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1

Wakefield: Community and Library Analysis.  

Science.gov (United States)

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

Trumpeter, Margo C.; Donahue, Mary Ellen

2

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

3

Evolutionary conceptual analysis: faith community nursing.  

Science.gov (United States)

The aim of the study was to report an evolutionary concept analysis of faith community nursing (FCN). FCN is a source of healthcare delivery in the USA which has grown in comprehensiveness and complexity. With increasing healthcare cost and a focus on access and prevention, FCN has extended beyond the physical walls of the faith community building. Faith communities and healthcare organizations invest in FCN and standardized training programs exist. Using Rodgers' evolutionary analysis, the literature was examined for antecedents, attributes, and consequences of the concept. This design allows for understanding the historical and social nature of the concept and how it changes over time. A search of databases using the keywords FCN, faith community nurse, parish nursing, and parish nurse was done. The concept of FCN was explored using research and theoretical literature. A theoretical definition and model were developed with relevant implications. The search results netted a sample of 124 reports of research and theoretical articles from multiple disciplines: medicine, education, religion and philosophy, international health, and nursing. Theoretical definition: FCN is a method of healthcare delivery that is centered in a relationship between the nurse and client (client as person, family, group, or community). The relationship occurs in an iterative motion over time when the client seeks or is targeted for wholistic health care with the goal of optimal wholistic health functioning. Faith integrating is a continuous occurring attribute. Health promoting, disease managing, coordinating, empowering and accessing health care are other essential attributes. All essential attributes occur with intentionality in a faith community, home, health institution and other community settings with fluidity as part of a community, national, or global health initiative. A new theoretical definition and corresponding conceptual model of FCN provides a basis for future nursing knowledge and model-based applications for evidence-based practice and research. PMID:25097106

Ziebarth, Deborah

2014-12-01

4

Link Analysis for Communities Detection on Facebook  

CERN Document Server

Social networks have become a part in the daily life of millions of users, which offer wide range of interests and practices. The main characteristic of social networks is its ability to gather different individuals around a common point of view or collective beliefs. Among the current social networking sites, Facebook is the most popular, which has the highest number of users. However, in Facebook, the existence of communities (groups)is a critical question; thus, many researchers focus on potential communities by using techniques like data mining and web mining. In this work, we present four approaches based on link analysis techniques to detect prospective groups and their members

Mellah, Mohamed Adnane; Hamou, Reda Mohamed; Kumar, A V Senthil

2014-01-01

5

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.

Wang Kui

2005-08-01

6

Sparse Quadratic Discriminant Analysis and Community Bayes  

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We develop a class of rules spanning the range between quadratic discriminant analysis and naive Bayes, through a path of sparse graphical models. A group lasso penalty is used to introduce shrinkage and encourage a similar pattern of sparsity across precision matrices. It gives sparse estimates of interactions and produces interpretable models. Inspired by the connected-components structure of the estimated precision matrices, we propose the community Bayes model, which par...

Le, Ya; Hastie, Trevor

2014-01-01

7

Metagenomic analysis of microbial communities and beyond  

DEFF Research Database (Denmark)

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

Schreiber, Lars

2014-01-01

8

Community detection algorithms: A comparative analysis  

Science.gov (United States)

Uncovering the community structure exhibited by real networks is a crucial step toward 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 [Proc. Natl. Acad. Sci. U.S.A. 99, 7821 (2002)] and on random graphs. As a result of our analysis, three recent algorithms introduced by Rosvall and Bergstrom [Proc. Natl. Acad. Sci. U.S.A. 104, 7327 (2007); Proc. Natl. Acad. Sci. U.S.A. 105, 1118 (2008)], Blondel [J. Stat. Mech.: Theory Exp. (2008), P10008], and Ronhovde and Nussinov [Phys. Rev. E 80, 016109 (2009)] have an excellent performance, with the additional advantage of low computational complexity, which enables one to analyze large systems.

Lancichinetti, Andrea; Fortunato, Santo

2009-11-01

9

Policy analysis of Health Community Council of Siauliai city municipality  

Digital Repository Infrastructure Vision for European Research (DRIVER)

In the Master‘s Thesis, the principles of health policy development and implementation from Health Community Council of Siauliai city municipality are analyzed. In the theoretical part, analysis of the Health Community Councils activity of Lithuanian municipalities, the European Union and the Lithuanian health policy documents and their implementation in the community are investigated in a theoretical aspect. Data results on Health Community Council health policy activities and inter-agency...

Pec?iuke?nas, Edvinas

2014-01-01

10

ALTERNATIVE FUTURES ANALYSIS: A FRAMEWORK FOR COMMUNITY DECISION-MAKING  

Science.gov (United States)

Alternative futures analysis is an assessment approach designed to inform community decisions about land and water use. We conducted an alternative futures analysis in Oregon's Willamette River Basin. Three alternative future landscapes for the year 2050 were depicted and compare...

11

Soil analysis for the community garden  

Science.gov (United States)

Kevin Svitana, Otterbein University, Westerville, OH Summary Otterbein is in the process of developing a community garden on its newly opened Equestrian Science facility. This facility was a former industrial ...

Svitana, Kevin

12

Link Analysis for Communities Detection on Facebook  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Social networks have become a part in the daily life of millions of users, which offer wide range of interests and practices. The main characteristic of social networks is its ability to gather different individuals around a common point of view or collective beliefs. Among the current social networking sites, Facebook is the most popular, which has the highest number of users. However, in Facebook, the existence of communities (groups)is a critical question; thus, many rese...

Mellah, Mohamed Adnane; Amine, Abdelmalek; Hamou, Reda Mohamed; Kumar, A. V. Senthil

2014-01-01

13

Port Community Learning Needs: Analysis and Design  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The port industry is facing a dramatic wave of changes that have transformed the structure of theindustry. Modern seaports are increasingly shifting from a “hardware-based” approach towards “knowhow intensive” configuration. In this context knowledge resources, learning processes and training initiatives increasingly represent key elements to guarantee the quality of service supplied and hence the competitiveness of modern seaport communities. This paper describes the learning needs a...

Sweeney, Edward; Evangelista, Pietro

2006-01-01

14

Plant Communities Analysis of Selected Urban Flora of Islamabad  

Directory of Open Access Journals (Sweden)

Full Text Available Variation of plant community composition with environmental parameters (Elevation, pH, nutrients in soil etc. was presented with the aim of determining the relationship of vegetation with environmental parameters in an urban area. Vegetation patterns of an area of 4 km2 were studied between 1300-1800 m in the selected areas of Islamabad city. This area is relatively having wider open spaces and consequently more species diversity. Taking into consideration the importance of soil characters in determining a certain type of vegetation, soil analysis is given due importance. Cluster analysis showed the existence of two major communities with different dominants due to environmental factors acting upon it. Broussonetia papyrifera an invasive species and Dalbergia sissoo an indigenous species are dominantly separated in different communities. Canonical Correspondence Analysis (CCA showed that soil moisture content, electrical conductivity, pH, Elevation, Ca+ and heavy metals were the major edaphic factors correlated with species distribution.

Syeda Maria Ali

2006-01-01

15

Metatranscriptomic analysis of extremely halophilic viral communities.  

Science.gov (United States)

Hypersaline environments harbour the highest number of viruses reported for aquatic environments. In crystallizer ponds from solar salterns, haloviruses coexist with extremely halophilic Archaea and Bacteria and present a high diversity although little is known about their activity. In this work, we analyzed the viral expression in one crystallizer using a metatranscriptomic approach in which clones from a metaviromic library were immobilized in a microarray and used as probes against total mRNA extracted from the hypersaline community. This approach has two advantages: (i) it overcomes the fact that there is no straightforward, unambiguous way to extract viral mRNA from bulk mRNAs and (ii) it makes the sequencing of all mRNAs unnecessary. Transcriptomic data indicated that the halovirus assemblage was highly active at the time of sampling and the viral groups with the highest expression levels were those related to high GC content haloarchaea and Salinibacter representatives, which are minor components in the environment. Moreover, the changes in the viral expression pattern and in the numbers of free viral particles were analyzed after submitting the samples to two stress conditions: ultraviolet-radiation and dilution. Results showed that Archaea were more sensitive than Bacteria to these stress conditions. The overexpression in the predicted archaeal virus fraction raised and the total numbers of free viruses increased. Furthermore, we identified some very closely related viral clones, displaying single-nucleotide polymorphisms, which were expressed only under certain conditions. These clones could be part of very closely related virus genomes for which we propose the term 'ecoviriotypes'. PMID:21490689

Santos, Fernando; Moreno-Paz, Mercedes; Meseguer, Inmaculada; López, Cristina; Rosselló-Mora, Ramon; Parro, Víctor; Antón, Josefa

2011-10-01

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An Analysis of Interaction and Participation Patterns in Online Community  

Science.gov (United States)

This paper presents findings from the pattern of participation and discourse analysis of the online interaction among in-service teachers in the teacher training institute in Singapore. It was found that the teachers formed a knowledge-building community and jointly discussed issues related to integrating information technology into the classroom.…

Sing, Chai Ching; Khine, Myint Swe

2006-01-01

17

Correlation network analysis applied to complex biofilm communities.  

Science.gov (United States)

The complexity of the human microbiome makes it difficult to reveal organizational principles of the community and even more challenging to generate testable hypotheses. It has been suggested that in the gut microbiome species such as Bacteroides thetaiotaomicron are keystone in maintaining the stability and functional adaptability of the microbial community. In this study, we investigate the interspecies associations in a complex microbial biofilm applying systems biology principles. Using correlation network analysis we identified bacterial modules that represent important microbial associations within the oral community. We used dental plaque as a model community because of its high diversity and the well known species-species interactions that are common in the oral biofilm. We analyzed samples from healthy individuals as well as from patients with periodontitis, a polymicrobial disease. Using results obtained by checkerboard hybridization on cultivable bacteria we identified modules that correlated well with microbial complexes previously described. Furthermore, we extended our analysis using the Human Oral Microbe Identification Microarray (HOMIM), which includes a large number of bacterial species, among them uncultivated organisms present in the mouth. Two distinct microbial communities appeared in healthy individuals while there was one major type in disease. Bacterial modules in all communities did not overlap, indicating that bacteria were able to effectively re-associate with new partners depending on the environmental conditions. We then identified hubs that could act as keystone species in the bacterial modules. Based on those results we then cultured a not-yet-cultivated microorganism, Tannerella sp. OT286 (clone BU063). After two rounds of enrichment by a selected helper (Prevotella oris OT311) we obtained colonies of Tannerella sp. OT286 growing on blood agar plates. This system-level approach would open the possibility of manipulating microbial communities in a targeted fashion as well as associating certain bacterial modules to clinical traits (e.g.: obesity, Crohn's disease, periodontal disease, etc). PMID:22163302

Duran-Pinedo, Ana E; Paster, Bruce; Teles, Ricardo; Frias-Lopez, Jorge

2011-01-01

18

[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 Hucho taimen, Thymallus arcticus, 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

2006-01-01

19

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

20

A microbial community analysis of the octocoral Eunicea fusca  

Scientific Electronic Library Online (English)

Full Text Available SciELO Chile | Language: English Abstract in english While there is a significant and growing body of knowledge describing the microbial communities of marine invertebrates such as sponges, there are very few such studies focused on octocorals. The octocoral Eunicea fusca is common on reefs in various regions of the Caribbean and has been the subject [...] of natural product investigations. As part of an effort to describe the microbial community associated with octocorals, a culture-independent analysis of the bacterial community of E. fusca was conducted. Specifically, a 16S rDNA clone library analysis was performed to provide baseline data. A total of 40 bacteria members from 11 groups were found. In general, Proteobacteria were the dominant group with a total of 24 species and ?-Proteobacteria represented the highest percentage of bacteria associated with E. fusca (27.5%). Other prominent groups observed were Acidobacteria, Actinobacteria, Cyanobacteria, Planctomycetes, ?-Proteobacteria, Lentisphaerae and Nitrospirae. This is the first analysis of bacterial populations associated with the gorgonian E. fusca.

Angela, Duque-Alarcón; Lory Z, Santiago-Vázquez; Russell G, Kerr.

2012-09-15

 
 
 
 
21

Microarray-Based Analysis of Microbial Community RNAs by Whole-Community RNA Amplification?  

Digital Repository Infrastructure Vision for European Research (DRIVER)

A new approach, termed whole-community RNA amplification (WCRA), was developed to provide sufficient amounts of mRNAs from environmental samples for microarray analysis. This method employs fusion primers (six to nine random nucleotides with an attached T7 promoter) for the first-strand synthesis. The shortest primer (T7N6S) gave the best results in terms of the yield and representativeness of amplification. About 1,200- to 1,800-fold amplification was obtained with amounts of the RNA templat...

Gao, Haichun; Yang, Zamin K.; Gentry, Terry J.; Wu, Liyou; Schadt, Christopher W.; Zhou, Jizhong

2007-01-01

22

A Large-Scale Community Structure Analysis In Facebook  

CERN Document Server

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

23

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

According to the authors of this paper, mass tourism does not generate the development of local communities but rather their devitalization. This paper presents a cross-literature survey on community-based tourism and local community development. It proposes some links between these two approaches and asserts that community-based tourism can be a strategy to trigger local community development. It address the conditions under which the convergence of these two approaches may allow the launchi...

Parent, Sylvie; Klein, Juan-luis; Jolin, Louis

2009-01-01

24

An ecosystem analysis of the activated sludge microbial community.  

Science.gov (United States)

This study was undertaken (i) to investigate the interactions of the activated sludge microbial community in a chemostat with the "environment", such as the substrate composition and variations, (ii) to investigate how these interactions affect the quality of the treated effluent and (iii) to determine the limits or applicability conditions to the indicators and to the prediction potential of the treated effluent quality. This work presents (a) the experimental results obtained from a reactor fed municipal wastewater (Data Set2-DS2) concerning the reactor's operating conditions and the microbial community of the sludge (b) comparisons between DS2 and an older Data Set (DS1) obtained when the reactor was fed synthetic substrate, all other experimental conditions being identical, and (c) simulation results and sensitivity analyses of two model runs (R1 and R2, corresponding to DS1 and DS2). The first trophic level (P(1)) of the DS2 microbial community consisted of bacteria, the second trophic level (P(2)) of bacteria-eating protozoa, rotifers and nematodes and the third trophic level (P(3)) of carnivorous protozoa and arthropods. Rotifers were an important constituent of the DS2 microbial community. The DS1 and DS1 communities differed in total size, trophic level sizes and species composition. Correlations between the major microbial groups of DS2 community and either loading rates or effluent quality attributes were generally low, but the correlation of bacteria with SVI and ammonia in the effluent was better. Also, the ratio of rotifers to protozoa in P(2) was correlated to BOD in the effluent. The results of this work indicate that predictions of the treated effluent quality based only on protozoa may not be safe. Sensitivity analysis of R2 run indicate that, when variation in Y and K(d) biokinetic coefficients of the sludge are combined with fluctuations in composition and quality of municipal wastewater entering the reactor, then sufficient significant prediction of bacteria in the aeration tank is not possible. In order to avoid erroneous oversimplifications regarding phenomena taking place in the sludge and to understand "unexplained" process failures, more ecologically sound methods for studying wastewater treatment (WWT) processes are needed, since WWT are primarily ecosystems interacting with technological systems. PMID:20390906

Yiannakopoulou, Trissevyene V

2010-01-01

25

ANALYSIS OF AQUATIC MICROBIAL COMMUNITIES IMPACTED BY LARGE POULTRY FORMS  

Science.gov (United States)

Microbial communities often respond more rapidly and extensively to environmental change than communities of higher organisms. Thus, characterizing shifts in the structure of native bacterial communities as a response to changes in nutrients, antimicrobials, and invading pathogen...

26

Seasonal and Spatial Changes of Microorganism Communities in Constructed Wetlands: A Community Level Physiological Profiling Analysis  

Directory of Open Access Journals (Sweden)

Full Text Available In constructed wetlands, microorganisms associated with plants are assumed to play a major role. A one-year survey was conducted in five vertical flow constructed wetland systems that had been operating from 2 months to 8 years in small French villages (100–500 People Equivalent to provide a better understanding of microbiological activity. The objective of our study was to highlight the most important factor generating variability between microorganisms communities compared to treatment performances. Results of community level physiological profiling using Biolog Ecoplates were analyzed using principal component analysis. The greatest microbial activity was observed in the oldest wetland during summer. Profiles of fed and rest bed were differentiated by the nature of the main carbon source metabolized. Whereas carbohydrates and carboxylic acids appeared to be better assimilated with fed beds, it seemed that phosphate compounds as well as amines allowed better growth in the plates inoculated with samples of rest beds. In all fed beds, the most important parameters affecting the diversity were the season and the age of the wetlands. There were only slight profile differences between surface and subsurface samples and between the first and second stage samples.

Gérard Merlin

2010-01-01

27

Microbial community analysis in biotrickling filters treating isopropanol air emissions.  

Science.gov (United States)

The evolution of the microbial community was analysed over one year in two biotrickling filters operating under intermittent feeding conditions and treating isopropanol emissions, a pollutant typically found in the flexography sector. Each reactor was packed with one media: plastic cross-flow-structured material or polypropylene rings. The communities were monitored by fluorescence in situ hybridization (FISH) and denaturing gradient gel electrophoresis (DGGE) analysis of the 16S rRNA region. After inoculation with activated sludge, the biotrickling filters were operated using inlet loads (ILs) from 20 to 65 g C m(-3) h(-1) and empty-bed residence times (EBRTs) from 14 to 160 s. Removal efficiencies higher than 80% were obtained with ILs up to 35 g C m(-3) h(-1) working at EBRTs as low as 24 s. There was an increase in the total percentage of the target domains of up to around 80% at the end of the experiment. Specifically, the Gammaproteobacteria domain group, which includes the well-known volatile organic compound (VOC)-degrading species such as Pseudomonas putida, showed a noticeable rise in the two biotrickling filters of 26% and 27%, respectively. DGGE pattern band analysis revealed a stable band of Pseudomonas putida in all the samples monitored, even in the lower diversity communities. In addition, at similar operational conditions, the biotrickling filter with a greater relative abundance of Pseudomonas sp. (19.2% vs. 8%) showed higher removal efficiency (90% vs. 79%). Results indicate the importance of undertaking a further in-depth study of the involved species in the biofiltration process and their specific function. PMID:24527643

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

2013-01-01

28

Rapid fingerprinting of methanogenic communities by high-resolution melting analysis.  

Science.gov (United States)

Characterizing microbial community structure using molecular techniques is becoming a popular approach in studies of waste/wastewater treatment processes. A rapid and robust tool to analyze microbial communities is required for efficient process monitoring and control. In this study, a new community fingerprinting method based on high-resolution melting (HRM) analysis was developed and applied to compare methanogenic community structures of five different anaerobic digesters. The new method produced robust community clustering and ordination results comparable to the results from the commonly used denaturing gradient gel electrophoresis (DGGE) performed in parallel. This method transforms melting peak plots (MPs) of community DNA samples generated by HRM analysis to molecular fingerprints and estimates the relationships between the communities based on the fingerprints. The MP-based fingerprinting would provide a good alternative to monitor variations in microbial community structure especially when handling large sample numbers due to its high-throughput capacity and short analysis time. PMID:25443624

Kim, Jaai; Lee, Changsoo

2014-12-01

29

Co-correspondence analysis: a new ordination method to relate two community compositions  

Digital Repository Infrastructure Vision for European Research (DRIVER)

A new ordination method, called co-correspondence analysis, is developed to relate two types of communities (e.g., a plant community and an animal community) sampled at a common set of sites in a direct way. The method improves the simple, indirect approach of applying correspondence analysis (reciprocal averaging) to the separate species data sets and correlating the resulting ordination axes. Co-correspondence analysis maximizes the weighted covariance between weighted averaged species scor...

Braak, C. J. F.; Schaffers, A. P.

2004-01-01

30

Microbial community analysis of a full-scale DEMON bioreactor.  

Science.gov (United States)

Full-scale applications of autotrophic nitrogen removal technologies for the treatment of digested sludge liquor have proliferated during the last decade. Among these technologies, the aerobic/anoxic deammonification process (DEMON) is one of the major applied processes. This technology achieves nitrogen removal from wastewater through anammox metabolism inside a single bioreactor due to alternating cycles of aeration. To date, microbial community composition of full-scale DEMON bioreactors have never been reported. In this study, bacterial community structure of a full-scale DEMON bioreactor located at the Apeldoorn wastewater treatment plant was analyzed using pyrosequencing. This technique provided a higher-resolution study of the bacterial assemblage of the system compared to other techniques used in lab-scale DEMON bioreactors. Results showed that the DEMON bioreactor was a complex ecosystem where ammonium oxidizing bacteria, anammox bacteria and many other bacterial phylotypes coexist. The potential ecological role of all phylotypes found was discussed. Thus, metagenomic analysis through pyrosequencing offered new perspectives over the functioning of the DEMON bioreactor by exhaustive identification of microorganisms, which play a key role in the performance of bioreactors. In this way, pyrosequencing has been proven as a helpful tool for the in-depth investigation of the functioning of bioreactors at microbiological scale. PMID:25245398

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

2014-09-23

31

Bacterial community analysis of contaminant soils from Chernobyl  

International Nuclear Information System (INIS)

Complete text of publication follows: Shortly after the Chernobyl accident in 1986, vegetation, contaminated soil and other radioactive debris were buried in situ in trenches. The aims of this work are to analyse the structure of bacterial communities evolving in this environment since 20 years, and to evaluate the potential role of microorganisms in radionuclide migration in soils. Therefore, soil samples exhibiting contrasted radionuclides content were collected in and around the trench number 22. Bacterial communities were examined using a genetic fingerprinting method that allowed a comparative profiling of the samples (DGGE), with universal and group-specific PCR primers. Our results indicate that Chernobyl soil samples host a wide diversity of Bacteria, with stable patterns for Firmicutes and Actinobacteria and more variable for Proteobacteria. A collection of 650 aerobic and anaerobic culturable isolates was also constructed. A phylogenetic analysis of 250 heterotrophic aerobic isolates revealed that 5 phyla are represented: Beta-, Gamma-proteobacteria, Actinobacteria, Bacteroidetes and spore-forming Firmicutes, which is largely dominant. These collection will be screened for the presence of radionuclide-accumulating species in order to estimate the potential influence of microorganisms in radionuclides migration in soils

32

Analysis of Intestinal Bacterial Community Diversity of Adult Dastarcus helophoroides  

Science.gov (United States)

Polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE), and a culturedependent technique were used to study the diversity of the intestinal bacterial community in adult Dastarcus helophoroides (Fairmaire) (Coleoptera: Bothrideridae). Universal bacterial primers targeting 200 bp regions of the 16S rDNA gene were used in the PCR-DGGE assay, and 14 bright bands were obtained. The intestinal bacteria detected by PCR-DGGE were classified to Enterococcus (Lactobacillales: Enterococcaceae), Bacillus (Bacillales: Bacillaceae), Cellvibrio (Pseudomonadales: Pseudomonadaceae), Caulobacter (Caulobacterales: Caulobacteraceae), and uncultured bacteria, whereas those isolated by the culture-dependent technique belonged to Staphylococcus (Bacillales: Staphylococcaceae), Pectobacterium Enterobacteriales: Enterobacteriaceae), and Enterobacter (Enterobacteriales: Enterobacteriaceae). These intestinal bacteria represented the groups Lactobacillales (Enterococcus), Pseudomonadales (Cellvibrio), Caulobacterales (Caulobacter), Bacilli (Bacillus and Staphylococcus), and Gammaproteobacteria (Pectobacterium and Enterobacter). Our results demonstrated that PCR-DGGE analysis and the culture-dependent technique were useful in determining the intestinal bacteria of D. helophoroides and the two methods should be integrated to characterize the microbial community and diversity. PMID:25200108

Zhang, Z. Q.; He, C.; Li, M. L.

2014-01-01

33

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

34

An Analysis of Valencia Community College's Policy Response to Local Community Agencies' Need for Student Volunteers.  

Science.gov (United States)

A study was conducted at Valencia Community College (VCC) to evaluate VCC's success in meeting the community's need for volunteers, to determine the needs of student volunteers, and to discover what kinds of students were participating in the student volunteer program. Results of a questionnaire completed by 72 student volunteers indicated that…

Bennett, Lula M.

35

Finding Astronomical Communities Through Co-readership Analysis  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Whenever a large group of people are engaged in an activity, communities will form. The nature of these communities depends on the relationship considered. In the group of people who regularly use scholarly literature, a relationship like ``person i and person j have cited the same paper'' might reveal communities of people working in a particular field. On this poster, we will investigate the relationship ``person i and person j have read the same paper''. Using the data lo...

Henneken, Edwin A.; Kurtz, Michael J.; Eichhorn, Guenther; Accomazzi, Alberto; Grant, Carolyn S.; Thompson, Donna; Bohlen, Elizabeth; Murray, Stephen S.

2007-01-01

36

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

2012-12-01

37

Community Development in Israel and the Netherlands. A Comparative Analysis.  

Science.gov (United States)

This exploratory study seeks to analyze and compare the practice of community work in The Netherlands and Israel, and the key variables shaping its character, role, and influence. The two countries are small, highly urbanized welfare democracies relying on central government financing of community and social work, and are characterized by…

Kramer, Ralph M.

38

Community characteristics that attract physicians in Japan: a cross-sectional analysis of community demographic and economic factors  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background In many countries, there is a surplus of physicians in some communities and a shortage in others. Population size is known to be correlated with the number of physicians in a community, and is conventionally considered to represent the power of communities to attract physicians. However, associations between other demographic/economic variables and the number of physicians in a community have not been fully evaluated. This study seeks other parameters that correlate with the physician population and show which characteristics of a community determine its "attractiveness" to physicians. Methods Associations between the number of physicians and selected demographic/economic/life-related variables of all of Japan's 3132 municipalities were examined. In order to exclude the confounding effect of community size, correlations between the physician-to-population ratio and other variable-to-population ratios or variable-to-area ratios were evaluated with simple correlation and multiple regression analyses. The equity of physician distribution against each variable was evaluated by the orenz curve and Gini index. Results Among the 21 variables selected, the service industry workers-to-population ratio (0.543, commercial land price (0.527, sales of goods per person (0.472, and daytime population density (0.451 were better correlated with the physician-to-population ratio than was population density (0.409. Multiple regression analysis showed that the service industry worker-to-population ratio, the daytime population density, and the elderly rate were each independently correlated with the physician-to-population ratio (standardized regression coefficient 0.393, 0.355, 0.089 respectively; each p Conclusion Daytime population and service industry population in a municipality are better parameters of community attractiveness to physicians than population. Because attractiveness is supposed to consist of medical demand and the amenities of urban life, the two parameters may represent the amount of medical demand and/or the extent of urban amenities of the community more precisely than population does. The conventional demand-supply analysis based solely on population as the demand parameter may overestimate the inequity of the physician distribution among communities.

Toyokawa Satoshi

2009-02-01

39

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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...

Li, Zhixin; Xu, Jingzhen; Zhang, Lihua

2013-01-01

40

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

Science.gov (United States)

We describe our initial efforts at implementing social network analysis to visualize and quantify student interactions in Florida International University's Physics Learning Center. 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 FIU. Our implementation of a research and learning community, embedded within a course reform effort, has led to increased recruitment and retention of physics majors. Finn and Rock [1997] link the academic and social integration of students to increased rates of retention. To identify these interactions, we have initiated an investigation that utilizes social network analysis to identify primary community participants. Community interactions are then characterized through the network's density and connectivity, shedding light on learning communities and participation. Preliminary results, further research questions, and future directions utilizing social network analysis are presented.

Brewe, Eric; Kramer, Laird H.; O'Brien, George

2010-01-19

 
 
 
 
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Building the Community Online Resource for Statistical Seismicity Analysis (CORSSA)  

Science.gov (United States)

Statistical seismology is critical to the understanding of seismicity, the testing of proposed earthquake prediction and forecasting methods, and the assessment of seismic hazard. Unfortunately, despite its importance to seismology - especially to those aspects with great impact on public policy - statistical seismology is mostly ignored in the education of seismologists, and there is no central repository for the existing open-source software tools. To remedy these deficiencies, and with the broader goal to enhance the quality of statistical seismology research, we have begun building the Community Online Resource for Statistical Seismicity Analysis (CORSSA). CORSSA is a web-based educational platform that is authoritative, up-to-date, prominent, and user-friendly. We anticipate that the users of CORSSA will range from beginning graduate students to experienced researchers. More than 20 scientists from around the world met for a week in Zurich in May 2010 to kick-start the creation of CORSSA: the format and initial table of contents were defined; a governing structure was organized; and workshop participants began drafting articles. CORSSA materials are organized with respect to six themes, each containing between four and eight articles. The CORSSA web page, www.corssa.org, officially unveiled on September 6, 2010, debuts with an initial set of approximately 10 to 15 articles available online for viewing and commenting with additional articles to be added over the coming months. Each article will be peer-reviewed and will present a balanced discussion, including illustrative examples and code snippets. Topics in the initial set of articles will include: introductions to both CORSSA and statistical seismology, basic statistical tests and their role in seismology; understanding seismicity catalogs and their problems; basic techniques for modeling seismicity; and methods for testing earthquake predictability hypotheses. A special article will compare and review available statistical seismology software packages.

Michael, A. J.; Wiemer, S.; Zechar, J. D.; Hardebeck, J. L.; Naylor, M.; Zhuang, J.; Steacy, S.; Corssa Executive Committee

2010-12-01

42

CORSSA: Community Online Resource for Statistical Seismicity Analysis  

Science.gov (United States)

Statistical seismology is critical to the understanding of seismicity, the evaluation of proposed earthquake prediction and forecasting methods, and the assessment of seismic hazard. Unfortunately, despite its importance to seismology-especially to those aspects with great impact on public policy-statistical seismology is mostly ignored in the education of seismologists, and there is no central repository for the existing open-source software tools. To remedy these deficiencies, and with the broader goal to enhance the quality of statistical seismology research, we have begun building the Community Online Resource for Statistical Seismicity Analysis (CORSSA, www.corssa.org). We anticipate that the users of CORSSA will range from beginning graduate students to experienced researchers. More than 20 scientists from around the world met for a week in Zurich in May 2010 to kick-start the creation of CORSSA: the format and initial table of contents were defined; a governing structure was organized; and workshop participants began drafting articles. CORSSA materials are organized with respect to six themes, each will contain between four and eight articles. CORSSA now includes seven articles with an additional six in draft form along with forums for discussion, a glossary, and news about upcoming meetings, special issues, and recent papers. Each article is peer-reviewed and presents a balanced discussion, including illustrative examples and code snippets. Topics in the initial set of articles include: introductions to both CORSSA and statistical seismology, basic statistical tests and their role in seismology; understanding seismicity catalogs and their problems; basic techniques for modeling seismicity; and methods for testing earthquake predictability hypotheses. We have also begun curating a collection of statistical seismology software packages.

Zechar, J. D.; Hardebeck, J. L.; Michael, A. J.; Naylor, M.; Steacy, S.; Wiemer, S.; Zhuang, J.

2011-12-01

43

A Unified Community Detection, Visualization and Analysis method  

CERN Document Server

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

44

Impact analysis and community development needs at the salt site  

International Nuclear Information System (INIS)

The Office of Nuclear Waste Isolation (ONWI) has developed a socioeconomic program for a nuclear waste repository constructed in salt. The program is comprised of three elements: impact assessment, impact mitigation, and impact monitoring. The first element, impact assessment, is the focus of ONWI's current activities. Socioeconomic data has been collected for seven salt sites in Texas, Utah, Mississippi and Louisiana. Demographic, economic, community service, governmental and social structure information has been assembled into data base reports for each site area. These socioeconomic reports will be the basis for analyzing community-related impacts. Socioeconomic effects are currently being evaluated for the environmental assessment document required by the Nuclear Waste Policy Act. The approach to evaluating socioeconomic impacts for the environmental assessment impact includes developing the data base necessary for evaluation; assessing impacts of baseline population projected by the states; assessing project-related impacts through the use of an inmigration model and responding to socioeconomic issues raised in public meetings and hearings. The siting, construction, and operation of nuclear repositories will involve an extended period of time and an increased workforce, which can result in some impacts similar to those of other large development projects. The communities affected by a repository site will face increased demands for housing, community services (tremands for housing, community services (transportation, sewer and water, schools, etc.) and land, as well as a desire to maintain the community's ''character''. The management of this expansion and other related community impacts should be structured to meet community needs and goals. The management process should include the formation of an impact management comment, a public participation program, and a technical assistance program

45

Analysis of Computer Science Communities Based on DBLP  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

Biryukov, Maria; Dong, Cailing

2010-01-01

46

Fuzzy analysis of community detection in complex networks  

Science.gov (United States)

A snowball algorithm is proposed to find community structures in complex networks by introducing the definition of community core and some quantitative conditions. A community core is first constructed, and then its neighbors, satisfying the quantitative conditions, will be tied to this core until no node can be added. Subsequently, one by one, all communities in the network are obtained by repeating this process. The use of the local information in the proposed algorithm directly leads to the reduction of complexity. The algorithm runs in O(n+m) time for a general network and O(n) for a sparse network, where n is the number of vertices and m is the number of edges in a network. The algorithm fast produces the desired results when applied to search for communities in a benchmark and five classical real-world networks, which are widely used to test algorithms of community detection in the complex network. Furthermore, unlike existing methods, neither global modularity nor local modularity is utilized in the proposal. By converting the considered problem into a graph, the proposed algorithm can also be applied to solve other cluster problems in data mining.

Zhang, Dawei; Xie, Fuding; Zhang, Yong; Dong, Fangyan; Hirota, Kaoru

2010-11-01

47

FUTISTREFFIT : Participatory Action Research: analysis and evaluation of football as a community youth development tool  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Wesseh Cucu. Thesis: Futistreffit – analysis and evaluation. Language: English. Content: 53 pages, 2 appendices. Degree: Bachelor of Social Services. Focus: Community Development. Institution: Diaconia University of Applied Sciences, Järvenpää The aim of this research is to examine football as a positive youth development tool for Learning-Integration. It focuses on community youth work and uses action research as the prime method of analysis and evaluation. The subject of re...

Wesseh, Cucu

2012-01-01

48

Analysis of Computer Science Communities Based on DBLP  

CERN Document Server

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

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

2010-01-01

49

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

50

High-resolution melt analysis for rapid comparison of bacterial community compositions.  

Science.gov (United States)

In the study of bacterial community composition, 16S rRNA gene amplicon sequencing is today among the preferred methods of analysis. The cost of nucleotide sequence analysis, including requisite computational and bioinformatic steps, however, takes up a large part of many research budgets. High-resolution melt (HRM) analysis is the study of the melt behavior of specific PCR products. Here we describe a novel high-throughput approach in which we used HRM analysis targeting the 16S rRNA gene to rapidly screen multiple complex samples for differences in bacterial community composition. We hypothesized that HRM analysis of amplified 16S rRNA genes from a soil ecosystem could be used as a screening tool to identify changes in bacterial community structure. This hypothesis was tested using a soil microcosm setup exposed to a total of six treatments representing different combinations of pesticide and fertilization treatments. The HRM analysis identified a shift in the bacterial community composition in two of the treatments, both including the soil fumigant Basamid GR. These results were confirmed with both denaturing gradient gel electrophoresis (DGGE) analysis and 454-based 16S rRNA gene amplicon sequencing. HRM analysis was shown to be a fast, high-throughput technique that can serve as an effective alternative to gel-based screening methods to monitor microbial community composition. PMID:24610853

Hjelmsø, Mathis Hjort; Hansen, Lars Hestbjerg; Baelum, Jacob; Feld, Louise; Holben, William E; Jacobsen, Carsten Suhr

2014-06-01

51

Finding Astronomical Communities Through Co-readership Analysis  

Science.gov (United States)

Whenever a large group of people are engaged in an activity, communities will form. The nature of these communities depends on the relationship considered. In the group of people who regularly use scholarly literature, a relationship like "person i and person j have cited the same paper" might reveal communities of people working in a particular field. On this poster, we will investigate the relationship "person i and person j have read the same paper". Using the data logs of the NASA/Smithsonian Astrophysics Data System (ADS), we first determine the population that will participate by requiring that a user queries the ADS at a certain rate. Next, we apply the relationship to this population. The result of this will be an abstract "relationship space", which we will describe in terms of various "representations". Examples of such "representations" are the projection of coread vectors onto Principal Components and the spectral density of the coread network. We will show that the coread relationship results in structure, we will describe this structure and we will provide a first attempt in the classification of this structure in terms of astronomical communities.

Henneken, Edwin A.; Kurtz, M. J.; Eichhorn, G.; Accomazzi, A.; Grant, C.; Thompson, D.; Bohlen, E.; Murray, S. S.

2006-12-01

52

Molecular Analysis of Endolithic Microbial Communities in Volcanic Glasses  

Science.gov (United States)

Terrestrial and marine volcanic glasses become mineralogically and chemically altered, and in many cases this alteration has been attributed to microbial activity. We have used molecular techniques to study the resident microbial communities from three different volcanic environments that may be responsible for this crustal alteration. Total microbial DNA was extracted from rhyolite glass of the 7 million year old Rattlesnake Tuff in eastern Oregon. The DNA was amplified using the polymerase chain reaction (PCR) with bacterial primers targeting the 16S rRNA gene. This 16S rDNA was cloned and screened with restriction fragment length polymorphism (RFLP). Out of 89 total clones screened, 46 belonged to 13 different clone families containing two or more members, while 43 clones were unique. Sequences of eight clones representing the most dominant clone families in the library were 92 to 97% similar to soil bacterial species. In a separate study, young pillow basalts (PCR. Repeated attempts with different primer sets yielded no bacterial genes, whereas archaeal genes were quite abundant. A genetic fingerprinting technique, terminal restriction fragment length polymorphism (T-RFLP), was used to compare the archaeal community compositions among the six different basalts. Filtered deep-sea water samples (~15 L) were examined in parallel to identify any overlap between rock- and seawater-associated archaea. The six rock community profiles were quite similar to each other, and the background water communities were also similar, respectively. Both the rock and water communities shared the same dominant peak. To identify the T-RFLP peaks corresponding to the individual members of the rock and seawater communities, clone libraries of the archaeal 16S rDNA for one basalt sample (Dive 3718) and its corresponding background water sample were constructed. The most abundant archaeal genes were closely related to uncultured Group I marine Crenarchaeota that have been previously identified from similar deep-sea habitats. These archaeal genes collectively correspond to the dominant T-RFLP peak present in both the rock and water samples. In a third study, we investigated the microbial community residing in a Hawaiian Scientific Drilling Program core collected near Hilo, Hawaii. Total microbial DNA was extracted from a depth of 1351 m in the drill core (ambient temperature in the drill hole ~16°C), where petrographic evidence suggested the presence of microbial alteration. Archaeal 16S rRNA genes were amplified, cloned, and twelve clones representing the most abundant groups were sequenced. Eleven out of the twelve clones were 97 to 99% similar to Group I marine Crenarchaeota, while the remaining clone was 95% similar to Euryarchaeota, based on BLAST searches of the GenBank database. Our community-level approach to studying microbes living in volcanic glasses has provided a greater understanding of the microbial communities that potentially alter these materials.

di Meo, C. A.; Giovannoni, S.; Fisk, M.

2002-12-01

53

Plant Communities Analysis of Selected Urban Flora of Islamabad  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Variation of plant community composition with environmental parameters (Elevation, pH, nutrients in soil etc.) was presented with the aim of determining the relationship of vegetation with environmental parameters in an urban area. Vegetation patterns of an area of 4 km2 were studied between 1300-1800 m in the selected areas of Islamabad city. This area is relatively having wider open spaces and consequently more species diversity. Taking into consideration the importance of soil c...

Syeda Maria Ali; Shamim Kauser

2006-01-01

54

Analysis of Intestinal Bacterial Community Diversity of Adult Dastarcus helophoroides  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE), and a culturedependent technique were used to study the diversity of the intestinal bacterial community in adult Dastarcus helophoroides (Fairmaire) (Coleoptera: Bothrideridae). Universal bacterial primers targeting 200 bp regions of the 16S rDNA gene were used in the PCR-DGGE assay, and 14 bright bands were obtained. The intestinal bacteria detected by PCR-DGGE were classified to Enterococcus (Lactobacillales: Ente...

Zhang, Z. Q.; He, C.; Li, M. L.

2014-01-01

55

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

Directory of Open Access Journals (Sweden)

Full Text Available 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 o f observations, interviews and document analysis. Purposive sampling and later theoretical sampling was used for selecting interviewees. This resulted in a total o f 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 o f 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 underresourced 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 o f the programmes.

Gloria Mtshali

2005-09-01

56

Benthic diatoms in the Gulf of Bothnia : Community analysis and diversity  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Benthic diatoms are valuable tools for biological monitoring and paleo-ecological reconstruction of past environmental conditions. This thesis aims at describing size-related properties of benthic diatoms and suggests that data assessment for community analysis can be improved by considering the importance of scale. It investigates which environmental factors structure epilithic diatom communities on the coast of the Gulf of Bothnia and identifies environmental factors correlated with phytobe...

Busse, Svenja

2002-01-01

57

Molecular analysis of the microbial community structures in water-flooding petroleum reservoirs with different temperatures  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Temperature is one of the most important environmental factors regulating the activity and determining the composition of the microbial community. Analysis of microbial communities from six water-flooding petroleum reservoirs at temperatures from 20 to 63 °C by 16S rRNA gene clone libraries indicates the presence of physiologically diverse and temperature-dependent microorganisms in these subterrestrial ecosystems. In high-temperature petroleum reservoirs, most of the archaeal ...

-y Wang, L.; -y Duan, R.; -f Liu, J.; -z Yang, S.; -d Gu, J.; -z Mu, B.

2012-01-01

58

Bacterial community analysis of activated sludge: an evaluation of four commonly used DNA extraction methods  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The effectiveness of three commercially available direct DNA isolation kits (Mobio, Fast, Qiagen) and one published direct DNA extraction protocol (Bead) for extracting bacterial DNA from different types of activated sludge was investigated and mutually compared. The DNA quantity and purity were determined using real-time PCR targeting the bacterial 16S rDNA gene. Microbial community fingerprints were assessed by automated ribosomal intergenic spacer analysis. The resulting community profiles...

Vanysacker, L.; Declerck, S. A. J.; Hellemans, B.; Meester, L.; Vankelecom, I.; Declerck, P.

2010-01-01

59

Community Violence, Protective Factors, and Adolescent Mental Health: A Profile Analysis  

Digital Repository Infrastructure Vision for European Research (DRIVER)

This study examined interrelationships among community violence exposure, protective factors, and mental health in a sample of urban, predominantly African American adolescents (N = 504). Latent Profile Analysis was conducted to identify profiles of adolescents based on a combination of community violence exposure, self-worth, parental monitoring, and parental involvement and to examine whether these profiles differentially predict adolescents' depressive symptoms and aggressive behavior. Thr...

Copeland-linder, Nikeea; Lambert, Sharon F.; Ialongo, Nicholas S.

2010-01-01

60

Investigation and analysis of microbiological communities in natural Ophiocordyceps sinensis.  

Science.gov (United States)

Ophiocordyceps sinensis is a fungus that parasitizes caterpillars, and more than 30 species of filamentous fungi have been isolated from its fruiting body. However, its microbiological diversity remains unclear. Based on the clone library and quantitative PCR techniques, the bacterial flora and mycobiota of 3 different samples (larva, stromata/sclerotia, and surface soil) from natural O. sinensis specimens were investigated using primer sets that targeted the 16S rRNA gene and internal transcribed spacer region of ribosomal DNA. The results showed that the abundance of bacterial and fungal communities in the soil attached to the surface of O. sinensis was (6.4 ± 1.4) × 10(6) and (6.0 ± 0.3) × 10(7) copies/g dry matter, respectively, which was the highest compared with that in the larva and stromal samples. The main groups of bacteria in the O. sinensis samples were Proteobacteria and Actinobacteria, while Ascomycota was the most dominant fungal group in the 3 samples. At the genus level, Geomyces, Phoma, and Trichocladium were the dominant genera in the larval sample, while Geomyces and Cladosporium were the dominant genera in the stromal sample. In conclusion, a great number of bacterial and fungal species were present in naturally occurring O. sinensis specimens, and there was a high diversity of bacterial and fungal communities. These findings contribute to the understanding of the bacterial and fungal community structure of this valuable medicinal fungus and lay the foundation for the future discovery of new medicinal microorganism resources. PMID:25578897

Xia, Fei; Liu, Yan; Shen, Guang-Rong; Guo, Lian-Xian; Zhou, Xuan-Wei

2015-02-01

 
 
 
 
61

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

CERN Document Server

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

Brewe, Eric; Sawtelle, Vashti

2011-01-01

62

Learning for Social Justice: A Cultural Historical Activity Theory Analysis of Community Leadership Empowerment in a Korean American Community Organization  

Science.gov (United States)

Community organizations, especially those aiming at social change, play a significant role in establishing societal health and contributing to adult learning in daily communities. Their existence secures marginalized groups' involvement in society and enhances community development by building community leadership with multiple stakeholders…

Kim, Junghwan

2012-01-01

63

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

Science.gov (United States)

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

Schofield, Dee

64

agriGO: a GO analysis toolkit for the agricultural community  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Gene Ontology (GO), the de facto standard in gene functionality description, is used widely in functional annotation and enrichment analysis. Here, we introduce agriGO, an integrated web-based GO analysis toolkit for the agricultural community, using the advantages of our previous GO enrichment tool (EasyGO), to meet analysis demands from new technologies and research objectives. EasyGO is valuable for its proficiency, and has proved useful in uncovering biological knowledge in massive data s...

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

2010-01-01

65

Analysis of prescriptions dispensed at community pharmacies in Nablus, Palestine.  

Science.gov (United States)

We investigated the prescription quality and prescribing trends of private clinicians in Nablus governorate, Palestine. A total of 363 prescriptions were collected from a random sample of 36 community pharmacies over a study period of 288 working hours. Data regarding elements in the prescription and the types of drugs prescribed were analysed. Physician-related variables were mostly noted, however, patient's address and weight were absent in all prescriptions and less than half included age and sex. Information regarding strength of the medications prescribed was missing in over 70% of prescriptions. Other drug-related variables like frequency and instruction of use were present in over 80% of prescriptions. Antimicrobial agents were the most commonly prescribed followed by NSAIDs/analgesics. Amoxicillin alone or in combination was the most commonly prescribed antimicrobial agents followed by cefuroxime. Prescription writing quality in Nablus is deficient in certain aspects and improvement is required. PMID:20799538

Sawalha, A F; Sweileh, W M; Zyoud, S H; Al-Jabi, S W; Shamseh, F F Bni; Odah, A

2010-07-01

66

An aetiological analysis of erythema nodosum in a community hospital  

Directory of Open Access Journals (Sweden)

Full Text Available Erythema nodosum (EN is a reaction pattern in the skin characterized by septal panniculitis. Infectious diseases are most common cause of EN. This study was aimed to find out the most common causes for EN as seen in a community hospital over a period of two years. Fifteen patients with EN were subjected to detailed clinical and laboratory investigations to establish the etiology. Immuno - fluorescence and PCR for Mycobacterium tuberculosis were performed in relevant patients. Seven cases were diagnosed to be secondary to tuberculosis that was confirmed by a complete resolution of the lesions after a full course of anti TB chemotherapy. In one patient, the EN was drug induced, two were due to polyarteritis nodosa, one was due to SLE, one was due to streptococcal infection, and three were idiopathic in aetiology. Though the number of patients is small, it still establishes the fact that tuberculosis continues to be the most common cause of EN.

Sarveswari K

2001-11-01

67

[Analysis on leaf forms in Quercus mongolica community].  

Science.gov (United States)

Leaf-size classes of 337 vascular plants in Quercus mongolica community in northeast, China were analyzed according to Raunkiaer system. The dominant type was microphyll which percentage is 45.4%, followed by compound leaf (23.1%), mesophyll (22.6%), nanophyll (6.8%), macrophyll (0.9%), aphyllous (0.9%), leptophyll (0.3%). The leaves edges of 337 plants were investigated and the percentage of entire leaves plants is 22.3%. Leaf-size classes spectra of trees, shrubs and herbs were figured out. The mesophyll ratio in trees was higher than that in shrubs and herbs. The mesophyll ratio in shrubs was the lowest. Different sites had different leaf-size classes spectra. Microphyll also was the dominant type in every site. No significant relationships were found between leaf-size classes spectra and latitude and altitude. PMID:12722461

Yu, Shunli; Ma, Keping; Chen, Lingzhi

2003-01-01

68

Temporal dynamics of bird community composition: an analysis of baseline conditions from long-term data.  

Science.gov (United States)

Numerous anthropogenic activities threaten the biodiversity found on earth. Because all ecological communities constantly experience temporal turnover due to natural processes, it is important to distinguish between change due to anthropogenic impact and the underlying natural rate of change. In this study, we used data sets on breeding bird communities that covered at least 20 consecutive years, from a variety of terrestrial ecosystems, to address two main questions. (1) How fast does the composition of bird communities change over time, and can we identify a baseline of natural change that distinguishes primeval systems from systems experiencing varying degrees of human impact? (2) How do patterns of temporal variation in composition vary among bird communities in ecosystems with different anthropogenic impacts? Time lag analysis (TLA) showed a pattern of increasing rate of temporal compositional change from large-scale primeval systems to disturbed and protected systems to distinctly successional systems. TLA slopes of natural turnover, while communities subjected to anthropogenic impact were characterised by TLA slopes of >0.04. Most of the temporal variability of breeding bird communities was explained by slow changes occurring over decades, regardless of the intensity of human impact. In most of the time series, medium- and short-wave periodicity was not detected, with the exception of breeding bird communities subjected to periodic pulses (e.g. caterpillar outbreaks causing food resource peaks). PMID:24929348

Kampichler, Christian; Angeler, David G; Holmes, Richard T; Leito, Aivar; Svensson, Sören; van der Jeugd, Henk P; Weso?owski, Tomasz

2014-08-01

69

Simulation and Strategy Analysis of the Eco-community Planning by Using of Computer Software Programs  

Directory of Open Access Journals (Sweden)

Full Text Available In order to improve the living comfort level of the low-income groups, and the belonging of the affordable housing community residents, the research group take Nanyang green community housing design as the research object, using the computer software for community planning phase of the thermal environment, wind environment, light environment for simulation analysis. The result showed the micro-climate, thermal environment, and adjusting the temperature of the district as well which is the affordable housing community worthy of promotion of green building technologies for small and medium-sized cities. It also provides the reference for the similar project planning in the process of ventilation, lighting, shading, such as green design strategy research.

Zhao Jingxin

2013-01-01

70

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

2012-01-01

71

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

Science.gov (United States)

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

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

2014-07-01

72

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

Science.gov (United States)

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

Simon, Merril A.; Tovar, Esau

2004-01-01

73

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

74

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

2012-09-01

75

Spectral methods for the detection of network community structure: a comparative analysis  

International Nuclear Information System (INIS)

Spectral analysis has been successfully applied to the detection of community structure of networks, respectively being based on the adjacency matrix, the standard Laplacian matrix, the normalized Laplacian matrix, the modularity matrix, the correlation matrix and several other variants of these matrices. However, the comparison between these spectral methods is less reported. More importantly, it is still unclear which matrix is more appropriate for the detection of community structure. This paper answers the question by evaluating the effectiveness of these five matrices against benchmark networks with heterogeneous distributions of node degree and community size. Test results demonstrate that the normalized Laplacian matrix and the correlation matrix significantly outperform the other three matrices at identifying the community structure of networks. This indicates that it is crucial to take into account the heterogeneous distribution of node degree when using spectral analysis for the detection of community structure. In addition, to our surprise, the modularity matrix exhibits very similar performance to the adjacency matrix, which indicates that the modularity matrix does not gain benefits from using the configuration model as a reference network with the consideration of the node degree heterogeneity

76

SAPAC: a SBF analysis pipeline for the astronomical community  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Large volumes of CCD imaging data that will become available from wide-field cameras at telescopes such as the CFHT, SUBARU, VST, or VISTA in the near future are highly suitable for systematic distance surveys of early-type galaxies using the Surface Brightness Fluctuation (SBF) method. For the efficient processing of such large data sets, we are developing the first semi-automatic SBF analysis pipeline named SAPAC. After a brief description of the SBF method we discuss the ...

Dunn, Laura P.; Jerjen, Helmut

2005-01-01

77

Preservation of Estuarine Sediments for Lipid Analysis of Biomass and Community Structure of Microbiota  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Various methods were tested for preserving estuarine sediments in the field before biochemical analysis of the microbiota. Total microbial biomass was determined as lipid phosphate (LP), and the fatty acids of the microbial lipids were used as indicators of community structure. Control samples were sieved to remove macroinvertebrates and plant materials and were extracted immediately in the field. Other samples were preserved both before and after sieving and stored for 5 days before analysis...

Federle, Thomas W.; White, David C.

1982-01-01

78

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

Energy Technology Data Exchange (ETDEWEB)

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

1978-03-22

79

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

DEFF Research Database (Denmark)

A mainstream viewpoint on sensitivity analysis in the wastewater modelling community is that it is a first-order differential analysis of outputs with respect to the parameters – typically obtained by perturbing one parameter at a time with a small factor. An alternative viewpoint on sensitivity analysis is related to uncertainty analysis, which attempts to relate the total uncertainty in the outputs to the uncertainty in the inputs. In this paper we evaluate and discuss two such sensitivity analysis methods for two different purposes/case studies: (i) Applying sensitivity analysis to a plant design (BSM1 plant layout) using Standardized Regression Coefficients (SRC) and (ii) Applying sensitivity analysis to help fine-tuning a fuzzy controller for a BNPR plant using Morris Screening. The results obtained from each case study are then critically discussed in view of practical applications of sensitivity analysis in day-to-day engineering projects.

Sin, Gürkan; Ruano, M.V.

2010-01-01

80

Spatial analysis of tuberculosis in four main ethnic communities in Taiwan during 2005 to 2009  

Directory of Open Access Journals (Sweden)

Full Text Available The aim of the present study was to assess spatial features of tuberculosis prevalence and their relationships with four main ethnic communities in Taiwan. Methods of spatial analysis were clustering pattern determination (such as global version of Moran’s test and local version of Gi*(d statistic, using logistic regression calculations to identify spatial distributions over a contiguous five years and identify significant similarities, discriminant analysis to classify variables, and geographically weighted regression (GWR to determine the strength of relationships between tuberculosis prevalence and ethnic variables in spatial features. Tuberculosis demonstrated decreasing trends in prevalence in both genders during 2005 to 2009. All results of the global Moran’s tests indicated spatial heterogeneity and clusters in the plain and mountainous Aboriginal townships. The Gi*(d statistic calculated z-score outcomes, categorized as clusters or non-clusters, at at 5% significance level. According to the stepwise Wilks’ lambda discriminant analysis, in the Aborigines and Hoklo communities townships with clusters of tuberculosis cases differentiated from townships without cluster cases, to a greater extent than in the other communities. In the GWR models, the explanatory variables demonstrated significant and positive signs of parameter estimates in clusters occurring in plain and mountainous aboriginal townships. The explanatory variables of both the Hoklo and Hakka communities demonstrated significant, but negative, signs of parameter estimates. The Mainlander community did not significantly associate with cluster patterns of tuberculosis in Taiwan. Results indicated that locations of high tuberculosis prevalence closely related to areas containing higher proportions of the Aboriginal community in Taiwan. This information is relevant for assessment of spatial risk factors, which, in turn, can facilitate the planning of the most advantageous types of health care policies, and implementation of effective health care services.

Pui-Jen Tsai

2011-11-01

 
 
 
 
81

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

2013-06-01

82

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.

Scheffler Brian E

2010-11-01

83

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.

Wang Xiaohang

2006-08-01

84

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

85

Community paediatrics moves on-an analysis of changing work patterns 1994-97.  

Science.gov (United States)

Objectives: To describe the current clinical workload of the modern community paediatrician; to outline the changes in this role over recent years and examine the reasons for these. Design and setting: The design is a retrospective analysis of data routinely collected for contracting purposes. Nottingham community paediatric service 1994-97 is the setting. Main outcome measures: These are the characteristics of patients seen, sources of referral, locations of clinical contact, referral rates by area. Results: 36 710 appointments were offered over the time period studied. The non-attendance rate was 17%. Pre-school children made up the largest group seen. Most referrals were from health visitors (23%) and school nurses (29%). There has been a small but significant increase in the numbers of children seen who have developmental problems and disability, and due to child protection issues between the time periods. There has been a shift in the proportions of children seen in a local health centre referral clinic (9.8% increase during 1994-97) rather than in a school setting. Twice as many children are referred to the community paediatrician from inner city areas than from the surrounding county areas. Conclusion: The transfer of child health surveillance to the primary health care team and the increased training of community paediatricians, has resulted in community paediatricians developing an increasingly specialised role particularly in the areas of child growth and development, disability, social and behavioural paediatrics. Public Health (2000) 114, 61-64. PMID:10800147

Blair; Pullan; Rands; Crown

2000-01-01

86

Data Management and Analysis in Support of Community Climate Science (Invited)  

Science.gov (United States)

An insightful analysis in climate science depends critically on the choices of software tools to discover, access, manipulate, and visualize the often large and unwieldy data sets of interest. These data exploration tasks can be complex and time-consuming, and they frequently involve many resources spread throughout the modeling and observational climate communities. The inability to find data, large data set sizes, lack of adequate metadata, poor documentation, and lack of sufficient computational and diagnostic/visualization resources serve to impede climate researchers from using the climate data already available. My talk will cover access and analysis of climate modeling, observation, and measurements data through the use of the Earth System Grid Federation (ESGF) and the Ultra-scale Visualization Climate Data Analysis Tools (UV-CDAT). Currently, the ESGF is supporting many multi-model and observational assessments by archiving multiple petabytes of data for community use. ESGF is a distributed federated system expressly designed to provide climate researchers worldwide with access to data, information, models, analysis tools, and computational resources for large-scale assessments. Among its many data holdings, it contains and disseminates the Coupled Model Intercomparison Project (CMIP) data sets used for the Intergovernmental Panel on Climate Change (IPCC) assessment reports. The Ultra-scale Visualization Climate Data Analysis Tools (UV-CDAT), in combination with ESGF, provides an end-to-end solution for data management, analysis, and visualization. Extreme value analysis plotting using an array of DV3D visualization techniques.

Williams, D. N.

2013-12-01

87

Does social media users’ commenting behavior differ by their local community tie? A computer–assisted linguistic analysis approach  

Digital Repository Infrastructure Vision for European Research (DRIVER)

This study is an exploratory attempt to use automatic linguistic analysis for understanding social media users’ news commenting behavior. The study addresses geographically–based dynamics in human–computer interaction, namely, users’ tie to a geographic community. Specifically, the study reveals that commenting behavior differs between users of different levels of local community tie. Comments by local users, those with higher level of local community tie, exhibit different linguistic...

Xu, Weiai Wayne Department Of Communication At The University At Buffalo; Li, Liangyue Department Of Electrical And Computer Engineering At Northeastern University In Boston; Stefanone, Michael A. Department Of Communication At The University At Buffalo; Fu, Yun Assistant Professor And Founding Director Of The Smile Lab In The Department Of Electrical And Computer Engineering At Northeastern University At Boston

2013-01-01

88

Phylogenetic analysis of the microbial community in hypersaline petroleum produced water from the Campos Basin.  

Science.gov (United States)

In this work the archaea and eubacteria community of a hypersaline produced water from the Campos Basin that had been transported and discharged to an onshore storage facility was evaluated by 16S recombinant RNA (rRNA) gene sequence analysis. The produced water had a hypersaline salt content of 10 (w/v), had a carbon oxygen demand (COD) of 4,300 mg/l and contains phenol and other aromatic compounds. The high salt and COD content and the presence of toxic phenolic compounds present a problem for conventional discharge to open seawater. In previous studies, we demonstrated that the COD and phenolic content could be largely removed under aerobic conditions, without dilution, by either addition of phenol degrading Haloarchaea or the addition of nutrients alone. In this study our goal was to characterize the microbial community to gain further insight into the persistence of reservoir community members in the produced water and the potential for bioremediation of COD and toxic contaminants. Members of the archaea community were consistent with previously identified communities from mesothermic reservoirs. All identified archaea were located within the phylum Euryarchaeota, with 98 % being identified as methanogens while 2 % could not be affiliated with any known genus. Of the identified archaea, 37 % were identified as members of the strictly carbon-dioxide-reducing genus Methanoplanus and 59 % as members of the acetoclastic genus Methanosaeta. No Haloarchaea were detected, consistent with the need to add these organisms for COD and aromatic removal. Marinobacter and Halomonas dominated the eubacterial community. The presence of these genera is consistent with the ability to stimulate COD and aromatic removal with nutrient addition. In addition, anaerobic members of the phyla Thermotogae, Firmicutes, and unclassified eubacteria were identified and may represent reservoir organisms associated with the conversion hydrocarbons to methane. PMID:24920265

Piubeli, Francine; Grossman, Matthew J; Fantinatti-Garboggini, Fabiana; Durrant, Lucia R

2014-10-01

89

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

90

Assessment of microbial community structure changes by amplified ribosomal DNA restriction analysis (ARDRA)  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Amplified ribosomal DNA restriction analysis (ARDRA) is a simple method based on restriction endonuclease digestion of the amplified bacterial 16S rDNA. In this study we have evaluated the suitability of this method to detect differences in activated sludge bacterial communities fed on domestic or industrial wastewater, and subject to different operational conditions. The ability of ARDRA to detect these differences has been tested in modified Ludzack-Ettinger (MLE) configurations. Samples fr...

Gich Batlle, Frederic; Amer Maistriau, Estefania; Abella? Ametller, Carles; Balaguer I Condom, Maria Dolors; Poch, Manuel

2000-01-01

91

An empirical analysis of the demand for health using the European Community Household Panel  

Digital Repository Infrastructure Vision for European Research (DRIVER)

This paper estimates demand for health equations using three waves of data from the European Community Household Panel. The economic model is a typical specification of Grossman's [1] proposal. The paper focuses on three specific points: i) the existence of two stages in the demand for health decision process (to contact a physician and how often to visit him). ii) the analysis of this double-hurdle process in different scenarios (visits to the general practitioners, the specialists and the d...

Jime?nez-marti?n, Sergi; Labeaga, Jose? M.; Marti?nez-granado, Maite

2000-01-01

92

Sputum gram's stain in community-acquired pneumococcal pneumonia. A meta-analysis.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The usefulness of the sputum Gram's stain is controversial. This meta-analysis was designed to evaluate the sensitivity and specificity of the sputum Gram's stain in community-acquired pneumococcal pneumonia. Using a predetermined protocol, articles were discovered through a MEDLINE search (1966 to 1993) and the examination of bibliographies and were graded for quality by three blinded reviewers. Information on the reference standard, blinding, stain interpreter, control for antibiotic use, a...

Reed, W. W.; Byrd, G. S.; Gates, R. H.; Howard, R. S.; Weaver, M. J.

1996-01-01

93

Meta-analysis: Epidemiology of Non-cardiac Chest Pain in the Community  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Abstract Background: Prevalence of, and risk factors for, non-cardiac chest pain in the community have not been well studied. Aims: To conduct a systematic review and meta-analysis to examine these issues. Methods: MEDLINE, EMBASE, and EMBASE Classic were searched (up to March 2011) to identify population-based studies reporting prevalence of non-cardiac chest pain in adults (?15 years) according to self-report, questionnaire, or specific symptom-based criteria. Prevalence...

Ford, Alexander; Suares, Nicole C.; Talley, Nicholas J.

2011-01-01

94

Transcriptome Fingerprinting Analysis: An Approach to Explore Gene Expression Patterns in Marine Microbial Communities  

Science.gov (United States)

Microbial transcriptomics are providing new insights into the functional processes of microbial communities. However, analysis of each sample is still expensive and time consuming. A rapid and low cost method that would allow the identification of the most interesting samples for posterior in-depth metatranscriptomics analysis would be extremely useful. Here we present Transcriptome Fingerprinting Analysis (TFA) as an approach to fulfill this objective in microbial ecology studies. We have adapted the differential display technique for mRNA fingerprinting based on the PCR amplification of expressed transcripts to interrogate natural microbial eukaryotic communities. Unlike other techniques, TFA does not require prior knowledge of the mRNA sequences to be detected. We have used a set of arbitrary primers coupled with a fluorescence labeled primer targeting the poly(A) tail of the eukaryotic mRNA, with further detection of the resulting labeled cDNA products in an automated genetic analyzer. The output represented by electropherogram peak patterns allowed the comparison of a set of genes expressed at the time of sampling. TFA has been optimized by testing the sensitivity of the method for different initial RNA amounts, and the repeatability of the gene expression patterns with increasing time after sampling both with cultures and environmental samples. Results show that TFA is a promising approach to explore the dynamics of gene expression patterns in microbial communities. PMID:21857972

Coll-Lladó, Montserrat; Acinas, Silvia G.; Pujades, Cristina; Pedrós-Alió, Carlos

2011-01-01

95

Prediction of symptomatic depression by discriminant analysis in Japanese community-dwelling elderly.  

Science.gov (United States)

Although a number of studies have examined depression risk factors for elderly persons, little attention has been paid to the prediction of individuals at risk. This study constructed a predictive model for discrimination between individuals at a higher risk of depression and normal subjects in Japanese community-dwelling elderly persons, using linear discriminant analysis. Data were collected from 754 non-institutionalized elderly men and women aged 65 years and older living in the community in Japan, using face-to-face interviews in 2002. Stepwise linear discrimination analysis was used to construct a predictive model to select individuals who have a higher risk of depression. The stepwise discriminant analysis selected the five predictor variables (frequent hearing problems, poor appetite, less financial leeway, low emotional support and less subjective usefulness) and yielded a statistically significant function (?=0.816; ?2=113.0, df=5, p<0.001). This function showed that the rate of correct prediction was 78.2% for depressed. The calculated discriminate function based on the above five predictor variables (hearing problem, less appetite, less financial leeway, low emotional support and less subjective usefulness) is useful for detecting individuals at high risk of depression and preventing its development among community-dwelling elderly persons. Prospective studies are needed to confirm the validity and feasibility of the model for earlier screening for depression among such people. PMID:20399517

Okamoto, Kazushi; Harasawa, Yuko

2011-01-01

96

A Community Analysis and Service Development Plan for the Reference Department, Stark County District Library, Canton, Ohio.  

Science.gov (United States)

Goals of this analysis of the community and its library users in Canton, Ohio, were to: (1) examine the community served and not served by the district reference department; (2) examine types of services provided for users by the department; (3) design a service policy; (4) make recommendations for service improvements; and (5) formulate action…

Yankus, Constance Opipare; Yankus, Anthony G.

97

Molecular analysis of the bacterial communities in crude oil samples from two brazilian offshore petroleum platforms.  

Science.gov (United States)

Crude oil samples with high- and low-water content from two offshore platforms (PA and PB) in Campos Basin, Brazil, were assessed for bacterial communities by 16S rRNA gene-based clone libraries. RDP Classifier was used to analyze a total of 156 clones within four libraries obtained from two platforms. The clone sequences were mainly affiliated with Gammaproteobacteria (78.2% of the total clones); however, clones associated with Betaproteobacteria (10.9%), Alphaproteobacteria (9%), and Firmicutes (1.9%) were also identified. Pseudomonadaceae was the most common family affiliated with these clone sequences. The sequences were further analyzed by MOTHUR, yielding 81 operational taxonomic units (OTUs) grouped at 97% stringency. Richness estimators also calculated by MOTHUR indicated that oil samples with high-water content were the most diverse. Comparison of bacterial communities present in these four samples using LIBSHUFF and Principal Component Analysis (PCA) indicated that the water content significantly influenced the community structure only of crude oil obtained from PA. Differences between PA and PB libraries were observed, suggesting the importance of the oil field as a driver of community composition in this habitat. PMID:22319534

Korenblum, Elisa; Souza, Diogo Bastos; Penna, Monica; Seldin, Lucy

2012-01-01

98

Phylogenetic Analysis of the Hyperthermophilic Pink Filament Community in Octopus Spring, Yellowstone National Park  

Science.gov (United States)

This journal article reports the molecular phylogenetic approach used to analyze a microbial community associated with the 84 to 88 degrees C outflow from Octopus Spring. The authors perform techniques such as microscopy, DNA extraction and amplification, cloning and sequence analysis of 16S rRNA genes, phylogenetic analysis, and in situ hybridization to determine the limited phylogenetic diversity of the pink filaments including hydrogen-oxidizing bacteria. Located in PubMed, this article contains a link to a printable PDF version.

Pace, Norman R.; Reysenbach, Anna-Louise; Wickham, Gene S.

2010-02-19

99

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

Science.gov (United States)

This study presents descriptive statistics and community analysis of adult biting midges trapped at 16 livestock farms by means of light traps on Zealand and Lolland-Falster, Denmark. A total of 9,047 male and female Culicoides divided into 24 species, were caught. Biotic and abiotic factors ranging from presence of different host species (cattle or sheep/goats), presence of small woody areas or wetlands in the surrounding landscape, and agricultural practice (organic or conventional) were included in the community analysis. Only differences in the Culicoides communities between conventional and organic practices were tested significantly different. Total numbers of Culicoides individuals were higher on the organic farms than on the conventional farms. The larger loads of biting midges on the organic farms may be due to free-ranging animals that attracted the midges on pastures and carried them to the stable environment (the cattle of the conventional farms were held inside the stables). Presence of deciduous trees within 500 m of the farms resulted in higher numbers of Culicoides obsoletus s.s., while presence of wetlands increased the numbers of Culicoides punctatus and Culicoides pulicaris. Furthermore, Culicoides riethi and Culicoides puncticollis (subgenus Monoculicoides) were recorded in high numbers on individual farms. C. puncticollis was found for the first time in Denmark and so far only recorded from Zealand. PMID:25326377

Nielsen, S A; Banta, G; Rasmussen, A-M; Skovgård, H

2014-12-01

100

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

Science.gov (United States)

Acid rock drainage (ARD) originating from the Yasumi-ishi tunnel near the main tunnel of the Yanahara mine in Japan was characterized to be moderately acidic (pH 4.1) and contained iron at a low concentration (51?mg/L). The composition of the microbial community was determined by sequence analysis of 16S rRNA genes using PCR and denaturing gradient gel electrophoresis. The analysis of the obtained sequences showed their similarity to clones recently detected in other moderately acidic mine drainages. Uncultured bacteria related to Ferrovum- and Gallionella-like clones were dominant in the microbial community. Analyses using specific primers for acidophilic iron- or sulfur-oxidizing bacteria, Acidithiobacillus ferrooxidans, Leptospirillum spp., Acidithiobacillus caldus, Acidithiobacillus thiooxidans, and Sulfobacillus spp. revealed the absence of these bacteria in the microbial community in ARD from the Yasumi-ishi tunnel. Clones affiliated with a member of the order Thermoplasmatales were detected as the dominant archaea in the ARD microbial population. PMID:25229870

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

2014-01-01

 
 
 
 
101

Molecular analysis of the microbial community structures in water-flooding petroleum reservoirs with different temperatures  

Directory of Open Access Journals (Sweden)

Full Text Available Temperature is one of the most important environmental factors regulating the activity and determining the composition of the microbial community. Analysis of microbial communities from six water-flooding petroleum reservoirs at temperatures from 20 to 63 °C by 16S rRNA gene clone libraries indicates the presence of physiologically diverse and temperature-dependent microorganisms in these subterrestrial ecosystems. In high-temperature petroleum reservoirs, most of the archaeal sequences belong to the thermophilic archaea including the genera Thermococcus, Methanothermobacter and Thermoplasmatales, most of the bacterial sequences belong to the phyla Firmicutes, Thermotogae and Thermodesulfobacteria; in low-temperature petroleum reservoirs, most of the archaeal sequences are affiliated with the genera Methanobacterium, Methanoculleus and Methanocalculus, most of the bacterial sequences to the phyla Proteobacteria, Bacteroidetes and Actinobacteria. Canonical correspondence analysis (CCA revealed that temperature, mineralization, ionic type as well as volatile fatty acids showed correlation with the microbial community structures. These organisms may be adapted to the environmental conditions of these petroleum reservoirs over geologic time by metabolizing buried organic matter from the original deep subsurface environment and became the common inhabitants in subsurface environments.

L.-Y. Wang

2012-04-01

102

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

DEFF Research Database (Denmark)

This study presents descriptive statistics and community analysis of adult biting midges trapped at 16 livestock farms by means of light traps on Zealand and Lolland-Falster, Denmark. A total of 9,047 male and female Culicoides divided into 24 species, were caught. Biotic and abiotic factors ranging from presence of different host species (cattle or sheep/goats), presence of small woody areas or wetlands in the surrounding landscape, and agricultural practice (organic or conventional) were included in the community analysis. Only differences in the Culicoides communities between conventional and organic practices were tested significantly different. Total numbers of Culicoides individuals were higher on the organic farms than on the conventional farms. The larger loads of biting midges on the organic farms may be due to free-ranging animals that attracted the midges on pastures and carried them to the stable environment (the cattle of the conventional farms were held inside the stables). Presence of deciduoustrees within 500 m of the farms resulted in higher numbers of Culicoides obsoletus s.s., while presence of wetlands increased the numbers of Culicoides punctatus and Culicoides pulicaris. Furthermore, Culicoides riethi and Culicoides puncticollis (subgenus Monoculicoides) were recorded in high numbers on individual farms. C. puncticollis was found for the first time in Denmark and so far only recorded from Zealand.

Nielsen, SØren Achim; Banta, Gary Thomas

2014-01-01

103

On the Analysis of a Label Propagation Algorithm for Community Detection  

CERN Document Server

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

104

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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 analysi...

Koichi Fujie; Hiroyuki Daimon; Yoichi Atsuta; Muhammad Hanif

2012-01-01

105

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

Science.gov (United States)

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

Gilgour, Joseph G.

2012-01-01

106

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

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: English Abstract in portuguese 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 su [...] stentabilidade na produção de alimentos. Apresenta-se uma comparação com outras metodologias de PO soft e relatam-se alguns resultados e ações. Abstract in english 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 comp [...] arison is made with other soft Operations Research (OR) methodologies and first actions and results are reported.

Anderson Amendoeira, Namen; Cláudio Thomás, Bornstein; Jonathan, Rosenhead.

2010-08-01

107

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

108

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

2010-08-01

109

High-Throughput Metagenomic Technologies for Complex Microbial Community Analysis: Open and Closed Formats  

Science.gov (United States)

ABSTRACT?  Understanding the structure, functions, activities and dynamics of microbial communities in natural environments is one of the grand challenges of 21st century science. To address this challenge, over the past decade, numerous technologies have been developed for interrogating microbial communities, of which some are amenable to exploratory work (e.g., high-throughput sequencing and phenotypic screening) and others depend on reference genes or genomes (e.g., phylogenetic and functional gene arrays). Here, we provide a critical review and synthesis of the most commonly applied “open-format” and “closed-format” detection technologies. We discuss their characteristics, advantages, and disadvantages within the context of environmental applications and focus on analysis of complex microbial systems, such as those in soils, in which diversity is high and reference genomes are few. In addition, we discuss crucial issues and considerations associated with applying complementary high-throughput molecular technologies to address important ecological questions. PMID:25626903

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

2015-01-01

110

Comparative analysis of the intestinal bacterial communities in different species of carp by pyrosequencing.  

Science.gov (United States)

Gut microbiota is increasingly regarded as an integral component of the host, due to important roles in the modulation of the immune system, the proliferation of the intestinal epithelium and the regulation of the dietary energy intake. Understanding the factors that influence the composition of these microbial communities is essential to health management, and the application to aquatic animals still requires basic investigation. In this study, we compared the bacterial communities harboured in the intestines and in the rearing water of grass carp (Ctenopharyngodon idellus), crucian carp (Carassius cuvieri), and bighead carp (Hypophthalmichthys nobilis), by using 454-pyrosequencing with barcoded primers targeting the V4 to V5 regions of the bacterial 16S rRNA gene. The specimens of the three species were cohabiting in the same pond. Between 6,218 and 10,220 effective sequences were read from each sample, resulting in a total of 110,398 sequences for 13 samples from gut microbiota and pond water. In general, the microbial communities of the three carps were dominated by Fusobacteria, Firmicutes, Proteobacteria and Bacteroidetes, but the abundance of each phylum was significantly different between species. At the genus level, the overwhelming group was Cetobacterium (97.29?±?0.46 %) in crucian carp, while its abundance averaged c. 40 and 60 % of the sequences read in the other two species. There was higher microbial diversity in the gut of filter-feeding bighead carp than the gut of the two other species, with grazing feeding habits. The composition of intestine microbiota of grass carp and crucian carp shared higher similarity when compared with bighead carp. The principal coordinates analysis (PCoA) with the weighted UniFrac distance and the heatmap analysis suggested that gut microbiota was not a simple reflection of the microbial community in the local habitat but resulted from species-specific selective pressures, possibly dependent on behavioural, immune and metabolic characteristics. PMID:25145494

Li, Tongtong; Long, Meng; Gatesoupe, François-Joël; Zhang, Qianqian; Li, Aihua; Gong, Xiaoning

2015-01-01

111

Metagenome analysis of a complex community reveals the metabolic blueprint of anammox bacterium ‘Candidatus Jettenia asiatica’  

Directory of Open Access Journals (Sweden)

Full Text Available Anammox bacteria are key players in the global nitrogen cycle and responsible for up to 50% of global nitrogen loss. Because of their cost effective application in anaerobic nitrogen removal, the anammox bacteria are widely implemented in wastewater treatment. Currently, five genera of anammox bacteria have been identified, together forming a deep branching order in the Planctomycetes-Verrucomicrobium- Chlamydiae (PVC superphylum. Members of all genera have been detected in wastewater treatment plants, but metagenomic information is not yet available for all genera. Here we report the metagenomic analysis of an enrichment dominated by ‘Candidatus Jettenia asiatica’. The whole microbial community o\tf a granular sludge anammox reactor was sequenced using both illumina and 454 pyrosequencing. The sludge was previously shown to have a ~50% enrichment of the anammox bacterium ‘Candidatus Jettenia asiatica’ by 16S rRNA gene analysis. 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 cd1-type nitrite reductase NirS that is responsible for the nitrite reduction of ‘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, methane producing microorganisms and denitrifying methanotroph 'Ca. Methylomirabilis oxyfera'.

ZiyeHu

2012-10-01

112

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.

Tyson Gene W

2007-10-01

113

Analysis of nanoplankton community structure using flow sorting and molecular techniques.  

Science.gov (United States)

We developed a method for the separate and simultaneous analysis of the community structure of heterotrophic nanopkankton (HNP) and autotrophic nanoplankton (ANP). This method consists of three steps. First, nanoplankton cells were concentrated using a cross-flow filtration system because cell densities in natural seawater are usually too low for genetic studies. Second, HNP and ANP were separated by flow cytometric sorting ("flow sorting") on the basis of the presence or absence of chlorophyll. Finally, the community structure was analyzed using denaturing gradient gel electrophoresis targeting 18S rRNA gene. The newly developed method was applied to the coastal surface water of Aburatsubo Inlet, Japan, in July 2008. The separation of nanoplankton into HNP and ANP was validated by phylogenetic analysis, and the trophic mode of uncultured nanoplankton was confirmed (e.g. Marine Alveolata group II [MALV II] and Marine Stramenopile clade-2 [MAST-2]). This new method involving cell concentration, flow sorting and phylogenetic analysis is a potentially powerful tool for evaluating the population dynamics and ecology of marine protozoa. PMID:21566389

Yoshida, Noriaki; Nishimura, Masahiko; Inoue, Katsuyuki; Yoshizawa, Susumu; Kamiya, Eriko; Taniguchi, Akito; Hamasaki, Koji; Kogure, Kazuhiro

2009-01-01

114

PIXE analysis of hair samples from artisanal mining communities in the Acupan region, Benguet, Philippines  

International Nuclear Information System (INIS)

The mountainous regions of Benguet Province in the Philippines is home to some 10,000 small-scale miners who make out a living by extracting gold. In these communities, the method of extraction still involves the use of mercury, via amalgamation. In the separation of gold from mercury the method involves the release of mercury vapor into the atmosphere. This is therefore expected to affect the people living in the nearby areas. This study involves the accumulation of baseline data on the extent of mercury contamination in humans through the analysis of their hair. In 1989, Hursh et al. [Arch. Environ. Health 44 (2) (1989) 120] studied human volunteers and found that uptake of mercury vapor through the skin is only about 1% of the uptake through inhalation [World Health Organization, IPCS, EHC118, Inorganic Mercury, Geneva, 1991, p. 42]. In this light, any residual mercury which might have deposited in human hair is speculated to give an indication of how much mercury vapor the subject could have actually inhaled. A high concentration of mercury in the sample can therefore be indicative of the high rate of intake of the mercury vapor through inhalation. A sampling of the community consisted of both male (83%) and female (17%) subjects who ranged in age from 8 to 66 years old. Hair analysis was done using particle induced X-ray emission at the Iwate Medical University through Dr. Sera. With Zn set as a standard element, the rest of the elements were determined using the of the elements were determined using the standard-free method. In order to obtain the conversion coefficient for hair samples, many hair samples were analyzed by this method and the internal standard method which involves the preparation of the hair samples by chemical ashing. The results obtained were comparable. The PIXE results for these samples showed the analysis of 26 elements but for our purposes, however, only the mercury analysis will be considered. Results of the analysis showed the hair samples to contain 0-27 ppm, with only seven of the 70 respondents showing no traces of mercury, while nine had levels beyond the 5 ppm limit set by the Human Biomonitor II [Bundesgesundheitsblatt 39 (1996) 221]. Further studies using PIXE analysis of hair is recommended on the same communities with a wider area base to show that PIXE analysis on hair samples as an alternative procedure which is faster without sacrificing reliability

115

Contaminants reduce the richness and evenness of marine communities: A review and meta-analysis  

International Nuclear Information System (INIS)

Biodiversity of marine ecosystems is integral to their stability and function and is threatened by anthropogenic processes. We conducted a literature review and meta-analysis of 216 studies to understand the effects of common contaminants upon diversity in various marine communities. The most common diversity measures were species richness, the Shannon-Wiener index (H') and Pielou evenness (J). Largest effect sizes were observed for species richness, which tended to be the most sensitive index. Pollution was associated with marine communities containing fewer species or taxa than their pristine counterparts. Marine habitats did not vary in their susceptibility to contamination, rather a ?40% reduction in richness occurred across all habitats. No class of contaminant was associated with significantly greater impacts on diversity than any other. Survey studies identified larger effects than laboratory or field experiments. Anthropogenic contamination is strongly associated with reductions in the species richness and evenness of marine habitats. - Contamination substantially reduces the biodiversity of marine communities in all major habitat types and across all major contaminant classes.

116

Optimization of preservation and processing of sea anemones for microbial community analysis using molecular tools.  

Science.gov (United States)

For several years, knowledge on the microbiome associated with marine invertebrates was impaired by the challenges associated with the characterization of bacterial communities. With the advent of culture independent molecular tools it is possible to gain new insights on the diversity and richness of microorganisms associated with marine invertebrates. In the present study, we evaluated if different preservation and processing methodologies (prior to DNA extraction) can affect the bacterial diversity retrieved from snakelocks anemone Anemonia viridis. Denaturing gradient gel electrophoresis (DGGE) community fingerprints were used as proxy to determine the bacterial diversity retrieved (H'). Statistical analyses indicated that preservation significantly affects H'. The best approach to preserve and process A. viridis biomass for bacterial community fingerprint analysis was flash freezing in liquid nitrogen (preservation) followed by the use of a mechanical homogenizer (process), as it consistently yielded higher H'. Alternatively, biomass samples can be processed fresh followed by cell lyses using a mechanical homogenizer or mortar &pestle. The suitability of employing these two alternative procedures was further reinforced by the quantification of the 16S rRNA gene; no significant differences were recorded when comparing these two approaches and the use of liquid nitrogen followed by processing with a mechanical homogenizer. PMID:25384534

Rocha, Joana; Coelho, Francisco J R C; Peixe, Luísa; Gomes, Newton C M; Calado, Ricardo

2014-01-01

117

A retrospective analysis of a community-based health program in Papua New Guinea.  

Science.gov (United States)

The Women and Children's Health Project was a large Australian funded aid Project that sought to improve the health of women and children in Papua New Guinea between 1998 and 2004. Community development and health promotion interventions aimed to increase community support for attended birth and children's health. Green and Kreuter's [Green, L. W. and Kreuter, M. W. (2005) Health Program Planning: An Educational and Ecological Approach, 4th edition. McGraw-Hill, New York] precede-proceed model of health program planning was applied retrospectively to critique the design, implementation and evaluation of the Project. An outcome evaluation (2006) provided data for this analysis and investigated long-term impact using a multi-methods approach. Application of the precede-proceed model was useful, but the model fails to sufficiently well identify 'inhibiting factors' as part of the educational and ecological assessment during the planning phase. Pre-defined objectives and contractually obligated outputs in a donor funded business model negatively influenced Project activity and outcomes. Despite this and the challenging context for implementation, Project interventions improved interaction between the community and health systems, and improved use of maternal child health services. PMID:19342392

Ashwell, Helen Elizabeth Scott; Barclay, Lesley

2009-06-01

118

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

Science.gov (United States)

High-throughput sequencing and analysis of microbial community cDNA (metatranscriptomics) are providing valuable insight into in situ microbial activity and metabolism in the oceans. A critical first step in metatranscriptomic studies is the preparation of high-quality cDNA. At the minimum, preparing cDNA for sequencing involves steps of biomass collection, RNA preservation, total RNA extraction, and cDNA synthesis. Each of these steps may present unique challenges for marine microbial samples, particularly for deep-sea samples whose transcriptional profiles may change between water collection and RNA preservation. Because bacterioplankton community RNA yields may be relatively low (RNA to obtain sufficient cDNA for downstream sequencing. Additionally, depending on the nature of the samples, budgetary considerations, and the choice of sequencing technology, steps may be required to deplete the amount of ribosomal RNA (rRNA) transcripts in a sample in order to maximize mRNA recovery. cDNA preparation may also involve the addition of internal RNA standards to biomass samples, thereby allowing for absolute quantification of transcript abundance following sequencing. This chapter describes a general protocol for cDNA preparation from planktonic microbial communities, from RNA preservation to final cDNA synthesis, with specific emphasis placed on topics of sampling bias and rRNA depletion. Consideration of these topics is critical for helping standardize metatranscriptomics methods as they become widespread in marine microbiology research. PMID:24060122

Stewart, Frank J

2013-01-01

119

Context based Expert Finding in Online Communities using Social Network Analysis  

Directory of Open Access Journals (Sweden)

Full Text Available Nowadays, online communities are one of the most popular collaborative environments in the Internet where people are free to express their opinions. These communities provide facilities for knowledge sharing in which, people can share their experience with each other. The main problem regarding to the knowledge sharing on online communities is the wide range of information on them without any mechanism to determine their validity. So, for knowledge seekers, it is important to recognize the expertise of each member based on contexts to find the best answers among all replies to his question. Although, lots of researches have been conducted so far to determine the level of people’s expertise, none of them has had context based approach to the problem. In this research a novel method based on social network analysis is proposed to find the experts in different contexts. For evaluation process of the proposed method, Metafilter Forum was chosen and the data has been processed in several steps. First, data were gathered by our crawling program and then extracted, transformed and loaded to data base by ETL operations. Then, experts on specified context were found by applying the proposed method on the processed data. Finally, accuracy of the method was calculated and compared with other methods.

Mojtaba Behzadi

2012-01-01

120

Contaminants reduce the richness and evenness of marine communities: A review and meta-analysis  

Energy Technology Data Exchange (ETDEWEB)

Biodiversity of marine ecosystems is integral to their stability and function and is threatened by anthropogenic processes. We conducted a literature review and meta-analysis of 216 studies to understand the effects of common contaminants upon diversity in various marine communities. The most common diversity measures were species richness, the Shannon-Wiener index (H') and Pielou evenness (J). Largest effect sizes were observed for species richness, which tended to be the most sensitive index. Pollution was associated with marine communities containing fewer species or taxa than their pristine counterparts. Marine habitats did not vary in their susceptibility to contamination, rather a approx40% reduction in richness occurred across all habitats. No class of contaminant was associated with significantly greater impacts on diversity than any other. Survey studies identified larger effects than laboratory or field experiments. Anthropogenic contamination is strongly associated with reductions in the species richness and evenness of marine habitats. - Contamination substantially reduces the biodiversity of marine communities in all major habitat types and across all major contaminant classes.

Johnston, Emma L., E-mail: e.johnston@unsw.edu.a [Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales 2052 (Australia); Roberts, David A. [Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales 2052 (Australia)

2009-06-15

 
 
 
 
121

Design and Analysis of the Community Youth Development Study Longitudinal Cohort Sample  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Communities That Care (CTC) is a prevention system designed to reduce adolescent substance use and delinquency through the selection of effective preventive interventions tailored to a community’s specific profile of risk and protection. A community-randomized trial of CTC, the Community Youth Development Study, is currently being conducted in 24 communities across the United States. This paper describes the rationale, multilevel analyses, and baseline comparability for the study’s longit...

Brown, Eric C.; Graham, John W.; Hawkins, J. David; Arthur, Michael W.; Baldwin, Megan M.; Oesterle, Sabrina; Briney, John S.; Catalano, Richard F.; Abbott, Robert D.

2009-01-01

122

[Correlation analysis on the damage of Mikania micrantha to plant communities in Neilingdind Island of Guandong Province, China].  

Science.gov (United States)

The analysis showed that 58 species of trees, short-trees and shrubs in Neilingding Island of Guangdong Province were damaged by M. micrantha, of which, woody trees accounted for 67%. Short-trees and sunny shrubs were damaged most seriously, followed by the communities with low canopy density consisted of only 2 dominant species, and those with high canopy density consisted of 5 or 6 dominant species. The coverage of M. micrantha mainly related to the vertical structure of plant communities. The taller the community height and the more the synusia, the lesser was the coverage of M. micrantha. The damaging ratio mainly related to species diversity and community density. The higher the species diversity and community density, the lower the damaging ratio was. The damaging degree mainly related to the coverage of other liana. The more the coverage of other liana, the higher was the damaging degree of M. micrantha. PMID:15852937

Zhou, Xianye; Wang, Bosun; Li, Mingguang; Liao, Wenbo; Zhou, Yunlong; Zan, Qijie; Wang, Yongjun

2005-02-01

123

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.

Parmanto Bambang

2008-06-01

124

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

DEFF Research Database (Denmark)

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 healthin 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, Thilde; Thanh Xuan, Le Thi

2012-01-01

125

Applying Social Network Analysis to Analyze a Web-Based Community  

Directory of Open Access Journals (Sweden)

Full Text Available this paper deals with a very renowned website (that is Book-Crossing from two angles: The first angle focuses on the direct relations between users and books. Many things can be inferred from this part of analysis such as who is more interested in book reading than others and why? Which books are most popular and which users are most active and why? The task requires the use of certain social network analysis measures (e.g. degree centrality. What does it mean when two users like the same book? Is it the same when other two users have one thousand books in common? Who is more likely to be a friend of whom and why? Are there specific people in the community who are more qualified to establish large circles of social relations? These questions (and of course others were answered through the other part of the analysis, which will take us to probe the potential social relations between users in this community. Although these relationships do not exist explicitly, they can be inferred with the help of affiliation network analysis and techniques such as m-slice. Book-Crossing dataset, which covered four weeks of users' activities during 2004, has always been the focus of investigation for researchers interested in discovering patterns of users' preferences in order to offer the most possible accurate recommendations. However; the implicit social relationships among users that emerge (when putting users in groups based on similarity in book preferences did not gain the same amount of attention. This could be due to the importance recommender systems attain these days (as compared to other research fields as a result to the rapid spread of e-commerce websites that seek to market their products online. Certain social network analysis software, namely Pajek, was used to explore different structural aspects of this community such as brokerage roles, triadic constraints and levels of cohesion. Some overall statistics were also obtained such as network density, average geodesic distance and average degree.

Mohammed Al-Taie

2012-02-01

126

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

Energy Technology Data Exchange (ETDEWEB)

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

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

1979-05-01

127

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

Science.gov (United States)

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. PMID:21586331

Ahmadlou, Mehran; Adeli, Hojjat

2011-09-15

128

Serial Analysis of rRNA Genes and the Unexpected Dominance of Rare Members of Microbial Communities?  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The accurate description of a microbial community is an important first step in understanding the roles of its components in ecosystem function. A method for surveying microbial communities termed serial analysis of rRNA genes (SARD) is described here. Through a series of molecular cloning steps, short DNA sequence tags are recovered from the fifth variable (V5) region of the prokaryotic 16S rRNA genes from microbial communities. These tags are ligated to form concatemers comprised of 20 to 4...

Ashby, Matthew N.; Rine, Jasper; Mongodin, Emmanuel F.; Nelson, Karen E.; Dimster-denk, Dago

2007-01-01

129

An analysis of the metabolic patterns of two rural communities affected by soy expansion in the North of Argentina  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The soy expansion model in Argentina generates structural changes in traditional lifestyles that can be associated with different biophysical and socioeconomic impacts. To explore this issue, we apply an innovative method for integrated assessment - the Multi Scale Integrated Analysis of Societal and Ecosystem Metabolism (MuSIASEM) framework - to characterize two communities in the Chaco Region, Province of Formosa, North of Argentina. These communities have recently experienced the expansion...

Arizpe Ramos, Nancy Guadalupe

2012-01-01

130

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

131

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

2013-02-01

132

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

Science.gov (United States)

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

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

2010-01-01

133

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

Science.gov (United States)

The permafrost soil of Mo-he in Northeast China presents a typical cold environment colonized by psychrophilic microorganisms. This study is aimed at assessing the bacterial communities of permafrost soil of Mo-he in China by sequencing the 16S rRNA genes and Mothur analysis. PCR products with universal 16S rRNA gene primers were cloned and partially sequenced, and bacterial identification at the species was performed by comparative analysis with the GenBank/EMBL/DDBJ database. A total of 266 clones were obtained with the average length of 1,050 bp. Mothur analysis showed that the coverage value of clone library was 53.78 %, Shannon diversity (H) was 4.03, Simpson diversity value was 0.018, and 74 operational taxonomic units were generated. Through phylogenetic assignment using BLASTN by more than 97 % similarity, a total of 87 tentative taxa were identified. The majority of bacterial sequences recovered in this study belonged to the Acidobacteria, Proteobacteria, Verrucomicrobia, Bacteroidetes, Chloroflexi and Chlorobi. Among them, Acidobacteria are dominant community, accounting for 30.1 % of total bacteria, followed by Proteobacteria which accounted for 22.2 %. This result reflected the acidic characteristics of the permafrost soil of which pH value was 6.0. Our study indicated that the permafrost soil of Mo-he in China has a high diversity of bacteria and represents a vast potential resource of novel bacteria. As far as we knew, this is the first report on bacterial diversity of permafrost soil of Mo-he in China. PMID:24426176

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

2014-03-01

134

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

Science.gov (United States)

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 (http://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. PMID:24098075

Ostraat, Michele L; Mills, Karmann C; Guzan, Kimberly A; Murry, Damaris

2013-01-01

135

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

Science.gov (United States)

Phospholipid fatty acid (PLFA) as biomarkers, is widely used to profile microbial communities in environmental samples. However, PLFA extraction and derivatization protocols are not standardized and have widely varied among published studies. Specifically investigators have used either HCl/MeOH or KOH/MeOH or both for the methylation step of PLFA analysis, without justification or research to support either one. It seems likely that each method could have very different outcomes and conclusions for PLFA based studies. Therefore, the objective of this study was to determine the effect of catalyst type for methylation on detecting PLFAs and implications for interpreting microbial profiling in soil. Fatty acid samples extracted from soils obtained from a wetland, an intermittently flooded site, and an adjacent upland site were subjected to HCl/MeOH or KOH/MeOH catalyzed methylation procedures during PLFA analyses. The methylation method using HCl/MeOH resulted in significantly higher concentrations of most PLFAs than the KOH/MeOH method. Another important outcome was that fatty acids with a methyl group (18:1?,7c 11Me, TBSA 10Me 18:0, 10Me 18:0, 17:0 10Me and 16:0 10Me being an actinomycetes biomarker) could not be detected by HCl/MeOH catalyzed methylation but were found in appreciable concentrations with KOH/MeOH method. From our results, because the HCl/MeOH method did not detect the fatty acids containing methyl groups that could strongly influence the microbial community profile, we recommend that the KOH/MeOH catalyzed transesterification method should become the standard procedure for PLFA profiling of soil microbial communities. PMID:22212759

Chowdhury, Taniya Roy; Dick, Richard P

2012-02-01

136

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

Science.gov (United States)

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

Wood, N. J.; Spielman, S.

2012-12-01

137

Cytobank: providing an analytics platform for community cytometry data analysis and collaboration.  

Science.gov (United States)

Cytometry is used extensively in clinical and laboratory settings to diagnose and track cell subsets in blood and tissue. High-throughput, single-cell approaches leveraging cytometry are developed and applied in the computational and systems biology communities by researchers, who seek to improve the diagnosis of human diseases, map the structures of cell signaling networks, and identify new cell types. Data analysis and management present a bottleneck in the flow of knowledge from bench to clinic. Multi-parameter flow and mass cytometry enable identification of signaling profiles of patient cell samples. Currently, this process is manual, requiring hours of work to summarize multi-dimensional data and translate these data for input into other analysis programs. In addition, the increase in the number and size of collaborative cytometry studies as well as the computational complexity of analytical tools require the ability to assemble sufficient and appropriately configured computing capacity on demand. There is a critical need for platforms that can be used by both clinical and basic researchers who routinely rely on cytometry. Recent advances provide a unique opportunity to facilitate collaboration and analysis and management of cytometry data. Specifically, advances in cloud computing and virtualization are enabling efficient use of large computing resources for analysis and backup. An example is Cytobank, a platform that allows researchers to annotate, analyze, and share results along with the underlying single-cell data. PMID:24590675

Chen, Tiffany J; Kotecha, Nikesh

2014-01-01

138

Community Analysis of Plant Biomass-Degrading Microorganisms from Obsidian Pool, Yellowstone National Park.  

Science.gov (United States)

The conversion of lignocellulosic biomass into biofuels can potentially be improved by employing robust microorganisms and enzymes that efficiently deconstruct plant polysaccharides at elevated temperatures. Many of the geothermal features of Yellowstone National Park (YNP) are surrounded by vegetation providing a source of allochthonic material to support heterotrophic microbial communities adapted to utilize plant biomass as a primary carbon and energy source. In this study, a well-known hot spring environment, Obsidian Pool (OBP), was examined for potential biomass-active microorganisms using cultivation-independent and enrichment techniques. Analysis of 33,684 archaeal and 43,784 bacterial quality-filtered 16S rRNA gene pyrosequences revealed that archaeal diversity in the main pool was higher than bacterial; however, in the vegetated area, overall bacterial diversity was significantly higher. Of notable interest was a flooded depression adjacent to OBP supporting a stand of Juncus tweedyi, a heat-tolerant rush commonly found growing near geothermal features in YNP. The microbial community from heated sediments surrounding the plants was enriched in members of the Firmicutes including potentially (hemi)cellulolytic bacteria from the genera Clostridium, Anaerobacter, Caloramator, Caldicellulosiruptor, and Thermoanaerobacter. Enrichment cultures containing model and real biomass substrates were established at a wide range of temperatures (55-85 °C). Microbial activity was observed up to 80 °C on all substrates including Avicel, xylan, switchgrass, and Populus sp. Independent of substrate, Caloramator was enriched at lower (65 °C) temperatures. PMID:25319238

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

2014-10-16

139

Aerobic remediation of petroleum sludge through soil supplementation: Microbial community analysis  

International Nuclear Information System (INIS)

Highlights: ? Enhanced aerobic-degradation of PAHs was noticed with increasing soil concentration. ? Lower ring PAHs showed superior degradation over higher ring PAHs. ? Role of dehydrogenase activity, redox pattern and dissolved oxygen was investigated. ? Community analysis detected survival of efficient aromatic degrading microorganisms. - Abstract: The effect of soil concentration on the aerobic degradation of real-field petroleum sludge was studied in slurry phase reactor. Total petroleum hydrocarbons (TPH) and polycyclic aromatic hydrocarbons (PAHs) showed effective removal but found to depend on the soil concentration. Aromatic fraction (48.12%) documented effective degradation compared to aliphatics (47.31%), NSO (28.69%) and asphaltenes (26.66%). PAHs profile showed efficient degradation of twelve individual aromatic compounds where lower ring compounds showed relatively higher degradation efficiency compared to the higher ring compounds. The redox behaviour and dehydrogenase activity showed a linear increment with the degradation pattern. Microbial community composition and changes during bioremediation were studied using denaturing gradient gel electrophoresis (DGGE). Among the 12 organisms identified, Proteobacteria was found to be dominant representing 50% of the total population (25% of ?-proteobacteria; 16.6% of ?-proteobacteria; 8.3% of ?-proteobacteria), while 33.3% were of uncultured bacteria and 16.6% were of firmicutes. firmicutes.

140

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

Science.gov (United States)

Biofiltration of ethylene provides an environmentally friendly and economically beneficial option relative to physical/chemical removal, where selection of appropriate bed material is crucial. Here the vermicompost with indigenous microorganisms as bed material was evaluated for ethylene removal through batch test and biofilter experiment. Temporal and spatial dynamics of bacterial community in the vermicompost-biofilter under different ethylene loads were characterized by culture and denaturing gradient gel electrophoresis (DGGE) methods. The results showed that ethylene was effectively degraded by the vermicompost under conditions of 25-50% moisture content and 25-35°C temperature. The vermicompost-biofilter achieved nearly 100% ethylene removal up to an inlet load of 11mg m(-3)h(-1). Local nitrogen lack of the vermicompost in the biofilter was observed over operation time, but the change of pH was slight. DGGE analysis demonstrated that the bacterial abundance and community structure of vermicompost-biofilter varied with the height of biofilter under different ethylene loads. Pseudomonads and Actinobacteria were predominant in the biofilter throughout the whole experiment. PMID:21665363

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

2011-08-30

 
 
 
 
141

Spatial analysis of falls in an urban community of Hong Kong  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Falls are an issue of great public health concern. This study focuses on outdoor falls within an urban community in Hong Kong. Urban environmental hazards are often place-specific and dependent upon the built features, landscape characteristics, and habitual activities. Therefore, falls must be examined with respect to local situations. Results This paper uses spatial analysis methods to map fall occurrences and examine possible environmental attributes of falls in an urban community of Hong Kong. The Nearest neighbour hierarchical (Nnh and Standard Deviational Ellipse (SDE techniques can offer additional insights about the circumstances and environmental factors that contribute to falls. The results affirm the multi-factorial nature of falls at specific locations and for selected groups of the population. Conclusion The techniques to detect hot spots of falls yield meaningful results that enable the identification of high risk locations. The combined use of descriptive and spatial analyses can be beneficial to policy makers because different preventive measures can be devised based on the types of environmental risk factors identified. The analyses are also important preludes to establishing research hypotheses for more focused studies.

Wong Wing C

2009-03-01

142

Characterization of bacterial communities in sediments receiving various wastewater effluents with high-throughput sequencing analysis.  

Science.gov (United States)

454 Pyrosequencing was applied to examine bacterial communities in sediment samples collected from a river receiving effluent discharge from rural domestic sewage (RDS) and various factories, including a tannery (TNS), clothing plant (CTS), and button factory (BTS), respectively. For each sample, 4,510 effective sequences were selected and utilized to do the bacterial diversity and abundance analysis, respectively. In total, 1,288, 2,036, 1,800, and 2,150 operational taxonomic units were obtained at 3% distance cutoff in TNS, CTS, BTS, and RDS, respectively. Bacterial phylotype richness in RDS was higher than the other samples, and TNS had the least richness. The most predominant class in the TNS, CTS, and BTS samples is Betaproteobacteria. Cyanobacteria (no_rank) is the most predominant one in the RDS sample. Circa 31% sequences in TNS were affiliated with the Rhodocyclales order. In the four samples, Aeromonas, Arcobacter, Clostridium, Legionella, Leptospira, Mycobacterium, Pseudomonas, and Treponema genera containing pathogenic bacteria were detected. Characterization of bacterial communities in sediments from various downstream branches indicated that distinct wastewater effluents have similar potential to reduce the natural variability in river ecosystems and contribute to the river biotic homogenization. PMID:24477925

Lu, Xiao-Ming; Lu, Peng-Zhen

2014-04-01

143

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

Science.gov (United States)

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. PMID:21637937

Liu, Jingjing; Wu, Weixiang; Chen, Chongjun; Sun, Faqian; Chen, Yingxu

2011-09-01

144

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

Science.gov (United States)

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 ( 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. PMID:14641591

Ranjard, Lionel; Lejon, David P H; Mougel, Christophe; Schehrer, Lucie; Merdinoglu, Didier; Chaussod, Rémi

2003-11-01

145

[On two ends of minority politics: an anthropological analysis of hattatsu sh?gai and hikikomori communities].  

Science.gov (United States)

This paper provides a comparative analysis of two communities in Japan based on long-term anthropological fieldwork: one is the community of those with hattatsu sh?gai (developmental disorder) and their families and the other is the community of those who have experienced hikikomori and their families. The purpose of this paper is to examine the similarities and differences between the two communities in terms of the ways in which medical diagnoses are understood, identities are formed and certain perspectives on society are shared. By doing so, we attempt to move beyond the clinical sphere to capture the sociocultural significance of "being" an individual with developmental disorder or hikikomori experience. PMID:23234196

Teruyama, Junko; Horiguchi, Sachiko

2012-01-01

146

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

147

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

Science.gov (United States)

The Southern California Earthquake Center (SCEC) has formed a Geoscience/IT partnership to develop an advanced information infrastructure for system-level earthquake science in Southern California. This SCEC/ITR partnership comprises SCEC, USC's Information Sciences Institute (ISI), the San Diego Supercomputer Center (SDSC), the Incorporated Institutions for Research in Seismology (IRIS), and the U.S. Geological Survey. This collaboration recently completed the second year in a five-year National Science Foundation (NSF) funded ITR project called the SCEC Community Modeling Environment (SCEC/CME). The goal of the SCEC/CME is to develop seismological applications and information technology (IT) infrastructure to support the development of Seismic Hazard Analysis (SHA) programs and other geophysical simulations. The SHA application programs developed by project collaborators include a Probabilistic Seismic Hazard Analysis system called OpenSHA [Field et al., this meeting]. OpenSHA computational elements that are currently available include a collection of attenuation relationships, and several Earthquake Rupture Forecasts (ERF's). Geophysicists in the collaboration have also developed Anelastic Wave Models (AWMs) using both finite-difference and finite-element approaches. Earthquake simulations using these codes have been run for a variety of earthquake sources. A Rupture Dynamic Model (RDM) has also been developed that couples a rupture dynamics simulation into an anelastic wave model. The collaboration has also developed IT software and hardware infrastructure to support the development, execution, and analysis of SHA programs. To support computationally expensive simulations, we have constructed a grid-based system utilizing Globus software [Kesselman et al., this meeting]. Using the SCEC grid, project collaborators can submit computations from the SCEC/CME servers to High Performance Computers at USC, NPACI and Teragrid High Performance Computing Centers. We have developed a SCEC Community Velocity Model server based on Internet standards (XML, SOAP, and WSDL) to provide access to the SCEC Community Velocity Model. We have also continued development of the SCEC Fault Information System (SCEC/FIS) to provide access to the SCEC Community Fault Model and the SCEC Fault Activity Database. Data generated and archived by the SCEC/CME is stored in a digital library system, the Storage Resource Broker (SRB) [Minster et al., this meeting]. This system provides a robust and secure system for maintaining the association between the data sets and their metadata. A browser-based computational pathway assembly web site has been developed [Gupta et al., this meeting]. Users can compose SHA calculations and call SCEC/CME computational programs to process the data and the output. By assembling a series of computational steps, users can develop complex computational pathways the validity of which can be verified with an ontology-based pathway assembly tool. Data visualization software developed by the collaboration to support analysis and validation of data sets includes 4D wave propagation visualization software based on OpenGL [Thiebaux et al., this meeting] and 3D Geowall-based visualization of earthquakes and faults.

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

2003-12-01

148

A study of microbial communities in selected samples using phospholipid fatty acids analysis  

International Nuclear Information System (INIS)

Fatty acid patterns of phospholipids were determined in different environmental samples using phospholipid fatty acids analysis (PLFA) in order to characterise microbial community structures. Hyporheic gravel-sand sediment samples were collected from Sitka Stream, muddy sediment samples from several weirs on Morava River, activated and digested sludge from Olomouc water purification plant and sand samples from filters in Olomouc-Cernovir water treatment plant. Profiles of PLFA indicate a clear difference between these types of samples. The muddy sediments showed high percentages of ester-linked polyunsaturated fatty acids contributed by river phytoplankton. The longer chain fatty acids (26 - 30 grad C), indicators for organic matter of allochthonous origin, increased in the hyporheic sediments. Activated and digested sludge contain much poorer profiles than other samples, probably because of the lower occurrence of bacteria. (authors)

149

Multiple deprivation, income and poverty in Italy: an analysis based on European Community Household Panel  

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Full Text Available The aim of this article is to examine both the diffusion and intensity of poverty in Italy by utilising two kinds of approach. The first is the usual one, which employs a threshold defined in terms of income in order to identify the poor families. The second, referring to the definition of functioning introduced by Sen, identifies the poor families on the basis of living conditions. The use of this specific approach allows us to take into account new aspects of the phenomenon that the income approach overcame. Our analyses refer to the results of the second wave of the European Community Household Panel, which was delivered in 1995. Regarding income poverty, a logistic discriminant analysis has been performed in order to detect the significantly connected variables, as for the living conditions approach. The latter approach is more effective in the detection of the family state of privation than the former.

Sergio Brasini

2007-10-01

150

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.

Childs Kevin L

2010-11-01

151

Microbial community analysis of perchlorate-reducing cultures growing on zero-valent iron  

International Nuclear Information System (INIS)

Anaerobic microbial mixed cultures demonstrated its ability to completely remove perchlorate in the presence of zero-valent iron. In order to understand the major microbial reaction in the iron-supported culture, community analysis comprising of microbial fatty acids and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) techniques was performed for perchlorate reducing cultures. Analysis of fatty acid methyl esters (FAMEs) and subsequent principal component analysis (PCA) showed clear distinctions not only between iron-supported perchlorate reducing culture and seed bacteria, but also among perchlorate-reducing cultures receiving different electron donors. The DGGE pattern targeting the chlorite dismutase (cld) gene showed that iron-supported perchlorate reducing culture is similar to hydrogen-fed cultures as compared to acetate-fed culture. The phylogenetic tree suggested that the dominant microbial reaction may be a combination of the autotrophic and heterotrophic reduction of perchlorate. Both molecular and chemotaxonomic experimental results support further understanding in the function of zero-valent iron as an adequate electron source for enhancing the microbial perchlorate reduction in natural and engineered systems.

152

Determinants of community health fund membership in Tanzania: a mixed methods analysis.  

Science.gov (United States)

BackgroundIn many developing countries, initiatives are underway to strengthen voluntary community based health insurance as a means of expanding access to affordable care among the informal sector. However, increasing coverage with voluntary health insurance in low income settings can prove challenging. There are limited studies on determinants of enrolling in these schemes using mixed methods. This study aims to shed light on the characteristics of those joining a community health fund, a type of community based health insurance, in Tanzania and the reasons for their membership and subsequent drop out using mixed methods.MethodsA cross sectional survey of households in four rural districts was conducted in 2008, covering a total of 1,225 (524 members of CHF and 701 non-insured) households and 7,959 individuals. In addition, 12 focus group discussions were carried out with CHF members, non-scheme members and members of health facility governing committees in two rural districts. Logistic regression was used to assess the determinants of CHF membership while thematic analysis was done to analyse qualitative data.ResultsThe quantitative analysis revealed that the three middle income quintiles were more likely to enrol in the CHF than the poorest and the richest. CHF member households were more likely to be large, and headed by a male than uninsured households from the same areas. The qualitative data supported the finding that the poor rather than the poorest were more likely to join as were large families and of greater risk of illness, with disabilities or persons with chronic diseases. Households with elderly members or children under-five years were also more likely to enrol. Poor understanding of risk pooling deterred people from joining the scheme and was the main reason for not renewing membership. On the supply side, poor quality of public care services, the limited benefit package and a lack of provider choice were the main factors for low enrolment.ConclusionsDeterminants of CHF membership are diverse and improving the quality of health services and expanding the benefit package should be prioritised to expand voluntary health insurance coverage. PMID:25411021

Macha, Jane; Kuwawenaruwa, August; Makawia, Suzan; Mtei, Gemini; Borghi, Josephine

2014-11-20

153

Impact of T-RFLP data analysis choices on assessments of microbial community structure and dynamics.  

Science.gov (United States)

BackgroundTerminal restriction fragment length polymorphism (T-RFLP) analysis is a common DNA-fingerprinting technique used for comparisons of complex microbial communities. Although the technique is well established there is no consensus on how to treat T-RFLP data to achieve the highest possible accuracy and reproducibility. This study focused on two critical steps in the T-RFLP data treatment: the alignment of the terminal restriction fragments (T-RFs), which enables comparisons of samples, and the normalization of T-RF profiles, which adjusts for differences in signal strength, total fluorescence, between samples.ResultsVariations in the estimation of T-RF sizes were observed and these variations were found to affect the alignment of the T-RFs. A novel method was developed which improved the alignment by adjusting for systematic shifts in the T-RF size estimations between the T-RF profiles. Differences in total fluorescence were shown to be caused by differences in sample concentration and by the gel loading. Five normalization methods were evaluated and the total fluorescence normalization procedure based on peak height data was found to increase the similarity between replicate profiles the most. A high peak detection threshold, alignment correction, normalization and the use of consensus profiles instead of single profiles increased the similarity of replicate T-RF profiles, i.e. lead to an increased reproducibility. The impact of different treatment methods on the outcome of subsequent analyses of T-RFLP data was evaluated using a data set from a longitudinal study of the bacterial community in an activated sludge wastewater treatment plant. Whether the alignment was corrected or not and if and how the T-RF profiles were normalized had a substantial impact on ordination analyses, assessments of bacterial dynamics and analyses of correlations with environmental parameters.ConclusionsA novel method for the evaluation and correction of the alignment of T-RF profiles was shown to reduce the uncertainty and ambiguity in alignments of T-RF profiles. Large differences in the outcome of assessments of bacterial community structure and dynamics were observed between different alignment and normalization methods. The results of this study can therefore be of value when considering what methods to use in the analysis of T-RFLP data. PMID:25381552

Fredriksson, Nils; Hermansson, Malte; Wilén, Britt-Marie

2014-11-01

154

Community-based physical activity interventions for treatment of type 2 diabetes: a systematic review with meta-analysis.  

Science.gov (United States)

Evidence suggests engaging in regular physical activity (PA) can have beneficial outcomes for adults with type 2 diabetes (TD2), including weight loss, reduction of medication usage and improvements in hemoglobin A1c (HbA1c)/fasting glucose. While a number of clinical-based PA interventions exist, community-based approaches are limited. The objective of this study is to conduct a systematic review with meta-analysis to assess the effectiveness of community-based PA interventions for the treatment of TD2 in adult populations. A search of peer-reviewed publications from 2002 to June 2012 was conducted across several electronic databases to identify interventions evaluated in community settings. Twenty-two studies were identified, and 11 studies reporting HbA1c as an outcome measure were pooled in the meta-analysis. Risk of bias assessment was also conducted. The findings demonstrate community-based PA interventions can be effective in producing increases in PA. Meta-analysis revealed a lowering of HbA1c levels by -0.32% [95% CI -0.65, 0.01], which approached statistical significance (p?community-based interventions in adult populations diagnosed with TD2. PMID:23372566

Plotnikoff, Ronald C; Costigan, Sarah A; Karunamuni, Nandini D; Lubans, David R

2013-01-01

155

Comparative molecular analysis of bacterial communities inhabiting pristine and polluted with polycyclic aromatic hydrocarbons Black Sea coastal sediments.  

Science.gov (United States)

Molecular analysis was applied to characterize bacterial community structure in sediment samples collected from pristine site and oil-polluted Black Sea harbor. Amplified Ribosomal DNA Restriction Analysis (ARDRA) revealed a high similarity in the restriction patterns of both samples thus not demonstrating the effect of the pollutant on the structure of the bacterial communities. Constructed 16S rRNA gene libraries gave more detailed assessment of members. Results showed that ?- and ?-Proteobacteria were dominant in the oil polluted site, whereas the pristine site was characterized by prevalence of Actinobacteria. The biodegradative potential of the adapted bacterial community in the oil-polluted sediments was demonstrated by the presence of the aromatic ring hydroxylating dioxygenase genes. PMID:24759506

Todorova, Nadezhda H; Mironova, Roumyana S; Karamfilov, Ventzislav K

2014-06-15

156

Social Development Needs Analysis as a tool for SIA to guide corporate-community investment: Applications in the minerals industry  

International Nuclear Information System (INIS)

Mining companies are faced with growing societal demands that a sufficient portion of the benefits from mining should flow to local communities to ensure they are adequately compensated for the negative social impacts they experience. This paper considers how a more equitable benefit distribution system can be achieved through voluntary initiatives, recognising companies as potential agents for social development through the provision of improved services and infrastructure, capacity-building, employment and local economic development initiatives. Social Development Needs Analysis is introduced as an enhancement to participatory Social Impact Assessment methods to give practical guidance to site managers in evaluating community investment alternatives. Social Development Needs Analysis aims to identify the priority social issues that need to be addressed in order for a company to contribute to a net positive impact in the community while building assets for the business

157

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

158

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

Energy Technology Data Exchange (ETDEWEB)

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

1978-03-22

159

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

Scientific Electronic Library Online (English)

Full Text Available SciELO Argentina | Language: Spanish 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" re [...] lacionadas a la propuesta de medicina integral y medicina preventiva. Su publicación en español en la sección Textos fundacionales, apunta a la reconstrucción histórica 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" rel [...] ated 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 movement 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.

Jairnilson, Silva Paim.

2009-04-01

160

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

Scientific Electronic Library Online (English)

Full Text Available SciELO Public Health | Language: Spanish 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" re [...] lacionadas a la propuesta de medicina integral y medicina preventiva. Su publicación en español en la sección Textos fundacionales, apunta a la reconstrucción histórica 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" rel [...] ated 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 movement 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.

Jairnilson Silva, Paim.

2009-04-01

 
 
 
 
161

Phylogenetic Microarray Analysis of a Microbial Community Performing Reductive Dechlorination at a TCE-contaminated Site  

Science.gov (United States)

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 two 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. PMID:22091783

Lee, Patrick K. H.; Warnecke, F.; Brodie, Eoin L.; Macbeth, Tamzen W.; Conrad, Mark E.; Andersen, Gary L.; Alvarez-Cohen, Lisa

2012-01-01

162

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.

2013-05-01

163

Analysis of composition and structure of coastal to mesopelagic bacterioplankton communities in the northern Gulf of Mexico  

Directory of Open Access Journals (Sweden)

Full Text Available 16S rRNA gene amplicons were pyrosequenced to assess bacterioplankton community composition, diversity and phylogenetic community structure for 17 stations in the northern Gulf of Mexico (nGoM sampled in March 2010. Statistical analyses showed that samples from depths ? 100 m differed distinctly from deeper samples. SAR 11 ?-Proteobacteria and Bacteroidetes dominated communities at depths ? 100 m, which were characterized by high ?-Proteobacteria/?-Proteobacteria ratios (?/? > 1.7. Thaumarchaeota, Firmicutes and ?-Proteobacteria were relatively abundant in deeper waters, and ?/? ratios were low (< 1. Canonical correlation analysis indicated that ?- and ?-Proteobacteria, Thaumarchaeota and Firmicutes correlated positively with depth; ?-Proteobacteria and Bacteroidetes correlated positively with temperature and dissolved oxygen; Actinobacteria, ?-Proteobacteria and Verrucomicrobia correlated positively with a measure of suspended particles. Diversity indices did not vary with depth or other factors, which indicated that richness and evenness elements of bacterioplankton communities might develop independently of nGoM physical-chemical variables. Phylogenetic community structure as measured by the net relatedness (NRI and nearest taxon (NTI indices also did not vary with depth. NRI values indicated that most of the communities were comprised of OTUs more distantly related to each other in whole community comparisons than expected by chance. NTI values derived from phylogenetic distances of the closest neighbor for each OTU in a given community indicated that OTUs tended to occur in clusters to a greater extent than expected by chance. This indicates that “habitat filtering” might play an important role in nGoM bacterioplankton species assembly, and that such filtering occurs throughout the water column.

GaryMKing

2013-01-01

164

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

Directory of Open Access Journals (Sweden)

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

ConnieLovejoy

2012-12-01

165

Aerobic degradation study of three fluoroanilines and microbial community analysis: the effects of increased fluorine substitution.  

Science.gov (United States)

The fate of fluorinated compounds in the environment, especially polyfluorinated aromatics, is a matter of great concern. In this work, 4-Fluoroaniline (4-FA), 2,4-Difluoroanilines (2,4-DFA), and 2,3,4-Trifluoroanilines (2,3,4-TFA), were chosen as the target pollutants to study their biodegradability under aerobic conditions. The required enriched time of the mixed bacterial culture for degrading 4-FA, 2,4-DFA, and 2,3,4-TFA was 26, 51, and 165 days, respectively, which suggested that the longer enrichment time was required with the increase of fluorine substitution. At the initial concentrations of 100-200 mg L(-1), the 4-FA, 2,4-DFA, and 2,3,4-TFA could be degraded completely by the mixed bacterial culture. The maximum specific degradation rates of 4-FA, 2,4-DFA, and 2,3,4-TFA were 22.48 ± 0.55, 15.27 ± 2.04, and 8.84 ± 0.93 mg FA (g VSS h)(-1), respectively. Also, the three FAs enriched cultures showed certain potential of degrading other two FAs. The results from enzyme assay suggested the expression of meta-cleavage pathways during three FAs degradation. The denaturing gradient gel electrophoresis analysis revealed that unique bacterial communities were formed after FAs enrichment and these were principally composed of ?-Proteobacteria, Oscillatoriophycideae, ?-Proteobacteria, ?-Proteobacteria, Thermales, Xanthomonadales, Deinococci, Flavobacteriia, and Actinobacteridae. The Shannon-Wiener indexes in three FAs enriched culture decreased with the increase of fluorine substitution, indicating the significant effect of fluorine substitution on the microbial diversity. These findings supply important information on the fate of three FAs under aerobic environment, and the bacterial communities in their degradation systems. PMID:25238671

Zhao, Zhi-Qing; Tian, Bao-Hu; Zhang, Xuan; Ghulam, Abbas; Zheng, Tu-Cai; Shen, Dong-Sheng

2015-02-01

166

Resource partitioning in freshwater turtle communities: A null model meta-analysis of available data  

Science.gov (United States)

Resource partitioning is one of the most intensely studied issues in ecology since the mid-1900s, nonetheless this issue has never been examined in detail for several important animal groups, including the freshwater turtles. In this paper I re-analyze by null models several studies on resource partitioning by freshwater turtles published in the peer-reviewed literature. These studies originated from all continents and from a variety of climatic and habitat conditions. I used data given in the original papers to recalculate dietary overlap between species. Then, the true datasets were compared to randomly generated datasets produced by 3 × 10 4 Monte Carlo permutations, by using two different randomization algorithms (RA2 and RA3 of Lawlor, 1980). Datasets were inspected to find non-random structure of the various communities along four resource dimensions: macro-habitat, micro-habitat, food, and time. Based on my meta-analysis, I concluded that the micro-habitat resource is the most important dimension (it was the resource partitioned in nearly 80% of the study cases), followed by the food resource dimension (nearly 70%), whereas macro-habitat and time were clearly less important. In relation to micro-habitat dimension, the selection of basking site typology is perhaps the main aspect of the microhabitat niche to be partitioned. Logistic regression models indicated that the presence of a resource partitioning structure in the dataset was influenced only by matrix size, and not by number of species, continent, presence of substantial body size differences among coexisting species, or tropical versus non-tropical origin. A combination of causes may explain the observed patterns: interspecific competition is likely important in shaping several turtle communities, but intrinsic and extrinsic constraints and predation are also relevant.

Luiselli, Luca

2008-07-01

167

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

Science.gov (United States)

Denaturing gradient gel electrophoresis (DGGE) is a powerful technique to reveal the community structures and composition of microorganisms in complex natural environments and samples. However, positive and reproducible polymerase chain reaction (PCR) products, which are difficult to acquire for some specific samples due to low abundance of the target microorganisms, significantly impair the effective applications of DGGE. Thus, nested PCR is often introduced to generate positive PCR products from the complex samples, but one problem is also introduced: The total number of thermocycling in nested PCR is usually unacceptably high, which results in skewed community structures by generation of random or mismatched PCR products on the DGGE gel, and this was demonstrated in this study. Furthermore, nested PCR could not resolve the uneven representative issue with PCR products of complex samples with unequal richness of microbial population. In order to solve the two problems in nested PCR, the general protocol was modified and improved in this study. Firstly, a general PCR procedure was used to amplify the target genes with the PCR primers without any guanine cytosine (GC) clamp, and then, the resultant PCR products were purified and diluted to 0.01 ?g ml(-1). Subsequently, the diluted PCR products were utilized as templates to amplify again with the same PCR primers with the GC clamp for 17 cycles, and the products were finally subjected to DGGE analysis. We demonstrated that this is a much more reliable approach to obtain a high quality DGGE profile with high reproducibility. Thus, we recommend the adoption of this improved protocol in analyzing microorganisms of low abundance in complex samples when applying the DGGE fingerprinting technique to avoid biased results. PMID:24728758

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

2014-06-01

168

Community-Based Physical Activity Interventions for Treatment of Type 2 Diabetes: A Systematic Review with Meta-Analysis  

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Evidence suggests engaging in regular physical activity (PA) can have beneficial outcomes for adults with type 2 diabetes (TD2), including weight loss, reduction of medication usage and improvements in hemoglobin A1c (HbA1c)/fasting glucose. While a number of clinical-based physical activity interventions exist, community-based approaches are limited. The objective of this study is to conduct a systematic review with meta-analysis to assess the effectiveness of community-based PA intervention...

RonaldCPlotnikoff; NandiniKarunamuni

2013-01-01

169

Meta-Transcriptomic Analysis of a Chromate-Reducing Aquifer Microbial Community  

Science.gov (United States)

A major challenge for microbial ecology that has become more tractable in the advent of new molecular techniques is characterizing gene expression in complex microbial communities. We are using meta-transcriptomic analysis to characterize functional changes in an aquifer-derived, chromate-reducing microbial community as it transitions through various electron-accepting conditions. 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, namely, nitrate, sulfate, and Fe(III). The microcosms progressed successively through various electron-accepting conditions (e.g., denitrifying, sulfate-reducing, and ferric iron-reducing conditions, as well as nitrate-dependent, chemolithotrophic Fe(II)-oxidizing conditions). Cr(VI) was rapidly reduced initially and again upon further Cr(VI) amendments. Extensive geochemical sampling and analysis (e.g., lactate, acetate, chloride, nitrate, nitrite, sulfate, dissolved Cr(VI), total Fe(II)), RNA/DNA harvesting, and PhyloChip analyses were conducted. Methods were developed for removal of rRNA from total RNA in preparation for meta-transcriptome sequencing. To date, samples representing denitrifying and fermentative/sulfate-reducing conditions have been sequenced using 454 Titanium technology. Of the non-rRNA related reads for the denitrifying sample (which was also actively reducing chromate), ca. 8% were associated with denitrification and ca. 0.9% were associated with chromate resistance/transport, in contrast to the fermentative/sulfate-reducing sample (in which chromate had already been reduced), which had zero reads associated with either of these categories but many predicted proteins associated with sulfate-reducing bacteria. We observed sequences for key functional transcripts that were unique at the nucleotide level compared to the GenBank non-redundant database [such as L-lactate dehydrogenase (iron-sulfur-cluster-binding subunit), cytochrome cd1 nitrite reductase (nirS) (from the denitrifying phase), and dissimilatory sulfite reductase (dsrA, dsrB) (from the sulfate-reducing phase)]. One potential advantage of this approach is that such important genes may not have been detected using more traditional techniques, including PCR-based methods and a priori functional microarrays.

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

2010-12-01

170

Design and analysis of the Community Youth Development Study longitudinal cohort sample.  

Science.gov (United States)

Communities That Care (CTC) is a prevention system designed to reduce adolescent substance use and delinquency through the selection of effective preventive interventions tailored to a community's specific profile of risk and protection. A community-randomized trial of CTC, the Community Youth Development Study, is currently being conducted in 24 communities across the United States. This article describes the rationale, multilevel analyses, and baseline comparability for the study's longitudinal cohort design. The cohort sample consists of 4,407 fifth- and sixth-grade students recruited in 2004 and 2005 and surveyed annually through ninth grade. Results of mixed-model ANOVAs indicated that students in CTC and control communities exhibited no significant differences (ps > .05) in baseline levels of student outcomes. PMID:19509119

Brown, Eric C; Graham, John W; Hawkins, J David; Arthur, Michael W; Baldwin, Megan M; Oesterle, Sabrina; Briney, John S; Catalano, Richard F; Abbott, Robert D

2009-08-01

171

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

CERN Document Server

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

172

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

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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 o...

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

2012-01-01

173

Analysis of Factors Affecting the Accuracy, Reproducibility, and Interpretation of Microbial Community Carbon Source Utilization Patterns  

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We determined factors that affect responses of bacterial isolates and model bacterial communities to the 95 carbon substrates in Biolog microtiter plates. For isolates and communities of three to six bacterial strains, substrate oxidation rates were typically nonlinear and were delayed by dilution of the inoculum. When inoculum density was controlled, patterns of positive and negative responses exhibited by microbial communities to each of the carbon sources were reproducible. Rates and exten...

Haack, S. K.; Garchow, H.; Klug, M. J.; Forney, L. J.

1995-01-01

174

Serial analysis of rRNA genes and the unexpected dominance of rare members of microbial communities.  

Science.gov (United States)

The accurate description of a microbial community is an important first step in understanding the roles of its components in ecosystem function. A method for surveying microbial communities termed serial analysis of rRNA genes (SARD) is described here. Through a series of molecular cloning steps, short DNA sequence tags are recovered from the fifth variable (V5) region of the prokaryotic 16S rRNA genes from microbial communities. These tags are ligated to form concatemers comprised of 20 to 40 tags which are cloned and identified by DNA sequencing. Four agricultural soil samples were profiled with SARD to assess the method's utility. A total of 37,008 SARD tags comprising 3,127 unique sequences were identified. A comparison of duplicate profiles from one soil genomic DNA preparation revealed that the method was highly reproducible. The large numbers of singleton tags, together with nonparametric richness estimates, indicated that a significant amount of sequence tag diversity remained undetected with this level of sampling. The abundance classes of the observed tags were scale-free and conformed to a power law distribution. Numerically, the majority of the total tags observed belonged to abundance classes that were each present at less than 1% of the community. Over 99% of the unique tags individually made up less than 1% of the community. Therefore, from either a numerical or diversity standpoint, taxa with low abundance comprised a significant proportion of the microbial communities examined and could potentially make a large contribution to ecosystem function. SARD may provide a means to explore the ecological roles of these rare members of microbial communities in qualitative and quantitative terms. PMID:17526780

Ashby, Matthew N; Rine, Jasper; Mongodin, Emmanuel F; Nelson, Karen E; Dimster-Denk, Dago

2007-07-01

175

Serial Analysis of rRNA Genes and the Unexpected Dominance of Rare Members of Microbial Communities?  

Science.gov (United States)

The accurate description of a microbial community is an important first step in understanding the roles of its components in ecosystem function. A method for surveying microbial communities termed serial analysis of rRNA genes (SARD) is described here. Through a series of molecular cloning steps, short DNA sequence tags are recovered from the fifth variable (V5) region of the prokaryotic 16S rRNA genes from microbial communities. These tags are ligated to form concatemers comprised of 20 to 40 tags which are cloned and identified by DNA sequencing. Four agricultural soil samples were profiled with SARD to assess the method's utility. A total of 37,008 SARD tags comprising 3,127 unique sequences were identified. A comparison of duplicate profiles from one soil genomic DNA preparation revealed that the method was highly reproducible. The large numbers of singleton tags, together with nonparametric richness estimates, indicated that a significant amount of sequence tag diversity remained undetected with this level of sampling. The abundance classes of the observed tags were scale-free and conformed to a power law distribution. Numerically, the majority of the total tags observed belonged to abundance classes that were each present at less than 1% of the community. Over 99% of the unique tags individually made up less than 1% of the community. Therefore, from either a numerical or diversity standpoint, taxa with low abundance comprised a significant proportion of the microbial communities examined and could potentially make a large contribution to ecosystem function. SARD may provide a means to explore the ecological roles of these rare members of microbial communities in qualitative and quantitative terms. PMID:17526780

Ashby, Matthew N.; Rine, Jasper; Mongodin, Emmanuel F.; Nelson, Karen E.; Dimster-Denk, Dago

2007-01-01

176

Connecting subsistence harvest and marine ecology: A cluster analysis of communities by fishing and hunting patterns  

Science.gov (United States)

Alaska Native subsistence hunters and fishers are engaged in environmental sampling, influenced by harvest technology and cultural preferences as well as biogeographical factors. We compared subsistence harvest patterns in 35 communities along the Bering, Chukchi, and Beaufort coasts of Alaska to identify affinities and groupings, and to compare those results with previous ecological analyses done for the same region. We used hierarchical cluster analysis to reveal spatial patterns in subsistence harvest records of coastal Alaska Native villages from the southern Bering Sea to the Beaufort Sea. Three main clusters were identified, correlating strongly with geography. The main division separates coastal villages of western Alaska from arctic villages along the northern Chukchi and Beaufort Seas and on islands of the Bering Sea. K-means groupings corroborate this result, with some differences. The second node splits the arctic villages, along the Chukchi, Beaufort and northern Bering Seas, where marine mammals dominate the harvest, from those on islands of the Bering Sea, characterized by seabird and seal harvests. These patterns closely resemble eco-regions proposed on biological grounds. Biogeography thus appears to be a significant factor in groupings by harvest characteristics, suggesting that subsistence harvests are a viable form of ecosystem sampling.

Renner, Martin; Huntington, Henry P.

2014-11-01

177

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

Science.gov (United States)

A two-stage aerobic membrane bioreactor (MBR) system for treating acrylonitrile butadiene styrene (ABS) resin wastewater was carried out in this study to evaluate the system performance on nitrification. The results showed that nitrification of the aerobic MBR system was significant and the highest TKN removal of approximately 90% was obtained at hydraulic retention time (HRT) 18 h. In addition, the result of nitrogen mass balance revealed that the percentage of TN removal due to denitrification was in the range of 8.7-19.8%. Microbial community analysis based on 16s rDNA molecular approach indicated that the dominant ammonia oxidizing bacteria (AOB) group in the system was a ?-class ammonia oxidizer which was identified as uncultured sludge bacterium (AF234732). A heterotrophic aerobic denitrifier identified as Thauera mechernichensis was found in the system. The results indicated that a sole aerobic MBR system for simultaneous removals of carbon and nitrogen can be designed and operated for neglect with an anaerobic unit. PMID:21236663

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

2011-05-01

178

Analysis of a microbial community associated with polychlorinated biphenyl degradation in anaerobic batch reactors.  

Science.gov (United States)

The degradation of polychlorinated biphenyls (PCBs) was investigated under fermentative-methanogenic conditions for up to 60 days in the presence of anaerobic biomass from a full-scale UASB reactor. The low methane yields in the PCBs-spiked batch reactors suggested that the biomass had an inhibitory effect on the methanogenic community. Reactors containing PCBs and co-substrates (ethanol/sodium formate) exhibited substantial PCB reductions from 0.7 to 0.2 mg mL(-1). For the Bacteria domain, the PCBs-spiked reactors were grouped with the PCB-free reactors with a similarity of 55 %, which suggested the selection of a specific population in the presence of PCBs. Three genera of bacteria were found exclusively in the PCB-spiked reactors and were identified using pyrosequencing analysis, Sedimentibacter, Tissierela and Fusibacter. Interestingly, the Sedimentibacter, which was previously correlated with the reductive dechlorination of PCBs, had the highest relative abundance in the RCS-PCB (7.4 %) and RCS-PCB-PF (12.4 %) reactors. Thus, the anaerobic sludge from the UASB reactor contains bacteria from the Firmicutes phylum that are capable of degrading PCBs. PMID:25104219

Gomes, B C; Adorno, M A T; Okada, D Y; Delforno, T P; Lima Gomes, P C F; Sakamoto, I K; Varesche, M B A

2014-11-01

179

Bacterial and Fungal Communities in Tempeh as Reveal by Amplified Ribosomal Intergenic Sequence Analysis  

Directory of Open Access Journals (Sweden)

Full Text Available Tempeh is an Indonesian traditional fermented food produced using Rhizopus as a starter culture. In practice, however, the starter culture as well as fermentation processes would yield a polymicrobial fermentation, which generated a unique tempeh flavor and texture. This condition makes Indonesian tempeh as one of the most complex fermented food, while at the same time would make it difficult to scale up tempeh production with uniform quality and consistency. The aim of this study was to compare a number of tempeh microbial communities employing Amplified Ribosomal Intergenic Sequence Analysis (ARISA. Fresh tempeh samples were obtained from tempeh producers in Java and Moluccas. 16S rRNA gene libraries and DNA sequencing were employed to analyze further the nature of bacterial diversity in two selected tempeh samples. The results of our study showed that different tempeh producer possessed different Bacterial ARISA (BARISA or fungi ARISA (FARISA profiles. However, BARISA profiles were found to be more discriminative than FARISA, and therefore BARISA would be more useful for tempeh genetic fingerprint or barcoding.

CECILIA ANNA SEUMAHU

2013-06-01

180

The gene regulatory network basis of the "community effect," and analysis of a sea urchin embryo example.  

Science.gov (United States)

The "Community Effect" denotes intra-territorial signaling amongst cells which constitute a particular tissue or embryonic progenitor field. The cells of the territory express the same transcriptional regulatory state, and the intra-territorial signaling is essential to maintenance of this specific regulatory state. The structure of the underlying gene regulatory network (GRN) subcircuitry explains the genomically wired mechanism by which community effect signaling is linked to the continuing transcriptional generation of the territorial regulatory state. A clear example is afforded by the oral ectoderm GRN of the sea urchin embryo where cis-regulatory evidence, experimental embryology, and network analysis combine to provide a complete picture. We review this example and consider less well known but similar cases in other developing systems where the same subcircuit GRN topology is present. To resolve mechanistic issues that arise in considering how community effect signaling could operate to produce its observed effects, we construct and analyze the behavior of a quantitative model of community effect signaling in the sea urchin embryo oral ectoderm. Community effect network topology could constitute part of the genomic regulatory code that defines transcriptional function in multicellular tissues composed of cells in contact, and hence may have arisen as a metazoan developmental strategy. PMID:19523466

Bolouri, Hamid; Davidson, Eric H

2010-04-15

 
 
 
 
181

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

Science.gov (United States)

A polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) approach for the detection and characterization of arbuscular mycorrhizal fungi (AMF) 18S ribosomal DNA (rDNA) was developed and applied to the study of AMF communities associated with the main sand-stabilizing plant species of the Dutch sand dunes, marram grass (Ammophila arenaria, L.). DNA was extracted directly from plant roots, soil or isolated AMF spores, and prominent bands resulting from AMF-specific DGGE profiles were excised for sequence analysis. This strategy provided a robust means of detecting and identifying AMF-like species without the use of trap plant cultivation methods. A number of Glomus-like and Scutellospora-like sequences was detected, including a putatively novel Glomus species, and differences were observed in the dominant AMF-like populations detected in healthy vs. degenerating stands of A. arenaria and in bulk sand dune soil. It has previously been suggested that plant pathogens, such as fungi and nematodes, may contribute to the decline of A. arenaria. Although no causal relationship can be drawn between the observed differences in the dominantly detected AMF-like populations and the vitality of plant growth, these results indicate that mutualistic interactions between this plant and AMF should not be overlooked when examining the role of soil-borne microorganisms in vegetation dynamics. In addition, there were discrepancies observed between the AMF-like groups detected in spore populations vs. direct 18S rDNA analysis of root material, corroborating previous suggestions that spore inspection alone may poorly represent actual AMF population structure. PMID:11928709

Kowalchuk, George A; de Souza, Francisco A; van Veen, Johannes A

2002-03-01

182

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

Energy Technology Data Exchange (ETDEWEB)

Peta-scale computing environments pose significant challenges for both system and application developers and addressing them required more than simply scaling up existing tera-scale solutions. Performance analysis tools play an important role in gaining this understanding, but previous monolithic tools with fixed feature sets have not sufficed. Instead, this project worked on the design, implementation, and evaluation of a general, flexible tool infrastructure supporting the construction of performance tools as “pipelines” of high-quality tool building blocks. These tool building blocks provide common performance tool functionality, and are designed for scalability, lightweight data acquisition and analysis, and interoperability. For this project, we built on Open|SpeedShop, a modular and extensible open source performance analysis tool set. The design and implementation of such a general and reusable infrastructure targeted for petascale systems required us to address several challenging research issues. All components needed to be designed for scale, a task made more difficult by the need to provide general modules. The infrastructure needed to support online data aggregation to cope with the large amounts of performance and debugging data. We needed to be able to map any combination of tool components to each target architecture. And we needed to design interoperable tool APIs and workflows that were concrete enough to support the required functionality, yet provide the necessary flexibility to address a wide range of tools. A major result of this project is the ability to use this scalable infrastructure to quickly create tools that match with a machine architecture and a performance problem that needs to be understood. Another benefit is the ability for application engineers to use the highly scalable, interoperable version of Open|SpeedShop, which are reassembled from the tool building blocks into a flexible, multi-user interface set of tools. This set of tools targeted at Office of Science Leadership Class computer systems and selected Office of Science application codes. We describe the contributions made by the team at the University of Wisconsin. The project built on the efforts in Open|SpeedShop funded by DOE/NNSA and the DOE/NNSA Tri-Lab community, extended Open|Speedshop to the Office of Science Leadership Class Computing Facilities, and addressed new challenges found on these cutting edge systems. Work done under this project at Wisconsin can be divided into two categories, new algorithms and techniques for debugging, and foundation infrastructure work on our Dyninst binary analysis and instrumentation toolkits and MRNet scalability infrastructure.

Miller, Barton

2014-06-30

183

Spatial organization and drivers of the virtual water trade: a community-structure analysis  

Science.gov (United States)

The trade of agricultural commodities can be associated with a virtual transfer of the local freshwater resources used for the production of these goods. Thus, trade of food products virtually transfers large amounts of water from areas of food production to far consumption regions, a process termed the ‘globalization of water’. We consider the (time-varying) community structure of the virtual water network for the years 1986-2008. The communities are groups of countries with dense internal connections, while the connections are sparser among different communities. Between 1986 and 2008, the ratio between virtual water flows within communities and the total global trade of virtual water has continuously increased, indicating the existence of well defined clusters of virtual water transfers. In some cases (e.g. Central and North America and Europe in recent years) the virtual water communities correspond to geographically coherent regions, suggesting the occurrence of an ongoing process of regionalization of water resources. However, most communities also include countries located on different ‘sides’ of the world. As such, geographic proximity only partly explains the community structure of virtual water trade. Similarly, the global distribution of people and wealth, whose effect on the virtual water trade is expressed through simple ‘gravity models’, is unable to explain the strength of virtual water communities observed in the past few decades. A gravity model based on the availability of and demand for virtual water in different countries has higher explanatory power, but the drivers of the virtual water fluxes are yet to be adequately identified.

D'Odorico, Paolo; Carr, Joel; Laio, Francesco; Ridolfi, Luca

2012-09-01

184

Analysis of Departmental Functions: The Department of Staff and Instructional Services, Houston Community College System.  

Science.gov (United States)

The Department of Staff and Instructional Services (SIS) in the Houston Community College System (HCCS) takes a leadership role in providing and promoting products and services required to empower the HCCS in the pursuit of quality service to the campus community. The goals of the SIS department are to adopt Total Quality Service orientation,…

Walke, Jean

185

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

Directory of Open Access Journals (Sweden)

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.

Koichi Fujie

2012-03-01

186

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

Directory of Open Access Journals (Sweden)

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

187

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

Scientific Electronic Library Online (English)

Full Text Available SciELO Cuba | Language: Spanish Abstract in spanish 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. Abstract in english 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 sys [...] tem. 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.

2010-03-21

188

ClimatePipes: User-Friendly Data Access, Manipulation, Analysis & Visualization of Community Climate Models  

Science.gov (United States)

The impact of climate change will resonate through a broad range of fields including public health, infrastructure, water resources, and many others. Long-term coordinated planning, funding, and action are required for climate change adaptation and mitigation. Unfortunately, widespread use of climate data (simulated and observed) in non-climate science communities is impeded by factors such as large data size, lack of adequate metadata, poor documentation, and lack of sufficient computational and visualization resources. We present ClimatePipes to address many of these challenges by creating an open source platform that provides state-of-the-art, user-friendly data access, analysis, and visualization for climate and other relevant geospatial datasets, making the climate data available to non-researchers, decision-makers, and other stakeholders. The overarching goals of ClimatePipes are: - Enable users to explore real-world questions related to climate change. - Provide tools for data access, analysis, and visualization. - Facilitate collaboration by enabling users to share datasets, workflows, and visualization. ClimatePipes uses a web-based application platform for its widespread support on mainstream operating systems, ease-of-use, and inherent collaboration support. The front-end of ClimatePipes uses HTML5 (WebGL, Canvas2D, CSS3) to deliver state-of-the-art visualization and to provide a best-in-class user experience. The back-end of the ClimatePipes is built around Python using the Visualization Toolkit (VTK, http://vtk.org), Climate Data Analysis Tools (CDAT, http://uv-cdat.llnl.gov), and other climate and geospatial data processing tools such as GDAL and PROJ4. ClimatePipes web-interface to query and access data from remote sources (such as ESGF). Shown in the figure is climate data layer from ESGF on top of map data layer from OpenStreetMap. The ClimatePipes workflow editor provides flexibility and fine grained control, and uses the VisTrails (http://www.vistrails.org) workflow engine in the backend.

Chaudhary, A.; DeMarle, D.; Burnett, B.; Harris, C.; Silva, W.; Osmari, D.; Geveci, B.; Silva, C.; Doutriaux, C.; Williams, D. N.

2013-12-01

189

Spontaneous Communities of Learning: A Social Analysis of Learning Ecosystems in Massively Multiplayer Online Gaming (MMOG) Environments  

Digital Repository Infrastructure Vision for European Research (DRIVER)

This research project is comprised of a cross-cultural ethnography and social network analysis that seeks to illuminate the spontaneous communities of learning/practice that emerge around the relatively recent phenomenon of massively multiplayer online games. While these games can be played individually to greater or lesser degrees depending on the game, the game play mechanics are generally such that true mastery of the game can often only be achieved by working collaboratively with other pl...

Galarneau, Lisa

2005-01-01

190

Characterization of Microbial Community Structure in the Surface Sediment of Osaka Bay, Japan, by Phospholipid Fatty Acid Analysis  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Twenty-eight sediment samples collected from Osaka Bay, Japan, were analyzed for phospholipid ester-linked fatty acids (PLFA) to determine regional differences in microbial community structure of the bay. The abundance of three major groups of C10 to C19 PLFA (saturated, branched, and monounsaturated PLFA), which accounted for 84 to 97% of the total PLFA, indicated the predominance of prokaryotes in the sediment. The distribution of six clusters obtained by similarity analysis in the bay reve...

Rajendran, Narasimmalu; Matsuda, Osamu; Urushigawa, Yoshikuni; Simidu, Usio

1994-01-01

191

High-Throughput Analysis of Ammonia Oxidiser Community Composition via a Novel, amoA-Based Functional Gene Array  

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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 am...

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

2012-01-01

192

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

2014-01-01

193

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

2013-01-01

194

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

Science.gov (United States)

On August 8, 2009, Typhoon Morakot brought heavy rain to Taiwan, causing numerous landslides and debris flows in the Taihe village area of Meishan Township, Chiayi County, in south-central Taiwan. In the Taihe land is primary used for agriculture and land use management may be a factor in the area's landslides. This study explores Typhoon Morakot-induced landslides and land use changes between 1999 and 2009 using GIS with the aid of field investigation. Spot 5 satellite images with a resolution of 2.5 m are used for landslide interpretation and manually digitalized in GIS. A statistical analysis for landslide frequency-area distribution was used to identify the landslide characteristics associated with different types of land use. There were 243 landslides with a total area of 2.75 km(2) in the study area. The area is located in intrinsically fragile combinations of sandstone and shale. Typhoon Morakot-induced landslides show a power-law distribution in the study area. Landslides were mainly located in steep slope areas containing natural forest and in areas planted with bamboo, tea, and betel nut. Land covered with natural forest shows the highest landslide ratio, followed by bamboo, betel nut, and tea. Landslides thus show a higher ratio in areas planted with shallow root vegetation such as bamboo, betel nut, and tea. Furthermore, the degree of basin development is proportional to the landslide ratio. The results show that a change in vegetation cover results in a modified landslide area and frequency and changed land use areas have higher landslide ratios than non-changed. Land use management and community-based disaster prevention are needed in mountainous areas of Taiwan for hazard mitigation. PMID:22961329

Chen, Chien-Yuan; Huang, Wen-Lin

2013-05-01

195

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

CERN Document Server

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

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

2013-01-01

196

Comparative Human Health Risk Analysis of Coastal Community Water and Waste Service Options  

Science.gov (United States)

As a pilot approach to describe adverse human health effects from alternative decentralized community water systems compared to conventional centralized services (business-as-usual [BAU]), selected chemical and microbial hazards were assessed using disability adjusted life years ...

197

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

2012-07-01

198

Manifestation of efficiency of “Olweus” children bullying prevention programme: analysis of experience of school community members  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The efficiency of bullying prevention programme “Olweus” (OBPP ) created by Mr D. Olweus, a professor of psychology at Bergen University, is analyzed in the article by referring to experience gained by the school community members during participation in this programme. The aim of the article is to reveal the experience of the school community members, who participate in the “Olweus” bullying prevention programme, in the prevention of bullying actions/ activities. Presenting the resul...

Baniuliene?, Aurelija; Juodaityte?, Audrone?

2011-01-01

199

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

Ramanadhan, Shoba; Mendez, Samuel R.; Rao, Megan; Viswanath, Kasisomayajula

2013-01-01

200

Comparative Molecular Analysis of Community- or Hospital-Acquired Methicillin-Resistant Staphylococcus aureus  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) is a growing public health concern that has been associated with pediatric fatalities. It is hypothesized that the evolution of CA-MRSA is a recent event due to the acquisition of mec DNA by previously methicillin-susceptible strains that circulated in the community. This study investigated the genetic relatedness between CA-MRSA, hospital-associated MRSA (HA-MRSA), and nonmenstrual toxic shock syndrome (nmTSS) isolates....

Fey, P. D.; Sai?d-salim, B.; Rupp, M. E.; Hinrichs, S. H.; Boxrud, D. J.; Davis, C. C.; Kreiswirth, B. N.; Schlievert, P. M.

2003-01-01

 
 
 
 
201

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

Directory of Open Access Journals (Sweden)

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

Fred Rovai and Hope Jordan

2004-08-01

202

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

Fred Rovai and Hope Jordan

2004-01-01

203

Spatial organization and drivers of the virtual water trade: a community-structure analysis  

International Nuclear Information System (INIS)

The trade of agricultural commodities can be associated with a virtual transfer of the local freshwater resources used for the production of these goods. Thus, trade of food products virtually transfers large amounts of water from areas of food production to far consumption regions, a process termed the ‘globalization of water’. We consider the (time-varying) community structure of the virtual water network for the years 1986–2008. The communities are groups of countries with dense internal connections, while the connections are sparser among different communities. Between 1986 and 2008, the ratio between virtual water flows within communities and the total global trade of virtual water has continuously increased, indicating the existence of well defined clusters of virtual water transfers. In some cases (e.g. Central and North America and Europe in recent years) the virtual water communities correspond to geographically coherent regions, suggesting the occurrence of an ongoing process of regionalization of water resources. However, most communities also include countries located on different ‘sides’ of the world. As such, geographic proximity only partly explains the community structure of virtual water trade. Similarly, the global distribution of people and wealth, whose effect on the virtual water trade is expressed through simple ‘gravity models’, is unable to explain the strength of virtual water communities observed in the past few decades. A gravihe past few decades. A gravity model based on the availability of and demand for virtual water in different countries has higher explanatory power, but the drivers of the virtual water fluxes are yet to be adequately identified. (letter)

204

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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 mic...

Keiko Fujita; Seiichi Furuya; Minako Kohno; et al.

2010-01-01

205

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

2007-11-01

206

Community Detecting and Feature Analysis in Real Directed Weighted Social Networks  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Real social networks usually have some structural features of the complex networks, such as community structure, the scale-free degree distribution, clustering, "small world" network, dynamic evolution and so on. A new community detecting algorithm for directed and weighted social networks is proposed in this paper. Due to the use of more reference information, the accuracy of the algorithm is better than some of the typical detecting algorithms. And because of the use of heap structure and m...

Yao Liu; Qiao Liu; Zhiguang Qin

2013-01-01

207

Quantitative Microbial Community Analysis of Three Different Sulfidic Mine Tailing Dumps Generating Acid Mine Drainage?  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The microbial communities of three different sulfidic and acidic mine waste tailing dumps located in Botswana, Germany, and Sweden were quantitatively analyzed using quantitative real-time PCR (Q-PCR), fluorescence in situ hybridization (FISH), catalyzed reporter deposition-FISH (CARD-FISH), Sybr green II direct counting, and the most probable number (MPN) cultivation technique. Depth profiles of cell numbers showed that the compositions of the microbial communities are greatly different at t...

Kock, Dagmar; Schippers, Axel

2008-01-01

208

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

Science.gov (United States)

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. PMID:23882444

Gregg, Ak; Hatay, M; Haas, Af; Robinett, Nl; Barott, K; Vermeij, Mja; Marhaver, Kl; Meirelles, P; Thompson, F; Rohwer, F

2013-01-01

209

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

Science.gov (United States)

Soil microbial diversity represents the largest global reservoir of novel microorganisms and enzymes. In this study, we coupled functional metagenomics and DNA stable-isotope probing (DNA-SIP) using multiple plant-derived carbon substrates and diverse soils to characterize active soil bacterial communities and their glycoside hydrolase genes, which have value for industrial applications. We incubated samples from three disparate Canadian soils (tundra, temperate rainforest, and agricultural) with five native carbon ((12)C) or stable-isotope-labeled ((13)C) carbohydrates (glucose, cellobiose, xylose, arabinose, and cellulose). Indicator species analysis revealed high specificity and fidelity for many uncultured and unclassified bacterial taxa in the heavy DNA for all soils and substrates. Among characterized taxa, Actinomycetales (Salinibacterium), Rhizobiales (Devosia), Rhodospirillales (Telmatospirillum), and Caulobacterales (Phenylobacterium and Asticcacaulis) were bacterial indicator species for the heavy substrates and soils tested. Both Actinomycetales and Caulobacterales (Phenylobacterium) were associated with metabolism of cellulose, and Alphaproteobacteria were associated with the metabolism of arabinose; members of the order Rhizobiales were strongly associated with the metabolism of xylose. Annotated metagenomic data suggested diverse glycoside hydrolase gene representation within the pooled heavy DNA. By screening 2,876 cloned fragments derived from the (13)C-labeled DNA isolated from soils incubated with cellulose, we demonstrate the power of combining DNA-SIP, multiple-displacement amplification (MDA), and functional metagenomics by efficiently isolating multiple clones with activity on carboxymethyl cellulose and fluorogenic proxy substrates for carbohydrate-active enzymes. Importance: The ability to identify genes based on function, instead of sequence homology, allows the discovery of genes that would not be identified through sequence alone. This is arguably the most powerful application of metagenomics for the recovery of novel genes and a natural partner of the stable-isotope-probing approach for targeting active-yet-uncultured microorganisms. We expanded on previous efforts to combine stable-isotope probing and metagenomics, enriching microorganisms from multiple soils that were active in degrading plant-derived carbohydrates, followed by construction of a cellulose-based metagenomic library and recovery of glycoside hydrolases through functional metagenomics. The major advance of our study was the discovery of active-yet-uncultivated soil microorganisms and enrichment of their glycoside hydrolases. We recovered positive cosmid clones in a higher frequency than would be expected with direct metagenomic analysis of soil DNA. This study has generated an invaluable metagenomic resource that future research will exploit for genetic and enzymatic potential. PMID:25028422

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

2014-01-01

210

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

2012-09-01

211

Technical, economic and environmental analysis of a MSW kerbside separate collection system applied to small communities.  

Science.gov (United States)

The main aim of this study was to evaluate the costs and environmental impacts induced by a fixed model of MSW kerbside separate collection system for communities up to 10,000 inhabitants, in order to evaluate the convenience for the smaller municipalities to unite and form more economically and environmentally sound systems. This topic is important not only due to the large number of small municipalities (e.g. in Italy 72% of the municipalities has less than 5000 inhabitants) but also to the fact that separate collection systems are typically designed to take into account only the technical and economic aspects, which is a practice but not acceptable in the light of the sustainable development paradigm. In economic terms, between 1000 and 4000 inhabitants, the annual per capita cost for vehicles and personnel decreased, with a maximum at approximately 180€/inhabitants/year; while, from 5000 up to 10,000 inhabitants, the annual per capita cost was practically constant and equal to about 80€/inhabitants/year. For the municipalities of less than 5000 inhabitants, from an economic point of view the aggregation is always advantageous. The environmental impacts were calculated by means of the Life Cycle Assessment tool SimaPro 7.1, while the economic-environmental convenience was evaluated by combining in a simple multicriteria analysis, the annual total per capita cost (€/inhabitants/year) and the annual total per capita environmental impact (kEco-indicator point/inhabitants/year), giving the same importance to each criteria. The analysis was performed by means of the Paired Comparison Technique using the Simple Additive Weighting method. The economic and environmental convenience of the aggregation diminishes with the size of the municipalities: for less than 4000 inhabitants, the aggregation was almost always advantageous (91.7%); while, for more than or equal to 5000 inhabitants, the aggregation was convenient only in 33.3% of the cases. On the whole, out of 45 cases examined, for the municipalities from 1000 to 9000 inhabitants, the aggregation was both economically and environmentally convenient in 60.0% of the cases. PMID:22677016

De Feo, G; Malvano, C

2012-10-01

212

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

Energy Technology Data Exchange (ETDEWEB)

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

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

2009-06-15

213

Functional gene array-based analysis of microbial community structure in groundwater with gradient of contaminant levels  

Energy Technology Data Exchange (ETDEWEB)

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

Wu, Liyou [University of Oklahoma, Norman; Van Nostrand, Joy [University of Oklahoma, Norman; Schadt, Christopher Warren [ORNL; Watson, David B [ORNL; Jardine, Philip M [ORNL; Palumbo, Anthony Vito [ORNL; Hazen, Terry [Lawrence Berkeley National Laboratory (LBNL); Zhou, Jizhong [University of Oklahoma, Norman

2009-04-01

214

The SCEC Community Modeling Environment(SCEC/CME): A Collaboratory for Seismic Hazard Analysis  

Science.gov (United States)

The SCEC Community Modeling Environment (SCEC/CME) Project is an NSF-supported Geosciences/IT partnership that is actively developing an advanced information infrastructure for system-level earthquake science in Southern California. This partnership includes SCEC, USC's Information Sciences Institute (ISI), the San Diego Supercomputer Center (SDSC), the Incorporated Institutions for Research in Seismology (IRIS), and the U.S. Geological Survey. The goal of the SCEC/CME is to develop seismological applications and information technology (IT) infrastructure to support the development of Seismic Hazard Analysis (SHA) programs and other geophysical simulations. The SHA application programs developed on the Project include a Probabilistic Seismic Hazard Analysis system called OpenSHA. OpenSHA computational elements that are currently available include a collection of attenuation relationships, and several Earthquake Rupture Forecasts (ERFs). Geophysicists in the collaboration have also developed Anelastic Wave Models (AWMs) using both finite-difference and finite-element approaches. Earthquake simulations using these codes have been run for a variety of earthquake sources. Rupture Dynamic Model (RDM) codes have also been developed that simulate friction-based fault slip. The SCEC/CME collaboration has also developed IT software and hardware infrastructure to support the development, execution, and analysis of these SHA programs. To support computationally expensive simulations, we have constructed a grid-based scientific workflow system. Using the SCEC grid, project collaborators can submit computations from the SCEC/CME servers to High Performance Computers at USC and TeraGrid High Performance Computing Centers. Data generated and archived by the SCEC/CME is stored in a digital library system, the Storage Resource Broker (SRB). This system provides a robust and secure system for maintaining the association between the data seta and their metadata. To provide an easy-to-use system for constructing SHA computations, a browser-based workflow assembly web portal has been developed. Users can compose complex SHA calculations, specifying SCEC/CME data sets as inputs to calculations, and calling SCEC/CME computational programs to process the data and the output. Knowledge-based software tools have been implemented that utilize ontological descriptions of SHA software and data can validate workflows created with this pathway assembly tool. Data visualization software developed by the collaboration supports analysis and validation of data sets. Several programs have been developed to visualize SCEC/CME data including GMT-based map making software for PSHA codes, 4D wavefield propagation visualization software based on OpenGL, and 3D Geowall-based visualization of earthquakes, faults, and seismic wave propagation. The SCEC/CME Project also helps to sponsor the SCEC UseIT Intern program. The UseIT Intern Program provides research opportunities in both Geosciences and Information Technology to undergraduate students in a variety of fields. The UseIT group has developed a 3D data visualization tool, called SCEC-VDO, as a part of this undergraduate research program.

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

2005-12-01

215

Evaluating community investments in the mining sector using multi-criteria decision analysis to integrate SIA with business planning  

International Nuclear Information System (INIS)

Gaining senior management's commitment to long-term social development projects, which are characterised by uncertainty and complexity, is made easier if projects are shown to benefit the site's strategic goals. However, even though the business case for community investment may have been accepted at a general level, as a strategy for competitive differentiation, risk mitigation and a desire to deliver - and to be seen to deliver - a 'net benefit' to affected communities, mining operations are still faced with implementation challenges. Case study research on mining companies, including interviews with social investment decision-makers, has assisted in developing the Social Investment Decision Analysis Tool (SIDAT), a decision model for evaluating social projects in order to create value for both the company and the community. Multi-criteria decision analysis techniques integrating business planning processes with social impact assessment have proved useful in assisting mining companies think beyond the traditional drivers (i.e. seeking access to required lands and peaceful relations with neighbours), to broader issues of how they can meet their business goals and contribute to sustainable development in the regions in which they operate

216

Pre-design and life cycle cost analysis of a hybrid power system for rural and remote communities in Afghanistan  

Directory of Open Access Journals (Sweden)

Full Text Available In view of the present situation of the Afghanistan electricity sector, the photovoltaic and diesel generator stand-alone hybrid power system is increasingly attractive for application in rural and remote communities. Thousands of rural communities in Afghanistan depend solely on traditional kerosene for illumination and rarely have access to electricity sources such as DC battery for radio and other small appliances. This study is conducted to offer real-life solution to this problem. The hybrid system is investigated to meet the domestic load demand that is estimated based on the communities’ electricity consumption culture. At first, customary pre-design is pursued. Afterwards, the break-even point and net present value algorithms are applied for economic analysis. That makes this study differ from the previous academic literature. The concepts developed in this study are targeted for a cost-effective hybrid system, which is appropriate for rural and remote residents’ lifestyle change and improvement. Based on the academic research methods, overall analysis procedures can fit as an analogy, especially for developing countries.

Mir Sayed Shah Danish

2014-08-01

217

Microbial Community Structure of the Japan Trench Cold Seeps Sediment Determined by Phospholipid Analysis  

Science.gov (United States)

Seafloor cold seeps support some of the most prolific and diverse ecosystems on Earth. A multitude of microbial habitats are associated with cold seeps. The seeping fluids are enriched in reduced chemical species such as sulfide and methane. These reduced species are utilized by microorganisms to gain energy from the reduction of sulfate and oxidation of methane, the so-called anaerobic oxidation of methane. The Japan Trench is characterized by abundant chemosynthesis-based communities associated with cold seeps. Chemosynthetic communities of Maorithyas hadalis and Calyptogena phaseoliformis have been discovered at depths of over 7,000 m. In this project, sediment samples were collected from communities dominated by thyasirid bivalve Maorithyas hadalis and the vesicomyid clam Calyptogena phaseoliformis and analyzed for phospholipid fatty acids (PLFA). Our objectives were to determine and compare the microbial biomass and community structure of the two sites with different megafaunal species. Result showed the average estimated microbial biomass was 2.97*109 and 4.78*109 cells (g dry wt)-1 for Calyptogena and Maorithyas sediment, respectively. Fatty acids ranging from 12 to 22 carbons were detected. The PLFA profiles suggest the presence of methanotrophic bacteria, sulfur-oxidizing bacteria as well as sulfate-reducers. The polyunsaturated fatty acids (C 18:2 and C20:5) also allow us to trace the possible source of the sediment to the piezophilic bacteria. The assemblage of fatty acids indicates the presence of complex microbial communities in the cold seeps sediments of the Japan Trench.

Chan, O.; Fang, J.; Kato, C.

2004-12-01

218

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

2012-08-01

219

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 SciELO Brazil | Language: English 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 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.

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

2010-06-01

220

Study on anaerobic ammonium oxidation process coupled with denitrification microbial fuel cells (MFCs) and its microbial community analysis.  

Science.gov (United States)

Denitrifying MFC was successfully coupled with anaerobic ammonium oxidation process in this study. With the help of cathode electrons, the stoichiometry relationship ?(-)NH3-N:?(-)NO2(-)-N:?(+)NO3(-)-N was approximate 1:1.37:0.03 during the stable operation, which demonstrated its further nitrite and nitrate reduction. According to microbial community analysis, Candidatus Brocadia sinica was the main anammox community, and Rhodopseudomonas palustris with electrochemical driven denitrifying ability, especially enriched in biofilm. Higher abundance of nirK genes in biofilm (compare to the control) and invariable amx genes in suspended sludge were responsible for its better nitrogen removal. The sludge and biofilm performed their own duties on anammox and denitrification, respectively, according to genes quantification. Under the totally autotrophic system, electron donors were "concentrated supplied" and easy to control, which avoided the suppression of anammox growth, making this autotrophic coupling process appears to be more promising. PMID:25459866

Li, Chao; Ren, Hongqiang; Xu, Ming; Cao, Jiashun

2014-11-01

 
 
 
 
221

Analysis of the archaeal sub-seafloor community at Suiyo Seamount on the Izu-Bonin Arc  

Science.gov (United States)

A sub-surface archaeal community at the Suiyo Seamount in the Western Pacific Ocean was investigated by 16S rRNA gene sequence and whole-cell in situ hybridization analyses. In this study, we drilled and cased holes at the hydrothermal area of the seamount to minimize contamination of the hydrothermal fluid in the sub-seafloor by penetrating seawater. PCR clone analysis of the hydrothermal fluid samples collected from a cased hole indicated the presence of chemolithoautotrophic primary biomass producers of Archaeoglobales and the Methanococcales-related archaeal HTE1 group, both of which can utilize hydrogen as an electron donor. We discuss the implication of the microbial community on the early history of life and on the search for extraterrestrial life.

Hara, Kurt; Kakegawa, Takeshi; Yamashiro, Kan; Maruyama, Akihiko; Ishibashi, Jun-Ichiro; Marumo, Katsumi; Urabe, Tetsuro; Yamagishi, Akihiko

222

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

Science.gov (United States)

The application of multivariate statistical analyses has become a consistent feature in microbial ecology. However, many microbial ecologists are still in the process of developing a deep understanding of these methods and appreciating their limitations. As a consequence, staying abreast of progress and debate in this arena poses an additional challenge to many microbial ecologists. To address these issues, we present the GUide to STatistical Analysis in Microbial Ecology (GUSTA ME): a dynamic, web-based resource providing accessible descriptions of numerous multivariate techniques relevant to microbial ecologists. A combination of interactive elements allows users to discover and navigate between methods relevant to their needs and examine how they have been used by others in the field. We have designed GUSTA ME to become a community-led and -curated service, which we hope will provide a common reference and forum to discuss and disseminate analytical techniques relevant to the microbial ecology community. PMID:25314312

Buttigieg, Pier Luigi; Ramette, Alban

2014-12-01

223

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

DEFF Research Database (Denmark)

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

2011-01-01

224

Communities and Hierarchical Structures in Dynamic Social Networks: Analysis and Visualization  

CERN Document Server

Detection of community structures in social networks has attracted lots of attention in the domain of sociology and behavioral sciences. Social networks also exhibit dynamic nature as these networks change continuously with the passage of time. Social networks might also present a hierarchical structure led by individuals that play important roles in a society such as Managers and Decision Makers. Detection and Visualization of these networks changing over time is a challenging problem where communities change as a function of events taking place in the society and the role people play in it. In this paper we address these issues by presenting a system to analyze dynamic social networks. The proposed system is based on dynamic graph discretization and graph clustering. The system allows detection of major structural changes taking place in social communities over time and reveals hierarchies by identifying influential people in a social networks. We use two different data sets for the empirical evaluation and...

Gilbert, Frédéric; Zaidi, Faraz; Jourdan, Fabien; Bourqui, Romain

2014-01-01

225

Microbial community analysis of a single chamber microbial fuel cell using potato wastewater.  

Science.gov (United States)

Microbial fuel cells (MFCs) convert chemical energy to electrical energy via bio-electrochemical reactions mediated by microorganisms. This study investigated the diversity of the microbial community in an air cathode single chamber MFC that used potato-process wastewater as substrate. Terminal restriction fragment length polymorphism results indicated that the bacterial communities on the anode, cathode, control electrode, and MFC bulk fluid were similar, but differed dramatically from that of the anaerobic domestic sludge and potato wastewater inoculum. The 16S ribosomal DNA sequencing results showed that microbial species detected on the anode were predominantly within the phyla of Proteobacteria, Firmicutes, and Bacteroidetes. Fluorescent microscopy results indicated that there was a clear enhancement of biofilm formation on the anode. Results of this study could help improve understanding of the complexity of microbial communities and optimize the microbial composition for generating electricity by MFCs that use potato wastewater. PMID:24851328

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

2014-04-01

226

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

Energy Technology Data Exchange (ETDEWEB)

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

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

2014-04-01

227

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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, Marinimicr...

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

2012-01-01

228

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

2013-11-01

229

An Analysis of the Community College Concept in the Socialist Republic of Viet Nam  

Science.gov (United States)

The purpose of this study was to discover if core characteristics exist forming a Vietnamese community college model and to determine if the characteristics would explain the model. This study utilized three theoretical orientations while reviewing the existing literature, formulating the research questions, examining the data and drawing…

Epperson, Cynthia K.

2010-01-01

230

The Faculty Identities of Community College Adjuncts Teaching in the Humanities: A Discourse Analysis Study  

Science.gov (United States)

Research has shown that forming a professional identity is central in the process of becoming an effective teacher (Alsup, 2006; Danielewicz, 2001). Yet, little is known about the faculty identity development of part-time faculty, who represent nearly 70% of all faculty at community colleges (AFT Higher Education, 2009). Addressing this critical…

Thirolf, Kathryn Q.

2012-01-01

231

Analysis of written advertising material distributed through community pharmacies in Riyadh, Saudi Arabia  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Background: Advertising is a crucial component of pharmaceutical industry promotion. Research indicates that information on advertisement materials might be inadequate, inaccurate, biased, and misleading. Objective: To analyse and critically assess the information presented in print pharmaceutical advertisements in Saudi Arabia.Methods: Pharmaceutical advertisements were collected from 280 community pharmacies in Riyadh city, Saudi Arabia. The advertisements were evaluated using criteria deri...

Sa, Al-aqeel; Jf, Al-sabhan; Ny, Sultan

2013-01-01

232

Career Stages of Community College Faculty: A Qualitative Analysis of their Career Paths, Roles, and Development.  

Science.gov (United States)

Reports findings from interviews of 22 faculty that elicited perceptions of their career paths, early-stage career roles, and the role played by faculty development. Finds that the majority chose the community college because of its emphasis on teaching and that their career roles changed over time. Makes recommendations for faculty recruitment,…

Fugate, Amy L.; Amey, Marilyn J.

2000-01-01

233

Workforce: Gap Analysis of a Rural Community College's Training and Local Business & Industry Needs  

Science.gov (United States)

In Mississippi, the bulk of the responsibility to conduct workforce training falls on the community colleges. With the recent trends of large industry relocating overseas, layoffs, and plant closures, these challenges have become prevalent in rural America. Through the development and delivery of workforce programs to local business and industry,…

Wilson, Delfina Acosta

2009-01-01

234

A Survey and Analysis of Part-Time Instructors at J. Sargeant Reynolds Community College [Virginia].  

Science.gov (United States)

During the 1975 fall quarter, J. Sargeant Reynolds Community College (Richmond, Virginia) conducted a survey of its part-time faculty members. Of the 346 part-time instructors at the college, 254 (73.4%) returned usable questionnaires. The factors investigated were: (1) their characteristics--age, race, sex, educational background, previous…

Grymes, Robert J., Jr.

235

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

Science.gov (United States)

The links between social capital and mental wellbeing are established but the direction of the social capital-wellbeing relationship is rarely systematically examined. This omission undermines the validity of social capital as a basis for health interventions. The aim of this paper was to explore the short-term (one-year) reciprocal relationship between community participation - an important component of social capital - and mental wellbeing. We used nationally representative Household, Income and Labour Dynamics in Australia (HILDA) Survey data, 2005-11. The HILDA Survey is an annual cohort study from which was extracted a sub-sample of panel data (the same people participating across multiple waves) enabling us to use fixed effects regression methods to model the longitudinal association of mental health and participation controlling for individual heterogeneity. The results showed that better mental wellbeing in one year was generally related to more community participation the next year, while greater past community participation was linked to better mental wellbeing the next year independent of (i) initial mental wellbeing, (ii) multiple potentially confounding factors and (iii) unobserved and time-constant heterogeneity. Political participation was marginally related to worse mental health in both directions. The results also showed that the association between community participation and mental wellbeing the next year is weaker for those with poor initial wellbeing than for initially healthier respondents. Our findings may inform the trial and scientific evaluation of programs aimed at increasing informal social connectedness and civic engagement to promote mental wellbeing. PMID:25633762

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

2015-03-01

236

Stable isotope analysis reveals community-level variation in fish trophodynamics across a fringing coral reef  

Science.gov (United States)

In contrast to trophodynamic variations, the marked zonation in physical and biological processes across coral reefs and the concomitant changes in habitat and community structure are well documented. In this study, we demonstrate consistent spatial changes in the community-level trophodynamics of 46 species of fish across the fringing Ningaloo Reef, Western Australia, using tissue stable isotope and fatty acid analyses. Increasing nitrogen (?15N) and decreasing carbon (?13C) isotope ratios in the tissues of herbivores, planktivores and carnivores with increasing proximity to the ocean were indicative of increased reliance on oceanic productivity. In contrast, detritivores and corallivores displayed no spatial change in ?15N or ?13C, indicative of the dependence on reef-derived material across the reef. Higher ?13C, as well as increased benthic- and bacterial-specific fatty acids, suggested reliance on reef-derived production increased in back-reef habitats. Genus-level analyses supported community- and trophic group-level trends, with isotope modelling of species from five genera ( Abudefduf sexfasciatus, Chromis viridis, Dascyllus spp., Pomacentrus spp. and Stegastes spp.), demonstrating declining access to oceanic zooplankton and, in the case of Pomacentrus spp. and Stegastes spp., a switch to herbivory in the back-reef. The spatial changes in fish trophodynamics suggest that the relative roles of oceanic and reef-derived nutrients warrant more detailed consideration in reef-level community ecology.

Wyatt, A. S. J.; Waite, A. M.; Humphries, S.

2012-12-01

237

Microbial Communities in Biofilms of an Acid Mine Drainage Site Determined by Phospholipid Analysis  

Science.gov (United States)

Phospholipids were extracted to determine the microbial biomass and community structure of biofims from an acid mine drainage (AMD) at the Green Valley coal mine site (GVS) in western Indiana. The distribution of specific biomarkers indicated the presence of a variety of microorganisms. Phototrophic microeukaryotes, which include Euglena mutabilis, algae, and cyanobacteria were the most dominant organisms, as indicated by the presence of polyunsaturated fatty acids. The presence of terminally methyl branched fatty acids suggests the presence of Gram-positive bacteria, and the mid-methyl branched fatty acids indicates the presence of sulfate-reducing bacteria. Fungi appear to also be an important part of the AMD microbial communities as suggested by the presence of 18:2 fatty acid. The acidophilic microeukaryotes Euglena dominated the biofilm microbial communities. These microorganisms appear to play a prominent role in the formation and preservation of stromatolites and in releasing oxygen to the atmosphere by oxygenic photosynthesis. Thus, the AMD environment comprises a host of microorganisms spreading out within the phylogenetic tree of life. Novel insights on the roles of microbial consortia in the formation and preservation of stromatolites and the production of oxygen through photosynthesis in AMD systems may have significance in the understanding of the interaction of Precambrian microbial communities in environments that produced microbially-mediated sedimentary structures and that caused oxygenation of Earth's atmosphere.

Das Gupta, S.; Fang, J.

2008-12-01

238

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

Science.gov (United States)

The diversity of the intestinal bacterial communities in Dastarcus helophoroides (Fairmaire) (Coleoptera: Bothrideridae) larvae and adults was assayed by PCR-DGGE to determine whether different artificial diets could influence these bacterial communities. Two diets were used for feeding the larvae and four for the adults. Escherichia, Desemzia, Staphylococcus, Asticcacaulis, Cellvibrio, Aurantimonas, and Planomicrobium were isolated from the gut of the adults, with Escherichia and Staphylococcus being the main bacterial communities, and the quantities of intestinal bacterial were different in the adults fed different diets. Specifically, the amount of intestinal bacteria from the adults fed different diets had the following ranking according to the major component of the diet: ant powder > darkling beetle pupa powder > cricket powder > silkworm pupa powder. Escherichia, Bacillus, Staphylococcus, Kurthia, Planococcaceae, Ralstonia, Leptothrix, Acinetobacter, and Pseudomonas were isolated from the gut of the larvae. The quantity of intestinal bacteria from the larvae fed the darkling beetle pupae was greater than that from the larvae fed other artificial diets. This study, for the first time, investigated the effect of artificial diets on the bacterial community and the intestinal microbial diversity of D. helophoroides. PMID:25373234

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

2014-01-01

239

An Analysis of Step-In/Step-Out Students at Valencia Community College.  

Science.gov (United States)

In order to determine the characteristics, educational motivations, and opinions of "step-in/step-out" students at Valencia Community College (VCC), the author sent questionnaires to 200 persons selected at random from those who had enrolled for less than 12 hours credit between September 1975 and January 1977 and who were eligible to return but…

Bennett, Lula M.

240

Comparative denaturing gradient gel electrophoresis analysis of fungal communities associated with whole plant corn silage.  

Science.gov (United States)

Significant portions of grain produced for livestock consumption are convened into ensiled forage. Silage producers have long recognized the positive effects of using an inoculant to insure the proper transformation of forage into a palatable and digestible feedstuff. When silage is fed from a storage structure, exposure to air stimulates the growth of epiphytic aerobes that may result in the loss of up to 50% of the dry matter. Moreover, fungi have been found to be associated with ensiled forage, but their growth is normally suppressed by the anaerobic conditions. However, the introduction of oxygen results in a fungal bloom, and the fungi and the associated metabolites may result in lost productivity in the livestock consuming the contaminated forage. In this study, we report on the diversity of the fungal community associated with whole plant corn silage during the ensiling process, and the effect of two different bacterial inoculants as compared with the uninoculated natural epiphytic fermentation on the distribution of the fungi associated with the silage. The fungal community from duplicate mini-silo packages of the same treatment was analyzed by denaturing gradient gel electrophoresis and direct sequencing of the resulting operational taxonomic units. This method proved useful in analyzing the complex microbial communities associated with the forage in that it was possible to determine that one inoculant dramatically influenced the fungal community associated with whole plant corn silage. PMID:11683465

May, L A; Smiley, B; Schmidt, M G

2001-09-01

 
 
 
 
241

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

242

Building ties: social capital network analysis of a forest community in a biosphere reserve in Chiapas, Mexico  

Directory of Open Access Journals (Sweden)

Full Text Available Governance of the commons depends on the capacity to generate collective action. Networks and rules that foster that collective action have been defined as social capital. However, their causal link is still not fully understood. We use social network analysis to assess social capital, decision-making, and collective action in a forest-based common pool resource management in La Sepultura Biosphere Reserve (Chiapas, Mexico. Our research analyzes the productive networks and the evolution of coffee groups in one community. The network shows some centrality, with richer landholders tending to occupy core positions and poorer landless peasants occupying peripheral ones. This has fostered the community's environmentally oriented development but has also caused internal conflicts. Market requirements have shaped different but complementary productive networks, where organic coffee commercialization is the main source of bridging ties, which has resulted in more connectivity and resilience. Conservation attitudes, along with the institutional setting of the community, have promoted collective action. The unresolved conflicts, however, still leave some concerns about governance in the future.

Felipe Reyes

2012-09-01

243

Community patterns of stigma towards persons living with HIV: A population-based latent class analysis from rural Vietnam  

LENUS (Irish Health Repository)

Abstract Background The negative effects of stigma on persons living with HIV (PLHIV) have been documented in many settings and it is thought that stigma against PLHIV leads to more difficulties for those who need to access HIV testing, treatment and care, as well as to limited community uptake of HIV prevention and testing messages. In order to understand and prevent stigma towards PLHIV, it is important to be able to measure stigma within communities and to understand which factors are associated with higher stigma. Methods To analyze patterns of community stigma and determinants to stigma toward PLHIV, we performed an exploratory population-based survey with 1874 randomly sampled adults within a demographic surveillance site (DSS) in rural Vietnam. Participants were interviewed regarding knowledge of HIV and attitudes towards persons living with HIV. Data were linked to socioeconomic and migration data from the DSS and latent class analysis and multinomial logistic regression were conducted to examine stigma group sub-types and factors associated with stigma group membership. Results We found unexpectedly high and complex patterns of stigma against PLHIV in this rural setting. Women had the greatest odds of belong to the highest stigma group (OR 1.84, 95% CI 1.42-2.37), while those with more education had lower odds of highest stigma group membership (OR 0.45, 95% CI 0.32-0.62 for secondary education; OR 0.19, 95% CI 0.10-0.35 for tertiary education). Long-term migration out of the district (OR 0.61, 95% CI 0.4-0.91), feeling at-risk for HIV (OR 0.42, 95% CI 0.27-0.66), having heard of HIV from more sources (OR 0.44, 95% CI 0.3-0.66), and knowing someone with HIV (OR 0.76, 95% CI 0.58-0.99) were all associated with lower odds of highest stigma group membership. Nearly 20% of the population was highly unsure of their attitudes towards PLHIV and persons in this group had significantly lower odds of feeling at-risk for HIV (OR 0.54, 95% CI 0.33-0.90) or of knowing someone with HIV (OR 0.32, 95% CI 0.22-0.46). Conclusions Stigma towards PLHIV is high generally, and very high in some sub-groups, in this community setting. Future stigma prevention efforts could be enhanced by analyzing community stigma sub-groups and tailoring intervention messages to community patterns of stigma.

Pharris, Anastasia

2011-09-18

244

The Financial Analysis of a Modern Scheme for Managing Waste Proposed for the Urban Community Arie?, Cluj County  

Directory of Open Access Journals (Sweden)

Full Text Available This paper presents a scheme for managingwaste, proposed for the urban community of Arie?,Cluj County, in which we are going to show themain activities that should be accomplished withthe support of the local public administration.Based on the analysis of the waste flows, thedemographic trends and the waste generatingtrends, we propose a scheme for managingwaste that has a major investment component,an administrative re-organizing component andan educational one. We suggest a scheme whichincludes advanced techniques and methods fortreating waste. Moreover, we demonstrated thatthe efficiency of the scheme cannot be conceivedoutside a circuit for valorizing and recycling theuseful materials contained in the waste.

Lucia Monica SCOR?AR

2009-10-01

245

Analysis of links between groundwater recharge and discharge areas and wetland plant communities distribution in Middle Biebrza Basin, Poland  

Science.gov (United States)

Natural evolution of wetlands is strongly dependent on groundwater dynamics, soil aeration and climate. These environmental factors determine the constant development of wetland plant communities and peat forming processes. Depending on spatial distribution of groundwater flow systems and recharge and discharge conditions, shallow groundwater can also be influenced by phreatophytic plants. Such feedback plays an important role in wetland development, especially when landuse or climate changes occur. Thus, understanding the links between dynamics of biotopic and biocenotic relations is crucial for wetland management aimed at the comprehensive set of conservation strategies. Main aim of this study was to review links between valuable wetland plant communities and the groundwater recharge/discharge conditions of particular habitats of Middle Biebrza Basin, Poland. The study area consists of various types of wetland landscapes, of which the dominant are fens. Organogenic top layer is intersected locally by sandy dunes and glaci-fluvial residual plateaus. The northern boundary of the study area is covered with an outwash plateau. A three-dimensional regional groundwater flow model was set up to quantify groundwater system and flow paths. Model calibration involved measured heads of the unconfined organogenic top layer and the underlaying, confined sandy aquifer. Measured thickness of unsaturated zone as well as physical parameters of organogenic layer were taken into account in interpretation of shallow groundwater dynamics. Recharge to groundwater was spatially distributed in accordance to analysis of measured precipitation-groundwater level relationships. Cell-by-cell flow analysis and groundwater exfiltration analysis were applied to map groundwater recharge and discharge areas within the modelled area. Results of groundwater modelling were validated with phytosociologic research combined with remote-sensing based spatial analysis of wetland habitats distribution. Results indicated spatial distibution of water balance components of different wetland habitats. In areas of fen plant communities, modelled intensity of vertical upward groundwater flow to the top layer is significantly higher than in ombrotrophic habitats. Research indicated, that spatial patterns of groundwater recharge/discharge intensity is strongly linked to areal distribution of water quality dependent phreatophytic plant communities. In certain areas, simulated drainage conditions increased the thickness of the unsaturated zone, which explains a crucial response of wetland evolution in the last centuries: redirection of groundwater flow towards artificial canals resulted in diminished throughflow in organogenic layer, which causes accumulation of acidic rain water and - consequently - development of ombrotrophic habitats.

Grygoruk, Mateusz; Batelaan, Okke; Okruszko, Tomasz; Kotowski, Wiktor; Rycharski, Marek; Chormanski, Jaroslaw; Miroslaw-Swiatek, Dorota

2010-05-01

246

Phylogenetic analysis of atmospheric halotolerant bacterial communities at high altitude in an Asian dust (KOSA) arrival region, Suzu City  

International Nuclear Information System (INIS)

The microbial communities transported by Asian desert dust (KOSA) events have attracted much attention as bioaerosols because the transported microorganisms are thought to influence the downwind ecosystems in Korea and Japan. However, the atmospheric microbial community has not been investigated at high altitude in the KOSA arrival area. In this study, to estimate the viability and diversity of atmospheric halotolerant bacteria, which are expected to resist to various environmental stresses as well as high salinities, bioaerosol samples were collected at 10 and 600 m above the ground within the KOSA arrival area, Suzu City, Japan, during KOSA events. During the sampling period, the particle numbers at 600 m were higher than those at 10 m, suggesting that large particles of aerosol fall from the high altitude of 600 m to the ground surface. The microorganisms in bioaerosol samples grew in media containing up to 15% NaCl concentrations demonstrating the viability of the halotolerant bacteria in bioaerosol samples. The PCR-DGGE analysis using 16S rDNA revealed that the bacterial species in NaCl-amended cultures were similar to the bacteria detected from the genomic DNA directly extracted from the bioaerosol samples. The 16S rDNA sequences of bacterial communities in bioaerosol samples were classified into 4 phylotypes belonging to the Bacilluscereus or Bacillussubtilis group. The bioaerosol samples collected at 600 m included 2 phylotypes belonging to B. subtilis, and onhylotypes belonging to B. subtilis, and one phylotype among all 4 phylotypes was identical between the samples at 10 and 600 m. In the atmosphere at 600 m, the halotolerant bacterial community was expected to remain viable, and the species composition was expected to include a few species of the genus Bacillus. During this investigation period, these atmospheric bacteria may have been vertically transported to the ground surface, where the long-range KOSA particle transport from China is frequently observed.

247

Community and Nihilism  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Developing the arguments put forward in books such as Communitas, in this article the political  philosopher Roberto Esposito tries to overcome the customary opposition between the notions of community and nihilism. His aim is to rethink what community might mean in an age of ‘completed nihilism’. In a subtle genealogical and etymological analysis of the concept of community, he demonstrates how, rather than establishing a substantial and positive bond, community is ...

Roberto Esposito

2009-01-01

248

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

249

Community Detecting and Feature Analysis in Real Directed Weighted Social Networks  

Directory of Open Access Journals (Sweden)

Full Text Available Real social networks usually have some structural features of the complex networks, such as community structure, the scale-free degree distribution, clustering, "small world" network, dynamic evolution and so on. A new community detecting algorithm for directed and weighted social networks is proposed in this paper. Due to the use of more reference information, the accuracy of the algorithm is better than some of the typical detecting algorithms. And because of the use of heap structure and multi-task modular architecture, the algorithm also got a high computational efficiency than other algorithms. The effectiveness and efficiency of the algorithm is validated by experiments on real social networks. Based on the theories and models of complex networks, the features of the real large social networks are analyzed.

Yao Liu

2013-06-01

250

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

International Nuclear Information System (INIS)

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

251

Geographic analysis of thermal equilibria: A bioenergetic model for predicting thermal response of aquatic insect communities  

International Nuclear Information System (INIS)

The thermal regime immediately downstream from bottom release reservoirs is often characterized by reduced diel and seasonal (winter warm/summer cool) conditions. These unusual thermal patterns have often been implicated as a primary factor underlying observed downstream changes in the species composition of aquatic macroinvertebrate communities. The potential mechanisms for selective elimination of benthic species by unusual thermal regimes has been reviewed. Although the effects of temperature on the rate and magnitude of larval growth and development has been included in the list of potential mechanisms, only recently have field studies below dams focused on this interrelationship. This study investigates the overall community structure as well as the seasonal pattern of larval growth and development for several univoltine species of insects in the Delaware River below or near the hypolimnetic discharge of the Cannonsville and Pepeacton dams. These dams, which are located on the West and East branches of the Delaware River, respectively, produce a thermal gradient extending about 70 km downstream

252

Community structure analysis of reverse osmosis membrane biofilms and the significance of Rhizobiales bacteria in biofouling.  

Science.gov (United States)

The biofilm community structure of a biofouled reverse osmosis (RO) membrane was examined using a polyphasic approach, and the dominant phylotypes retrieved were related to the order Rhizobiales, a group of bacteria that is hitherto not implicated in membrane biofouling. A comparison with two other membrane biofilms using T-RFLP fingerprinting also revealed the dominance of Rhizobiales organisms. When pure culture RO biofilm isolates were cultivated aerobically in BIOLOG microplates, most Rhizobiales were metabolically versatile in their choice of carbon substrates. Nitrate reduction was observed in five RO isolates related to Castellaniella, Ochrobactrum, Stenotrophomonas, and Xanthobacter. Many of the key Rhizobiales genera including Bosea, Ochrobactrum, Shinella, and Rhodopseudomonas were detected by PCR to contain the nirK gene responsible for nitrite reductase activity. These findings suggest that Rhizobiales organisms are ecologically significant in membrane biofilm communities under both aerobic and anoxic conditions and may be responsible for biofouling in membrane separation systems. PMID:17695921

Pang, Chee Meng; Liu, Wen-Tso

2007-07-01

253

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

International Nuclear Information System (INIS)

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.)

254

Comparative analysis of microbial community of novel lactic acid fermentation inoculated with different undefined mixed cultures.  

Science.gov (United States)

Three undefined mixed cultures (activated sludge) from different municipal wastewater treatment plants were used as seeds in a novel lactic acid fermentation process fed with potato peel waste (PPW). Anaerobic sequencing batch fermenters were run under identical conditions to produce predominantly lactic acid. Illumina sequencing was used to examine the 16S rRNA genes of bacteria in the three seeds and fermenters. Results showed that the structure of microbial communities of three seeds were different. All three fermentation products had unique community structures that were dominated (>96%) by species of the genus Lactobacillus, while members of this genus constituted lactic acid fermentation of PPW with undefined mixed cultures were robust and resilient, which provided engineering prospects for the microbial utilization of carbohydrate wastes to produce lactic acid. PMID:25545096

Liang, Shaobo; Gliniewicz, Karol; Mendes-Soares, Helena; Settles, Matthew L; Forney, Larry J; Coats, Erik R; McDonald, Armando G

2015-03-01

255

Relevant risk factors analysis of diabetic retinopathy in patients with type 2 diabetes mellitus from community  

Directory of Open Access Journals (Sweden)

Full Text Available AIM: To investigate the related risk factors of diabetic retinopathy(DRin patients with type 2 diabetes mellitus(DMin residents of community in our local area and provide a clinical evidence for prevention and treatment for the complication of DM. METHODS: The residents who lived in our local community with type 2 DM and hospitalized were studied. The stages of DR and duration of DM, blood pressure, level of blood glucose, blood lipids and other factors were analyzed statistically.RESULTS: Fifty-three patients(30.1%were found with DR in 176 cases. The risk factors included the diabetic duration and glycosylated hemoglobin(all PP>0.05. CONCLUSION: Diabetic duration and glycosylated hemoglobin are the risk factors of DR.

Sheng-Li Hao

2013-10-01

256

The Australian Information Systems Research Community: an analysis of mainstream publication outlets  

Directory of Open Access Journals (Sweden)

Full Text Available This paper reports on an investigation of the nature of and interactions among the Information Systems academic research community in Australia. The 382 refereed papers from the two mainstream IS refereed publication outlets in Australia were analysed for the period 1990-1996 to determine the contributions of individual universities, departments and authors to the pattern of collaboration, and to examine the nature of the contributors. The study revealed that several institutions, departments and authors dominated the publication outlets and that the majority of the collaboration that occurred took place within university departments. Collaboration between and among different disciplines and nations, and between practitioners and academics was limited. It was found that although the Australian academic IS research community had only recently emerged, it was growing strongly.

Gail Ridley

1998-05-01

257

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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 older youth) completed a web-based survey comprised of 15 drug-related problem situations and 413 responses developed by Hawaiian youth. The findings ...

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

2011-01-01

258

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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 investi...

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

2006-01-01

259

Community analysis of betaproteobacterial ammonia-oxidizing bacteria using the amoCAB operon  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The genes and intergenic regions of the amoCAB operon were analyzed to establish their potential as molecular markers for analyzing ammonia-oxidizing betaproteobacterial (beta-AOB) communities. Initially, sequence similarity for related taxa, evolutionary rates from linear regressions, and the presence of conserved and variable regions were analyzed for all available sequences of the complete amoCAB operon. The gene amoB showed the highest sequence variability of the thre...

Junier, P.; Kim, Ok-sun; Junier, T.; Ahn, T. -s; Imhoff, Johannes F.; Witzel, K. -p

2013-01-01

260

Design and validation of an analysis grid of social networks (virtual communities)  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The Internet and communication technologies have caused profound changes in the circulation of information, and consequently in the ways we teach, learn, and interact with each other. A research project was initiated in the year 2009 in order to investigate whether virtual communities, created from the existing social software on the web, provide the development of meaningful learning, the result of interactions, and knowledge sharing among its members. The first phase of the pres...

Lisbo?a, Eliana Santana; Coutinho, Clara Pereira

2010-01-01

 
 
 
 
261

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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,...

Jeon, Yoon-seong; Chun, Jongsik; Kim, Bong-soo

2013-01-01

262

Rural Communities on the Cambodian Central Plain: A Comparative Analysis Based on Five Communes  

Directory of Open Access Journals (Sweden)

Full Text Available Introduction Rural Development in Cambodia in Transition With nearly 85 percent of its population living in rural communities, it is obvious that rural development issues occupy a prominent place in the overall development of Cambodia. As the country’s population rapidly increases, people in rural areas depend upon agriculture as their means of subsistence. In parallel, agriculture must meet the growing and diversifying urban food demand, while generating resources for export. The complex pro...

Jean-Christophe Diepart

2013-05-01

263

A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Recent advances in massively parallel sequencing technology have created new opportunities to probe the hidden world of microbes. Taxonomy-independent clustering of the 16S rRNA gene is usually the first step in analyzing microbial communities. Dozens of algorithms have been developed in the last decade, but a comprehensive benchmark study is lacking. Here, we survey algorithms currently used by microbiologists, and compare seven representative methods in a large-scale benchmark study that ad...

Sun, Yijun; Cai, Yunpeng; Huse, Susan M.; Knight, Rob; Farmerie, William G.; Wang, Xiaoyu; Mai, Volker

2012-01-01

264

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

Abstract 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 functiona...

Yousuf Basit; Sanadhya Payal; Keshri Jitendra; Jha Bhavanath

2012-01-01

265

Analysis of Fuel Cell Driven Ground Source Heat Pump Systems in Community Buildings  

Digital Repository Infrastructure Vision for European Research (DRIVER)

In the present study, a fuel cell driven ground source heat pump (GSHP) system is applied in a community building and heat pump system performance is analyzed by computational methods. Conduction heat transfer between the brine pipe and ground is analyzed by TEACH code in order to predict the performance of the heat pump system. The predicted coefficient of performance (COP) of the heat pump system and the energy cost were compared with the variation of the location of the objective building,...

Jong-Keun Shin; Young-Don Choi; Dong-Hwa Jeong; Jae-Ki Byun

2013-01-01

266

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 applied to analyse the economic and geopolitical motivations for cooperating on energy as a mean to ensure the gas transit dimension of EU energy security on the one side and as a mean to solve the e...

Petersen, Anne Hald

2012-01-01

267

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

Two aerobic, lab-scale, slurry-phase bioreactors were used to examine the biodegradation of polycyclic aromatic hydrocarbons (PAHs) in contaminated soil and the associated bacterial communities. The two bioreactors were operated under semi-continuous (draw-and-fill) conditions at a residence time of 35 days, but one was fed weekly and the other monthly. Most of the quantified PAHs, including high-molecular-weight compounds, were removed to a greater extent in the weekly-fed bioreactor, which ...

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

2011-01-01

268

A multiple criteria analysis for-household solid waste management in the urban community of Dakar  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Household solid waste management is a severe problem in big cities of developing countries. Mismanaged solid waste dumpsites produce bad sanitary, ecological and economic consequences for the whole population, especially for the poorest urban inhabitants. Dealing with this problem, this paper utilizes field data collected in the urban community of Dakar, in view of ranking nine areas of the city with respect to multiple criteria of nuisance. Nine criteria are built and organized in three fami...

Kapepula, K. M.; Colson, Ge?rard; Sabri, Karim; Thonart, Philippe

2007-01-01

269

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

Crude oil samples with high- and low-water content from two offshore platforms (PA and PB) in Campos Basin, Brazil, were assessed for bacterial communities by 16S rRNA gene-based clone libraries. RDP Classifier was used to analyze a total of 156 clones within four libraries obtained from two platforms. The clone sequences were mainly affiliated with Gammaproteobacteria (78.2% of the total clones); however, clones associated with Betaproteobacteria (10.9%), Alphaproteobacteria (9%), and Firmic...

Elisa Korenblum; Diogo Bastos Souza; Monica Penna; Lucy Seldin

2012-01-01

270

Multisubstrate Isotope Labeling and Metagenomic Analysis of Active Soil Bacterial Communities  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Soil microbial diversity represents the largest global reservoir of novel microorganisms and enzymes. In this study, we coupled functional metagenomics and DNA stable-isotope probing (DNA-SIP) using multiple plant-derived carbon substrates and diverse soils to characterize active soil bacterial communities and their glycoside hydrolase genes, which have value for industrial applications. We incubated samples from three disparate Canadian soils (tundra, temperate rainforest, and agricultural) ...

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

2014-01-01

271

Microbial Community Analysis of a Coastal Salt Marsh Affected by the Deepwater Horizon Oil Spill  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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 ...

Beazley, Melanie J.; Martinez, Robert J.; Rajan, Suja; Powell, Jessica; Piceno, Yvette M.; Tom, Lauren M.; Andersen, Gary L.; Hazen, Terry C.; Nostrand, Joy D.; Zhou, Jizhong; Mortazavi, Behzad; Sobecky, Patricia A.

2012-01-01

272

Human Helminth Co-Infection: Analysis of Spatial Patterns and Risk Factors in a Brazilian Community  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Helminth species such as Necator americanus and Schistosoma mansoni are among the most prevalent of chronic human infections in the developing world. Individuals living in endemic areas are commonly infected with both species. Although the implications of being co-infected with helminths are increasingly recognized, factors influencing patterns of co-infection within human communities remain ill-defined. Here, we describe spatial patterns and risk factors for co-infection with N. americanus a...

Pullan, Rachel L.; Bethony, Jeffrey M.; Geiger, Stefan M.; Cundill, Bonnie; Correa-oliveira, Rodrigo; Quinnell, Rupert J.; Brooker, Simon

2008-01-01

273

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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 a...

Popoola, K. O. K.; Otalekor, A.

2011-01-01

274

Direct ribosome isolation from soil to extract bacterial rRNA for community analysis.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

A simple method that combines an adapted ribosome isolation method and a common RNA extraction step has been developed for selective recovery of intact rRNA from natural microbial communities in soil. After mechanical cell lysis, ribosomes are separated by centrifugation steps, avoiding massive humic acid contamination and RNA degradation. The protocol accommodates the complex composition of soils by blocking adsorbing surfaces and humic acids with polyvinylpyrrolidone and bovine serum albumi...

Felske, A.; Engelen, B.; Nu?bel, U.; Backhaus, H.

1996-01-01

275

Integrated metagenomics and network analysis of soil microbial community of the forest timberline.  

Science.gov (United States)

The forest timberline responds quickly and markedly to climate changes, rendering it a ready indicator. Climate warming has caused an upshift of the timberline worldwide. However, the impact on belowground ecosystem and biogeochemical cycles remain elusive. To understand soil microbial ecology of the timberline, we analyzed microbial communities via 16s rRNA Illumina sequencing, a microarray-based tool named GeoChip 4.0 and a random matrix theory-based association network approach. We selected 24 sampling sites at two vegetation belts forming the timberline of Shennongjia Mountain in Hubei Province of China, a region with extraordinarily rich biodiversity. We found that temperature, among all of measured environmental parameters, showed the most significant and extensive linkages with microbial biomass, microbial diversity and composition at both taxonomic and functional gene levels, and microbial association network. Therefore, temperature was the best predictor for microbial community variations in the timberline. Furthermore, abundances of nitrogen cycle and phosphorus cycle genes were concomitant with NH4(+)-N, NO3(-)-N and total phosphorus, offering tangible clues to the underlying mechanisms of soil biogeochemical cycles. As the first glimpse at both taxonomic and functional compositions of soil microbial community of the timberline, our findings have major implications for predicting consequences of future timberline upshift. PMID:25613225

Ding, Junjun; Zhang, Yuguang; Deng, Ye; Cong, Jing; Lu, Hui; Sun, Xin; Yang, Caiyun; Yuan, Tong; Van Nostrand, Joy D; Li, Diqiang; Zhou, Jizhong; Yang, Yunfeng

2015-01-01

276

Phylogenetic analysis of epibacterial communities on the surfaces of four red macroalgae  

Science.gov (United States)

Macroalgal surfaces are prone to being attached by bacteria. Epibacterial community structures on marine macroalgae are host-specific but temporally and spatially variable. In this study, we investigated the structure of epibacterial communities on the surfaces of four red macroalgae, Gracilaria lemaneiformis, Gloiopeltis furcata, Mazzaella sp. and Porphyra yezoensis, by analyzing the sequences of 16S rRNA gene libraries. Healthy individuals of all macroalgae species were collected in winter from a farm at Dalian, China. The results showed that the epibacterial communities were mainly dominated by ?-Proteobacteria, ?-Proteobacteria and Bacteroidetes. Deinococcus-Thermus, Spirochaetes and ?-Proteobacteria were also found. The majority of cloned sequences shared the greatest similarity to those of culturable organisms. A large portion of sequences from the ?-Proteobacteria homed in Roseobacter clade, i.e., genera Ahrensia, Roseovarius, Litoreibacter, Octadecabacter, Thaiassobacter and Sulfitobacter, while members of Bacteroidetes mainly belonged to family Flavobacteriaceae. The cloned sequences could be separated into 66 OTUs at 0.01 distance value, and rare common OTUs were found among libraries. At genus level, Pseudoalteromonas dominated Gr. lemaneiformis and Gl. furcata libraries, accounting for 72.2% and 47.3%, respectively. Sulfitobacter dominated P. yezoensis library, accounting for 35.4%. A previously undefined cluster within Deinococcus-Thermus dominated Mazzaella sp. library, accounting for 24.6% of the all. These results indicated that a broad range of bacteria inhabited the surfaces of these macroalgae.

Wu, Hongqing; Liu, Min; Zhang, Wuchang; Xiao, Tian

2014-12-01

277

Cultivation-independent analysis of microbial communities on Austrian raw milk hard cheese rinds.  

Science.gov (United States)

"Vorarlberger Bergkäse" (VB) is an Austrian artisanal hard cheese produced from raw cow's milk. The composition of its rind microbiota and the changes in the microbial communities during ripening have not previously been investigated. This study used 16S and 18S rRNA gene cloning and sequencing to characterize the bacterial and fungal communities of seven pooled cheese rind samples taken in seven different ripening cellars of three Austrian dairy facilities. A total of 408 clones for 16S and 322 clones for 18S rRNA gene libraries were used for taxonomic classification, revealing 39 bacterial and seven fungal operational taxonomic units (OTUs). Bacterial OTUs belonged to four different phyla. Most OTUs were affiliated to genera often found in cheese, including high numbers of coryneforms. The most abundant OTU from 16S rRNA gene libraries showed highest similarity to Halomonas. Young cheese rinds were dominated by Actinobacteria or Proteobacteria, particularly by Halomonas and Brevibacterium aurantiacum, while Staphyloccocus equorum was most abundant in old cheeses. The most abundant 18S rRNA OTU had highest similarity to the filamentous fungus Scopulariopsis brevicaulis. Pairwise correlation analyses revealed putative co-occurrences between a number of OTUs. It was possible to discriminate the different cheese rind microbiota at the community-level by facility affiliation and ripening time. This work provides insights into the microbial composition of VB cheese rinds and might allow the processing- and ripening conditions to be improved to enhance the quality of the product. PMID:24794620

Schornsteiner, Elisa; Mann, Evelyne; Bereuter, Othmar; Wagner, Martin; Schmitz-Esser, Stephan

2014-06-16

278

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

2012-03-01

279

Integrated metagenomics and network analysis of soil microbial community of the forest timberline  

Science.gov (United States)

The forest timberline responds quickly and markedly to climate changes, rendering it a ready indicator. Climate warming has caused an upshift of the timberline worldwide. However, the impact on belowground ecosystem and biogeochemical cycles remain elusive. To understand soil microbial ecology of the timberline, we analyzed microbial communities via 16s rRNA Illumina sequencing, a microarray-based tool named GeoChip 4.0 and a random matrix theory-based association network approach. We selected 24 sampling sites at two vegetation belts forming the timberline of Shennongjia Mountain in Hubei Province of China, a region with extraordinarily rich biodiversity. We found that temperature, among all of measured environmental parameters, showed the most significant and extensive linkages with microbial biomass, microbial diversity and composition at both taxonomic and functional gene levels, and microbial association network. Therefore, temperature was the best predictor for microbial community variations in the timberline. Furthermore, abundances of nitrogen cycle and phosphorus cycle genes were concomitant with NH4+-N, NO3--N and total phosphorus, offering tangible clues to the underlying mechanisms of soil biogeochemical cycles. As the first glimpse at both taxonomic and functional compositions of soil microbial community of the timberline, our findings have major implications for predicting consequences of future timberline upshift.

Ding, Junjun; Zhang, Yuguang; Deng, Ye; Cong, Jing; Lu, Hui; Sun, Xin; Yang, Caiyun; Yuan, Tong; van Nostrand, Joy D.; Li, Diqiang; Zhou, Jizhong; Yang, Yunfeng

2015-01-01

280

Integrated metagenomics and network analysis of soil microbial community of the forest timberline  

Science.gov (United States)

The forest timberline responds quickly and markedly to climate changes, rendering it a ready indicator. Climate warming has caused an upshift of the timberline worldwide. However, the impact on belowground ecosystem and biogeochemical cycles remain elusive. To understand soil microbial ecology of the timberline, we analyzed microbial communities via 16s rRNA Illumina sequencing, a microarray-based tool named GeoChip 4.0 and a random matrix theory-based association network approach. We selected 24 sampling sites at two vegetation belts forming the timberline of Shennongjia Mountain in Hubei Province of China, a region with extraordinarily rich biodiversity. We found that temperature, among all of measured environmental parameters, showed the most significant and extensive linkages with microbial biomass, microbial diversity and composition at both taxonomic and functional gene levels, and microbial association network. Therefore, temperature was the best predictor for microbial community variations in the timberline. Furthermore, abundances of nitrogen cycle and phosphorus cycle genes were concomitant with NH4+-N, NO3?-N and total phosphorus, offering tangible clues to the underlying mechanisms of soil biogeochemical cycles. As the first glimpse at both taxonomic and functional compositions of soil microbial community of the timberline, our findings have major implications for predicting consequences of future timberline upshift. PMID:25613225

Ding, Junjun; Zhang, Yuguang; Deng, Ye; Cong, Jing; Lu, Hui; Sun, Xin; Yang, Caiyun; Yuan, Tong; Van Nostrand, Joy D.; Li, Diqiang; Zhou, Jizhong; Yang, Yunfeng

2015-01-01

 
 
 
 
281

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

282

Multi criteria analysis for sustainability assessments of electricity generation systems in a rural community in South Africa  

Energy Technology Data Exchange (ETDEWEB)

One of the key challenges of the energy policy in South Africa is to ensure that rural areas have access to electricity. This is reflected in the key energy policy documents (the 1998 Energy White Paper and the 2002 Renewable Energy White Paper). Both these documents identified renewable energy resources as immediate alternatives to grid electricity in especially remote rural communities that are characterised by low population densities. Centralised energy generation and transmission is very costly and inefficient in these areas due to greater transmission and distribution losses. While the cost of electricity in South Africa is relatively cheaper, it is not accessible for many rural households. There are still over two million households in rural areas without access to electricity. This paper presents a multi-criteria decision analysis (MCDA) using the Analytical Hierarchy Process (AHP) technique to compare various electricity technologies (mainly renewables) in a specific rural community of South Africa using social, economic, environment and technical indicators. These technologies were than ranked against each indicator assuming that the high-level criteria have equal importance for sustainable development. It is demonstrated that energy from wind is the most sustainable, followed by photovoltaic, anaerobic digestion (biogas) and then gasification. A sensitivity analysis was also performed to verify the stability of the priority ranking. The outcome of this study will specifically assist energy planners and decision-makers to choose the best alternative from a range of technology alternatives in a milieu of conflicting and competing criteria. (orig.)

Amigun, B.; Mehlwana, M. [Council for Scientific and Industrial Research, Pretoria (South Africa). Sustainable Energy Futures, Natural Resources and the Environment; Musango, J.K. [Department of Energy (DoE), Pretoria (South Africa); Brent, A.C. [Stellenbosch Univ. (South Africa). Centre for Renewable and Sustainable Energy Studies

2011-07-01

283

Municipal solid waste management: Identification and analysis of engineering indexes representing demand and costs generated in virtuous Italian communities  

International Nuclear Information System (INIS)

Highlights: • Collection and analysis of real life data in the field of Municipal Solid Waste (MSW) generation and costs for management. • Study of 92 virtuous Italian communities. • Elaboration of trends of engineering indexes useful during design and evaluation of MSWM systems. - Abstract: The definition and utilisation of engineering indexes in the field of Municipal Solid Waste Management (MSWM) is an issue of interest for technicians and scientists, which is widely discussed in literature. Specifically, the availability of consolidated engineering indexes is useful when new waste collection services are designed, along with when their performance is evaluated after a warm-up period. However, most published works in the field of MSWM complete their study with an analysis of isolated case studies. Conversely, decision makers require tools for information collection and exchange in order to trace the trends of these engineering indexes in large experiments. In this paper, common engineering indexes are presented and their values analysed in virtuous Italian communities, with the aim of contributing to the creation of a useful database whose data could be used during experiments, by indicating examples of MSWM demand profiles and the costs required to manage them

284

Community analysis of arbuscular mycorrhizal fungi in roots of Poncirus trifoliata and Citrus reticulata based on SSU rDNA.  

Science.gov (United States)

Morphological observation of arbuscular mycorrhizal fungi (AMF) species in rhizospheric soil could not accurately reflect the actual AMF colonizing status in roots, while molecular identification of indigenous AMF colonizing citrus rootstocks at present was rare in China. In our study, community of AMF colonizing trifoliate orange (Poncirus trifoliata L. Raf.) and red tangerine (Citrus reticulata Blanco) were analyzed based on small subunit of ribosomal DNA genes. Morphological observation showed that arbuscular mycorrhizal (AM) colonization, spore density, and hyphal length did not differ significantly between two rootstocks. Phylogenetic analysis showed that 173 screened AMF sequences clustered in at least 10 discrete groups (GLO1~GLO10), all belonging to the genus of Glomus Sensu Lato. Among them, GLO1 clade (clustering with uncultured Glomus) accounting for 54.43% clones was the most common in trifoliate orange roots, while GLO6 clade (clustering with Glomus intraradices) accounting for 35.00% clones was the most common in red tangerine roots. Although, Shannon-Wiener indices exhibited no notable differences between both rootstocks, relative proportions of observed clades analysis revealed that composition of AMF communities colonizing two rootstocks varied severely. The results indicated that native AMF species in citrus rhizosphere had diverse colonization potential between two different rootstocks in the present orchards. PMID:25162057

Wang, Peng; Wang, Yin

2014-01-01

285

Oral versus i.v. antibiotics for community-acquired pneumonia in children: a cost-minimisation analysis.  

Science.gov (United States)

Community-acquired pneumonia represents a high financial burden to healthcare providers. This manuscript seeks to estimate and compare the costs of treating children hospitalised with community-acquired pneumonia, with oral and intravenous antibiotics, thus determining which treatment is cost minimising. A cost-minimisation analysis was undertaken alongside a randomised controlled non-blinded equivalence trial. 232 children (from eight paediatric centres in England) diagnosed with pneumonia, who required admission to hospital, were randomised to receive oral amoxicillin or i.v. benzyl penicillin. The analysis considered the cost to the health service, patients and society, from pre-admission until the child was fully recovered. Oral amoxicillin and i.v. benzyl penicillin have equivalent efficacy. Children treated with i.v. antibiotics were found to have significantly longer in-patient stays (3.12 versus 1.93 days; ppneumonia with oral amoxicillin would result in savings of between pound473 and pound518 per child (euro545 and euro596 per child) admitted. The findings demonstrate that oral amoxicillin is a cost-effective treatment for the majority of children admitted to hospital with pneumonia. PMID:19717479

Lorgelly, P K; Atkinson, M; Lakhanpaul, M; Smyth, A R; Vyas, H; Weston, V; Stephenson, T

2010-04-01

286

Community Media: Muting the Democratic Media Discourse?  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Focuses on the concept of community media. Components that construct the identity of community media; Multi-theoretical approaches for analysis of community media; Definition of community media based on the concept of alternative media; Link between community media and civil society; Problems faced by community media organizations in European countries.

Carpentier, N.; Lie, R.; Servaes, J.

2003-01-01

287

Analysis of behavioral change techniques in community-led total sanitation programs.  

Science.gov (United States)

The lack of sanitation facilitates the spread of diarrheal diseases-a leading cause of child deaths worldwide. As of 2012, an estimated 1 billion people still practiced open defecation (OD). To address this issue, one behavioral change approach used is community-led total sanitation (CLTS). It is now applied in an estimated 66 countries worldwide, and many countries have adopted this approach as their main strategy for scaling up rural sanitation coverage. While it appears that many of the activities used in CLTS-that target community-level changes in sanitation behaviors instead of household-level changes-have evolved out of existing behavior change frameworks and techniques, it is less clear how these activities are adapted by different organizations and applied in different country contexts. The aims of this study are to (i) show which behavior change frameworks and techniques are the most common in CLTS interventions; (ii) describe how activities are implemented in CLTS interventions by region and context; and (3) determine which activities program implementers considered the most valuable in achieving open defecation free (ODF) status and sustaining it. The results indicate that a wide range of activities are conducted across the different programs and often go beyond standard CLTS activities. CLTS practitioners ranked follow-up and monitoring activities as the most important activities for achieving an ODF community, yet only 1 of 10 organizations conducted monitoring and follow-up throughout their project. Empirical studies are needed to determine which specific behavioral change activities are most effective at ending OD and sustaining it. PMID:25209916

Sigler, Rachel; Mahmoudi, Lyana; Graham, Jay Paul

2014-09-10

288

Simazine biodegradation in soil: analysis of bacterial community structure by in situ hybridization.  

Science.gov (United States)

Pesticide and nitrate contamination of soil and groundwater from agriculture is an environmental and public health concern worldwide. Simazine, 6-chloro-N2,N4-diethyl-1,3,5-triazine-2,4-diamine, is a triazine herbicide used in agriculture for selective weed control with several types of crops and it is frequently applied to soils receiving N-fertilizers. Degradation experiments were performed in the laboratory to assess whether the biodegradation of simazine in soil may be influenced by the presence of urea. Simazine degradation rates under different experimental conditions (presence/absence of urea, microbiologically active/sterilized soil) were assessed together with the formation, degradation and transformation of its main metabolites in soil. Simazine degradation was affected by the presence of urea, in terms both of a smaller half-life (t(1/2)) and of a higher amount of desethyl-simazine formed. The soil bacterial community was also studied. Microbial abundances were determined by epifluorescence direct counting. Moreover in situ hybridization with rRNA-targeted fluorescent oligonucleotide probes was used to analyze the bacterial community structure. Fluorescent in situ hybridization (FISH) was used to detect specific groups of bacteria such as the alpha,beta,gamma-subdivisions of Proteobacteria, Gram-positive bacteria with a high G + C DNA content, Planctomycetes, Betaproteobacterial ammonia-oxidizing bacteria and nitrifying bacteria. The presence of the herbicide and/or urea affected the bacterial community structure, showing that FISH is a valuable tool for determining the response of bacterial populations to different environmental conditions. PMID:16015577

Caracciolo, Anna Barra; Grenni, Paola; Ciccoli, Roberto; Di Landa, Giuseppe; Cremisini, Carlo

2005-09-01

289

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

290

Spatial point process analysis for a plant community with high biodiversity  

DEFF Research Database (Denmark)

A complex multivariate spatial point pattern for a plant community with high biodiversity is modelled using a hierarchical multivariate point process model. In the model, interactions between plants with different post-fire regeneration strategies are of key interest. We consider initially 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.

Illian, Janine; MØller, Jesper

2006-01-01

291

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

292

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

293

A trait-interpersonal analysis of suicide proneness among lesbian, gay, and bisexual community members.  

Science.gov (United States)

Suicide remains a concerning issue for lesbian, gay, and bisexual (LGB) persons. The integrated effects of five-factor model personality traits and interpersonal-psychological theory of suicide (IPTS) constructs on suicide proneness in a community sample of 336 LGB adults were examined. Results supported a model inclusive of all five-factor model domains predicting IPTS constructs leading to suicide proneness. Effects of neuroticism and extraversion were both mediated by perceived burdensomeness and thwarted belongingness. Thwarted belongingness mediated the effect of agreeableness on suicide proneness. Identified mediation pathways build on existing trait-interpersonal theory and may inform clinical services for sexual minority persons. PMID:24702204

Cramer, Robert J; Stroud, Caroline H; Fraser, Theresa; Graham, James

2014-12-01

294

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

2010-09-01

295

Analysis of bacterial communities associated with the benthic amphipod Diporeia in the Laurentian Great Lakes Basin.  

Science.gov (United States)

Bacterial communities play important roles in the biological functioning of crustaceans, yet little is known about their diversity, structure, and dynamics. This study was conducted to investigate the bacterial communities associated with the benthic amphipod Diporeia, an important component in the Great Lakes foodweb that has been declining over the past 3 decades. In this study, the combination of 16S rRNA gene sequencing and terminal restriction fragment length polymorphism revealed a total of 175 and 138 terminal restriction fragments (T-RFs) in Diporeia samples following treatment with the endonucleases HhaI and MspI, respectively. Relatively abundant and prevalent T-RFs were affiliated with the genera Flavobacterium and Pseudomonas and the class Betaproteobacteria. T-RFs affiliated with the order Rickettsiales were also detected. A significant difference in T-RF presence and abundance (P = 0.035) was detected among profiles generated for Diporeia collected from 4 sites in Lake Michigan. Comparison of profiles generated for Diporeia samples collected in 2 years from lakes Superior and Michigan showed a significant change in diversity for Lake Superior Diporeia but not Lake Michigan Diporeia. Profiles from one Lake Michigan site contained multiple unique T-RFs compared with other Lake Michigan Diporeia profiles, most notably one that represents the genus Methylotenera. This study generated the most extensive list of bacteria associated with Diporeia and sheds useful insights on the microbiome of Great Lakes Diporeia that may help to reveal potential causes of the decline of Diporeia populations. PMID:25494536

Winters, Andrew D; Marsh, Terence L; Brenden, Travis O; Faisal, Mohamed

2015-01-01

296

Stream Community Structure: An Analysis of Riparian Forest Buffer Restoration in the Chesapeake Bay Watershed  

Science.gov (United States)

Forested riparian buffer zones have been proposed as an important aid in curtailing upland sources of pollution before they reach stream surface waters, and enhancing habitat for stream organisms. Our objective was to test the efficacy of restored forest riparian buffers along streams in the Chesapeake Bay watershed by examining the stream macrobenthic community structure. To test our hypothesis, we collected riffle benthic and water samples, and performed habitat evaluations at 30 stream sites in the mid-Atlantic Piedmont, ranging in buffer age from 0 to greater than 50 years of age. Results showed that habitat, water quality, and benthic macroinvertebrate metrics improved with age of restored buffer. Habitat scores were driven mostly by instream substrate availability and width and age of riparian buffer zones. Water quality parameters varied within buffer age groups depending age of surrounding forest vegetation. Benthic invertebrate taxa richness, % EPT, % Plecoptera, % Ephemeroptera, and the FBI all improved with age of buffer zone. Instream habitat quality was the greatest driver of benthic macroinvertebrate community diversity and health, and appeared to plateau within 10-15 years of restoration with noticeable improvements occurring within 5-10 years post restoration.

Orzetti, L. L.; Jones, R. C.

2005-05-01

297

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. PMID:23029440

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

298

Analysis of Fuel Cell Driven Ground Source Heat Pump Systems in Community Buildings  

Directory of Open Access Journals (Sweden)

Full Text Available In the present study, a fuel cell driven ground source heat pump (GSHP system is applied in a community building and heat pump system performance is analyzed by computational methods. Conduction heat transfer between the brine pipe and ground is analyzed by TEACH code in order to predict the performance of the heat pump system. The predicted coefficient of performance (COP of the heat pump system and the energy cost were compared with the variation of the location of the objective building, the water saturation rate of the soil, and the driven powers of the heat pump system. Compared to the late-night electricity driven system, a significant reduction of energy cost can be accomplished by employing the fuel cell driven heat pump system. This is due to the low cost of electricity production of the fuel cell system and to the application of the recovered waste heat generated during the electricity production process to the heating of the community building.

Jong-Keun Shin

2013-05-01

299

The effects of community factors on school participation in Turkey: A multilevel analysis  

Science.gov (United States)

Turkey, like many developing countries, is facing considerable problems in terms of low school attendance rates, late enrolment and early dropout of girls in particular. Numerous studies have already been conducted, both in Turkey and elsewhere, to determine the factors affecting school enrolment of boys and girls. Existing studies in Turkey, however, have focused extensively on the association between household-level factors and school participation, ignoring the role of the broader environment in which children live. Using a recent, large-scale and nationally representative data set, this paper investigates school participation at both primary and secondary levels in Turkey, giving specific attention to community- level factors. In taking into account socioeconomic context variables using the multilevel modelling method, this study contributes significantly to current school participation literature in Turkey. The author's findings highlight the importance of community/context factors in explaining low school enrolment in Turkey. The results of the study can help policy makers develop a systematic understanding of the relationship between socioeconomic context and school participation, and enable them to make more appropriate decisions for improving school participation across the country.

Gumus, Sedat

2014-05-01

300

Microbial community in anoxic-oxic-settling-anaerobic sludge reduction process revealed by 454 pyrosequencing analysis.  

Science.gov (United States)

Modification of the anoxic-oxic (AO) process by inserting a sludge holding tank (SHT) into the sludge return line forms an anoxic-oxic-settling-anaerobic (A+OSA) process that can achieve a 48.98% sludge reduction rate. The 454 pyrosequencing method was used to obtain the microbial communities of the AO and A+OSA processes. Results showed that the microbial community structures of the 2 processes were different as a result of the SHT insertion. Bacteria assigned to the phyla Proteobacteria and Bacteroidetes commonly existed and dominated the microbial populations of the 2 processes. However, the relative abundance of these populations shifted in the presence of SHT. The relative abundance of Proteobacteria decreased during the A+OSA process. A specific comparison at the class level showed that Sphingobacteria was enriched in the A+OSA process. The result suggested that the fermentative bacteria Sphingobacteria may have key functions in reducing the sludge from the A+OSA process. Uncultured Nitrosomonadaceae gradually became the dominant ammonia-oxidizing bacteria, and the nitrite-oxidizing bacterium Nitrospira was enriched in the A+OSA process. Both occurrences were favorable for stabilized nitrogen removal. The known denitrifying species in the A+OSA process were similar to those in the AO process; however, their relative abundance also decreased. PMID:25388228

Ning, Xinqiang; Qiao, Wenwen; Zhang, Lei; Gao, Xu

2014-12-01

 
 
 
 
301

Factors associated with use of community mental health services by schizophrenia patients using multilevel analysis  

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Full Text Available Abstract Background Persons with schizophrenia and related disorders may be particularly sensitive to a number of determinants of service use, including those related with illness, socio-demographic characteristics and organizational factors. The objective of this study is to identify factors associated with outpatient contacts at community mental health services of patients with schizophrenia or related disorders. Methods This cross-sectional study analyzed 1097 patients. The main outcome measure was the total number of outpatient consultations during one year. Independent variables were related to socio-demographic, clinical and use of service factors. Data were collected from clinical records. Results The multilevel linear regression model explained 46.35% of the variance. Patients with significantly more contacts with ambulatory services were not working and were receiving welfare benefits (p = 0.02, had no formal education (p = 0.02, had a global level of severity of two or three (four being the most severe (p Conclusions As expected, the variables that explained the use of community service could be viewed as proxies for severity of illness. The most surprising finding, however, was that a group of four psychiatrists was also independently associated with use of ambulatory services by patients with schizophrenia or related disorders. More research is needed to carefully examine how professional support networks interact to affect use of mental health.

Moreno Patricia

2011-10-01

302

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

2013-01-01

303

Poverty in Mozambique Discourse, Analysis and Monitoring. Suggestions for National Stakeholders and the Donor Community  

Digital Repository Infrastructure Vision for European Research (DRIVER)

This report was prepared for the Norwegian Embassy in Mozambique and NORAD. Its purpose is to advise the Norwegian and other cooperation authorities on how best to support poverty analysis and monitoring in Mozambique, generally and in the sectors of health, energy and fisheries in particular. The following scope of work is highlighted in the Terms of Reference: • map ongoing poverty analysis and identify institutions which could be involved in such analysis • assess the latest poverty an...

Isaksen, Jan; Staaland, Anette; Weimer, Bernhard

2005-01-01

304

Microbial community analysis and identification of alternative host-specific fecal indicators in fecal and river water samples using pyrosequencing.  

Science.gov (United States)

It is important to know the comprehensive microbial communities of fecal pollution sources and receiving water bodies for microbial source tracking. Pyrosequencing targeting the V1-V3 hypervariable regions of the 16S rRNA gene was used to investigate the characteristics of bacterial and Bacteroidales communities in major fecal sources and river waters. Diversity analysis indicated that cow feces had the highest diversities in the bacterial and Bacteroidales group followed by the pig sample, with human feces having the lowest value. The Bacteroidales, one of the potential fecal indicators, totally dominated in the fecal samples accounting for 31%-52% of bacterial sequences, but much less (0.6%) in the river water. Clustering and Venn diagram analyses showed that the human sample had a greater similarity to the pig sample in the bacterial and Bacteroidales communities than to samples from other hosts. Traditional fecal indicators, i.e., Escherichia coli, were detected in the human and river water samples at very low rates and Clostridium perfringens and enterococci were not detected in any samples. Besides the Bacteroidales group, some microorganisms detected in the specific hosts, i.e., Parasutterella excrementihominis, Veillonella sp., Dialister invisus, Megamonas funiformis, and Ruminococcus lactaris for the human and Lactobacillus amylovorus and Atopostipes sp. for the pig, could be used as potential host-specific fecal indicators. These microorganisms could be used as multiple fecal indicators that are not dependent on the absence or presence of a single indicator. Monitoring for multiple indicators that are highly abundant and host-specific would greatly enhance the effectiveness of fecal pollution source tracking. PMID:21887641

Jeong, Ju-Yong; Park, Hee-Deung; Lee, Kyong-Hee; Weon, Hang-Yeon; Ka, Jong-Ok

2011-08-01

305

Trayectorias Organizacionales y Empoderamiento Comunitario: Un Análisis de Interfaz en Dos Localidades de la Región de la Araucanía Organizational Trajectories and Community Empowerment: An Interface Analysis in Two Communities of the Araucanía Region  

Directory of Open Access Journals (Sweden)

Full Text Available Se reportan los principales resultados de una investigación cuyo propósito fue indagar sobre las variables psico-socio-culturales presentes en la interfaz entre organizaciones comunitarias de base y agentes públicos que potencian o restringen procesos de empoderamiento organizacional y comunitario. Se empleó una metodología cualitativa, apoyada por el análisis estructural de redes, analizándose en 2 localidades de la región de la Araucanía 4 tipos de organizaciones comunitarias. Los resultados muestran que en las localidades predomina un interfaz de tipo semiclientelar, clientelar y paternalista, formas de relación que se centran en la entrega de recursos por parte del municipio para resolver algunas necesidades inmediatas de la comunidad, tendiendo a predominar en las organizaciones objetivos inmediatos y una participación centrada en conseguir estos recursos.The main findings of a study that investigated the psychosocial cultural factors affecting the interface between community organizations and public agencies are reported. Four types of organizations are analyzed in 2 different communities, using a qualitative methodology and a structural networks analysis. In both communities the paternalistic, client and semi-client interface type predominate. These types of relationships focus on the delivery of resources by the municipal institution as a way of addressing the immediate needs of the community. In turn, the community organizations center their efforts on short-term objectives and participation aimed at obtaining these resources.

Alba Zambrano

2009-11-01

306

New Agilent platform DNA microarrays for transcriptome analysis of Plasmodium falciparum and Plasmodium berghei for the malaria research community  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background DNA microarrays have been a valuable tool in malaria research for over a decade but remain in limited use in part due their relatively high cost, poor availability, and technical difficulty. With the aim of alleviating some of these factors next-generation DNA microarrays for genome-wide transcriptome analysis for both Plasmodium falciparum and Plasmodium berghei using the Agilent 8x15K platform were designed. Methods Probe design was adapted from previously published methods and based on the most current transcript predictions available at the time for P. falciparum or P. berghei. Array performance and transcriptome analysis was determined using dye-coupled, aminoallyl-labelled cDNA and streamlined methods for hybridization, washing, and array analysis were developed. Results The new array design marks a notable improvement in the number of transcripts covered and average number of probes per transcript. Array performance was excellent across a wide range of transcript abundance, with low inter-array and inter-probe variability for relative abundance measurements and it recapitulated previously observed transcriptional patterns. Additionally, improvements in sensitivity permitted a 20-fold reduction in necessary starting RNA amounts, further reducing experimental costs and widening the range of application. Conclusions DNA microarrays utilizing the Agilent 8x15K platform for genome-wide transcript analysis in P. falciparum and P. berghei mark an improvement in coverage and sensitivity, increased availability to the research community, and simplification of the experimental methods.

Kafsack Björn F C

2012-06-01

307

Project Final Report: Building a Community Infrastructure for Scalable On-Line Performance Analysis Tools around Open|SpeedShop  

Energy Technology Data Exchange (ETDEWEB)

In this project we created a community tool infrastructure for program development tools targeting Petascale class machines and beyond. This includes tools for performance analysis, debugging, and correctness tools, as well as tuning and optimization frameworks. The developed infrastructure provides a comprehensive and extensible set of individual tool building components. We started with the basic elements necessary across all tools in such an infrastructure followed by a set of generic core modules that allow a comprehensive performance analysis at scale. Further, we developed a methodology and workflow that allows others to add or replace modules, to integrate parts into their own tools, or to customize existing solutions. In order to form the core modules, we built on the existing Open|SpeedShop infrastructure and decomposed it into individual modules that match the necessary tool components. At the same time, we addressed the challenges found in performance tools for petascale systems in each module. When assembled, this instantiation of community tool infrastructure provides an enhanced version of Open|SpeedShop, which, while completely different in its architecture, provides scalable performance analysis for petascale applications through a familiar interface. This project also built upon and enhances capabilities and reusability of project partner components as specified in the original project proposal. The overall project team’s work over the project funding cycle was focused on several areas of research, which are described in the following sections. The reminder of this report also highlights related work as well as preliminary work that supported the project. In addition to the project partners funded by the Office of Science under this grant, the project team included several collaborators who contribute to the overall design of the envisioned tool infrastructure. In particular, the project team worked closely with the other two DOE NNSA laboratories Los Alamos and Sandia leveraging co-funding for Krell by ASC’s Common Computing Environment (CCE) program as laid out in the original proposal. The ASC CCE co-funding, coordinated through LLNL, was for 50% of the total project funding, with the ASC CCE portion of the funding going entirely to Krell, while the ASCR funding itself was split between Krell and the funded partners. This report covers the entire project from both funding sources. Additionally, the team leveraged the expertise of software engineering researchers from Carnegie Mellon University, who specialize in software framework design, in order to achieve a broadly acceptable component framework. The Component Based Tool Framework (CBTF) software has been released to the community. Information related to the project and the released software can be found on the CBTF wiki page at: http://sourceforge.net/p/cbtf/wiki/Home

Galarowicz, James

2014-01-06

308

COMMUNITY RIGHT-TO-KNOW AND EMERGENCY PLANNING: USING COMPUTERS TO CONDUCT HAZARDS ANALYSIS  

Science.gov (United States)

The paper discusses the process of hazards analysis and the basic building blocks of systems used for data storage, retrieval, correlation, and analysis, to better inform people choosing and/or evaluating the systems. The remainder of the paper discusses: (1) the process of hazar...

309

Fluorescence in situ hybridization analysis of the prokaryotic community inhabiting crystallizer ponds.  

Science.gov (United States)

A fluorescence in situ hybridization (FISH) protocol suitable for the identification of prokaryotes inhabiting hypersaline environments was developed and applied to several crystallizer ponds with salinities above 36% from a multipond solar saltern in Alicante, Spain. Two morphotypes were abundant in these environments: rods and square or square-like prokaryotes that could be affiliated to Bacteria and Archaea, respectively, by FISH with domain-specific probes. FISH with a newly designed probe proved that the archaeal 16S rDNA sequence most frequently recovered from the crystallizers, SPhT, originated from the dominant square-like prokaryotes. These uncultured prokaryotes have the morphology of Walsby's square bacteria. Additionally, FISH with a probe targeted to the genus Haloarcula, members of which are frequently isolated from this environment, indicated that this genus accounts for less than 0.1% of the total prokaryotic community. PMID:11207773

Antón, J; Llobet-Brossa, E; Rodríguez-Valera, F; Amann, R

1999-12-01

310

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

311

A Fast-Track East African Community Monetary Union? Convergence Evidence from a Cointegration Analysis.  

Directory of Open Access Journals (Sweden)

Full Text Available There is a proposal for a fast-tracked approach to the African Community (EAC monetary union. This paper uses cointegration techniques to determine whether the member countries would form a successful monetary union based on the long-run behavior of nominal and real exchange rates and monetary base. The three variables are each analyzed for co-movements among the five countries. The empirical results indicate only partial convergence for the variables considered, suggesting there could be substantial costs for the member countries from a fast-tracked process. This implies the EAC countries need significant adjustments to align their monetary policies and to allow a period of monetary policy coordination to foster convergence that will improve the chances of a sustainable currency union.

Steven Buigut

2011-01-01

312

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

2011-06-01

313

Measures of precision for dissimilarity-based multivariate analysis of ecological communities.  

Science.gov (United States)

Ecological studies require key decisions regarding the appropriate size and number of sampling units. No methods currently exist to measure precision for multivariate assemblage data when dissimilarity-based analyses are intended to follow. Here, we propose a pseudo multivariate dissimilarity-based standard error (MultSE) as a useful quantity for assessing sample-size adequacy in studies of ecological communities. Based on sums of squared dissimilarities, MultSE measures variability in the position of the centroid in the space of a chosen dissimilarity measure under repeated sampling for a given sample size. We describe a novel double resampling method to quantify uncertainty in MultSE values with increasing sample size. For more complex designs, values of MultSE can be calculated from the pseudo residual mean square of a permanova model, with the double resampling done within appropriate cells in the design. R code functions for implementing these techniques, along with ecological examples, are provided. PMID:25438826

Anderson, Marti J; Santana-Garcon, Julia

2015-01-01

314

Network analysis suggests a potentially 'evil' alliance of opportunistic pathogens inhibited by a cooperative network in human milk bacterial communities.  

Science.gov (United States)

The critical importance of human milk to infants and even human civilization has been well established. Yet our understanding of the milk microbiome has been limited to cataloguing OTUs and computation of community diversity. To the best of our knowledge, there has been no report on the bacterial interactions within the milk microbiome. To bridge this gap, we reconstructed a milk bacterial community network based on Hunt et al. Our analysis revealed that the milk microbiome network consists of two disconnected sub-networks. One sub-network is a fully connected complete graph consisting of seven genera as nodes and all of its pair-wise interactions among the bacteria are facilitative or cooperative. In contrast, the interactions in the other sub-network of eight nodes are mixed but dominantly cooperative. Somewhat surprisingly, the only 'non-cooperative' nodes in the second sub-network are mutually cooperative Staphylococcus and Corynebacterium that include some opportunistic pathogens. This potentially 'evil' alliance between Staphylococcus and Corynebacterium could be inhibited by the remaining nodes that cooperate with one another in the second sub-network. We postulate that the 'confrontation' between the 'evil' alliance and 'benign' alliance and the shifting balance between them may be responsible for dysbiosis of the milk microbiome that permits mastitis. PMID:25651890

Sam Ma, Zhanshan; Guan, Qiong; Ye, Chengxi; Zhang, Chengchen; Foster, James A; Forney, Larry J

2015-01-01

315

Neighborhood social cohesion and disorder in relation to walking in community-dwelling older adults: a multilevel analysis.  

Science.gov (United States)

Objectives. To examine the role of neighborhood social conditions and walking in community-dwelling older adults. Methods. A multi-level analysis of data from 4,317 older adults (mean age = 74.5; 73% black) from a geographically-defined urban community. Participants completed structured interviews including 14 questions on neighborhood conditions and self-reported walking. The neighborhood questions were summarized into individual-level measures of perceived neighborhood social cohesion and disorder. These measures were aggregated by neighborhood to construct neighborhood-level measures of social cohesion and disorder. Results. Neighborhood-level disorder, but not social cohesion, was significantly associated with walking, independent individual-level neighborhood perceptions and other correlates of walking. Further adjustment for race weakened this association to a marginally significant level. Discussion. Neighborhood conditions may shape walking behavior in older adults, especially conditions that reflect physical neglect or social threat. Promotion of walking behavior in older adults may require improvement of the safety and upkeep of the neighborhood environment. PMID:19144973

Mendes de Leon, Carlos F; Cagney, Kathleen A; Bienias, Julia L; Barnes, Lisa L; Skarupski, Kimberly A; Scherr, Paul A; Evans, Denis A

2009-02-01

316

Neighborhood Social Cohesion and Disorder in Relation to Walking in Community-Dwelling Older Adults: A Multi-Level Analysis  

Science.gov (United States)

Objectives To examine the role of neighborhood social conditions and walking in community-dwelling older adults. Methods A multi-level analysis of data from 4,317 older adults (mean age = 74.5; 73% black) from a geographically-defined urban community. Participants completed structured interviews including 14 questions on neighborhood conditions and self-reported walking. The neighborhood questions were summarized into individual-level measures of perceived neighborhood social cohesion and disorder. These measures were aggregated by neighborhood to construct neighborhood-level measures of social cohesion and disorder. Results Neighborhood-level disorder, but not social cohesion, was significantly associated with walking, independent individual-level neighborhood perceptions and other correlates of walking. Further adjustment for race weakened this association to a marginally significant level. Discussion Neighborhood conditions may shape walking behavior in older adults, especially conditions that reflect physical neglect or social threat. Promotion of walking behavior in older adults may require improvement of the safety and upkeep of the neighborhood environment. PMID:19144973

Mendes de Leon, Carlos F.; Cagney, Kathleen A.; Bienias, Julia L.; Barnes, Lisa L.; Skarupski, Kimberly A.; Scherr, Paul A.; Evans, Danis A.

2008-01-01

317

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

318

??????????????????????? 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.

???

2012-09-01

319

Patterns and Regularities in the European Marketing Academic Community : A Social Network Analysis of EMAC Annual Conferences  

DEFF Research Database (Denmark)

Recent years have seen a growing interest in the nature of scientific collaboration, as researchers have become interested in how knowledge is generated in research communities. The aim of the current paper is to provide insights into the structure of the European Marketing Academy (EMAC) and to examine the appearance of patterns and regularities in the way EMAC members choose collaboration partners. The work is based on a Social Network Analysis of the co-authored publications presented at the 2000-2010 EMAC conferences. Results show that the main selection criteria for choosing collaboration partners is socio-cultural and geographical) proximity rather than marketing sub-discipline, pointing towards a very systematic tendency for EMAC members to be organised around institutions in the same or culturally related countries.

Krystallis Krontalis, Athanasios; Ormrod, Robert P.

2011-01-01

320

New Visualization and Analysis Tools for Magnetospheric, Heliospheric, and Solar Models from the Community Coordinated Modeling Center  

Science.gov (United States)

The Community Coordinated Modeling Center (CCMC) at NASA Goddard Space Flight Center has developed new analysis tools to help scientists analyze space weather simulation data executed at the CCMC. Space Weather Explorer 2 is a Java-based application that can visualize, in 2D and 3D, large data files on common hardware. A new WebGL and HTML5-based version of Space Weather Explorer, along with a data streaming server, allows even more users to access larger datasets than normally possible. The tool allows users to remotely and easily share visualization data with others, bringing collaborative research to a new level. We will demonstrate how these tools enable new insights into the structures and dynamics of complex heliophysics phenomena such as coronal mass ejections (CMEs), flux transfer events (FTEs), and Kelvin-Helmholtz vortices.

Berrios, D.; LaSota, J.; Donti, N.; Boblitt, J.; Mullinix, R.; Maddox, M. M.

2011-12-01

 
 
 
 
321

Analysis of Bidding Networks in eBay: Aggregate Preference Identification through Community Detection  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Statistical analysis of networks plays a critical role in the context of economics and the social sciences. Here we construct a bidding network to represent the behavior of users of the eBay marketplace. We study the eBay markets for digital cameras and liquid crystal display screens, and employ network analysis to identify aggregate structure in bidder preferences. The network that we construct associates auctions with nodes, and weighted edges between nodes capture the number of bidders com...

Jin, R. Kang-xing; Parkes, David C.; Wolfe, Patrick J.

2007-01-01

322

Cultivable bacterial community from South China Sea sponge as revealed by DGGE fingerprinting and 16S rDNA phylogenetic analysis.  

Science.gov (United States)

The cultivable bacterial communities associated with four South China Sea sponges-Stelletta tenuis, Halichondria rugosa, Dysidea avara, and Craniella australiensis in mixed cultures-were investigated by microbial community DNA-based DGGE fingerprinting and 16S rDNA phylogenetic analysis. Diverse bacteria such as alpha-, gamma-, delta-Proteobacteria, Bacteroidetes, and Firmicutes were cultured, some of which were previously uncultivable bacteria, potential novel strains with less than 95% similarity to their closest relatives and sponge symbionts growing only in the medium with the addition of sponge extract. According to 16S rDNA BLAST analysis, most of the bacteria were cultured from sponge for the first time, although similar phyla of bacteria have been previously recognized. The selective pressure of sponge extract on the cultured bacterial species was suggested, although the effect of sponge extract on bacterial community in high nutrient medium is not significant. Although alpha- and gamma-Proteobacteria appeared to form the majority of the dominant cultivable bacterial communities of the four sponges, the composition of the cultivable bacterial community in the mixed culture was different, depending on the medium and sponge species. Greater bacterial diversity was observed in media C and CS for Stelletta tenuis, in media F and FS for Halichondria rugosa and Craniella australiensis. S. tenuis was found to have the highest cultivable bacterial diversity including alpha-, gamma-, delta-Proteobacteria, Bacteroidetes, and Firmicutes, followed by sponge Dysidea avara without delta-Proteobacteria, sponge Halichondria rugosa with only alpha-, gamma-Proteobacteria and Bacteroidetes, and sponge C. australiensis with only alpha-, gamma-Proteobacteria and Firmicutes. Based on this study, by the strategy of mixed cultivation integrated with microbial community DNA-based DGGE fingerprinting and phylogenetic analysis, the cultivable bacterial community of sponge could be revealed effectively. PMID:17896134

Li, Zhiyong; He, Liming; Miao, Xiaoling

2007-12-01

323

Community extraction for social networks  

CERN Document Server

Analysis of networks and in particular discovering communities within networks has been a focus of recent work in several fields, with applications ranging from citation and friendship networks to food webs and gene regulatory networks. Most of the existing community detection methods focus on partitioning the entire network into communities, with the expectation of many ties within communities and few ties between. However, many networks contain nodes that do not fit in with any of the communities, and forcing every node into a community can distort results. Here we propose a new framework that focuses on community extraction instead of partition, extracting one community at a time. The main idea behind extraction is that the strength of a community should not depend on ties between members of other communities, but only on ties within that community and its ties to the outside world. We show that the new extraction criterion performs well on simulated and real networks, and establish asymptotic consistency ...

Zhao, Yunpeng; Zhu, Ji

2010-01-01

324

Shaping Communities out of Triangles  

CERN Document Server

Community detection has arisen as one of the most relevant topics in the field of graph data mining due to its importance in many fields such as biology, social networks or network traffic analysis. The metrics proposed to shape communities are generic and follow two approaches: maximizing the internal density of such communities or reducing the connectivity of the internal vertices with those outside the community. However, these metrics take the edges as a set and do not consider the internal layout of the edges in the community. We define a set of properties oriented to social networks that ensure that communities are cohesive, structured and well defined. Then, we propose the Weighted Community Clustering (WCC), which is a community metric based on triangles. We proof that analyzing communities by triangles gives communities that fulfill the listed set of properties, in contrast to previous metrics. Finally, we experimentally show that WCC correctly captures the concept of community in social networks usi...

Prat-Pérez, Arnau; Brunat, Josep M; Larriba-Pey, Josep-Lluis

2012-01-01

325

HydroDesktop as a Community Designed and Developed Resource for Hydrologic Data Discovery and Analysis  

Science.gov (United States)

As has been seen in other informatics fields, well-documented and appropriately licensed open source software tools have the potential to significantly increase both opportunities and motivation for inter-institutional science and technology collaboration. The CUAHSI HIS (and related HydroShare) projects have aimed to foster such activities in hydrology resulting in the development of many useful community software components including the HydroDesktop software application. HydroDesktop is an open source, GIS-based, scriptable software application for discovering data on the CUAHSI Hydrologic Information System and related resources. It includes a well-defined plugin architecture and interface to allow 3rd party developers to create extensions and add new functionality without requiring recompiling of the full source code. HydroDesktop is built in the C# programming language and uses the open source DotSpatial GIS engine for spatial data management. Capabilities include data search, discovery, download, visualization, and export. An extension that integrates the R programming language with HydroDesktop provides scripting and data automation capabilities and an OpenMI plugin provides the ability to link models. Current revision and updates to HydroDesktop include migration of core business logic to cross platform, scriptable Python code modules that can be executed in any operating system or linked into other software front-end applications.

Ames, D. P.

2013-12-01

326

Microbiological community analysis of vermicompost tea and its influence on the growth of vegetables and cereals.  

Science.gov (United States)

Vermicompost, the digestion product of organic material by earthworms, has been widely reported to have a more positive effect on plant growth and plant health than conventional compost. A study was conducted to investigate the effects of different vermicompost elutriates (aerated compost teas) on soils and plant growth. The teas were analyzed by chemical, microbiological, and molecular methods accompanied by plant growth tests at laboratory and field scale. The number of microorganisms in the teas increased during the extraction process and was affected by substrate addition. The vermicompost tea found to increase plant growth best under laboratory tests was applied to cereals (wheat and barley) and vegetables (Raphanus sativus, Rucola selvatica, and Pisum sativum) in a field study. The results revealed no effects of tea application on plant yield; however, sensoric tests indicated an improvement in crop quality. The soils from laboratory and field studies were investigated to detect possible microbial or chemical changes. The results indicated that minor changes to the soil microbial community occurred following tea application by foliar spray in both the laboratory-scale and field-scale experiments. PMID:22712623

Fritz, J I; Franke-Whittle, I H; Haindl, S; Insam, H; Braun, R

2012-07-01

327

Nucleic acid based quantitative microbial community analysis in different marine and terrestrial sediments  

Science.gov (United States)

Sub-seafloor sediments harbour over half of all prokaryotic cells on Earth. This immense cell number is calculated from numerous microscopic cell counts (AODC) in ODP sediment cores. Since AODC can not differentiate between living or dead cells, the population size of living microorganisms and the abundance of different prokaryotic groups are unknown. Recent molecular nucleic acid and biomarker analyses showed that a high proportion of the cells are alive and that the microbial communities of deep marine sediments harbour members of distinct, uncultured bacterial and archaeal lineages. The main objective of our project is the quantification of living prokaryotes in various sediments. Deep sediment samples from the Pacific and the Atlantic Oceans (ODP Legs 201 and 207, IODP Exp. 307 and 308), sediments from the Indian Ocean (RV Sonne 189-2) and the Black Sea (RV Meteor 51/4) as well as terrestrial Chesapeake Bay Sediments (ICDP) were analyzed using Catalyzed Reporter Deposition - Fluorescence In Situ Hybridisation (CARD - FISH) and quantitative, real-time PCR (Q-PCR), targeting either the 16S rRNA gene or the functional genes dsrA, mcrA and aprA to quantify microorganisms of various phylogenetic or physiological groups (e.g. JS1 cluster and Chloroflexi). At all sediment sites, cell numbers decreased with depth, however, the abundance of particular microbial groups varied at different sites and depths. The results indicate that global estimates of the deep biosphere should be reconsidered.

Schippers, A.; Blazejak, A.; Köweker, G.

2009-12-01

328

The death drive: conceptual analysis and relevance in the Spanish psychoanalytic community.  

Science.gov (United States)

Based on a six-year doctoral research, the author carries out a historical, epistemological and paradigmatic assessment of the controversial concept of the death instinct. The author analyses this notion's speculative nature; its relation with the second principle of thermodynamics; the feasibility of a return to an inorganic state; the death drive's metaphorical and isomorphic uses, as well as its theoretical and doctrinaire approaches; its relationship with repetition compulsion and masochism; the influence of Freud 's scientific background on its formulation; and its context-dependent meaning. Although this paper stems mainly from the theoretical aspects of the study, it also offers some clinical thoughts on the basis of a clinical vignette. The author stresses the underlying healing aspects of repetition in the analytic situation. Next, he presents concise comments on his empirical research on the current professional usage of the death drive in the Spanish psychoanalytical community. This research covered more than 27% of Spanish psychoanalysts (IPA) and psychotherapists (EFPP). The essay's conclusions point to the ambiguous character of the death drive concept and its literal unacceptability and the absence of consistent arguments for its acceptance. PMID:19382960

Armengou, Frank García-Castrillón

2009-04-01

329

Implementation Cost Analysis of a Community-Based Exercise Program for Seniors in South Florida.  

Science.gov (United States)

The objective of the study was to measure the costs of implementing the EnhanceFitness program to elderly residents of South Florida. The Health Foundation of South Florida's Healthy Aging Regional Collaborative implemented EnhanceFitness as part of their initiative to make evidence-based healthy aging programs available to South Florida seniors. Cost data were collected from agencies participating in the delivery of EnhanceFitness classes in South Florida. Cost questionnaires were e-mailed to program coordinators from agencies participating in the delivery of EnhanceFitness classes. Program coordinators worked with accounting staff to complete the questionnaires. Questionnaires were returned via e-mail. Costs were presented from the perspective of participating agencies. Total costs were divided by the number of classes being offered by each agency to determine cost per class per month. Average monthly costs per class were $1,713 during the first year of implementation and $873 during the second year of implementation. The cost measurements, combined with information from the literature on cost savings attributable to EnhanceFitness participation, suggest that EnhanceFitness has the potential to generate a net societal cost savings among program participants. The results are useful for community agencies considering implementing EnhanceFitness for their populations. PMID:24440919

Page, Timothy F; Batra, Anamica; Ghouse, Muddasir M; Palmer, Richard C

2014-01-17

330

Black Males in Education: Learning and Achievement. A Summative Community Analysis Response from the Kwanzaa Adult Forum (December 27, 2010)  

Science.gov (United States)

Background: Educating black males is critical. No longer can the black community blame the school for the academic failure of this population. The black community must address this pervasive issue. Purpose: The purpose for this inquiry was to explore community support and recommendations for educating black males. Setting: The setting took place…

Bell, Edward Earl

2011-01-01

331

Virus Pathogen Database and Analysis Resource (ViPR: A Comprehensive Bioinformatics Database and Analysis Resource for the Coronavirus Research Community  

Directory of Open Access Journals (Sweden)

Full Text Available Several viruses within the Coronaviridae family have been categorized as either emerging or re-emerging human pathogens, with Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV being the most well known. The NIAID-sponsored Virus Pathogen Database and Analysis Resource (ViPR, www.viprbrc.org supports bioinformatics workflows for a broad range of human virus pathogens and other related viruses, including the entire Coronaviridae family. ViPR provides access to sequence records, gene and protein annotations, immune epitopes, 3D structures, host factor data, and other data types through an intuitive web-based search interface. Records returned from these queries can then be subjected to web-based analyses including: multiple sequence alignment, phylogenetic inference, sequence variation determination, BLAST comparison, and metadata-driven comparative genomics statistical analysis. Additional tools exist to display multiple sequence alignments, view phylogenetic trees, visualize 3D protein structures, transfer existing reference genome annotations to new genomes, and store or share results from any search or analysis within personal private ‘Workbench’ spaces for future access. All of the data and integrated analysis and visualization tools in ViPR are made available without charge as a service to the Coronaviridae research community to facilitate the research and development of diagnostics, prophylactics, vaccines and therapeutics against these human pathogens.

Yun Zhang

2012-11-01

332

Fusion Energy: Contextual Analysis of the Information Panels Developed by the Scientific Community versus Citizen Discourse  

International Nuclear Information System (INIS)

The report presents an exploratory study on the impact of scientific dissemination, particularly a comparative analysis of two discourses on fusion energy as an alternative energy future. The report introduces a comparative analysis of the institutional discourse, as portrayed by the scientific jargon used in a European travelling exhibition on nuclear fusion Fusion Expo, and the social discourse, as illustrated by a citizen deliberation on this very same exhibition. Through textual analysis, the scientific discourse as deployed in the informative panels at the Fusion Expo is compared with the citizen discourse as developed in the discussions within the citizen groups. The ConText software was applied for such analysis. The purpose is to analyze how visitors assimilate, capture and understand highly technical information. Results suggest that, in despite of convergence points, the two discourses present certain differences, showing diverse levels of communication. The scientific discourse shows a great profusion of formalisms and technicalities of scientific jargon. The citizen discourse shows abundance of words associated with daily life and the more practical aspects (economy, efficiency), concerning institutional and evaluative references. In sum, the study shows that although there are a few common communicative spaces, there are still very few turning points. These data indicate that although exhibitions can be a good tool to disseminate advances in fusion energy in informal learning contexts, public feedback is a powerful tool for improving the quality of social dialogue. (Author)

333

Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw  

Science.gov (United States)

Permafrost contains an estimated 1672????????Pg carbon (C), an amount roughly equivalent to the total currently contained within land plants and the atmosphere. This reservoir of C is vulnerable to decomposition as rising global temperatures cause the permafrost to thaw. During thaw, trapped organic matter may become more accessible for microbial degradation and result in greenhouse gas emissions. Despite recent advances in the use of molecular tools to study permafrost microbial communities, their response to thaw remains unclear. Here we use deep metagenomic sequencing to determine the impact of thaw on microbial phylogenetic and functional genes, and relate these data to measurements of methane emissions. Metagenomics, the direct sequencing of DNA from the environment, allows the examination of whole biochemical pathways and associated processes, as opposed to individual pieces of the metabolic puzzle. Our metagenome analyses reveal that during transition from a frozen to a thawed state there are rapid shifts in many microbial, phylogenetic and functional gene abundances and pathways. After one week of incubation at 5 ??C, permafrost metagenomes converge to be more similar to each other than while they are frozen. We find that multiple genes involved in cycling of C and nitrogen shift rapidly during thaw. We also construct the first draft genome from a complex soil metagenome, which corresponds to a novel methanogen. Methane previously accumulated in permafrost is released during thaw and subsequently consumed by methanotrophic bacteria. Together these data point towards the importance of rapid cycling of methane and nitrogen in thawing permafrost. ?? 2011 Macmillan Publishers Limited. All rights reserved.

MacKelprang, R.; Waldrop, M.P.; Deangelis, K.M.; David, M.M.; Chavarria, K.L.; Blazewicz, S.J.; Rubin, E.M.; Jansson, J.K.

2011-01-01

334

An Analysis of the Equitability of the Full-time Equivalent Enrollment Formula for the Distribution of State Aid Among Iowa Community Colleges.  

Science.gov (United States)

The full-time equivalent enrollment (FTEE) has been a significant factor to Iowa's 15 area community colleges for cost analysis, production comparisons, and for the distribution of state aid. The FTEE formula calculates units of production according to the ratio of reimbursable contact hours (RCH) to total contact hours generated by student…

Schorzmann, Eugene F.

335

Brief Report: Impact of Applied Behaviour Analysis (ABA) on Carer Burden and Community Participation in Challenging Behaviour--Results from a Randomised Controlled Trial  

Science.gov (United States)

Background: Applied behaviour analysis (ABA) reduces challenging behaviour in people with intellectual disability. There is interest, however, in whether such interventions reduce carer burden and increase community participation in this group. Methods: A 6-month randomised controlled trial was followed by a longer-term naturalistic follow-up of…

Hassiotis, A.; Robotham, D.; Canagasabey, A.; Marston, L.; Thomas, B.; King, M.

2012-01-01

336

“Until they know how much you care”: A qualitative analysis of an innovative practice in community pharmacy  

Directory of Open Access Journals (Sweden)

Full Text Available Purpose: This qualitative study was concerned with investigating community pharmacists’ thoughts on the use of two brief scales to measure patient outcomes and therapeutic alliance in the context of their Medication Therapy Management (MTM services. The scales were originally developed for use in behavioral healthcare, but were used in a novel (community pharmacy setting as part of a previous parent study. We describe this practice (using these scales in a novel setting as an innovative practice, report on the pharmacists’ experiences with the practice, and discuss relative advantages and disadvantages for integrating the use of the scales as part of routine practice.Methods: Six community pharmacy practitioners participated in a semi-structured interview pertaining to the use of the scales in their MTM services. Pharmacist interviews were transcribed, analyzed according to qualitative content analysis methodology, and presented in relation to the guiding interview questions.Results: Pharmacists had varying opinions on the use of the scales as part of their practice. Initial concerns included patient (misunderstanding about the purpose and proper completion of the scales, as well as apprehension about the use of the information. These concerns were largely resolved through education, repeated use, and routinization. Pharmacists, in general, saw a value to using these scales in clinical practice, for clinical and professional reasons, although there was variability on the degree to which pharmacists integrated the scales into practice after the study completion. Pharmacists had varied opinions as well as on the degree to which the use of the scales would impact medication adherence. Pharmacists were most surprised by how much participation in this study prompted them to reflect on their interactions with patients.Conclusions: Pharmacists, in general, were receptive to participating in the parent study and using two brief scales to measure patient outcomes and therapeutic alliance. Pharmacists had varying opinions on the degree to which the use of these scales could impact patient medication adherence, although they perceived other value and benefits secondary to the interactions. While most pharmacists did not maintain formal use of the scales after study end, they took away general principles of patient-centered care and individualized feedback.

Michael Melczak, PhD

2011-01-01

337

Dietary Patterns Associated with Risk for Metabolic Syndrome in Urban Community of Karachi Defined by Cluster Analysis  

Directory of Open Access Journals (Sweden)

Full Text Available Dietary trends have been found to be related with metabolic syndrome in various studies. To identify dietary patterns and study associations between the dietary patterns of subjects with high and low risk of metabolic syndrome in a Karachi based community. A group of 871 men and women were selected randomly from 532 households. Data about consumption of specific foods was available for 867 adults. Participants completed a health and lifestyle questionnaire and 363 subjects provided fasting blood samples for glucose and lipids. Dietary intake was assessed by a questionnaire to identify consumption of 33 specific food items and the dietary patterns categorized into 6 food groups was assessed by cluster analysis. Five dietary patterns were identified through cluster analysis. Cluster 1 had the lowest proportion of persons with metabolic syndrome i.e. 42.7% while cluster 2 had the highest percentage of metabolic syndrome subjects (56.3% (p = 0.09. Consumption of fat and caloric dense foods was significantly higher among highest risk group (cluster 2 compared to lowest risk group (cluster 1 (p = 0.0001. The consumption of food groups containing fruit, milk and meat was also more than twice in high risk compared to low risk group (p = 0.0001. Even within the same population there are marked differences in dietary patterns and these apparently contribute to the risk of developing metabolic syndrome. Dietary pattern studies will help elucidate links between diet and disease and contribute to developing healthy eating guidelines.

Rubina Hakeem

2010-01-01

338

LC/IRMS analysis: A powerful technique to trace carbon flow in microphytobenthic communities in intertidal sediments  

Science.gov (United States)

Microphytobenthic communities are important for primary production in intertidal marine sediments. Extracellular polymeric substances (EPS), comprising polysaccharides and proteins, play a key role in the structure and functioning of microphytobenthic biofilms and allow interactions between the benthic microalgae and the associated heterotrophic bacteria. The use of stable isotopes has provided major insights into the functioning of these microbial ecosystems. Until recently, gas chromatography-isotope ratio mass spectrometry (GC/IRMS) was the principal method for compound specific stable isotope analysis in these studies. Liquid chromatography linked to IRMS (LC/IRMS) is a more recently developed technique that broadens the range of compounds that can be targeted, in particular enabling the analysis of 13C in non-volatile, aqueous soluble organic compounds, such as carbohydrates and amino acids. In this paper we present an overview of the possibilities and limitations of the LC/IRMS technique to study metabolic processes in microphytobenthic biofilms consisting of mainly diatoms. With a preliminary in-situ labeling experiment, we show that the biosynthesis of carbohydrates and amino acids in EPS and total carbohydrate and amino acid pools can be determined by LC/IRMS. Water extractable EPS were composed predominantly of carbohydrates, whereas amino acids played a minor role, both in terms of content and production. By using LC/IRMS, we will be able to quantify the biosynthesis of metabolites and, hence, to unravel in detail the metabolic pathways of the transfer of carbon from the diatoms via EPS to the bacteria.

Moerdijk-Poortvliet, Tanja C. W.; Stal, Lucas J.; Boschker, Henricus T. S.

2014-09-01

339

GeoChip-based analysis of the microbial community functional structures in simultaneous desulfurization and denitrification process.  

Science.gov (United States)

The elemental sulfur (S°) recovery was evaluated in the presence of nitrate in two development models of simultaneous desulfurization and denitrification (SDD) process. At the loading rates of 0.9 kg S/(m³·day) for sulfide and 0.4 kg N/(m³·day) for nitrate, S° conversion rate was 91.1% in denitrifying sulfide removal (DSR) model which was higher than in integrated simultaneous desulfurization and denitrification (ISDD) model (25.6%). A comprehensive analysis of functional diversity, structure and metabolic potential of microbial communities was examined in two models by using functional gene array (GeoChip 2.0). GeoChip data indicated that diversity indices, community structure, and abundance of functional genes were distinct between two models. Diversity indices (Simpson's diversity index (1/D) and Shannon-Weaver index (H')) of all detected genes showed that with elevated influent loading rate, the functional diversity decreased in ISDD model but increased in DSR model. In contrast to ISDD model, the overall abundance of dsr genes was lower in DSR model, while some functional genes targeting from nitrate-reducing sulfide-oxidizing bacteria (NR-SOB), such as Thiobacillus denitrificans, Sulfurimonas denitrificans, and Paracoccus pantotrophus were more abundant in DSR model which were highly associated with the change of S(0) conversion rate obtained in two models. The results obtained in this study provide additional insights into the microbial metabolic mechanisms involved in ISDD and DSR models, which in turn will improve the overall performance of SDD process. PMID:25079984

Yu, Hao; Chen, Chuan; Ma, Jincai; Liu, Wenzong; Zhou, Jizhong; Lee, Duu-Jong; Ren, Nanqi; Wang, Aijie

2014-07-01

340

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

Michele L Ostraat, Karmann C Mills, Kimberly A Guzan, Damaris MurryRTI International, Durham, NC, USAAbstract: The amount of data being generated in the nanotechnology research space is significant, and the coordination, sharing, and downstream analysis of the data is complex and consistently deliberated. The complexities of the data are due in large part to the inherently complicated characteristics of nanomaterials. Also, testing protocols and assays used for nanomaterials are diverse and l...

Ml, Ostraat; Kc, Mills; Ka, Guzan; Murry D

2013-01-01

 
 
 
 
341

Cyanobacterial community structure as seen from RNA polymerase gene sequence analysis.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

PCR was used to amplify DNA-dependent RNA polymerase gene sequences specifically from the cyanobacterial population in a seawater sample from the Sargasso Sea. Sequencing and analysis of the cloned fragments suggest that the population in the sample consisted of two distinct clusters of Prochlorococcus-like cyanobacteria and four clusters of Synechococcus-like cyanobacteria. The diversity within these clusters was significantly different, however. Clones within each Synechococcus-like cluster...

Palenik, B.

1994-01-01

342

Crowdsourcing education on the Web: a role-based analysis of online learning communities  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Learning online has significantly evolved over the past decade due to the emergence of Web 2.0 and 3.0 technologies that facilitate social learning in adaptive online environments. The open content movement and the associated techniques of crowdsourcing (i.e. assimilating several small contributions into resources of high quality) have further influenced education on the Web. This chapter investigates the concept of crowdsourcing in education through an analysis of case studies dealing with t...

Corneli, Joseph; Mikroyannidis, Alexander

2012-01-01

343

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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, knowl...

Khadka C; Vacik H

2012-01-01

344

Analysis of photosynthetic picoeukaryote community structure along an extended Ellett Line transect in the northern North Atlantic reveals a dominance of novel prymnesiophyte and prasinophyte phylotypes  

Science.gov (United States)

Photosynthetic picoeukaryotes (PPEs) of a size situ hybridization (FISH) analysis of seawater samples collected along the transect to provide a PCR-independent survey of class level PPE distribution patterns. We found the PPE community was dominated by members of the Prymnesiophyceae, Prasinophyceae and Mamiellophyceae. Interestingly, phylogenetic analysis revealed several novel Prymnesiophyceae and Prasinophyceae phylotypes (with only 85-96% identity to neighbouring sequences) within lineages for which cultured counterparts are unknown.

Kirkham, Amy R.; Jardillier, Ludwig E.; Holland, Ross; Zubkov, Mikhail V.; Scanlan, Dave J.

2011-07-01

345

Community contextual predictors of endoscopic colorectal cancer screening in the USA: spatial multilevel regression analysis  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Colorectal cancer (CRC is the second leading cause of cancer death in the United States, and endoscopic screening can both detect and prevent cancer, but utilization is suboptimal and varies across geographic regions. We use multilevel regression to examine the various predictors of individuals' decisions to utilize endoscopic CRC screening. Study subjects are a 100% population cohort of Medicare beneficiaries identified in 2001 and followed through 2005. The outcome variable is a binary indicator of any sigmoidoscopy or colonoscopy use over this period. We analyze each state separately and map the findings for all states together to reveal patterns in the observed heterogeneity across states. Results We estimate a fully adjusted model for each state, based on a comprehensive socio-ecological model. We focus the discussion on the independent contributions of each of three community contextual variables that are amenable to policy intervention. Prevalence of Medicare managed care in one's neighborhood was associated with lower probability of screening in 12 states and higher probability in 19 states. Prevalence of poor English language ability among elders in one's neighborhood was associated with lower probability of screening in 15 states and higher probability in 6 states. Prevalence of poverty in one's neighborhood was associated with lower probability of screening in 36 states and higher probability in 5 states. Conclusions There are considerable differences across states in the socio-ecological context of CRC screening by endoscopy, suggesting that the current decentralized configuration of state-specific comprehensive cancer control programs is well suited to respond to the observed heterogeneity. We find that interventions to mediate language barriers are more critically needed in some states than in others. Medicare managed care penetration, hypothesized to affect information about and diffusion of new endoscopic technologies, has a positive association in only a minority of states. This suggests that managed care plans' promotion of this cost-increasing technology has been rather limited. Area poverty has a negative impact in the vast majority of states, but is positive in five states, suggesting there are some effective cancer control policies in place targeting the poor with supplemental resources promoting CRC screening.

Mobley Lee R

2010-09-01

346

The methodology for developing a prospective meta-analysis in the family planning community  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Prospective meta-analysis (PMA is a collaborative research design in which individual sites perform randomized controlled trials (RCTs and pool the data for meta-analysis. Members of the PMA collaboration agree upon specific research interventions and outcome measures, ideally before initiation but at least prior to any individual trial publishing results. This allows for uniform reporting of primary and secondary outcomes. With this approach, heterogeneity among trials contributing data for the final meta-analysis is minimized while each site maintains the freedom to design a specific trial. This paper describes the process of creating a PMA collaboration to evaluate the impact of misoprostol on ease of intrauterine device (IUD insertion in nulliparous women. Methods After the principal investigator developed a preliminary PMA protocol, he identified potential collaborating investigators at other sites. One site already had a trial underway and another site was in the planning stages of a trial meeting PMA requirements. Investigators at six sites joined the PMA collaborative. Each site committed to enroll subjects to meet a pre-determined total sample size. A final common research plan and site responsibilities were developed and agreed upon through email and face-to-face meetings. Each site committed to contribute individual patient data to the PMA collaboration, and these data will be analyzed and prepared as a multi-site publication. Individual sites retain the ability to analyze and publish their site's independent findings. Results All six sites have obtained Institutional Review Board approval and each has obtained individual funding to meet the needs of that site's study. Sites have shared resources including study protocols and consents to decrease costs and improve study flow. This PMA protocol is registered with the Cochrane Collaboration and data will be analyzed according to Cochrane standards for meta-analysis. Conclusions PMA is a novel research method that improves meta-analysis by including several study sites, establishing uniform reporting of specific outcomes, and yet allowing some independence on the part of individual sites with respect to the conduct of research. The inclusion of several sites increases statistical power to address important clinical questions. Compared to multi-center trials, PMA methodology encourages collaboration, aids in the development of new investigators, decreases study costs, and decreases time to publication. Trial Registration ClinicalTrials.gov: NCT00613366, NCT00886834, NCT01001897, NCT01147497 and NCT01307111

Jacobson Janet C

2011-04-01

347

Building Safer Communities: The Integrated Community Safety Approach  

Energy Technology Data Exchange (ETDEWEB)

This paper discusses an integrated community safety approach to creating safer communities. It defines community broadly to include two categories of community members: “industry” and “neighbors.” Potential community members within the “industry” category include facilities, government/regulators, customers, stockholders, and suppliers. Within the “neighbors” category are towns, cities, counties, states; people/commodity flow systems; news media and special interest groups; environment; and families of employees. Each of these potential community members and its characteristics are discussed. The integrated community safety approach consists of three major activities: (1) define the boundaries of the community; (2) facilitate the sense of community; and (3) address the needs of the community. Defining the boundaries of the community includes determining the geographical and social boundaries; this is accomplished through conducting a hazard analysis and community involvement to identify all of the community members. Facilitating the sense of community includes conducting a capability/needs assessment and continuing community involvement to identify the issues and concerns of community members. Addressing the needs of the community involves master planning to consider safety issues in all community development actions and continuing community education and involvement. The integrated community safety approach is a workable approach for existing industries and their neighbors as well as new projects that industries and their neighbors might be considering. By using this socio-technical approach to integrating industry and all of its neighbors into a safer community, the integrated community safety approach will better assure the viability and safety of industry and its neighbors while maintaining or improving the overall quality of life.

Fawcett, Ricky Lee; Kerr, Thomas A; Jordan, Steven Albert

2001-03-01

348

Oligonucleotide Fingerprinting of rRNA Genes for Analysis of Fungal Community Composition  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Thorough assessments of fungal diversity are currently hindered by technological limitations. Here we describe a new method for identifying fungi, oligonucleotide fingerprinting of rRNA genes (OFRG). ORFG sorts arrayed rRNA gene (ribosomal DNA [rDNA]) clones into taxonomic clusters through a series of hybridization experiments, each using a single oligonucleotide probe. A simulated annealing algorithm was used to design an OFRG probe set for fungal rDNA. Analysis of 1,536 fungal rDNA clones d...

Valinsky, Lea; Della Vedova, Gianluca; Jiang, Tao; Borneman, James

2002-01-01

349

Energy analysis of the coal fuel cycle: Community health and resource change in an Appalachian coal county  

International Nuclear Information System (INIS)

In spite of steadily expanding coal development in this decade in the USA, there has been little systematic assessment of occupational and public health implications of increased production in specific regions of the USA. Preliminary analysis of a prototype Appalachian area is presented. Anderson County, Tennessee, the prototype area chosen for evaluation, lies in the Upper East Tennessee Coalfield. This county is uniquely suited for study since every process of the coal fuel cycle (extraction, transport, combustion, power production and waste disposal) takes place within the county boundary. By extensive exploitation of both surface and underground methods of extraction, this county has maintained a leading position in Tennessee's coal production for several years. Concepts of energy analysis and systematized data presentation were used to convert information gathered from diverse sources into comparable energy units (kcal). Concepts and methodology implemented in the analysis can be applied most appropriately to existing conditions in other counties of the Appalachian Coal Basin. Findings are presented for calendar year 1978. For the year of study, the major energy loss to the county was depletion of the coal resource base by use of inefficient mining techniques (a loss of 10.5x1012kcal fuel equivalents). Another loss is to community health, which is depleted by lost productivity of, and compensation payments to, victims of mining accidents and occupationvictims of mining accidents and occupational disease such as 'black lung' (15x109kcal). Another countywide depletion process is roadbed and bridge deterioration caused by large volumes of heavy coal-haul vehicular traffic (10x109kcal). These losses are being borne mainly by residents of the Appalachian host region, with little systematic compensation by consumers of the coal resource. It is expected that these losses will increase in magnitude as national coal use increases. (author)

350

Comparative Metagenomic Analysis Of Microbial Communities From Active Layer And Permafrost After Short-Term Thaw  

Science.gov (United States)

.Permafrost areas occupy 20-25% of the Earth and extend of 1 km depths. The total number of prokaryotes and their biomass in cold regions are estimated to be 1 x 1030 cells and 140 x1015 g of C, respectively. Thus these environments serve as a reservoir of microbial and biogeochemical activity, which is likely to increase upon thawing. We are currently performing long-term thawing experiments at 4o C on 18, geochemically well-characterized, 1 meter long, intact cores consisting of active-layer (0-70 cm depth) and permafrost, collected from a 7 meter diameter ice-wedge polygon located at the McGill Arctic Research Station on Axel Heiberg Island, Nunavut, Canada. The organic carbon content of these cores averages ~1% at depth but increases to 5.4% in the top 10 cm. The cores were subdivided into four treatment groups: saturated cores (thawed while receiving artificial rain), drained cores (being thawed under natural hydrological conditions), dark cores (thawed under natural hydrological conditions with no light input) and control cores (maintain permafrost table at 70 cm depth). Over the course of 10 weeks the cores were progressively thawed from -4oC to 4oC from the top down to simulate spring thaw conditions in the Arctic. The temperatures at 5 cm, 35 cm, 65 cm, and below the permafrost table in the core were recorded continuously. Pore water and gas samples from 4 depths in each core were collected every two weeks and analyzed for pH, anions, cations, H2, CH4, CO, O2, N2, CO2 and ?13C of CO2. Headspace gas samples were collected weekly and analyzed for the same gases as the pore gases. Sediment sub-samples from the 4 depths were collected and total community genomic DNA (gDNA) was isolated using FastDNA SPIN kit followed by Qiagen column purification. The average yield of gDNA was ~3.5 ?g/g of soil for the upper 5 cm active layers and decreased to ~1.5 ?g/g of soil in the permafrost. The bacterial 16S copy numbers estimated by real-time quantitative PCR decreased with depth from 7x108 to 1x108 copies /g of soil. Characterization of the metagenomic sequences derived from the samples before thawing elucidated differences between the permafrost and active-layer with Acidobacteria and Alpha-Proteobacteria are being significantly higher in active layer than in permafrost, on the contrary permafrost had higher abundance of Actinobacteria and Bacteroidetes than active layer. Currently additional metagenomic DNA illumina libraries for 20 samples after 1 week thawing are in preparation and will be analyzed to determine whether variations in the metagenomic sequences are correlated to the geochemical data.

Vishnivetskaya, T. A.; Chauhan, A.; Saarunya, G.; Murphy, J.; Williams, D.; Layton, A. C.; Pfiffner, S. M.; Stackhouse, B. T.; Sanders, R.; Lau, C. M.; myneni, S.; Phelps, T. J.; Fountain, A. G.; Onstott, T. C.

2012-12-01

351

Constant Communities in Complex Networks  

CERN Document Server

Identifying community structure is a fundamental problem in network analysis. Most community detection algorithms are based on optimizing a combinatorial parameter, for example modularity. This optimization is generally NP-hard, thus merely changing the vertex order can alter their assignments to the community. However, there has been very less study on how vertex ordering influences the results of the community detection algorithms. Here we identify and study the properties of invariant groups of vertices (constant communities) whose assignment to communities are, quite remarkably, not affected by vertex ordering. The percentage of constant communities can vary across different applications and based on empirical results we propose metrics to evaluate these communities. Using constant communities as a pre-processing step, one can significantly reduce the variation of the results. Finally, we present a case study on phoneme network and illustrate that constant communities, quite strikingly, form the core func...

Chakraborty, Tanmoy; Ganguly, Niloy; Bhowmick, Sanjukta; Mukherjee, Animesh

2013-01-01

352

Intercomparison of the community multiscale air quality model and CALGRID using process analysis.  

Science.gov (United States)

This study was designed to examine the similarities and differences between two advanced photochemical air quality modeling systems: EPA Models-3/CMAQ and CALGRID/CALMET. Both modeling systems were applied to an ozone episode that occurred along the I-5 urban corridor in western Washington and Oregon during July 11-14, 1996. Both models employed the same modeling domain and used the same detailed gridded emission inventory. The CMAQ model was run using both the CB-IV and RADM2 chemical mechanisms, while CALGRID was used with the SAPRC-97 chemical mechanism. Outputfrom the Mesoscale Meteorological Model (MM5) employed with observational nudging was used in both models. The two modeling systems, representing three chemical mechanisms and two sets of meteorological inputs, were evaluated in terms of statistical performance measures for both 1- and 8-h average observed ozone concentrations. The results showed that the different versions of the systems were more similar than different, and all versions performed well in the Portland region and downwind of Seattle but performed poorly in the more rural region north of Seattle. Improving the meteorological input into the CALGRID/CALMET system with planetary boundary layer (PBL) parameters from the Models-3/CMAQ meteorology preprocessor (MCIP) improved the performance of the CALGRID/CALMET system. The 8-h ensemble case was often the best performer of all the cases indicating that the models perform better over longer analysis periods. The 1-h ensemble case, derived from all runs, was not necessarily an improvement over the five individual cases, but the standard deviation about the mean provided a measure of overall modeling uncertainty. Process analysis was applied to examine the contribution of the individual processes to the species conservation equation. The process analysis results indicated that the two modeling systems arrive at similar solutions by very different means. Transport rates are faster and exhibit greater fluctuations in the CMAQ cases than in the CALGRID cases, which lead to different placement of the urban ozone plumes. The CALGRID cases, which rely on the SAPRC97 chemical mechanism, exhibited a greater diurnal production/loss cycle of ozone concentrations per hour compared to either the RADM2 or CBIV chemical mechanisms in the CMAQ cases. These results demonstrate the need for specialized process field measurements to confirm whether we are modeling ozone with valid processes. PMID:16124311

O'Neill, Susan M; Lamb, Brian K

2005-08-01

353

RegaDB: community-driven data management and analysis for infectious diseases  

Science.gov (United States)

Summary: RegaDB is a free and open source data management and analysis environment for infectious diseases. RegaDB allows clinicians to store, manage and analyse patient data, including viral genetic sequences. Moreover, RegaDB provides researchers with a mechanism to collect data in a uniform format and offers them a canvas to make newly developed bioinformatics tools available to clinicians and virologists through a user friendly interface. Availability and implementation: Source code, binaries and documentation are available on http://rega.kuleuven.be/cev/regadb. RegaDB is written in the Java programming language, using a web-service-oriented architecture. Contact: pieter.libin@rega.kuleuven.be PMID:23645815

Libin, Pieter; Beheydt, Gertjan; Deforche, Koen; Imbrechts, Stijn; Ferreira, Fossie; Van Laethem, Kristel; Theys, Kristof; Carvalho, Ana Patricia; Cavaco-Silva, Joana; Lapadula, Giuseppe; Torti, Carlo; Assel, Matthias; Wesner, Stefan; Snoeck, Joke; Ruelle, Jean; De Bel, Annelies; Lacor, Patrick; De Munter, Paul; Van Wijngaerden, Eric; Zazzi, Maurizio; Kaiser, Rolf; Ayouba, Ahidjo; Peeters, Martine; de Oliveira, Tulio; Alcantara, Luiz C. J.; Grossman, Zehava; Sloot, Peter; Otelea, Dan; Paraschiv, Simona; Boucher, Charles; Camacho, Ricardo J.; Vandamme, Anne-Mieke

2013-01-01

354

A geostatistical analysis of small-scale spatial variability in bacterial abundance and community structure in salt marsh creek bank sediments  

Science.gov (United States)

Small-scale variations in bacterial abundance and community structure were examined in salt marsh sediments from Virginia's eastern shore. Samples were collected at 5 cm intervals (horizontally) along a 50 cm elevation gradient, over a 215 cm horizontal transect. For each sample, bacterial abundance was determined using acridine orange direct counts and community structure was analyzed using randomly amplified polymorphic DNA fingerprinting of whole-community DNA extracts. A geostatistical analysis was used to determine the degree of spatial autocorrelation among the samples, for each variable and each direction (horizontal and vertical). The proportion of variance in bacterial abundance that could be accounted for by the spatial model was quite high (vertical: 60%, horizontal: 73%); significant autocorrelation was found among samples separated by 25 cm in the vertical direction and up to 115 cm horizontally. In contrast, most of the variability in community structure was not accounted for by simply considering the spatial separation of samples (vertical: 11%, horizontal: 22%), and must reflect variability from other parameters (e.g., variation at other spatial scales, experimental error, or environmental heterogeneity). Microbial community patch size based upon overall similarity in community structure varied between 17 cm (vertical) and 35 cm (horizontal). Overall, variability due to horizontal position (distance from the creek bank) was much smaller than that due to vertical position (elevation) for both community properties assayed. This suggests that processes more correlated with elevation (e.g., drainage and redox potential) vary at a smaller scale (therefore producing smaller patch sizes) than processes controlled by distance from the creek bank. c2002 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.

Franklin, Rima B.; Blum, Linda K.; McComb, Alison C.; Mills, Aaron L.

2002-01-01

355

Cyanobacterial community structure as seen from RNA polymerase gene sequence analysis  

Energy Technology Data Exchange (ETDEWEB)

PCR was used to amplify DNA-dependent RNA polymerase gene sequences specifically from the cyanobacterial population in a seawater sample from the Sargasso Sea. Sequencing and analysis of the cloned fragments suggests that the population in the sample consisted of two distinct clusters of Prochlorococcus-like cyanobacteria and four clusters of Synechococcus-like cyanobacteria. The diversity within these clusters was significantly different, however. Clones within each Synechococcus-like cluster were 99 to 100% identical, while each Prochlorococcus-like cluster was only 91% identical at the nucleotide level. One Prochlorococcus-like cluster was significantly more closely related to a Mediterranean Sea (surface) Prochlorococcus isolate than to the other cluster, showing the highly divergent nature of this group even in one sample. The approach described here can be used as a general method for examining cyanobacterial diversity, while an oligotrophic ocean ecosystem such as the Sargasso Sea may be an ideal model for examining diversity in relation to environmental parameters. 51 refs., 3 figs., 2 tabs.

Palenik, B. [Univ. of California, San Diego, La Jolla, CA (United States)

1994-09-01

356

Purification of high ammonia wastewater in a biofilm airlift loop bioreactor with microbial communities analysis.  

Science.gov (United States)

A 70 m(3) gas-liquid-solid three-phase flow airlift loop bioreactor, in which biofilm attached on granular active carbon carriers, was used for purification of the high ammonia wastewater from bioethanol production. Under the optimum operating conditions, COD and NH4 (+)-N average removal rate of 89.0 and 98.6 % were obtained at hydraulic retention time of 10 h. Scanning electron microscopy was applied for observation of the biofilm formation. High contaminants removal efficiency was achieved by holding high biomass concentration in the reactor due to the attached biofilm over the carriers. The 16S rRNA gene clone library analysis indicated that 68.6 % of the clones were affiliated with the two phyla Bacteroidetes and Proteobacteria, and residual clones clustered with various sequences from uncultured bacteria. The presence of various anoxic/anaerobic bacteria indicated that the oxygen gradient inside the biofilm could provide appropriate micro-environment for nitrogen removal through simultaneous nitrification and denitrification. PMID:25344088

Qiu, Chunsheng; Zhang, Dandan; Sun, Liping; Wen, Jianping

2015-01-01

357

Analysis of bacterial communities and bacterial pathogens in a biogas plant by the combination of ethidium monoazide, PCR and Ion Torrent sequencing  

DEFF Research Database (Denmark)

The present study investigated the changes of bacterial community composition including bacterial pathogens along a biogas plant, i.e. from the influent, to the biogas reactor and to the post-digester. The effects of post-digestion temperature and time on the changes of bacterial community composition and bacterial pathogens were also studied. Microbial analysis was made by Ion Torrent sequencing of the PCR amplicons from ethidium monoazide treated samples, and ethidium monoazide was used to cleave DNA from dead cells and exclude it from PCR amplification. Both similarity and taxonomic analysis showed that the bacterial community composition in the influent was changed after anaerobic digestion. Firmicutes were dominant in all the samples, while Proteobacteria decreased in the biogas reactor compared with the influent. Variations of bacterial community composition in the biogas reactor with time were also observed. This could be attributed to varying composition of the influent. Batch experiments showed that the methane recovery from the digested residues (obtained from biogas reactor) was mainly related with post-digestion temperature. However, post-digestion time rather than temperature had a significant effect on the changes of bacterial community composition. The changes of bacterial community composition were also reflected in the changes of relative abundance of bacterial pathogens. The richness and relative abundance of bacterial pathogens were reduced after anaerobic digestion in the biogas reactor. It was found in batch experiments that bacterial pathogens showed the highest relative abundance and richness after 30days' post-digestion. Streptococcus bovis was found in all the samples. Our results showed that special attention should be paid to the post-digestion since the increase in relative abundance of bacterial pathogens after post-digestion might reflect regrowth of bacterial pathogens and limit biosolids disposal vectors. © 2014 Elsevier Ltd.

Luo, Gang; Angelidaki, Irini

2014-01-01

358

Analysis of bacterial communities and bacterial pathogens in a biogas plant by the combination of ethidium monoazide, PCR and Ion Torrent sequencing.  

Science.gov (United States)

The present study investigated the changes of bacterial community composition including bacterial pathogens along a biogas plant, i.e. from the influent, to the biogas reactor and to the post-digester. The effects of post-digestion temperature and time on the changes of bacterial community composition and bacterial pathogens were also studied. Microbial analysis was made by Ion Torrent sequencing of the PCR amplicons from ethidium monoazide treated samples, and ethidium monoazide was used to cleave DNA from dead cells and exclude it from PCR amplification. Both similarity and taxonomic analysis showed that the bacterial community composition in the influent was changed after anaerobic digestion. Firmicutes were dominant in all the samples, while Proteobacteria decreased in the biogas reactor compared with the influent. Variations of bacterial community composition in the biogas reactor with time were also observed. This could be attributed to varying composition of the influent. Batch experiments showed that the methane recovery from the digested residues (obtained from biogas reactor) was mainly related with post-digestion temperature. However, post-digestion time rather than temperature had a significant effect on the changes of bacterial community composition. The changes of bacterial community composition were also reflected in the changes of relative abundance of bacterial pathogens. The richness and relative abundance of bacterial pathogens were reduced after anaerobic digestion in the biogas reactor. It was found in batch experiments that bacterial pathogens showed the highest relative abundance and richness after 30 days' post-digestion. Streptococcus bovis was found in all the samples. Our results showed that special attention should be paid to the post-digestion since the increase in relative abundance of bacterial pathogens after post-digestion might reflect regrowth of bacterial pathogens and limit biosolids disposal vectors. PMID:24852413

Luo, Gang; Angelidaki, Irini

2014-09-01

359

Methanethiol degradation in anaerobic bioreactors at elevated pH (8): reactor performance and microbial community analysis.  

Science.gov (United States)

The degradation of methanethiol (MT) at 30 degrees C under saline-alkaline (pH 8-10, 0.5M Na(+)) conditions was studied in a lab-scale Upflow Anaerobic Sludge Blanket (UASB) reactor inoculated with estuarine sediment from the Wadden Sea (The Netherlands). At a sodium concentration of 0.5M and a pH between 8 and 9 complete MT degradation to sulfide, methane and carbon dioxide was possible at a maximum loading rate of 22mmolMTL(-1)day(-1) and a hydraulic retention time of 6h. The presence of yeast extract (100mg/L) in the medium was essential for complete MT degradation. 16S rRNA based DGGE and sequence analysis revealed that species related to the genera Methanolobus and Methanosarcina dominated the archaeal community in the reactor sludge. Their relative abundance fluctuated in time, possibly as a result of the changing operational conditions in the reactor. The most dominant MT-degrading archaeon was enriched from the reactor and obtained in pure culture. This strain WR1, which was most closely related to Methanolobus taylorii, degraded MT, dimethyl sulfide (DMS), methanol and trimethylamine. Its optimal growth conditions were 0.2M NaCl, 30 degrees C and pH 8.4. In batch and reactor experiments operated at pH 10, MT was not degraded. PMID:18562196

van Leerdam, Robin C; de Bok, Frank A M; Bonilla-Salinas, Monica; van Doesburg, Wim; Lomans, Bart P; Lens, Piet N L; Stams, Alfons J M; Janssen, Albert J H

2008-12-01

360

Genetic analysis in a variant of limb girdle muscular dystrophy in an inbred aboriginal community  

Energy Technology Data Exchange (ETDEWEB)

Limb girdle muscular dystrophy (LGMD) is a heterogeneous group of disorders with variable inheritance patterns, age-of-onset, rates of progression and patterns of muscle involvement. To date, 4 different chromosomal assignments have been described; LGMD1 to chromosome 5q, LGMD2 to chromosome 15q, SCARMD to chromosome 13q and a fourth locus on chromosome 2p. Because of this genetic heterogeneity, only large unambiguous multiplex families which are clearly linked to a particular locus can be utilized in a genetic analysis. We now report preliminary findings in a large highly inbred aboriginal kindred with 8 probands (5 females, 3 males) from 6 nuclear families with a progressive LMD. All presented in their mid- to late teens with gait disturbances. At time of presentation all except one had both proximal as well as distal muscle involvement, facial muscle sparing, CK levels 25 to 100 times normal (3762-20,400 U/l), dystrophic muscle biopsies and normal dystrophin and dystrophin-associated glycoprotein expression. We have studied the segregation of highly informative microsatellite markers for FBN1, D15S132 and the gene for thrombospondin on chromosome 15q and D2S134, D2S136, D2S147, and D2S166 on chromosome 2. Linkage to chromosome 15q has been excluded and two-point lod scores are not significant as yet to either confirm or exclude linkage to chromosome 2p. However, visual inspection reveals that affected individuals are not consistently homozygous for the chromosome 2p markers as would be predicted in such an inbred population. Clinically, SCARMD is unlikely and if the locus on chromosomes 2p and 5q can also be excluded, a genome-wide search using evenly spaced microsatellites will be initiated. A second geographically distinct aboriginal kindred with a similar clinical phenotype has now also been identified.

Greenberg, C.R.; Nylen, E.G.; Halliday, W. [Univ. of Manitoba, Winnipeg (Canada)] [and others

1994-09-01

 
 
 
 
361

Determinants of marital behaviour in five Apennine communities of Central Italy inferred by surname analysis, repeated pairs and kinship estimates.  

Science.gov (United States)

The work makes use of surname analysis, repeated pairs and kinship estimates in 11,009 marriage records celebrated in five communities of the Italian Central Apennine (Celano, Lecce dei Marsi, Ortucchio, Roio, Villavallelonga) from 1802 to 1965 with the objective to deepen knowledge of the relative influence of several determinants on their marital behaviour. These towns are part of the same geographic and economic environment: the slopes of the ancient Fucino Lake. This work further elaborates the results from previous studies on the bio-demographic model of the region. The data were analyzed according to three periods of approximately 50 years. Results show the highest inbreeding coefficients in the pastoral towns of Roio and Villavallelonga. Repeated pair analysis highlights a certain degree of population subdivision which declined in time in Celano, Lecce dei Marsi and Ortucchio. The highest and increasing values of RP-RPr in time in Roio suggest a general reduction in genetic heterogeneity. This is possibly due to the celebration of marriages among families selected on the economic basis of pastoralism, as this town historically has had a leading tradition of sheep-farming. Villavallelonga, excluding isonymous marriages, shows an increase in repeated pair unions in time, thus revealing a substructure with marriages among preferred lineages. This is in line with previous results on consanguineous marriages which indicated the tendency of avoiding unions between close relatives in this small geographic isolate. This study demonstrates the influence of geographical (altitude) and social factors (pastoralism) on the marital structures of the investigated populations. PMID:24012323

Capocasa, M; Taglioli, L; Anagnostou, P; Paoli, G; Danubio, M E

2014-02-01

362

Community Schools. ACSA School Management Digest, Series 1, Number 15. ERIC/CEM Research Analysis Series, Number 42.  

Science.gov (United States)

Utilizing material in the ERIC network, this paper briefly investigates the theory, history, and current state of community schools. Planning guidelines for alternative uses of school facilities are discussed and some examples are given of effective shared facilities. Financial requirements for starting a community school and possible sources of…

Schofield, Dee

363

Forest Policy Scenario Analysis: Sensitivity of Songbird Community to Changes in Forest Cover Amount and Configuration  

Directory of Open Access Journals (Sweden)

Full Text Available Changes in mature forest cover amount, composition, and configuration can be of significant consequence to wildlife populations. The response of wildlife to forest patterns is of concern to forest managers because it lies at the heart of such competing approaches to forest planning as aggregated vs. dispersed harvest block layouts. In this study, we developed a species assessment framework to evaluate the outcomes of forest management scenarios on biodiversity conservation objectives. Scenarios were assessed in the context of a broad range of forest structures and patterns that would be expected to occur under natural disturbance and succession processes. Spatial habitat models were used to predict the effects of varying degrees of mature forest cover amount, composition, and configuration on habitat occupancy for a set of 13 focal songbird species. We used a spatially explicit harvest scheduling program to model forest management options and simulate future forest conditions resulting from alternative forest management scenarios, and used a process-based fire-simulation model to simulate future forest conditions resulting from natural wildfire disturbance. Spatial pattern signatures were derived for both habitat occupancy and forest conditions, and these were placed in the context of the simulated range of natural variation. Strategic policy analyses were set in the context of current Ontario forest management policies. This included use of sequential time-restricted harvest blocks (created for Woodland caribou (Rangifer tarandus conservation and delayed harvest areas (created for American marten (Martes americana atrata conservation. This approach increased the realism of the analysis, but reduced the generality of interpretations. We found that forest management options that create linear strips of old forest deviate the most from simulated natural patterns, and had the greatest negative effects on habitat occupancy, whereas policy options that specify deferment and timing of harvest for large blocks helped ensure the stable presence of an intact mature forest matrix over time. The management scenario that focused on maintaining compositional targets best supported biodiversity objectives by providing the composition patterns required by the 13 focal species, but this scenario may be improved by adding some broad-scale spatial objectives to better maintain large blocks of interior forest habitat through time.

Jim Baker

2007-06-01

364

Community Organization And Community Assets  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Community assets are acquired to deliver services. Ongoing service delivery depends on the acquisition or creation, maintenance and renewal of community assets. Where a community asset can no longer deliver the services required by the community it needs to be renewed or replaced. Legally, municipalities and local self -governments are responsible for the community assets under their control. Facilities and infrastructure should operate efficiently and deliver the desired level of service to ...

Mukesh Kanaskar; Kulkarni, V. V.; Balakrishna Prasad; Aparajita Rajwade

2013-01-01

365

Phylogenetic analysis and in situ identification of the intestinal microbial community of rainbow trout ( Oncorhynchus mykiss , Walbaum)  

DEFF Research Database (Denmark)

Aims: To identify the dominant culturable and nonculturable microbiota of rainbow trout intestine.Methods and Results: Microbial density of rainbow trout intestine was estimated by direct microscopic counts (4('),6-diamidino-2-phenylindole, DAPI) and by culturing on tryptone soya agar (TSA). Differential gradient gel electrophoresis analysis of bacterial DNA from intestinal samples, re-amplification of bands and sequence analysis was used to identify the bacteria that dominated samples where aerobic counts were less than or equal to2% of the DAPI counts. 16S rDNA gene sequences of 146 bacterial isolates and three sequences of uncultured bacteria were identified. A set of oligonucleotide probes was constructed and used to detect and enumerate the bacterial community structure of the gastrointestinal tract of rainbow trout by fluorescence in situ hybridization (FISH). Members of the gamma subclass of Proteobacteria (mainly Aeromonas and Enterobacteriaceae) dominated the bacterial population structure. Acinetobacter, Pseudomonas, Shewanella, Plesiomonas and Proteus were also identified together with isolates belonging to the beta subclass of Proteobacteria and Gram-positive bacteria with high and low DNA G + C content. In most samples, the aerobic count (on TSA) was 50-90% of the direct (DAPI) count. A bacterium representing a previously unknown phylogenetic lineage with only 89% 16S rRNA gene sequence similarity to Anaerofilum pentosovorans was detected in intestinal samples where aerobic counts were less than or equal to2% of direct (DAPI) counts. Ten to 75% of the microbial population in samples with low aerobic counts hybridized (FISH) with a probe constructed against this not-yet cultured bacterium.Conclusions: Proteobacteria belonging to the gamma subclass dominated the intestinal microbiota of rainbow trout. However, in some samples the microflora was dominated by uncultivated, presumed anaerobic, micro-organisms. The bacterial population structure of rainbow trout intestine, as well as total bacterial counts, varied from fish to fish.Significance and Impact of the Study: Good correlation was seen between cultivation results and in situ analysis, however, a molecular approach was crucial for the identification of organisms uncultivated on TSA

Huber, I.; Spanggaard, Bettina

2004-01-01

366

Shaping Communities out of Triangles  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Community detection has arisen as one of the most relevant topics in the field of graph data mining due to its importance in many fields such as biology, social networks or network traffic analysis. The metrics proposed to shape communities are generic and follow two approaches: maximizing the internal density of such communities or reducing the connectivity of the internal vertices with those outside the community. However, these metrics take the edges as a set and do not c...

Prat-pe?rez, Arnau; Dominguez-sal, David; Brunat, Josep M.; Larriba-pey, Josep-lluis

2012-01-01

367

Comparative analysis of bacterial community-metagenomics in coastal Gulf of Mexico sediment microcosms following exposure to Macondo oil (MC252).  

Science.gov (United States)

The indigenous bacterial communities in sediment microcosms from Dauphin Island (DI), Petit Bois Island (PB) and Perdido Pass (PP) of the coastal Gulf of Mexico were compared following treatment with Macondo oil (MC252) using pyrosequencing and culture-based approaches. After quality-based trimming, 28,991 partial 16S rRNA sequence reads were analyzed by rarefaction, confirming that analyses of bacterial communities were saturated with respect to species diversity. Changes in the relative abundances of Proteobacteria, Bacteroidetes and Firmicutes played an important role in structuring bacterial communities in oil-treated sediments. Proteobacteria were dominant in oil-treated samples, whereas Firmicutes and Bacteroidetes were either the second or the third most abundant taxa. Tenericutes, members of which are known for oil biodegradation, were detected shortly after treatment, and continued to increase in DI and PP sediments. Multivariate statistical analyses (ADONIS) revealed significant dissimilarity of bacterial communities between oil-treated and untreated samples and among locations. In addition, a similarity percentage analysis showed the contribution of each species to the contrast between untreated and oil-treated samples. PCR amplification using DNA from pure cultures of Exiguobacterium,  Pseudoalteromonas,  Halomonas and Dyadobacter, isolated from oil-treated microcosm sediments, produced amplicons similar to polycyclic aromatic hydrocarbon-degrading genes. In the context of the 2010 Macondo blowout, the results from our study demonstrated that the indigenous bacterial communities in coastal Gulf of Mexico sediment microcosms responded to the MC252 oil with altered community structure and species composition. The rapid proliferation of hydrocarbonoclastic bacteria suggests their involvement in the degradation of the spilt oil in the Gulf of Mexico ecosystem. PMID:25205599

Koo, Hyunmin; Mojib, Nazia; Thacker, Robert W; Bej, Asim K

2014-11-01

368

NIMBY syndrome and public consultation policy: the implications of a discourse analysis of local responses to the establishment of a community mental health facility.  

Science.gov (United States)

The relocation of mental health services from an institutional to community base in different parts of the UK has witnessed incidents of public opposition in relation to the establishment of community mental health projects. It has been argued that this not-in-my-backyard (NIMBY) syndrome is partly a result of the attitudes held by the public towards people with mental health problems. The present paper reports some findings from a study of community attitudes towards individuals with mental health problems in a Scottish community, and discusses their implications for the development of public consultation guidelines with respect to the establishment of community mental health facilities. Discourse analysis was used to explore people's views about individuals with mental health problems. The study examined the ways in which their views were expressed in letters to the local press, and in subsequent discussions and interviews, when arguing for or against a supported accommodation project in their neighbourhood. Participants formulated their arguments around a number of issues which they claimed were of public concern. One of these related to the way in which the project was set up. In particular, participants argued that it had been established without any prior consultation with local people and in circumstances of secrecy. The findings demonstrate that, while consultation is relatively unproblematically defined in terms of its function, the specific nature of consultation is more problematic. The implications of these findings for mental health policy and practice are considered in the light of current official guidelines on public consultation relating to the establishment of community mental health facilities. It is argued that existing guidelines fail to take account of the concerns of local people, and therefore, that any intervention based on such guidelines is likely to be ineffective. It is suggested that the findings of this study will be of interest to policy makers and practitioners seeking to devise future public consultation strategies. PMID:14498834

Cowan, Sue

2003-09-01

369

A Biopsychosocial Profile of Adult Canadians with and without Chronic Back Disorders: A Population-Based Analysis of the 2009-2010 Canadian Community Health Surveys  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Chronic back disorders (CBD) are a significant public health concern. Profiling Canadians with CBD and the associated biopsychosocial factors at a national population level is important to understand the burden of this condition and how clinicians, health systems, and related policies might address this potentially growing problem. We performed a secondary analysis of the 2009 and 2010 Canadian Community Health Surveys to calculate prevalence and to better understand the differences between p...

Brenna Bath; Catherine Trask; Jesse McCrosky; Josh Lawson

2014-01-01

370

Has the Emergence of Community-Associated Methicillin-Resistant Staphylococcus aureus Increased Trimethoprim-Sulfamethoxazole Use and Resistance?: a 10-Year Time Series Analysis  

Digital Repository Infrastructure Vision for European Research (DRIVER)

There are an increasing number of indications for trimethoprim-sulfamethoxazole use, including skin and soft tissue infections due to community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA). Assessing the relationship between rates of use and antibiotic resistance is important for maintaining the expected efficacy of this drug for guideline-recommended conditions. Using interrupted time series analysis, we aimed to determine whether the 2005 emergence of CA-MRSA and recomme...

Wood, Jameson B.; Smith, Donald B.; Baker, Errol H.; Brecher, Stephen M.; Gupta, Kalpana

2012-01-01

371

Rapid Method for Coextraction of DNA and RNA from Natural Environments for Analysis of Ribosomal DNA- and rRNA-Based Microbial Community Composition  

Digital Repository Infrastructure Vision for European Research (DRIVER)

A rapid protocol for the extraction of total nucleic acids from environmental samples is described. The method facilitates concomitant assessment of microbial 16S rRNA diversity by PCR and reverse transcription-PCR amplification from a single extraction. Denaturing gradient gel electrophoresis microbial community analysis differentiated the active component (rRNA derived) from the total bacterial diversity (ribosomal DNA derived) down the horizons of an established grassland soil.

Griffiths, Robert I.; Whiteley, Andrew S.; O Donnell, Anthony G.; Bailey, Mark J.

2000-01-01

372

[Revelation and phylogenetic analysis of the predominant bacterial community associated with sponges in the South China Sea based on PCR- DGGE fingerprints].  

Science.gov (United States)

The predominant bacterial community structure of Dysidea avara and Craniella australiensis in the South China Sea were revealed by PCR- DGGE fingerprinting in the present study. With further cloning, sequencing and phylogenetic analysis, it was found that Proteobacteria predominated in these two sponges. Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria were found in Dysidea avara and only Gammaproteobacteria found in Craniella australiensis. Although Bacteroidetes were found in both sponges, they differed in the species. These bacteria were found in sponges firstly. The bacteria in Craniella australiensis show more complex diversity than that in Dysidea avara. Because compared with Dysidea avara, Craniella australiensis include Actinobacteria, Firmicutes, etc. The bacterial community diversity in these two sponges indicates that the sponge-associated bacteria are host-specific even if the hosts are from the same marine location. DGGE fingerprint-based analysis should integrate with band cloning and sequencing, phylogenetic analysis, etc., molecular techniques to get precise results for the microbial community and diversity revelation. The research of studying sponge microbe by DGGE technique is initial work, that will accelerate the development of sponge microorganisms item. PMID:16933628

He, Li-Ming; Li, Zhi-Yong; Wu, Jie; Hu, Ye; Jiang, Qun

2006-06-01

373

The topography of poverty in the United States: a spatial analysis using county-level data from the Community Health Status Indicators project.  

Science.gov (United States)

Socioeconomic and health-related data at the county level are now available through the Community Health Status Indicators (CHSI) database. These data are useful for assessing the health of communities and regions. Users of the CHSI data can access online reports and an online mapping application for visualizing patterns in various community-related measures. It also is possible to download these data to conduct local analyses. This paper describes a spatial analysis of poverty in the United States at the county level for 2000. Spatial statistical techniques in a geographic information system were used to quantify significant spatial patterns, such as concentrated poverty rates and spatial outliers. The analysis revealed significant and stark patterns of poverty. A distinctive north-south demarcation of low versus high poverty concentrations was found, along with isolated pockets of high and low poverty within areas in which the predominant poverty rates were opposite. This pattern can be described as following a continental poverty divide. These insights can be useful in explicating the underlying processes involved in forming such spatial patterns that result in concentrated wealth and poverty. The spatial analytic techniques are broadly applicable to socioeconomic and health-related data and can provide important information about the spatial structure of datasets, which is important for choosing appropriate analysis methods. PMID:17875255

Holt, James B

2007-10-01

374

The Topography of Poverty in the United States: A Spatial Analysis Using County-Level Data From the Community Health Status Indicators Project  

Directory of Open Access Journals (Sweden)

Full Text Available Socioeconomic and health-related data at the county level are now available through the Community Health Status Indicators (CHSI database. These data are useful for assessing the health of communities and regions. Users of the CHSI data can access online reports and an online mapping application for visualizing patterns in various community-related measures. It also is possible to download these data to conduct local analyses. This paper describes a spatial analysis of poverty in the United States at the county level for 2000. Spatial statistical techniques in a geographic information system were used to quantify significant spatial patterns, such as concentrated poverty rates and spatial outliers. The analysis revealed significant and stark patterns of poverty. A distinctive north–south demarcation of low versus high poverty concentrations was found, along with isolated pockets of high and low poverty within areas in which the predominant poverty rates were opposite. This pattern can be described as following a continental poverty divide. These insights can be useful in explicating the underlying processes involved in forming such spatial patterns that result in concentrated wealth and poverty. The spatial analytic techniques are broadly applicable to socioeconomic and health-related data and can provide important information about the spatial structure of datasets, which is important for choosing appropriate analysis methods.

James B. Holt, PhD, MPA

2007-10-01

375

Metagenome sequence analysis of filamentous microbial communities obtained from geochemically distinct geothermal channels reveals specialization of three aquificales lineages.  

DEFF Research Database (Denmark)

The Aquificales are thermophilic microorganisms that inhabit hydrothermal systems worldwide and are considered one of the earliest lineages of the domain Bacteria. We analyzed metagenome sequence obtained from six thermal "filamentous streamer" communities (?40 Mbp per site), which targeted three different groups of Aquificales found in Yellowstone National Park (YNP). Unassembled metagenome sequence and PCR-amplified 16S rRNA gene libraries revealed that acidic, sulfidic sites were dominated by Hydrogenobaculum (Aquificaceae) populations, whereas the circum-neutral pH (6.5-7.8) sites containing dissolved sulfide were dominated by Sulfurihydrogenibium spp. (Hydrogenothermaceae). Thermocrinis (Aquificaceae) populations were found primarily in the circum-neutral sites with undetectable sulfide, and to a lesser extent in one sulfidic system at pH 8. Phylogenetic analysis of assembled sequence containing 16S rRNA genes as well as conserved protein-encoding genes revealed that the composition and function of thesecommunities varied across geochemical conditions. Each Aquificales lineage contained genes for CO2 fixation by the reverse-TCA cycle, but only the Sulfurihydrogenibium populations perform citrate cleavage using ATP citrate lyase (Acl). The Aquificaceae populations use an alternative pathway catalyzed by two separate enzymes, citryl-CoA synthetase (Ccs), and citryl-CoA lyase (Ccl). All three Aquificales lineages contained evidence of aerobic respiration, albeit due to completely different types of heme Cu oxidases (subunit I) involved in oxygen reduction. The distribution of Aquificales populations and differences among functional genes involved in energy generation and electron transport is consistent with the hypothesis that geochemical parameters (e.g., pH, sulfide, H2, O2) have resulted in niche specialization among members of the Aquificales.

Takacs-Vesbach, Cristina; Inskeep, William P

2013-01-01

376

Patterns of comorbidity in community-dwelling older people hospitalised for fall-related injury: A cluster analysis  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Community-dwelling older people aged 65+ years sustain falls frequently; these can result in physical injuries necessitating medical attention including emergency department care and hospitalisation. Certain health conditions and impairments have been shown to contribute independently to the risk of falling or experiencing a fall injury, suggesting that individuals with these conditions or impairments should be the focus of falls prevention. Since older people commonly have multiple conditions/impairments, knowledge about which conditions/impairments coexist in at-risk individuals would be valuable in the implementation of a targeted prevention approach. The objective of this study was therefore to examine the prevalence and patterns of comorbidity in this population group. Methods We analysed hospitalisation data from Victoria, Australia's second most populous state, to estimate the prevalence of comorbidity in patients hospitalised at least once between 2005-6 and 2007-8 for treatment of acute fall-related injuries. In patients with two or more comorbid conditions (multicomorbidity we used an agglomerative hierarchical clustering method to cluster comorbidity variables and identify constellations of conditions. Results More than one in four patients had at least one comorbid condition and among patients with comorbidity one in three had multicomorbidity (range 2-7. The prevalence of comorbidity varied by gender, age group, ethnicity and injury type; it was also associated with a significant increase in the average cumulative length of stay per patient. The cluster analysis identified five distinct, biologically plausible clusters of comorbidity: cardiopulmonary/metabolic, neurological, sensory, stroke and cancer. The cardiopulmonary/metabolic cluster was the largest cluster among the clusters identified. Conclusions The consequences of comorbidity clustering in terms of falls and/or injury outcomes of hospitalised patients should be investigated by future studies. Our findings have particular relevance for falls prevention strategies, clinical practice and planning of follow-up services for these patients.

Finch Caroline F

2011-08-01

377

Critical analysis of science-related texts in a breastfeeding information, support, and advocacy community of practice  

Science.gov (United States)

This study examines the way in which women in a breastfeeding information, support, and advocacy (BISA) community of practice critically engage with written/oral science-related texts. The range of texts that these participants encounter is explored and two critical reading approaches are investigated: (1) critical science reading, or reading to assess text validity; and (2) critical science-related text analysis (CSTA), or reading to determine the way in which a text positions subjects or reality, is indicative of particular interests, or leaves out particular voices. The former has been addressed by science education research; the latter is based upon feminist poststructuralism and critical literacy literature. Participants in BISA encounter a wide range of science-related texts, and, to varying degrees, assess the validity of these texts based upon what they know about science, their own and others' experiences, and practical knowledge. Participants also engage in CSTA to greater and lesser extents. Also, experts in BISA are entrusted by participants in the organization to identify valid and trustworthy texts. Differences in critical science reading across participants and texts are discussed, as are the purposes for critical science reading and conditions in BISA that support these critical practices. This study informs both science education and critical literacy research, argues that critical science reading and CSTA are worthwhile practices of both everyday folks and students, and suggests that educators encourage engagement in these practices by presenting students with conflicting science-related texts, encouraging doubt in and epistemic distancing from science-related texts, and modeling critical engagement with science-related texts for students.

Lottero-Perdue, Pamela S.

378

Outcome Analysis of Patients Requiring Mechanical Ventilation with Severe Community-Acquired Pneumonia and Identified Bacterial Pathogens.  

Directory of Open Access Journals (Sweden)

Full Text Available Background: Severe community-acquired pneumonia (CAP is associated with high mortality.The choice of antibiotics should be guided by the distribution of bacterialpathogens. The purpose of this study was to analyze the causative bacteriaand outcomes of patients with severe CAP in a medical intensive careunit (MICU in Taiwan. The results may provide a basis of guidance forfuture empirical antibiotic treatments.Methods: We enrolled patients with severe CAP who were intubated and who requiredmechanical ventilation in an MICU in 2001. Only patients with identifiedbacterial pathogens were included. The bacterial distribution was determined,while differences in age, acute physiology and chronic health evaluation(APACHE II scores, and initial PaO2/FiO2 ratio between surviving andexpired patients were compared.Results: Fifty-nine patients were enrolled and 75 isolates were obtained. Klebsiellapneumoniae was the most common bacteria (21.3%, followed byPseudomonas aeruginosa and Acinetobacter baumannii. Staphylococcusaureus (8% was the most-commonly isolated gram-positive organism, andhalf of its isolates were oxacillin-resistant (ORSA. The overall mortalitywas 55.9%. Multiple logistic regression analysis revealed that survivors hada significantly younger age and lower APACHE II scores.Conclusions: Gram-negative bacilli were the most-common causative pathogens amongpatients with severe CAP requiring mechanical ventilation. Antipseudomonalantibiotics or a carbapenem should be considered to cover Pseudomonasspecies, extended-spectrum ?-lactamase-producing strains, andAcinetobacter species. If the isolated bacteria are gram-positive, care shouldbe taken to cover the possibility of ORSA. Old age and higher APACHE IIscores were associated with higher mortality.

Han-Chung Hu

2005-04-01

379

Analysis of the effectiveness of physical rehabilitation according spirographic indicators in community-acquired pneumonia during convalescence  

Directory of Open Access Journals (Sweden)

Full Text Available Purpose : to make a program of physical rehabilitation for convalescents after community-acquired pneumonia, promotes normalization of respiratory function. The objectives of the study was to evaluate the dynamics spirographic indicators during convalescence community-acquired pneumonia. Material: the study involved 28 women aged 19 to 24 years with a diagnosis of community-acquired pneumonia after convalescent. Results: the positive influence of physiotherapy based dance aerobics; morning hygienic gymnastics; therapeutic massage and physical therapy on indicators of lung volumes, ventilation and bronchial patency according spirographic research. Conclusion: in community-acquired pneumonia during the convalescence period recommended physical rehabilitation, which includes curative gymnastics based on dance aerobics, morning hygienic gymnastics, massage therapy, physiotherapy. It improves the functionality of the cardiorespiratory system, nonspecific immunity and overall physical performance level.

Kalmykova Y.S.

2014-05-01

380

Economic analysis and evaluation of community pharmacists' practices : Application to the screeming for chronic disease : the obstructive sleep apnea syndrome  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Facing the issues of access, quality and proximity, the "Hospital, Patients, Health and Territories" (HPST) law, passed in 2009, constitutes a basis for the reorganization of primary care in France. The healthcare reform emphasizes on the collaboration between healthcare professionals and the optimization of their skills. The community pharmacist is on the forefront of this reform. Through its accessibility, its training and its proximity with healthy and sick patients, community pharmacists ...

Perraudin, Cle?mence

2013-01-01