lower ratio of cy17:0 to 16:1?7c compared to that of tillage, indicating that microbial stress decreased because the soils were not disturbed (P < 0.05). Fungi should be considered as a potential factor responsible for the obvious microbial community differentiation that was observed between the no-till and tillage areas in a controlled horticultural field.

Yang SK; Kim MK; Seo YW; Choi KJ; Lee ST; Kwak YS; Lee YH

2012-04-01

280

??????????????????????? Analysis of Endophytic Fungal Community from Roots of Two Transgenic Rice  

Directory of Open Access Journals (Sweden)

Full Text Available ????????????????????????????????????????????????????????????????????????????????????????Gaeumannomyces??????????????????23.23%?????????????????????????????????????????????????????????????????????????????????21.25%?26.56%??????????????????????????????????????????????? Endophytic fungal community in roots of two transgenic rice (antifungal genes) was studied by isolation and staining observation. Compared with non-transgenic rice, the isolation frequency and diversity of the endophytic fungi from two transgenic rice in different growth stages exhibited no significant differences in contrast with the control. Gaeumannomyces was the dominant population of endophytic fungi in the roots of rice with the dominance of 23.23%, and could be isolated in either the two transgenic rice or the control, and any growth stages. By staining observation, the infection rates of endophytic fungi in seedlings of transgenic rice were significantly lower than the control by 21.25% and 26.56% respectively, but there were no significant differences in tillering and maturity. Therefore, it is inferred that the transgenic rice had no significant effect on fungal communities in rice roots.

???; ???; ???; ???; ??; ???

2012-01-01

 
 
 
 
281

Analysis of a benthic community food web using isotopically labelled potential food  

International Nuclear Information System (INIS)

[en] A series of experiments was designed to reveal the trophic structure of a benthic community using kelp holdfasts as microcosms within the kelp-bed community. The experimental food comprised zooplankton represented by 3H2O-labelled Artemia sp. eggs and nauplii (200 to 300 ?m), detritus derived from 14C-labelled kelp (60 to 90 ?m), and phytoplankton represented by 14C-labelled Dunaliella primolecta (5 to 10 ?m) cultures. Separate experiments of short duration (1 to 2 h) were used to indicate the primary consumers on each type of food, while longer experiments (4, 8 and 16 h) suggested the secondary consumers (coprophagous and carnivorous species). Several species were found to be omnivorous. (orig.)

1982-09-15

282

Dry anaerobic digestion of food waste under mesophilic conditions: performance and methanogenic community analysis.  

UK PubMed Central (United Kingdom)

The performance of dry anaerobic digestion (AD) of food waste was investigated under mesophilic conditions and the methanogenic community was investigated using 454 pyrosequencing. Stable dry AD was achieved by hydraulic retention time (HRT) control without the addition of alkali agents. The average CH4 production rate, CH4 content, and volatile solid reduction rate were 2.51±0.17m(3)/m(3)/d, 66±2.1%, and 65.8±1.22%, respectively, at an HRT of 40d. The methanogenic community of the seed sludge experienced a significant reduction in genus diversity from 18 to 4 and a dominant methanogenic shift from hydrogenotrophic to acetoclastic groups after the acclimation under dry condition. Almost all sequences of the dry anaerobic digester were closely related with those of Methanosarcina thermophila with similarity of 96.4-99.1%. The experimental results would serve as useful information to understand the dry AD system.

Cho SK; Im WT; Kim DH; Kim MH; Shin HS; Oh SE

2013-03-01

283

Comparative analysis of two community stressors' long-term mental health effects  

Energy Technology Data Exchange (ETDEWEB)

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.

Dew, M.A.; Bromet, E.J.; Schulberg, H.C.

1987-04-01

284

Community analysis reveals close affinities between endophytic and endolichenic fungi in mosses and lichens.  

UK PubMed Central (United Kingdom)

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 endophytes of mosses.

U'ren JM; Lutzoni F; Miadlikowska J; Arnold AE

2010-08-01

285

Financial analysis of afforestation of community lands in Ramganga catchment in Uttar Pradesh hills  

Energy Technology Data Exchange (ETDEWEB)

The main objectives of the study are: (1) to determine the financial feasibility of afforestation of community lands in the Ramganga catchment; and (2) to project the income and employment effects of afforestation at the catchment level. A two-stage stratified random sampling design was used for selecting a sample of 12 sabhas (an organized group of people) from the catchment. To achieve the first objective, discounted cash flows were computed for pure chir plantation, pure bhimal plantation at a ratio of 9:1, and the following three measures of financial feasibility were worked out: (1) net present value; (2) gross benefit-cost ratio; and (3) financial internal rate of return. To attain the second objective, uniform series of annual income were completed by dividing the total net present value per ha over the rotation period by the appropriate annuity factor and multiplying the resultant quotient by the area of community land in the catchment. Each of the three types of plantation i.e. bhimal, chir and bhimal + chir, was found to be financially feasible at 5% and 10% discount rates in terms of both GBCR and the NPV criteria. A mixed plantation of bhimal + chir is recommended for the community lands in the catchment.

Tewari, D.D.; Singh, K.

1984-01-01

286

Identification of Household Bacterial Community and Analysis of Species Shared with Human Microbiome.  

UK PubMed Central (United Kingdom)

Microbial populations in indoor environments, where we live and eat, are important for public health. Various bacterial species reside in the kitchen, and refrigerators, the major means of food storage within kitchens, can be a direct source of food borne illness. Therefore, the monitoring of microbiota in the refrigerator is important for food safety. We investigated and compared bacterial communities that reside in the vegetable compartment of the refrigerator and on the seat of the toilet, which is recognized as highly colonized by microorganisms, in ten houses using high-throughput sequencing. Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes were predominant in refrigerator and toilet samples. However, Proteobacteria was more abundant in the refrigerator, and Firmicutes was more abundant in the toilet. These household bacterial communities were compared with those of human skin and gut to identify potential sources of household bacteria. Bacterial communities from refrigerators and toilets shared more species in common with human skin than gut. Opportunistic pathogens, including Propionibacterium acnes, Bacteroides vulgatus, and Staphylococcus epidermidis, were identified as species shared with human skin and gut microbiota. This approach can provide a general background of the household microbiota and a potential method of source-tracking for public health purposes.

Jeon YS; Chun J; Kim BS

2013-06-01

287

Preventing waterborne diseases: analysis of a community health worker program in rural Tamil Nadu, India.  

UK PubMed Central (United Kingdom)

Community health worker (CHW) programs have become popular tools in reducing the burden of childhood illnesses. However, the efficacy of CHWs in facilitating behavior change, as a means of preventing waterborne diseases, remains unclear. Using a household survey (n = 225),in rural Tamil Nadu, South India, we assessed the effects of a CHW program on knowledge, attitudes and practices related to diarrheal illness through comparison with a control population that was not enrolled in the program. The CHW program in the experimental village entailed behavior change aimed at preventing diarrheal illness through home visits, community events and health education. Correlates of four key variables on knowledge of drinking water contamination and behavior change were examined by using logistic regression models. We found that while the program was effective in raising awareness of drinking water contamination, it did not significantly increase hygiene and water sanitation practices in the village community in comparison to the control population. Furthermore, villagers enrolled in the CHW program were unable to recognize the connections between contaminated drinking water and disease. The results of our survey indicated the CHW program did not significantly affect behavior in the experimental village. Possible shortcomings in the program are discussed.

Gupta N; Mutukkanu T; Nadimuthu A; Thiyagaran I; Sullivan-Marx E

2012-04-01

288

Mangrove community in an abandoned crick kiln: A structural and association analysis  

Directory of Open Access Journals (Sweden)

Full Text Available Background: The presence of brick kiln along the Hoogly river sites of lower Bengal is very usualand this phenomenon is not only restricted to India alone but also to other south Asian countries.The abandoned brick kiln are important habitat for the formation of mangrove community due totidal action, loose silty substratum and less anthropogenic interference. In this context, the aim ofthe present study is to visualize how the structural and association pattern regulate the communitydynamics 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 andground truthing. Association indices (Ochiai, Dice and Jaccard) were measured based on 2X2contingency/species association table.Results: Out of 10 species under 10 genera and 9 families found in the present habitat, Sonneratiacaseolaris is the only mangrove tree species with 155 individuals along with other mangroveassociates like Cryptocoryne ciliata, Crinum viviparum, Acanthus ilicifolius and Derris scandens. Thehigh importance value index of Sonneratia caseolaris, Cryptocoryne ciliata, and Crinum viviparumindicated their significant role in community formation. The strong positive association of these 3species also suggests helping in developing community in stressed environment.Conclusion: Identification of such potential mangrove habitat and study of their communitydynamics would be helpful to find out the nature of mangrove establishment for futureafforestation programme of threatened mangrove species.

Sumit Manna; Anirban Roy; Tushar Kanti Ghara

2012-01-01

289

Analysis of fecal Lactobacillus community structure in patients with early rheumatoid arthritis.  

UK PubMed Central (United Kingdom)

The objective of this study was to analyze human fecal Lactobacillus community and its relationship with rheumatoid arthritis. Samples taken from rheumatoid arthritis (RA) patients and healthy individuals were analyzed by quantitative real-time PCR. Bacterial DNA was extracted from feces, and amplicons of the Lactobacillus-specific regions of 16S rRNA were analyzed by denaturing gradient gel electrophoresis. The richness, Shannon-Wiener index, and evenness of gut microbiota of both groups were analyzed to compare fecal Lactobacillus community structures. Results of this study demonstrated that fecal microbiota of RA patients contained significantly more Lactobacillus (10.62 ± 1.72 copies/g) than the control group (8.93 ± 1.60 copies/g). Significant increases were observed in RA patients in terms of the richness, Shannon-Wiener, and evenness measures, indicating more bacterial species, and increased bacterial diversity and abundance. These results suggest a potential relationship between Lactobacillus communities and the development and progression of rheumatoid arthritis.

Liu X; Zou Q; Zeng B; Fang Y; Wei H

2013-08-01

290

Diversity and community analysis of ammonia oxidizing bacteria in a streambed surrounding an artificial dam.  

UK PubMed Central (United Kingdom)

The degree to which small natural dams affect the native bacterial nitrogen cycling community was explored by molecular methods. The identities and relative abundances of ammonia oxidizing bacteria in the sediment surrounding an artificial dam both at the surface and in the hyporheic zone were characterized. Analyses were performed using tRFLP of the conserved amoA gene using a semi-nested degenerate PCR approach. Additionally, an amoA gene library was constructed to characterize the most dominant sediment genotypes. The results of the tRFLP analyses showed clear differences between the upstream and downstream communities at different depths in the sediment column. Non-metric multidimensional scaling ordination of the tRFLP data set produced a stable one-dimensional solution with significant correlations to oxygen, pH, nitrate, and dissolved organic nitrogen levels. The sample corresponding to the hyporheic zone downstream of the dam showed 28-50% higher amoA richness and higher diversity than the other samples. All gene fragments sequenced from the samples grouped with sequences of the Nitrosospira type. Ordination of 16S rDNA tRFLP data revealed a two dimensional data structure, one axis of which had similar chemical correlation characteristics as the amoA model axis. Taken together, the results from this study suggest that the presence of the dam creates physical and chemical heterogeneity that may foster genetic diversity and community changes amongst ammonia oxidizing bacteria.

Murdoch RW; Costello Staniec A

2013-09-01

291

Effectiveness analysis on the physical activity and the health benefit of a community population based program.  

UK PubMed Central (United Kingdom)

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.

Jiang YY; Yang ZX; Ni R; Zhu YQ; Li ZY; Yang LC; Zhai Y; Zhao WH

2013-06-01

292

Identification of Household Bacterial Community and Analysis of Species Shared with Human Microbiome.  

Science.gov (United States)

Microbial populations in indoor environments, where we live and eat, are important for public health. Various bacterial species reside in the kitchen, and refrigerators, the major means of food storage within kitchens, can be a direct source of food borne illness. Therefore, the monitoring of microbiota in the refrigerator is important for food safety. We investigated and compared bacterial communities that reside in the vegetable compartment of the refrigerator and on the seat of the toilet, which is recognized as highly colonized by microorganisms, in ten houses using high-throughput sequencing. Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes were predominant in refrigerator and toilet samples. However, Proteobacteria was more abundant in the refrigerator, and Firmicutes was more abundant in the toilet. These household bacterial communities were compared with those of human skin and gut to identify potential sources of household bacteria. Bacterial communities from refrigerators and toilets shared more species in common with human skin than gut. Opportunistic pathogens, including Propionibacterium acnes, Bacteroides vulgatus, and Staphylococcus epidermidis, were identified as species shared with human skin and gut microbiota. This approach can provide a general background of the household microbiota and a potential method of source-tracking for public health purposes. PMID:23743600

Jeon, Yoon-Seong; Chun, Jongsik; Kim, Bong-Soo

2013-06-01

293

Analysis of the predator community of a subterranean herbivorous insect based on polymerase chain reaction.  

Science.gov (United States)

The identity and impact of trophic linkages within subterranean arthropod communities are challenging to establish, a fact that hinders the development of conservation biological control programs of subterranean herbivores. Diabrotica virgifera (the western corn rootworm) is a severe agricultural pest that lives subterraneously during its pre-imaginal stages and succumbs to high levels of pre-imaginal mortality from unknown agents. The guts of 1500 field-collected arthropod predators were analyzed for D. virgifera-specific DNA sequences using quantitative polymerase chain reaction (qPCR). These gut analyses were used to generate relative and taxon-specific prey consumption indices for the major predator taxa and to determine relative consumption levels during D. virgifera egg and larval stages by predator feeding guilds. Laboratory feeding assays were used to determine the meal size consumed during 5 min and digestion rates of D. virgifera DNA of four predators abundant in D. virgifera-infested cornfields. More than 17 taxa consumed D. virgifera in the field. Harvestmen and small rove beetles were the most abundant predators captured, and the most frequent predators within the community to consume D. virgifera. The largest proportions of individual species' populations testing positive for D. virgifera DNA were found in ground beetles (Scarites quadriceps and Poecilus chalcites) and spiders, wolf spiders, and predaceous mites. Because of the longer duration of the egg stage, significantly more predators consumed D. virgifera eggs than larvae, but a similar proportion of the predator community fed on eggs and larvae. Predators with sucking mouthparts had a higher consumption index than chewing predators. Laboratory assays confirmed that sucking predators consume more D. virgifera DNA during 5 min than the chewing predators, and all four predators digested this DNA at a similar rate. This research substantiates that a diverse community of soil-dwelling and subterranean predators contribute to the high level of mortality incurred by D. virgifera in cornfields (approximately 99% pre-adult mortality). Moreover, qPCR is a useful tool for describing trophic relationships within subterranean food webs, a crucial step in determining the relative contributions of a diverse predator community to the population dynamics of an herbivorous arthropod. PMID:20014585

Lundgren, Jonathan G; Ellsbury, Michael E; Prischmann, Deirdre A

2009-12-01

294

Analysis of the predator community of a subterranean herbivorous insect based on polymerase chain reaction.  

UK PubMed Central (United Kingdom)

The identity and impact of trophic linkages within subterranean arthropod communities are challenging to establish, a fact that hinders the development of conservation biological control programs of subterranean herbivores. Diabrotica virgifera (the western corn rootworm) is a severe agricultural pest that lives subterraneously during its pre-imaginal stages and succumbs to high levels of pre-imaginal mortality from unknown agents. The guts of 1500 field-collected arthropod predators were analyzed for D. virgifera-specific DNA sequences using quantitative polymerase chain reaction (qPCR). These gut analyses were used to generate relative and taxon-specific prey consumption indices for the major predator taxa and to determine relative consumption levels during D. virgifera egg and larval stages by predator feeding guilds. Laboratory feeding assays were used to determine the meal size consumed during 5 min and digestion rates of D. virgifera DNA of four predators abundant in D. virgifera-infested cornfields. More than 17 taxa consumed D. virgifera in the field. Harvestmen and small rove beetles were the most abundant predators captured, and the most frequent predators within the community to consume D. virgifera. The largest proportions of individual species' populations testing positive for D. virgifera DNA were found in ground beetles (Scarites quadriceps and Poecilus chalcites) and spiders, wolf spiders, and predaceous mites. Because of the longer duration of the egg stage, significantly more predators consumed D. virgifera eggs than larvae, but a similar proportion of the predator community fed on eggs and larvae. Predators with sucking mouthparts had a higher consumption index than chewing predators. Laboratory assays confirmed that sucking predators consume more D. virgifera DNA during 5 min than the chewing predators, and all four predators digested this DNA at a similar rate. This research substantiates that a diverse community of soil-dwelling and subterranean predators contribute to the high level of mortality incurred by D. virgifera in cornfields (approximately 99% pre-adult mortality). Moreover, qPCR is a useful tool for describing trophic relationships within subterranean food webs, a crucial step in determining the relative contributions of a diverse predator community to the population dynamics of an herbivorous arthropod.

Lundgren JG; Ellsbury ME; Prischmann DA

2009-12-01

295

Availability of substance abuse treatment services in Spanish: a GIS analysis of Latino communities in Los Angeles County, California.  

UK PubMed Central (United Kingdom)

BACKGROUND: The percentage of Latino clients entering outpatient substance abuse treatment (OSAT) in the United States has increased significantly in the past 10 years. Evidence suggests that a lack of services in Spanish is a significant barrier to treatment access among Latinos. METHODS: Using a geographic information system (GIS) approach, data from the U.S. Census Bureau and the National Survey of Substance Abuse Treatment Services (N-SSATS) were analyzed to determine the geographic distance between OSAT facilities with services in Spanish and Latino communities throughout Los Angeles County, CA. Data from N-SSATS were also analyzed using logistic regression models to examine organizational characteristics and their association with offering services in Spanish. Our GIS methods are tested in their ability to provide baseline measures to inform future analysis comparing changes in demography and service infrastructure. RESULTS: GIS analysis revealed cold spots representing high-density Latino communities with extensive travel distance to facilities offering services in Spanish. The average linear distance between Latino communities and facilities offering Spanish-language services ranged from 2 to 6 miles, while the location of the cold spots pointed to a need for services in Spanish in a particular subregion of the county. Further, secondary data analysis revealed that, on average, being privately owned (OR = .23, 95% CI = 0.06-0.90) was associated with a lower likelihood of providing services in Spanish compared to public facilities. Additionally, a facility with a state license (OR = 2.08, 95% CI = 1.12-3.88) or a higher number of Medicaid recipients (OR = 2.98, 95% CI = 1.76-5.05) was twice as likely to offer services in Spanish. CONCLUSION: Despite the significant presence of Latinos in L.A. County in 2000, low capacity was found in discrete Latino communities in terms of offering OSAT services in Spanish. Funding and regulation play a significant role in facilities' capacity to offer these services. Future studies should build from our multi-method approach to compare changes in population demography and system infrastructure and inform health care policy that seeks to improve providers' capacity to provide linguistically competent care.

Guerrero EG; Pan KB; Curtis A; Lizano EL

2011-01-01

296

Availability of substance abuse treatment services in Spanish: A GIS analysis of Latino communities in Los Angeles County, California  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background The percentage of Latino clients entering outpatient substance abuse treatment (OSAT) in the United States has increased significantly in the past 10 years. Evidence suggests that a lack of services in Spanish is a significant barrier to treatment access among Latinos. Methods Using a geographic information system (GIS) approach, data from the U.S. Census Bureau and the National Survey of Substance Abuse Treatment Services (N-SSATS) were analyzed to determine the geographic distance between OSAT facilities with services in Spanish and Latino communities throughout Los Angeles County, CA. Data from N-SSATS were also analyzed using logistic regression models to examine organizational characteristics and their association with offering services in Spanish. Our GIS methods are tested in their ability to provide baseline measures to inform future analysis comparing changes in demography and service infrastructure. Results GIS analysis revealed cold spots representing high-density Latino communities with extensive travel distance to facilities offering services in Spanish. The average linear distance between Latino communities and facilities offering Spanish-language services ranged from 2 to 6 miles, while the location of the cold spots pointed to a need for services in Spanish in a particular subregion of the county. Further, secondary data analysis revealed that, on average, being privately owned (OR = .23, 95% CI = 0.06-0.90) was associated with a lower likelihood of providing services in Spanish compared to public facilities. Additionally, a facility with a state license (OR = 2.08, 95% CI = 1.12-3.88) or a higher number of Medicaid recipients (OR = 2.98, 95% CI = 1.76-5.05) was twice as likely to offer services in Spanish. Conclusion Despite the significant presence of Latinos in L.A. County in 2000, low capacity was found in discrete Latino communities in terms of offering OSAT services in Spanish. Funding and regulation play a significant role in facilities' capacity to offer these services. Future studies should build from our multi-method approach to compare changes in population demography and system infrastructure and inform health care policy that seeks to improve providers' capacity to provide linguistically competent care.

Guerrero Erick G; Pan Karen B; Curtis Andrew; Lizano Erica L

2011-01-01

297

Nitrifying Community Analysis in a Single Submerged Attached-Growth Bioreactor for Treatment of High-Ammonia Waste Stream  

DEFF Research Database (Denmark)

This study investigated the nitrifying community structure in a single-stage submerged attached-growth bioreactor (SAGB) that successfully achieved stable nitrogen removal over nitrite of a high-strength ammonia wastewater. The reactor was operated with intermittent aeration and external carbon addition (methanol). With influent ammonia and total Kjeldahl nitrogen ranging from 537 to 968 mg/L and 643 to1510 mg/L, respectively, 85% nitrogen removal was obtained, and effluent was dominated by nitrite (NO2 ?/NOx >0.95). Nitrifying community analysis using fluorescence in situ hybridization (FISH), with a hierarchical set of probes targeting known ammonia-oxidizing bacteria (AOB) within beta-proteobacteria, showed that the AOB community of the biofilter consists almost entirely of members of the Nitrosomonas europaea/eutropha and the Nitrosococcus mobilis lineages. Image analysis of FISH pictures was used to quantify the identified AOB, and it was estimated that Nitrosomonas europaea/eutropha-like AOB accounted for 4.3% of the total volume of the biofilm, while Nitrosococcus mobilis-like AOB made up 1.2%; these numbers summed up to a total AOB fraction of 5.5% of the total volume on the biofilm. Nitrite-oxidizing bacteria (NOB) were not detectable in the biofilm samples with probes for either Nitrospira sp. or Nitrobacter sp., which indicated that NOB were either absent from the biofilters or present in numbers below the detection limit of FISH (<0.1% of the total biofilm). Nitrite oxidizers were likely outcompeted from the system because of the free ammonia inhibition and the possibility that the aeration period (from intermittent aeration) was not sufficiently long for the NOB to be released from the competition for oxygen with heterotrophs and AOB. The nitrogen removal via nitrite in a SAGB reactor described in this study is applicable for high-ammonia-strength wastewater treatment, such as centrate or industrial wastes. Udgivelsesdato: December 2007

Gu, April Z.; Pedros, Philip B

2007-01-01

298

Comparative analysis of bacterial community and antibiotic-resistant strains in different developmental stages of the housefly (Musca domestica).  

UK PubMed Central (United Kingdom)

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.

Wei T; Hu J; Miyanaga K; Tanji Y

2013-02-01

299

Terminal-restriction fragment length polymorphism and automated ribosomal intergenic spacer analysis profiling of fungal communities in Camembert cheese  

UK PubMed Central (United Kingdom)

Identifying and isolating yeasts and moulds within a fungal community is challenging. The main goal of the present study was to assess a new approach for the detection and identification of fungi involved in Camembert cheese rind formation to replace the use of traditional microbiological techniques. Two molecular methods, terminal-restriction fragment length polymorphism (T-RFLP) and automated ribosomal intergenic spacer analysis (ARISA), were adapted and compared for their potential to determine fungal composition directly from cheese samples. The two techniques in combination with principal component analysis showed differences in the fungal composition of cheeses when comparing surface with centre, different batches, manufacturing processes and ripening times. Moreover, cheese stabilisation induced changes in the flora at the cheese centre, and difference in size (150 g versus 1 kg) modified surface flora. Nine fungal genera were identified in cheese samples: Cladosporium, Debaryomyces, Geotrichum, Kluyveromyces, Mucor, Penicillium, Pichia, Saccharomyces and Yarrowia.

Arteau Marianne; Labrie Steve; Roy Denis

2010-08-01

300

Comparative analysis of bacterial communities in a potato field as determined by pyrosequencing  

DEFF Research Database (Denmark)

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 Deltaproteobacteria flourished under different ecological conditions than the Acidobacteria.

Inceoglu, Özgül; Abu Al-Soud, Waleed

2011-01-01

 
 
 
 
301

Comparative analysis of bacterial communities in a potato field as determined by pyrosequencing.  

UK PubMed Central (United Kingdom)

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 Deltaproteobacteria flourished under different ecological conditions than the Acidobacteria.

Inceo?lu Ö; Al-Soud WA; Salles JF; Semenov AV; van Elsas JD

2011-01-01

302

[Clinical analysis of mortality in elderly patients with community-acquired pneumonia].  

UK PubMed Central (United Kingdom)

AIM: Community-acquired pneumonia remains a common and serious disease for elderly persons. The incidence and mortality rates of pneumonia are higher in the elderly. We analyzed the mortality and prognostic factors in 200 elderly patients with community-acquired pneumonia. METHODS: The subjects were 200 elderly patients aged 65 years or older who needed hospitalization after initial visit to Geriatric Medicine, Juntedo Tokyo Koto Geriatric Medical Center, between January 2005 and December 2006. The subjects were divided into two groups, those who died, and those who survived on admission, we examined mortality rates and compared the background, underlying disease, laboratory data, chest X-ray findings, severity classification using A-DROP, between the two groups. RESULTS: The mortality rate was 15.0%. Circulating diseases, cerebrovacscular diseases and dementia were the most common underlying diseases. It took a longer period to enter the hospital in the cases that died. In laboratory findings, total protein, serum albumin and percutaneous oxygen saturation were lower, and BUN was higher in the fatality group. There were many more patients who had extending infiltration shadow on chest X-ray films and severe condition on A-DROP classification in the fatality group. CONCLUSIONS: We concluded that delay of diagnosis and treatment, dehydration, low levels of protein and albumin were important prognostic factors. The extent of infiltration shadow in chest X-ray findings was also important. A-DROP might be useful for estimating the prognosis in elderly patients with community-acquired pneumonia. We should consider the prognostic factors and severity at the initial stage when treating elderly patients with pneumonia.

Sakamoto N; Sugihara E; Boku S; Fukuda H; Isonuma H; Aiba M; Dambara T

2010-01-01

303

Community mental-health services and suicide rate in Finland: a nationwide small-area analysis.  

UK PubMed Central (United Kingdom)

BACKGROUND: In many countries, psychiatric services have been reformed by reducing the size of hospitals and developing community mental-health services. We investigated this reform by assessing the relation between suicide risk and different ways of organising mental-health services. METHODS: We did a nationwide comprehensive survey of Finnish adult mental-health service units between Sept 1, 2004, and March 31, 2005. From health-care or social-care officers of 428 municipalities, we asked for information, classified according to the European service mapping schedule, about adult mental-health services. For each municipality, we measured age-adjusted and sex-adjusted suicide risk, pooled between 2000 and 2004, and then adjusted for register-derived socioeconomic factors. FINDINGS: A wide variety of outpatient services (relative risk [RR] 0.92, 95% CI 0.87-0.96), prominence of outpatient versus inpatient services (0.93, 0.89-0.97), and 24-h emergency services (0.84, 0.75-0.92) were associated with decreased death rates from suicide. However, after adjustment for socioeconomic factors, only the prominence of outpatient services was associated with low suicide rate (0.94, 0.90-0.98). We replicated this finding even after adjustment for organisational changes and inpatient treatment. INTERPRETATION: Well-developed community mental-health services are associated with lower suicide rates than are services oriented towards inpatient treatment provision. These data are consistent with the idea that population mental health can be improved by use of multifaceted, community-based, specialised mental-health services. FUNDING: Academy of Finland.

Pirkola S; Sund R; Sailas E; Wahlbeck K

2009-01-01

304

Microbial community characterization, activity analysis and purifying efficiency in a biofilter process.  

UK PubMed Central (United Kingdom)

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 COD(Mn) 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, COD(Mn), 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.

Xiang H; Lu X; Yin L; Yang F; Zhu G; Liu W

2013-04-01

305

Wisdom Way Solar Village: Design, Construction, and Analysis of a Low Energy Community  

Energy Technology Data Exchange (ETDEWEB)

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.

Aldrich, R.

2012-08-01

306

rRNA-based analysis to monitor succession of faecal bacterial communities in Holstein calves.  

UK PubMed Central (United Kingdom)

AIMS: To quantitatively analyse the faecal bacterial communities of Holstein calves and track their succession up to 12 weeks of age. METHODS AND RESULTS: Faecal samples obtained from four female Holstein calves were analysed by the RNA-based, sequence-specific rRNA cleavage method. Twelve scissor probes covering major rumen bacterial groups were used, detecting c. 60-90% of the total 16S rRNAs. At 1 week of age, 16S rRNAs from members of the Bacteroides-Prevotella group (40·0% of the total 16S rRNAs), Faecalibacterium (21·7%), the Clostridium coccoides-Eubacterium rectale group (16·7%) and the Atopobium cluster (10·9%) were detected at high levels. Throughout the 12-week period, rRNAs of the Bacteroides-Prevotella and the Cl. coccoides-Eu. rectale groups constituted the major fraction of microbiota (c. 50-70% of the total). The relative abundances of the Atopobium cluster, Faecalibacterium, and some probiotic bacteria (such as those of the genera Lactobacillus and Bifidobacterium) decreased as the animal aged. Instead, an uncultivated rumen bacterial group, as well as Ruminococcus flavefaciens and Fibrobacter emerged at the detectable levels (1-2%) in the faeces sampled at a postweaning age. In addition, certain bacterial groups that were not covered by the probe suite increased as the animals aged. CONCLUSIONS: Young calves undergo dynamic changes in their intestinal bacterial community during the first 12 weeks of life. As young ruminants undergo metabolic and physiological development in their digestive tracts in the transition from a monogastric to a ruminant animal at an early age, the intestinal bacterial community may reflect such development. SIGNIFICANCE AND IMPACT OF THE STUDY: The succession of the bacterial communities in the faeces of calves was quantitatively monitored in the present study for the first time. The approach used here was demonstrated to be a useful means for determining the populations of predominant faecal bacterial groups in a variety of calf experiments in response to diet, stress and disease.

Uyeno Y; Sekiguchi Y; Kamagata Y

2010-11-01

307

Comparative molecular analysis of chemolithoautotrophic bacterial diversity and community structure from coastal saline soils, Gujarat, India.  

UK PubMed Central (United Kingdom)

BACKGROUND: Soils harbour high diversity of obligate as well as facultative chemolithoautotrophic bacteria that contribute significantly to CO2 dynamics in soil. In this study, we used culture dependent and independent methods to assess the community structure and diversity of chemolithoautotrophs in agricultural and coastal barren saline soils (low and high salinity). We studied the composition and distribution of chemolithoautotrophs by means of functional marker gene cbbL encoding large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase and a phylogenetic marker 16S rRNA gene. The cbbL form IA and IC genes associated with carbon fixation were analyzed to gain insight into metabolic potential of chemolithoautotrophs in three soil types of coastal ecosystems which had a very different salt load and sulphur content. RESULTS: In cbbL libraries, the cbbL form IA was retrieved only from high saline soil whereas form IC was found in all three soil types. The form IC cbbL was also amplified from bacterial isolates obtained from all soil types. A number of novel monophyletic lineages affiliated with form IA and IC phylogenetic trees were found. These were distantly related to the known cbbL sequences from agroecosystem, volcanic ashes and marine environments. In 16S rRNA clone libraries, the agricultural soil was dominated by chemolithoautotrophs (Betaproteobacteria) whereas photoautotrophic Chloroflexi and sulphide oxidizers dominated saline ecosystems. Environmental specificity was apparently visible at both higher taxonomic levels (phylum) and lower taxonomic levels (genus and species). The differentiation in community structure and diversity in three soil ecosystems was supported by LIBSHUFF (P = 0.001) and UniFrac. CONCLUSION: This study may provide fundamentally new insights into the role of chemolithoautotrophic and photoautotrophic bacterial diversity in biochemical carbon cycling in barren saline soils. The bacterial communities varied greatly among the three sites, probably because of differences in salinity, carbon and sulphur contents. The cbbL form IA-containing sulphide-oxidizing chemolithotrophs were found only in high saline soil clone library, thus giving the indication of sulphide availability in this soil ecosystem. This is the first comparative study of the community structure and diversity of chemolithoautotrophic bacteria in coastal agricultural and saline barren soils using functional (cbbL) and phylogenetic (16S rDNA) marker genes.

Yousuf B; Sanadhya P; Keshri J; Jha B

2012-01-01

308

[Comparative analysis of the treatment of inpatients with community-acquired pneumonia and its different outcomes].  

Science.gov (United States)

The aim of the work was to compare the quality of medical care provided to patients with severe community-acquired pneumonia (CAP) and its different outcomes. (complete recovery, or death--25 patients in either group). In the latter group, the patients did not undergo adequate clinical and instrumental examination at the pre-hospital stage). Most recovered patients were given high doses of ceftriaxone, clarithromycin and ambroxol or low doses of systemic glucocorticoids. A pulmonologist participated in the treatment of these patients twice as frequently as in the treatment of the patients of the latter group. Effects of high doses of systemic glucocorticoids remains debatable. PMID:23789451

Vizel', A A; Lysenko, G V

2013-01-01

309

[Comparative analysis of the treatment of inpatients with community-acquired pneumonia and its different outcomes].  

UK PubMed Central (United Kingdom)

The aim of the work was to compare the quality of medical care provided to patients with severe community-acquired pneumonia (CAP) and its different outcomes. (complete recovery, or death--25 patients in either group). In the latter group, the patients did not undergo adequate clinical and instrumental examination at the pre-hospital stage). Most recovered patients were given high doses of ceftriaxone, clarithromycin and ambroxol or low doses of systemic glucocorticoids. A pulmonologist participated in the treatment of these patients twice as frequently as in the treatment of the patients of the latter group. Effects of high doses of systemic glucocorticoids remains debatable.

Vizel' AA; Lysenko GV

2013-01-01

310

Hierarchical spatial point process analysis for a plant community with high biodiversity  

DEFF Research Database (Denmark)

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 likelihood approach to inference where problems arise due to unknown interaction radii for the plants. We next demonstrate that a Bayesian approach provides a flexible framework for incorporating prior information concerning the interaction radii. From an ecological perspective, we are able both to confirm existing knowledge on species' interactions and to generate new biological questions and hypotheses on species' interactions. Udgivelsesdato: September

Illian, Janine B.; MØller, Jesper

2009-01-01

311

Cost-Benefit Analysis of a Community-Based Stroke Prevention Program in Bao Shan District, Shanghai, China  

Directory of Open Access Journals (Sweden)

Full Text Available Background: Stroke is a serious problem faced by society. This disease brings not only health problems to individuals suffering from it, but also a serious economic burden to patients and their families. Moreover, it reduces social benefits and the labor force. Therefore, it is important to think about the efficient control and prevention of this disease. It is well known that hypertension is the main cause of stroke. In Bao Shan District, located in Shanghai, China, a community-based prevention program has been in place since 1995. The program is trying to reduce the number of stroke patients and the costs to treat them, mainly by hypertension control and treatment.Objectives: The purpose of this paper is to show the data, describe the results and give a cost-benefit analysis of the program according to data from 1995 to 1997. Methods: The data is calculated by using the method of cost-benefit analysis. Results: According to the cost-benefit analysis of the program, because the incidence of stroke goes down after the hypertension prevention work is taken, the16 patients will not face economic loss because of stoke after the prevention. This is the biggest benefit of this community-based program. The input of this program is RMB 293,573 and the output is RMB 1,062.204; the ratio of cost and benefit is: cost: benefit=1:3.57. (the official currency of the People's Republic of China; RMB/USD currency exchange rate is 1: 0.1473).Conclusion: The economic burden and the Cost-Benefit Analysis can provide important data to the medical and public health departments in order to make the pertinent prevention policy.

Yan Huang; Jing Ren

2010-01-01

312

Social Audits for Community Action: A tool to Initiate Community Action for Reducing Child Mortality  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Research question : (i) What is the community?s perception (assessment & analysis) of causes underlying neonatal, infant and under five deaths? (ii) What action does the community take thereafter? Objectives : To stimulate the community to assess and analyze the causes...

Nandan D; Misra S; Jain M; Singh D; Verma M; Sethi V

313

Phylogenetic analysis of the succession of bacterial communities in the Great South Bay (Long Island).  

UK PubMed Central (United Kingdom)

Bacterial community composition and succession were examined over the course of the summer season in the Great South Bay, Long Island, NY, USA, using a 16S rDNA clone library approach. There was a progression of changes in dominant species in the libraries during the summer of 1997. The July library had several groups dominant, the SAR407 relatives of the alpha-Proteobacteria (24%) and the SAR86 (18%), sulfur-oxidizing symbiont relatives (8%) of the gamma-Proteobacteria, and unidentified Cytophaga-Flexibacter representatives (22%). In August, the Cytophaga-Flexibacter (Gelidibacter sp. and unidentified Cytophaga-Flexibacter representative) and Cyanobacteria (Synechococcus sp.) increased to 28% and 14%, respectively. High GC Gram-positives appeared at 18%, and beta-Proteobacteria (Ralstonia sp.) at 10%. By September these groups had either declined or were absent, while the SAR86 cluster, Pseudoalteromonas and Alteromonas of the gamma-Proteobacteria were dominant in the community (61%). The dominance of open ocean bacteria along with the presence of Aureococcus anophagefferens (Pelagophyceae) in July suggests possible open ocean coupling to bloom events. Many clones in this study were related to previously described clones from a wide distribution of marine environments, substantiating the cosmopolitan nature of pelagic bacteria. Only one isolated bacterium was closely related to 16S rDNA found in the August library.

Kelly KM; Chistoserdov AY

2001-03-01

314

Comparative metagenomic analysis of soil microbial communities across three hexachlorocyclohexane contamination levels.  

UK PubMed Central (United Kingdom)

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.

Sangwan N; Lata P; Dwivedi V; Singh A; Niharika N; Kaur J; Anand S; Malhotra J; Jindal S; Nigam A; Lal D; Dua A; Saxena A; Garg N; Verma M; Kaur J; Mukherjee U; Gilbert JA; Dowd SE; Raman R; Khurana P; Khurana JP; Lal R

2012-01-01

315

Comparative Metagenomic Analysis of Soil Microbial Communities across Three Hexachlorocyclohexane Contamination Levels  

Science.gov (United States)

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.

Sangwan, Naseer; Lata, Pushp; Dwivedi, Vatsala; Singh, Amit; Niharika, Neha; Kaur, Jasvinder; Anand, Shailly; Malhotra, Jaya; Jindal, Swati; Nigam, Aeshna; Lal, Devi; Dua, Ankita; Saxena, Anjali; Garg, Nidhi; Verma, Mansi; Kaur, Jaspreet; Mukherjee, Udita; Gilbert, Jack A.; Dowd, Scot E.; Raman, Rajagopal; Khurana, Paramjit; Khurana, Jitendra P.; Lal, Rup

2012-01-01

316

Analysis of the Community Health Agent Training Course in relation to violence against women  

Directory of Open Access Journals (Sweden)

Full Text Available Violence has caused a worldwide impact, being considered a Public Health problem. The World Health Organization (WHO) definesviolence as “the intentional use of physical force or power, threatened or actual, against oneself, another person or against a group or community, which either results in or has a high likelihood of resulting in injury, death, psychological harm, maldevelopment or deprivation”.There are several kinds of violence (domestic, sexual, etc) which make it an endemism that affects individual and collective health both in Brazil and other countries. Therefore, the Casa da Mulher Catarina (Catarina Women’s House), which is an extension Project of the Federal University of Santa Catarina (UFSC), organized a qualification course for 403 Community Health Agents (CHA) from Local Health Units of Florianopolis aiming to sensitize these professionals regarding violence against women. Six courses of 12 hours each were carried out to discuss violence, health, violence and gender, violence and media, violence and racism and the Maria da Penha Law. Results highlighted the most appreciated topics (subjects related to the Maria da Penha Law and lecturers) and the least appreciated ones (place of the course and topics about racism). This shows the qualification fulfilled participants´ expectations, and that they are now able to identify signs of violence against women in their groups and also multiply actions against other types of violence.

Jane Maria de Souza Philippi; Patrícia Alves de Souza; Patrícia Alves de Souza

2010-01-01

317

Incidence of Staphylococcus aureus and analysis of associated bacterial communities on food industry surfaces.  

UK PubMed Central (United Kingdom)

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.

Gutiérrez D; Delgado S; Vázquez-Sánchez D; Martínez B; Cabo ML; Rodríguez A; Herrera JJ; García P

2012-12-01

318

Bacterial community structure analysis of sediment in the Sagami River, Japan using a rapid approach based on two-dimensional DNA gel electrophoresis mapping with selective primer pairs.  

Science.gov (United States)

A rapid approach based on two-dimensional DNA gel electrophroesis (2-DGE) mapping with selective primer pairs was employed to analyze bacterial community structure in sediments from upstream, midstream and downstream of Sagami River in Japan. The 2-DGE maps indicated that Alpha- and Delta-proteobacteria were major bacterial populations in the upstream and midstream sediments. Further bacterial community structure analysis showed that richness proportion of Alpha- and Delta-proteobacterial groups reflected a trend toward decreasing from the upstream to downstream sediments. The biomass proportion of bacterial populations in the midstream sediment showed a significantly difference from that in the other sediments, suggesting that there may be an environmental pressure on the midstream bacterial community. Lorenz curves, together with Gini coefficients were successfully applied to the 2-DGE mapping data for resolving evenness of bacterial populations, and showed that the plotted curve from high-resolution 2-DGE mapping became less linear and more an exponential function than that of the 1-DGE methods such as chain length analysis and denaturing gradient gel electrophoresis, suggesting that the 2-DGE mapping may achieve a more detailed evaluation of bacterial community. In conclusion, the 2-DGE mapping combined with the selective primer pairs enables bacterial community structure analysis in river sediment and thus it can also monitor sediment pollution based on the change of bacterial community structure. PMID:21222030

Liu, Guo-hua; Rajendran, Narasimmalu; Amemiya, Takashi; Itoh, Kiminori

2011-01-08

319

Bacterial community structure analysis of sediment in the Sagami River, Japan using a rapid approach based on two-dimensional DNA gel electrophoresis mapping with selective primer pairs.  

UK PubMed Central (United Kingdom)

A rapid approach based on two-dimensional DNA gel electrophroesis (2-DGE) mapping with selective primer pairs was employed to analyze bacterial community structure in sediments from upstream, midstream and downstream of Sagami River in Japan. The 2-DGE maps indicated that Alpha- and Delta-proteobacteria were major bacterial populations in the upstream and midstream sediments. Further bacterial community structure analysis showed that richness proportion of Alpha- and Delta-proteobacterial groups reflected a trend toward decreasing from the upstream to downstream sediments. The biomass proportion of bacterial populations in the midstream sediment showed a significantly difference from that in the other sediments, suggesting that there may be an environmental pressure on the midstream bacterial community. Lorenz curves, together with Gini coefficients were successfully applied to the 2-DGE mapping data for resolving evenness of bacterial populations, and showed that the plotted curve from high-resolution 2-DGE mapping became less linear and more an exponential function than that of the 1-DGE methods such as chain length analysis and denaturing gradient gel electrophoresis, suggesting that the 2-DGE mapping may achieve a more detailed evaluation of bacterial community. In conclusion, the 2-DGE mapping combined with the selective primer pairs enables bacterial community structure analysis in river sediment and thus it can also monitor sediment pollution based on the change of bacterial community structure.

Liu GH; Rajendran N; Amemiya T; Itoh K

2011-11-01

320

Assessing community-based conservation projects: A systematic review and multilevel analysis of attitudinal, behavioral, ecological, and economic outcomes  

Directory of Open Access Journals (Sweden)

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 projects from previous reviews for a total of 136 projects. The analyses suggest that project design, particularly capacity building in local communities, is critical in generating success across all outcomes. In addition, some community characteristics, such as tenure regimes and supportive cultural beliefs and institutions, are important for some aspects of project success. Surprisingly, there is less evidence that national context systematically influences project outcomes. Conclusions Our study supports the idea that conservation projects should be carefully designed to be effective and that some characteristics of local communities can facilitate success. That well-designed projects can prevail over disadvantages relating to the pre-existing national and local context is encouraging. As the evidence base on CBC grows, it will be useful to repeat this analysis with additional search terms, and consider additional variables related to national context to further evaluate the role of broader socio-political and economic contexts.

Brooks Jeremy; Waylen Kerry; Mulder Monique

2013-01-01

 
 
 
 
321

Microarray-based analysis of survival of soil microbial community during ozonation  

Energy Technology Data Exchange (ETDEWEB)

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 indigenous soil microorganisms, a fraction of the key functional gene-containing microorganisms survived during ozonation and kept the community functional.

Wang, Jian; Van Nostrand, Joy D.; He, Zhili; Wu, Liyou; Deng, Ye; Zhang, Xu; Zhou, Jizhong; Li, Guanghe

2010-05-17

322

Metagenomic and Meta-transcriptomic Analysis of a Chromate-Reducing Aquifer Microbial Community  

Science.gov (United States)

As part of a highly interdisciplinary study of in situ reductive immobilization of Cr at DOE's Hanford 100H site, we are developing a systems biology approach (employing metagenomic and meta-transcriptomic data) to identify highly expressed genes in the native microbial community under conditions of interest, without requiring any a priori sequence information or assumptions about what processes might be occurring. A key scientific goal is to determine if there are diagnostic biomolecular signatures indicative of important aquifer biogeochemical processes that can be used to (a) help discriminate between direct (enzymatic) and indirect (abiotic) oxidation-reduction processes relevant to bioremediation and (b) to inform and constrain reactive transport models even when geochemical field measurements do not reveal all relevant processes. We are in the process of collecting metagenomic and meta-transcriptomic sequence information from various experimental systems under conditions relevant to in situ chromate reduction at Hanford 100H. This poster focuses on Hanford microcosm studies. To characterize functional changes in an aquifer-derived, chromate-reducing microbial community as it transitions successively through electron-accepting conditions relevant to the Hanford subsurface, we inoculated anaerobic microcosms with groundwater from the Cr-contaminated Hanford 100H site and supplemented them with lactate and electron acceptors present at the site [e.g., nitrate, sulfate, and Fe(III)]. Metagenomic and meta-transcriptomic "snapshots" were taken during denitrification, sulfate and Fe(III) reduction, and nitrate-dependent oxidation of Fe(II) and sulfide. We conducted Illumina paired-end sequencing, assembled with ABySS-pe, and initially annotated using MG-RAST and CAMERA. cDNA samples for meta-transcriptome sequencing represented mRNA enriched using a new subtractive hybridization method resulting in 61-78% of reads mapping to their corresponding metagenomes. Observations from the analyses to date include the following: (1) consistent phylogenetic community transitions were documented by 16S rRNA pyrotag and metagenome sequence data as Hanford microcosms passed successively through denitrifying conditions (dominated initially by beta-Proteobacteria) to fermentative and sulfate- and iron-reducing conditions (dominated by Firmicutes); (2) the greatest diversity of denitrification genes occurred during initial denitrifying phase; (3) high expression of nitrate reductase (nar) and S oxidation (soxWXYZABCD) genes occurred after nitrate was added to cultures following sulfate-reducing phase, even though S oxidation was not detectable based on sulfate measurements; and (4) highly expressed genes in Hanford microcosms and groundwater included "hypothetical proteins", which supports the monitoring approach that we are pursuing, namely, to focus on highly expressed genes specific to Hanford rather than genes chosen a priori.

Beller, H. R.; Lim, H.; Han, R.; Karaoz, U.; Brodie, E. L.

2011-12-01

323

Cost-Benefit Analysis of a Community-Based Stroke Prevention Program in Bao Shan District, Shanghai, China  

Directory of Open Access Journals (Sweden)

Full Text Available Background: Stroke is a serious problem faced by society. This disease brings not only health problemsto individuals suffering from it, but also a serious economic burden to patients and their families.Moreover, it reduces social benefits and the labor force. Therefore, it is important to think about theefficient control and prevention of this disease. It is well known that hypertension is the main cause ofstroke. In Bao Shan District, located in Shanghai, China, a community-based prevention program hasbeen in place since 1995. The program is trying to reduce the number of stroke patients and the costs totreat them, mainly by hypertension control and treatment.Objectives: The purpose of this paper is to show the data, describe the results and give a cost-benefitanalysis of the program according to data from 1995 to 1997.Methods: The data is calculated by using the method of cost-benefit analysis.Results: According to the cost-benefit analysis of the program, because the incidence of stroke goesdown after the hypertension prevention work is taken, the16 patients will not face economic loss becauseof stoke after the prevention. This is the biggest benefit of this community-based program. The input ofthis program is RMB 293,573 and the output is RMB 1,062.204; the ratio of cost and benefit is: cost:benefit=1:3.57. (The official currency of the People's Republic of China; RMB/USD currency exchangerate is 1: 0.1473).Conclusion: The economic burden and the Cost-Benefit Analysis can provide important data to themedical and public health departments in order to make the pertinent prevention policy.

Yan Huang; Jing Ren

2011-01-01

324

Microbial community analysis of Deepwater Horizon oil-spill impacted sites along the Gulf coast using functional and phylogenetic markers.  

UK PubMed Central (United Kingdom)

We investigated the impact of the Deepwater Horizon oil spill on microbial communities in wetland sediment and seawater samples collected from sites along the Gulf shore. Based on GC/MS analysis, the sediment from Bay Jimmy, LA had detectable signs of hydrocarbon contamination, identified as n-alkanes in the GC/MS spectrum similar to that of the Deepwater Horizon source oil (MC-252). To identify changes in microbial assemblage structure and functional diversity in response to hydrocarbon contamination, five genes (bacterial 16S rRNA, Pseudomonas-specific 16S rRNA, alkB, P450, and PAH-RHD?) were selected based on the specific enzymes encoded by bacteria to degrade alkanes or polycyclic aromatic hydrocarbons. A quantitative PCR analysis revealed the presence of alkane and PAH-degrading genes in both contaminated and non-contaminated samples with no significant difference in gene content between contaminated and non-contaminated samples. However, the ribotype analysis based on pyrosequencing identified 17 bacteria genera known for their capacity to degrade hydrocarbons, including Mycobacterium, Novosphingobium, Parvibaculum, Pseudomonas, and Sphingomonas, in the contaminated sediment sample. Furthermore, the contaminated sample had a very high relative abundance of 16S rRNA gene sequences affiliated with the genus Parvibaculum, members of which have been characterized for their degradative abilities. These data suggest that specific bacterial taxa within the genus Parvibaculum have the capacity for hydrocarbon degradation and could use the hydrocarbons as a carbon and energy source, resulting in a dominant population in a hydrocarbon-contaminated soil. In summary, when exposed to the spilled oil, the distinct wetland microbial communities responded with decreased diversity and increased abundance of selective degradative species.

Looper JK; Cotto A; Kim BY; Lee MK; Liles MR; Ní Chadhain SM; Son A

2013-10-01

325

Integrated proteomic and metabolomic analysis of an artificial microbial community for two-step production of vitamin C.  

UK PubMed Central (United Kingdom)

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.

Ma Q; Zhou J; Zhang W; Meng X; Sun J; Yuan YJ

2011-01-01

326

Microbial community analysis of Deepwater Horizon oil-spill impacted sites along the Gulf coast using functional and phylogenetic markers.  

UK PubMed Central (United Kingdom)

We investigated the impact of the Deepwater Horizon oil spill on microbial communities in wetland sediment and seawater samples collected from sites along the Gulf shore. Based on GC/MS analysis, the sediment from Bay Jimmy, LA had detectable signs of hydrocarbon contamination, identified as n-alkanes in the GC/MS spectrum similar to that of the Deepwater Horizon source oil (MC-252). To identify changes in microbial assemblage structure and functional diversity in response to hydrocarbon contamination, five genes (bacterial 16S rRNA, Pseudomonas-specific 16S rRNA, alkB, P450, and PAH-RHD?) were selected based on the specific enzymes encoded by bacteria to degrade alkanes or polycyclic aromatic hydrocarbons. A quantitative PCR analysis revealed the presence of alkane and PAH-degrading genes in both contaminated and non-contaminated samples with no significant difference in gene content between contaminated and non-contaminated samples. However, the ribotype analysis based on pyrosequencing identified 17 bacteria genera known for their capacity to degrade hydrocarbons, including Mycobacterium, Novosphingobium, Parvibaculum, Pseudomonas, and Sphingomonas, in the contaminated sediment sample. Furthermore, the contaminated sample had a very high relative abundance of 16S rRNA gene sequences affiliated with the genus Parvibaculum, members of which have been characterized for their degradative abilities. These data suggest that specific bacterial taxa within the genus Parvibaculum have the capacity for hydrocarbon degradation and could use the hydrocarbons as a carbon and energy source, resulting in a dominant population in a hydrocarbon-contaminated soil. In summary, when exposed to the spilled oil, the distinct wetland microbial communities responded with decreased diversity and increased abundance of selective degradative species.

Looper JK; Cotto A; Kim BY; Lee MK; Liles MR; Ní Chadhain SM; Son A

2013-09-01

327

Analysis of Aquatic Insects’ Communities of Awba Reservoir and its Physico-Chemical Properties  

Directory of Open Access Journals (Sweden)

Full Text Available This study was conducted to assess the Awba reservoir insects’ communities and the health status through the determination of insects’ abundance, composition, distribution and water qualities parameters. Water samples and insects were collected bi-weekly from August through December, 2009. Insects were sampled using standard entomological methods, while water samples was analyzed using standard Winkler’s titrimetric and APHA methods to determine the chemical properties. Water analyses and insects’ identifications were conducted in the laboratory in Department of Zoology, University of Ibadan, Oyo State. The results show that only DO and phosphate-phosphorus had significant difference (p<0.05). A total of 1,154 insects were recorded, Chironomidae and Culicidae were most abundance. The chemical properties and the distinct taxa found in the water suggest that the water body is polluted and may be dangerous to the health of people around the reservoir.

K.O.K. Popoola; A. Otalekor

2011-01-01

328

An experimental analysis of spatial competition in a dense infaunal community: The importance of relative effects  

Science.gov (United States)

A densely populated soft-sediment community was experimentally analysed for interspecific competition for space in laboratory experiments. No interspecific competitive interactions leading to a decrease in survivorship could be documented over a five-week period. The four most abundant species all coexisted in laboratory microcosms. The two tube-buiding species, the tanaid Leptochelia dubia and the polychaete Rhynchospio arenincola, could not exclude the mobile bivalve Transennella tantilla or the burrowing amphipod Paraphoxus spinosus. None of the species increases its emigration frequency when other species are present. Paraphoxus is found to be a browsing predator on Phynchospio but inflicts no detectable mortality. The coexistence of these species is permitted by virtue of the fact that none of the species can alter the soft-sediment habitat sufficiently to make the habitat unsuitable for the other species.

Wilson, W. Herbert

1984-06-01

329

Metaproteomic Analysis of a Chemosynthetic Hydrothermal Vent Community Reveals Insights into Key-Metabolic Processes  

Science.gov (United States)

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 internal sulfur cycle within the community. The community contained expressed enzymes of a variety of carbon metabolism pathways. Key enzymes of the reverse TCA cycle for fixation of CO2 and the Wood-Ljungdahl pathway for oxidation of acetyl-CoA and / or the fixation of CO2 were found. Key enzymes of aerobic and anaerobic methane-oxidation pathways were identified as well, namely particulate methane monooxygenase and methyl-Coenzyme M reductase. Various house-keeping gene-products, like cold- and heat shock proteins as well as ribosomal proteins and ATP synthases were identified. This approach has a future potential of broadening our understanding of environmental complexity and regulation in response to geochemical constraints. [1] Dupierris, V., Masselon, C., Court, M., Kieffer-Jaquinod, S., and Bruley, C. (2009) A toolbox for validation of mass spectrometry peptides identification and generation of database: IRMa. Bioinformatics 25, 1980-1981.

Steen, I.; Stokke, R.; Lanzen, A.; Pedersen, R.; Øvreås, L.; Urich, T.

2010-12-01

330

Analysis: the impact of needle, syringe, and lancet disposal on the community.  

UK PubMed Central (United Kingdom)

There are over 7.5 billion needles and syringes used outside of the health care system each year by individuals with diabetes, migraines, allergies, infertility, arthritis, HIV, hepatitis, multiple sclerosis, osteoporosis, psoriasis, or other conditions. Disposal of needles, syringes, lancets, and other medical products are not regulated in the home, while these same products used in health care facilities are strictly regulated. Home-generated medical waste is routinely placed into curbside trash, placing sanitation workers and custodial personnel at personal risk of a needle-stick injury. The Coalition for Safe Community Needle Disposal is working to establish a solution that is satisfactory to all stakeholders, sharing the burden of these programs with the pharmaceutical industry, medical device industry, waste management industry, recycling companies, and local and state governments.

Gold K

2011-07-01

331

Hydrocephalus is a rare outcome in community-acquired bacterial meningitis in adults : a retrospective analysis  

DEFF Research Database (Denmark)

BACKGROUND: Community-acquired bacterial meningitis (CABM) continues to have a high mortality rate and often results in severe sequelae among survivors. Lately, an increased effort has been focused on describing the neurological complications of meningitis including hydrocephalus. To aid in this field of research we set out to ascertain the risk and outcome of hydrocephalus in patients with community-acquired bacterial meningitis (CABM) in North Denmark Region. METHODS: We conducted a retrospective population-based cohort study of CABM cases above 14 years of age. Cases diagnosed during a 13-year period, 1998 through 2010, were identified in a laboratory register and data were acquired through patient records. Cases not confirmed by culture met other strict inclusion criteria. The diagnosis of hydrocephalus relied upon the radiologists' reports on cranial imaging. Outcome was graded according to the Glasgow Outcome Scale at discharge from the primary admission. Long-term sequelae were based upon any subsequent hospital contacts until the end of 2011. RESULTS: Hydrocephalus was diagnosed in five of 165 episodes (3%) and all were classified as communicating. Only 120 patients had cranial imaging done and in this group the rate was 4.2%. In three cases hydrocephalus was present at admission, while two cases were diagnosed on days 44 and 99, respectively, due to altered mental status. The aetiology was either Eschericia coli (n = 2) or Streptococcus pneumoniae (n = 3). Case fatality was 60% among cases with hydrocephalus and 17% among other cases. Case fatality was similar irrespective of whether patients had a cranial CT or not. CONCLUSIONS: Hydrocephalus was diagnosed in 3% of adolescent and adult cases with CABM and had a high case fatality rate in spite of specialised medical care and neurosurgical interventions. Our findings are comparable with a recent Dutch national prospective study.

Bodilsen, Jacob; SchØnheyder, Henrik Carl

2013-01-01

332

Hydrocephalus is a rare outcome in community-acquired bacterial meningitis in adults: a retrospective analysis  

Science.gov (United States)

Background Community-acquired bacterial meningitis (CABM) continues to have a high mortality rate and often results in severe sequelae among survivors. Lately, an increased effort has been focused on describing the neurological complications of meningitis including hydrocephalus. To aid in this field of research we set out to ascertain the risk and outcome of hydrocephalus in patients with community-acquired bacterial meningitis (CABM) in North Denmark Region. Methods We conducted a retrospective population-based cohort study of CABM cases above 14 years of age. Cases diagnosed during a 13-year period, 1998 through 2010, were identified in a laboratory register and data were acquired through patient records. Cases not confirmed by culture met other strict inclusion criteria. The diagnosis of hydrocephalus relied upon the radiologists’ reports on cranial imaging. Outcome was graded according to the Glasgow Outcome Scale at discharge from the primary admission. Long-term sequelae were based upon any subsequent hospital contacts until the end of 2011. Results Hydrocephalus was diagnosed in five of 165 episodes (3%) and all were classified as communicating. Only 120 patients had cranial imaging done and in this group the rate was 4.2%. In three cases hydrocephalus was present at admission, while two cases were diagnosed on days 44 and 99, respectively, due to altered mental status. The aetiology was either Eschericia coli (n?=?2) or Streptococcus pneumoniae (n?=?3). Case fatality was 60% among cases with hydrocephalus and 17% among other cases. Case fatality was similar irrespective of whether patients had a cranial CT or not. Conclusions Hydrocephalus was diagnosed in 3% of adolescent and adult cases with CABM and had a high case fatality rate in spite of specialised medical care and neurosurgical interventions. Our findings are comparable with a recent Dutch national prospective study.

2013-01-01

333

Hydrocephalus is a rare outcome in community-acquired bacterial meningitis in adults: a retrospective analysis.  

UK PubMed Central (United Kingdom)

BACKGROUND: Community-acquired bacterial meningitis (CABM) continues to have a high mortality rate and often results in severe sequelae among survivors. Lately, an increased effort has been focused on describing the neurological complications of meningitis including hydrocephalus. To aid in this field of research we set out to ascertain the risk and outcome of hydrocephalus in patients with community-acquired bacterial meningitis (CABM) in North Denmark Region. METHODS: We conducted a retrospective population-based cohort study of CABM cases above 14 years of age. Cases diagnosed during a 13-year period, 1998 through 2010, were identified in a laboratory register and data were acquired through patient records. Cases not confirmed by culture met other strict inclusion criteria. The diagnosis of hydrocephalus relied upon the radiologists' reports on cranial imaging. Outcome was graded according to the Glasgow Outcome Scale at discharge from the primary admission. Long-term sequelae were based upon any subsequent hospital contacts until the end of 2011. RESULTS: Hydrocephalus was diagnosed in five of 165 episodes (3%) and all were classified as communicating. Only 120 patients had cranial imaging done and in this group the rate was 4.2%. In three cases hydrocephalus was present at admission, while two cases were diagnosed on days 44 and 99, respectively, due to altered mental status. The aetiology was either Eschericia coli (n = 2) or Streptococcus pneumoniae (n = 3). Case fatality was 60% among cases with hydrocephalus and 17% among other cases. Case fatality was similar irrespective of whether patients had a cranial CT or not. CONCLUSIONS: Hydrocephalus was diagnosed in 3% of adolescent and adult cases with CABM and had a high case fatality rate in spite of specialised medical care and neurosurgical interventions. Our findings are comparable with a recent Dutch national prospective study.

Bodilsen J; Schønheyder HC; Nielsen HI

2013-07-01

334

Hypertension Control in Community Health Centers Across China: Analysis of Antihypertensive Drug Treatment Patterns.  

UK PubMed Central (United Kingdom)

BACKGROUND: Blood pressure (BP) control in China is generally poor. It is assumed that an important cause of this unsatisfactory situation is the present standard of care provided by primary care physicians. METHODS: One thousand community health centers (CHCs) were selected across China based on geographical location, previous cooperative experience, and acceptance of an invitation to implement a standardized protocol of community-based BP management. Baseline information for each hypertensive patient under the care of these CHCs was collected, and the present pattern of hypertensive drug treatment was analyzed. RESULTS: Of all identified hypertensive patients (n = 249,830), 37% were treated with drugs. Characteristics linked with hypertension treatment included systolic BP, age, sex, region, smoking and alcohol consumption status, body mass index, comorbidities, and family history. The most frequently prescribed classes of antihypertensive drugs were diuretics (56.0%), followed by centrally active drugs (CADs) (38.3%), calcium channel blockers (CCBs) (36.8%), vasodilators (26.5%), and angiotensin-converting enzyme inhibitors (ACEIs) (23.3%). In regards to drug combination patterns, diuretics plus CADs was the most frequently used 2-drug combination (61.4%) and vasodilators plus CADs plus diuretics was the most frequently used 3-drug therapy (69.2%). Seventy-seven percent of patients on combination therapy were prescribed single pill combinations, 87.2% of which were composed of CADs and vasodilators and 12.8% of which were composed of ACEIs and diuretics. The control rates of patients on monotherapy and combination therapy were 27.7% and 24.1% (P < 0.05), respectively. CONCLUSIONS: Our study identified major shortcomings in the present status of antihypertensive pharmacotherapy in routine medical practice in China. It is essential to implement a program of professional education regarding the appropriate use of antihypertensive drugs.

Wang Z; Wang X; Chen Z; Wang W; Zhu H; Chen W; Zhu M; Hu S; Staessen JA; Liu L; Fodor JG

2013-10-01

335

ABC-VED Analysis of a Drug Store in the Department of Community Medicine of a Medical College in Delhi  

Science.gov (United States)

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.

Anand, T.; Ingle, G. K.; Kishore, J.; Kumar, R

2013-01-01

336

The Analysis of Sula’s Eccentricity in Character: Family and Community’s Influence on a Person’s Character  

Directory of Open Access Journals (Sweden)

Full Text Available Sula, the heroine in the second novel by Toni Morrison, has attracted the attention of many critics and readers. There are many discussions and reviews on Sula, especially on Sula’s character from every perspective. Based on the previous reviews, this paper mainly analyzes Sula’s eccentricity in character from the family and community’s influence in shaping a person’s character, which is of great help for readers to better understand Sula.  Key words: Sula;  Character;  Eccentricity

Guiqin AN

2011-01-01

337

Molecular analysis of the catechol-degrading bacterial community in a coal wasteland heavily contaminated with PAHs.  

UK PubMed Central (United Kingdom)

A PCR-based molecular tool was developed to estimate the diversity of the catechol-degrading bacterial community in a coal wasteland heavily contaminated with PAHS. A degenerate primer pair specific to catA sequences was designed by multiple alignment of known sequences coding a key intermediate of the beta-ketoadiapate pathway degrading catechol, namely catechol 1,2-dioxygenase. The specificity of this primer pair was assessed in 21 pure strains by PCR and sequencing. Comparison of the 16S rDNA and catA phylogenies revealed an absence of congruence between these two genes. The primer set was able to amplify catA sequences in DNA extracts from an industrial soil highly contaminated with heavy metals and polycyclic aromatic hydrocarbons (PAHs). RFLP screening of the catA library (95 clones) yielded 32 RFLP families. All of the 43 clone sequences obtained exhibited 86% identity on average to known CatA. Phylogenetic analysis revealed that these CatA sequences were related to Actinobacteria, alpha-, beta- and gamma-Proteobacteria phyla and confirmed the absence of congruence with 16S rDNA sequences, which implies horizontal gene transfer of the cat gene cluster between soil microbiota. Our results suggest that the diversity of the catA bacterial community is maintained in highly contaminated soil.

El Azhari N; Devers-Lamrani M; Chatagnier G; Rouard N; Martin-Laurent F

2010-05-01

338

The role of Streptococcus pneumoniae in community-acquired pneumonia among adults in Europe: a meta-analysis.  

UK PubMed Central (United Kingdom)

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.

Rozenbaum MH; Pechlivanoglou P; van der Werf TS; Lo-Ten-Foe JR; Postma MJ; Hak E

2013-03-01

339

Determinants of coverage in community-based therapeutic care programmes: towards a joint quantitative and qualitative analysis.  

Science.gov (United States)

One of the most important elements behind the success of Community-based Therapeutic Care (CTC) programmes for the treatment of severe acute malnutrition has been their ability to achieve high levels of coverage. In CTC, coverage is measured using the Centric System Area Sampling (CSAS) method, which provides accurate and reliable estimates of programme coverage as well as information on the primary reasons for non-attendance. Another important feature of CTC programmes is their use of socio-cultural assessments to determine potential barriers to access and to develop context-specific responses. By analysing data on non-attendance provided by CSAS surveys, in conjunction with data from socio-cultural assessments, it is possible to identify common factors responsible for failures in programme coverage. This paper focuses on an analysis of data from 12 CTC programmes across five African countries. It pinpoints three common factors (distance to sites, community awareness of the programme, and the way in which rejections are handled at the sites) that, together, account for approximately 75 per cent of non-attendance. PMID:20002705

Guerrero, Saúl; Myatt, Mark; Collins, Steve

2009-12-11

340

Evaluation and optimization of nucleic acid extraction methods for the molecular analysis of bacterial communities associated with corroded carbon steel.  

Science.gov (United States)

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. PMID:22500778

Marty, Florence; Ghiglione, Jean-François; Païssé, Sandrine; Gueuné, Hervé; Quillet, Laurent; van Loosdrecht, Mark C M; Muyzer, Gerard

2012-01-01

 
 
 
 
341

Evaluation and optimization of nucleic acid extraction methods for the molecular analysis of bacterial communities associated with corroded carbon steel.  

UK PubMed Central (United Kingdom)

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.

Marty F; Ghiglione JF; Païssé S; Gueuné H; Quillet L; van Loosdrecht MC; Muyzer G

2012-01-01

342

Distance learning students in “communities of practice” An analysis of nursing education offered in three different learning programmes.  

Directory of Open Access Journals (Sweden)

Full Text Available The purpose of this study was to understand the impact of the distance learning programme on learning processes in nursing education. It was the purpose to highlight the differences and similarities in the traditional nursing programme vs. the distance learning programme. Empirically, the article builds on a comparative study of two Danish nursing schools and three different nursing classes, including one based on the distance learning programme. The three different nursing classes cover the ways of studying in nursing education in Denmark. Observations were conducted with the classes as a whole. Interviews were conducted with 7 students from the distance learning programme, 6 from the traditional programme and 5 from the credit transfer class. The interpretative approach was selected to form the background of this study. The observation, as well as the interview guide was formed on the basis of Etienne Wengers theory: “Learning in communities of practice”. The analysis was based on concepts from the same theoretical background, as the observations and interviews. Findings from the study show that the distance-learning students have a selective and targeted way of engaging in communities of practice. Findings in relation to age, to being well prepared and feeling responsible for own learning, in relation to doing a self study and to knowledge forms, seem to have precise relevance for the differences between the ways of studying in nursing education.

Trine Ungermann Fredskild

2008-01-01