WorldWideScience

Sample records for gene wiki community

  1. EcoliWiki: a wiki-based community resource for Escherichia coli.

    Science.gov (United States)

    McIntosh, Brenley K; Renfro, Daniel P; Knapp, Gwendowlyn S; Lairikyengbam, Chanchala R; Liles, Nathan M; Niu, Lili; Supak, Amanda M; Venkatraman, Anand; Zweifel, Adrienne E; Siegele, Deborah A; Hu, James C

    2012-01-01

    EcoliWiki is the community annotation component of the PortEco (http://porteco.org; formerly EcoliHub) project, an online data resource that integrates information on laboratory strains of Escherichia coli, its phages, plasmids and mobile genetic elements. As one of the early adopters of the wiki approach to model organism databases, EcoliWiki was designed to not only facilitate community-driven sharing of biological knowledge about E. coli as a model organism, but also to be interoperable with other data resources. EcoliWiki content currently covers genes from five laboratory E. coli strains, 21 bacteriophage genomes, F plasmid and eight transposons. EcoliWiki integrates the Mediawiki wiki platform with other open-source software tools and in-house software development to extend how wikis can be used for model organism databases. EcoliWiki can be accessed online at http://ecoliwiki.net.

  2. WikiGenomes: an open web application for community consumption and curation of gene annotation data in Wikidata.

    Science.gov (United States)

    Putman, Tim E; Lelong, Sebastien; Burgstaller-Muehlbacher, Sebastian; Waagmeester, Andra; Diesh, Colin; Dunn, Nathan; Munoz-Torres, Monica; Stupp, Gregory S; Wu, Chunlei; Su, Andrew I; Good, Benjamin M

    2017-01-01

    With the advancement of genome-sequencing technologies, new genomes are being sequenced daily. Although these sequences are deposited in publicly available data warehouses, their functional and genomic annotations (beyond genes which are predicted automatically) mostly reside in the text of primary publications. Professional curators are hard at work extracting those annotations from the literature for the most studied organisms and depositing them in structured databases. However, the resources don't exist to fund the comprehensive curation of the thousands of newly sequenced organisms in this manner. Here, we describe WikiGenomes (wikigenomes.org), a web application that facilitates the consumption and curation of genomic data by the entire scientific community. WikiGenomes is based on Wikidata, an openly editable knowledge graph with the goal of aggregating published knowledge into a free and open database. WikiGenomes empowers the individual genomic researcher to contribute their expertise to the curation effort and integrates the knowledge into Wikidata, enabling it to be accessed by anyone without restriction. www.wikigenomes.org.

  3. Using Wikis to Develop Collaborative Communities in an Environmental Chemistry Course

    Science.gov (United States)

    Pence, Laura E.; Pence, Harry E.

    2015-01-01

    Group construction of wikis in an environmental chemistry course provided an effective framework for students to develop and to manage collaborative communities, characterized by interactive projects designed to deepen learning. A sequence of assignments facilitated improvement of the students' wiki construction and editing skills and these…

  4. Wiki Writers: Students and Teachers Making Connections across Communities

    Science.gov (United States)

    Andes, Laurie; Claggett, Elizabeth

    2011-01-01

    Expressions of delight and anticipation are a direct result of a schoolwide writing program designed by teachers to develop language skills in special education students. These second graders participated in a writing project that made use of wikis to facilitate collaboration among the students, parents, teachers, and university members of their…

  5. Wikis, Workshops and Writing: Strategies for Flipping a College Community Engagement Course

    Science.gov (United States)

    Maloy, Robert W.; Edwards, Sharon A.; Evans, Allison

    2014-01-01

    This paper describes utilizing wiki technology, small group workshops, and reflective writing assignments to "flip" a community engagement/service-learning course for college undergraduates who are tutoring culturally and linguistically diverse students in K-12 schools. Flipped classrooms are gaining popularity in the teaching of…

  6. Community-based Ontology Development, Annotation and Discussion with MediaWiki extension Ontokiwi and Ontokiwi-based Ontobedia.

    Science.gov (United States)

    Ong, Edison; He, Yongqun

    2016-01-01

    Hundreds of biological and biomedical ontologies have been developed to support data standardization, integration and analysis. Although ontologies are typically developed for community usage, community efforts in ontology development are limited. To support ontology visualization, distribution, and community-based annotation and development, we have developed Ontokiwi, an ontology extension to the MediaWiki software. Ontokiwi displays hierarchical classes and ontological axioms. Ontology classes and axioms can be edited and added using Ontokiwi form or MediaWiki source editor. Ontokiwi also inherits MediaWiki features such as Wikitext editing and version control. Based on the Ontokiwi/MediaWiki software package, we have developed Ontobedia, which targets to support community-based development and annotations of biological and biomedical ontologies. As demonstrations, we have loaded the Ontology of Adverse Events (OAE) and the Cell Line Ontology (CLO) into Ontobedia. Our studies showed that Ontobedia was able to achieve expected Ontokiwi features.

  7. Wikis and Collaborative Inquiry

    Science.gov (United States)

    Lamb, Annette; Johnson, Larry

    2009-01-01

    Wikis are simply Web sites that provide easy-to-use tools for creating, editing, and sharing digital documents, images, and media files. Multiple participants can enter, submit, manage, and update a single Web workspace creating a community of authors and editors. Wiki projects help young people shift from being "consumers" of the Internet to…

  8. Wiki portals

    OpenAIRE

    Kočar, Anja

    2013-01-01

    In our everyday life we are faced with the internet and various web pages that are created on a particular topic. Construction of these can be addressed in different ways. One of them is the usage of wiki portals. Wiki is a collection of web pages, whose content is simple to create and modify, we only need a web browser and an internet connection. If we want to start our own wiki, we need a software called wiki engine. In this thesis we treat wiki as a system of websites, which enables ...

  9. Audio Wiki for mobile communities: information system for the rest of Us

    CSIR Research Space (South Africa)

    Leinonen, T

    2006-09-01

    Full Text Available it possible to use MediaWiki server as the Content Management System of an audio information system. User can make a query to the MediaWiki server by sending a search term as an SMS message to the service number. After a while the user will receive a call back...

  10. Inquiry Resources Collection as a Boundary Object Supporting Meaningful Collaboration in a Wiki-Based Scientist-Teacher Community

    Science.gov (United States)

    Kim, Hye Jeong; Herbert, Bruce

    2012-08-01

    Different interpretations of scientific inquiry exist between the two different communities of scientists and science teachers. Thus, in order to achieve a successful partnership between science teachers and scientists in establishing effective communities of practice, the framework for instructional practice in teacher professional development needs to be carefully designed. To respond to this challenge, we developed the Inquiry Resources Collection (IRC), which offers a wiki-based inquiry resource collection developed by scientists to support novice science teachers' inquiry lesson design. The collaborative managing and sharing of knowledge in a professional development program via a wiki environment is the key to developing a practical resource for novice teachers teaching scientific inquiry. Based on our reflection of data gathered during 4 years of our project, we invoked the ideas of boundary objects and reflective apprenticeship between scientists and teachers to design the IRC.

  11. Technical Evaluation Report 27: Educational Wikis: Features and selection criteria

    Directory of Open Access Journals (Sweden)

    Jim Rudolph

    2004-04-01

    Full Text Available This report discusses the educational uses of the ‘wiki,’ an increasingly popular approach to online community development. Wikis are defined and compared with ‘blogging’ methods; characteristics of major wiki engines are described; and wiki features and selection criteria are examined.

  12. RTI Wiki

    Data.gov (United States)

    National Aeronautics and Space Administration — Under files is the link to the RTI wiki. Research Test and Integration (RTI) focuses on the development of long term plans for test and integration opportunities for...

  13. Review: Ullrich Dittler, Michael Kindt & Christine Schwarz (Eds. (2007. Online-Communities als soziale Systeme. Wikis, Weblogs und Social Software im E-Learning [Online-Communities as Social Systems: Wikis, Weblogs and Social Software in E-Learning

    Directory of Open Access Journals (Sweden)

    Martin Welker

    2008-01-01

    Full Text Available The book Online-Communities as Social Systems: Wikis, Weblogs and Social Software in E-Learning by DITTLER, KINDT and SCHWARZ discusses the practice of new collaborative applications for learning and teaching in universities and schools. The authors summarize online communities from the perspective of German-speaking E-Learning researchers. The core questions under debate are whether, and how, new online platforms and communities will promote new forms of knowledge transfer and learning, and if there is a clash between free and institutionalized forms of learning. The empirical results presented here show that conflicts exist and that these arise through the use of social software in hierarchical organizations. URN: urn:nbn:de:0114-fqs0801467

  14. "The Isle Is Full of Noises": Using Wiki Software to Establish a Discourse Community in a Shakespeare Classroom

    Science.gov (United States)

    Farabaugh, Robin

    2007-01-01

    For the last four semesters my courses in Shakespeare have used QwikiWiki and MediaWiki, two versions of the wiki software, for writing exercises and directed reflection on language--including both by the students about Shakespeare's language, and by the teacher/researcher regarding the students' performance in "Writing to Learn". In experimenting…

  15. Wiki社区中基于信誉的激励机制研究%Research on incentive mechanism based on reputation in wiki community

    Institute of Scientific and Technical Information of China (English)

    毕振坤; 蔡国永

    2011-01-01

    针对wiki社区中存在的大量干扰者,个体节点由于自身得不到现实利益以及时间因素等,不愿积极参与wiki社区交互的问题.在参考P2P网络中信誉模型的基础上,结合wiki社区特点建立相应信誉模型,并在wiki社区信誉模型中利用角色划分方式引入激励机制.实验结果表明,该机制能够减少wiki社区中干扰者节点的恶意行为,提高节点参与wiki社区协同交互的积极性,从而促使wiki社区健康发展.%There exist intruders in wiki communities because individuals will not take part in the community interaction actively for time limitation or self-interest. An appropriate wiki reputation mdoel is proposed on basis of large number of P2P reputation models. An incentive mechanism is introduced into wiki community reputation model in the way of community role division. Experimental results show that this incentive mechanism can effectively decrease intruders' evil interaction, improve the positive interaction and make the growth of wiki community much better and healthier.

  16. Knowledge management by wikis

    CERN Document Server

    Spek, Sander

    2008-01-01

    Wikis provide a new way of collaboration and knowledge sharing. Wikis are software that allows users to work collectively on a web-based knowledge base. Wikis are characterised by a sense of anarchism, collaboration, connectivity, organic development and self-healing, and they rely on trust. We list several concerns about applying wikis in professional organisation. After these concerns are met, wikis can provide a progessive, new knowledge sharing and collaboration tool.

  17. Wikis supporting PLM and Technical Documentation

    CERN Document Server

    Høimyr, Nils-Joar; CERN. Geneva. IT Department

    2007-01-01

    Over the last years, Wikis have arisen as powerful tools for collaborative documentation on the Internet. The Encyclopaedia Wikipedia has become a reference, and the power of community editing in a Wiki allows for capture of knowledge from contributors all over the world. Use of a Wiki for Technical Documentation, along with hyper-links to other data sources such as a Product Lifecycle Management (PLM) system, provides a very effective collaboration tool as information can be easily feed into the system throughout the project life-cycle. In particular for software- and hardware projects with rapidly evolving documentation, the Wiki approach has proved to be successful. Certain Wiki implementations, such as TWiki, are project-oriented and include functionality such as automatic page revisioning. This paper addresses the use of TWiki to document hardware and software projects at CERN, from the requirements and brain-storming phase to end-product documentation. 2 examples are covered: large scale engineering for...

  18. Wikis, Blogs, & More, Oh My!

    Science.gov (United States)

    Villano, Matt

    2008-01-01

    Everyone seems to have a different definition for "Web 2.0," but most people agree the phrase describes a second generation of web-based communities and hosted services that aim to facilitate creativity, collaboration, and sharing between users. Technically speaking, these new technologies include blogs, wikis, folksonomies (collaborative or…

  19. Wikis, Blogs, & More, Oh My!

    Science.gov (United States)

    Villano, Matt

    2008-01-01

    Everyone seems to have a different definition for "Web 2.0," but most people agree the phrase describes a second generation of web-based communities and hosted services that aim to facilitate creativity, collaboration, and sharing between users. Technically speaking, these new technologies include blogs, wikis, folksonomies…

  20. Taking Down Walls: An International Wiki Creates a Community of Thinkers

    Science.gov (United States)

    Maltese, Denise; Naughter, Kate

    2010-01-01

    This article explores collaboration between a rural school in upstate New York and an international school in Amman, Jordan. The authors describe how they provided their students with real audiences for their writing, and, over time, built an international community of writers. Classroom walls were blurred as the authors "team-taught"…

  1. Collaborative trust evaluation for wiki security

    DEFF Research Database (Denmark)

    Lindberg, Kasper; Jensen, Christian D.

    2012-01-01

    Wiki systems form a subclass of the more general Open Collaborative Authoring Systems, where content is created and maintained by a user community. The ability of anyone to edit the content is, at the same time, their strength and their weakness. Anyone can write documents that improve the value...... of the wiki-system, but at the same time, anyone can also introduce errors into these documents, by accident or on purpose. A security model for wiki-style authoring systems has previously been proposed. This model is based on both static and dynamic document access controls that enforce a simple integrity...... based security policy. In this paper, we present a new policy for the existing wiki security model, which provides a higher degree of parameterization and adaptability. The new policy is analyzed and compared to the original policy. Our evaluation shows that this new policy provides stronger security...

  2. Mining biological pathways using WikiPathways web services.

    Directory of Open Access Journals (Sweden)

    Thomas Kelder

    Full Text Available WikiPathways is a platform for creating, updating, and sharing biological pathways [1]. Pathways can be edited and downloaded using the wiki-style website. Here we present a SOAP web service that provides programmatic access to WikiPathways that is complementary to the website. We describe the functionality that this web service offers and discuss several use cases in detail. Exposing WikiPathways through a web service opens up new ways of utilizing pathway information and assisting the community curation process.

  3. Mining biological pathways using WikiPathways web services.

    Science.gov (United States)

    Kelder, Thomas; Pico, Alexander R; Hanspers, Kristina; van Iersel, Martijn P; Evelo, Chris; Conklin, Bruce R

    2009-07-30

    WikiPathways is a platform for creating, updating, and sharing biological pathways [1]. Pathways can be edited and downloaded using the wiki-style website. Here we present a SOAP web service that provides programmatic access to WikiPathways that is complementary to the website. We describe the functionality that this web service offers and discuss several use cases in detail. Exposing WikiPathways through a web service opens up new ways of utilizing pathway information and assisting the community curation process.

  4. Documentation Resources on the ESIP Wiki

    Science.gov (United States)

    Habermann, Ted; Kozimor, John; Gordon, Sean

    2017-01-01

    The ESIP community includes data providers and users that communicate with one another through datasets and metadata that describe them. Improving this communication depends on consistent high-quality metadata. The ESIP Documentation Cluster and the wiki play an important central role in facilitating this communication. We will describe and demonstrate sections of the wiki that provide information about metadata concept definitions, metadata recommendation, metadata dialects, and guidance pages. We will also describe and demonstrate the ISO Explorer, a tool that the community is developing to help metadata creators.

  5. MediaWiki Grammar Recovery

    CERN Document Server

    Zaytsev, Vadim

    2011-01-01

    The paper describes in detail the recovery effort of one of the official MediaWiki grammars. Over two hundred grammar transformation steps are reported and annotated, leading to delivery of a level 2 grammar, semi-automatically extracted from a community created semi-formal text using at least five different syntactic notations, several non-enforced naming conventions, multiple misspellings, obsolete parsing technology idiosyncrasies and other problems commonly encountered in grammars that were not engineered properly. Having a quality grammar will allow to test and validate it further, without alienating the community with a separately developed grammar.

  6. From Wiki Woes to Wiki Wows. Tips

    Science.gov (United States)

    Spencer, Lynn

    2007-01-01

    Library media specialists hear about Web 2.0 in numerous professional journals and during conference workshops. They know that using this aspect of the Internet is second nature to many of their students, and therefore they feel a need to become knowledgeable about this means of information sharing. What better way to learn about blogs, wikis, or…

  7. A Runyakitara Culture Wiki

    African Journals Online (AJOL)

    Frederick Iraki

    Our wiki is available to be read by everyone, though only members are ..... illustrating language aspects such as spelling and vowel assimilation. ... taught in schools, discussed the key problem of the school approach as the transformation of.

  8. Document and author promotion strategies in the secure wiki model

    DEFF Research Database (Denmark)

    Lindberg, Kasper; Jensen, Christian D.

    2012-01-01

    Wiki systems form a subclass of the more general Open Collaborative Authoring Systems, where content is created by a user community. The ability of anyone to edit the content is, at the same time, their strength and their weakness. Anyone can write documents that improve the value of the wiki...... quality to edit all other documents of similar or poorer quality. Moreover, authors who consistently produce top quality documents will eventually be allowed to edit all documents in the wiki. Collaborative filtering is used to evaluate the quality of documents that an author has contributed to the system...

  9. Wiki Web Collaboration

    CERN Document Server

    Ebersbach, Anja; Heigl, Richard

    2006-01-01

    A book about wikis! That's what people need. Because with wiki technology, lots of people can freely work - gether - they can even generate very large works in the intellectual realm. See for yourself: Today, we still marvel at our massive church buildings, each c- structed over a period of centuries, requiring an immense amount of labor and often bearing the cultural stamp of all of the epochs during which it was created. Someone just has to begin by placing stone upon stone and motivate the people nearby to help out a bit. In places where such enthusiastic fellow men and women lend a hand an

  10. Supporting Personal Semantic Annotations in P2P Semantic Wikis

    Science.gov (United States)

    Torres, Diego; Skaf-Molli, Hala; Díaz, Alicia; Molli, Pascal

    In this paper, we propose to extend Peer-to-Peer Semantic Wikis with personal semantic annotations. Semantic Wikis are one of the most successful Semantic Web applications. In semantic wikis, wikis pages are annotated with semantic data to facilitate the navigation, information retrieving and ontology emerging. Semantic data represents the shared knowledge base which describes the common understanding of the community. However, in a collaborative knowledge building process the knowledge is basically created by individuals who are involved in a social process. Therefore, it is fundamental to support personal knowledge building in a differentiated way. Currently there are no available semantic wikis that support both personal and shared understandings. In order to overcome this problem, we propose a P2P collaborative knowledge building process and extend semantic wikis with personal annotations facilities to express personal understanding. In this paper, we detail the personal semantic annotation model and show its implementation in P2P semantic wikis. We also detail an evaluation study which shows that personal annotations demand less cognitive efforts than semantic data and are very useful to enrich the shared knowledge base.

  11. Using wikis to stimulate collaborative learning in two online health sciences courses.

    Science.gov (United States)

    Zitzelsberger, Hilde; Campbell, Karen A; Service, Dorothea; Sanchez, Otto

    2015-06-01

    The use of wiki technology fits well in courses that encourage constructive knowledge building and social learning by a community of learners. Pedagogically, wikis have attracted interest in higher education environments because they facilitate the collaborative processes required for developing student group assignments. This article describes a pilot project to assess the implementation of wikis in two online small- and mid-sized elective courses comprising nursing students in third- or fourth-year undergraduate levels within interdisciplinary health sciences courses. The need exists to further develop the pedagogical use of wiki environments before they can be expected to support collaboration among undergraduate nursing students. Adapting wiki implementation to suitable well-matched courses will make adaptation of wikis into nursing curricula more effective and may increase the chances that nursing students will hone the collaborative abilities that are essential in their future professional roles in communities of practice. Copyright 2015, SLACK Incorporated.

  12. CulturalWiki: A Semantic Map-Based Wiki for Interdisciplinary Collaboration

    Directory of Open Access Journals (Sweden)

    Stefano Valtolina

    2013-11-01

    Full Text Available The use of digital maps capitalizes on the long tradition of using paper maps as mean of communication and learning among people. More than ever, maps are becoming one of the most used metaphors to present concepts and knowledge. This paper presents a wiki infrastructure for map-based information systems’ design that, through an ontology, defines a semantic model able to minimize the problems in communication across interdisciplinary communities by putting together cultural information from different data sources. Using map-oriented solution, the wiki is aimed at enabling intercultural collaboration and learning among all the stakeholders involved in cultural heritage projects. A living lab based on the use of the CulturalWiki framework is described and the results of evaluations are presented.

  13. Wiki-talk Datasets

    OpenAIRE

    Sun, Jun; Kunegis, Jérôme

    2016-01-01

    User interaction networks of Wikipedia of 28 different languages. Nodes (orininal wikipedia user IDs) represent users of the Wikipedia, and an edge from user A to user B denotes that user A wrote a message on the talk page of user B at a certain timestamp. More info: http://yfiua.github.io/academic/2016/02/14/wiki-talk-datasets.html

  14. Reassessing the Gravity’s Rainbow Pynchon Wiki: a new research paradigm?

    Directory of Open Access Journals (Sweden)

    Simon Peter Rowberry

    2012-07-01

    Full Text Available Since the 'Against the Day 'Wiki launched in October 2006, the Pynchon Wiki collection has received over twenty thousand edits, making it one of the largest, dedicated literary reference Wikis. One can now view and add annotations to all seven of Pynchon’s novels – only 'Slow Learner 'and his non-fiction remain 'sans 'Wiki -, and a loose community of over four hundred contributors have done so. This paper will assess the importance of the 'Gravity’s Rainbow 'Wiki in transforming understanding and interpretation through asking four different questions: does the Wiki count as a disruptive force in the Pynchon interpretive industry, who contributes to the Wiki, what types of contribution they make, and how do they exploit the hypertextual features on offer through the MediaWiki package. I will suggest that the Pynchon Wiki does not fully depart from old media forms of interpretation and remains fragmented in both community, resembling a symphony of soloists, and potential connections. This is a version of Web 2.0 synthesizing both Darcy DiNucci’s original dystopian vision of fragmentation (DiNucci and Tim O’Reilly’s utopian idea of harnessing ‘collective intelligence’ (O’Reilly.

  15. Reassessing the Gravity’s Rainbow Pynchon Wiki: a new research paradigm?

    Directory of Open Access Journals (Sweden)

    Simon Peter Rowberry

    2012-07-01

    Full Text Available Since the Against the Day Wiki launched in October 2006, the Pynchon Wiki collection has received over twenty thousand edits, making it one of the largest, dedicated literary reference Wikis. One can now view and add annotations to all seven of Pynchon’s novels – only Slow Learner and his non-fiction remain sans Wiki -, and a loose community of over four hundred contributors have done so. This paper will assess the importance of the Gravity’s Rainbow Wiki in transforming understanding and interpretation through asking four different questions: does the Wiki count as a disruptive force in the Pynchon interpretive industry, who contributes to the Wiki, what types of contribution they make, and how do they exploit the hypertextual features on offer through the MediaWiki package. I will suggest that the Pynchon Wiki does not fully depart from old media forms of interpretation and remains fragmented in both community, resembling a symphony of soloists, and potential connections. This is a version of Web 2.0 synthesizing both Darcy DiNucci’s original dystopian vision of fragmentation (DiNucci and Tim O’Reilly’s utopian idea of harnessing ‘collective intelligence’ (O’Reilly.

  16. AstroBetter: A Blog and Wiki for Professional Astronomers

    Science.gov (United States)

    Rigby, Jane

    2011-01-01

    AstroBetter.com is a multi-contributor blog and wiki website designed for information sharing among professional astronomers. The goal of the site is to increase the productivity of astronomers by creating a centralized location for tips and tools of our multifaceted trade. Our content includes topics related to data reduction and analysis, general computing, writing papers and proposals, giving talks, teaching, career planning, productivity, organization, and diversity and equity in science and education. While we have several contributors, the site is intended to be community driven and we encourage everyone to publish to the wiki, submit guest posts, suggest post ideas, and to comment on blog entries. One of our primary goals is to consolidate and reduce the transient nature of the astronomy community's collective knowledge base by having an active wiki. Currently, the most common way to share astro-centric tools and tips that are not appropriate for a published paper, is to put them on an individual's website. However, the average astronomer's website will have at least four different addresses over the course of their career and only the site owner can edit the content. As a result, information on personal websites goes stale very quickly and deal links to such sites abound. It is our hope that community maintained wikis, such as the one hosted on AstroBetter, will gradually replace the personal website. In this poster we introduce the contributors to AstroBetter, show statistics about our current readership, give excerpts of some of our most popular posts and wiki entries, and show how anyone can add or edit content on the wiki. The goal of this poster is to spread the work about AstroBetter and increase our community of readers and wiki editors, because together, we can AstroBetter.

  17. NASA Human Research Wiki - An Online Collaboration Tool

    Science.gov (United States)

    Barr, Y. R.; Rasbury, J.; Johnson, J.; Barsten, K.; Saile, L.; Watkins, S. D.

    2011-01-01

    In preparation for exploration-class missions, the Exploration Medical Capability (ExMC) element of NASA's Human Research Program (HRP) has compiled a large evidence base, which previously was available only to persons within the NASA community. The evidence base is comprised of several types of data, for example: information on more than 80 medical conditions which could occur during space flight, derived from several sources (including data on incidence and potential outcomes of these medical conditions, as captured in the Integrated Medical Model's Clinical Finding Forms). In addition, approximately 35 gap reports are included in the evidence base, identifying current understanding of the medical challenges for exploration, as well as any gaps in knowledge and/or technology that would need to be addressed in order to provide adequate medical support for these novel missions. In an effort to make the ExMC information available to the general public and increase collaboration with subject matter experts within and outside of NASA, ExMC has developed an online collaboration tool, very similar to a wiki, titled the NASA Human Research Wiki. The platform chosen for this data sharing, and the potential collaboration it could generate, is a MediaWiki-based application that would house the evidence, allow "read only" access to all visitors to the website, and editorial access to credentialed subject matter experts who have been approved by the Wiki's editorial board. Although traditional wikis allow users to edit information in real time, the NASA Human Research Wiki includes a peer review process to ensure quality and validity of information. The wiki is also intended to be a pathfinder project for other HRP elements that may want to use this type of web-based tool. The wiki website will be released with a subset of the data described and will continue to be populated throughout the year.

  18. AceWiki: A Natural and Expressive Semantic Wiki

    CERN Document Server

    Kuhn, Tobias

    2008-01-01

    We present AceWiki, a prototype of a new kind of semantic wiki using the controlled natural language Attempto Controlled English (ACE) for representing its content. ACE is a subset of English with a restricted grammar and a formal semantics. The use of ACE has two important advantages over existing semantic wikis. First, we can improve the usability and achieve a shallow learning curve. Second, ACE is more expressive than the formal languages of existing semantic wikis. Our evaluation shows that people who are not familiar with the formal foundations of the Semantic Web are able to deal with AceWiki after a very short learning phase and without the help of an expert.

  19. WikiWikiWebs: New Ways to Communicate in a Web Environment

    Directory of Open Access Journals (Sweden)

    Brenda Chawner

    2006-03-01

    Full Text Available This paper introduces WikiWikiWeb software, also known as Wiki, for use in library and information management contexts. Wikis provide an environment for Web-based collaboration and can also be used for Web site content management. The article includes an overview of the history and development of Wiki, as well as discussing basic and advanced Wiki features. It compares three Wiki engines and describes seven case studies of real-world library and library-related Wiki applications. The paper concludes with a discussion of factors that can contribute to a successful Wiki project.

  20. WikiPrints: rendering enterprise Wiki content for printing

    Science.gov (United States)

    Berkner, Kathrin

    2010-02-01

    Wikis have become a tool of choice for collaborative, informative communication. In contrast to the immense Wikipedia, that serves as a reference web site and typically covers only one topic per web page, enterprise wikis are often used as project management tools and contain several closely related pages authored by members of one project. In that scenario it is useful to print closely related content for review or teaching purposes. In this paper we propose a novel technique for rendering enterprise wiki content for printing called WikiPrints, that creates a linearized version of wiki content formatted as a mixture between web layout and conventional document layout suitable for printing. Compared to existing print options for wiki content, Wikiprints automatically selects content from different wiki pages given user preferences and usage scenarios. Meta data such as content authors or time of content editing are considered. A preview of the linearized content is shown to the user and an interface for making manual formatting changes provided.

  1. 基于Wiki的高校科研知识社群的共享模式研究%Research on the Knowledge Sharing Mode of University Scientific Research Knowledge Community Based on Wiki

    Institute of Scientific and Technical Information of China (English)

    钟克吟

    2015-01-01

    With the help of the communication and sharing mechanism of university scientific research knowledge community, the collegial scientific researcher’s implicit knowledge can be made explicit ,and it also can promote knowledge sharing, innovation and value-added. In view of the functional requirements of the knowledge sharing platform, the system uses the prominent wiki engine MediaWiki to build a knowledge sharing platform for university scientific research knowledge community. For forming a perfect community knowledge sharing mode it establishes an incentive mechanism to inspire college teachers' interest and builds some function-al modules such as the module for mining the community knowledge resources in order to integrate academic re-source, the module of the platform of scientific research projects and an academic frontier forum.%利用高校科研知识社群的交流和分享机制,将高校科研人员的隐性知识外显化,促进高校知识的共享、创新与增值。针对知识共享平台的系统功能需求,选用较为著名的Wiki引擎MediaWiki构建高校科研知识社群共享平台,建立激励机制以激发高校教师的参与积极性,分析和挖掘社群知识资源,通过整合学术资源库、设立科研专题支撑平台、学术前沿讨论区等功能模块,以完善社群知识共享模式。

  2. LACO-WIKI: AN OPEN ACCESS ONLINE PORTAL FOR LAND COVER VALIDATION

    Directory of Open Access Journals (Sweden)

    L. See

    2015-08-01

    Full Text Available The LACO-Wiki tool represents an open access, online portal that offers standardized land cover validation at local to global scales. LACO-Wiki integrates the LACOVAL prototype for land cover validation and the Geo-Wiki system for visualization, validation and crowdsourcing of land cover. This paper presents a conceptual overview of the LACO-Wiki system and describes the main validation workflow, in which the user uploads the map for validation, creates a validation sample, carries out the sample interpretation and generates a report detailing the accuracy assessment. In addition to a land cover validation tool, LACO-Wiki is also intended to become an open access repository for calibration and validation data that can be used by the land monitoring community to improve future land cover products.

  3. Wiki keys on mobile devices

    OpenAIRE

    Weber, Gisela; Hagedorn, Gregor

    2010-01-01

    The development of increasingly powerful mobile devices like PDAs (Personal Digital Assistants) and Smartphones, with larger displays and greater resolution makes them increasingly suitable for identification tools available directly “in the field”. One of several approaches towards this aim in the KeyToNature project is based on wiki-stored documents. Important features of wiki-based keys, such as hidden text and media information as well as links to glossary entries are su...

  4. Untangling knowledge creation and knowledge integration in enterprise wikis

    DEFF Research Database (Denmark)

    Beck, Roman; Rai, Arun; Fischbach, Kai

    2015-01-01

    , but the motivating factors that drive individuals to contribute their knowledge to these systems is not very well understood. We theorize that enterprise wiki initiatives require two separate and distinct types of knowledge-sharing behaviors to succeed: knowledge creation (KC) and knowledge integration (KI). We...... examine a Wiki initiative at a major German bank to untangle the motivating factors behind KC and KI. Our results suggest KC and KI are indeed two distinct behaviors, reconcile inconsistent findings from past studies on the role of motivational factors for knowledge sharing to establish shared electronic......A central challenge organizations face is how to build, store, and maintain knowledge over time. Enterprise wikis are community-based knowledge systems situated in an organizational context. These systems have the potential to play an important role in managing knowledge within organizations...

  5. Untangling knowledge creation and knowledge integration in enterprise wikis

    DEFF Research Database (Denmark)

    Beck, Roman; Rai, Arun; Fischbach, Kai;

    2015-01-01

    , but the motivating factors that drive individuals to contribute their knowledge to these systems is not very well understood. We theorize that enterprise wiki initiatives require two separate and distinct types of knowledge-sharing behaviors to succeed: knowledge creation (KC) and knowledge integration (KI). We......A central challenge organizations face is how to build, store, and maintain knowledge over time. Enterprise wikis are community-based knowledge systems situated in an organizational context. These systems have the potential to play an important role in managing knowledge within organizations...... examine a Wiki initiative at a major German bank to untangle the motivating factors behind KC and KI. Our results suggest KC and KI are indeed two distinct behaviors, reconcile inconsistent findings from past studies on the role of motivational factors for knowledge sharing to establish shared electronic...

  6. KYOTO: A Wiki for Establishing Semantic Interoperability for Knowledge Sharing Across Languages and Cultures

    OpenAIRE

    Marchetti, Andrea; Ronzano, Francesco; Tesconi, Maurizio; Vossen, Piek; Agirre, Eneko; Bond, Francis; Bosma, Wauter; Herold, Axel; Hicks, Amanda; Hsieh, Shu-Kai; Isahara, Hitoshi; Huang, Chu-Ren; Kanzaki, Kyoko; Rigau, German; Segers, Roxane

    2010-01-01

    KYOTO is an Asian-European project developing a community platform for modeling knowledge and finding facts across languages and cultures. The platform operates as a Wiki system that multilingual and multi-cultural communities can use to agree on the meaning of terms in specific domains. The Wiki is fed with terms that are automatically extracted from documents in different languages. The users can modify these terms and relate them across languages. The system generates complex, language-neu...

  7. EVA Wiki - Transforming Knowledge Management for EVA Flight Controllers and Instructors

    Science.gov (United States)

    Johnston, Stephanie S.; Alpert, Brian K.; Montalvo, Edwin James; Welsh, Lawrence Daren; Wray, Scott; Mavridis, Costa

    2016-01-01

    The EVA Wiki was recently implemented as the primary knowledge database to retain critical knowledge and skills in the EVA Operations group at NASA's Johnson Space Center by ensuring that information is recorded in a common, easy to search repository. Prior to the EVA Wiki, information required for EVA flight controllers and instructors was scattered across different sources, including multiple file share directories, SharePoint, individual computers, and paper archives. Many documents were outdated, and data was often difficult to find and distribute. In 2011, a team recognized that these knowledge management problems could be solved by creating an EVA Wiki using MediaWiki, a free and open-source software developed by the Wikimedia Foundation. The EVA Wiki developed into an EVA-specific Wikipedia on an internal NASA server. While the technical implementation of the wiki had many challenges, one of the biggest hurdles came from a cultural shift. Like many enterprise organizations, the EVA Operations group was accustomed to hierarchical data structures and individually-owned documents. Instead of sorting files into various folders, the wiki searches content. Rather than having a single document owner, the wiki harmonized the efforts of many contributors and established an automated revision controlled system. As the group adapted to the wiki, the usefulness of this single portal for information became apparent. It transformed into a useful data mining tool for EVA flight controllers and instructors, as well as hundreds of others that support EVA. Program managers, engineers, astronauts, flight directors, and flight controllers in differing disciplines now have an easier-to-use, searchable system to find EVA data. This paper presents the benefits the EVA Wiki has brought to NASA's EVA community, as well as the cultural challenges it had to overcome.

  8. Impact of Implementing a Wiki to Develop Structured Electronic Order Sets on Physicians' Intention to Use Wiki-Based Order Sets

    Science.gov (United States)

    Beaupré, Pierre; Bégin, Laura; Dupuis, Audrey; Côté, Mario; Légaré, France

    2016-01-01

    Background Wikis have the potential to promote best practices in health systems by sharing order sets with a broad community of stakeholders. However, little is known about the impact of using a wiki on clinicians’ intention to use wiki-based order sets. Objective The aims of this study were: (1) to describe the use of a wiki to create structured order sets for a single emergency department; (2) to evaluate whether the use of this wiki changed emergency physicians’ future intention to use wiki-based order sets; and (3) to understand the impact of using the wiki on the behavioral determinants for using wiki-based order sets. Methods This was a pre/post-intervention mixed-methods study conducted in one hospital in Lévis, Quebec. The intervention was comprised of receiving access to and being motivated by the department head to use a wiki for 6 months to create electronic order sets designed to be used in a computer physician order entry system. Before and after our intervention, we asked participants to complete a previously validated questionnaire based on the Theory of Planned Behavior. Our primary outcome was the intention to use wiki-based order sets in clinical practice. We also assessed participants’ attitude, perceived behavioral control, and subjective norm to use wiki-based order sets. Paired pre- and post-Likert scores were compared using Wilcoxon signed-rank tests. The post-questionnaire also included open-ended questions concerning participants’ comments about the wiki, which were then classified into themes using an existing taxonomy. Results Twenty-eight emergency physicians were enrolled in the study (response rate: 100%). Physicians’ mean intention to use a wiki-based reminder was 5.42 (SD 1.04) before the intervention, and increased to 5.81 (SD 1.25) on a 7-point Likert scale (P=.03) after the intervention. Participants’ attitude towards using a wiki-based order set also increased from 5.07 (SD 0.90) to 5.57 (SD 0.88) (P=.003). Perceived

  9. Wiki-Based Data and Information Integration (WikiDI2) System Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The proposed innovation is: A data and information integration (DI2) system built from the methods and tools used to create Wiki websites. Wiki (Hawaiian for...

  10. Posibilidades educativas de la wiki Educational possibilities of wiki

    Directory of Open Access Journals (Sweden)

    Francisco Mora Vicarioli

    2012-11-01

    Full Text Available El artículo presenta el recurso wiki como una herramientaflexiblequeaportagrandesposibilidades a la educación. Su principal característica es que permite a un conjunto de usuarios interactuar de forma asincrónica para crear algún tipo de contenido y que cada uno puede agregar, quitar o editar los aportes propios o de los demás.The article presents the use of wiki as a flexible tool that provides great opportunities for education. The main feature of this resource is that it allows a set of users to interact asynchronously to create some content and everyone can add, remove or edit the contributions from themselves or others.

  11. Using Wikis to Learn Computer Programming

    Science.gov (United States)

    González-Ortega, David; Díaz-Pernas, Francisco Javier; Martínez-Zarzuela, Mario; Antón-Rodríguez, Míriam; Díez-Higuera, José Fernando; Boto-Giralda, Daniel; de La Torre-Díez, Isabel

    In this paper, we analyze the suitability of wikis in education, especially to learn computer programming, and present a wiki-based teaching innovation activity carried out in the first course of Telecommunication Engineering during two academic courses. The activity consisted in the creation of a wiki to collect errors made by students while they were coding programs in C language. The activity was framed in a collaborative learning strategy in which all the students had to collaborate and be responsible for the final result, but also in a competitive learning strategy, in which the groups had to compete to make original meaningful contributions to the wiki. The use of a wiki for learning computer programming was very satisfactory. A wiki allows to monitor continuously the work of the students, who become publishers and evaluators of contents rather than mere consumers of information, in an active learning approach.

  12. The Executive Wiki: Wikis Can Be a Multitasking Administrators' Best Friend

    Science.gov (United States)

    Warlick, David

    2007-01-01

    The poster child for the Web 2.0 movement, the wiki, demonstrates the spirit of open content more clearly than any other application. Wikipedia, the most famous wiki and the world's largest encyclopedia, defines a wiki as a Web site that "allows visitors to add, remove, edit, and change content." Even though it is a controversial information…

  13. Combining Semantic Wikis and Controlled Natural Language

    CERN Document Server

    Kuhn, Tobias

    2008-01-01

    We demonstrate AceWiki that is a semantic wiki using the controlled natural language Attempto Controlled English (ACE). The goal is to enable easy creation and modification of ontologies through the web. Texts in ACE can automatically be translated into first-order logic and other languages, for example OWL. Previous evaluation showed that ordinary people are able to use AceWiki without being instructed.

  14. WIKI4, a novel inhibitor of tankyrase and Wnt/ß-catenin signaling.

    Directory of Open Access Journals (Sweden)

    Richard G James

    Full Text Available The Wnt/ß-catenin signaling pathway controls important cellular events during development and often contributes to disease when dysregulated. Using high throughput screening we have identified a new small molecule inhibitor of Wnt/ß-catenin signaling, WIKI4. WIKI4 inhibits expression of ß-catenin target genes and cellular responses to Wnt/ß-catenin signaling in cancer cell lines as well as in human embryonic stem cells. Furthermore, we demonstrate that WIKI4 mediates its effects on Wnt/ß-catenin signaling by inhibiting the enzymatic activity of TNKS2, a regulator of AXIN ubiquitylation and degradation. While TNKS has previously been shown to be the target of small molecule inhibitors of Wnt/ß-catenin signaling, WIKI4 is structurally distinct from previously identified TNKS inhibitors.

  15. Wikis og blogs i undervisningen

    DEFF Research Database (Denmark)

    Dohn, Nina Bonderup

    2010-01-01

    I denne artikel diskuteres muligheder og problemstillinger forbundet med at inddrage wikis og blogs i undervisning inden for det humanistiske og sam-fundsvidenskabelige fagfelt på universitetsniveau. Fokus er på de former for brug, hvor de studerende er aktive i produktionen af indhold, og hvor der...... lægges vægt på stadig brug og genbrug af indholdet på tværs af kontekster. Der redegøres først for, hvad ’web 2.0’ er, og hvad der forstås ved ’web 2.0-medieret læring’. På den baggrund opstilles en række læringsteoretisk og didaktisk begrundede potentialer ved at inddrage wiki- og blog-aktiviteter i...

  16. Wikis og blogs i undervisningen

    DEFF Research Database (Denmark)

    Dohn, Nina Bonderup

    2010-01-01

    I denne artikel diskuteres muligheder og problemstillinger forbundet med at inddrage wikis og blogs i undervisning inden for det humanistiske og sam-fundsvidenskabelige fagfelt på universitetsniveau. Fokus er på de former for brug, hvor de studerende er aktive i produktionen af indhold, og hvor der...... lægges vægt på stadig brug og genbrug af indholdet på tværs af kontekster. Der redegøres først for, hvad ’web 2.0’ er, og hvad der forstås ved ’web 2.0-medieret læring’. På den baggrund opstilles en række læringsteoretisk og didaktisk begrundede potentialer ved at inddrage wiki- og blog-aktiviteter i...

  17. Using Wikis to Promote Collaborative EFL Writing

    Science.gov (United States)

    Aydin, Zelilha; Yildiz, Senem

    2014-01-01

    This study focuses on the use of wikis in collaborative writing projects in foreign language learning classrooms. A total of 34 intermediate level university students learning English as a foreign language (EFL) were asked to accomplish three different wiki-based collaborative writing tasks, (argumentative, informative and decision-making) working…

  18. Critical assessment of using wikis in legal education

    NARCIS (Netherlands)

    Hoorn, E.; Hoorn, M.D. van

    2007-01-01

    Wikis serve to support collaborative writing on the web. The best known example of a wiki is Wikipedia, an open encyclopedia on the web. This paper is meant to explore possible uses of a wiki-environment in legal education. Firstly, it describes the actual use of a closed wiki environment in a class

  19. The Wiki as a Virtual Space for Qualitative Data Collection

    Science.gov (United States)

    Castanos, Carolina; Piercy, Fred P.

    2010-01-01

    The authors make a case for using wiki technology in qualitative research. A wiki is an online database that allows users to create, edit, and/or reflect on the content of a web page. Thus, wiki technology can support qualitative research that attempts to understand the shared thinking of participants. To illustrate the use of the wiki for this…

  20. Critical assessment of using wikis in legal education

    NARCIS (Netherlands)

    Hoorn, E.; Hoorn, M.D. van

    2007-01-01

    Wikis serve to support collaborative writing on the web. The best known example of a wiki is Wikipedia, an open encyclopedia on the web. This paper is meant to explore possible uses of a wiki-environment in legal education. Firstly, it describes the actual use of a closed wiki environment in a class

  1. Promoting Professional Identity: A Within Group Comparison of Wiki-Based and Traditional Assignments on School Counselling Students' Learning, Sense of Community and Computer Anxiety

    Science.gov (United States)

    Rockinson-Szapkiw, Amanda J.; Pritchard, Tracey; McComb-Beverage, Shanna; Schellenberg, Rita

    2013-01-01

    The purpose of this study is to compare traditional and non-traditional instructional practices used in a counsellor education programme to determine their effect on pre-service school counsellors' learning and sense of community, thus leading to enhanced professional identity. Traditional and non-traditional assignments were examined: (a) a…

  2. Wiki Storyline in Second Language Teaching

    Directory of Open Access Journals (Sweden)

    Hege Emma Rimmereide

    2011-07-01

    Full Text Available Wiki Storyline is a web-based Storyline project. The interdisciplinary approach to second language teaching provided by combining the Storyline method and ICT is dynamic, and ideal for practicing receptive and productive skills in English. Being a learner-centered approach, the Storyline creates motivation for written and oral communication and this is facilitated by digital tools. The Wiki Storyline project has been carried out with two inservice courses and this study presents a comparative analysis of the various technical solutions, as well as of the pedagogical potential explored in the two courses. In addition to the wiki, Etherpad and a blog were the key digital media tools included in the project. In the wiki a virtual world was created, while Etherpad served as a tool for real time collaborative text editing, and the blog as an arena for reflection for the participants, outside the virtual world.

  3. Using Wiki Technology in the Classroom

    DEFF Research Database (Denmark)

    Majgaard, Gunver

    2013-01-01

    as a collaborative learning tool for encyclopaedia articles on learning and technology. There were several potential dilemmas in the students’ collaborative work: Inspiration versus imitation of others’ ideas and solutions; academic achievements versus friendships; varying work ethics and academic levels......How do engineering students develop norms and standards for collaborative work in a Wiki society? Students from first and second semesters participated in two experiments. In the first semester they used the Wiki as project logs and in the second semester the same students used the Wiki......; and editing or adding text. From these dilemmas and potential conflicts emerged social norms, such as norms for structuring, editing and collaborating on Wiki pages. The emerging social norms were answers to the potential dilemmas and conflicts....

  4. Large Formal Wikis: Issues and Solutions

    CERN Document Server

    Alama, Jesse; Mamane, Lionel; Urban, Josef

    2011-01-01

    We present several steps towards large formal mathematical wikis. The Coq proof assistant together with the CoRN repository are added to the pool of systems handled by the general wiki system described in \\cite{DBLP:conf/aisc/UrbanARG10}. A smart re-verification scheme for the large formal libraries in the wiki is suggested for Mizar/MML and Coq/CoRN, based on recently developed precise tracking of mathematical dependencies. We propose to use features of state-of-the-art filesystems to allow real-time cloning and sandboxing of the entire libraries, allowing also to extend the wiki to a true multi-user collaborative area. A number of related issues are discussed.

  5. WikiLeaks: neue Dimensionen des Medienaktivismus

    OpenAIRE

    Stalder, Felix

    2011-01-01

    "Mit WikiLeaks hat der Medienaktivismus eine neue Dimension erreicht. WikiLeaks versteht die neuen sozio-technischen Möglichkeiten und institutionellen Widersprüche, die die gegenwärtige Phase der Entwicklung der Netzwerkgesellschaft kennzeichnen, für sein Projekt nutzbar zu machen. Politisch bleibt das Projekt allerdings schwer kategorisierbar, da es gleichzeitig eine markt-libertäre und eine institutionskritische Haltung vertritt, gleichermassen staatliche wie privat-wirtscha...

  6. A Wiki Way Of Programming For The Web Of Data

    OpenAIRE

    Arapov, Pavel; Buffa, Michel; Ben Othmane, Amel

    2014-01-01

    International audience; WikiNEXT is a wiki engine that enables users to write rapidly applications directly from the browser, in particular applications that can exploit the web of data. WikiNEXT relies on semantic web formalisms and technologies (RDF/RDFa lite) to describe wiki page content and embedded metadata, and to manipulate them (for example, using the SPARQL language). WikiNEXT is a mix between a web-based IDE (Integrated Development Environment) and a semantic wiki. It embeds severa...

  7. Investment and Return: Wiki Engagement in a "Remedial" ESL Writing Course

    Science.gov (United States)

    Nakamaru, Sarah

    2012-01-01

    This study explores the extent to which students in a community college remedial English as a second language (ESL) course engaged with a class wiki and the relationship between their pattern of engagement over time and success in exiting remediation. Participants included 47 students in two sections of ESL writing during the spring 2009 semester.…

  8. The Way of the Wiki: Using a Wiki as a Management Tool for Online Programs

    Science.gov (United States)

    Huett, Jason B.; Huett, Kimberly C.; Bennett, Elizabeth

    2010-01-01

    Many universities are struggling to meet student demand for quality online course offerings. As an online program grows, it can become more difficult to manage information, resources, and people. Adopting useful knowledge management tools, such as wikis, could help better position an online program in a competitive marketplace. Wikis promote…

  9. ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses.

    Science.gov (United States)

    Stokes, Todd H; Torrance, J T; Li, Henry; Wang, May D

    2008-05-28

    A survey of microarray databases reveals that most of the repository contents and data models are heterogeneous (i.e., data obtained from different chip manufacturers), and that the repositories provide only basic biological keywords linking to PubMed. As a result, it is difficult to find datasets using research context or analysis parameters information beyond a few keywords. For example, to reduce the "curse-of-dimension" problem in microarray analysis, the number of samples is often increased by merging array data from different datasets. Knowing chip data parameters such as pre-processing steps (e.g., normalization, artefact removal, etc), and knowing any previous biological validation of the dataset is essential due to the heterogeneity of the data. However, most of the microarray repositories do not have meta-data information in the first place, and do not have a a mechanism to add or insert this information. Thus, there is a critical need to create "intelligent" microarray repositories that (1) enable update of meta-data with the raw array data, and (2) provide standardized archiving protocols to minimize bias from the raw data sources. To address the problems discussed, we have developed a community maintained system called ArrayWiki that unites disparate meta-data of microarray meta-experiments from multiple primary sources with four key features. First, ArrayWiki provides a user-friendly knowledge management interface in addition to a programmable interface using standards developed by Wikipedia. Second, ArrayWiki includes automated quality control processes (caCORRECT) and novel visualization methods (BioPNG, Gel Plots), which provide extra information about data quality unavailable in other microarray repositories. Third, it provides a user-curation capability through the familiar Wiki interface. Fourth, ArrayWiki provides users with simple text-based searches across all experiment meta-data, and exposes data to search engine crawlers (Semantic Agents

  10. Using Wikis and Collaborative Learning for Science Teachers' Professional Development

    Science.gov (United States)

    Chen, Y-H.; Jang, S-J.; Chen, P-J.

    2015-01-01

    Wiki bears great potential to transform learning and instruction by scaffolding personal and social constructivism. Past studies have shown that proper application of wiki benefits both students and teachers; however, few studies have integrated wiki and collaborative learning to examine the growth of science teachers' "Technological,…

  11. Using Wikis and Collaborative Learning for Science Teachers' Professional Development

    Science.gov (United States)

    Chen, Y-H.; Jang, S-J.; Chen, P-J.

    2015-01-01

    Wiki bears great potential to transform learning and instruction by scaffolding personal and social constructivism. Past studies have shown that proper application of wiki benefits both students and teachers; however, few studies have integrated wiki and collaborative learning to examine the growth of science teachers' "Technological,…

  12. WikiScience: Wikipedia for science and technology

    OpenAIRE

    Aibar Puentes, Eduard

    2015-01-01

    Peer-reviewed Presentació de la conferència "WikiScience: Wikipedia for science and technology". Presentación de la conferencia "WikiScience: Wikipedia for science and technology". Presentation of the conference "Science Wiki: Wikipedia for science and technology".

  13. Using a Wiki as a Group Communications Tool

    Science.gov (United States)

    Mihm, Barbara

    2009-01-01

    The research explains wiki development and use in industry and potential benefits in higher education as a collaborative communication tool. The findings of a study conducted in a business administration class involving the use of wikis is discussed. The paper concludes with useful guidelines for college instructors incorporating wikis as a…

  14. Prototype for Extended XDB Using Wiki

    Directory of Open Access Journals (Sweden)

    Wook-Sung Yoo

    2012-11-01

    Full Text Available This paper describes a prototype of extended XDB. XDB is an open-source and extensible database architecture developed by National Aeronautics and Space Administration (NASA to provide integration of heterogeneous and distributed information resources for scientific and engineering applications. XDB enables an unlimited number of desktops and distributed information sources to be linked seamlessly and efficiently into an information grid using Data Access and Retrieval Composition (DARC protocol whichprovides a contextual search and retrieval capability useful for lightweight web applications. This paper shows the usage of XDB on common data management in the enterprise without burdening users and application developers with unnecessary complexity and formal schemas. Supported by NASA Ames Research Center through NASA Exploration System Mission Directorate (ESMD Higher Education grant, a project team at Fairfield University extended this concept and developed an extended XDB protocol and a prototype providing text-searches for Wiki. The technical specification of the protocol was posted to Source Forge (sourceforge.net and a prototype providing text-searches for Wiki was developed. The prototype was created for 16 tags of the MediaWiki dialect. As part of future works, the prototype will be further extended to the complete Wiki markups and other dialects of Wiki.

  15. A fielded wiki for personality genetics

    DEFF Research Database (Denmark)

    Nielsen, Finn Årup

    2010-01-01

    I describe a fielded wiki, where a Web form interface allows the entry, analysis and visualization of results from scientific papers in the personality genetics domain. Papers in this domain typically report the mean and standard deviation of multiple personality trait scores from statistics on h......-analysis can compute individual and combined effect sizes. The meta-analytic results are displayed in on-the-fly computed hyperlinked graphs and tables. Revision control on the basic data tracks changes and data may be exported to comma-separated files or in a MediaWiki template format....

  16. Learning Assessment Using Wikis: Integrated or LMS Independent?

    Science.gov (United States)

    Forment, Marc Alier; de Pedro, Xavier; Casañ, Maria Jose; Piguillem, Jordi; Galanis, Nikolas

    Wikis have a potentially huge educational value. This article outlines a feature set that wiki engines need in order to successfully host collaborative educational scenarios using wiki technology. One of the first issues to solve is the need for assessment methodologies supported by the software. And the second one is to choose between using an integrated wiki engine inside the Learning Management System (LMS), or an external standalone wiki engine. Advantages and disadvantages from both options of this second issue are discussed, with each choice presenting different implications as far as individual student assessment, feedback and grading are concerned. Among the expected results, the most notable are incentives to incorporate wikis in the teaching procedure, significant enhancements in usability, as well as allowing teachers to provide more timely written feedback on their students' individual contributions on wiki based activities, on top of the usual numerical grading.

  17. Wikis and Collaborative Learning in Higher Education

    Science.gov (United States)

    Zheng, Binbin; Niiya, Melissa; Warschauer, Mark

    2015-01-01

    While collaborative learning and collaborative writing can be of great value to student learning, the implementation of a technology-supported collaborative learning environment is a challenge. With their built-in features for supporting collaborative writing and social communication, wikis are a promising platform for collaborative learning;…

  18. Within the Wiki: Best Practices for Educators

    Science.gov (United States)

    Schroeder, Barbara

    2009-01-01

    With the increasing emphasis in higher education to provide opportunities for students to work and collaborate in groups, enhancing problem-solving and critical-thinking skills, instructors are looking beyond traditional course management tools to emerging technologies. One technology that supports group collaboration is a wiki. However, many…

  19. Teaching and Learning Physics using Wikis

    Science.gov (United States)

    Mohottala, Hashini

    2010-03-01

    The use of new teaching tools and technologies in modern classrooms in universities, colleges and even schools is essential. Here we report an adaptation of a new and powerful teaching tool, Wiki, in teaching Physics. Wiki is an interactive webpage which can be accessed and updated collaboratively by a group of users via any web browser. This new teaching tool was first used in an introductory level Physics course. The students were assigned different tasks and as a part of the learning procedure, they were encouraged to do independent research to explore applications related to the Physics concepts learned in the class. As a result, students often brought interesting findings into the class that led to insightful class discussions. Although Physics is not the most popular science subject among undergraduate students, the adaptation of Wiki showed a notable change in the students' perceptions. As we have experienced, there are number of advantages of using Wikis in a Physics classroom - improves the writing and research skills; helps students explore and understand the subject in depth and most of all enhances their desire and ability to learn Physics.

  20. Social Media and Organizing – An Empirical Analysis of the Role of Wiki Affordances in Organizing Practices

    DEFF Research Database (Denmark)

    Mansour, Osama; Askenäs, Linda; Ghazawneh, Ahmad

    2013-01-01

    The evolution of social media has introduced novel possibilities for work and interaction in organizations. The wiki technology is one important kind of social media technologies that is increasingly used to facilitate the creation and sharing of organizational knowledge within communities. Given...... the increasing use of social media in organizations and the lack of knowledge on their consequences for organizing, we use an affordance lens to explore the enactment of organizational wiki affordances. Using qualitative data obtained through interviews, field visits, and documents from two multinational...... organizations –CCC and IBM– we first identified eight affordances that describe various wiki possibilities and practices. We then identified four properties of these affordances including multiplicity, referential, situatedness, and communal. These properties represent the main contribution of the paper...

  1. Collaborate, Engage, and Interact in Online Learning: Successes with Wikis and Synchronous Virtual Classrooms at Athens State University

    Science.gov (United States)

    Rich, Lisa Logan; Cowan, Wendy; Herring, Susan D.; Wilkes, William

    2009-01-01

    The purpose of this paper is to provide faculty with creative ways to use tools such as wikis and synchronous virtual classrooms to build a sense of community within their distance classes. A review of the literature provides an understanding of the many significant benefits of including collaboration, engagement, and interaction in e-learning…

  2. Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources.

    Science.gov (United States)

    Waagmeester, Andra; Kutmon, Martina; Riutta, Anders; Miller, Ryan; Willighagen, Egon L; Evelo, Chris T; Pico, Alexander R

    2016-06-01

    The diversity of online resources storing biological data in different formats provides a challenge for bioinformaticians to integrate and analyse their biological data. The semantic web provides a standard to facilitate knowledge integration using statements built as triples describing a relation between two objects. WikiPathways, an online collaborative pathway resource, is now available in the semantic web through a SPARQL endpoint at http://sparql.wikipathways.org. Having biological pathways in the semantic web allows rapid integration with data from other resources that contain information about elements present in pathways using SPARQL queries. In order to convert WikiPathways content into meaningful triples we developed two new vocabularies that capture the graphical representation and the pathway logic, respectively. Each gene, protein, and metabolite in a given pathway is defined with a standard set of identifiers to support linking to several other biological resources in the semantic web. WikiPathways triples were loaded into the Open PHACTS discovery platform and are available through its Web API (https://dev.openphacts.org/docs) to be used in various tools for drug development. We combined various semantic web resources with the newly converted WikiPathways content using a variety of SPARQL query types and third-party resources, such as the Open PHACTS API. The ability to use pathway information to form new links across diverse biological data highlights the utility of integrating WikiPathways in the semantic web.

  3. User Defined Structural Searches in MediaWiki

    DEFF Research Database (Denmark)

    Bouvin, Niels Olof; Albertsen, Johannes

    2008-01-01

    Wikipedia has been the poster child of user contributed content using the space of MediaWiki as the canvas on which to write. While well suited for authoring simple hypermedia documents, MediaWiki does not lend itself easily to let the author create dynamically assembled documents, or create pages...... that monitor other pages. While it is possible to create such "special" pages, it requires PHP coding and thus administrative rights to the MediaWiki server. We present in this paper work on a structural query language (MediaWiki Query Language - MWQL) to allow users to add dynamically evaluated searches...

  4. AceWiki: Collaborative Ontology Management in Controlled Natural Language

    CERN Document Server

    Kuhn, Tobias

    2008-01-01

    AceWiki is a prototype that shows how a semantic wiki using controlled natural language - Attempto Controlled English (ACE) in our case - can make ontology management easy for everybody. Sentences in ACE can automatically be translated into first-order logic, OWL, or SWRL. AceWiki integrates the OWL reasoner Pellet and ensures that the ontology is always consistent. Previous results have shown that people with no background in logic are able to add formal knowledge to AceWiki without being instructed or trained in advance.

  5. T-search : buscador con tesauro para wikis

    OpenAIRE

    Sagredo Olivenza, Ismael

    2009-01-01

    El auge de los entornos wiki, cada vez más extendidos, hace necesarias herramientas que permitan recuperar de forma eficiente la información de estos entornos. Hasta ahora los buscadores genéricos como Google son las mejores herramientas para encontrar en wikis como Wikipedia, pero no para wikis de menor difusión, donde Google y otros buscadores sólo tienen indizada una pequeña parte del sitio. Por otro lado, los buscadores que incorporan los entornos wiki son muy limitados, y sólo realizan b...

  6. VuWiki: An Ontology-Based Semantic Wiki for Vulnerability Assessments

    Science.gov (United States)

    Khazai, Bijan; Kunz-Plapp, Tina; Büscher, Christian; Wegner, Antje

    2014-05-01

    The concept of vulnerability, as well as its implementation in vulnerability assessments, is used in various disciplines and contexts ranging from disaster management and reduction to ecology, public health or climate change and adaptation, and a corresponding multitude of ideas about how to conceptualize and measure vulnerability exists. Three decades of research in vulnerability have generated a complex and growing body of knowledge that challenges newcomers, practitioners and even experienced researchers. To provide a structured representation of the knowledge field "vulnerability assessment", we have set up an ontology-based semantic wiki for reviewing and representing vulnerability assessments: VuWiki, www.vuwiki.org. Based on a survey of 55 vulnerability assessment studies, we first developed an ontology as an explicit reference system for describing vulnerability assessments. We developed the ontology in a theoretically controlled manner based on general systems theory and guided by principles for ontology development in the field of earth and environment (Raskin and Pan 2005). Four key questions form the first level "branches" or categories of the developed ontology: (1) Vulnerability of what? (2) Vulnerability to what? (3) What reference framework was used in the vulnerability assessment?, and (4) What methodological approach was used in the vulnerability assessment? These questions correspond to the basic, abstract structure of the knowledge domain of vulnerability assessments and have been deduced from theories and concepts of various disciplines. The ontology was then implemented in a semantic wiki which allows for the classification and annotation of vulnerability assessments. As a semantic wiki, VuWiki does not aim at "synthesizing" a holistic and overarching model of vulnerability. Instead, it provides both scientists and practitioners with a uniform ontology as a reference system and offers easy and structured access to the knowledge field of

  7. Wikis: A Knowledge Platform for Collaborative Learning in ESL Reading

    Science.gov (United States)

    Wiseman, Cynthia S.; Belknap, Joshua P.

    2013-01-01

    Wikis provide an effective technological tool to meet the pedagogical goals outlined in the new TESOL Technology Standards (Healey et al.,2009). A wiki, a cross between a website and a word document, is an interactive webpage that allows students to read, generate, and publish content online in an environment of collaboration. The flexibility and…

  8. Attitudinal Factors Affecting Wiki Group Collaboration for English Writing

    Science.gov (United States)

    Chen, Chwen Jen; Chuah, Kee Man; Tho, Jimmy; Teh, Chee Siong

    2015-01-01

    Wikis, being one of the popular Web 2.0 tools, have impacted students' engagement and performance particularly in the aspects of second and foreign language learning. While an increasing number of studies have focused on the effectiveness of wiki in improving students' writing skills, this study was conducted to examine the attitudinal factors…

  9. Collaborative Tasks in Wiki-Based Environment in EFL Learning

    Science.gov (United States)

    Zou, Bin; Wang, Dongshuo; Xing, Minjie

    2016-01-01

    Wikis provide users with opportunities to post and edit messages to collaborate in the language learning process. Many studies have offered findings to show positive impact of Wiki-based language learning for learners. This paper explores the effect of collaborative task in error correction for English as a Foreign Language learning in an online…

  10. Cooperative Learning at a Distance: An Experiment with Wikis

    Science.gov (United States)

    Campbell, Katherine; Ellingson, Dee Ann

    2010-01-01

    The merits of incorporating group work into learning environments are well established. Online classes and other distance learning settings, however, can make it challenging to introduce traditional group projects. Wikis use technology to facilitate group work in distance learning settings. Wikis allow individuals in different locations to…

  11. Evaluating the Use of a Wiki for Collaborative Learning

    Science.gov (United States)

    Su, Feng; Beaumont, Chris

    2010-01-01

    A wiki is able to provide a learning environment which is closely aligned with the social-constructivist approach and is more natural than many tools where open collaboration and the exchange of ideas are important. This case study analyses and evaluates essential aspects for the successful deployment of a wiki in a higher education setting using…

  12. Wiki Uses in Higher Education: Exploring Barriers to Successful Implementation

    Science.gov (United States)

    Karasavvidis, Ilias

    2010-01-01

    E-learning 2.0 is expected to address some of the problems which characterized the first generation of E-learning implementations. Wikis are among the most promising E-learning 2.0 tools because they require active student engagement which facilitates constructivist learning. The present article focuses on the use of wikis in a university…

  13. "Wiki-Ed Poetry": Transforming Preservice Teachers' Preconceptions about Poetry and Poetry Teaching

    Science.gov (United States)

    Hughes, Janette; Dymoke, Sue

    2011-01-01

    This article focuses specifically on teacher candidates' preconceptions about poetry and poetry teaching and how these preconceptions shift as they work through various tasks on a wiki. Through an analysis of their definitions of poetry and ideas about poetry pedagogy captured in online discussion, survey, and interview responses, the authors…

  14. Use of Semantic Wikis to support collaborative learning

    Directory of Open Access Journals (Sweden)

    Mauro Coccoli

    2012-08-01

    Full Text Available Semantic Wiki consentono, tramite un linguaggio comprensibile agli elaboratori e formalmente definito, l’annotazione semantica dei contenuti delle pagine Wiki e la rappresentazione esplicita delle relazioni di significato tra essi presenti. Essi offrono la possibilità di sfruttare sia i vantaggi delle tecnologie basate su ontologie sia i meccanismi collaborativi propri dei Wiki. L’articolo descrive un progetto, denominato Semantic WikiSUN, avviato per indagare le prospettive didattiche di tali sistemi. Esso è basato su un quadro teorico complesso che integra evidenze neurocognitive, teorie dell’apprendimento e modelli costruttivisti-sociali della conoscenza. Obiettivo del contributo è, sulla base della esperienza intrapresa, discutere potenzialità e criticità didattiche dei Semantic Wiki, estendendo talvolta la riflessione a considerazioni più generali sui processi di apprendimento mediati da tecnologie semantiche.

  15. The impact of group membership on collaborative learning with wikis.

    Science.gov (United States)

    Matschke, Christina; Moskaliuk, Johannes; Kimmerle, Joachim

    2013-02-01

    The social web stimulates learning through collaboration. However, information in the social web is often associated with information about its author. Based on previous evidence that ingroup information is preferred to outgroup information, the current research investigates whether group memberships of wiki authors affect learning. In an experimental study, we manipulated the group memberships (ingroup vs. outgroup) of wiki authors by using nicknames. The designated group memberships (being fans of a soccer team or not) were completely irrelevant for the domain of the wiki (the medical disorder fibromyalgia). Nevertheless, wiki information from the ingroup led to more integration of information into prior knowledge as well as more increase of factual knowledge than information from the outgroup. The results demonstrate that individuals apply social selection strategies when considering information from wikis, which may foster, but also hinder, learning and collaboration. Practical implications for collaborative learning in the social web are discussed.

  16. A Neutral Control Condition for Hypnosis Experiments: "Wiki" Text.

    Science.gov (United States)

    Varga, Katalin; Kekecs, Zoltán; Myhre, P S; Józsa, Emese

    2017-01-01

    A new control condition called Wiki is introduced. Key themes of each test suggestion of the Stanford Hypnotic Susceptibility Scale, Form C, were matched by a corresponding extract from Wikipedia.org. The authors compared phenomenological reports of participants across 4 conditions: hypnosis split into high and low hypnotizable subgroups, music, and Wiki condition, using the Phenomenology of Consciousness Inventory. High hypnotizables undergoing hypnosis reported higher altered experience and altered states of awareness than individuals in the Wiki condition, supporting the authors' hypothesis that the Wiki condition does not evoke an altered state of consciousness (internal dialogue, volitional control, and self-awareness did not differ). Wiki might be a viable control condition in hypnosis research given further examination.

  17. Building a Virtual Cultural Intelligence Community

    Science.gov (United States)

    2007-06-01

    stuff quick-web.” “Wiki Wiki” is a reduplication of “wiki,” a Hawaiian -language word for fast. Wikipedia, “What Is Wiki,” Wiki.Org, http... wedded to organizations, the capacity for change is reduced due to bureaucratic cultures and requirements. It is Andrus’ 55 James Moffatt...academic community as a whole has a great deal of variety, individual academics can be insular. The casual expert may tend to be less “ wedded ” to a

  18. MetaBase—the wiki-database of biological databases

    Science.gov (United States)

    Bolser, Dan M.; Chibon, Pierre-Yves; Palopoli, Nicolas; Gong, Sungsam; Jacob, Daniel; Angel, Victoria Dominguez Del; Swan, Dan; Bassi, Sebastian; González, Virginia; Suravajhala, Prashanth; Hwang, Seungwoo; Romano, Paolo; Edwards, Rob; Bishop, Bryan; Eargle, John; Shtatland, Timur; Provart, Nicholas J.; Clements, Dave; Renfro, Daniel P.; Bhak, Daeui; Bhak, Jong

    2012-01-01

    Biology is generating more data than ever. As a result, there is an ever increasing number of publicly available databases that analyse, integrate and summarize the available data, providing an invaluable resource for the biological community. As this trend continues, there is a pressing need to organize, catalogue and rate these resources, so that the information they contain can be most effectively exploited. MetaBase (MB) (http://MetaDatabase.Org) is a community-curated database containing more than 2000 commonly used biological databases. Each entry is structured using templates and can carry various user comments and annotations. Entries can be searched, listed, browsed or queried. The database was created using the same MediaWiki technology that powers Wikipedia, allowing users to contribute on many different levels. The initial release of MB was derived from the content of the 2007 Nucleic Acids Research (NAR) Database Issue. Since then, approximately 100 databases have been manually collected from the literature, and users have added information for over 240 databases. MB is synchronized annually with the static Molecular Biology Database Collection provided by NAR. To date, there have been 19 significant contributors to the project; each one is listed as an author here to highlight the community aspect of the project. PMID:22139927

  19. Technoeconomic analysis of biofuels: A wiki-based platform for lignocellulosic biorefineries

    DEFF Research Database (Denmark)

    Klein-Marcuschamer, Daniel; Oleskowicz-Popiel, Piotr; Simmons, Blake A.

    2010-01-01

    We present a process model for a lignocellulosic ethanol biorefinery that is open to the biofuels academic community. Beyond providing a series of static results, the wiki-based platform provides a dynamic and transparent tool for analyzing, exploring, and communicating the impact of process...... advances and alternatives for biofuels production. The model is available for download (at http://econ.jbei.org) and will be updated based on feedback from the community of experts in biofuel-related fields. By making the assumptions and performance metrics of this model transparent, we anticipate...... this tool can provide a consensus on the energy-related, environmental, and economic performance of lignocellulosic ethanol....

  20. Towards a Conceptual Framework for WikiGIS

    Directory of Open Access Journals (Sweden)

    Wided Batita

    2014-10-01

    Full Text Available As an emerging complex concept, GeoDesign requires an innovative theoretical basis, tools, supports and practices. For this reason, we propose a new concept, “WikiGIS”, designed to answer some dimensions of the GeoDesign process. WikiGIS focuses on the needs of GeoDesign, but we leave the door open for future improvement when tested in other areas that may have additional needs. WikiGIS is built on Web 2.0 technologies—and primarily on wiki—to manage the tracking of participants’ editing (i.e., managing the contributions history. It also offers GIS functions for geoprocessing and a design-based approach for sketching proposals. One of the main strengths of WikiGIS is its ability to manage the traceability of contributions with an easy and dynamical access, data quality and deltification. The core of this paper consists of presenting a conceptual framework for WikiGIS using UML diagrams. A user interface is presented later to show how our WikiGIS proposal works. This interface is simply a means to illustrate the concepts underlying WikiGIS.

  1. Effective use of Wikis in College Mathematics Classes

    Directory of Open Access Journals (Sweden)

    Paul Martin

    2010-12-01

    Full Text Available Wikis are used in mathematics education in a variety of ways [3]. As with Wikipedia, mathematics related Wikis provide pages and links that describe many different branches of mathematics. Another common use is as a portal for distributing and collecting mathematics course materials [1]. This article describes the authors' use of course wikis for two different purposes in two undergraduate math courses. In Calculus-I, a wiki was utilized to share and present the outcome of an optimization problem that required small groups to collect information about student homes' attic insulation status and eventually to compute the optimal amount of new insulation to add that maximizes heating savings. The second wiki was for a small seminar-style course on Mathematical Mysteries where students collected and posted the results of their research relating to famous unsolved problems in mathematics. This wiki was also used as a platform for in-class presentations by the students and the instructors. In both cases, the bulk of the wiki contribution was by students.

  2. Index wiki database: design and experiments

    CERN Document Server

    Krizhanovsky, A A

    2008-01-01

    With the fantastic growth of Internet usage, information search in documents of a special type called a "wiki page" that is written using a simple markup language, has become an important problem. This paper describes the software architectural model for indexing wiki texts in three languages (Russian, English, and German) and the interaction between the software components (GATE, Lemmatizer, and Synarcher). The inverted file index database was designed using visual tool DBDesigner. The rules for parsing Wikipedia texts are illustrated by examples. Two index databases of Russian Wikipedia (RW) and Simple English Wikipedia (SEW) are built and compared. The size of RW is by order of magnitude higher than SEW (number of words, lexemes), though the growth rate of number of pages in SEW was found to be 12% higher than in Russian, and the rate of acquisition of new words in SEW lexicon was 6% higher during a period of five months (from September 2007 to February 2008). The Zipf's law was tested with both Russian an...

  3. WhatisKT wiki: a case study of a platform for knowledge translation terms and definitions — descriptive analysis

    Directory of Open Access Journals (Sweden)

    McKibbon Kathleen Ann

    2013-01-01

    Full Text Available Abstract Background More than a hundred terms, often with unclear definitions and varying emphases, are used by health research and practice communities across the world who are interested in getting the best possible evidence applied (e.g., knowledge translation, implementation science, diffusion of innovations, and technology transfer. This makes finding published evidence difficult and can result in reduced, misinterpreted, or challenging interactions among professionals. Open dialogue and interaction among various professionals is needed to achieve consolidation of vocabulary. We use case report methods to describe how we sought to build an online tool to present the range of terms and facilitate the dialogue process across groups and disciplines interested in harnessing research evidence for healthcare. Methods We used a wiki platform from Wikispaces to present the problem of terminology and make a case and opportunity for collaboration on usage. Wikis are web sites where communities of users can collaborate online to build content and discuss progress. We gathered terms related to getting research into practice, sought published definitions, and posted these on the wiki (WhatisKT http://whatiskt.wikispaces.com/. We built the wiki in mid-2008 and promoted it through various groups and publications. This report describes the content of the site, our promotion efforts, use of the site, and how the site was used for collaboration up to the end of 2011. Results The WhatisKT wiki site now includes more than 120 pages. Traffic to the site has increased substantially from an average of 200 monthly visits in 2008 to 1700 in 2011. Visitors from 143 countries viewed the wiki in 2011, compared with 12 countries in 2008. However, most use has been limited to short term accesses of about 40 seconds per visit, and discussion of consolidation and solidifying terminology is conspicuously absent. Conclusions Although considerable interest exists in the

  4. Creating an open access cal/val repository via the LACO-Wiki online validation platform

    Science.gov (United States)

    Perger, Christoph; See, Linda; Dresel, Christopher; Weichselbaum, Juergen; Fritz, Steffen

    2017-04-01

    There is a major gap in the amount of in-situ data available on land cover and land use, either as field-based ground truth information or from image interpretation, both of which are used for the calibration and validation (cal/val) of products derived from Earth Observation. Although map producers generally publish their confusion matrices and the accuracy measures associated with their land cover and land use products, the cal/val data (also referred to as reference data) are rarely shared in an open manner. Although there have been efforts in compiling existing reference datasets and making them openly available, e.g. through the GOFC/GOLD (Global Observation for Forest Cover and Land Dynamics) portal or the European Commission's Copernicus Reference Data Access (CORDA), this represents a tiny fraction of the reference data collected and stored locally around the world. Moreover, the validation of land cover and land use maps is usually undertaken with tools and procedures specific to a particular institute or organization due to the lack of standardized validation procedures; thus, there are currently no incentives to share the reference data more broadly with the land cover and land use community. In an effort to provide a set of standardized, online validation tools and to build an open repository of cal/val data, the LACO-Wiki online validation portal has been developed, which will be presented in this paper. The portal contains transparent, documented and reproducible validation procedures that can be applied to local as well as global products. LACO-Wiki was developed through a user consultation process that resulted in a 4-step wizard-based workflow, which supports the user from uploading the map product for validation, through to the sampling process and the validation of these samples, until the results are processed and a final report is created that includes a range of commonly reported accuracy measures. One of the design goals of LACO-Wiki has been

  5. What Does Wiki Reveal about the Knowledge Processing Strategies of School Pupils? Seventh-Graders as Users of Wiki and Processors of Knowledge in a Collaborative Writing Project

    Science.gov (United States)

    Ahlholm, Maria; Grünthal, Satu; Harjunen, Elina

    2017-01-01

    On the basis of one teaching project carried out in a school, this article discusses collaborative writing in wiki platforms. It aims to find out what wiki reveals about pupils' knowledge construction, creation, and division and their collaborative writing skills. In this project, wiki is treated as a useful tool for analyzing these processes…

  6. Using Semantic Wikis for Structured Argument in Medical Domain

    CERN Document Server

    Groza, Adrian

    2010-01-01

    This research applies ideas from argumentation theory in the context of semantic wikis, aiming to provide support for structured-large scale argumentation between human agents. The implemented prototype is exemplified by modelling the MMR vaccine controversy.

  7. Introduction of a Wiki in an Enterprise: Motives and Challenges

    Directory of Open Access Journals (Sweden)

    Fernando L. F. Almeida

    2011-10-01

    Full Text Available Among the tools available to implement the collaborative production of knowledge in organizations, the use of wikis has been gaining momentum and showing a low-cost and high efficiency. However, some difficulties still arise when attempting to introduce this kind of technology in an organization. In addition to technological limitations, the cultural issues inherent in companies can also origin problems and promising projects can be abandoned without achieving all the objectives planned. In this work, we study the motives, challenges as well as the more common problems that appear during the wiki implantation process in an organization and the purposed solutions on the literature. The main objective is to identify forms for the wiki to become a tool that everyone can use in the organization and identify the best practices related, so that the project of creating a functional wiki for an organization can aspire to befall a success and not simply abandoned.

  8. Kui WikiLeaks asuks Eestis... / Karmen Turk

    Index Scriptorium Estoniae

    Turk, Karmen, 1982-

    2010-01-01

    WikiLeaksi tegutsemise õiguspärasusest Eesti ja Euroopa õiguses. Internetiteenuse pakkuja vastutusest, info avaldamise ja vahendamise seaduslikkusest ja sõnavabaduse piiridest. Eesti Riigikohtu ja Euroopa Inimõiguste Kohtu praktika põhjal

  9. Wikis and blogs: consider the possibilities for continuing nursing education.

    Science.gov (United States)

    Billings, Diane M

    2009-12-01

    Wikis and blogs are software programs that promote communication and collaboration through the development of written documents. Nurse educators can use them to facilitate teaching and learning in a variety of health care settings.

  10. Formal Mathematics on Display: A Wiki for Flyspeck

    OpenAIRE

    Tankink, C.; Kaliszyk, C.; Urban, J.; Geuvers, H.

    2013-01-01

    The Agora system is a prototype "Wiki for Formal Mathematics", with an aim to support developing and documenting large formalizations of mathematics in a proof assistant. The functions implemented in Agora include in-browser editing, strong AI/ATP proof advice, verification, and HTML rendering. The HTML rendering contains hyperlinks and provides on-demand explanation of the proof state for each proof step. In the present paper we show the prototype Flyspeck Wiki as an instance of Agora for HO...

  11. Linking NCBI to Wikipedia: a wiki-based approach

    OpenAIRE

    Page, R.D.M.

    2011-01-01

    The NCBI Taxonomy underpins many bioinformatics and phyloinformatics databases, but by itself provides limited information on the taxa it contains. One readily available source of information on many taxa is Wikipedia. This paper describes iPhylo Linkout, a Semantic wiki that maps taxa in NCBI's taxonomy database onto corresponding pages in Wikipedia. Storing the mapping in a wiki makes it easy to edit, correct, or otherwise annotate the links between NCBI and Wikipedia. The mapping currently...

  12. Pembuatan Wiki Legenda Indonesia dengan Menggunakan CMS Mediawiki

    Directory of Open Access Journals (Sweden)

    Adityo Roosdiono

    2013-03-01

    Full Text Available Indonesia adalah negara yang terdiri dari berbagai suku bangsa dan budaya. Salah satu bentuk kekayaan suku bangsa di Indonesia dapat dilihat dari banyaknya legenda yang tersebar di Indonesia. Hampir setiap daerah di Indonesia memiliki cerita rakyat yang kental dengan suasana mistik, budaya dan tradisi di daerah masing-masing.Sayangnya cerita rakyat ini jarang sekali diekspos sehingga tidak jarang warga negara Indonesia tidak tahu cerita sejarah yang ada di Indonesia.  Berdasarkan pemikiran itulah, perlu diadakannya sebuah Wiki legenda Indonesia terkait mitos dan sejarah di Indonesia.Wiki legenda Indonesia menggunakan teknologi CMS MediaWiki, yang telah digunakan oleh Wikipedia sendiri. MediaWiki ini akan dipakai sebagai model awal pembuatan Wiki legenda Indonesia sehingga dapat digunakan sebagai media penyimpanan cerita rakyat. Selain sebagai media penyimpanan, Wiki legenda Indonesia juga berfungsi sebagai media diskusi para peminat cerita rakyat yang ada di Indonesia. Sehingga kedepannya, cerita legenda di Indonesia mampu diketahui oleh seluruh masyarakat Indonesia pada khususnya, dan dunia pada umumnya.

  13. The NASA Human Research Wiki - An Online Collaboration Tool

    Science.gov (United States)

    Barr, Yael; Rasbury, Jack; Johnson, Jordan; Barstend, Kristina; Saile, Lynn; Watkins, Sharmi

    2012-01-01

    The Exploration Medical Capability (ExMC) element is one of six elements of the Human Research Program (HRP). ExMC is charged with decreasing the risk of: "Inability to adequately recognize or treat an ill or injured crew member" for exploration-class missions In preparation for exploration-class missions, ExMC has compiled a large evidence base, previously available only to persons within the NASA community. ExMC has developed the "NASA Human Research Wiki" in an effort to make the ExMC information available to the general public and increase collaboration within and outside of NASA. The ExMC evidence base is comprised of several types of data, including: (1)Information on more than 80 medical conditions which could occur during space flight (a)Derived from several sources (b)Including data on incidence and potential outcomes, as captured in the Integrated Medical Model s (IMM) Clinical Finding Forms (CliFFs). (2)Approximately 25 gap reports (a)Identify any "gaps" in knowledge and/or technology that would need to be addressed in order to provide adequate medical support for these novel missions.

  14. Refactoring affordances in corporate wikis: a case for the use of mind maps

    Science.gov (United States)

    Puente, Gorka; Díaz, Oscar; Azanza, Maider

    2015-11-01

    The organisation of corporate wikis tends to deteriorate as time goes by. Rearranging categories, structuring articles and even moving sections among articles are cumbersome tasks in current wiki engines. This discourages the layman. But, it is the layman who writes the articles, knows the wiki content and detects refactoring opportunities. Our goal is to improve the refactoring affordances of current wiki engines by providing an alternative front-end tuned to refactoring. This is achieved by (1) surfacing the structure of the wiki corpus as a mind map, and (2) conducting refactoring as mind map reshaping. To this end, we introduce WikiWhirl, a domain-specific language for wiki refactoring. WikiWhirl is supported as an extension of FreeMind, a popular mind mapping tool. In this way, refactoring operations are intuitively conducted as actions upon mind map nodes. In a refactoring session a user imports the wiki structure as a FreeMind map; next, conducts the refactoring operations on the map, and finally, the effects are saved in the wiki database. The operational semantics of the WikiWhirl operations follow refactoring good practices (e.g., authorship preservation). Results from a controlled experiment suggest that WikiWhirl outperforms MediaWiki in three main affordance enablers: understandability, productivity and fulfillment of refactoring good practices.

  15. Sediment denitrifier community composition and nirS gene expression investigated with functional gene microarrays

    DEFF Research Database (Denmark)

    Francis, C.A.; Jackson, G.A.; Ward, B.B.

    2008-01-01

    total RNA extracts) targets were hybridized to the same array to compare the profiles of community composition at the DNA (relative abundance) and mRNA (gene expression) levels. Only the three dominant denitrifying groups (in terms of relative strength of DNA hybridization signal) were detected at the m......A functional gene microarray was used to investigate denitrifier community composition and nitrite reductase (nirS) gene expression in sediments along the estuarine gradient in Chesapeake Bay, USA. The nirS oligonucleotide probe set was designed to represent a sequence database containing 539...

  16. Using Wikis to Teach History Education to 21st Century Learners: A ...

    African Journals Online (AJOL)

    Salmon's five-stage model of online learning. The findings indicate ... Keywords: Gadamer, Gilly Salmon, Hermeneutics, History education, Wikis and Dialogue,. Online .... share their understanding of a history artifact hosted on a Wiki platform.

  17. Using Wikis to Foster Collaborative Writing: Exploring Influencing Factors to Successful Implementation

    Science.gov (United States)

    Hadjerrouit, Said

    2012-01-01

    Wiki technology provides new opportunities to foster collaborative learning in various educational settings. To empirically examine the impact of wikis on learning, this article explores students' collaborative writing activities performed on MediaWiki. The activities were analyzed using a taxonomy with ten categories (clarify content, add…

  18. Collaborative Learning with a Wiki: Differences in Perceived Usefulness in Two Contexts of Use

    Science.gov (United States)

    Naismith, L.; Lee, B.-H.; Pilkington, R. M.

    2011-01-01

    This paper investigates the potential of a wiki (FlexWiki) to support collaborative authoring of web resources in authentic coursework by two different sets of education students at different stages of their professional development. Research questions included: (1) how the selected wiki could be blended with curriculum activities and existing…

  19. Electures-Wiki--Toward Engaging Students to Actively Work with Lecture Recordings

    Science.gov (United States)

    Hermann, Christoph; Ottmann, Thomas

    2011-01-01

    In this paper, we present the integration of a Wiki with lecture recordings using a tool called "aofconvert", enabling the students to visually reference lecture recordings in the Wiki at a precise moment in time of the lecture. This tight integration between a Wiki and lecture materials allows the students to elaborate on the topics…

  20. The Use of Wikis in a Science Inquiry-Based Project in a Primary School

    Science.gov (United States)

    Lau, Wilfred W. F.; Lui, Vicky; Chu, Samuel K. W.

    2017-01-01

    This study explored the use of wikis in a science inquiry-based project conducted with Primary 6 students (aged 11-12). It used an online wiki-based platform called PBworks and addressed the following research questions: (1) What are students' attitudes toward learning with wikis? (2) What are students' interactions in online group collaboration…

  1. More than Just Wikipedia: Creating a Collaborative Research Library Using a Wiki

    Science.gov (United States)

    Munoz, Caroline Lego

    2012-01-01

    Increasingly, wiki technology is being used in education and business settings. Although most students are aware of Wikipedia, many do not understand that a wiki is a malleable platform that has a multitude of uses. Wiki technology is one of many social media tools that students need to not only become familiar with but also be able to effectively…

  2. Using a Wiki to Enhance Cooperative Learning in a Real Analysis Course

    Science.gov (United States)

    Peterson, Elisha

    2009-01-01

    This article describes how the author used a wiki-based website in a real analysis course, and assesses its effectiveness. The wiki was used to post course materials, maintain a forum, enable students to write collaborative projects, and enable students to develop a glossary of important terms. The wiki proved to be very successful; it facilitated…

  3. Wikis as a Tool for Collaborative Learning: Implications for Literacy, Language Education and Multilingualism

    Science.gov (United States)

    Aydin, Selami

    2014-01-01

    This study presents a review of the literature concerning the use of wikis as a tool for collaborative learning in the second language acquisition and foreign language learning process, as research on the use of wikis is relatively new. The study first introduces the theoretical background behind the use of wikis in the mentioned processes. Then,…

  4. Using Wikis to Enhance and Develop Writing Skills among Secondary School Students in Hong Kong

    Science.gov (United States)

    Mak, Barley; Coniam, David

    2008-01-01

    This paper investigates authentic writing through the use of wikis by Year 7 ESL learners in a secondary school in Hong Kong. The wikis were used as a collaborative writing platform to produce--with minimal input and support from their teachers--wiki content that describes the different facilities and features of their school. Over a period of two…

  5. Making Group Assessment Transparent: What Wikis Can Contribute to Collaborative Projects

    Science.gov (United States)

    Caple, Helen; Bogle, Mike

    2013-01-01

    This paper investigates the use of new media technologies, in particular wikis, for the compiling and grading of group assessment tasks. Wikis are open web pages that can be viewed and modified by anyone with internet access and are well known for their collaborative nature. Wikis are also transparent, which means that any edit/modification is…

  6. More than Just Wikipedia: Creating a Collaborative Research Library Using a Wiki

    Science.gov (United States)

    Munoz, Caroline Lego

    2012-01-01

    Increasingly, wiki technology is being used in education and business settings. Although most students are aware of Wikipedia, many do not understand that a wiki is a malleable platform that has a multitude of uses. Wiki technology is one of many social media tools that students need to not only become familiar with but also be able to effectively…

  7. Wiki surveys: open and quantifiable social data collection.

    Science.gov (United States)

    Salganik, Matthew J; Levy, Karen E C

    2015-01-01

    In the social sciences, there is a longstanding tension between data collection methods that facilitate quantification and those that are open to unanticipated information. Advances in technology now enable new, hybrid methods that combine some of the benefits of both approaches. Drawing inspiration from online information aggregation systems like Wikipedia and from traditional survey research, we propose a new class of research instruments called wiki surveys. Just as Wikipedia evolves over time based on contributions from participants, we envision an evolving survey driven by contributions from respondents. We develop three general principles that underlie wiki surveys: they should be greedy, collaborative, and adaptive. Building on these principles, we develop methods for data collection and data analysis for one type of wiki survey, a pairwise wiki survey. Using two proof-of-concept case studies involving our free and open-source website www.allourideas.org, we show that pairwise wiki surveys can yield insights that would be difficult to obtain with other methods.

  8. Wikis as the Knowledge Management Tools in Organizations

    Directory of Open Access Journals (Sweden)

    Hossein Pashaeizad

    2012-02-01

    Full Text Available In an attempt to enhance knowledge, firms and corporations have been overwhelmed with assorted methods for retaining employee wisdom. To pay attention to the benefits of a successful knowledge management program can help create competitive advantage. Therefore, numerous knowledge management solutions have been developed and implemented. Some of these knowledge management initiatives provide a means to accumulate, organize, and access the firm’s most essential asset. With the advent and spread of information and communication technologies, especially Internet, social software and communication tools has risen to the challenge of capturing knowledge with a variety of methods. One of these tools is wiki that provides a new way of collaboration and knowledge sharing. Wiki is a software that allows users to work collectively on a web-based knowledge base. This paper reviews the role of wikis in knowledge creation and management

  9. Wiki as a tool for microbiology teaching, learning and assessment.

    Science.gov (United States)

    Sampaio-Maia, B; Maia, J S; Leitão, S; Amaral, M; Vieira-Marques, P

    2014-05-01

    Evidence suggests that cooperative learning and peer-assessment fosters students' ability to work with others and may lead to better cognitive outcomes and higher achievement. This work aimed to assess the use of an online collaborative tool for the teaching/learning and assessment of Microbiology. A total of 144 students were grouped and assigned to create wiki entries as well as to peer review wikis created by colleagues (peer-assessment process) using the Wiki module from Moodle Virtual Learning Environment (MVLE). MVLE actions log was used for tracking students' activity. The number of student's actions within wiki did not present a strong correlation with wiki scores, so it should not be used as a heavy evaluation parameter. The amount of work developed between members of the same group differed significantly, suggesting that final scores should be attributed individually. When peer-assessment process was implemented, the number of editing actions increased, suggesting that the peer-assessment strategy encourages the development of a better work. The vast majority of students execute the work in the last 10% of the period assigned for task development, which can be counter-productive for a truly collaborative work. Wiki revealed to be a useful tool for Microbiology teaching/learning and assessment, promoting collaborative work, promoting virtual mobility and facilitating the real-time monitoring of the students' work. This pedagogical project promoted also the involvement of students in their assessment process, encouraging their critical sense and quest for Excellency. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  10. A Simple Application Program Interface for Saving Java Program Data on a Wiki

    OpenAIRE

    Takashi Yamanoue; Kentaro Oda; Koichi Shimozono

    2012-01-01

    A simple application program interface (API) for Java programs running on a wiki is implemented experimentally. A Java program with the API can be running on a wiki, and the Java program can save its data on the wiki. The Java program consists of PukiWiki, which is a popular wiki in Japan, and a plug-in, which starts up Java programs and classes of Java. A Java applet with default access privilege cannot save its data at a local host. We have constructed an API of applets for easy and unified...

  11. How Wikis can be Used to Manage Knowledge in SMEs

    DEFF Research Database (Denmark)

    Razmerita, Liana; Kirchner, Kathrin

    2011-01-01

    and reports a small case study in an IT consulting company following the introduction of a wiki-based solution into its daily practices. The usage of the wiki and its impact on knowledge work are explored. The authors then compare the findings from the literature review with those from the case study....... The comparison shows that introducing knowledge processes can start ‘bottom-up’ through an initiative to better manage personal knowledge. Furthermore, the articulation of personal and collective knowledge is possible synergistically and in a more transparent manner....

  12. Proposing a Wiki-Based Technique for Collaborative Essay Writing

    Directory of Open Access Journals (Sweden)

    Mabel Ortiz Navarrete

    2014-10-01

    Full Text Available This paper aims at proposing a technique for students learning English as a foreign language when they collaboratively write an argumentative essay in a wiki environment. A wiki environment and collaborative work play an important role within the academic writing task. Nevertheless, an appropriate and systematic work assignment is required in order to make use of both. In this paper the proposed technique when writing a collaborative essay mainly attempts to provide the most effective way to enhance equal participation among group members by taking as a base computer mediated collaboration. Within this context, the students’ role is clearly defined and individual and collaborative tasks are explained.

  13. Linking NCBI to Wikipedia: a wiki-based approach.

    Science.gov (United States)

    Page, Roderic D M

    2011-03-31

    The NCBI Taxonomy underpins many bioinformatics and phyloinformatics databases, but by itself provides limited information on the taxa it contains. One readily available source of information on many taxa is Wikipedia. This paper describes iPhylo Linkout, a Semantic wiki that maps taxa in NCBI's taxonomy database onto corresponding pages in Wikipedia. Storing the mapping in a wiki makes it easy to edit, correct, or otherwise annotate the links between NCBI and Wikipedia. The mapping currently comprises some 53,000 taxa, and is available at http://iphylo.org/linkout. The links between NCBI and Wikipedia are also made available to NCBI users through the NCBI LinkOut service.

  14. A semantic geographical knowledge wiki system mashed up with Google Maps

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    A wiki system is a typical Web 2.0 application that provides a bi-directional platform for users to collaborate and share much useful information online.Unfortunately,computers cannot well understand the wiki pages in plain text.The user-generated geographical content via wiki systems cannot be manipulated properly and efficiently unless the geographical semantics is explicitly represented.In this paper,a geographical semantic wiki system,Geo-Wiki,is introduced to solve this problem.Geo-Wiki is a semantic geographical knowledge-sharing web system based on geographical ontologies so that computers can parse and storage the multi-source geographical knowledge.Moreover,Geo-Wiki mashed up with map services enriches the representation and helps users to find spatial distribution patterns,and thus can serve geospatial decision-making by customizing the Google Maps APIs.

  15. The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability.

    Science.gov (United States)

    Li, Jing-Woei; Bolser, Dan; Manske, Magnus; Giorgi, Federico Manuel; Vyahhi, Nikolay; Usadel, Björn; Clavijo, Bernardo J; Chan, Ting-Fung; Wong, Nathalie; Zerbino, Daniel; Schneider, Maria Victoria

    2013-09-01

    Next-generation sequencing (NGS) is increasingly being adopted as the backbone of biomedical research. With the commercialization of various affordable desktop sequencers, NGS will be reached by increasing numbers of cellular and molecular biologists, necessitating community consensus on bioinformatics protocols to tackle the exponential increase in quantity of sequence data. The current resources for NGS informatics are extremely fragmented. Finding a centralized synthesis is difficult. A multitude of tools exist for NGS data analysis; however, none of these satisfies all possible uses and needs. This gap in functionality could be filled by integrating different methods in customized pipelines, an approach helped by the open-source nature of many NGS programmes. Drawing from community spirit and with the use of the Wikipedia framework, we have initiated a collaborative NGS resource: The NGS WikiBook. We have collected a sufficient amount of text to incentivize a broader community to contribute to it. Users can search, browse, edit and create new content, so as to facilitate self-learning and feedback to the community. The overall structure and style for this dynamic material is designed for the bench biologists and non-bioinformaticians. The flexibility of online material allows the readers to ignore details in a first read, yet have immediate access to the information they need. Each chapter comes with practical exercises so readers may familiarize themselves with each step. The NGS WikiBook aims to create a collective laboratory book and protocol that explains the key concepts and describes best practices in this fast-evolving field.

  16. Peer Evaluation in Chemical Engineering Capstone Design via Wikis

    Science.gov (United States)

    Heldt, Caryn L.

    2012-01-01

    Inter-group peer evaluation through wikis was implemented as a method for senior capstone design teams to improve writing and the critical evaluation of data. Each group was evaluated by peers using a qualitative discussion and evaluated quantitatively by instructors. Students had an increased interest in contributing to online knowledge centers,…

  17. Evaluating WikiTrust: a trust support tool for Wikipedia

    NARCIS (Netherlands)

    Lucassen, Teun; Schraagen, Jan Maarten

    2011-01-01

    Because of the open character of Wikipedia readers should always be aware of the possibility of false information. WikiTrust aims at helping readers to judge the trustworthiness of articles by coloring the background of less trustworthy words in a shade of orange. In this study we look into the effe

  18. Identifying Collaborative Behaviours Online: Training Teachers in Wikis

    Science.gov (United States)

    Vinagre Laranjeira, Margarita

    2016-01-01

    In this paper we explore the data gathered from a group of nine in-service teachers who were trained online to become future telecollaborative teachers. Participants from different countries worked in two small groups in a wiki designed specially to facilitate discussion and collaboration. Tasks included reading and reviewing articles on…

  19. Online Open Neuroimaging Mass Meta-Analysis with a Wiki

    DEFF Research Database (Denmark)

    Nielsen, Finn Arup; Kempton, Matthew J.; Williams, Steven C. R.

    2015-01-01

    We describe a system for meta-analysis where a wiki stores numerical data in a simple comma-separated values format and a web service performs the numerical statistical computation. We initially apply the system on multiple meta-analyses of structural neuroimaging data results. The described system...

  20. Pedagogical Significance of Wikis: Towards Gaining Effective Learning Outcomes

    Science.gov (United States)

    Hewege, Chandana Rathnasiri; Perera, Liyanage Chamila Roshani

    2013-01-01

    Purpose: The purpose of this paper is to explore the effectiveness and pedagogical implications of integrating wikis into the curriculum and the subsequent learning outcomes of a group of Net-Gens who enrolled in an International Marketing course. The research problem of the study is: "What are the learning outcomes and pedagogical…

  1. Contenido generado por usuarios (UGC, wikis y derecho de autor

    Directory of Open Access Journals (Sweden)

    Juan Sebastián Sereno Restrepo

    2010-11-01

    Full Text Available El contenido generado mediante wiki por sus usuarios plantea dos problemas. El primero (“formal”, establecer a qué figura de atribución y coordinación de facultades de derecho de autor corresponde; el segundo (“deontológico”, determinar si los jurídicos efectos derivados de tal adecuación son consistentes con una de las finalidades legitimadoras del derecho de autor (incentivar la creación, y en caso negativo, qué mecanismo se debe utilizar para resolver la contradicción. El contenido generado mediante wiki (abierta corresponde, por regla general, a la figura de obra originaria y derivada; adicionalmente, los efectos jurídicos derivados no son claramente compatibles con la promoción de la creación. Tal contradicción se resuelve implementando en la wiki una licencia general (vinculante para todos usuarios de la wiki, estándar y uniforme (vr. g., la licencia creative commons.

  2. Contenido generado por usuarios (UGC, wikis y derecho de autor

    Directory of Open Access Journals (Sweden)

    Juan Sebastián Sereno Restrepo

    2010-11-01

    Full Text Available El contenido generado mediante Wiki por sus usuarios plantea dos problemas. El primero ("formal", establecer a qué figura de atribución y coordinación de facultades de derecho de autor corresponde; el segundo ("deontológico", determinar si los jurídicos efectos derivados de tal adecuación son consistentes con una de las finalidades legitimadoras del derecho de autor (incentivar la creación, y en caso negativo, qué mecanismo se debe utilizar para resolver la contradicción. El contenido generado mediante wiki (abierta corresponde por regla general a la figura de obra originaria y derivada; adicionalmente, los efectos jurídicos derivados no son claramente compatibles con la promoción de la creación. Tal contradicción se resuelve implementando en la Wiki una licencia general (vinculante para todos usuarios de la wiki, estándar y uniforme (vrg, la licencia creative commons.

  3. A Wiki-based Key to Garden and Village Birds

    OpenAIRE

    Trilar, Tomi

    2010-01-01

    A Wiki-based Key to Garden and Village Birds is available in two versions: a dichotomous, hyperlinked and printable version, and as step-bystep identification version. It is supported by jKey Player in English, Slovenian, Spanish, Romanian and German.

  4. Group Projects in Chemical Engineering Using a Wiki

    Science.gov (United States)

    Heys, Jeffrey J.

    2008-01-01

    Group projects are common in undergraduate chemical engineering course. Wikis are a new medium for group projects because they are Webpages that are edited using the same software used to view the Webpage. Advantages include the ability to record changes made by each individual (helpful for grading), ability to continuously monitor progress, and a…

  5. Muscle Research and Gene Ontology: New standards for improved data integration

    Directory of Open Access Journals (Sweden)

    Nori Alessandra

    2009-01-01

    Full Text Available Abstract Background The Gene Ontology Project provides structured controlled vocabularies for molecular biology that can be used for the functional annotation of genes and gene products. In a collaboration between the Gene Ontology (GO Consortium and the muscle biology community, we have made large-scale additions to the GO biological process and cellular component ontologies. The main focus of this ontology development work concerns skeletal muscle, with specific consideration given to the processes of muscle contraction, plasticity, development, and regeneration, and to the sarcomere and membrane-delimited compartments. Our aims were to update the existing structure to reflect current knowledge, and to resolve, in an accommodating manner, the ambiguity in the language used by the community. Results The updated muscle terminologies have been incorporated into the GO. There are now 159 new terms covering critical research areas, and 57 existing terms have been improved and reorganized to follow their usage in muscle literature. Conclusion The revised GO structure should improve the interpretation of data from high-throughput (e.g. microarray and proteomic experiments in the area of muscle science and muscle disease. We actively encourage community feedback on, and gene product annotation with these new terms. Please visit the Muscle Community Annotation Wiki http://wiki.geneontology.org/index.php/Muscle_Biology.

  6. Use of Wiki software for the knowledge management at the IEN

    Energy Technology Data Exchange (ETDEWEB)

    Augusto, Silas C.; Oliveira, Mauro V.; Almeida, Jose Carlos S.; Marques, Luana F.S.; Antunes, Joao Francisco O., E-mail: silas@ien.gov.br, E-mail: mvitor@ien.gov.br, E-mail: jcsa@ien.gov.br, E-mail: lsales@ien.gov.br, E-mail: jfantunes@ien.gov.br [Instituto de Engenharia Nuclear (IEN/CNEN-RJ), Rio de Janeiro, RJ (Brazil)

    2015-07-01

    Thanks to the broad availability of internet access and the development of browser-based web applications known as 'wikis' (Hawaiian word for 'quick, fast'), it became possible for internet users to participate on big collaborative encyclopedic projects. The best example is Wikipedia, an online encyclopedia based on MediaWiki that receives contributions from internet users around the world. In this context, the word 'wiki' usually refers to the wiki software itself, and/or the collection of hypertext documents managed by it. Wiki software allows creating, editing and managing online-shared documents, which become available immediately after they are created/edited. With such capabilities, wikis can also be used within organizations as tools to allow its employees to collaborate in the construction of a common knowledge base containing information relevant to the organization. In such context, the wiki becomes a tool for knowledge management. This article describes the implementation of the WikiIEN, which is based on MediaWiki, as a tool for knowledge management at the IEN - Instituto de Engenharia Nuclear. This tool aims to improve the sharing of information among institute researchers, thorough a dynamic common knowledge base that can be on-line updated. In the article are presented the logical and computational structure of the wiki created for deposit of the knowledge generated at the IEN. (author)

  7. SOIL Geo-Wiki: A tool for improving soil information

    Science.gov (United States)

    Skalský, Rastislav; Balkovic, Juraj; Fritz, Steffen; See, Linda; van der Velde, Marijn; Obersteiner, Michael

    2014-05-01

    Crowdsourcing is increasingly being used as a way of collecting data for scientific research, e.g. species identification, classification of galaxies and unravelling of protein structures. The WorldSoilProfiles.org database at ISRIC is a global collection of soil profiles, which have been 'crowdsourced' from experts. This system, however, requires contributors to have a priori knowledge about soils. Yet many soil parameters can be observed in the field without specific knowledge or equipment such as stone content, soil depth or color. By crowdsourcing this information over thousands of locations, the uncertainty in current soil datasets could be radically reduced, particularly in areas currently without information or where multiple interpretations are possible from different existing soil maps. Improved information on soils could benefit many research fields and applications. Better soil data could enhance assessments of soil ecosystem services (e.g. soil carbon storage) and facilitate improved process-based ecosystem modeling from local to global scales. Geo-Wiki is a crowdsourcing tool that was developed at IIASA for land cover validation using satellite imagery. Several branches are now available focused on specific aspects of land cover validation, e.g. validating cropland extent or urbanized areas. Geo-Wiki Pictures is a smart phone application for collecting land cover related information on the ground. The extension of Geo-Wiki to a mobile environment provides a tool for experts in land cover validation but is also a way of reaching the general public in the validation of land cover. Here we propose a Soil Geo-Wiki tool that builds on the existing functionality of the Geo-Wiki application, which will be largely designed for the collection and sharing of soil information. Two distinct applications are envisaged: an expert-oriented application mainly for scientific purposes, which will use soil science related language (e.g. WRB or any other global reference

  8. Distributed scaffolding: Wiki collaboration among Latino high school chemistry students

    Science.gov (United States)

    O'Sullivan, Edwin Duncan, Jr.

    The primary purpose of this study was to evaluate if wiki collaboration among Latino high school chemistry students can help reduce the science achievement gap between Latino and White students. The study was a quasi-experimental pre/post control group mixed-methods design. It used three intact sections of a high school chemistry course. The first research question asked if there is a difference in academic achievement between a treatment and control group on selected concepts from the topics of bonding, physical changes, and chemical changes, when Latino high school chemistry students collaborate on a quasi-natural wiki project. Overall results for all three activities (Bonding, Physical Changes, and Chemical Changes) indicated no significant difference between the wiki and control group. However, students performing the chemical changes activity did significantly better than their respective control group. Furthermore, there was a significant association, with large effect size, between group membership and ability to overcome the misconception that aqueous ionic reactants in precipitation reactions exist as molecular pairs of ions. Qualitative analysis of classroom and computer lab dialogue, discussion board communication, student focus groups, teacher interviews, and wiki content attributes the better performance of the chemical changes wiki group to favorable differences in intersubjectivity and calibrated assistance, as well as learning about submicroscopic representations of precipitation reactions in multiple contexts. Furthermore, the nonsignificant result overall points to an aversion to peer editing as a possible cause. Drawing considerably on Vygotsky and Piaget, the results are discussed within the context of how distributed scaffolding facilitated medium levels of cognitive conflict. The second research question asked what the characteristics of distributed metacognitive scaffolding are when Latino high school chemistry students collaborate on a quasi

  9. Using a Poetry Wiki: How Can the Medium Support Pre-Service Teachers of English in Their Professional Learning about Writing Poetry and Teaching Poetry Writing in a Digital Age?

    Science.gov (United States)

    Dymoke, Sue; Hughes, Janette

    2009-01-01

    In this paper we report on one aspect of a qualitative study about an online wiki community, which was developed to build collaborative knowledge about poetry among a group of pre-service English teachers. Our paper explores pre-service teachers' experiences of writing in a digital medium and their perceptions of themselves as writers. We focus…

  10. Extraction of Hidden Social Networks from Wiki-Environment Involved in Information Conflict

    OpenAIRE

    Alguliyev, Rasim M.; Ramiz M. Aliguliyev; Irada Y. Alakbarova

    2016-01-01

    Social network analysis is a widely used technique to analyze relationships among wiki-users in Wikipedia. In this paper the method to identify hidden social networks participating in information conflicts in wiki-environment is proposed. In particular, we describe how text clustering techniques can be used for extraction of hidden social networks of wiki-users caused information conflict. By clustering unstructured text articles caused information conflict we ...

  11. Extraction of Hidden Social Networks from Wiki-Environment Involved in Information Conflict

    Directory of Open Access Journals (Sweden)

    Rasim M. Alguliyev

    2016-03-01

    Full Text Available Social network analysis is a widely used technique to analyze relationships among wiki-users in Wikipedia. In this paper the method to identify hidden social networks participating in information conflicts in wiki-environment is proposed. In particular, we describe how text clustering techniques can be used for extraction of hidden social networks of wiki-users caused information conflict. By clustering unstructured text articles caused information conflict we create social network of wiki-users. For clustering of the conflict articles a hybrid weighted fuzzy-c-means method is proposed.

  12. Semantic Search in Wiki using HTML5 Microdata for Semantic Annotation

    Directory of Open Access Journals (Sweden)

    P Pabitha

    2011-05-01

    Full Text Available Wiki, the collaborative web authoring system makes Web a huge collection of information, as the Wiki pages are authored by anybody all over the world. These Wiki pages, if annotated semantically, will serve as a universal pool of intellectual resources that can be read by machines too. This paper presents an analytical study and implementation of making the Wiki pages semantic by using HTML5 semantic elements and annotating with microdata. And using the semantics the search module is enhanced to provide accurate results.

  13. Wiki surveys: Open and quantifiable social data collection

    CERN Document Server

    Salganik, Matthew J

    2012-01-01

    Research about attitudes and opinions is central to social science and relies on two common methodological approaches: surveys and interviews. While surveys enable the quantification of large amounts of information quickly and at a reasonable cost, they are routinely criticized for being "top-down" and rigid. In contrast, interviews allow unanticipated information to "bubble up" directly from respondents, but are slow, expensive, and difficult to quantify. Advances in computing technology now enable a hybrid approach that combines the quantifiability of a survey and the openness of an interview; we call this new class of data collection tools wiki surveys. Drawing on principles underlying successful information aggregation projects, such as Wikipedia, we propose three general criteria that wiki surveys should satisfy: they should be greedy, collaborative, and adaptive. We then present results from www.allourideas.org, a free and open-source website we created that enables groups all over the world to deploy w...

  14. Kajian Pembelajaran Online Berbasis Wiki Di Lingkup Perguruan Tinggi

    Directory of Open Access Journals (Sweden)

    Soetam Rizky Wicaksono

    2012-01-01

    Full Text Available Scope of online learning in higher education now more widely assumed to be a repository of teaching materials for both teachers and students. Nevertheless there are still many things that can still be developed and studied with an experimental model for online learning can be more participatory in the learning context given that the scope of the college is more directed to andragogik. One innovation that leads to this is to make the application of model-based learning wiki adopting crowdsourcing. This paper explores theoretical study attempted as a first step in the research development of wiki-based online learning model. The results of this study should be the basis for experiments to be conducted in order to adapt contextually in real state.

  15. SWiM -- A Semantic Wiki for Mathematical Knowledge Management

    CERN Document Server

    Lange, Christoph

    2010-01-01

    SWiM is a semantic wiki for collaboratively building, editing and browsing mathematical knowledge represented in the domain-specific structural semantic markup language OMDoc. It motivates users to contribute to collections of mathematical knowledge by instantly sharing the benefits of knowledge-powered services with them. SWiM is currently being used for authoring content dictionaries, i. e. collections of uniquely identified mathematical symbols, and prepared for managing a large-scale proof formalisation effort.

  16. Knowledge construction and knowledge sharing: A Wiki-based approach

    OpenAIRE

    Montero Fleta, Maria Begoña; Pérez Sabater, Carmen

    2011-01-01

    The present research, based on constructivist learning paradigms, describes the outcomes of a project which complies with real life projection into the professional world: a Wiki-based approach is devised to construct knowledge, manage own learning and develop communication and linguistic skills in English. The paper aims to analyze the process and product of students¿ contribution to group work. A qualitative analysis reveals the students¿ positive and negative feedback. The stud...

  17. Twelve tips for using blogs and wikis in medical education.

    Science.gov (United States)

    Sandars, John

    2006-12-01

    Blogs and wikis are an emerging area in medical education but are widely used by the general public. These easily accessed websites can be used for a variety of purposes. They can provide a learning resource that can be read by learners, they can be written by learners as a portfolio, and they can be used as a collaborative learning space. The exact use will depend on the requirements of the learner and the educator.

  18. Wikis in education - After ten years of experience

    Directory of Open Access Journals (Sweden)

    Miran Hladnik

    2016-12-01

    Full Text Available In the recent ten years, the use of Wikimedia projects in classroom has become a daily necessity. On the Wikiversity subject pages, students can enroll into the seminar schedule, teachers can publish links to their educational resources and instructions, as well as summarize experiences. Students can document their activities on their personal Wikiversity pages, where they can also report about their assignments and exchange information with teachers and their peers. They often use Wikiversity as a sandbox, in order to sketch the encyclopedic entries for Wikipedia. They can link Wikiversity with Wikisource. The latter is a space to which they can upload the literary texts that are found in the national digital library. They can also correct the errors, which have been caused by OCR process, and equip the texts with metadata. Wikis thus force their users to depart from the school “ghetto” and enter the realm of their discipline through the participatory establishment of its sustainable, digital infrastructure. Considering the valuable potential that the wikis have in the context of the paradigm shift, during which competition retreats in favor of the participation and exchange, the article concludes that wikis are still insufficiently represented in the education processes.

  19. Wiki-pi: a web-server of annotated human protein-protein interactions to aid in discovery of protein function.

    Directory of Open Access Journals (Sweden)

    Naoki Orii

    Full Text Available Protein-protein interactions (PPIs are the basis of biological functions. Knowledge of the interactions of a protein can help understand its molecular function and its association with different biological processes and pathways. Several publicly available databases provide comprehensive information about individual proteins, such as their sequence, structure, and function. There also exist databases that are built exclusively to provide PPIs by curating them from published literature. The information provided in these web resources is protein-centric, and not PPI-centric. The PPIs are typically provided as lists of interactions of a given gene with links to interacting partners; they do not present a comprehensive view of the nature of both the proteins involved in the interactions. A web database that allows search and retrieval based on biomedical characteristics of PPIs is lacking, and is needed. We present Wiki-Pi (read Wiki-π, a web-based interface to a database of human PPIs, which allows users to retrieve interactions by their biomedical attributes such as their association to diseases, pathways, drugs and biological functions. Each retrieved PPI is shown with annotations of both of the participant proteins side-by-side, creating a basis to hypothesize the biological function facilitated by the interaction. Conceptually, it is a search engine for PPIs analogous to PubMed for scientific literature. Its usefulness in generating novel scientific hypotheses is demonstrated through the study of IGSF21, a little-known gene that was recently identified to be associated with diabetic retinopathy. Using Wiki-Pi, we infer that its association to diabetic retinopathy may be mediated through its interactions with the genes HSPB1, KRAS, TMSB4X and DGKD, and that it may be involved in cellular response to external stimuli, cytoskeletal organization and regulation of molecular activity. The website also provides a wiki-like capability allowing users

  20. Ensino-aprendizagem colaborativo mediado pelo Wiki do Moodle Collaborative learning-teaching mediated by Wiki Moodle

    Directory of Open Access Journals (Sweden)

    Ilse Abegg

    2010-12-01

    Full Text Available Mediados pela ferramenta Wiki do Moodle, desenvolvemos atividades a distância no Curso de Física da UFSM com o intuito de produzir um objeto escolar hipermídia tematizado pelo Tema Estruturador do Ensino de Física 2: Calor, Ambiente e usos de Energia (oriundo dos PCN+ , locando o diálogo-problematizador na transversalidade curricular "Meio Ambiente". Problematizamos esta atividade, caracterizada como uma produção colaborativa de hipermídia de divulgação científico-tecnológica, ao longo do período letivo da disciplina Didática I da Física da instância curricular integradora. O trabalho em grupo mediado pelo wiki do Moodle tem sido implementado através do PEA (Planejamento, Execução e Avaliação de forma cíclico-espiralada, estudando os casos. Os resultados indicam boa potencialidade da mediação tecnológica, no âmbito do diálogo-problematizador e empowerment, para este tipo de trabalho escolar colaborativo a distância.Through the wiki Moodle, we developed distance education activities in the Physics Course at UFSM, aiming at producing a hypermedia school subject related to the discipline Physics 2 structuring teaching theme: Heat, Environment and uses of Energy (coming from the PCN+, placing the problematic dialogue in the transversal theme "Environment". We designed this activity, described as a collaborative production of hypermedia for scientific-technological dissemination, over the period of school discipline Didactic I from the Physics Course. The working group mediated by the wiki Moodle has been implemented through the PEA (Planning, Execution, and Assessment. The results are positive on the use of technology mediation concerning problematic dialogue and empowerment, in this type of collaborative and distance education.

  1. Collaborative Knowledge Building with Wikis: The Impact of Redundancy and Polarity

    Science.gov (United States)

    Moskaliuk, Johannes; Kimmerle, Joachim; Cress, Ulrike

    2012-01-01

    Wikis as shared digital artifacts may enable users to participate in processes of knowledge building. To what extent and with which quality knowledge building can take place is assumed to depend on the interrelation between people's prior knowledge and the information available in a wiki. In two experimental studies we examined the impact on…

  2. Students' Engagement with a Collaborative Wiki Tool Predicts Enhanced Written Exam Performance

    Science.gov (United States)

    Stafford, Tom; Elgueta, Herman; Cameron, Harriet

    2014-01-01

    We introduced voluntary wiki-based exercises to a long-running cognitive psychology course, part of the core curriculum for an undergraduate degree in psychology. Over 2 yearly cohorts, students who used the wiki more also scored higher on the final written exam. Using regression analysis, it is possible to account for students' tendency to score…

  3. Scaffolding Strategies for Wiki-Based Collaboration: Action Research in a Multicultural Japanese Language Program

    Science.gov (United States)

    Jung, Insung; Suzuki, Yoko

    2015-01-01

    Wikis can be used to encourage and support collaborative constructivist learning. However, their effectiveness depends upon the use of scaffolding strategies to guide the students in their use. This action research investigated three scaffolding strategies for wiki-based multicultural Japanese language learning: worked examples, grouping and peer…

  4. Use of a Wiki-Based Software to Manage Research Group Activities

    Science.gov (United States)

    Wang, Ting; Vezenov, Dmitri V.; Simboli, Brian

    2014-01-01

    This paper discusses use of the wiki software Confluence to organize research group activities and lab resources. Confluence can serve as an electronic lab notebook (ELN), as well as an information management and collaboration tool. The article provides a case study in how researchers can use wiki software in "home-grown" fashion to…

  5. Wiki as a Corporate Learning Tool: Case Study for Software Development Company

    Science.gov (United States)

    Milovanovic, Milos; Minovic, Miroslav; Stavljanin, Velimir; Savkovic, Marko; Starcevic, Dusan

    2012-01-01

    In our study, we attempted to further investigate how Web 2.0 technologies influence workplace learning. Our particular interest was on using Wiki as a tool for corporate exchange of knowledge with the focus on informal learning. In this study, we collaborated with a multinational software development company that uses Wiki as a corporate tool…

  6. The Ecosystem Factor in Supporting Wiki Initiative for Knowledge Sharing in Malaysian Public Organisation

    Science.gov (United States)

    Khuzaimah, Khairil Hizar Md; Affandi, Haryanti Mohd; Hassan, Fadzil

    2015-01-01

    The purpose of this paper is to highlight the significance of considering the organizational ecosystem in implementing wikis for knowledge sharing.The findings suggest that a prerequisite of an effective wiki is the appreciation of the factors that make up the organizational ecosystem; technical and organizational factors are variable elements of…

  7. Investigating Technical and Pedagogical Usability Issues of Collaborative Learning with Wikis

    Science.gov (United States)

    Hadjerrouit, Said

    2012-01-01

    Wikis have been recently promoted as tools that foster collaborative learning. However, there has been little research devoted to the criteria that are suitable to address issues pertinent to collaborative learning. This paper proposes a set of criteria to explore technical and pedagogical usability issues of collaborative learning with wikis. The…

  8. Analysis of tag-based Recommendation Performance for a Semantic Wiki

    DEFF Research Database (Denmark)

    Durao, Frederico; Dolog, Peter

    2009-01-01

    Recommendations play a very important role for revealing related topics addressed in the wikis beyond the currently viewed page. In this paper, we extend KiWi, a semantic wiki with three different recommendation approaches. The first approach is implemented as a traditional tag-based retrieval, t...

  9. Students' Engagement with a Collaborative Wiki Tool Predicts Enhanced Written Exam Performance

    Science.gov (United States)

    Stafford, Tom; Elgueta, Herman; Cameron, Harriet

    2014-01-01

    We introduced voluntary wiki-based exercises to a long-running cognitive psychology course, part of the core curriculum for an undergraduate degree in psychology. Over 2 yearly cohorts, students who used the wiki more also scored higher on the final written exam. Using regression analysis, it is possible to account for students' tendency to…

  10. Beyond WikiLeaks implications for the future of communications, journalism and society

    CERN Document Server

    Brevini, Benedetta; McCurdy, Patrick

    2013-01-01

    The 2010 release of US embassy diplomatic cables put WikiLeaks into the international spotlight. Revelations by the leaks sparked intense debate within international diplomacy, journalism and society. This book reflects on the implications of WikiLeaks across politics and media, and on the results of leak journalism and transparency activism.

  11. Writing with Wikis: A Cautionary Tale of Technology in the Classroom

    Science.gov (United States)

    Allwardt, Debra E.

    2011-01-01

    Learning to write a scholarly literature review is often difficult for undergraduate students. This teaching note examines a pilot study of BSW students' use of a wiki to collaboratively write a literature review in a research course (N=36). Students expressed negative responses toward the assignment and were reluctant to use the wiki. Their…

  12. Scaffolding Strategies for Wiki-Based Collaboration: Action Research in a Multicultural Japanese Language Program

    Science.gov (United States)

    Jung, Insung; Suzuki, Yoko

    2015-01-01

    Wikis can be used to encourage and support collaborative constructivist learning. However, their effectiveness depends upon the use of scaffolding strategies to guide the students in their use. This action research investigated three scaffolding strategies for wiki-based multicultural Japanese language learning: worked examples, grouping and peer…

  13. Wiki as a Corporate Learning Tool: Case Study for Software Development Company

    Science.gov (United States)

    Milovanovic, Milos; Minovic, Miroslav; Stavljanin, Velimir; Savkovic, Marko; Starcevic, Dusan

    2012-01-01

    In our study, we attempted to further investigate how Web 2.0 technologies influence workplace learning. Our particular interest was on using Wiki as a tool for corporate exchange of knowledge with the focus on informal learning. In this study, we collaborated with a multinational software development company that uses Wiki as a corporate tool…

  14. Wiki og læringsstier gav overblik på kursus i entrepreneurship

    DEFF Research Database (Denmark)

    Rasmussen, Pia

    2010-01-01

    Om on-lineredskaber som wiki og læringstier som redskaber i procesorienteret undervisning i entreprenørskab.......Om on-lineredskaber som wiki og læringstier som redskaber i procesorienteret undervisning i entreprenørskab....

  15. Students' Confidence and Perceived Value for Participating in Cross-Cultural Wiki-Based Collaborations

    Science.gov (United States)

    Ertmer, Peggy A.; Newby, Timothy J.; Liu, Wei; Tomory, Annette; Yu, Ji Hyun; Lee, Young Mi

    2011-01-01

    An international wiki-based collaboration was integrated into a large introductory educational technology course enrolling 346 students, divided into 43 teams. Student teams participated in a 5-week project in which they created wiki chapters about the educational uses of specific Web 2.0 tools. Two to four international students, located in their…

  16. Assessing Collaboration in a Wiki: The Reliability of University Students' Peer Assessment

    Science.gov (United States)

    De Wever, Bram; Van Keer, Hilde; Schellens, Tammy; Valcke, Martin

    2011-01-01

    This study focuses on the reliability of intra-group peer assessment (PA) of the collaboration processes in a wiki. First-year university students (N = 659) were subdivided in groups of 8 to create wikis. They were to assess their group members on four criteria (contribution, discussion, sources, and social). The main research question focused on…

  17. USING WIKIS AS A SUPPORT AND ASSESSMENT TOOL IN COLLABORATIVE DIGITAL GAME-BASED LEARNING ENVIRONMENTS

    Directory of Open Access Journals (Sweden)

    Yavuz SAMUR

    2011-04-01

    Full Text Available In computer-supported collaborative learning (CSCL environments, there are many researches done on collaborative learning activities; however, in game-based learning environments, more research and literature on collaborative learning activities are required. Actually, both game-based learning environments and wikis enable us to use new chances for learning, especially in collaborative learning activities. Therefore, in this paper, related literature on wikis and how game & instructional designers can leverage from wikis in game-based learning settings for enhancing students’ collaborative learning activities are examined. Based on the reviewed literature, two main suggestions are given in this paper with their underlying reasons. First, using wikis as a support tool for enhancing collaboration in digital game-based learning (DGBL environments, and second using wikis as an assessment tool in DGBL are suggested.

  18. Study on University Knowledge Management Based on Wiki%基于 Wiki 的高校知识管理研究

    Institute of Scientific and Technical Information of China (English)

    王永卫

    2012-01-01

      高校知识管理不仅对于提高高校的整体竞争力,而且对于高校的发展,都起着很重要的作用。但是,目前来看,对高校知识管理的实施并不太好。首先分析了高校知识管理存在的障碍因素,介绍了 Wiki 所具有的特点,特别是其具有知识管理的社会功能,指出了将 Wiki 引入高校知识管理的可行性,并对基于 Wiki 的高校知识管理的意义进行了阐述,最后提出了基于 Wiki 的高校知识管理模型构想。%  University knowledge management not only for improving the overall competitiveness of the universities, but also for the development of colleges and universities play a very important role. However, the present situation, the implementation of the university knowledge management is not good enough. The article first analyzes the university knowledge management barriers,described the characteristics of Wiki, and described the social function of knowledge management, Pointed out the Wiki the feasibility of the university knowledge management, and a Wiki-based Knowledge Management in Higher significance was explained, proposed a Wiki-based Knowledge Management in Higher model idea.

  19. Plant interactions with multiple insect herbivores: from community to genes

    NARCIS (Netherlands)

    Stam, J.M.; Kroes, A.; Li, Y.; Gols, R.; Loon, van J.J.A.; Poelman, E.H.; Dicke, M.

    2014-01-01

    Every plant is a member of a complex insect community that consists of tens to hundreds of species that belong to different trophic levels. The dynamics of this community are critically influenced by the plant, which mediates interactions between community members that can occur on the plant simulta

  20. Plant interactions with multiple insect herbivores: from community to genes

    NARCIS (Netherlands)

    Stam, J.M.; Kroes, A.; Li, Y.; Gols, R.; Loon, van J.J.A.; Poelman, E.H.; Dicke, M.

    2014-01-01

    Every plant is a member of a complex insect community that consists of tens to hundreds of species that belong to different trophic levels. The dynamics of this community are critically influenced by the plant, which mediates interactions between community members that can occur on the plant

  1. [Radiological knowledge management with the help of departmental wikis].

    Science.gov (United States)

    Schuster, A; Brachthäuser, D; Mansour, M; Alfke, H

    2016-09-01

    In times of RIS (radiology information system) and KIS (hospital information system) systems, patient-related data are at the radiologist's disposal at the push of a button. However, this is not the case for other important data. The increasing complexity of modern medicine demands that up-to-date information like protocols, SOPs (Standards of Practice), news and modifications are constantly accessible to all employees. This aspect of quality assurance becomes increasingly important in the context of certification. For such knowledge management purposes we have built a wiki in our department. Here we report our positive experiences with this technology.

  2. Wikis y el nuevo estudiante de lenguas extranjeras

    Directory of Open Access Journals (Sweden)

    Ana Gimeno Sanz

    2010-01-01

    Full Text Available Los entornos digitales cada vez son más comunes en la enseñanza de lenguas extranjeras, además de jugar un papel muy importante como organizadores de tareas, proveedores de input y como gestores de recursos para la enseñanza de idiomas. Permiten, asimismo, a los profesores organizar la interacción de los estudiantes y, al mismo tiempo, proporcionar un magnífico entorno para presentar distintos géneros informativos. Las wikis son hoy en día una de las redes sociales que cada vez se utilizan más para dar apoyo al aprendizaje cooperativo y para fomentar el aprendizaje autónomo. Están estrechamente relacionadas con las metodologías docentes que se basan en el desarrollo de un proyecto o en la resolución de problemas, prácticas docentes éstas en las que tanto alumnos como profesores contribuyen a la construcción del conocimiento y comparten experiencias. Las wikis también han contribuido a crear las llamadas "comunidades de práctica", a las que pueden acudir los estudiantes en contextos de autoaprendizaje o en aquellas situaciones donde se carece del apoyo de un tutor o profesor para encontrar apoyo y consejo. Añadido a esto, la proliferación de herramientas que fomentan la comunicación mediatizada por ordenador han multiplicado los métodos docentes que se aplican en el aula y fuera de ella y han tenido una influencia muy significativa en el surgimiento de un nuevo perfil de estudiante; es decir, aquél que está plenamente acostumbrado a utilizar estas herramientas para relacionarse socialmente con otras personas aunque no sea con fines educativos. Por último, mediante el uso de las wikis se ha desarrollado el concepto de "enseñanza entre pares" y "tutorización entre pares", especialmente en contextos de creación de textos escritos mediante la cooperación colectiva. Este hecho ha contribuido, asimismo, a que el estudiante tenga mayor conciencia de los procesos implícitos en la construcción y edición textual. Este cap

  3. Bacterial community and arsenic functional genes diversity in arsenic contaminated soils from different geographic locations

    Science.gov (United States)

    Gu, Yunfu; D. Van Nostrand, Joy; Wu, Liyou; He, Zhili; Qin, Yujia; Zhao, Fang-Jie; Zhou, Jizhong

    2017-01-01

    To understand how soil microbial communities and arsenic (As) functional genes respond to soil arsenic (As) contamination, five soils contaminated with As at different levels were collected from diverse geographic locations, incubated for 54 days under flooded conditions, and examined by both MiSeq sequencing of 16S rRNA gene amplicons and functional gene microarray (GeoChip 4.0). The results showed that both bacterial community structure and As functional gene structure differed among geographical locations. The diversity of As functional genes correlated positively with the diversity of 16S rRNA genes (Pcontaminated with different levels of As at different geographic locations, and the impact of environmental As contamination on the soil bacterial community. PMID:28475654

  4. Robust detection of hierarchical communities from Escherichia coli gene expression data.

    Directory of Open Access Journals (Sweden)

    Santiago Treviño

    Full Text Available Determining the functional structure of biological networks is a central goal of systems biology. One approach is to analyze gene expression data to infer a network of gene interactions on the basis of their correlated responses to environmental and genetic perturbations. The inferred network can then be analyzed to identify functional communities. However, commonly used algorithms can yield unreliable results due to experimental noise, algorithmic stochasticity, and the influence of arbitrarily chosen parameter values. Furthermore, the results obtained typically provide only a simplistic view of the network partitioned into disjoint communities and provide no information of the relationship between communities. Here, we present methods to robustly detect co-regulated and functionally enriched gene communities and demonstrate their application and validity for Escherichia coli gene expression data. Applying a recently developed community detection algorithm to the network of interactions identified with the context likelihood of relatedness (CLR method, we show that a hierarchy of network communities can be identified. These communities significantly enrich for gene ontology (GO terms, consistent with them representing biologically meaningful groups. Further, analysis of the most significantly enriched communities identified several candidate new regulatory interactions. The robustness of our methods is demonstrated by showing that a core set of functional communities is reliably found when artificial noise, modeling experimental noise, is added to the data. We find that noise mainly acts conservatively, increasing the relatedness required for a network link to be reliably assigned and decreasing the size of the core communities, rather than causing association of genes into new communities.

  5. Functional gene composition, diversity and redundancy in microbial stream biofilm communities.

    Directory of Open Access Journals (Sweden)

    Andrew Dopheide

    Full Text Available We surveyed the functional gene composition and diversity of microbial biofilm communities in 18 New Zealand streams affected by different types of catchment land use, using a comprehensive functional gene array, GeoChip 3.0. A total of 5,371 nutrient cycling and energy metabolism genes within 65 gene families were detected among all samples (342 to 2,666 genes per stream. Carbon cycling genes were most common, followed by nitrogen cycling genes, with smaller proportions of sulphur, phosphorus cycling and energy metabolism genes. Samples from urban and native forest streams had the most similar functional gene composition, while samples from exotic forest and rural streams exhibited the most variation. There were significant differences between nitrogen and sulphur cycling genes detected in native forest and urban samples compared to exotic forest and rural samples, attributed to contrasting proportions of nitrogen fixation, denitrification, and sulphur reduction genes. Most genes were detected only in one or a few samples, with only a small minority occurring in all samples. Nonetheless, 42 of 65 gene families occurred in every sample and overall proportions of gene families were similar among samples from contrasting streams. This suggests the existence of functional gene redundancy among different stream biofilm communities despite contrasting taxonomic composition.

  6. Functional gene composition, diversity and redundancy in microbial stream biofilm communities.

    Science.gov (United States)

    Dopheide, Andrew; Lear, Gavin; He, Zhili; Zhou, Jizhong; Lewis, Gillian D

    2015-01-01

    We surveyed the functional gene composition and diversity of microbial biofilm communities in 18 New Zealand streams affected by different types of catchment land use, using a comprehensive functional gene array, GeoChip 3.0. A total of 5,371 nutrient cycling and energy metabolism genes within 65 gene families were detected among all samples (342 to 2,666 genes per stream). Carbon cycling genes were most common, followed by nitrogen cycling genes, with smaller proportions of sulphur, phosphorus cycling and energy metabolism genes. Samples from urban and native forest streams had the most similar functional gene composition, while samples from exotic forest and rural streams exhibited the most variation. There were significant differences between nitrogen and sulphur cycling genes detected in native forest and urban samples compared to exotic forest and rural samples, attributed to contrasting proportions of nitrogen fixation, denitrification, and sulphur reduction genes. Most genes were detected only in one or a few samples, with only a small minority occurring in all samples. Nonetheless, 42 of 65 gene families occurred in every sample and overall proportions of gene families were similar among samples from contrasting streams. This suggests the existence of functional gene redundancy among different stream biofilm communities despite contrasting taxonomic composition.

  7. Community specificity: life and afterlife effects of genes.

    Science.gov (United States)

    Whitham, Thomas G; Gehring, Catherine A; Lamit, Louis J; Wojtowicz, Todd; Evans, Luke M; Keith, Arthur R; Smith, David Solance

    2012-05-01

    Community-level genetic specificity results when individual genotypes or populations of the same species support different communities. Our review of the literature shows that genetic specificity exhibits both life and afterlife effects; it is a widespread phenomenon occurring in diverse taxonomic groups, aquatic to terrestrial ecosystems, and species-poor to species-rich systems. Such specificity affects species interactions, evolution, ecosystem processes and leads to community feedbacks on the performance of the individuals expressing the traits. Thus, genetic specificity by communities appears to be fundamentally important, suggesting that specificity is a major driver of the biodiversity and stability of the world's ecosystems.

  8. Experiences of Wiki topic teaching in postgraduate orthodontics: what do the learners think?

    Science.gov (United States)

    Ireland, A J; Atack, N E; Sandy, J R

    2013-02-01

    Traditionally, the academic content of many 3-year full-time postgraduate courses in orthodontics in the UK has been delivered using tutorial and lecture-based teaching. This is often teacher lead rather than learner centred. Even with the advent of teaching modules on the national virtual learning environment, although well liked by students, is still often teacher lead. An alternative on-line approach to learner-centred teaching is to use Wikis. Nine postgraduate students in the first term of their full-time 3-year specialist training programme at Bristol Dental School were divided into three groups and wrote a Wiki on three interrelated topics. This process was repeated in the second term using three different, but still interrelated topics. Following each, they were asked to give detailed feedback on their Wiki topic teaching. The results showed that students felt writing the Wikis was useful for team work, provided a more learner-centred approach, created a body of work in a live format that would be useful for revision and was a welcome variation on traditional teaching methods. The biggest problem encountered was the IT platform used to create the Wikis. The students also felt the Wikis should be assessed as a piece of group work rather than as separate individuals. Wiki topic teaching is a useful tool in the teaching of postgraduate orthodontics providing variation and a more learner-centred approach. Further exploration of the available IT platforms is required. © 2012 John Wiley & Sons A/S.

  9. BOWiki: an ontology-based wiki for annotation of data and integration of knowledge in biology

    Directory of Open Access Journals (Sweden)

    Gregorio Sergio E

    2009-05-01

    Full Text Available Abstract Motivation Ontology development and the annotation of biological data using ontologies are time-consuming exercises that currently require input from expert curators. Open, collaborative platforms for biological data annotation enable the wider scientific community to become involved in developing and maintaining such resources. However, this openness raises concerns regarding the quality and correctness of the information added to these knowledge bases. The combination of a collaborative web-based platform with logic-based approaches and Semantic Web technology can be used to address some of these challenges and concerns. Results We have developed the BOWiki, a web-based system that includes a biological core ontology. The core ontology provides background knowledge about biological types and relations. Against this background, an automated reasoner assesses the consistency of new information added to the knowledge base. The system provides a platform for research communities to integrate information and annotate data collaboratively. Availability The BOWiki and supplementary material is available at http://www.bowiki.net/. The source code is available under the GNU GPL from http://onto.eva.mpg.de/trac/BoWiki.

  10. WikiGIS Basic Concepts: Web 2.0 for Geospatial Collaboration

    Directory of Open Access Journals (Sweden)

    Mathieu Rondeau

    2012-03-01

    Full Text Available With the emergence of Web 2.0, new applications arise and evolve into more interactive forms of collective intelligence. These applications offer to both professionals and citizens an open and expanded access to geographic information. In this paper, we develop the conceptual foundations of a new technology solution called WikiGIS. WikiGIS’s strength lies in its ability to ensure the traceability of changes in spatial-temporal geographic components (geometric location and shape, graphics: iconography and descriptive generated by users. The final use case highlights to what extent WikiGIS could be a relevant and useful technological innovation in Geocollaboration.

  11. Use and acceptance of Wiki systems for students of veterinary medicine.

    Science.gov (United States)

    Kolski, Darius; Arlt, Sebastian; Birk, Stephan; Heuwieser, Wolfgang

    2013-01-01

    Zielsetzung: Wiki-Systeme gewinnen im universitären Bereich überwiegend bei jungen Nutzern an Bedeutung. Anhand einer Umfrage sollte untersucht werden, wie Studierende der Tiermedizin Wiki-Systeme bisher nutzen, ob sie ein fachspezifisches, tiermedizinisches Wiki-System als sinnvoll erachten und wie hoch die Bereitschaft zur Mitgestaltung ist.Methodik: Die Datenerhebung erfolgte als empirische Untersuchung mit Hilfe eines Fragebogens, der Studierenden (n=210) des Fachbereiches Veterinärmedizin (Freie Universität Berlin) ausgehändigt wurde. Der Fragebogen enthielt Fragen zur Nutzung von Wikipedia allgemein und für den universitären Gebrauch und zur Nutzung und Akzeptanz von speziellen tiermedizinischen Wiki-Systemen. Ergebnisse: Die meisten Befragten hatten vorwiegend Leseerfahrungen mit Wikipedia und tiermedizinischen Wiki-Systemen, vor allem jüngere Semester. Im Gegensatz dazu war die aktive Nutzung hinsichtlich Schreiben oder Verändern von Informationen gering (8,6% Wikipedia, 15,3% tiermedizinische Wiki-Systeme). Sie war bei männlichen Nutzern (p=0,008) und in höheren Semestern (7,4% Anteil am 7. Semester) stärker vorhanden. Die bisherige Nutzung universitär genutzter tiermedizinischer Wiki-Systeme war ebenfalls gering. Die Mehrheit der Studierenden (96,2%) gab jedoch an, tiermedizinische Wiki-Systeme als Informationsmedium (d.h. passiv) in Zukunft nutzen zu wollen. Auch hier wurde eine niedrige Bereitschaft zur aktiven Erstellung von Inhalten angegeben. Allerdings erwarten viele Studierende beim Verfassen eigener Texte einen größeren Lernerfolg. Ein Vertrauen in die Informationsqualität eines Wiki-Systems ist bei den Studierenden grundsätzlich vorhanden. Schlussfolgerung: Die Einschätzung der Wiki-Systeme als nützliche Nachschlagewerke (94,8%) und die Befürwortung tiermedizinischer Wiki-Systeme (95,7%) lässt eine erfolgreiche Etablierung von veterinärmedizinischen Wiki-Systemen erwarten. Hierbei sollten insbesondere Methoden zur Erh

  12. Improving Critical Skills Using Wikis and CGPS in a Physics Classroom

    Science.gov (United States)

    Mohottala, H. E.

    2016-10-01

    We report the combined use of Wikispaces (wikis) and collaborative group problem solving (CGPS) sessions conducted in introductory-level calculus-based physics classes. As a part of this new teaching tool, some essay-type problems were posted on the wiki page on a weekly basis and students were encouraged to participate in problem solving without providing numerical final answers but only the steps. Each week students were further evaluated on problem solving skills, opening up more opportunity for peer interaction through CGPS. Students developed a set of skills in decision making, problem solving, communication, negotiation, critical and independent thinking, and teamwork through the combination of wikis and CGPS.

  13. 基于Wiki-IC的知识服务研究

    Institute of Scientific and Technical Information of China (English)

    余波

    2011-01-01

    Wiki-IC是信息共享空间(IC)的Wiki化,是在虚拟层面建立信息共享空间的知识服务模式的创新.文章以Wiki为应用平台,在分析Wiki知识构建特征的基础上,研究Wiki-IC的构成要素、工作原理、知识服务内容等方面,最后对Wiki-IC存在的问题作出了探讨.

  14. Center for fetal monkey gene transfer for heart, lung, and blood diseases: an NHLBI resource for the gene therapy community.

    Science.gov (United States)

    Tarantal, Alice F; Skarlatos, Sonia I

    2012-11-01

    The goals of the National Heart, Lung, and Blood Institute (NHLBI) Center for Fetal Monkey Gene Transfer for Heart, Lung, and Blood Diseases are to conduct gene transfer studies in monkeys to evaluate safety and efficiency; and to provide NHLBI-supported investigators with expertise, resources, and services to actively pursue gene transfer approaches in monkeys in their research programs. NHLBI-supported projects span investigators throughout the United States and have addressed novel approaches to gene delivery; "proof-of-principle"; assessed whether findings in small-animal models could be demonstrated in a primate species; or were conducted to enable new grant or IND submissions. The Center for Fetal Monkey Gene Transfer for Heart, Lung, and Blood Diseases successfully aids the gene therapy community in addressing regulatory barriers, and serves as an effective vehicle for advancing the field.

  15. Primer Sets Developed for Functional Genes Reveal Shifts in Functionality of Fungal Community in Soils

    NARCIS (Netherlands)

    Hannula, S.E.; van Veen, J.A.

    2016-01-01

    Phylogenetic diversity of soil microbes is a hot topic at the moment. However, the molecular tools for the assessment of functional diversity in the fungal community are less developed than tools based on genes encoding the ribosomal operon. Here 20 sets of primers targeting genes involved mainly in

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

    Institute of Scientific and Technical Information of China (English)

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

    2008-01-01

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

  17. Students’ engagement with a collaborative wiki tool predicts enhanced written exam performance

    Directory of Open Access Journals (Sweden)

    Tom Stafford

    2014-08-01

    Full Text Available We introduced voluntary wiki-based exercises to a long-running cognitive psychology course, part of the core curriculum for an undergraduate degree in psychology. Over 2 yearly cohorts, students who used the wiki more also scored higher on the final written exam. Using regression analysis, it is possible to account for students’ tendency to score well on other psychology exams, thus statistically removing some obvious candidate third factors, such as general talent or enthusiasm for psychology, which might drive this correlation. Such an analysis shows that both high- and low-grading students who used the wiki got higher scores on the final exam, with engaged wiki users scoring an average of an extra 5 percentage points. We offer an interpretation of the mechanisms of action in terms of the psychological literature on learning and memory.

  18. Development of generic and strategic skills through a wiki platform in industrial engineering programs

    Directory of Open Access Journals (Sweden)

    L. Celorrio-Barragué

    2016-03-01

    Full Text Available This paper describes the collaborative learning task carried out in the framework of a Strength of Materials course in an undergraduate degree program in Industrial Engineering using a wiki platform as a support tool. Stages of the teaching/learning process are described. These are: organization of the wiki to host the work of student groups, creation of working groups and assignation of projects, delivery of guidance material and model, editing the project and publishing pages on the wiki, assessments performed using rubrics, and the results obtained. The wiki platform provides interesting statistics for evaluating cooperation between students and time variation of students’ effort. The final quality of the projects is very high because a midterm evaluation in the form of a “peer review rubric” is carried out. Then, students improve their projects. The paper concludes by gathering the opinions made by students; the benefits provided by this teaching experience are then analyzed.

  19. Paper-pen peer-correction versus wiki-based peer-correction

    Directory of Open Access Journals (Sweden)

    Froldova Vladimira

    2016-01-01

    Full Text Available This study reports on the comparison of the students’ achievement and their attitudes towards the use of paper-pen peer-correction and wiki-based peer-correction within English language lessons and CLIL Social Science lessons at the higher secondary school in Prague. Questionnaires and semi-structured interviews were utilized to gather information. The data suggests that students made considerable use of wikis and showed higher degrees of motivation in wiki-based peer-correction during English language lessons than in CLIL Social Science lessons. In both cases wikis not only contributed to developing students’ writing skills, but also helped students recognize the importance of collaboration.

  20. Primer Sets Developed for Functional Genes Reveal Shifts in Functionality of Fungal Community in Soils

    Science.gov (United States)

    Hannula, S. Emilia; van Veen, Johannes A.

    2016-01-01

    Phylogenetic diversity of soil microbes is a hot topic at the moment. However, the molecular tools for the assessment of functional diversity in the fungal community are less developed than tools based on genes encoding the ribosomal operon. Here 20 sets of primers targeting genes involved mainly in carbon cycling were designed and/or validated and the functioning of soil fungal communities along a chronosequence of land abandonment from agriculture was evaluated using them. We hypothesized that changes in fungal community structure during secondary succession would lead to difference in the types of genes present in soils and that these changes would be directional. We expected an increase in genes involved in degradation of recalcitrant organic matter in time since agriculture. Out of the investigated genes, the richness of the genes related to carbon cycling was significantly higher in fields abandoned for longer time. The composition of six of the genes analyzed revealed significant differences between fields abandoned for shorter and longer time. However, all genes revealed significant variance over the fields studied, and this could be related to other parameters than the time since agriculture such as pH, organic matter, and the amount of available nitrogen. Contrary to our initial hypothesis, the genes significantly different between fields were not related to the decomposition of more recalcitrant matter but rather involved in degradation of cellulose and hemicellulose. PMID:27965632

  1. Primer Sets Developed for Functional Genes Reveal Shifts in Functionality of Fungal Community in Soils.

    Science.gov (United States)

    Hannula, S Emilia; van Veen, Johannes A

    2016-01-01

    Phylogenetic diversity of soil microbes is a hot topic at the moment. However, the molecular tools for the assessment of functional diversity in the fungal community are less developed than tools based on genes encoding the ribosomal operon. Here 20 sets of primers targeting genes involved mainly in carbon cycling were designed and/or validated and the functioning of soil fungal communities along a chronosequence of land abandonment from agriculture was evaluated using them. We hypothesized that changes in fungal community structure during secondary succession would lead to difference in the types of genes present in soils and that these changes would be directional. We expected an increase in genes involved in degradation of recalcitrant organic matter in time since agriculture. Out of the investigated genes, the richness of the genes related to carbon cycling was significantly higher in fields abandoned for longer time. The composition of six of the genes analyzed revealed significant differences between fields abandoned for shorter and longer time. However, all genes revealed significant variance over the fields studied, and this could be related to other parameters than the time since agriculture such as pH, organic matter, and the amount of available nitrogen. Contrary to our initial hypothesis, the genes significantly different between fields were not related to the decomposition of more recalcitrant matter but rather involved in degradation of cellulose and hemicellulose.

  2. Primer sets developed for fungal functional genes reveal shifts in functionality of fungal community in soils

    Directory of Open Access Journals (Sweden)

    Emilia Silja Hannula

    2016-11-01

    Full Text Available Phylogenetic diversity of soil microbes is a hot topic at the moment. However, the molecular tools for the assessment of functional diversity in the fungal community are less developed than tools based on genes encoding the ribosomal operon. Here 20 sets of primers targeting genes involved mainly in carbon cycling were designed and/or validated and the functioning of soil fungal communities along a chronosequence of land abandonment from agriculture was evaluated using them. We hypothesized that changes in fungal community structure during secondary succession would lead to difference in the types of genes present in soils and that these changes would be directional. We expected an increase in genes involved in degradation of recalcitrant organic matter in time since agriculture. Out of the investigated genes, the richness of the genes related to carbon cycling was significantly higher in fields abandoned for longer time. The composition of six of the genes analyzed revealed significant differences between fields abandoned for shorter and longer time. However, all genes revealed significant variance over the fields studied, and this could be related to other parameters than the time since agriculture such as pH, organic matter and the amount of available nitrogen. Contrary to our initial hypothesis, the genes significantly different between fields were not related to the decomposition of more recalcitrant matter but rather involved in degradation of cellulose and hemicellulose.

  3. Evaluating Wiki as a tool to promote quality academic writing skills

    OpenAIRE

    Wheeler, Steve; Wheeler, Dawn

    2007-01-01

    In this study we investigated undergraduate teacher trainees' use of wikis, focusing on the use of shared spaces to communicate ideas and generate course specific content. We explored how students, through such activities, were to able to improve their academic writing skills. We discuss writing as a social practice and discuss how wikis might promote better academic writing. With data derived from student discussion boards and a post-module e-mail questionnaire (N=35) our findings indicate t...

  4. Developing Student Science and Information Literacy through Contributions to the Society of Exploration Geophysicists (SEG) Wiki

    Science.gov (United States)

    Guertin, L. A.; Farley, I.; Geary, A.

    2016-12-01

    Introductory-level Earth science courses provide the opportunity for science and non-science majors to expand discipline-specific content knowledge while enhancing skill sets applicable to all disciplines. The outcomes of the student work can then benefit the education and outreach efforts of an international organization - in this case, a wiki devoted exclusively to the geosciences, managed by the Society of Exploration Geophysicists (SEG). The course Environment Earth at Penn State Brandywine is a general education science course with the overarching course goal for students to understand, communicate examples, and make informed decisions relating to big ideas and fundamental concepts of Earth science. To help accomplish this goal, students carry out a semester-long digital engaged scholarship project that benefits the users of the SEG Wiki (http://wiki.seg.org/). To begin with developing the literacy of students and their ability to read, interpret, and evaluate sources of scientific news, the first assignment requires students to write an annotated bibliography on a specific topic that serves as the foundation for a new SEG Wiki article. Once students have collected and summarized information from reliable sources, students learn how writing for a wiki is different than writing a term paper and begin drafting their wiki page. Students peer review each other's work for content and clarity before publishing their work on the SEG wiki. Students respond positively to this project, reporting a better understanding of and respect towards the authors of online wiki pages, as well as an overall satisfaction of knowing their work will benefit others. Links to student-generated pages and instructional materials can be found at: http://sites.psu.edu/segwiki/.

  5. CSIR at INEX 2008 Link-the-Wiki Track

    Science.gov (United States)

    Lu, Wei; Liu, Dan; Fu, Zhenzhen

    In this paper, we describe methods taken by CSIR in the INEX 2008 Link-the-Wiki track. For the incoming link detection, we use p(d|t), the probability to generate a document, when given the topic file, to judge which documents are proper link sources for the given topic. For the file-to-file task of outgoing link detection, we take a two-step approach: first, we identify a group of candidate target documents by literally matching the topic file title and document content; then, candidate documents are ranked by the number of incoming links. For the anchor-to-BEP task, we use p(d|a,t), the probability to generate a document, when given the topic file and an anchor name, to select anchors and link targets for a given topic.

  6. The Use of a Wiki to Facilitate Collaborative Learning in a South African Physiotherapy Department

    Directory of Open Access Journals (Sweden)

    M. Rowe

    2012-12-01

    Full Text Available The dominant form of teaching in higher education remains the lecture,even though evidence suggests that it alone is inadequate to facilitate the development ofthe higher order thinking skills required in clinical practice. The use of wikis may have a roleto play in facilitating collaborative learning practices that are important for professionaldevelopment. This descriptive survey evaluated the use of a wiki for a collaborative learningactivity within small groups of undergraduate physiotherapy students in a South Africanuniversity. Students participated in a wiki-based assignment and were then surveyedusing open- and closed-ended questions to determine their perceptions and experiences of the process. The results indicate thatalthough a wiki can be used to develop relevant content, there were significant challenges in its implementation. These included apoor understanding by students of how to work effectively in groups, a lack of physical and epistemological access to the internet,and the need for adequate preparation and support. Some features of the wiki were found to have an impact on the quality ofthe work produced, including the use of Discussion pages, peer review, and the public nature of the wiki. The conclusion is thatwikis may have a role to play in collaborative groupwork, but that that students need to be adequately prepared and supportedthroughout the process.

  7. Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community.

    Science.gov (United States)

    Hemme, Christopher L; Green, Stefan J; Rishishwar, Lavanya; Prakash, Om; Pettenato, Angelica; Chakraborty, Romy; Deutschbauer, Adam M; Van Nostrand, Joy D; Wu, Liyou; He, Zhili; Jordan, I King; Hazen, Terry C; Arkin, Adam P; Kostka, Joel E; Zhou, Jizhong

    2016-04-05

    Unraveling the drivers controlling the response and adaptation of biological communities to environmental change, especially anthropogenic activities, is a central but poorly understood issue in ecology and evolution. Comparative genomics studies suggest that lateral gene transfer (LGT) is a major force driving microbial genome evolution, but its role in the evolution of microbial communities remains elusive. To delineate the importance of LGT in mediating the response of a groundwater microbial community to heavy metal contamination, representative Rhodanobacter reference genomes were sequenced and compared to shotgun metagenome sequences. 16S rRNA gene-based amplicon sequence analysis indicated that Rhodanobacter populations were highly abundant in contaminated wells with low pHs and high levels of nitrate and heavy metals but remained rare in the uncontaminated wells. Sequence comparisons revealed that multiple geochemically important genes, including genes encoding Fe(2+)/Pb(2+) permeases, most denitrification enzymes, and cytochrome c553, were native to Rhodanobacter and not subjected to LGT. In contrast, the Rhodanobacter pangenome contained a recombinational hot spot in which numerous metal resistance genes were subjected to LGT and/or duplication. In particular, Co(2+)/Zn(2+)/Cd(2+) efflux and mercuric resistance operon genes appeared to be highly mobile within Rhodanobacter populations. Evidence of multiple duplications of a mercuric resistance operon common to most Rhodanobacter strains was also observed. Collectively, our analyses indicated the importance of LGT during the evolution of groundwater microbial communities in response to heavy metal contamination, and a conceptual model was developed to display such adaptive evolutionary processes for explaining the extreme dominance of Rhodanobacter populations in the contaminated groundwater microbiome. Lateral gene transfer (LGT), along with positive selection and gene duplication, are the three main

  8. CYP1A1, GCLC, AGT, AGTR1 gene-gene interactions in community-acquired pneumonia pulmonary complications.

    Science.gov (United States)

    Salnikova, Lyubov E; Smelaya, Tamara V; Golubev, Arkadiy M; Rubanovich, Alexander V; Moroz, Viktor V

    2013-11-01

    This study was conducted to establish the possible contribution of functional gene polymorphisms in detoxification/oxidative stress and vascular remodeling pathways to community-acquired pneumonia (CAP) susceptibility in the case-control study (350 CAP patients, 432 control subjects) and to predisposition to the development of CAP complications in the prospective study. All subjects were genotyped for 16 polymorphic variants in the 14 genes of xenobiotics detoxification CYP1A1, AhR, GSTM1, GSTT1, ABCB1, redox-status SOD2, CAT, GCLC, and vascular homeostasis ACE, AGT, AGTR1, NOS3, MTHFR, VEGFα. Risk of pulmonary complications (PC) in the single locus analysis was associated with CYP1A1, GCLC and AGTR1 genes. Extra PC (toxic shock syndrome and myocarditis) were not associated with these genes. We evaluated gene-gene interactions using multi-factor dimensionality reduction, and cumulative gene risk score approaches. The final model which included >5 risk alleles in the CYP1A1 (rs2606345, rs4646903, rs1048943), GCLC, AGT, and AGTR1 genes was associated with pleuritis, empyema, acute respiratory distress syndrome, all PC and acute respiratory failure (ARF). We considered CYP1A1, GCLC, AGT, AGTR1 gene set using Set Distiller mode implemented in GeneDecks for discovering gene-set relations via the degree of sharing descriptors within a given gene set. N-acetylcysteine and oxygen were defined by Set Distiller as the best descriptors for the gene set associated in the present study with PC and ARF. Results of the study are in line with literature data and suggest that genetically determined oxidative stress exacerbation may contribute to the progression of lung inflammation.

  9. In situ gene expression in mixed-culture biofilms: Evidence of metabolic interactions between community members

    DEFF Research Database (Denmark)

    Møller, Søren; Sternberg, Claus; Andersen, Jens Bo;

    1998-01-01

    Microbial communities growing in laboratory-based pow chambers were investigated in order to study compartmentalization of specific gene expression. Among the community members studied, the focus,vas in particular on Pseudomonas putida and a strain of an Acinetobacter sp., and the genes studied...... are involved in the biodegradation of toluene and related aromatic compounds. The upper-pathway promoter (Pu) and the meta-pathway promoter (Pm) from the TOL plasmid were fused independently to the gene coding for the green fluorescent protein (GFP), and expression from these promoters was studied in P. putida......, which was a dominant community member. Biofilms were cultured in flow chambers, which in combination with scanning confocal laser microscopy allowed direct monitoring of promoter activity with single-cell spatial resolution. Expression from the Pu promoter was homogeneously induced by benzyl alcohol...

  10. Connected Gene Communities Underlie Transcriptional Changes in Cornelia de Lange Syndrome.

    Science.gov (United States)

    Boudaoud, Imène; Fournier, Éric; Baguette, Audrey; Vallée, Maxime; Lamaze, Fabien C; Droit, Arnaud; Bilodeau, Steve

    2017-09-01

    Cornelia de Lange syndrome (CdLS) is a complex multisystem developmental disorder caused by mutations in cohesin subunits and regulators. While its precise molecular mechanisms are not well defined, they point toward a global deregulation of the transcriptional gene expression program. Cohesin is associated with the boundaries of chromosome domains and with enhancer and promoter regions connecting the three-dimensional genome organization with transcriptional regulation. Here, we show that connected gene communities, structures emerging from the interactions of noncoding regulatory elements and genes in the three-dimensional chromosomal space, provide a molecular explanation for the pathoetiology of CdLS associated with mutations in the cohesin-loading factor NIPBL and the cohesin subunit SMC1A NIPBL and cohesin are important constituents of connected gene communities that are centrally positioned at noncoding regulatory elements. Accordingly, genes deregulated in CdLS are positioned within reach of NIPBL- and cohesin-occupied regions through promoter-promoter interactions. Our findings suggest a dynamic model where NIPBL loads cohesin to connect genes in communities, offering an explanation for the gene expression deregulation in the CdLS. Copyright © 2017 by the Genetics Society of America.

  11. “Build It and They Will Come?” A Case Study of the Use of a Wiki in a Higher Education Research Unit

    Directory of Open Access Journals (Sweden)

    Ting Yuan

    2010-08-01

    Full Text Available With collaborative web technologies such as wikis becoming increasingly popular in the workplace, this case study examined how workers at an education research unit within a graduate school of education perceive the wiki as a platform for communication and collaboration, and the extent to which they actually use a workplace wiki for that purpose. Twenty staff members, for whom a wiki was built, were surveyed, while records of their activities on the wiki over a 6-month period were retrieved and analyzed. Findings reveal that though most of these staff members have positive views towards the wiki as a space that can effectively promote information sharing and collaboration, they are not quite as enthusiastic about engaging the wiki as a medium for their daily collaborative work activities. The possible reasons for this discrepancy are discussed together with recommendations on the strategies similar organizations can adopt to help encourage and maximize wiki usage in the workplace.

  12. Wiki Laboratory Notebooks: Supporting Student Learning in Collaborative Inquiry-Based Laboratory Experiments

    Science.gov (United States)

    Lawrie, Gwendolyn Angela; Grøndahl, Lisbeth; Boman, Simon; Andrews, Trish

    2016-06-01

    Recent examples of high-impact teaching practices in the undergraduate chemistry laboratory that include course-based undergraduate research experiences and inquiry-based experiments require new approaches to assessing individual student learning outcomes. Instructors require tools and strategies that can provide them with insight into individual student contributions to collaborative group/teamwork throughout the processes of experimental design, data analysis, display and communication of their outcomes in relation to their research question(s). Traditional assessments in the form of laboratory notebooks or experimental reports provide limited insight into the processes of collaborative inquiry-based activities. A wiki environment offers a collaborative domain that can potentially support collaborative laboratory processes and scientific record keeping. In this study, the effectiveness of the wiki in supporting laboratory learning and assessment has been evaluated through analysis of the content and histories for three consenting, participating groups of students. The conversational framework has been applied to map the relationships between the instructor, tutor, students and laboratory activities. Analytics that have been applied to the wiki platform include: character counts, page views, edits, timelines and the extent and nature of the contribution by each student to the wiki. Student perceptions of both the role and the impact of the wiki on their experiences and processes have also been collected. Evidence has emerged from this study that the wiki environment has enhanced co-construction of understanding of both the experimental process and subsequent communication of outcomes and data. A number of features are identified to support success in the use of the wiki platform for laboratory notebooks.

  13. Education in health research methodology: use of a wiki for knowledge translation.

    Directory of Open Access Journals (Sweden)

    Michele P Hamm

    Full Text Available INTRODUCTION: A research-practice gap exists between what is known about conducting methodologically rigorous randomized controlled trials (RCTs and what is done. Evidence consistently shows that pediatric RCTs are susceptible to high risk of bias; therefore novel methods of influencing the design and conduct of trials are required. The objective of this study was to develop and pilot test a wiki designed to educate pediatric trialists and trainees in the principles involved in minimizing risk of bias in RCTs. The focus was on preliminary usability testing of the wiki. METHODS: The wiki was developed through adaptation of existing knowledge translation strategies and through tailoring the site to the identified needs of the end-users. The wiki was evaluated for usability and user preferences regarding the content and formatting. Semi-structured interviews were conducted with 15 trialists and systematic reviewers, representing varying levels of experience with risk of bias or the conduct of trials. Data were analyzed using content analysis. RESULTS: Participants found the wiki to be well organized, easy to use, and straightforward to navigate. Suggestions for improvement tended to focus on clarification of the text or on esthetics, rather than on the content or format. Participants liked the additional features of the site that were supplementary to the text, such as the interactive examples, and the components that focused on practical applications, adding relevance to the theory presented. While the site could be used by both trialists and systematic reviewers, the lack of a clearly defined target audience caused some confusion among participants. CONCLUSIONS: Participants were supportive of using a wiki as a novel educational tool. The results of this pilot test will be used to refine the risk of bias wiki, which holds promise as a knowledge translation intervention for education in medical research methodology.

  14. Bioremediation of petroleum hydrocarbons: catabolic genes, microbial communities, and applications.

    Science.gov (United States)

    Fuentes, Sebastián; Méndez, Valentina; Aguila, Patricia; Seeger, Michael

    2014-06-01

    Bioremediation is an environmental sustainable and cost-effective technology for the cleanup of hydrocarbon-polluted soils and coasts. In spite of that longer times are usually required compared with physicochemical strategies, complete degradation of the pollutant can be achieved, and no further confinement of polluted matrix is needed. Microbial aerobic degradation is achieved by the incorporation of molecular oxygen into the inert hydrocarbon molecule and funneling intermediates into central catabolic pathways. Several families of alkane monooxygenases and ring hydroxylating dioxygenases are distributed mainly among Proteobacteria, Actinobacteria, Firmicutes and Fungi strains. Catabolic routes, regulatory networks, and tolerance/resistance mechanisms have been characterized in model hydrocarbon-degrading bacteria to understand and optimize their metabolic capabilities, providing the basis to enhance microbial fitness in order to improve hydrocarbon removal. However, microbial communities taken as a whole play a key role in hydrocarbon pollution events. Microbial community dynamics during biodegradation is crucial for understanding how they respond and adapt to pollution and remediation. Several strategies have been applied worldwide for the recovery of sites contaminated with persistent organic pollutants, such as polycyclic aromatic hydrocarbons and petroleum derivatives. Common strategies include controlling environmental variables (e.g., oxygen availability, hydrocarbon solubility, nutrient balance) and managing hydrocarbon-degrading microorganisms, in order to overcome the rate-limiting factors that slow down hydrocarbon biodegradation.

  15. Functional Gene Diversity and Metabolic Potential of the Microbial Community in an Estuary-Shelf Environment

    Directory of Open Access Journals (Sweden)

    Yu Wang

    2017-06-01

    Full Text Available Microbes play crucial roles in various biogeochemical processes in the ocean, including carbon (C, nitrogen (N, and phosphorus (P cycling. Functional gene diversity and the structure of the microbial community determines its metabolic potential and therefore its ecological function in the marine ecosystem. However, little is known about the functional gene composition and metabolic potential of bacterioplankton in estuary areas. The East China Sea (ECS is a dynamic marginal ecosystem in the western Pacific Ocean that is mainly affected by input from the Changjiang River and the Kuroshio Current. Here, using a high-throughput functional gene microarray (GeoChip, we analyzed the functional gene diversity, composition, structure, and metabolic potential of microbial assemblages in different ECS water masses. Four water masses determined by temperature and salinity relationship showed different patterns of functional gene diversity and composition. Generally, functional gene diversity [Shannon–Weaner’s H and reciprocal of Simpson’s 1/(1-D] in the surface water masses was higher than that in the bottom water masses. The different presence and proportion of functional genes involved in C, N, and P cycling among the bacteria of the different water masses showed different metabolic preferences of the microbial populations in the ECS. Genes involved in starch metabolism (amyA and nplT showed higher proportion in microbial communities of the surface water masses than of the bottom water masses. In contrast, a higher proportion of genes involved in chitin degradation was observed in microorganisms of the bottom water masses. Moreover, we found a higher proportion of nitrogen fixation (nifH, transformation of hydroxylamine to nitrite (hao and ammonification (gdh genes in the microbial communities of the bottom water masses compared with those of the surface water masses. The spatial variation of microbial functional genes was significantly correlated

  16. Proposing a Wiki-Based Technique for Collaborative Essay Writing (Propuesta de un modelo pedagógico para la escritura colaborativa de ensayos en un entorno virtual wiki)

    Science.gov (United States)

    Ortiz Navarrete, Mabel; Ferreira Cabrera, Anita

    2014-01-01

    This paper aims at proposing a technique for students learning English as a foreign language when they collaboratively write an argumentative essay in a wiki environment. A wiki environment and collaborative work play an important role within the academic writing task. Nevertheless, an appropriate and systematic work assignment is required in…

  17. Crowdsourcing the nodulation gene network discovery environment.

    Science.gov (United States)

    Li, Yupeng; Jackson, Scott A

    2016-05-26

    The Legumes (Fabaceae) are an economically and ecologically important group of plant species with the conspicuous capacity for symbiotic nitrogen fixation in root nodules, specialized plant organs containing symbiotic microbes. With the aim of understanding the underlying molecular mechanisms leading to nodulation, many efforts are underway to identify nodulation-related genes and determine how these genes interact with each other. In order to accurately and efficiently reconstruct nodulation gene network, a crowdsourcing platform, CrowdNodNet, was created. The platform implements the jQuery and vis.js JavaScript libraries, so that users are able to interactively visualize and edit the gene network, and easily access the information about the network, e.g. gene lists, gene interactions and gene functional annotations. In addition, all the gene information is written on MediaWiki pages, enabling users to edit and contribute to the network curation. Utilizing the continuously updated, collaboratively written, and community-reviewed Wikipedia model, the platform could, in a short time, become a comprehensive knowledge base of nodulation-related pathways. The platform could also be used for other biological processes, and thus has great potential for integrating and advancing our understanding of the functional genomics and systems biology of any process for any species. The platform is available at http://crowd.bioops.info/ , and the source code can be openly accessed at https://github.com/bioops/crowdnodnet under MIT License.

  18. The State of Wiki Usage in U.S. K-12 Schools: Leveraging Web 2.0 Data Warehouses to Study Quality and Equality in Online Learning Environments

    Science.gov (United States)

    Reich, Blair Justin Fire

    2012-01-01

    In the first part of this dissertation, I document wiki usage in U.S. K-12 settings by analyzing data on a representative sample drawn from a population of nearly 180,000 wikis. My research group, which I lead and managed, measured the opportunities wikis provide for students to develop 21st century skills such as expert thinking, complex…

  19. The State of Wiki Usage in U.S. K-12 Schools: Leveraging Web 2.0 Data Warehouses to Assess Quality and Equity in Online Learning Environments

    Science.gov (United States)

    Reich, Justin; Murnane, Richard; Willett, John

    2012-01-01

    To document wiki usage in U.S. K-12 settings, this study examined a representative sample drawn from a population of nearly 180,000 wikis. The authors measured the opportunities wikis provide for students to develop 21st-century skills such as expert thinking, complex communication, and new media literacy. The authors found four types of wiki…

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

    Directory of Open Access Journals (Sweden)

    Nishida Mutsumi

    2009-09-01

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

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

    Science.gov (United States)

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

    2014-07-01

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

  2. Developing Collaborative Autonomous Learning Abilities in Computer Mediated Language Learning: Attention to Meaning among Students in Wiki Space

    Science.gov (United States)

    Kessler, Greg; Bikowski, Dawn

    2010-01-01

    This study reports on attention to meaning among 40 NNS pre-service EFL teachers as they collaboratively constructed a wiki in a 16-week online course. Focus is placed upon the nature of individual and group behavior when attending to meaning in a long-term wiki-based collaborative activity as well as the students' collaborative autonomous…

  3. The Making of a History Standards Wiki: "Covering", "Uncovering", and "Discovering" Curriculum Frameworks Using a Highly Interactive Technology

    Science.gov (United States)

    Maloy, Robert W.; Poirier, Michelle; Smith, Hilary K.; Edwards, Sharon A.

    2010-01-01

    This article explores using a wiki, one of the newest forms of interactive computer-based technology, as a resource for teaching the Massachusetts K-12 History and Social Science Curriculum Framework, a set of state-mandated learning standards. Wikis are web pages that can be easily edited by multiple authors. They invite active involvement by…

  4. Scaffolding Wiki-Supported Collaborative Learning for Small-Group Projects and Whole-Class Collaborative Knowledge Building

    Science.gov (United States)

    Lin, C-Y.; Reigeluth, C. M.

    2016-01-01

    While educators value wikis' potential, wikis may fail to support collaborative constructive learning without careful scaffolding. This article proposes literature-based instructional methods, revised based on two expert instructors' input, presents the collected empirical evidence on the effects of these methods and proposes directions for future…

  5. Scaffolding Wiki-Supported Collaborative Learning for Small-Group Projects and Whole-Class Collaborative Knowledge Building

    Science.gov (United States)

    Lin, C-Y.; Reigeluth, C. M.

    2016-01-01

    While educators value wikis' potential, wikis may fail to support collaborative constructive learning without careful scaffolding. This article proposes literature-based instructional methods, revised based on two expert instructors' input, presents the collected empirical evidence on the effects of these methods and proposes directions for future…

  6. An Exploratory Study on Using Wiki to Foster Student Teachers' Learner-Centered Learning and Self and Peer Assessment

    Science.gov (United States)

    Ng, Eugenia M. W.; Lai, Yiu Chi

    2012-01-01

    This article discusses an exploratory study that examined whether a wiki-based project could foster student-centered learning. Student teachers were divided into five groups to tackle a group project which involved creating digital learning materials on wiki that could teach information technology (IT) to secondary school students. As assessment…

  7. The Role of the Constructivist Learning Theory and Collaborative Learning Environment on Wiki Classroom, and the Relationship between Them

    Science.gov (United States)

    Alzahrani, Ibraheem; Woollard, John

    2013-01-01

    This paper seeks to discover the relationship between both the social constructivist learning theory and the collaborative learning environment. This relationship can be identified by giving an example of the learning environment. Due to wiki characteristics, Wiki technology is one of the most famous learning environments that can show the…

  8. Empirical Testing of a Theoretical Extension of the Technology Acceptance Model: An Exploratory Study of Educational Wikis

    Science.gov (United States)

    Liu, Xun

    2010-01-01

    This study extended the technology acceptance model and empirically tested the new model with wikis, a new type of educational technology. Based on social cognitive theory and the theory of planned behavior, three new variables, wiki self-efficacy, online posting anxiety, and perceived behavioral control, were added to the original technology…

  9. T2Ku: Building a Semantic Wiki of Mathematics

    CERN Document Server

    Pan, Minqi

    2012-01-01

    We introduce T2Ku, an open source project that aims at building a semantic wiki of mathematics featuring automated reasoning(AR) techniques. We want to utilize AR techniques in a way that truly helps mathematical researchers solve problems in the real world, instead of building another ambitious yet useless system. By setting this as our objective, we exploit pragmatic design decisions that have proven feasible in other projects, while still employs a loosely coupled architecture to allow better inference programs to be integrated in the future. In this paper, we state the motivations and examine state-of-the-art systems, why we are not satisfied with those systems and how we are going to improve. We then describe our architecture and the way we implemented the system. We present examples showing how to use its facilities. T2Ku is an on-going project. We conclude this paper by summarizing the development progress and encouraging the reader to join the project.

  10. BCD: a wiki-based decommissioning knowledge management tool

    Energy Technology Data Exchange (ETDEWEB)

    Fontaine, V.; Coudouneau, L.; Goursaud, V. [CEA Marcoule (DEN/MAR/DPAD/SECAD), 30 (France)

    2008-07-01

    Knowledge management allows decommissioning stakeholders to take advantage of past experience (in terms of efficiency, quality, safety, cost, etc.), avoid repeating previous errors, and identify good ideas and practices. It is usually broken down into three processes: collecting information, supplementing and enriching it, and making it available to all decommissioning stakeholders. The CEA has been collecting and centralizing data for many years: the first qualitative assessment of operational experience began in 1991. However, the documents collected were not always relevant for this assessment and, for lack of enrichment and distribution, were generally not used to a significant extent. In order to take advantage of the existing and future body of knowledge and to share this knowledge among decommissioning stakeholders, the CEA decommissioning review unit decided to develop an intranet site known as BCD (from the French acronym for Central Decommissioning Database) using the same wiki technology as the collaborative web encyclopedia, Wikipedia. The objective of BCD is to develop a decommissioning encyclopedia comprising definitions and terminology, the regulatory framework, the lessons of experience with technical or contractual projects, guidelines, statements of results, etc. This article describes BCD and its potential, together with the results observed to date and its prospects for future development. (authors)

  11. Bacterial community composition and chitinase gene diversity of vermicompost with antifungal activity.

    Science.gov (United States)

    Yasir, Muhammad; Aslam, Zubair; Kim, Seon Won; Lee, Seon-Woo; Jeon, Che Ok; Chung, Young Ryun

    2009-10-01

    Bacterial communities and chitinase gene diversity of vermicompost (VC) were investigated to clarify the influence of earthworms on the inhibition of plant pathogenic fungi in VC. The spore germination of Fusarium moniliforme was reduced in VC aqueous extracts prepared from paper sludge and dairy sludge (fresh sludge, FS). The bacterial communities were examined by culture-dependent and -independent analyses. Unique clones selected from 16S rRNA libraries of FS and VC on the basis of restriction fragment length polymorphism (RFLP) fell into the major lineages of the domain bacteria Proteobacteria, Bacteroidetes, Verrucomicrobia, Actinobacteria and Firmicutes. Among culture isolates, Actinobacteria dominated in VC, while almost equal numbers of Actinobacteria and Proteobacteria were present in FS. Analysis of chitinolytic isolates and chitinase gene diversity revealed that chitinolytic bacterial communities were enriched in VC. Populations of bacteria that inhibited plant fungal pathogens were higher in VC than in FS and particularly chitinolytic isolates were most active against the target fungi.

  12. Detection of gene communities in multi-networks reveals cancer drivers

    Science.gov (United States)

    Cantini, Laura; Medico, Enzo; Fortunato, Santo; Caselle, Michele

    2015-12-01

    We propose a new multi-network-based strategy to integrate different layers of genomic information and use them in a coordinate way to identify driving cancer genes. The multi-networks that we consider combine transcription factor co-targeting, microRNA co-targeting, protein-protein interaction and gene co-expression networks. The rationale behind this choice is that gene co-expression and protein-protein interactions require a tight coregulation of the partners and that such a fine tuned regulation can be obtained only combining both the transcriptional and post-transcriptional layers of regulation. To extract the relevant biological information from the multi-network we studied its partition into communities. To this end we applied a consensus clustering algorithm based on state of art community detection methods. Even if our procedure is valid in principle for any pathology in this work we concentrate on gastric, lung, pancreas and colorectal cancer and identified from the enrichment analysis of the multi-network communities a set of candidate driver cancer genes. Some of them were already known oncogenes while a few are new. The combination of the different layers of information allowed us to extract from the multi-network indications on the regulatory pattern and functional role of both the already known and the new candidate driver genes.

  13. Community dynamics in the mouse gut microbiota: a possible role for IRF9-regulated genes in community homeostasis.

    Directory of Open Access Journals (Sweden)

    Claire L Thompson

    Full Text Available BACKGROUND: Gut microbial communities of mammals are thought to show stable differences between individuals. This means that the properties imparted by the gut microbiota become a unique and constant characteristic of the host. Manipulation of the microbiota has been proposed as a useful tool in health care, but a greater understanding of mechanisms which lead to community stability is required. Here we have examined the impact of host immunoregulatory phenotype on community dynamics. METHODS AND FINDINGS: Denaturing gradient gel electrophoresis was used to analyse the faecal bacterial community of BALB/c and C57BL/6 mice and C57BL/6 mice deficient for either type I interferon (IFN signalling (IRF9 KO mice or type I and type II IFN signalling (STAT1 KO mice. Temporal variation was found in all mouse strains. A measure of the ability for a community structure characteristic of the host to be maintained over time, the individuality index, varied between mouse strains and available data from pigs and human models. IRF9 KO mice had significantly higher temporal variation, and lower individuality, than other mouse strains. Examination of the intestinal mucosa of the IRF9 KO mice revealed an increased presence of T-cells and neutrophils in the absence of inflammation. SIGNIFICANCE: The high temporal variation observed in the gut microbiota of inbred laboratory mice has implications for their use as experimental models for the human gut microbiota. The distinct IRF9 and STAT1 phenotypes suggest a role for IRF9 in immune regulation within the gut mucosa and that further study of interferon responsive genes is necessary to understand host-gut microbe relationships.

  14. Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community

    Directory of Open Access Journals (Sweden)

    Christopher L. Hemme

    2016-04-01

    Full Text Available Unraveling the drivers controlling the response and adaptation of biological communities to environmental change, especially anthropogenic activities, is a central but poorly understood issue in ecology and evolution. Comparative genomics studies suggest that lateral gene transfer (LGT is a major force driving microbial genome evolution, but its role in the evolution of microbial communities remains elusive. To delineate the importance of LGT in mediating the response of a groundwater microbial community to heavy metal contamination, representative Rhodanobacter reference genomes were sequenced and compared to shotgun metagenome sequences. 16S rRNA gene-based amplicon sequence analysis indicated that Rhodanobacter populations were highly abundant in contaminated wells with low pHs and high levels of nitrate and heavy metals but remained rare in the uncontaminated wells. Sequence comparisons revealed that multiple geochemically important genes, including genes encoding Fe2+/Pb2+ permeases, most denitrification enzymes, and cytochrome c553, were native to Rhodanobacter and not subjected to LGT. In contrast, the Rhodanobacter pangenome contained a recombinational hot spot in which numerous metal resistance genes were subjected to LGT and/or duplication. In particular, Co2+/Zn2+/Cd2+ efflux and mercuric resistance operon genes appeared to be highly mobile within Rhodanobacter populations. Evidence of multiple duplications of a mercuric resistance operon common to most Rhodanobacter strains was also observed. Collectively, our analyses indicated the importance of LGT during the evolution of groundwater microbial communities in response to heavy metal contamination, and a conceptual model was developed to display such adaptive evolutionary processes for explaining the extreme dominance of Rhodanobacter populations in the contaminated groundwater microbiome.

  15. In situ gene expression in mixed-culture biofilms: Evidence of metabolic interactions between community members

    DEFF Research Database (Denmark)

    Møller, Søren; Sternberg, Claus; Andersen, Jens Bo

    1998-01-01

    in both community and pure-culture biofilms, while the Pm promoter was induced in the mixed community but not in a pure-culture biofilm. By sequentially adding community members, induction of Pm was shown to be a consequence of direct metabolic interactions between an Acinetobacter species and P. putida...... are involved in the biodegradation of toluene and related aromatic compounds. The upper-pathway promoter (Pu) and the meta-pathway promoter (Pm) from the TOL plasmid were fused independently to the gene coding for the green fluorescent protein (GFP), and expression from these promoters was studied in P. putida......, which was a dominant community member. Biofilms were cultured in flow chambers, which in combination with scanning confocal laser microscopy allowed direct monitoring of promoter activity with single-cell spatial resolution. Expression from the Pu promoter was homogeneously induced by benzyl alcohol...

  16. Using a Semantic Wiki for Documentation Management in Very Small Projects

    Science.gov (United States)

    Ribaud, Vincent; Saliou, Philippe

    The emerging ISO/IEC 29110 standard Lifecycle profiles for Very Small Entities is targeted at very small entity (VSE) having up to 25 people, to assist them unlock the potential benefits of using software engineering standards. VSEs may use semantic web technologies to improve documentation management infrastructure and processes. We proposed to use a semantic wiki for documentation management based on an identification scheme inspired from an IFLA proposition called Functional Requirements for Bibliographic Records. The document identification scheme allows documents to be managed by the internal resource management of the semantic wiki, hence benefiting from a straightforward but powerful version control. With few inputs of semantic annotations by VSE employees - through usable semantic forms and templates, the semantic wiki acts as a library catalog, and users can find, identify, select, obtain, and navigate resources.

  17. Profiling Hyporheic Microbial Community Nitrogen Cycle and Carbohydrate Active Enzyme Gene Abundances across Seasons

    Science.gov (United States)

    Nelson, W. C.; Graham, E.; Stegen, J.

    2016-12-01

    The hyporheic zone (HZ) is the permanently inundated sediment layer between a surface channel and adjacent groundwater-saturated sediments. It has been hypothesized to play a major role in macronutrient (C, N, P) cycling in rivers. The correlation between community taxonomic composition dynamics and functional gene representation is poorly understood for hyporheic communities. To explore how microbial communities respond to temporal changes in environmental conditions, metagenomes were derived from communities captured in sterile sandpacks deployed within the HZ of the Columbia River. HMM databases were used to enumerate protein families present. Functional classification of reads allowed a general assessment of community function over time, while targeted assembly of specific genes enabled investigation of the diversity of organisms encoding these functions. Preliminary analysis of nitrogen cycle pathways shows most gene families examined to have quite steady representation across seasons, with most observed changes being less than an order of magnitude. Analysis of ammonia oxidation genes showed bacterial ammonia oxidizers (AOB) to be stably present across the year, while the archaeal amoA gene increased in late summer, peaking sharply in November, mirroring results from 16S rRNA amplicon analysis which showed an increase in Thaumarcheal OTUs during that same period. Most glycosyl hydrolase GH families had low representation. Highly abundant classes of GH included the GH94 (beta-glucosidase), GH95 (1-2-alpha-L-fucosidase) and GH103 (lytic transglycosylase) families, suggesting activity on plant, fungus and insect polysaccharides and peptidoglycans. Further work is investigating the taxonomy of the sequences identified, to determine how changes in the community composition contribute to the stable gene family profiles observed. These results are intended to work towards a greater understanding of the role of species diversity and functional redundancy in the

  18. PyPedia: using the wiki paradigm as crowd sourcing environment for bioinformatics protocols.

    Science.gov (United States)

    Kanterakis, Alexandros; Kuiper, Joël; Potamias, George; Swertz, Morris A

    2015-01-01

    Today researchers can choose from many bioinformatics protocols for all types of life sciences research, computational environments and coding languages. Although the majority of these are open source, few of them possess all virtues to maximize reuse and promote reproducible science. Wikipedia has proven a great tool to disseminate information and enhance collaboration between users with varying expertise and background to author qualitative content via crowdsourcing. However, it remains an open question whether the wiki paradigm can be applied to bioinformatics protocols. We piloted PyPedia, a wiki where each article is both implementation and documentation of a bioinformatics computational protocol in the python language. Hyperlinks within the wiki can be used to compose complex workflows and induce reuse. A RESTful API enables code execution outside the wiki. Initial content of PyPedia contains articles for population statistics, bioinformatics format conversions and genotype imputation. Use of the easy to learn wiki syntax effectively lowers the barriers to bring expert programmers and less computer savvy researchers on the same page. PyPedia demonstrates how wiki can provide a collaborative development, sharing and even execution environment for biologists and bioinformaticians that complement existing resources, useful for local and multi-center research teams. PyPedia is available online at: http://www.pypedia.com. The source code and installation instructions are available at: https://github.com/kantale/PyPedia_server. The PyPedia python library is available at: https://github.com/kantale/pypedia. PyPedia is open-source, available under the BSD 2-Clause License.

  19. Wiki management a revolutionary new model for a rapidly changing and collaborative world

    CERN Document Server

    Collins, Rod

    2013-01-01

    We now live in a "wiki" world where mass collaboration is not only possible-it's often the best solution. Conventional management thought assumes that command-and-control is the most effective way to organize the efforts of large numbers of people, but rapid change and increasing complexity have rendered that model obsolete. As a result, most managers today lack the skills and knowledge needed to succeed in an age when networks are proving smarter and faster than hierarchies. Designing organizations for mass collaboration demands a new and very different model-wiki management.

  20. WikiHyperGlossary (WHG): an information literacy technology for chemistry documents.

    Science.gov (United States)

    Bauer, Michael A; Berleant, Daniel; Cornell, Andrew P; Belford, Robert E

    2015-01-01

    The WikiHyperGlossary is an information literacy technology that was created to enhance reading comprehension of documents by connecting them to socially generated multimedia definitions as well as semantically relevant data. The WikiHyperGlossary enhances reading comprehension by using the lexicon of a discipline to generate dynamic links in a document to external resources that can provide implicit information the document did not explicitly provide. Currently, the most common method to acquire additional information when reading a document is to access a search engine and browse the web. This may lead to skimming of multiple documents with the novice actually never returning to the original document of interest. The WikiHyperGlossary automatically brings information to the user within the current document they are reading, enhancing the potential for deeper document understanding. The WikiHyperGlossary allows users to submit a web URL or text to be processed against a chosen lexicon, returning the document with tagged terms. The selection of a tagged term results in the appearance of the WikiHyperGlossary Portlet containing a definition, and depending on the type of word, tabs to additional information and resources. Current types of content include multimedia enhanced definitions, ChemSpider query results, 3D molecular structures, and 2D editable structures connected to ChemSpider queries. Existing glossaries can be bulk uploaded, locked for editing and associated with multiple social generated definitions. The WikiHyperGlossary leverages both social and semantic web technologies to bring relevant information to a document. This can not only aid reading comprehension, but increases the users' ability to obtain additional information within the document. We have demonstrated a molecular editor enabled knowledge framework that can result in a semantic web inductive reasoning process, and integration of the WikiHyperGlossary into other software technologies, like

  1. Tecnología y filosofía wiki aplicadas al electromagnetismo computacional

    OpenAIRE

    De la Cruz Calvo, Daniel

    2007-01-01

    Este trabajo de fin de carrera se ha realizado en la Escola Politècnica Superior de Castelldefels (EPSC) en colaboración con el Centre Internacional de Mètodes Numèrics en Enginyeria (CIMNE) con el objetivo de explorar las posibilidades de la tecnología wiki aplicada al ámbito de investigación de CIMNE: el electromagnetismo computacional. De acuerdo con la Wikipedia, “un (o una) wiki es un sitio web colaborativo que puede ser editado por varios usuarios. Los usuarios de una ...

  2. "Blogs" and "wikis" are valuable software tools for communication within research groups.

    Science.gov (United States)

    Sauer, Igor M; Bialek, Dominik; Efimova, Ekaterina; Schwartlander, Ruth; Pless, Gesine; Neuhaus, Peter

    2005-01-01

    Appropriate software tools may improve communication and ease access to knowledge for research groups. A weblog is a website which contains periodic, chronologically ordered posts on a common webpage, whereas a wiki is hypertext-based collaborative software that enables documents to be authored collectively using a web browser. Although not primarily intended for use as an intranet-based collaborative knowledge warehouse, both blogs and wikis have the potential to offer all the features of complex and expensive IT solutions. These tools enable the team members to share knowledge simply and quickly-the collective knowledge base of the group can be efficiently managed and navigated.

  3. Brug af WIKI til fremme af lærende fællesskaber i entrepreneurskabsundervisning

    DEFF Research Database (Denmark)

    Rasmussen, Pia

    2011-01-01

    Artikel om WIKI-brug som bringer teknologi, web 2.0 og problemet med ansvarliggørelse af studerende for egen og gruppebaseret læring i fokus, kombineret med en ændret og mere tilbagetrukket lærerrolle......Artikel om WIKI-brug som bringer teknologi, web 2.0 og problemet med ansvarliggørelse af studerende for egen og gruppebaseret læring i fokus, kombineret med en ændret og mere tilbagetrukket lærerrolle...

  4. Genetic diversity of bacterial communities and gene transfer agents in northern South China Sea.

    Directory of Open Access Journals (Sweden)

    Fu-Lin Sun

    Full Text Available Pyrosequencing of the 16S ribosomal RNA gene (rDNA amplicons was performed to investigate the unique distribution of bacterial communities in northern South China Sea (nSCS and evaluate community structure and spatial differences of bacterial diversity. Cyanobacteria, Proteobacteria, Actinobacteria, and Bacteroidetes constitute the majority of bacteria. The taxonomic description of bacterial communities revealed that more Chroococcales, SAR11 clade, Acidimicrobiales, Rhodobacterales, and Flavobacteriales are present in the nSCS waters than other bacterial groups. Rhodobacterales were less abundant in tropical water (nSCS than in temperate and cold waters. Furthermore, the diversity of Rhodobacterales based on the gene transfer agent (GTA major capsid gene (g5 was investigated. Four g5 gene clone libraries were constructed from samples representing different regions and yielded diverse sequences. Fourteen g5 clusters could be identified among 197 nSCS clones. These clusters were also related to known g5 sequences derived from genome-sequenced Rhodobacterales. The composition of g5 sequences in surface water varied with the g5 sequences in the sampling sites; this result indicated that the Rhodobacterales population could be highly diverse in nSCS. Phylogenetic tree analysis result indicated distinguishable diversity patterns among tropical (nSCS, temperate, and cold waters, thereby supporting the niche adaptation of specific Rhodobacterales members in unique environments.

  5. Beyond classification: gene-family phylogenies from shotgun metagenomic reads enable accurate community analysis.

    Science.gov (United States)

    Riesenfeld, Samantha J; Pollard, Katherine S

    2013-06-22

    Sequence-based phylogenetic trees are a well-established tool for characterizing diversity of both macroorganisms and microorganisms. Phylogenetic methods have recently been applied to shotgun metagenomic data from microbial communities, particularly with the aim of classifying reads. But the accuracy of gene-family phylogenies that characterize evolutionary relationships among short, non-overlapping sequencing reads has not been thoroughly evaluated. To quantify errors in metagenomic read trees, we developed MetaPASSAGE, a software pipeline to generate in silico bacterial communities, simulate a sample of shotgun reads from a gene family represented in the community, orient or translate reads, and produce a profile-based alignment of the reads from which a gene-family phylogenetic tree can be built. We applied MetaPASSAGE to a variety of RNA and protein-coding gene families, built trees using a range of different phylogenetic methods, and compared the resulting trees using topological and branch-length error metrics. We identified read length as one of the major sources of error. Because phylogenetic methods use a reference database of full-length sequences from the gene family to guide construction of alignments and trees, we found that error can also be substantially reduced through increasing the size and diversity of the reference database. Finally, UniFrac analysis, which compares metagenomic samples based on a summary statistic computed over all branches in a read tree, is very robust to the level of error we observe. Bacterial community diversity can be quantified using phylogenetic approaches applied to shotgun metagenomic data. As sequencing reads get longer and more genomes across the bacterial tree of life are sequenced, the accuracy of this approach will continue to improve, opening the door to more applications.

  6. Stress-Survival Gene Identification From an Acid Mine Drainage Algal Mat Community

    Science.gov (United States)

    Urbina-Navarrete, J.; Fujishima, K.; Paulino-Lima, I. G.; Rothschild-Mancinelli, B.; Rothschild, L. J.

    2014-12-01

    Microbial communities from acid mine drainage environments are exposed to multiple stressors to include low pH, high dissolved metal loads, seasonal freezing, and desiccation. The microbial and algal communities that inhabit these niche environments have evolved strategies that allow for their ecological success. Metagenomic analyses are useful in identifying species diversity, however they do not elucidate the mechanisms that allow for the resilience of a community under these extreme conditions. Many known or predicted genes encode for protein products that are unknown, or similarly, many proteins cannot be traced to their gene of origin. This investigation seeks to identify genes that are active in an algal consortium during stress from living in an acid mine drainage environment. Our approach involves using the entire community transcriptome for a functional screen in an Escherichia coli host. This approach directly targets the genes involved in survival, without need for characterizing the members of the consortium.The consortium was harvested and stressed with conditions similar to the native environment it was collected from. Exposure to low pH (stress-induced genes that were transcribed into messenger RNA (mRNA). These mRNA transcripts were harvested to build complementary DNA (cDNA) libraries in E. coli. The transformed E. coli were exposed to the same stressors as the original algal consortium to select for surviving cells. Successful cells incorporated the transcripts that encode survival mechanisms, thus allowing for selection and identification of the gene(s) involved. Initial selection screens for freeze and desiccation tolerance have yielded E. coli that are 1 order of magnitude more resistant to freezing (0.01% survival of control with no transcript, 0.2% survival of E. coli with transcript) and 3 orders of magnitude more resistant to desiccation (0.005% survival of control cells with no transcripts, 5% survival of cells with transcript).This work

  7. Bottleneck genes and community structure in the cell cycle network of S. pombe.

    Directory of Open Access Journals (Sweden)

    Cécile Caretta-Cartozo

    2007-06-01

    Full Text Available The identification of cell cycle-related genes is still a difficult task, even for organisms with relatively few genes such as the fission yeast. Several gene expression studies have been published on S. pombe showing similarities but also discrepancies in their results. We introduce a network in which the weight of each link is a function of the phase difference between the expression peaks of two genes. The analysis of the stability of the clustering through the computation of an entropy parameter reveals a structure made of four clusters, the first one corresponding to a robustly connected M-G1 component, the second to genes in the S phase, and the third and fourth to two G2 components. They are separated by bottleneck structures that appear to correspond to cell cycle checkpoints. We identify a number of genes that are located on these bottlenecks. They represent a novel group of cell cycle regulatory genes. They all show interesting functions, and they are supposed to be involved in the regulation of the transition from one phase to the next. We therefore present a comparison of the available studies on the fission yeast cell cycle and a general statistical bioinformatics methodology to find bottlenecks and gene community structures based on recent developments in network theory.

  8. El proyecto Wiki Learning: Wikipedia como entorno de aprendizaje abierto

    Directory of Open Access Journals (Sweden)

    2016-10-01

    Full Text Available Los enfoques predominantes en el sistema educativo tradicional circunscriben las posibilidades de aprendizaje a entornos formales y cerrados. Sin embargo, las tecnologías móviles y plataformas digitales están transformando este paradigma, expandiendo las posibilidades de aprendizaje. A partir de esta condición y en el marco de la producción del conocimiento entre pares, sostenemos que Wikipedia puede ser utilizada como un entorno de aprendizaje abierto que cumple varios propósitos: a permite adquirir competencias básicas; b contribuye a la inteligencia colectiva; c acorta la brecha global de conocimiento; y, d facilita la construcción de redes globales de aprendizaje. Este estudio de caso tiene como objetivo presentar el proceso, estrategias y resultados del proyecto Wiki Learning, como modelo de aprendizaje abierto a través del uso de Wikipedia en una universidad mexicana. El proyecto abarcó desde la producción de artículos hasta talleres para el desarrollo de capacidades de profesores y estudiantes. Se realizaron encuestas a 57 docentes y 115 alumnos para identificar la percepción acerca de Wikipedia, su uso y posibilidades como herramienta educativa. Los resultados demostraron que a pesar de que todos son usuarios de Wikipedia, existe un desconocimiento general sobre su funcionamiento, estructura y comunidades, además de cierta desconfianza. Se presenta un desafío para romper el estigma y recuperar el valor de la gestión compartida del conocimiento, el propósito de la enciclopedia y su lugar como producto de la inteligencia colectiva.

  9. Organic micropollutants in aerobic and anaerobic membrane bioreactors: Changes in microbial communities and gene expression

    KAUST Repository

    Harb, Moustapha

    2016-07-09

    Organic micro-pollutants (OMPs) are contaminants of emerging concern in wastewater treatment due to the risk of their proliferation into the environment, but their impact on the biological treatment process is not well understood. The purpose of this study is to examine the effects of the presence of OMPs on the core microbial populations of wastewater treatment. Two nanofiltration-coupled membrane bioreactors (aerobic and anaerobic) were subjected to the same operating conditions while treating synthetic municipal wastewater spiked with OMPs. Microbial community dynamics, gene expression levels, and antibiotic resistance genes were analyzed using molecular-based approaches. Results showed that presence of OMPs in the wastewater feed had a clear effect on keystone bacterial populations in both the aerobic and anaerobic sludge while also significantly impacting biodegradation-associated gene expression levels. Finally, multiple antibiotic-type OMPs were found to have higher removal rates in the anaerobic MBR, while associated antibiotic resistance genes were lower.

  10. Daphnia as a refuge for an antibiotic resistance gene in an experimental freshwater community.

    Science.gov (United States)

    Eckert, Ester M; Di Cesare, Andrea; Stenzel, Birgit; Fontaneto, Diego; Corno, Gianluca

    2016-11-15

    Mechanisms that enable the maintenance of antibiotic resistance genes in the environment are still greatly unknown. Here we show that the tetracycline resistance gene tet(A) is largely removed from the pelagic aquatic bacterial community through filter feeding by Daphnia obtusa while it becomes detectable within the microbiome of the daphniids themselves, where it was not present prior to the experiment. We moreover show that a multitude of Daphnia-associated bacterial taxa are potential carriers of tet(A) and postulated that the biofilm-like structures, where bacteria grow in, may enable horizontal transfer of such genes. This experiment highlights the need to take ecological interactions and a broad range of niches into consideration when studying and discussing the fate of antibiotic resistance genes in nature.

  11. Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes.

    Science.gov (United States)

    Bálint, Miklós; Bahram, Mohammad; Eren, A Murat; Faust, Karoline; Fuhrman, Jed A; Lindahl, Björn; O'Hara, Robert B; Öpik, Maarja; Sogin, Mitchell L; Unterseher, Martin; Tedersoo, Leho

    2016-09-01

    With high-throughput sequencing (HTS), we are able to explore the hidden world of microscopic organisms to an unpre-cedented level. The fast development of molecular technology and statistical methods means that microbial ecologists must keep their toolkits updated. Here, we review and evaluate some of the more widely adopted and emerging techniques for analysis of diversity and community composition, and the inference of species interactions from co-occurrence data generated by HTS of marker genes. We emphasize the importance of observational biases and statistical properties of the data and methods. The aim of the review is to critically discuss the advantages and disadvantages of established and emerging statistical methods, and to contribute to the integration of HTS-based marker gene data into community ecology.

  12. Antibiotic resistance genes occurrence and bacterial community composition in the Liuxi River

    Directory of Open Access Journals (Sweden)

    Wenguang eXiong

    2014-12-01

    Full Text Available Antibiotic resistance genes (ARGs in the environment have paid great concern due to their health risk. We investigated antibiotics concentrations (tetracyclines, sulfonamides and fluoroquinolones, ARGs abundances (tetracycline, sulfonamide and plasmid-mediated quinolone resistance (PMQR genes, and bacterial community composition in sediment and water samples in the Liuxi River, China. Antibiotics concentrations were determined by ultra-performance liquid chromatography-electrospray tandem mass spectrometry. ARGs abundances were quantified by a culture-independent method. Bacterial community composition was analyzed by metagenomic approach based on Ion Torrent Personal Genome Machine platform. Antibiotics concentrations were at the levels of 1.19 to 622 ug kg-1 in sediment samples and below the limit of detection to 127 ng L-1 in water samples. Relative abundances (ARGs copies/16S rRNA gene copies of detected ARGs were at the range of 10-5 to 10-2. The dominant phyla were Proteobacteria, Bacteroidetes and Verrucomicrobia in sediment samples, and were Proteobacteria, Actinobacteria and Bacteroidetes in water samples. The results indicated that the river environment was contaminated by antibiotics and may be as a reservoir of ARGs. This study provided quantitative data on antibiotics, ARGs and bacterial community composition in the Liuxi River, a geographical location different from the reported studies.

  13. Microbial community gene expression within colonies of the diazotroph, Trichodesmium, from the Southwest Pacific Ocean.

    Science.gov (United States)

    Hewson, Ian; Poretsky, Rachel S; Dyhrman, Sonya T; Zielinski, Brian; White, Angelicque E; Tripp, H James; Montoya, Joseph P; Zehr, Jonathan P

    2009-11-01

    Trichodesmium are responsible for a large fraction of open ocean nitrogen fixation, and are often found in complex consortia of other microorganisms, including viruses, prokaryotes, microbial eukaryotes and metazoa. We applied a community gene expression (metatranscriptomic) approach to study the patterns of microbial gene utilization within colonies of Trichodesmium collected during a bloom in the Southwest Pacific Ocean in April 2007. The survey generated 5711-day and 5385-night putative mRNA reads. The majority of mRNAs were from the co-occurring microorganisms and not Trichodesmium, including other cyanobacteria, heterotrophic bacteria, eukaryotes and phage. Most transcripts did not share homology with proteins from cultivated microorganisms, but were similar to shotgun sequences and unannotated proteins from open ocean metagenomic surveys. Trichodesmium transcripts were mostly expressed photosynthesis, N(2) fixation and S-metabolism genes, whereas those in the co-occurring microorganisms were mostly involved in genetic information storage and processing. Detection of Trichodesmium genes involved in P uptake and As detoxification suggest that local enrichment of N through N(2) fixation may lead to a P-stress response. Although containing similar dominant transcripts to open ocean metatranscriptomes, the overall pattern of gene expression in Trichodesmium colonies was distinct from free-living pelagic assemblages. The identifiable genes expressed by Trichodesmium and closely associated microorganisms reflect the constraints of life in well-lit and nutrient-poor waters, with biosynthetic investment in nutrient acquisition and cell maintenance, which is in contrast to gene transcription by soil and coastal seawater microbial assemblages. The results provide insight into aggregate microbial communities in contrast to planktonic free-living assemblages that are the focus of other studies.

  14. Wikis to facilitate patient participation in developing information leaflets: first experiences

    NARCIS (Netherlands)

    Belt, T.H. van de; Faber, M.J.; Knijnenburg, J.M.; Duijnhoven, N.T.L. van; Nelen, W.L.D.M.; Kremer, J.A.M.

    2014-01-01

    OBJECTIVE: Although patients have gained a wealth of experienced based knowledge they are usually not involved in the development of patient information. We sought to determine the technical feasibility of wikis in generating dynamic patient information leaflets with participation from patients and

  15. Peer-Feedback and Revision Process in a Wiki Mediated Collaborative Writing

    Science.gov (United States)

    Woo, Matsuko Mukumoto; Chu, Samuel Kai Wah; Li, Xuanxi

    2013-01-01

    This study investigated the use of a wiki for collaborative writing among primary levels five (P5) and six (P6) students (n = 119) in a Chinese primary school in Hong Kong where English is taught as a second language (L2). Three classes of students and their English subject teachers participated in a three-month English language writing programme…

  16. Interdisciplinary Project-Based Learning: An Online Wiki Experience in Teacher Education

    Science.gov (United States)

    Biasutti, Michele; EL-Deghaidy, Heba

    2015-01-01

    In the current research study the use of Wikis as an online didactic tool to apply project-based learning in higher education was reported. The study was conducted in university teacher education programmes. During the online activities, participants developed interdisciplinary projects for the primary school working collaboratively in small…

  17. Wikis and collaborative writing applications in healthcare: a scoping review protocol.

    NARCIS (Netherlands)

    Archambault, P.M.; Belt, T.H. van de; Grajales III, F.J.; Eysenbach, G.; Aubin, K.; Gold, I.; Gagnon, M.P.; Kuziemsky, C.E.; Turgeon, A.F.; Poitras, J.; Faber, M.J.; Kremer, J.A.M.; Heldoorn, M.; Bilodeau, A.; Legare, F.

    2012-01-01

    ABSTRACT The rapid rise in the use of collaborative writing applications (eg, wikis, Google Documents, and Google Knol) has created the need for a systematic synthesis of the evidence of their impact as knowledge translation (KT) tools in the health care sector and for an inventory of the factors th

  18. Geography Geo-Wiki in the Classroom: Using Crowdsourcing to Enhance Geographical Teaching

    Directory of Open Access Journals (Sweden)

    Christoph Perger

    2014-09-01

    Full Text Available Geo-Wiki is a crowdsourcing tool used to derive information, based on satellite imagery, to validate and enhance global land cover. Around 5000 users are registered, who contribute to different campaigns to collect data across various domains (e.g., agriculture, biomass, human impact, etc.. However, seeing the Earth’s surface from above does not provide all of the necessary information for understanding what is happening on the ground. Instead, we need to enhance this experience with local knowledge or with additional information, such as geo-located photographs of surface features with annotation. The latest development in enhancing Geo-Wiki in this context has been achieved through collaboration with the University of Waterloo to set up a separate branch called Geography Geo-Wiki for use in undergraduate teaching. We provide the pedagogical objectives for this branch and describe two modules that we have introduced in first and third year Physical Geography classes. The majority of the feedback was positive and in, many cases, was part of what the student liked best about the course. Future plans include the development of additional assignments for the study of environmental processes using Geo-Wiki that would engage students in a manner that is very different from that of conventional teaching.

  19. Using Wiki in Teacher Education: Impact on Knowledge Management Processes and Student Satisfaction

    Science.gov (United States)

    Biasutti, Michele; EL-Deghaidy, Heba

    2012-01-01

    The current study reports on the use of Wiki as an online didactic tool to develop knowledge management (KM) processes in higher education. This study integrates social constructivist principles to learning where learners are pro-active and collaborative through higher order cognitive processes. The study was administered in two countries, namely…

  20. A Wiki-Based Group Project in an Inorganic Chemistry Foundation Course

    Science.gov (United States)

    Kristian, Kathleen E.

    2015-01-01

    A semester-long group project that utilizes wiki sites to enhance collaboration was developed for a foundation course in inorganic chemistry. Through structured assignments, student groups use metal-based or metal-combating therapeutic agents as a model for applying and understanding course concepts; they also gain proficiency with scientific- and…

  1. A Collaborative, Wiki-Based Organic Chemistry Project Incorporating Free Chemistry Software on the Web

    Science.gov (United States)

    Evans, Michael J.; Moore, Jeffrey S.

    2011-01-01

    In recent years, postsecondary instructors have recognized the potential of wikis to transform the way students learn in a collaborative environment. However, few instructors have embraced in-depth student use of chemistry software for the creation of interactive chemistry content on the Web. Using currently available software, students are able…

  2. Using Wikis and Blogs for Assessment in First-Year Engineering

    Science.gov (United States)

    Smith, Elizabeth Joy; Mills, Julie Evelyn; Myers, Baden

    2009-01-01

    Purpose: This paper aims to examine some of the strengths and weaknesses of the use of online tools such as wikis and blogs for assessment purposes, with the aim of proposing future developments and improvements. Design/methodology/approach: The paper utilises a case study approach by examining the outcomes of a new first-year course for all…

  3. Toward a Better Understanding of Culture: Wikis in the Beginning German Classroom

    Science.gov (United States)

    Ducate, Lara; Steckenbiller, Christiane

    2017-01-01

    The questions of how to teach culture, which culture(s) to teach and how to lead students to intercultural competence and understanding are common questions for language teachers. The current project employed wikis to systematically integrate culture and authentic texts into beginning German courses at a large south-eastern university in the…

  4. Using Wikis as a Support and Assessment Tool in Collaborative Digital Game-Based Learning Environments

    Science.gov (United States)

    Samur, Yavuz

    2011-01-01

    In computer-supported collaborative learning (CSCL) environments, there are many researches done on collaborative learning activities; however, in game-based learning environments, more research and literature on collaborative learning activities are required. Actually, both game-based learning environments and wikis enable us to use new chances…

  5. Attacks by “Anonymous” WikiLeaks Proponents not Anonymous

    NARCIS (Netherlands)

    Pras, Aiko; Sperotto, Anna; Moura, Giovane C.M.; Drago, Idilio; Barbosa, Rafael; Sadre, Ramin; Schmidt, Ricardo; Hofstede, Rick

    2010-01-01

    On November 28, 2010, the world started watching the whistle blower website WikiLeaks to begin publishing part of the 250,000 US Embassy Diplomatic cables. These confidential cables provide an insight on U.S. international affairs from 274 different embassies, covering topics such as analysis of hos

  6. Wiki and Digital Video Use in Strategic Interaction-Based Experiential EFL Learning

    Science.gov (United States)

    Dehaan, Jonathan; Johnson, Neil H.; Yoshimura, Noriko; Kondo, Takako

    2012-01-01

    This paper details the use of a free and access-controlled wiki as the learning management system for a four-week teaching module designed to improve the oral communication skills of Japanese university EFL students. Students engaged in repeated experiential learning cycles of planning, doing, observing, and evaluating their performance of a role…

  7. "A Learning Journey for All": American Elementary Teachers' Use of Classroom Wikis

    Science.gov (United States)

    Lee, Lena

    2012-01-01

    In response to the needs for understanding teaching practices and approaches with a technology tool in actual elementary classrooms, this paper examines the perspectives of American elementary teachers who use classroom wikis. Specially, it examines three main ideas: (a) teaching approaches and strategies across subject areas in the primary and…

  8. Wikis and collaborative writing applications in healthcare: a scoping review protocol.

    NARCIS (Netherlands)

    Archambault, P.M.; Belt, T.H. van de; Grajales III, F.J.; Eysenbach, G.; Aubin, K.; Gold, I.; Gagnon, M.P.; Kuziemsky, C.E.; Turgeon, A.F.; Poitras, J.; Faber, M.J.; Kremer, J.A.M.; Heldoorn, M.; Bilodeau, A.; Legare, F.

    2012-01-01

    ABSTRACT The rapid rise in the use of collaborative writing applications (eg, wikis, Google Documents, and Google Knol) has created the need for a systematic synthesis of the evidence of their impact as knowledge translation (KT) tools in the health care sector and for an inventory of the factors

  9. A Collaborative, Wiki-Based Organic Chemistry Project Incorporating Free Chemistry Software on the Web

    Science.gov (United States)

    Evans, Michael J.; Moore, Jeffrey S.

    2011-01-01

    In recent years, postsecondary instructors have recognized the potential of wikis to transform the way students learn in a collaborative environment. However, few instructors have embraced in-depth student use of chemistry software for the creation of interactive chemistry content on the Web. Using currently available software, students are able…

  10. A Wiki-Based Group Project in an Inorganic Chemistry Foundation Course

    Science.gov (United States)

    Kristian, Kathleen E.

    2015-01-01

    A semester-long group project that utilizes wiki sites to enhance collaboration was developed for a foundation course in inorganic chemistry. Through structured assignments, student groups use metal-based or metal-combating therapeutic agents as a model for applying and understanding course concepts; they also gain proficiency with scientific- and…

  11. A cloud-based semantic wiki for user training in healthcare process management.

    Science.gov (United States)

    Papakonstantinou, D; Poulymenopoulou, M; Malamateniou, F; Vassilacopoulos, G

    2011-01-01

    Successful healthcare process design requires active participation of users who are familiar with the cooperative and collaborative nature of healthcare delivery, expressed in terms of healthcare processes. Hence, a reusable, flexible, agile and adaptable training material is needed with the objective to enable users instill their knowledge and expertise in healthcare process management and (re)configuration activities. To this end, social software, such as a wiki, could be used as it supports cooperation and collaboration anytime, anywhere and combined with semantic web technology that enables structuring pieces of information for easy retrieval, reuse and exchange between different systems and tools. In this paper a semantic wiki is presented as a means for developing training material for healthcare providers regarding healthcare process management. The semantic wiki should act as a collective online memory containing training material that is accessible to authorized users, thus enhancing the training process with collaboration and cooperation capabilities. It is proposed that the wiki is stored in a secure virtual private cloud that is accessible from anywhere, be it an excessively open environment, while meeting the requirements of redundancy, high performance and autoscaling.

  12. Using Wiki in Teacher Education: Impact on Knowledge Management Processes and Student Satisfaction

    Science.gov (United States)

    Biasutti, Michele; EL-Deghaidy, Heba

    2012-01-01

    The current study reports on the use of Wiki as an online didactic tool to develop knowledge management (KM) processes in higher education. This study integrates social constructivist principles to learning where learners are pro-active and collaborative through higher order cognitive processes. The study was administered in two countries, namely…

  13. Wiki Technology as a Design Tool for a Capstone Design Course

    Science.gov (United States)

    Hadley, Kevin R.; Debelak, Kenneth A.

    2009-01-01

    Technology is a key component to the net generation's social, study, and professional skills. It is prudent to investigate the applications of new technology in education. In this study, a wiki was incorporated into a senior design course, and its utility was investigated with respect to process design. The results of the study indicate wikis…

  14. Using Wikis to Enhance Website Peer Evaluation in an Online Website Development Course: An Exploratory Study

    Science.gov (United States)

    He, Wu

    2011-01-01

    Peer evaluations are often used to improve learning in educational settings. As more and more online courses are offered, it is becoming increasingly important to explore new techniques for conducting peer evaluation in online courses. In recent years, wikis have increasingly been used in higher education to support learning and group work.…

  15. WikiTranslate: Query Translation for Cross-lingual Information Retrieval using only Wikipedia

    NARCIS (Netherlands)

    Nguyen, D.; Nguyen, Dong-Phuong; Overwijk, A.; Hauff, C.; Trieschnigg, Rudolf Berend; Hiemstra, Djoerd; de Jong, Franciska M.G.; Peters, Carol; Deselaers, Thomas; Ferro, Nicola; Gonzalo, Julio

    2009-01-01

    This paper presents WikiTranslate, a system which performs query translation for cross-lingual information retrieval (CLIR) using only Wikipedia to obtain translations. Queries are mapped to Wikipedia concepts and the corresponding translations of these concepts in the target language are used to

  16. Developing Business Writing Skills and Reducing Writing Anxiety of EFL Learners through Wikis

    Science.gov (United States)

    Kassem, Mohamed Ali Mohamed

    2017-01-01

    The present study aimed at investigating the effect of using wikis on developing business writing skills and reducing writing anxiety of Business Administration students at Prince Sattam bin Abdul Aziz University, KSA. Sixty students, who were randomly chosen and divided into two equivalent groups: control and experimental, participated in the…

  17. Experience with the use of online lectures, video Modules, and wiki-websites in engineering education

    DEFF Research Database (Denmark)

    Pedersen, Anders Gorm; Wernersson, Rasmus

    2011-01-01

    We here present our experience with three computer-based teaching methodologies that we have used for a number of years in engineering education: Online lectures, video modules, and wiki websites. The aim is to provide the reader with concrete tools that can be used directly in teaching situations...

  18. Students' Perceptions of Wiki-Based Collaborative Writing for Learners of English as a Foreign Language

    Science.gov (United States)

    Chao, Yu-Chuan Joni; Lo, Hao-Chang

    2011-01-01

    This study proposes a Wiki-based collaborative writing approach to the writing process for EFL (English as a foreign language) learners. A five-stage computer-mediated collaborative writing project including collaborative planning, partitioned drafting, peer-revising, peer-editing, and individual publishing was blended with on-campus English…

  19. Wikis and collaborative writing applications in health care: a scoping review

    NARCIS (Netherlands)

    Archambault, P.M.; Belt, T.H. van de; Grajales, F.J., 3rd; Faber, M.J.; Kuziemsky, C.E.; Gagnon, S.; Bilodeau, A.; Rioux, S.; Nelen, W.L.D.M.; Gagnon, M.P.; Turgeon, A.F.; Aubin, K.; Gold, I.; Poitras, J.; Eysenbach, G.; Kremer, J.A.M.; Legare, F.

    2013-01-01

    BACKGROUND: Collaborative writing applications (eg, wikis and Google Documents) hold the potential to improve the use of evidence in both public health and health care. The rapid rise in their use has created the need for a systematic synthesis of the evidence of their impact as knowledge translatio

  20. The Zones of Proximal and Distal Development in Chinese Language Studies with the Use of Wikis

    Science.gov (United States)

    Chew, Esyin; Ding, Seong Lin

    2014-01-01

    Educational practitioners in the higher education institutions of the UK have increasingly promoted the use of wikis. The technology enhanced learning experience of the UK was transferred to a local higher educational agency in Malaysia through a collaborative research project called WiLearn. By examining a student cohort enrolled in Chinese…

  1. Feasibility of a wiki as a participatory tool for patients in clinical guideline development

    NARCIS (Netherlands)

    Breejen, E.M. den; Nelen, W.L.D.M.; Knijnenburg, J.M.; Burgers, J.S.; Hermens, R.P.M.G.; Kremer, J.A.M.

    2012-01-01

    BACKGROUND: Patient participation is essential in developing high-quality guidelines but faces practical challenges. Evidence on timing, methods, evaluations, and outcomes of methodologies for patient participation in guideline development is lacking. OBJECTIVE: To assess the feasibility of a wiki a

  2. Key respiratory genes elucidate bacterial community respiration in a seasonally anoxic estuary.

    Science.gov (United States)

    Eggleston, Erin M; Lee, Dong Y; Owens, Michael S; Cornwell, Jeffrey C; Crump, Byron C; Hewson, Ian

    2015-07-01

    Intense annual spring phytoplankton blooms and thermohaline stratification lead to anoxia in Chesapeake Bay bottom waters. Once oxygen becomes depleted in the system, microbial communities use energetically favourable alternative electron acceptors for respiration. The extent to which changes in respiration are reflected in community gene expression have only recently been investigated. Metatranscriptomes prepared from near-bottom water plankton over a 4-month time series in central Chesapeake Bay demonstrated changes consistent with terminal electron acceptor availability. The frequency of respiration-related genes in metatranscriptomes was examined by BLASTx against curated databases of genes intimately and exclusively involved in specific electron acceptor utilization pathways. The relative expression of genes involved in denitrification and dissimilatory nitrate reduction to ammonium were coincident with changes in nitrate, nitrite and ammonium concentrations. Dissimilatory iron and manganese reduction transcript ratios increase during anoxic conditions and corresponded with the highest soluble reactive phosphate and manganese concentrations. The sulfide concentration peaked in late July and early August and also matched dissimilatory sulfate reduction transcript ratios. We show that rather than abrupt transitions between terminal electron acceptors, there is substantial overlap in time and space of these various anaerobic respiratory processes in Chesapeake Bay.

  3. Wikis and collaborative writing applications in health care: a scoping review protocol.

    Science.gov (United States)

    Archambault, Patrick Michel; van de Belt, Tom H; Grajales Iii, Francisco J; Eysenbach, Gunther; Aubin, Karine; Gold, Irving; Gagnon, Marie-Pierre; Kuziemsky, Craig E; Turgeon, Alexis F; Poitras, Julien; Faber, Marjan J; Kremer, Jan A M; Heldoorn, Marcel; Bilodeau, Andrea; Légaré, France

    2012-04-11

    The rapid rise in the use of collaborative writing applications (eg, wikis, Google Documents, and Google Knol) has created the need for a systematic synthesis of the evidence of their impact as knowledge translation (KT) tools in the health care sector and for an inventory of the factors that affect their use. While researchers have conducted systematic reviews on a range of software-based information and communication technologies as well as other social media (eg, virtual communities of practice, virtual peer-to-peer communities, and electronic support groups), none have reviewed collaborative writing applications in the medical sector. The overarching goal of this project is to explore the depth and breadth of evidence for the use of collaborative writing applications in health care. Thus, the purposes of this scoping review will be to (1) map the literature on collaborative writing applications; (2) compare the applications' features; (3) describe the evidence of each application's positive and negative effects as a KT intervention in health care; (4) inventory and describe the barriers and facilitators that affect the applications' use; and (5) produce an action plan and a research agenda. A six-stage framework for scoping reviews will be used: (1) identifying the research question; (2) identifying relevant studies within the selected databases (using the EPPI-Reviewer software to classify the studies); (3) selecting studies (an iterative process in which two reviewers search the literature, refine the search strategy, and review articles for inclusion); (4) charting the data (using EPPI-Reviewer's data-charting form); (5) collating, summarizing, and reporting the results (performing a descriptive, numerical, and interpretive synthesis); and (6) consulting knowledge users during three planned meetings. Since this scoping review concerns the use of collaborative writing applications as KT interventions in health care, we will use the Knowledge to Action (KTA

  4. Activities Based on Wiki Platform for Engineering Higher Education: Students' Point of View

    Directory of Open Access Journals (Sweden)

    Gláucia Nolasco de Almeida Mello

    2017-08-01

    Full Text Available The fast evolution of Information and Communication Technology (ICT introduced a new generation of learners that have been adopted mobile devices and Web 2.0 technologies to get information and communicate. The Web 2.0-based tools, such as blogs, wikis, Facebook, Instagram, etc, offer huge possibilities for collaboration. In this way, the main purpose of this research was plan an activity on wiki platform for Reinforced Concrete discipline in Civil Engineering course and answer the questions: (1 How should collaboration be effectively measured on wiki platform? (2 What is the students' point of view about using wiki platform for a collaboration activity? Wikispaces Classroom platform was chosen for the project because it is a free social writing platform, suitable for collaborative learning. Furthermore it works on modern browsers, tablets, and smart phone. A total of 167 students of Civil Engineering course were monitored on Wikispaces® platform. All students’ actions were analyzed and classified as low, medium or high level of collaboration. At the end of the project 111 students answered a questionnaire and 10 students participated of an informal interview where they expressed their opinion about the platform, the activities and the relationship with online peers. A descriptive statistical analysis of the data collected from the platform and the questionnaires answered by the students was performed. The results indicated that wiki platform is an important way to develop innovative activities and tasks for the purpose of to improve skills of engineering students such as: writing communication, organization, collaboration and critical thinking.

  5. Functional profiling of mercuric reductase (mer A genes in biofilm communities of a technical scale biocatalyzer

    Directory of Open Access Journals (Sweden)

    von Canstein Harald

    2003-10-01

    Full Text Available Abstract Background Bacterial mercury resistance is based on enzymatic reduction of ionic mercury to elemental mercury and has recently been demonstrated to be applicable for industrial wastewater clean-up. The long-term monitoring of such biocatalyser systems requires a cultivation independent functional community profiling method targeting the key enzyme of the process, the merA gene coding for the mercuric reductase. We report on the development of a profiling method for merA and its application to monitor changes in the functional diversity of the biofilm community of a technical scale biocatalyzer over 8 months of on-site operation. Results Based on an alignment of 30 merA sequences from Gram negative bacteria, conserved primers were designed for amplification of merA fragments with an optimized PCR protocol. The resulting amplicons of approximately 280 bp were separated by thermogradient gelelectrophoresis (TGGE, resulting in strain specific fingerprints for mercury resistant Gram negative isolates with different merA sequences. The merA profiling of the biofilm community from a technical biocatalyzer showed persistence of some and loss of other inoculum strains as well as the appearance of new bands, resulting in an overall increase of the functional diversity of the biofilm community. One predominant new band of the merA community profile was also detected in a biocatalyzer effluent isolate, which was identified as Pseudomonas aeruginosa. The isolated strain showed lower mercury reduction rates in liquid culture than the inoculum strains but was apparently highly competitive in the biofilm environment of the biocatalyzer where moderate mercury levels were prevailing. Conclusions The merA profiling technique allowed to monitor the ongoing selection for better adapted strains during the operation of a biocatalyzer and to direct their subsequent isolation. In such a way, a predominant mercury reducing Ps. aeruginosa strain was identified by

  6. Characterization of microbial community and the alkylscccinate synthase genes in petroleum reservoir fluids of China

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Lei; Mu, Bo-Zhong [University of Science and Technology (China)], email: bzmu@ecust.edu.cn; Gu, Ji-Dong [The University of Hong Kong (China)], email: jdgu@hkucc.hku.hk

    2011-07-01

    Petroleum reservoirs represent a special ecosystem consisting of specific temperature, pressure, salt concentration, oil, gas, water, microorganisms and, enzymes among others. This paper presents the characterization of microbial community and the alkyl succinate synthase genes in petroleum reservoir fluids in China. A few samples were analyzed and the physical and chemical characteristics are given in a tabular form. A flow chart shows the methods and procedures for microbial activities. Six petroleum reservoirs were studied using an archaeal 16S rRNA gene-based approach to establish the presence of archaea and the results are given. The correlation of archaeal and bacterial communities with reservoir conditions and diversity of the arachaeal community in water-flooding petroleum reservoirs at different temperatures is also shown. From the study, it can be summarized that, among methane producers, CO2-reducing methanogens are mostly found in oil reservoir ecosystems and as more assA sequences are revealed, more comprehensive molecular probes can be designed to track the activity of anaerobic alkane-degrading organisms in the environment.

  7. Functional genes based analysis of sulfur-oxidizing bacteria community in sulfide removing bioreactor.

    Science.gov (United States)

    Luo, Jian-Fei; Lin, Wei-Tie; Guo, Yong

    2011-04-01

    Sulfur-oxidizing bacteria (SOB) are the main microorganisms that participate in the bioremediation of sulfide-rich wastewater. To reveal the SOB community structure and determine which members of SOB contribute to the sulfide oxidation in a sulfide-rich cloth printing and dyeing wastewater treatment plant, specific primer pairs dsrA 625F/877R, soxB 704F/1199R, and sqr 473F/982R based on the SOB functional genes encoding dissimilatory sulfite reductase, sulfate thioesterase/thiohydrolase, and sulfide: quinone oxidoreductase were designed. The restriction fragment length polymorphism analysis showed that the diversity indices and the abundance of each OTU have no significant changes after time, which suggested the SOB community in the sulfide removing bioreactor have high steady phylogenetic analysis of functional gene-based clone libraries detected the SOB from Chlorobia, α-proteobacteria, β-proteobacteria, and γ-proteobacteria. The combined clone library showed the presence of dominant members of the SOB species closely related to families Halothiobacillaceae (17%), Hydrogenophilaceae (14%), and Rhodocyclaceae (13%), which may contribute to the sulfide oxidation in wastewater treatment process. This work provides a precise understanding of SOB microbial community within sulfide removing bioreactor, and the result gives assistance for the optimization of the treatment systems for sulfide biological degradation. © Springer-Verlag 2011

  8. Importance of Mobile Genetic Elements and Conjugal Gene Transfer for Subsurface Microbial Community Adaptation to Biotransformation of Metals

    Energy Technology Data Exchange (ETDEWEB)

    Sorensen, Soren J.

    2005-06-01

    The overall goal of this project is to investigate the effect of mobile genetic elements and conjugal gene transfer on subsurface microbial community adaptation to mercury and chromium stress and biotransformation. Our studies focus on the interaction between the fate of these metals in the subsurface and the microbial community structure and activity.

  9. Empirical phylogenies and species abundance distributions are consistent with pre-equilibrium dynamics of neutral community models with gene flow

    KAUST Repository

    Bonnet-Lebrun, Anne-Sophie

    2017-03-17

    Community characteristics reflect past ecological and evolutionary dynamics. Here, we investigate whether it is possible to obtain realistically shaped modelled communities - i.e., with phylogenetic trees and species abundance distributions shaped similarly to typical empirical bird and mammal communities - from neutral community models. To test the effect of gene flow, we contrasted two spatially explicit individual-based neutral models: one with protracted speciation, delayed by gene flow, and one with point mutation speciation, unaffected by gene flow. The former produced more realistic communities (shape of phylogenetic tree and species-abundance distribution), consistent with gene flow being a key process in macro-evolutionary dynamics. Earlier models struggled to capture the empirically observed branching tempo in phylogenetic trees, as measured by the gamma statistic. We show that the low gamma values typical of empirical trees can be obtained in models with protracted speciation, in pre-equilibrium communities developing from an initially abundant and widespread species. This was even more so in communities sampled incompletely, particularly if the unknown species are the youngest. Overall, our results demonstrate that the characteristics of empirical communities that we have studied can, to a large extent, be explained through a purely neutral model under pre-equilibrium conditions. This article is protected by copyright. All rights reserved.

  10. Antibiotics, Antibiotic Resistance Genes, and Bacterial Community Composition in Fresh Water Aquaculture Environment in China.

    Science.gov (United States)

    Xiong, Wenguang; Sun, Yongxue; Zhang, Tong; Ding, Xueyao; Li, Yafei; Wang, Mianzhi; Zeng, Zhenling

    2015-08-01

    Environmental antibiotic resistance has drawn increasing attention due to its great threat to human health. In this study, we investigated concentrations of antibiotics (tetracyclines, sulfonamides and (fluoro)quinolones) and abundances of antibiotic resistance genes (ARGs), including tetracycline resistance genes, sulfonamide resistance genes, and plasmid-mediated quinolone resistance genes, and analyzed bacterial community composition in aquaculture environment in Guangdong, China. The concentrations of sulfametoxydiazine, sulfamethazine, sulfamethoxazole, oxytetracycline, chlorotetracycline, doxycycline, ciprofloxacin, norfloxacin, and enrofloxacin were as high as 446 μg kg(-1) and 98.6 ng L(-1) in sediment and water samples, respectively. The relative abundances (ARG copies/16S ribosomal RNA (rRNA) gene copies) of ARGs (sul1, sul2, sul3, tetM, tetO, tetW, tetS, tetQ, tetX, tetB/P, qepA, oqxA, oqxB, aac(6')-Ib, and qnrS) were as high as 2.8 × 10(-2). The dominant phyla were Proteobacteria, Bacteroidetes, and Firmicutes in sediment samples and Proteobacteria, Actinobacteria and Bacteroidetes in water samples. The genera associated with pathogens were also observed, such as Acinetobacter, Arcobacter, and Clostridium. This study comprehensively investigated antibiotics, ARGs, and bacterial community composition in aquaculture environment in China. The results indicated that fish ponds are reservoirs of ARGs and the presence of potential resistant and pathogen-associated taxonomic groups in fish ponds might imply the potential risk to human health.

  11. Fungal community structure in disease suppressive soils assessed by 28S LSU gene sequencing.

    Directory of Open Access Journals (Sweden)

    C Ryan Penton

    Full Text Available Natural biological suppression of soil-borne diseases is a function of the activity and composition of soil microbial communities. Soil microbe and phytopathogen interactions can occur prior to crop sowing and/or in the rhizosphere, subsequently influencing both plant growth and productivity. Research on suppressive microbial communities has concentrated on bacteria although fungi can also influence soil-borne disease. Fungi were analyzed in co-located soils 'suppressive' or 'non-suppressive' for disease caused by Rhizoctonia solani AG 8 at two sites in South Australia using 454 pyrosequencing targeting the fungal 28S LSU rRNA gene. DNA was extracted from a minimum of 125 g of soil per replicate to reduce the micro-scale community variability, and from soil samples taken at sowing and from the rhizosphere at 7 weeks to cover the peak Rhizoctonia infection period. A total of ∼ 994,000 reads were classified into 917 genera covering 54% of the RDP Fungal Classifier database, a high diversity for an alkaline, low organic matter soil. Statistical analyses and community ordinations revealed significant differences in fungal community composition between suppressive and non-suppressive soil and between soil type/location. The majority of differences associated with suppressive soils were attributed to less than 40 genera including a number of endophytic species with plant pathogen suppression potentials and mycoparasites such as Xylaria spp. Non-suppressive soils were dominated by Alternaria, Gibberella and Penicillum. Pyrosequencing generated a detailed description of fungal community structure and identified candidate taxa that may influence pathogen-plant interactions in stable disease suppression.

  12. 维基在OPAC的应用与影响%Wiki's Influences and Its Application in OPAC in Libraries

    Institute of Scientific and Technical Information of China (English)

    杨亚晶; 张立肖

    2007-01-01

    文章结合OCLC的Wiki WorldCat(WikiD)项目,重点介绍了维基在OPAC中的应用.指出维基化OPAC将会丰富书目数据库的内容,完善OPAC的功能;为图书馆资源建设提供新思路;有可能提升图书馆的服务水平.

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

    Directory of Open Access Journals (Sweden)

    Ke Yu

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

  14. Experimenting with a Wiki-based collaborative process writing pedagogy for teaching and learning of Chinese writing among upper primary school students in China

    OpenAIRE

    2014-01-01

    This research mainly aims to design a Wiki-based Collaborative Process Writing Pedagogy (WCPWP) to help Mainland Chinese upper primary school students with their writing. A wiki-based learning environment (www.joyouswriting.com) named Joyous Writing Club (JWC) was designed and developed by the researcher using MediaWiki software. This study was conducted in a primary school in Shenzhen, Mainland China. This research applied Design-based Research (DBR) methodology, and included three itera...

  15. Methopedia - Pedagogical Design Community for European Educators

    DEFF Research Database (Denmark)

    Ryberg, Thomas; Niemczik, Christian; Brenstein, Elke

    2009-01-01

    The paper will discuss theoretical, methodological and technical aspects of the community based Methopedia wiki (www.methopedia.eu), which has been developed as a part of the EU-funded collaborative research project “Community of Integrated Blended Learning in Europe” (COMBLE; www.......comble-project.eu). Methopedia is a wiki and social community aimed at facilitating knowledge transfer between trainers/educators from different institutions or countries through interactive peer-to-peer support, and sharing of learning practices.   We describe how Methopedia has been developed though engaging practitioners...... informed the practical design and theoretical issues regarding the design of Methopedia. The workshops have led to redesigns and also a number of important issues and problems have emerged. In the paper, we therefore present and discuss the socio-technical design of Methopedia, which is based on open...

  16. Tillage Management and Seasonal Effects on Denitrifier Community Abundance, Gene Expression and Structure over Winter.

    Science.gov (United States)

    Tatti, Enrico; Goyer, Claudia; Burton, David L; Wertz, Sophie; Zebarth, Bernie J; Chantigny, Martin; Filion, Martin

    2015-10-01

    Tillage effects on denitrifier communities and nitrous oxide (N2O) emissions were mainly studied during the growing season. There is limited information for the non-growing season, especially in northern countries where winter has prolonged periods with sub-zero temperatures. The abundance and structure of the denitrifier community, denitrification gene expression and N2O emissions in fields under long-term tillage regimes [no-tillage (NT) vs conventional tillage (CT)] were assessed during two consecutive winters. NT exerted a positive effect on nirK and nosZ denitrifier abundance in both winters compared to CT. Moreover, the two contrasting managements had an opposite influence on nirK and nirS RNA/DNA ratios. Tillage management resulted in different denitrifier community structures during both winters. Seasonal changes were observed in the abundance and the structure of denitrifiers. Interestingly, the RNA/DNA ratios were greater in the coldest months for nirK, nirS and nosZ. N2O emissions were not influenced by management but changed over time with two orders of magnitude increase in the coldest month of both winters. In winter of 2009-2010, emissions were mainly as N2O, whereas in 2010-2011, when soil temperatures were milder due to persistent snow cover, most emissions were as dinitrogen. Results indicated that tillage management during the growing season induced differences in denitrifier community structure that persisted during winter. However, management did not affect the active cold-adapted community structure.

  17. Transfer of energy pathway genes in microbial enhanced biological phosphorus removal communities.

    Science.gov (United States)

    Wong, Dennis H-J; Beiko, Robert G

    2015-07-16

    Lateral gene transfer (LGT) is an important evolutionary process in microbial evolution. In sewage treatment plants, LGT of antibiotic resistance and xenobiotic degradation-related proteins has been suggested, but the role of LGT outside these processes is unknown. Microbial communities involved in Enhanced Biological Phosphorus Removal (EBPR) have been used to treat wastewater in the last 50 years and may provide insights into adaptation to an engineered environment. We introduce two different types of analysis to identify LGT in EBPR sewage communities, based on identifying assembled sequences with more than one strong taxonomic match, and on unusual phylogenetic patterns. We applied these methods to investigate the role of LGT in six energy-related metabolic pathways. The analyses identified overlapping but non-identical sets of transferred enzymes. All of these were homologous with sequences from known mobile genetic elements, and many were also in close proximity to transposases and integrases in the EBPR data set. The taxonomic method had higher sensitivity than the phylogenetic method, identifying more potential LGTs. Both analyses identified the putative transfer of five enzymes within an Australian community, two in a Danish community, and none in a US-derived culture. Our methods were able to identify sequences with unusual phylogenetic or compositional properties as candidate LGT events. The association of these candidates with known mobile elements supports the hypothesis of transfer. The results of our analysis strongly suggest that LGT has influenced the development of functionally important energy-related pathways in EBPR systems, but transfers may be unique to each community due to different operating conditions or taxonomic composition.

  18. Assessing the microbial community and functional genes in a vertical soil profile with long-term arsenic contamination.

    Directory of Open Access Journals (Sweden)

    Jinbo Xiong

    Full Text Available Arsenic (As contamination in soil and groundwater has become a serious problem to public health. To examine how microbial communities and functional genes respond to long-term arsenic contamination in vertical soil profile, soil samples were collected from the surface to the depth of 4 m (with an interval of 1 m after 16-year arsenic downward infiltration. Integrating BioLog and functional gene microarray (GeoChip 3.0 technologies, we showed that microbial metabolic potential and diversity substantially decreased, and community structure was markedly distinct along the depth. Variations in microbial community functional genes, including genes responsible for As resistance, carbon and nitrogen cycling, phosphorus utilization and cytochrome c oxidases were detected. In particular, changes in community structures and activities were correlated with the biogeochemical features along the vertical soil profile when using the rbcL and nifH genes as biomarkers, evident for a gradual transition from aerobic to anaerobic lifestyles. The C/N showed marginally significant correlations with arsenic resistance (p = 0.069 and carbon cycling genes (p = 0.073, and significant correlation with nitrogen fixation genes (p = 0.024. The combination of C/N, NO(3 (- and P showed the highest correlation (r = 0.779, p = 0.062 with the microbial community structure. Contradict to our hypotheses, a long-term arsenic downward infiltration was not the primary factor, while the spatial isolation and nutrient availability were the key forces in shaping the community structure. This study provides new insights about the heterogeneity of microbial community metabolic potential and future biodiversity preservation for arsenic bioremediation management.

  19. Assessing the microbial community and functional genes in a vertical soil profile with long-term arsenic contamination.

    Science.gov (United States)

    Xiong, Jinbo; He, Zhili; Van Nostrand, Joy D; Luo, Guosheng; Tu, Shuxin; Zhou, Jizhong; Wang, Gejiao

    2012-01-01

    Arsenic (As) contamination in soil and groundwater has become a serious problem to public health. To examine how microbial communities and functional genes respond to long-term arsenic contamination in vertical soil profile, soil samples were collected from the surface to the depth of 4 m (with an interval of 1 m) after 16-year arsenic downward infiltration. Integrating BioLog and functional gene microarray (GeoChip 3.0) technologies, we showed that microbial metabolic potential and diversity substantially decreased, and community structure was markedly distinct along the depth. Variations in microbial community functional genes, including genes responsible for As resistance, carbon and nitrogen cycling, phosphorus utilization and cytochrome c oxidases were detected. In particular, changes in community structures and activities were correlated with the biogeochemical features along the vertical soil profile when using the rbcL and nifH genes as biomarkers, evident for a gradual transition from aerobic to anaerobic lifestyles. The C/N showed marginally significant correlations with arsenic resistance (p = 0.069) and carbon cycling genes (p = 0.073), and significant correlation with nitrogen fixation genes (p = 0.024). The combination of C/N, NO(3) (-) and P showed the highest correlation (r = 0.779, p = 0.062) with the microbial community structure. Contradict to our hypotheses, a long-term arsenic downward infiltration was not the primary factor, while the spatial isolation and nutrient availability were the key forces in shaping the community structure. This study provides new insights about the heterogeneity of microbial community metabolic potential and future biodiversity preservation for arsenic bioremediation management.

  20. EnviWiki – the Czech Multimedia Toolkit for Education for Sustainable Development (ESD (reviewed text

    Directory of Open Access Journals (Sweden)

    Jana Dlouhá

    2008-05-01

    Full Text Available EnviWiki, The educational encyclopaedia for ESD literacy has been selected to be part of the EC DG EAC Inventory of innovative good practice on education for sustainable development. The main purpose of the Inventory is to show concrete examples which have been implemented in the Member States under the concept of ESD in formal and non-formal learning contexts and which are at the forefront as regards innovative approaches. Projects/programmes selected as innovative good practice will be used to inform the preparation of the next Progress Report on the EU Sustainable Development Strategy in Education. See European Commission DG Education and Culture Inventory of innovative practices in education for sustainable development, the case study EnviWiki - Environmental Literacy for Teachers (CZECH REPUBLIC, page 51.

  1. The Impact of a Collaborative Wiki Assignment on Teaching and Learning in a Teacher Education Program

    Directory of Open Access Journals (Sweden)

    Vanessa Joy Bravo

    2011-10-01

    Full Text Available This study explored students’ perceptions and behaviors of public wiki use during a collaborative Wikipedia assignment in a graduate technology and literacy education course. Results confirmed that the majority of students had an overall positive experience posting content on Wikipedia. Students learned how to use Wikipedia through collaborative practice, including, how to adhere to its standards and cite work properly, the importance of critically evaluating online information, and the value of publishing work to an authentic audience. Students (prospective and current teachers reported numerous ways in which collaboration on Wikipedia could be integrated into their K-12 classrooms in order to promote higher order thinking and foster meaningful knowledge construction. Pedagogical practices for the effective integration of public wiki assignments in higher education and K-12 settings are recommended.

  2. Evaluating the Effectiveness of a Wiki Internet Site for Medical Topics

    OpenAIRE

    2012-01-01

    To evaluate the iterative process of a collaborative public database (a Wiki) as a reference for information on hand illnesses we tested the null hypothesis that the number and type of edits are comparable for web pages covering different topics. The history of 4 hand surgery related web pages on the English language Wikipedia (Trigger finger, Complex Regional Pain Syndrome (CRPS), Ganglion cyst, and de Quervain Syndrome) were analyzed from inception to July 2011. Each edit was classified as ...

  3. METHODS AND TOOLS FOR DEVELOPING COMPUTER LEARNING SOFTWARE ON ELECTRICAL ENGINEERING BASED ON WIKI TECHNOLOGY

    Directory of Open Access Journals (Sweden)

    Roman V. Alekhin

    2014-01-01

    Full Text Available This work is devoted to issues related to the development of learning software and, in particular, digital libraries and knowledge bases in different fields and disciplines. Main attention is paid to the development of computer learning software for electrical engineering on the base of rapidly growing and popular wiki technology. This work was supported by RFBR (projects 12-08-00358, 14-01-00427, 12-07-00508. 

  4. INTERVIEW: Quick, Social and Collaborative - wiki-based user documentation at APC by Schneider Electric

    DEFF Research Database (Denmark)

    Møller, Margrethe H.; Pernille Bagger Nielsen, Pernille; Kalianov, Stanislav

    2013-01-01

    In the software documentation department at APC by Schneider Electric in Kolding, Denmark, Technical Writer Pernille Bagger Nielsen writes user documentation for the software developed by the company. In cooperation with Localization Manager Stanislav Kalianov she reorganised the user documentation...... for publication as wiki-based documentation on the internet. The new platform supports their strategy of using agile and iterative, topic-based, collaborative writing when developing user documentation. Their experience will interest readers who consider introducing a similar new strategy....

  5. The Leaky Pipe: Lead Pipers Weigh in on WikiLeaks

    Directory of Open Access Journals (Sweden)

    Editorial Board

    2010-12-01

    Full Text Available Introduction Let’s start off with a little background and context, just in case you haven’t been glued to the news to catch every nuance of the WikiLeaks story. The Guardian has a helpful timeline of the saga to get you (at least partially up to speed, and if you don’t like theirs, there are plenty [...

  6. Utilidad para el aprendizaje de anatomia del uso de wiki en el campus virtual

    OpenAIRE

    Garrido Astray, María Concepción; Pintor Holguín, Emilio; Reinoso Barbero, Luis; Fernández Fernández, Miguel; Colino Cortizo, Ignacio; Gómez Gallego, Félix

    2013-01-01

    Hemos implantado una nueva estrategia docente empleando dos herramientas disponibles dentro de las actividades interactivas que nos permite el campus virtual: wikis y cuestionarios on line. Esta experiencia se ha desarrollado en la asignatura de “Anatomía del Aparato Locomotor y Sistema Nervioso” que se imparte en el segundo cuatrimestre del 1º curso del Grado de Fisioterapia. Para conocer el impacto de este instrumento sobre el aprendizaje hemos evaluado los conocimientos adquiridos medi...

  7. Introducing New Undergraduates Into a Research Group Through Use of a Wiki

    Science.gov (United States)

    Whittlesey, Phyllis; Lopez, Ramon

    2009-04-01

    In a large research group it can be difficult to communicate fundamental group-specific concepts and data collection procedures to new or inexperienced members. Our research group utilizes a type of website called a wiki, which allows members to update and change content quickly and easily. A page on our group's wiki details fundamental concepts in the space physics research group, oriented at incoming undergraduate researchers, including a detailed description of what each of the most-used data sites is used for and a step by step procedure on how to use each one. The nature of the wiki as a dynamic and member-edited project means that descriptions and procedures can be revised and updated as new data sets become available. Our efforts include weekly meetings with the new undergraduates to explore these concepts and frequently-used data websites until these new members have learned enough to understand their assigned research projects. Our group has successfully incorporated undergraduates as early as their freshman year into the research group on scientifically significant research projects using these methods.

  8. Uso de wikis en ingeniería informática

    Directory of Open Access Journals (Sweden)

    Alicia Villanueva García

    2010-01-01

    Full Text Available Este texto describe la experiencia del desarrollo de una actividad de trabajo colaborativo en una asignatura del último curso de Ingeniería Informática. Los alumnos usan el wiki como un instrumento para el desarrollo de la actividad, mientras que el profesor aprovecha la tecnología wiki para hacer el seguimiento del trabajo realizado por los alumnos, proporcionando feedback a los alumnos en base a dicho seguimiento y evaluando tanto el trabajo de los estudiantes como el modo de trabajo en grupo. En primer lugar se presenta el contexto en el que se lleva a cabo la actividad. Relacionado con el contexto, describiremos cómo intentamos conseguir el clima adecuado para llevar a cabo la actividad mediante la realización de alguna actividad más breve complementaria. Describimos en detalle tanto el diseño como algunos aspectos de ejecución de la actividad que hace uso del wiki. También hablaremos de los problemas que se han presentado durante su desarrollo, de las soluciones que se han adoptado y nuestras reflexiones finales.

  9. Wiki en la Universitat Autònoma de Barcelona. Alcance y perspectivas

    Directory of Open Access Journals (Sweden)

    Sergi Robles

    2010-01-01

    Full Text Available Desde mayo del año 2004, un grupo de profesores de la Universitat Autònoma de Barcelona ha llevado a cabo distintas experiencias docentes en educación superior enfocadas a los nuevos planes piloto definidos en el marco del Espacio Europeo de Educación Superior (EEES basadas en la utilización del wiki, con el fin de mejorar el proceso de enseñanza-aprendizaje de los estudiantes. Se han desarrollado distintos materiales docentes para el aprendizaje autónomo y semi-presencial, diseñados para potenciar el trabajo colaborativo y a distancia. El análisis de los resultados obtenidos con la aplicación del wiki a la docencia ha permitido identificar las ventajas y las carencias del sistema de trabajo inicial y ampliar sus posibilidades con herramientas que aseguran una mejor adaptación de esta plataforma al EEES. La labor desarrollada por el grupo y el interés despertado en la comunidad universitaria son el punto de partida de la integración del wiki en el Campus Virtual (la plataforma institucional de soporte virtual del aprendizaje de la Universitat Autònoma de Barcelona que se está llevando a cabo actualmente.

  10. Mouse Social Network Dynamics and Community Structure are Associated with Plasticity-Related Brain Gene Expression.

    Science.gov (United States)

    Williamson, Cait M; Franks, Becca; Curley, James P

    2016-01-01

    Laboratory studies of social behavior have typically focused on dyadic interactions occurring within a limited spatiotemporal context. However, this strategy prevents analyses of the dynamics of group social behavior and constrains identification of the biological pathways mediating individual differences in behavior. In the current study, we aimed to identify the spatiotemporal dynamics and hierarchical organization of a large social network of male mice. We also sought to determine if standard assays of social and exploratory behavior are predictive of social behavior in this social network and whether individual network position was associated with the mRNA expression of two plasticity-related genes, DNA methyltransferase 1 and 3a. Mice were observed to form a hierarchically organized social network and self-organized into two separate social network communities. Members of both communities exhibited distinct patterns of socio-spatial organization within the vivaria that was not limited to only agonistic interactions. We further established that exploratory and social behaviors in standard behavioral assays conducted prior to placing the mice into the large group was predictive of initial network position and behavior but were not associated with final social network position. Finally, we determined that social network position is associated with variation in mRNA levels of two neural plasticity genes, DNMT1 and DNMT3a, in the hippocampus but not the mPOA. This work demonstrates the importance of understanding the role of social context and complex social dynamics in determining the relationship between individual differences in social behavior and brain gene expression.

  11. The use of virtual microscopy and a wiki in pathology education: Tracking student use, involvement, and response

    Directory of Open Access Journals (Sweden)

    Zev Leifer

    2015-01-01

    Full Text Available Background: The pathology laboratory course at the New York College of Podiatric Medicine involves the use of Virtual Microscopy. The students can scan the whole slide, section by section, and zoom in or out. Methods: Using the advantages of digital pathology, the students can, in addition, access the slide collections from other medical schools and put up normal histology (control slides side-by-side with the pathology. They can cut and paste and preserve the region of interest that they find. They can edit and annotate their slides. A wiki was created (http://pathlab2014.wikifoundry.com for the Class of 2014. The students saved, edited and uploaded their slides. In the wiki format, other students could comment, further edit, and even delete the slides. Results: The students studied Basic Mechanisms and System Pathology. During this time, they saved, edited, shared, and uploaded their slides to the wiki. These were available in one full presentation and were also grouped into 16 albums. They were available to all. Student access was followed by Google analytics. At the end of the course, a questionnaire was distributed, assessing their impression of the wiki format and soliciting strengths and weaknesses. Conclusions: The use of a wiki has a number of important advantages in pathology education. It trains the students in the more sophisticated skills that they will use as professional pathologists or as clinicians: (1 Telepathology-it enables them to share slides and discuss observations. (2 Archiving and retrieval - It models the challenge faced by hospitals, diagnostic labs and physicians in maintaining a collection of slides in a form that is easily accessible. (3 Image analysis-familiarity with the wiki format allows them to jump easily to capturing and storing images found in the literature or in a pathologist′s report. Experience with the use of a wiki in pathology education has been quite satisfactory from both the faculty and the

  12. Sulfamethoxazole and COD increase abundance of sulfonamide resistance genes and change bacterial community structures within sequencing batch reactors.

    Science.gov (United States)

    Guo, Xueping; Pang, Weihai; Dou, Chunling; Yin, Daqiang

    2017-05-01

    The abundant microbial community in biological treatment processes in wastewater treatment plants (WWTPs) may potentially enhance the horizontal gene transfer of antibiotic resistance genes with the presence of antibiotics. A lab-scale sequencing batch reactor was designed to investigate response of sulfonamide resistance genes (sulI, sulII) and bacterial communities to various concentrations of sulfamethoxazole (SMX) and chemical oxygen demand (COD) of wastewater. The SMX concentrations (0.001 mg/L, 0.1 mg/L and 10 mg/L) decreased with treatment time and higher SMX level was more difficult to remove. The presence of SMX also significantly reduced the removal efficiency of ammonia nitrogen, affecting the normal function of WWTPs. All three concentrations of SMX raised both sulI and sulII genes with higher concentrations exhibiting greater increases. The abundance of sul genes was positive correlated with treatment time and followed the second-order reaction kinetic model. Interestingly, these two genes have rather similar activity. SulI and sulII gene abundance also performed similar response to COD. Simpson index and Shannon-Weiner index did not show changes in the microbial community diversity. However, the 16S rRNA gene cloning and sequencing results showed the bacterial community structures varied during different stages. The results demonstrated that influent antibiotics into WWTPs may facilitate selection of ARGs and affect the wastewater conventional treatment as well as the bacteria community structures. Copyright © 2017 Elsevier Ltd. All rights reserved.

  13. Responses of bacterial community and functional marker genes of nitrogen cycling to biochar, compost and combined amendments in soil.

    Science.gov (United States)

    Wu, Haipeng; Zeng, Guangming; Liang, Jie; Chen, Jin; Xu, Jijun; Dai, Juan; Li, Xiaodong; Chen, Ming; Xu, Piao; Zhou, Yaoyu; Li, Fei; Hu, Liang; Wan, Jia

    2016-10-01

    Biochar and compost are seen as two attractive waste management options and are used for soil amendment and pollution remediation. The interaction between biochar and composting may improve the potential benefits of biochar and compost. We investigated soil physicochemical properties, bacterial community, bacterial 16S rRNA, and functional marker genes of nitrogen cycling of the soil remedied with nothing (S), compost (SC), biochar (SB), a mixture of compost and biochar (SBC), composted biochar (SBced), and a composted mixture of biochar and biomass (SBCing). The results were that all amendments (1) increased the bacterial community richness (except SB) and SBCing showed the greatest efficiency; (2) increased the bacterial community diversity (SBCing > SBC > SC > SBced > SB > S); and (3) changed the gene copy numbers of 16S rRNA, nirK, nirS, and nosZ genes of bacteria, ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB). All amendments (except SB) could increase the gene copy number of 16S rRNA, and SBCing had the greatest efficiency. The changes of soil bacterial community richness and diversity and the gene copy numbers of 16S rRNA, nirK, nirS, nosZ, AOA, and AOB would affect carbon and nitrogen cycling of the ecosystem and also implied that BCing had the greatest efficiency on soil amendment.

  14. A Capstone Wiki Knowledge Base: A Case Study of an Online Tool Designed to Promote Life-Long Learning through Engineering Literature Research

    Science.gov (United States)

    Clarke, James B.; Coyle, James R.

    2011-01-01

    This article reports the results of a case study in which an experimental wiki knowledge base was designed, developed, and tested by the Brill Science Library at Miami University for an undergraduate engineering senior capstone project. The wiki knowledge base was created to determine if the science library could enhance the engineering literature…

  15. Linking genes to communities and ecosystems: Daphnia as an ecogenomic model

    Science.gov (United States)

    Miner, Brooks E.; De Meester, Luc; Pfrender, Michael E.; Lampert, Winfried; Hairston, Nelson G.

    2012-01-01

    How do genetic variation and evolutionary change in critical species affect the composition and functioning of populations, communities and ecosystems? Illuminating the links in the causal chain from genes up to ecosystems is a particularly exciting prospect now that the feedbacks between ecological and evolutionary changes are known to be bidirectional. Yet to fully explore phenomena that span multiple levels of the biological hierarchy requires model organisms and systems that feature a comprehensive triad of strong ecological interactions in nature, experimental tractability in diverse contexts and accessibility to modern genomic tools. The water flea Daphnia satisfies these criteria, and genomic approaches capitalizing on the pivotal role Daphnia plays in the functioning of pelagic freshwater food webs will enable investigations of eco-evolutionary dynamics in unprecedented detail. Because its ecology is profoundly influenced by both genetic polymorphism and phenotypic plasticity, Daphnia represents a model system with tremendous potential for developing a mechanistic understanding of the relationship between traits at the genetic, organismal and population levels, and consequences for community and ecosystem dynamics. Here, we highlight the combination of traits and ecological interactions that make Daphnia a definitive model system, focusing on the additional power and capabilities enabled by recent molecular and genomic advances. PMID:22298849

  16. Simulated atmospheric N deposition alters fungal community composition and suppresses ligninolytic gene expression in a northern hardwood forest.

    Directory of Open Access Journals (Sweden)

    Ivan P Edwards

    Full Text Available High levels of atmospheric nitrogen (N deposition may result in greater terrestrial carbon (C storage. In a northern hardwood ecosystem, exposure to over a decade of simulated N deposition increased C storage in soil by slowing litter decay rates, rather than increasing detrital inputs. To understand the mechanisms underlying this response, we focused on the saprotrophic fungal community residing in the forest floor and employed molecular genetic approaches to determine if the slower decomposition rates resulted from down-regulation of the transcription of key lignocellulolytic genes, by a change in fungal community composition, or by a combination of the two mechanisms. Our results indicate that across four Acer-dominated forest stands spanning a 500-km transect, community-scale expression of the cellulolytic gene cbhI under elevated N deposition did not differ significantly from that under ambient levels of N deposition. In contrast, expression of the ligninolytic gene lcc was significantly down-regulated by a factor of 2-4 fold relative to its expression under ambient N deposition. Fungal community composition was examined at the most southerly of the four sites, in which consistently lower levels of cbhI and lcc gene expression were observed over a two-year period. We recovered 19 basidiomycete and 28 ascomycete rDNA 28S operational taxonomic units; Athelia, Sistotrema, Ceratobasidium and Ceratosebacina taxa dominated the basidiomycete assemblage, and Leotiomycetes dominated the ascomycetes. Simulated N deposition increased the proportion of basidiomycete sequences recovered from forest floor, whereas the proportion of ascomycetes in the community was significantly lower under elevated N deposition. Our results suggest that chronic atmospheric N deposition may lower decomposition rates through a combination of reduced expression of ligninolytic genes such as lcc, and compositional changes in the fungal community.

  17. Potential for horizontal gene transfer in microbial communities of the terrestrial subsurface.

    Science.gov (United States)

    Coombs, Jonna M

    2009-01-01

    The deep terrestrial subsurface is a vast, largely unexplored environment that is oligotrophic, highly heterogeneous, and may contain extremes of both physical and chemical factors. In spite of harsh conditions, subsurface studies at several widely distributed geographic sites have revealed diverse communities of viable organisms, which have provided evidence of low but detectable metabolic activity. Although much of the terrestrial subsurface may be considered to be distant and isolated, the concept of horizontal gene transfer (HGT) in this environment has far-reaching implications for bioremediation efforts and groundwater quality, industrial harvesting of subsurface natural resources such as petroleum, and accurate assessment of the risks associated with DNA release and transport from genetically modified organisms. This chapter will explore what is known about some of the major mechanisms of HGT, and how the information gained from surface organisms might apply to conditions in the terrestrial subsurface. Evidence for the presence of mobile elements in subsurface bacteria and limited retrospective studies examining genetic signatures of potential past gene transfer events will be discussed.

  18. Ponder over the Pluralism of Wiki Current Situation and Wiki Development%Wiki的应用领域与发展分析

    Institute of Scientific and Technical Information of China (English)

    洪跃; 崔海峰

    2008-01-01

    Wiki作为Web2.0时代的标志性技术和应用形式之一,在知识管理、信息传播等领域有着明显的优势,并在国外得到广泛应用,但在国内,由于种种原因人们对Wiki的认识和了解还处于初级阶段.本文以Wiki的历史、应用及发展模式为主线,对Wiki的相关知识进行了梳理和整合,从多元视角出发解读Wiki,以期为国内Wiki的发展提出一孔之见.

  19. VITCOMIC: visualization tool for taxonomic compositions of microbial communities based on 16S rRNA gene sequences

    Directory of Open Access Journals (Sweden)

    Kurokawa Ken

    2010-06-01

    Full Text Available Abstract Background Understanding the community structure of microbes is typically accomplished by sequencing 16S ribosomal RNA (16S rRNA genes. These community data can be represented by constructing a phylogenetic tree and comparing it with other samples using statistical methods. However, owing to high computational complexity, these methods are insufficient to effectively analyze the millions of sequences produced by new sequencing technologies such as pyrosequencing. Results We introduce a web tool named VITCOMIC (VIsualization tool for Taxonomic COmpositions of MIcrobial Community that can analyze millions of bacterial 16S rRNA gene sequences and calculate the overall taxonomic composition for a microbial community. The 16S rRNA gene sequences of genome-sequenced strains are used as references to identify the nearest relative of each sample sequence. With this information, VITCOMIC plots all sequences in a single figure and indicates relative evolutionary distances. Conclusions VITCOMIC yields a clear representation of the overall taxonomic composition of each sample and facilitates an intuitive understanding of differences in community structure between samples. VITCOMIC is freely available at http://mg.bio.titech.ac.jp/vitcomic/.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-06-15

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

  1. Pseudomonas community structure and antagonistic potential in the rhizosphere : insights gained by combining phylogenetic and functional gene-based analyses

    NARCIS (Netherlands)

    Costa, Rodrigo; Gomes, Newton C. M.; Kroegerrecklenfort, Ellen; Opelt, Katja; Berg, Gabriele; Smalla, Kornelia

    2007-01-01

    The Pseudomonas community structure and antagonistic potential in the rhizospheres of strawberry and oilseed rape (host plants of the fungal phytopathogen Verticillium dahliae) were assessed. The use of a new PCR-DGGE system, designed to target Pseudomonas-specific gacA gene fragments in environment

  2. The diversity and abundance of phytase genes (beta-propeller phytases) in bacterial communities of the maize rhizosphere

    NARCIS (Netherlands)

    Cotta, S.R.; Cavalcante Franco Dias, A.; Seldin, L.; Andreote, F. D.; van Elsas, J. D.

    2016-01-01

    The ecology of microbial communities associated with organic phosphorus (P) mineralization in soils is still understudied. Here, we assessed the abundance and diversity of bacteria harbouring genes encoding beta-propeller phytases (BPP) in the rhizosphere of traditional and transgenic maize cultivat

  3. Healthcare professionals' intentions to use wiki-based reminders to promote best practices in trauma care: a survey protocol

    Directory of Open Access Journals (Sweden)

    Lapointe Jean

    2010-06-01

    Full Text Available Abstract Background Healthcare professionals are increasingly using wikis as collaborative tools to create, synthesize, share, and disseminate knowledge in healthcare. Because wikis depend on collaborators to keep content up-to-date, healthcare professionals who use wikis must adopt behaviors that foster this collaboration. This protocol describes the methods we will use to develop and test the metrological qualities of a questionnaire that will assess healthcare professionals' intentions and the determinants of those intentions to use wiki-based reminders that promote best practices in trauma care. Methods Using the Theory of Planned Behavior, we will conduct semi-structured interviews of healthcare professionals to identify salient beliefs that may affect their future use of wikis. These beliefs will inform our questionnaire on intended behavior. A test-retest of the survey will verify the questionnaire's stability over time. We will interview 50 healthcare professionals (25 physicians and 25 allied health professionals working in the emergency departments of three trauma centers in Quebec, Canada. We will analyze the content of the interviews and construct and pilot a questionnaire. We will then test the revised questionnaire with 30 healthcare professionals (15 physicians and 15 allied health professionals and retest it two weeks later. We will assess the internal consistency of the questionnaire constructs using Cronbach's alpha coefficients and determine their stability with the intra-class correlation (ICC. Discussion To our knowledge, this study will be the first to develop and test a theory-based survey that measures healthcare professionals' intentions to use a wiki-based intervention. This study will identify professionals' salient beliefs qualitatively and will quantify the psychometric capacities of the questionnaire based on those beliefs.

  4. Develop Semantic Wiki System for Tradition Chinese Medicine%中医药语义维基系统研发

    Institute of Scientific and Technical Information of China (English)

    于彤; 陈华钧; 李敬华

    2013-01-01

    Semantic Wiki is an emerging technology that empowers wiki systems with Semantic Web technologies.Semantic Wiki systems not only retain the advantages of wiki systems in social knowledge engineering,but also enhance the support for structured data.Traditional Chinese Medicine (TCM)Encyclopedia is a Website for TCM knowledge sharing,developed by using Semantic Wiki technology.This system utilizes a TCM domain ontology to integrate the knowledge and artifacts in TCM domain,and provides Encyclopedia-like knowledge services for Web users.In this paper,we give a brief introduction to the Semantic Wiki technology,and articulate the technical background,use paradigm,and user interface of TCM Encyclopedia,in order to provide useful information for researchers and developers in TCM informatics.%语义维基是语义Web技术与维基系统相结合的产物,它既保持了维基系统在社会化知识工程方面的优势,又强化了对结构性数据的支持。中医百科是通过语义维基技术构建的中医药知识共享网站,它基于中医药领域本体来整合中医药领域的知识与作品,向网络用户提供百科全书式的知识服务。本文对语义维基技术进行了简要介绍,并阐述了中医百科的后台技术、交互方式和交互方式,以期为中医药信息化领域的研究和开发人员提供参考。

  5. Changes of microbial community structures and functional genes during biodegradation of phenolic compounds under high salt condition

    Institute of Scientific and Technical Information of China (English)

    WANG Ping; QU Yuanyuan; ZHOU Jiti

    2009-01-01

    The changes of microbial community structures and functional genes during the biodegradation of single phenol and phenol plus p-cresol under high salt condition were explored.It was found that the phenol-fed system (PFS) exhibited stronger degrading abilities and more stable biomass than that of the phenol plus p-cresol-fed system (PCFS).The microbial community structures were revealed by a modern DNA fingerprint technique,ribosomal intergenic spacer analysis (RISA).The results indicated that the microbial community of PFS changed obviously when gradually increased phenol concentration,while PCFS showed a little change.16S rRNA sequence analysis of the major bands showed that Alcanivorax sp.genus was predominant species during phenolic compounds degradation.Furthermore,amplified functional DNA restriction analysis (AFDRA) on phenol hydroxylase genes showed that the fingerprints were substantially different in the two systems,and the fingerprints were not the same during the different operational periods.

  6. Ensino na comunidade e inteligência coletiva: partilhando saberes com o WIKI

    Directory of Open Access Journals (Sweden)

    Antonio Pithon Cyrino

    Full Text Available As novas tecnologias de informação e comunicação têm permitido a produção de inovações no processo de ensino-aprendizagem no ensino superior. Neste estudo de intervenção e pesquisa em disciplina de ensino em comunidade da Faculdade de Medicina de Botucatu - Unesp (FMB-Unesp, procura-se explorar tais possibilidades mediante o envolvimento de alunos, professores e membros da própria comunidade. Para tanto, desenvolveu-se uma página Wiki, com informações produzidas pelos alunos a respeito de um bairro da cidade de Botucatu, com o objetivo de criar um ambiente de troca, interação, cooperação e produção compartilhada de conhecimentos entre esses sujeitos. Um grupo de jovens dessa comunidade recebeu treinamento no uso do Wiki, o que lhes permitiu incluir na página informações novas sobre o território. A análise mostra que na produção textual desses jovens ganhou destaque alguns elementos significativos de seu cotidiano. A presença de um professor tutor na comunidade foi essencial para o êxito do processo. Os resultados alcançados apontam a viabilidade e potencialidade do uso do Wiki como ferramenta de inteligência coletiva, por permitir a troca de saberes entre alunos e comunidade, valorizando toda forma de conhecimento e a expressão das singularidades.

  7. Virtual strategies to improve transversal competences, using wikis in a collaborative work

    Science.gov (United States)

    Guinau, Marta; Playa, Elisabet

    2016-04-01

    A major educational aim in university degrees since the implementation of the European Credit Transfer System (ECTS) on the European universities is the work based on transversal competences. However, the first course students arrive at the Spanish universities with important deficiencies on some of these competences, especially regarding on oral and written expression, time management and collaborative work. The experience of the teachers involved in this work has revealed the coordination difficulty between the students to work in group, important deficiencies on information management and the stress caused by the oral presentations. The results presented here correspond to a teaching innovation project. It is based on: a) the development of works in groups of 3 or 4 students, proposed as flipped classrooms strategy and b) the implementation of a virtual tool (a wiki). This tool helps the students with scientific information management and facilitates the access of all the students belonging to the work group at the information provided by colleagues. The wiki also improves the monitoring and evaluation of the work and contributions of each student by teachers. Each group must develop a topic related to the subject - General Geology and Geochemistry - that the group chose from a list of earth sciences topics proposed by teachers. The resulting works are presented in poster and oral presentations (10 min. per group and 5 min. for questions). Each work is evaluated by teachers using the evidences provided on the wiki and by means of evaluation guides. Moreover, the students must self and co-evaluate the presented works. The implementation of this project has provided information to analyze the impact of these strategies and to quantify it in terms of 'Learning Analytics'.

  8. WIKI::SCORE - A Collaborative Environment For Music Transcription And Publishing

    OpenAIRE

    J.João Almeida; N.Ramos Carvalho; J.Nuno Oliveira

    2012-01-01

    Music sources are most commonly shared in music scores scanned or printed on paper sheets. These artifacts are rich in information, but since they are images it is hard to re-use and share their content in todays’ digital world. There are modern languages that can be used to transcribe music sheets, this is still a time consuming task, because of the complexity involved in the process and the typical huge size of the original documents. WIKI::SCORE is a collaborative environment where seve...

  9. Wiki como herramienta de aprendizaje en grupo y evaluación al alumno

    Directory of Open Access Journals (Sweden)

    María Jesús Miró Obradors

    2013-11-01

    Full Text Available “Estimular el aprendizaje autónomo, incentivar el estudio individual y colectivo y reducir las formas pasivas de enseñanza" es uno de los objetivos de los nuevos planes de estudios. Siendo una Wiki aquél espacio de trabajo en línea que posibilita la creación colectiva de documentos utilizando un navegador web, consideramos ésta, una buena herramienta para el desarrollo del trabajo en grupo de los alumnos, así como para realizar una evaluación continuada de los mismos. Metodología: 1 Establecer grupos de estudiantes, 2 Crear wikis en las asignaturas abiertas en Moodle del Campus Virtual UCM (CV, 2 Introducción por el profesor de las actividades, 3 Abrir un foro, 4 Envío de las tareas (CV, 5 Calificación. Resultados y conclusiones: Alumnos de asignaturas en el Área de Bioquímica y Biología Molecular y Celular del Grado en Farmacia (UCM, han trabajado en wikis: a Una tabla, en la cual cada grupo de estudiantes introduce dos palabras clave (sin repetir de cada tema impartido y a su vez, redacta el enunciado de dos preguntas relativas a palabras clave que han incluido previamente otro grupo de alumnos. La lista resultante y revisada de unas 75 cuestiones, se utilizó para elaborar exámenes, realizados en clase tras la finalización de cada bloque de contenidos. b Cuestiones relativas a seminarios y películas de cine proyectadas previamente. El módulo Wiki de Moodle ha permitido a cada estudiante trabajar en páginas web on line con sus compañeros, habiendo podido añadir, expandir o modificar su contenido en ellas. Las versiones antiguas nunca se eliminan y pueden restaurarse. Esto ha permitido, además de calificar el trabajo de grupo, hacer un seguimiento del trabajo individual de cada estudiante, para su mejor evaluación. PIMCD 2013 nº 3 (UCM.

  10. Wiki-Based Stochastic Programming and Statistical Modeling System for the Cloud

    Directory of Open Access Journals (Sweden)

    Vaidas Giedrimas

    2016-03-01

    Full Text Available Scientific software is a special type of software because its quality has a huge impact on the quality of scientific conclusions and scientific progress. However, it is hard to ensure required quality of the software because of the misunderstandings between the scientists and the software engineers. In this paper, we present a system for improving the quality of scientific software using elements of wikinomics and cloud computing and its implementation details. The system enables scientists to collaborate and make direct evolution of the models, algorithms, and programs. WikiSPSM expands the limits of mathematical software.

  11. Frequencies of single nucleotide polymorphisms in genes regulating inflammatory responses in a community-based population

    Directory of Open Access Journals (Sweden)

    Comstock George W

    2007-03-01

    Full Text Available Abstract Background Allele frequencies reported from public databases or articles are mostly based on small sample sizes. Differences in genotype frequencies by age, race and sex have implications for studies designed to examine genetic susceptibility to disease. In a community-based cohort of 9,960 individuals, we compared the allele frequencies of 49 single nucleotide polymorphisms (SNPs of genes involved in inflammatory pathways to the frequencies reported on public databases, and examined the genotypes frequencies by age and sex. The genes in which SNPs were analyzed include CCR2, CCR5, COX1, COX2, CRP, CSF1, CSF2, IFNG, IL1A, IL1B, IL2, IL4, IL6, IL8, IL10, IL13, IL18, LTA, MPO, NOS2A, NOS3, PPARD, PPARG, PPARGC1 and TNF. Results Mean(SD age was 53.2(15.5; 98% were Caucasians and 62% were women. Only 1 out of 33 SNPs differed from the SNP500Cancer database in allele frequency by >10% in Caucasians (n = 9,831, whereas 12 SNPs differed by >10% (up to 50% in African Americans (n = 105. Two out of 15 SNPs differed from the dbSNP database in allele frequencies by >10% in Caucasians, and 5 out of 15 SNPs differed by >10% in African Americans. Age was similar across most genotype groups. Genotype frequencies did not differ by sex except for TNF(rs1799724, IL2(rs2069762, IL10(rs1800890, PPARG(rs1801282, and CRP(rs1800947 with differences of less than 4%. Conclusion When estimating the size of samples needed for a study, particularly if a reference sample is used, one should take into consideration the size and ethnicity of the reference sample. Larger sample size is needed for public databases that report allele frequencies in non-Caucasian populations.

  12. Metatranscriptome Sequencing of a Reef-building Coral Elucidates Holobiont Community Gene Functions in Health and Disease

    Science.gov (United States)

    Timberlake, S.; Helbig, T.; Fernando, S.; Penn, K.; Alm, E.; Thompson, F.; Thompson, J. R.

    2012-12-01

    The coral reefs of the Abrolhos Bank of Brazil play a vital ecological role in the health of the Southern Atlantic Ocean, but accelerating rates of disease, particularly white plague, threaten this ecosystem. Thus, an understanding of white plague disease and diagnostic tests for it are urgently needed. The coral animal is associated with a distinct microbiome, a diverse assemblage of eukaryotes, bacteria, and viruses. That these microbes have a great influence on the health of the coral has been long known, however, most of their functions are still mysterious. While recent studies have contrasted healthy and white-plague-associated communities, the causative agents and mechanisms of the disease remain unknown. We collected fragments of healthy and diseased corals, as well as post-disease skeleton, from 12 colonies of the genus Mussismilia, the major component of the reef structure in the Abrolhos bank, and increasingly, a victim of white-plague disease. Fragments were flash-frozen in situ, and prepped for culture-free high throughput sequencing of gene transcripts with the Illumina II-G. While the membership of the microbial communities associated with coral has been previously described, the a coral holobiont community's gene function has, to date, never been assayed by this powerful approach. We designed a bioinformatics pipeline to analyze the short-read data from this complex sample: identifying the functions of genes expressed in the holobiont, and describing the active community's taxonomic composition. We show that gene functions expressed by the coral's bacterial assemblage are distinct from those of the underlying skeleton, and we highlight differences in the disease samples. We find that gene markers for the dissimilatory sulfate reduction pathway more abundant in the disease state, and we further quantify this difference with qPCR. Finally, we report the abundant expression of highly repetitive transcripts in the diseased coral samples, and highlight

  13. The Collaborative Learning Activity Design of The High School Information Technology Course Based on Wiki%基于Wiki的《高中信息技术》课协作学习活动设计

    Institute of Scientific and Technical Information of China (English)

    杨好利; 曲凯歌

    2013-01-01

    As one of the emerging social software of information society, Wiki supports collaborative collaboration oriented com?munity, and provides a good collaboration platform for carrying out cooperative learning. In this paper, taking the high school in?formation technology courses as an example, we design the collaborative learning activity based on Wiki from several aspects, such as the learner characteristics, learning objectives, learning tasks, learning environment and resources, study groups, the collab?oration process, and collaborative evaluation.%Wiki作为信息社会新兴的社会性软件之一,支持面向社群的协作式协作,为开展协作学习提供了良好的协作平台。文章以《高中信息技术》课为例,从学习者特征、学习目标、学习任务、学习环境和资源、学习小组、协作过程、协作评价等方面设计了基于Wiki的协作学习活动。

  14. Effect of different biochars on antibiotic resistance genes and bacterial community during chicken manure composting.

    Science.gov (United States)

    Cui, Erping; Wu, Ying; Zuo, Yiru; Chen, Hong

    2016-03-01

    Rice straw biochar (RSB) and mushroom biochar (MB) were added to lab-scale chicken manure composting to evaluate their effects on the behaviors of antibiotic resistance genes (ARGs) and on total and bio-available heavy metals (Cu, Zn and As). The associated bacterial community was characterized by 16SrRNA high-throughput sequencing. The abundance of pathogenic bacteria was also calculated. At the end of the control composting experiment, the average removal rate of ARGs was 0.86 log units and the removal rate of pathogenic bacteria was 57.1%. MB addition resulted in a higher removal rate than that in the control composting experiment. However, RSB addition yielded opposite results, which may be due to the higher abundance of Erysipelotrichaceae, Lactobacillaceae, Family_XI_Incertae_Sedis (belonging to Firmicutes carrying and disseminating ARGs) and pathogenic bacteria carrying ARGs. Furthermore, the correlations between bio-available heavy metals and ARGs were more obvious than those between total heavy metals and ARGs.

  15. Effects of polycyclic aromatic hydrocarbons on microbial community structure and PAH ring hydroxylating dioxygenase gene abundance in soil.

    Science.gov (United States)

    Sawulski, Przemyslaw; Clipson, Nicholas; Doyle, Evelyn

    2014-11-01

    Development of successful bioremediation strategies for environments contaminated with recalcitrant pollutants requires in-depth knowledge of the microorganisms and microbial processes involved in degradation. The response of soil microbial communities to three polycyclic aromatic hydrocarbons, phenanthrene (3-ring), fluoranthene (4-ring) and benzo(a)pyrene (5-ring), was examined. Profiles of bacterial, archaeal and fungal communities were generated using molecular fingerprinting techniques (TRFLP, ARISA) and multivariate statistical tools were employed to interpret the effect of PAHs on community dynamics and composition. The extent and rate of PAH removal was directly related to the chemical structure, with the 5-ring PAH benzo(a)pyrene degraded more slowly than phenathrene or fluoranthene. Bacterial, archaeal and fungal communities were all significantly affected by PAH amendment, time and their interaction. Based on analysis of clone libraries, Actinobacteria appeared to dominate in fluoranthene amended soil, although they also represented a significant portion of the diversity in phenanthrene amended and unamended soils. In addition there appeared to be more γ-Proteobacteria and less Bacteroidetes in soil amended with either PAH compared to the control. The soil bacterial community clearly possessed the potential to degrade PAHs as evidenced by the abundance of PAH ring hydroxylating (PAH-RHDα) genes from both gram negative (GN) and gram positive (GP) bacteria in PAH-amended and control soils. Although the dioxygenase gene from GP bacteria was less abundant in soil than the gene associated with GN bacteria, significant (p PAH-RHDα gene were observed during phenanthrene and fluoranthene degradation, whereas there was no significant difference in the abundance of the GN PAH-RHDα gene during the course of the experiment. Few studies to-date have examined the effect of pollutants on more than one microbial community in soil. The current study provides

  16. Wiki-mediated Writing: design, media, writing strategies and feedback in online text production

    Directory of Open Access Journals (Sweden)

    Sylvana Sofkova Hashemi

    2013-10-01

    Full Text Available Bringing social media arenas, such as wikis, into the classroom invites teaching approaches that engage students in authentic, participatory and creative writing processes. This case study examines the online text production of primary school students in a wiki environment and how the key functionalities for commentary, discussion, logging skills of text and multimodal expression are utilized in practice to develop writing. Exploring the design of assignments and analysing the nature of final texts, writing strategies and feedback reveals an iterative process of writing dominated by strategies of expanding texts with new information and occasional surface editing. The students composed individual narratives on selected themes augmented by drawings, images, speaking avatars and video clips. Feedback was mainly provided by the teachers in the form of encouraging comments and corrective revisions directly in the students’ texts. Peer response was rare, in one project taking the form of discussion posts. Revising indicating increased language awareness was observed among second language learners. Overall, the study demonstrates a tension between instructional design, the affordances of the writing arena and the space for creativity when engaging students in advanced, participatory and reflective composing and revising of texts.

  17. A Collaborative Web-Based Approach to Planning Research, Integration, and Testing Using a Wiki

    Science.gov (United States)

    Delaney, Michael M.; Koshimoto, Edwin T.; Noble, Deleena; Duggan, Christopher

    2010-01-01

    The National Aeronautics and Space Administration Integrated Vehicle Health Management program touches on many different research areas while striving to enable the automated detection, diagnosis, prognosis, and mitigation of adverse events at the aircraft and system level. At the system level, the research focus is on the evaluation of multidisciplinary integrated methods, tools, and technologies for achieving the program goal. The participating program members form a diverse group of government, industry, and academic researchers. The program team developed the Research and Test Integration Plan in order to track significant test and evaluation activities, which are important for understanding, demonstrating, and communicating the overall project state and project direction. The Plan is a living document, which allows the project team the flexibility to construct conceptual test scenarios and to track project resources. The Plan also incorporates several desirable feature requirements for Plan users and maintainers. A wiki has proven to be the most efficient and effective means of implementing the feature requirements for the Plan. The wiki has proven very valuable as a research project management tool, and there are plans to expand its scope.

  18. Open Content, Open Learning 2.0: Using Wikis and Blogs in Higher Education

    Science.gov (United States)

    Wheeler, Steve

    This chapter focuses on the use of open content social software (wikis and blogs) as online supporting and enabling tools for students in higher education. The chapter presents arguments from both strategic and pedagogical perspectives and focuses particularly on the reality of pedagogical change where self-directed and self-organized "informal" learning, open content, and open learning are challenging the traditionally accepted roles of both students and teachers. The chapter describes approaches used to promote best practice in the use of blogs and wikis for reflective practice, knowledge creation, and the promotion of a culture of sharing and collaboration. It introduces a new five-stage model of online learning activities presented as an adaptive framework and a second model which has been created to enable visualization of Web 2.0 tool integration. The chapter argues that open content tools present opportunities to promote positive changes in university education to enhance quality and extend access, by encouraging student-generated content, knowledge creation, and self-organized learning processes, wherever students are located.

  19. FoodWiki: a Mobile App Examines Side Effects of Food Additives Via Semantic Web.

    Science.gov (United States)

    Çelik Ertuğrul, Duygu

    2016-02-01

    In this article, a research project on mobile safe food consumption system (FoodWiki) is discussed that performs its own inferencing rules in its own knowledge base. Currently, the developed rules examines the side effects that are causing some health risks: heart disease, diabetes, allergy, and asthma as initial. There are thousands compounds added to the processed food by food producers with numerous effects on the food: to add color, stabilize, texturize, preserve, sweeten, thicken, add flavor, soften, emulsify, and so forth. Those commonly used ingredients or compounds in manufactured foods may have many side effects that cause several health risks such as heart disease, hypertension, cholesterol, asthma, diabetes, allergies, alzheimer etc. according to World Health Organization. Safety in food consumption, especially by patients in these risk groups, has become crucial, given that such health problems are ranked in the top ten health risks around the world. It is needed personal e-health knowledge base systems to help patients take control of their safe food consumption. The systems with advanced semantic knowledge base can provide recommendations of appropriate foods before consumption by individuals. The proposed FoodWiki system is using a concept based search mechanism that performs on thousands food compounds to provide more relevant information.

  20. [Podcasts, wikis and blogs: the web 2.0 tools for medical and health education].

    Science.gov (United States)

    Santoro, Eugenio

    2007-10-01

    In the recent years, we have witnessed a new revolution in the field of communication through Internet. Web 2.0, whose contents are provided by the collaboration, discussion, and sharing between more users, is replacing the traditional web (the web 1.0). The use of podcasts, wikis, and blogs is rapidly increasing, and today they are proposed as educational tools for health professionals, physicians, and medical students. Medical podcasts have been developed by online medical journals (such as the New England Journal of Medicine, the Lancet, the British Medical Journal, and the JAMA), and by medical societies, medical schools and health institutions to communicate to and educate the physicians, the students, the patients, and the health consumers. Following the example of Wikipedia, medical wikis and blogs are being developed to support the medical education, the collaboration among researchers, and the clinical practice. However, these tools present some limitations related to their openness and ease of use which virtually allows anybody to alter and edit existing contents or to create new ones. This could make the contents unreliable and inaccurate, and could introduce risks for a correct medical education and for the health of those patients deciding to follow the medical advice included. Studies are needed to evaluate limits, benefits, and efficacy of these tools when used in the contexts of medical education and clinical practice. Other studies are needed to evaluate the reliability and the accuracy of the medical contents posted online through the web 2.0 services.

  1. Arquitectura en territorios informados y transparentes Una wiki en la escuela de arquitectura

    Directory of Open Access Journals (Sweden)

    Javier Fernández García

    2010-01-01

    Full Text Available El marco general de nuestra investigación en la universidad son los espacios de convivencia, información y formación que configuran los habitantes en un territorio online. La Web 2.0 nos ha dotado de nuevas herramientas con la que construir espacios. Desde la fundación en agosto de 2006 de CityWiki, indagamos en la arquitectura de estos lugares que se articulan en un espacio común en el que, a falta de jerarquía y policía, la acción en él la define el empoderamiento y la libertad del ciudadano responsable. A modo de laboratorio, desde entonces, embarcamos la actividad investigadora y docente en la actitud 2.0 incluida en la WWW. En la primera parte de este artículo se expone el pensamiento actualizado que empíricamente evoluciona emparejado a la actualidad de nuestras investigaciones. El objetivo es hacer entender el territorio wiki como informado y transparente llamado a añadir capas de información a la realidad para de esta forma no sustituirla sino ampliarla. Seguidamente, en la segunda parte, se describe y analiza la experiencia de innovación llevada a cabo durante el curso 2007/2008 en la que se ensayó un modelo docente instrumentados en los modos y paisajes previamente descritos.

  2. What Does the Digital Student Want? Cross-Cultural Collaboration and Wikis in Academic Literacy

    Directory of Open Access Journals (Sweden)

    Agnes Pisanski Peterlin

    2015-12-01

    Full Text Available New online educational tools have opened new possibilities for cross-cultural collaboration which supports critical thinking and encourages learner autonomy. Nevertheless, the success of a crosscultural collaborative experience cannot be taken for granted, since it inevitably involves the need to bridge transcultural differences. This paper presents an American-Slovene cross-cultural collaborative project with a focus on the perceptions of the Slovene student-participants. In particular, it examines their views of one of the components of the collaborative project, specifically, the collaborative wiki writing assignment, introduced to develop the students’ academic literacy skills. The findings of the questionnaire study show that the participants’ experiences with the cross-cultural collaboration were positive, although their answers reveal a slight preference for less challenging activities. Nevertheless, even the fairly demanding writing assignment was generally perceived to be interesting and useful: while its full interactive potential was not realized due to the participants’ reluctance to engage in editing, the wiki is clearly an efficient tool for promoting academic literacy.

  3. Fiction et forme encyclopédique : Wookieepedia, Dragon Ball Wiki et Cie.

    Directory of Open Access Journals (Sweden)

    Benoît Berthou

    2011-06-01

    Full Text Available Wookieepedia, Final Fantasy Wiki, Dragon Ball Wiki, Memory Alpha, WoWWiki… Autant d’encyclopédies en ligne abordant de célèbres fictions pour la jeunesse à travers un nombre parfois considérable d’articles abordant toutes sortes de sujets (récits, technologies, personnages, lieux, auteurs, fans…. Que nous apprennent ces dispositifs entendant prendre des fictions au sérieux, c’est-à-dire aborder un domaine relevant de l’imaginaire avec des outils relevant du domaine de la connaissance ? Deux pratiques se dégagent : la référence à des produits culturels prenant des formes fort diverses (romans, bandes dessinées, films, jeux vidéo… et le lien entre les divers articles. Ces deux pratiques montrent comment se développe une expertise quant à une fiction, une capacité à se situer dans une construction imaginaire.

  4. The Comparison of the Opinions of the University Students on the Usage of Blog and Wiki for Their Courses

    Science.gov (United States)

    Avci, Ummuhan; Askar, Petek

    2012-01-01

    The purpose of this study was to investigate the use of blogs and wikis as constructive tools in the computer courses of prospective teachers and compare them with respect to perceived usefulness, perceived ease of use, intention, self efficacy, and anxiety. Ninety-two students who were enrolled in various teacher education programs used blog and…

  5. Is Julian Assange an International Version of Daniel Ellsberg and WikiLeaks the Modern Equivalent of the Pentagon Papers?

    Science.gov (United States)

    Freivogel, William H.

    2011-01-01

    History has placed the stamp of approval on the publication of the Pentagon Papers, the top-secret history of the Vietnam War. If WikiLeaks editor-in-chief Julian Assange is another Daniel Ellsberg, then it is possible the website's disclosures will be viewed over time as similarly in the public interest. A classroom discussion on the release of…

  6. Research and Teaching: WikiED--Using Web 2.0 Tools to Teach Content and Critical Thinking

    Science.gov (United States)

    Frisch, Jennifer K.; Jackson, Paula C.; Murray, Meg C.

    2013-01-01

    WIKIed Biology is a National Science Foundation Transforming Undergraduate Education in Science, Technology, Engineering, and Mathematics interdisciplinary project in which the authors developed and implemented a model for student centered, inquiry-driven instruction using Web 2.0 technologies to increase inquiry and conceptual understanding in…

  7. Using a Wiki-Based Collaborative Process Writing Pedagogy to Facilitate Collaborative Writing among Chinese Primary School Students

    Science.gov (United States)

    Li, Xuanxi; Chu, Samuel Kai Wah; Ki, Wing Wah; Woo, Matsuko

    2012-01-01

    This case study explored collaborative writing in Chinese among 59 primary four Chinese students using a "Wiki-based Collaborative Process Writing Pedagogy" (WCPWP) in Shenzhen, China. It aimed mainly to design and orchestrate a WCPWP in order to facilitate students' Chinese writing. It investigated students' collaborative writing process and…

  8. Is Julian Assange an International Version of Daniel Ellsberg and WikiLeaks the Modern Equivalent of the Pentagon Papers?

    Science.gov (United States)

    Freivogel, William H.

    2011-01-01

    History has placed the stamp of approval on the publication of the Pentagon Papers, the top-secret history of the Vietnam War. If WikiLeaks editor-in-chief Julian Assange is another Daniel Ellsberg, then it is possible the website's disclosures will be viewed over time as similarly in the public interest. A classroom discussion on the release of…

  9. Social Media and Peer Feedback: What Do Students Really Think about Using Wiki and Facebook as Platforms for Peer Feedback?

    Science.gov (United States)

    Demirbilek, Muhammet

    2015-01-01

    Web 2.0 tools are becoming increasingly pervasive in higher education, and as a result, there is increasing interest in the use of online feedback activities. This study investigated students' actual experiences and perceptions using social media, Wiki and Facebook, tools to provide peer feedback on students' instructional material projects and to…

  10. "I Felt Like the Enemy and the Savior All at Once": English Teacher Identity in a Methods Course Wiki

    Science.gov (United States)

    Jewett, Michelle Ann

    2012-01-01

    This study explores the identity constructions of two cohorts of preservice teachers enrolled in English methods courses during a semester of field experience. This research employs a qualitative methodology and documents the nature of participant's responses posted to online wiki forum. Data sources include archived electronic interactions…

  11. Using the Integrated Vehicle Health Management Research Test and Integration Plan Wiki to Identify Synergistic Test Opportunities

    Science.gov (United States)

    Koelfgen, Syri J.; Faber, James J.

    2010-01-01

    The National Aeronautics and Space Administration (NASA) and the aviation industry have recognized a need for developing a method to identify and combine resources to carry out research and testing more efficiently. The Integrated Vehicle Health Management (IVHM) Research Test and Integration Plan (RTIP) Wiki is a tool that is used to visualize, plan, and accomplish collaborative research and testing. Synergistic test opportunities are developed using the RTIP Wiki, and include potential common resource testing that combines assets and personnel from NASA, industry, academia, and other government agencies. A research scenario is linked to the appropriate IVHM milestones and resources detailed in the wiki, reviewed by the research team members, and integrated into a collaborative test strategy. The scenario is then implemented by creating a test plan when appropriate and the research is performed. The benefits of performing collaborative research and testing are achieving higher Technology Readiness Level (TRL) test opportunities with little or no additional cost, improved quality of research, and increased communication among researchers. In addition to a description of the method of creating these joint research scenarios, examples of the successful development and implementation of cooperative research using the IVHM RTIP Wiki are given.

  12. Evaluating the Effectiveness of the Open-Access ChemWiki Resource as a Replacement for Traditional General Chemistry Textbooks

    Science.gov (United States)

    Allen, Gregory; Guzman-Alvarez, Alberto; Smith, Amy; Gamage, Alan; Molinaro, Marco; Larsen, Delmar S.

    2015-01-01

    Open educational resources (OERs) provide a potential alternative to costly textbooks and can allow content to be edited and adapted to a variety of classroom environments. At the University of California, Davis, the OER "ChemWiki" project, as part of the greater STEMWiki Hyperlibrary, was developed to supplant traditional post-secondary…

  13. Social Media and Peer Feedback: What Do Students Really Think about Using Wiki and Facebook as Platforms for Peer Feedback?

    Science.gov (United States)

    Demirbilek, Muhammet

    2015-01-01

    Web 2.0 tools are becoming increasingly pervasive in higher education, and as a result, there is increasing interest in the use of online feedback activities. This study investigated students' actual experiences and perceptions using social media, Wiki and Facebook, tools to provide peer feedback on students' instructional material projects and to…

  14. Effects of Blackboard's Discussion Boards, Blogs and Wikis on Effective Integration and Development of Literacy Skills in EFL Students

    Science.gov (United States)

    Alharbi, Majed

    2015-01-01

    This study aimed to investigate the effects of the online course tools, specifically discussion boards, blogs and wikis, the built-in facilities of Blackboard as computer-mediated communication integrated in e-learning environments on improving integrated reading and writing and on the attitudes of EFL college students towards literacy skills in…

  15. Evaluation of bacterial communities by bacteriome analysis targeting 16S rRNA genes and quantitative analysis of ammonia monooxygenase gene in different types of compost.

    Science.gov (United States)

    Kitamura, Rika; Ishii, Kazuo; Maeda, Isamu; Kozaki, Toshinori; Iwabuchi, Kazunori; Saito, Takahiro

    2016-01-01

    Biofiltration technology based on microbial degradation and assimilation is used for the removal of malodorous compounds, such as ammonia. Microbes that degrade malodorous and/or organic substances are involved in composting and are retained after composting; therefore, mature composts can serve as an ideal candidate for a biofilter medium. In this study, we focused on different types of raw compost materials, as these are important factors determining the bacterial community profile and the chemical component of the compost. Therefore, bacterial community profiles, the abundance of the bacterial ammonia monooxygenase gene (amoA), and the quantities of chemical components were analyzed in composts produced from either food waste or cattle manure. The community profiles with the lowest beta diversity were obtained from single type of cattle manure compost. However, cattle manure composts showed greater alpha diversity, contained higher amounts of various rRNA gene fragments than those of food waste composts and contained the amoA gene by relative quantification, and Proteobacteria were abundantly found and nitrifying bacteria were detected in it. Nitrifying bacteria are responsible for ammonia oxidation and mainly belong to the Proteobacteria or Nitrospira phyla. The quantities of chemical components, such as salt, phosphorus, and nitrogen, differed between the cattle manure and food waste composts, indicating that the raw materials provided different fermentation environments that were crucial for the formation of different community profiles. The results also suggest that cattle manure might be a more suitable raw material for the production of composts to be used in the biofiltration of ammonia. Copyright © 2015 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  16. Wiki協作系統應用於數位典藏之內容加值與知識匯集 Application of Wiki Collaboration System for Value Adding and Knowledge Aggregation in a Digital Archive Project

    Directory of Open Access Journals (Sweden)

    Sinn-Cheng Lin

    2006-03-01

    Full Text Available 本文提出一個由「系統」、「內容」與「社群」三要素所構成的「維基協作金三角模型」,並應用於數位典藏計畫中,作為內容加值與知識匯集平台。基於此一模型,我們首先對眾多維基引擎進行比較分析,以選擇最適合的系統;接著,以台灣棒球新聞數位典藏庫為基礎,以維基協作系統為平台,運用知識組織技術,如分類、索引、索引典與控制詞彙等,進行內容加值與知識匯集,以提升數位內容品質;最後,隨著資料量及社群規模日益成長,則探討如何提高社群成員的互動與參與,使社群之運作與經營更上軌道。This paper proposes a model called “The Golden Triangle for Wiki Collaboration”, composed of three elements: system, content, and community. The proposed model is used in a Digital Archives Project as a means of value adding and knowledge aggregation. We first compared and analyzed multiple wiki engines to select the best system for our research purpose. We chose Taiwanese Baseball News Digital Archive as the base of the research project and the wiki collaboration system as the platform. In order to improve and enhance the quality of digital content, we took the approach of applying techniques of knowledge organization, such as classification, indexing, thesaurus, and controlled vocabularies, so that value and knowledge can be added and aggregated. As the data and community grow, interaction of community members becomes crucial. Therefore, we discussed ways to encourage group interaction and participation from the operational and managerial point of view.

  17. Prevalence of antibiotic resistance genes and bacterial community composition in a river influenced by a wastewater treatment plant.

    Directory of Open Access Journals (Sweden)

    Elisabet Marti

    Full Text Available Antibiotic resistance represents a global health problem, requiring better understanding of the ecology of antibiotic resistance genes (ARGs, their selection and their spread in the environment. Antibiotics are constantly released to the environment through wastewater treatment plant (WWTP effluents. We investigated, therefore, the effect of these discharges on the prevalence of ARGs and bacterial community composition in biofilm and sediment samples of a receiving river. We used culture-independent approaches such as quantitative PCR to determine the prevalence of eleven ARGs and 16S rRNA gene-based pyrosequencing to examine the composition of bacterial communities. Concentration of antibiotics in WWTP influent and effluent were also determined. ARGs such as qnrS, bla TEM, bla CTX-M, bla SHV, erm(B, sul(I, sul(II, tet(O and tet(W were detected in all biofilm and sediment samples analyzed. Moreover, we observed a significant increase in the relative abundance of ARGs in biofilm samples collected downstream of the WWTP discharge. We also found significant differences with respect to community structure and composition between upstream and downstream samples. Therefore, our results indicate that WWTP discharges may contribute to the spread of ARGs into the environment and may also impact on the bacterial communities of the receiving river.

  18. Evaluating the effectiveness of a wiki internet site for medical topics.

    Science.gov (United States)

    Burgos, Clinton; Bot, Arjan; Ring, David

    2012-06-01

    To evaluate the iterative process of a collaborative public database (a Wiki) as a reference for information on hand illnesses we tested the null hypothesis that the number and type of edits are comparable for web pages covering different topics. The history of 4 hand surgery related web pages on the English language Wikipedia (Trigger finger, Complex Regional Pain Syndrome (CRPS), Ganglion cyst, and de Quervain Syndrome) were analyzed from inception to July 2011. Each edit was classified as one of six types: an addition is an edit that adds material; a deletion removes material; a modification is a combination of addition and deletion, or any rearrangement; a minor edit is a correction of spelling, grammar, or formatting errors; vandalism is any edit that is intended to harm the page; a vandalism fixed is an edit that addresses harm. The edits were also rated as possibly controversial or not (defined as edits that present information with a clear bias or do not list reliable sources). For both the Ganglion cyst and Trigger Finger pages, readability was measured at 1 year increments. Our primary null hypothesis was that the proportion of constructive edits (addition, deletion or modification) did not differ between the 4 web pages. The percentage of constructive edits (additions, deletions, and modifications) was significantly different for each page: 121/234 (52 %) for de Quervain, 258/448 (58 %) for CRPS, 103/156 (66 %) for Trigger Finger, and 160/389 (41 %) for Ganglion cyst. The percentage of edits related to vandalism was also significantly different: 28/234 (12 %) for de Quervain, 33/156 (7 %) for CRPS, 21/156 (14 %) for Trigger Finger, and 135/389 (35 %) for Ganglion cyst. Vandalism was quickly identified and addressed. Twenty-six percent of all edits were classified as potentially controversial. Forty percent of possibly controversial edits were deletions. The topic of a Wiki web page for information on hand illness influences the degree to which

  19. Investigation of energy gene expressions and community structures of free and attached acidophilic bacteria in chalcopyrite bioleaching.

    Science.gov (United States)

    Zhu, Jianyu; Jiao, Weifeng; Li, Qian; Liu, Xueduan; Qin, Wenqing; Qiu, Guanzhou; Hu, Yuehua; Chai, Liyuan

    2012-12-01

    In order to better understand the bioleaching mechanism, expression of genes involved in energy conservation and community structure of free and attached acidophilic bacteria in chalcopyrite bioleaching were investigated. Using quantitative real-time PCR, we studied the expression of genes involved in energy conservation in free and attached Acidithiobacillus ferrooxidans during bioleaching of chalcopyrite. Sulfur oxidation genes of attached A. ferrooxidans were up-regulated while ferrous iron oxidation genes were down-regulated compared with free A. ferrooxidans in the solution. The up-regulation may be induced by elemental sulfur on the mineral surface. This conclusion was supported by the results of HPLC analysis. Sulfur-oxidizing Acidithiobacillus thiooxidans and ferrous-oxidizing Leptospirillum ferrooxidans were the members of the mixed culture in chalcopyrite bioleaching. Study of the community structure of free and attached bacteria showed that A. thiooxidans dominated the attached bacteria while L. ferrooxidans dominated the free bacteria. With respect to available energy sources during bioleaching of chalcopyrite, sulfur-oxidizers tend to be on the mineral surfaces whereas ferrous iron-oxidizers tend to be suspended in the aqueous phase. Taken together, these results indicate that the main role of attached acidophilic bacteria was to oxidize elemental sulfur and dissolution of chalcopyrite involved chiefly an indirect bioleaching mechanism.

  20. The Effects of Wiki-based Recursive Process Writing on Chinese Narrative Essays for Chinese as a Second Language (CSL) Students in Singapore

    OpenAIRE

    Chee Kuen Chin; Cheng Gong; Boon Pei Tay

    2015-01-01

    This paper reports on the effects of using wiki-based process writing in Singapore’s Chinese as a Second Language (CSL) scenarios. A group of 32 Secondary 1 (Seventh Grade) students (“Students”) received various forms of online scaffolding at different steps of the writing process over two years. A whole set of teaching materials on 45 writing skills was developed and uploaded to the Wiki platform through five recursive cycles. In each cycle, the students were encouraged to app...

  1. From Finding Aids to Wiki Pages: Remixing Archival Metadata with RAMP

    Directory of Open Access Journals (Sweden)

    David González

    2013-10-01

    Full Text Available The Remixing Archival Metadata Project (RAMP is a lightweight web-based editing tool that is intended to let users do two things: (1 generate enhanced authority records for creators of archival collections and (2 publish the content of those records as Wikipedia pages. The RAMP editor can extract biographical and historical data from EAD finding aids to create new authority records for persons, corporate bodies, and families associated with archival and special collections (using the EAC-CPF format. It can then let users enhance those records with additional data from sources like VIAF and WorldCat Identities. Finally, it can transform those records into wiki markup so that users can edit them directly, merge them with any existing Wikipedia pages, and publish them to Wikipedia through its API.

  2. Experiencia del uso conjunto de WebQuests y Wikis en una asignatura universitaria no presencial

    Directory of Open Access Journals (Sweden)

    Torrico González, Ängel

    2007-01-01

    Full Text Available Desde hace unos años se viene investigando el uso de WebQuests para hacer posible una enseñanza de calidad en aulas no universitarias. El uso de estas técnicas en recintos universitarios es pequeño y habitualmente en asignaturas presenciales.Nosotros hemos realizado una experiencia en una asignatura de libre configuración no presencial dentro del Campus Andaluz Virtual, que nos ha servido para configurar una metodología propia, en la que destacamos el uso obligado de una herramienta con la que los alumnos puedan realizar una puesta en común de los resultados obtenidos: el Wiki, que unido al uso de la WebQuest nos ha proporcionado unos resultados muy positivos para el alumnado, tanto a nivel de enseñanza como de aprendizaje.

  3. Ciberativismo: a guerra da WikiLeaks contra os segredos de Estado

    Directory of Open Access Journals (Sweden)

    Carole Ferreira da Cruz

    2012-12-01

    Full Text Available http://dx.doi.org/10.5007/1806-5023.2012v9n1p90 Resenha do livro WikiLeaks: a guerra de Julian Assange contra os Segredos de Estado (Editora Verus, 2011, 336 p., no qual os repórteres investigativos do The Guardian, David Leigh e Luke Harding, contam os bastidores do maior vazamento da história, que revelou ao mundo detalhes obscuros da diplomacia mundial e das guerras do Afeganistão e do Iraque. A partir da análise do livro-reportagem sobre a organização WikliLeaks, pretendemos refletir sobre os mecanismos de resistência e atuação contra-hegemônica no contexto das redes abertas pelas tecnologias digitais.

  4. EnviWiki – výuková pomůcka na principu hypertextu

    Directory of Open Access Journals (Sweden)

    Jana Dlouhá

    2006-12-01

    Full Text Available Výukové texty, které jsou přístupné v elektronickém prostředí, mají kromě snadné dostupnosti a propojení s jinými informačními zdroji, i přednosti „hermeneutické“. Hypertext, který je základem jejich tvorby, totiž předstvuje nový metodologický nástroj lépe reprezentující fenomenální povahu skutečnosti. Příspěvek hodnotí tuto stránku reálně existující elektronické výukové pomůcky EnviWiki.

  5. 内容管理的明日之星——Wiki

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Wiki.org将Wiki定义为”可以运行的最简单的在线数据库”。受Apple的HyperCard编程环境的启发.Ward Cunningham在1995年.作为一种管理Portland Pattern Repository的网站内容的工具,开发了第一种Wiki软件。Wiki一词出自Wiki—Wiki。Wiki—Wiki在檀香山当地的语言里的含意是”快”。Wiki实际上是任何人——或者至少任何拥有权限的人——都可以创建或编辑的网页。

  6. Methods for the isolation of genes encoding novel PHB cycle enzymes from complex microbial communities.

    Science.gov (United States)

    Nordeste, Ricardo F; Trainer, Maria A; Charles, Trevor C

    2010-01-01

    Development of different PHAs as alternatives to petrochemically derived plastics can be facilitated by mining metagenomic libraries for diverse PHA cycle genes that might be useful for synthesis of bioplastics. The specific phenotypes associated with mutations of the PHA synthesis pathway genes in Sinorhizobium meliloti allows for the use of powerful selection and screening tools to identify complementing novel PHA synthesis genes. Identification of novel genes through their function rather than sequence facilitates finding functional proteins that may otherwise have been excluded through sequence-only screening methodology. We present here methods that we have developed for the isolation of clones expressing novel PHA metabolism genes from metagenomic libraries.

  7. Chronic exposure to triclosan sustains microbial community shifts and alters antibiotic resistance gene levels in anaerobic digesters.

    Science.gov (United States)

    Carey, Daniel E; Zitomer, Daniel H; Kappell, Anthony D; Choi, Melinda J; Hristova, Krassimira R; McNamara, Patrick J

    2016-08-10

    Triclosan, an antimicrobial chemical found in consumer personal care products, has been shown to stimulate antibiotic resistance in pathogenic bacteria. Although many studies focus on antibiotic resistance pertinent to medical scenarios, resistance developed in natural and engineered environments is less studied and has become an emerging concern for human health. In this study, the impacts of chronic triclosan (TCS) exposure on antibiotic resistance genes (ARGs) and microbial community structure were assessed in lab-scale anaerobic digesters. TCS concentrations from below detection to 2500 mg kg(-1) dry solids were amended into anaerobic digesters over 110 days and acclimated for >3 solid retention time values. Four steady state TCS concentrations were chosen (30-2500 mg kg(-1)). Relative abundance of mexB, a gene coding for a component of a multidrug efflux pump, was significantly higher in all TCS-amended digesters (30 mg kg(-1) or higher) relative to the control. TCS selected for bacteria carrying tet(L) and against those carrying erm(F) at concentrations which inhibited digester function; the pH decrease associated with digester failure was suspected to cause this selection. Little to no impact of TCS was observed on intI1 relative abundance. Microbial communities were also surveyed by high-throughput 16S rRNA gene sequencing. Compared to the control digesters, significant shifts in community structure towards clades containing commensal and pathogenic bacteria were observed in digesters containing TCS. Based on these results, TCS should be included in studies and risk assessments that attempt to elucidate relationships between chemical stressors (e.g. antibiotics), antibiotic resistance genes, and public health.

  8. Utilizing semantic Wiki technology for intelligence analysis at the tactical edge

    Science.gov (United States)

    Little, Eric

    2014-05-01

    Challenges exist for intelligence analysts to efficiently and accurately process large amounts of data collected from a myriad of available data sources. These challenges are even more evident for analysts who must operate within small military units at the tactical edge. In such environments, decisions must be made quickly without guaranteed access to the kinds of large-scale data sources available to analysts working at intelligence agencies. Improved technologies must be provided to analysts at the tactical edge to make informed, reliable decisions, since this is often a critical collection point for important intelligence data. To aid tactical edge users, new types of intelligent, automated technology interfaces are required to allow them to rapidly explore information associated with the intersection of hard and soft data fusion, such as multi-INT signals, semantic models, social network data, and natural language processing of text. Abilities to fuse these types of data is paramount to providing decision superiority. For these types of applications, we have developed BLADE. BLADE allows users to dynamically add, delete and link data via a semantic wiki, allowing for improved interaction between different users. Analysts can see information updates in near-real-time due to a common underlying set of semantic models operating within a triple store that allows for updates on related data points from independent users tracking different items (persons, events, locations, organizations, etc.). The wiki can capture pictures, videos and related information. New information added directly to pages is automatically updated in the triple store and its provenance and pedigree is tracked over time, making that data more trustworthy and easily integrated with other users' pages.

  9. Improved Vote Aggregation Techniques for the Geo-Wiki Cropland Capture Crowdsourcing Game

    Science.gov (United States)

    Baklanov, Artem; Fritz, Steffen; Khachay, Michael; Nurmukhametov, Oleg; Salk, Carl; See, Linda; Shchepashchenko, Dmitry

    2016-04-01

    Crowdsourcing is a new approach for solving data processing problems for which conventional methods appear to be inaccurate, expensive, or time-consuming. Nowadays, the development of new crowdsourcing techniques is mostly motivated by so called Big Data problems, including problems of assessment and clustering for large datasets obtained in aerospace imaging, remote sensing, and even in social network analysis. By involving volunteers from all over the world, the Geo-Wiki project tackles problems of environmental monitoring with applications to flood resilience, biomass data analysis and classification of land cover. For example, the Cropland Capture Game, which is a gamified version of Geo-Wiki, was developed to aid in the mapping of cultivated land, and was used to gather 4.5 million image classifications from the Earth's surface. More recently, the Picture Pile game, which is a more generalized version of Cropland Capture, aims to identify tree loss over time from pairs of very high resolution satellite images. Despite recent progress in image analysis, the solution to these problems is hard to automate since human experts still outperform the majority of machine learning algorithms and artificial systems in this field on certain image recognition tasks. The replacement of rare and expensive experts by a team of distributed volunteers seems to be promising, but this approach leads to challenging questions such as: how can individual opinions be aggregated optimally, how can confidence bounds be obtained, and how can the unreliability of volunteers be dealt with? In this paper, on the basis of several known machine learning techniques, we propose a technical approach to improve the overall performance of the majority voting decision rule used in the Cropland Capture Game. The proposed approach increases the estimated consistency with expert opinion from 77% to 86%.

  10. Wikis og blogs i undervisningen – Teoretiske perspektiver og praktiske erfaringer

    Directory of Open Access Journals (Sweden)

    Nina Bonderup Dohn

    2010-10-01

    Full Text Available I denne artikel diskuteres muligheder og problemstillinger forbundet med at inddrage wikis og blogs i undervisning inden for det humanistiske og samfundsvidenskabelige fagfelt på universitetsniveau. Fokus er på de former for brug, hvor de studerende er aktive i produktionen af indhold, og hvor der lægges vægt på stadig brug og genbrug af indholdet på tværs af kontekster. Der redegøres først for, hvad 'web 2.0' er, og hvad der forstås ved 'web 2.0-medieret læring'. På den baggrund opstilles en række læringsteoretisk og didaktisk begrundede potentialer ved at inddrage wiki- og blog-aktiviteter i undervisningen. Herefter præsenteres to eksempler fra egen undervisning, og det diskuteres, i hvilken grad de teoretiske potentialer blev realiseret, og hvilke problemstillinger der viste sig i de to cases. Dette danner afsæt for en mere generel påpegning af spændinger involveret i at bruge web 2.0 i undervisningen. For det første er der teoretiske spændinger mellem 'uddannelses-logik' og 'web 2.0-logik'. For det andet er der en spænding mellem på den ene side den mangfoldighed af kontekster, som web 2.0-medieret læring lægger op til at inddrage, og på den anden side behovet for mere faste forankringspunkter for læringsaktiviteter.

  11. Uso de wikis para la realización de trabajos colaborativos en el aula

    Directory of Open Access Journals (Sweden)

    Galache Laza, T.

    2006-01-01

    Full Text Available Habitualmente, la evaluación del alumnado que realizamos en la Universidad se basa únicamente en uno o varios exámenes individuales. Este hecho contrasta con su vida laboral posterior, donde se potenciará el trabajo en equipo, obteniendo la mayoría de los resultados a través de trabajos colaborativos. Con esta idea hemos realizado una experiencia docente en una asignatura optativa de la Diplomatura en Ciencias Empresariales, Investigación Operativa. Los alumnos de esta asignatura están distribuidos en tres grupos homogéneos de unos 20 alumnos. En cada uno de ellos hemos dedicado una parte importante de la calificación final a la realización de trabajos programados por los profesores, consistentes en realizar dentro de una plataforma Moodle, Wikis en los que cada grupo desarrolla un material predeterminado y conocido desde la programación del curso. Para cada grupo, cada uno de sus alumnos, deberá evaluar los Wikis realizados por los alumnos de los otros grupos, evaluación que ha de ser justificada y razonada, pudiendo cada profesor a su vez evaluarla de forma negativa o positiva. Con todo ello, los alumnos deben formar equipos para trabajar con sus compañeros en una tarea común a todos ellos y a su vez deben evaluar, de forma razonada, los trabajos realizados por sus compañeros de los otros grupos. Los resultados que hemos obtenido en cuanto a participación de los alumnos y rendimiento académico de los mismos son muy interesantes y nos llevan a la realización de importantes consideraciones de tipo práctico en trabajos colaborativos.

  12. Wikis en lenguas para fines específicos y su traducción

    Directory of Open Access Journals (Sweden)

    Raquel Lázaro Gutiérrez

    2010-01-01

    Full Text Available Las herramientas Wiki pueden llegar a ser muy útiles tanto en la enseñanza de lenguas en general como en la traducción, sobre todo si se tiene en cuenta que, hoy en día, dentro del nuevo marco del Espacio Europeo de Educación Superior, los docentes tienen que enfrentarse a dificultades como grupos numerosos de alumnos, pocas clases presenciales y competencias transversales añadidas al contenido de las materias. Por este motivo, que una herramienta como las wikis, que permita trabajar fuera del aula y con la cual el estudiante puede realizar trabajos individuales y en grupo, conectado y en contacto con el resto de sus compañeros y profesores, resulta especialmente útil. Mientras que la sencillez de estas herramientas permite al docente diseñar actividades atractivas y útiles con un esfuerzo y conocimientos tecnológicos relativamente mínimos, para los estudiantes supone una gran oportunidad para aprender a trabajar con las TIC y de manera grupal y colaborativa. En este capítulo se describen las tareas y actividades que se diseñaron y pusieron en práctica para las asignaturas del Máster Oficial en Comunicación Intercultural, Interpretación y Traducción en los Servicios Públicos y para las asignaturas de inglés para fines específicos del postgrado y grado de la Facultad de Derecho de la Universidad de Alcalá, centrándonos de manera especial en su diseño, las dificultades y ventajas que plantearon y la respuesta que se obtuvo por parte del alumnado.

  13. Building Semantic Wiki System Based on Research Environment%基于科研环境的语文Wiki系统构建

    Institute of Scientific and Technical Information of China (English)

    杨锐; 汤怡洁; 刘毅; 李崴

    2012-01-01

    The authors analyze the characteristics of the semantic Wiki system firstly, and then take the research environment as the starting point, describe the scenarios of semantic Wiki applications, conduct a detailed study for the open-source semantic Wiki sys- tem, and on this basis construct the semantic Wiki system from four aspects of research Ontology, semantic Wiki page construction, se- mantic annotation and semantic inference, to form a semantic Wiki research environment to support knowledge sharing and knowledge innovation.%首先对语义Wiki系统进行特性分析,然后以科研环境为出发点进行语义Wiki应用场景描述,针对开源语义Wiki系统进行详细研究,并在此基础上从语义Wiki使用的科研本体、页面构建、语义标注和语义推理四个方面进行语义Wiki系统构建,从而形成支持知识共享和知识创新的语义Wiki科研环境。

  14. Prevalence of antibiotic resistance genes in bacterial communities associated with Cladophora glomerata mats along the nearshore of Lake Ontario.

    Science.gov (United States)

    Ibsen, Michael; Fernando, Dinesh M; Kumar, Ayush; Kirkwood, Andrea E

    2017-05-01

    The alga Cladophora glomerata can erupt in nuisance blooms throughout the lower Great Lakes. Since bacterial abundance increases with the emergence and decay of Cladophora, we investigated the prevalence of antibiotic resistance (ABR) in Cladophora-associated bacterial communities up-gradient and down-gradient from a large sewage treatment plant (STP) on Lake Ontario. Although STPs are well-known sources of ABR, we also expected detectable ABR from up-gradient wetland communities, since they receive surface run-off from urban and agricultural sources. Statistically significant differences in aquatic bacterial abundance and ABR were found between down-gradient beach samples and up-gradient coastal wetland samples (ANOVA, Holm-Sidak test, p floating Cladophora sampled near the STP had the highest bacterial densities overall, including on ampicillin- and vancomycin-treated plates. However, quantitative polymerase chain reaction analysis of the ABR genes ampC, tetA, tetB, and vanA from environmental communities showed a different pattern. Some of the highest ABR gene levels occurred at the 2 coastal wetland sites (vanA). Overall, bacterial ABR profiles from environmental samples were distinguishable between living and decaying Cladophora, inferring that Cladophora may control bacterial ABR depending on its life-cycle stage. Our results also show how spatially and temporally dynamic ABR is in nearshore aquatic bacteria, which warrants further research.

  15. Antimicrobial susceptibility, risk factors and prevalence of bla cefotaximase, temoneira, and sulfhydryl variable genes among Escherichia coli in community-acquired pediatric urinary tract infection

    Directory of Open Access Journals (Sweden)

    Kallyadan V Nisha

    2017-01-01

    Conclusion: ESBL-producing E. coli from community-acquired pediatric UTI carries more than one type of beta-lactamase coding genes correlating their increased antibiotic resistance. Aggressive infection control policy, routine screening for detecting ESBL isolates in clinical samples, and antimicrobial stewardship are the keys to prevent their dissemination in community settings.

  16. Community structure and functional gene profile of bacteria on healthy and diseased thalli of the red seaweed Delisea pulchra.

    Directory of Open Access Journals (Sweden)

    Neil Fernandes

    Full Text Available Disease is increasingly viewed as a major factor in the ecology of marine communities and its impact appears to be increasing with environmental change, such as global warming. The temperate macroalga Delisea pulchra bleaches in Southeast Australia during warm summer periods, a phenomenon which previous studies have indicated is caused by a temperature induced bacterial disease. In order to better understand the ecology of this disease, the bacterial communities associated with threes type of samples was investigated using 16S rRNA gene and environmental shotgun sequencing: 1 unbleached (healthy D. pulchra 2 bleached parts of D. pulchra and 3 apparently healthy tissue adjacent to bleached regions. Phylogenetic differences between healthy and bleached communities mainly reflected relative changes in the taxa Colwelliaceae, Rhodobacteraceae, Thalassomonas and Parvularcula. Comparative metagenomics showed clear difference in the communities of healthy and diseased D. pulchra as reflected by changes in functions associated with transcriptional regulation, cation/multidrug efflux and non-ribosomal peptide synthesis. Importantly, the phylogenetic and functional composition of apparently healthy tissue adjacent to bleached sections of the thalli indicated that changes in the microbial communities already occur in the absence of visible tissue damage. This shift in unbleached sections might be due to the decrease in furanones, algal metabolites which are antagonists of bacterial quorum sensing. This study reveals the complex shift in the community composition associated with bleaching of Delisea pulchra and together with previous studies is consistent with a model in which elevated temperatures reduce levels of chemical defenses in stressed thalli, leading to colonization or proliferation by opportunistic pathogens or scavengers.

  17. Metagenomic analysis of bacterial community composition and antibiotic resistance genes in a wastewater treatment plant and its receiving surface water.

    Science.gov (United States)

    Tang, Junying; Bu, Yuanqing; Zhang, Xu-Xiang; Huang, Kailong; He, Xiwei; Ye, Lin; Shan, Zhengjun; Ren, Hongqiang

    2016-10-01

    The presence of pathogenic bacteria and the dissemination of antibiotic resistance genes (ARGs) may pose big risks to the rivers that receive the effluent from municipal wastewater treatment plants (WWTPs). In this study, we investigated the changes of bacterial community and ARGs along treatment processes of one WWTP, and examined the effects of the effluent discharge on the bacterial community and ARGs in the receiving river. Pyrosequencing was applied to reveal bacterial community composition including potential bacterial pathogen, and Illumina high-throughput sequencing was used for profiling ARGs. The results showed that the WWTP had good removal efficiency on potential pathogenic bacteria (especially Arcobacter butzleri) and ARGs. Moreover, the bacterial communities of downstream and upstream of the river showed no significant difference. However, the increase in the abundance of potential pathogens and ARGs at effluent outfall was observed, indicating that WWTP effluent might contribute to the dissemination of potential pathogenic bacteria and ARGs in the receiving river. Copyright © 2016 Elsevier Inc. All rights reserved.

  18. Taxonomic analysis of the microbial community in stored sugar beets using high-throughput sequencing of different marker genes.

    Science.gov (United States)

    Liebe, Sebastian; Wibberg, Daniel; Winkler, Anika; Pühler, Alfred; Schlüter, Andreas; Varrelmann, Mark

    2016-02-01

    Post-harvest colonization of sugar beets accompanied by rot development is a serious problem due to sugar losses and negative impact on processing quality. Studies on the microbial community associated with rot development and factors shaping their structure are missing. Therefore, high-throughput sequencing was applied to describe the influence of environment, plant genotype and storage temperature (8°C and 20°C) on three different communities in stored sugar beets, namely fungi (internal transcribed spacers 1 and 2), Fusarium spp. (elongation factor-1α gene fragment) and oomycetes (internal transcribed spacers 1). The composition of the fungal community changed during storage mostly influenced by the storage temperature followed by a weak environmental effect. Botrytis cinerea was the prevalent species at 8°C whereas members of the fungal genera Fusarium and Penicillium became dominant at 20°C. This shift was independent of the plant genotype. Species richness within the genus Fusarium also increased during storage at both temperatures whereas the oomycetes community did not change. Moreover, oomycetes species were absent after storage at 20°C. The results of the present study clearly show that rot development during sugar beet storage is associated with pathogens well known as causal agents of post-harvest diseases in many other crops.

  19. Uso de wikis como herramienta de trabajo colaborativo en un proceso de formación inicial docente

    Directory of Open Access Journals (Sweden)

    Ilich Silva-Peña

    2013-01-01

    Full Text Available A través del presente artículo queremos compartir el desarrollo de una experiencia de utilización de wikis como estrategia de trabajo colaborativo en un curso de formación inicial docente. La experiencia se enmarcó en el contexto de un proyecto de Investigación+Desarrollo donde se exploraron mejoras tecnológicas a incorporar en la formación docente. Se utilizó el software Moodle ®, con características Open source. Para sistematizar los resultados desde la mirada de los/as estudiantes se aplicaron cuestionarios con respuestas abiertas, que fueron codificadas utilizando una metodología cualitativa. Los resultados muestran una alta valoración de los wikis como herramienta de aprendizaje, especialmente por el apoyo que otorga al trabajo pedagógico no presencial y asincrónico.

  20. Bacterial community structure in High-Arctic snow and freshwater as revealed by pyrosequencing of 16S rRNA genes and cultivation

    DEFF Research Database (Denmark)

    Møller, Annette K.; Søborg, Ditte A.; Abu Al-Soud, Waleed;

    2013-01-01

    The bacterial community structures in High-Arctic snow over sea ice and an ice-covered freshwater lake were examined by pyrosequencing of 16S rRNA genes and 16S rRNA gene sequencing of cultivated isolates. Both the pyrosequence and cultivation data indicated that the phylogenetic composition...

  1. Bacterial community structure in High-Arctic snow and freshwater as revealed by pyrosequencing of 16S rRNA genes and cultivation

    DEFF Research Database (Denmark)

    Møller, Annette; Søborg, Ditte Andreasen; Al-Soud, Waleed Abu

    2013-01-01

    The bacterial community structures in High-Arctic snow over sea ice and an ice-covered freshwater lake were examined by pyrosequencing of 16S rRNA genes and 16S rRNA gene sequencing of cultivated isolates. Both the pyrosequence and cultivation data indicated that the phylogenetic composition...

  2. The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community.

    Science.gov (United States)

    Arnaud, Martha B; Chibucos, Marcus C; Costanzo, Maria C; Crabtree, Jonathan; Inglis, Diane O; Lotia, Adil; Orvis, Joshua; Shah, Prachi; Skrzypek, Marek S; Binkley, Gail; Miyasato, Stuart R; Wortman, Jennifer R; Sherlock, Gavin

    2010-01-01

    The Aspergillus Genome Database (AspGD) is an online genomics resource for researchers studying the genetics and molecular biology of the Aspergilli. AspGD combines high-quality manual curation of the experimental scientific literature examining the genetics and molecular biology of Aspergilli, cutting-edge comparative genomics approaches to iteratively refine and improve structural gene annotations across multiple Aspergillus species, and web-based research tools for accessing and exploring the data. All of these data are freely available at http://www.aspgd.org. We welcome feedback from users and the research community at aspergillus-curator@genome.stanford.edu.

  3. Effects of chlortetracycline and copper on tetracyclines and copper resistance genes and microbial community during swine manure anaerobic digestion.

    Science.gov (United States)

    Wang, Rui; Chen, Meixue; Feng, Feng; Zhang, Junya; Sui, Qianwen; Tong, Juan; Wei, Yuansong; Wei, Dongbin

    2017-08-01

    As antibiotic and heavy metals are over used in the livestock industry, animal manure is a reservoir of antibiotic resistance genes (ARGs). Anaerobic digestion has been reported to have the potential to reduce ARGs. However, few studies investigated whether reduction of ARGs would be affected by different external pressures including antibiotics and heavy metals during anaerobic digestion. The purpose of this study was thus to investigate effects of both chlortetracycline (CTC) and Cu on reduction of ARGs, heavy metal resistance genes (HMRGs) and mobile genetic elements (MGEs) during the swine manure anaerobic digestion. The results showed that the predominant ARGs (tetO, tetW, tetX, tetL) could be effectively reduced (approximately 1.00 log copies/g TS) through mesophilic anaerobic digestion. Microbial community evolution was the main driver. It was interesting that Treponema might indicate the termination of anaerobic digestion and compete with ARGs host bacteria. Addition of CTC, Cu and CTC+Cu affected microbial community change and hindered removal of ARGs, especially, CTC+Cu seriously affected Treponema and ARGs during anaerobic digestion. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Evaluación de la wiki como herramienta de trabajo colaborativo en la docencia universitaria

    Directory of Open Access Journals (Sweden)

    Marisela Montenegro

    2010-01-01

    Full Text Available La herramienta wiki se está consolidando como una herramienta de trabajo colaborativo y colectivo que tiene su máxima expresión en el desarrollo de la wikipedia. La herramienta wiki consiste en una página virtual para la escritura colaborativa, en la cual cada una de las personas que participa puede ir añadiendo y cambiando los contenidos de la página. Esta herramienta permite recoger el proceso de construcción del texto, visualizando las formas de trabajo de los estudiantes, guardando un historial de las diferentes versiones y las aportaciones realizadas por cada participante. El uso de esta herramienta pone de manifiesto que la interacción e interdependencia en la creación colectiva necesita de diferentes elementos de soporte a fin de que la deseada interacción se produzca. Entre los aspectos a incidir resaltan la necesidad de reconocer y dar valor al trabajo del otro, al mismo tiempo que se desarrolla una concepción compartida de la autoría que ofrece la suficiente seguridad para modificar el trabajo que otra persona ha realizado. Esta herramienta virtual ha sido implementada en varias asignaturas de la Licenciatura de Psicología de la UAB -como por ejemplo "Psicología Social de la Comunicación", "Prácticum interno" o "Prácticas de Psicología Social: Cultura y conocimiento", mediante una plataforma virtual de trabajo hecha con Moodle. Los docentes diseñaron los espacios virtuales a partir de los objetivos del programa de las asignaturas y cada uno de los grupos de trabajo tuvo su propia página para el desarrollo del trabajo a lo largo del semestre. Además, se han implementado espacios presenciales de seguimiento de las tareas de los estudiantes. En este capítulo se describe el proceso seguido, poniendo como ejemplo algunas de estas asignaturas. Se describen las diferentes opciones implementadas, se muestran los hitos conseguidos en el uso de esta herramienta y se reflexiona sobre las implicaciones de su uso para los

  5. Bacterial Community Diversity of Oil-Contaminated Soils Assessed by High Throughput Sequencing of 16S rRNA Genes

    Directory of Open Access Journals (Sweden)

    Mu Peng

    2015-09-01

    Full Text Available Soil bacteria play a major role in ecological and biodegradable function processes in oil-contaminated soils. Here, we assessed the bacterial diversity and changes therein in oil-contaminated soils exposed to different periods of oil pollution using 454 pyrosequencing of 16S rRNA genes. No less than 24,953 valid reads and 6246 operational taxonomic units (OTUs were obtained from all five studied samples. OTU richness was relatively higher in contaminated soils than clean samples. Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Planctomycetes and Proteobacteria were the dominant phyla among all the soil samples. The heatmap plot depicted the relative percentage of each bacterial family within each sample and clustered five samples into two groups. For the samples, bacteria in the soils varied at different periods of oil exposure. The oil pollution exerted strong selective pressure to propagate many potentially petroleum degrading bacteria. Redundancy analysis (RDA indicated that organic matter was the highest determinant factor for explaining the variations in community compositions. This suggests that compared to clean soils, oil-polluted soils support more diverse bacterial communities and soil bacterial community shifts were mainly controlled by organic matter and exposure time. These results provide some useful information for bioremediation of petroleum contaminated soil in the future.

  6. Bacterial Community Diversity of Oil-Contaminated Soils Assessed by High Throughput Sequencing of 16S rRNA Genes.

    Science.gov (United States)

    Peng, Mu; Zi, Xiaoxue; Wang, Qiuyu

    2015-09-24

    Soil bacteria play a major role in ecological and biodegradable function processes in oil-contaminated soils. Here, we assessed the bacterial diversity and changes therein in oil-contaminated soils exposed to different periods of oil pollution using 454 pyrosequencing of 16S rRNA genes. No less than 24,953 valid reads and 6246 operational taxonomic units (OTUs) were obtained from all five studied samples. OTU richness was relatively higher in contaminated soils than clean samples. Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Planctomycetes and Proteobacteria were the dominant phyla among all the soil samples. The heatmap plot depicted the relative percentage of each bacterial family within each sample and clustered five samples into two groups. For the samples, bacteria in the soils varied at different periods of oil exposure. The oil pollution exerted strong selective pressure to propagate many potentially petroleum degrading bacteria. Redundancy analysis (RDA) indicated that organic matter was the highest determinant factor for explaining the variations in community compositions. This suggests that compared to clean soils, oil-polluted soils support more diverse bacterial communities and soil bacterial community shifts were mainly controlled by organic matter and exposure time. These results provide some useful information for bioremediation of petroleum contaminated soil in the future.

  7. Microbial community structure of Arctic multiyear sea ice and surface seawater by 454 sequencing of the 16S RNA gene.

    Science.gov (United States)

    Bowman, Jeff S; Rasmussen, Simon; Blom, Nikolaj; Deming, Jody W; Rysgaard, Søren; Sicheritz-Ponten, Thomas

    2012-01-01

    Dramatic decreases in the extent of Arctic multiyear ice (MYI) suggest this environment may disappear as early as 2100, replaced by ecologically different first-year ice. To better understand the implications of this loss on microbial biodiversity, we undertook a detailed census of the microbial community in MYI at two sites near the geographic North Pole using parallel tag sequencing of the 16S rRNA gene. Although the composition of the MYI microbial community has been characterized by previous studies, microbial community structure has not been. Although richness was lower in MYI than in underlying surface water, we found diversity to be comparable using the Simpson and Shannon's indices (for Simpson t=0.65, P=0.56; for Shannon t=0.25, P=0.84 for a Student's t-test of mean values). Cyanobacteria, comprising 6.8% of reads obtained from MYI, were observed for the first time in Arctic sea ice. In addition, several low-abundance clades not previously reported in sea ice were present, including the phylum TM7 and the classes Spartobacteria and Opitutae. Members of Coraliomargarita, a recently described genus of the class Opitutae, were present in sufficient numbers to suggest niche occupation within MYI.

  8. Identification of polybacterial communities in patients with postoperative, posttraumatic, and endogenous endophthalmitis through 16S rRNA gene libraries.

    Science.gov (United States)

    Jayasudha, Rajagopalaboopathi; Narendran, Venkatapathy; Manikandan, Palanisamy; Prabagaran, Solai Ramatchandirane

    2014-05-01

    Endophthalmitis is a potential vision-threatening complication following surgical procedures (postoperative endophthalmitis [POE]), trauma (posttraumatic endophthalmitis [PTE]), and bacteremic seeding of the eye from a distant infection site (endogenous endophthalmitis [EE]). Several studies have revealed the polybacterial characteristics of endophthalmitis, which make the administration of antibiotics to treat the disease challenging. However, until now, the polybacterial communities of POE, PTE, and EE have not been precisely studied. Hence, the present study was designed to identify the bacterial community of endophthalmitis through 16S rRNA gene libraries. Of the 40 intraocular samples tested, 30 libraries were constructed with bacterial nested-PCR-positive samples. The obtained recombinant clones were screened through amplified rRNA gene restriction analysis (ARDRA) to identify unique clones. The multiple types of ARDRA patterns (P=0.345) and diverse bacterial sequences (P=0.277) within the libraries revealed the polybacterial nature of infection in POE, PTE, and EE. Moreover, to the best of our knowledge, this is the first report on polybacterial infection in EE. Gram-positive bacteria, including Bacillus spp. (n=19), Streptococcus spp. (n=18), Staphylococcus spp. (n=6), Exiguobacterium spp. (n=3), Gemella spp. (n=2), Enterococcus spp. (n=2), a Lysinibacillus sp. (n=1), a Clostridium sp. (n=1), and a Nocardia sp. (n=1), and Gram-negative bacteria, including Serratia spp. (n=18), Pseudomonas spp. (n=10), Enterobacter spp. (n=8), Acinetobacter spp. (n=3), Pantoea spp. (n=3), a Haemophilus sp. (n=1), and a Massilia sp. (n=1), were identified. Interestingly, among them, 10 bacterial species were not previously reported to be associated with endophthalmitis or other ocular infections. Besides, the presence of 4 unidentifiable clones suggests the possibility of novel organisms that might cause eye infections. Therefore, it is recommended that, in addition to the

  9. Identification of Carbohydrate Metabolism Genes in the Metagenome of a Marine Biofilm Community Shown to Be Dominated by Gammaproteobacteria and Bacteroidetes

    Directory of Open Access Journals (Sweden)

    Jennifer L. Edwards

    2010-10-01

    Full Text Available Polysaccharides are an important source of organic carbon in the marine environment and degradation of the insoluble and globally abundant cellulose is a major component of the marine carbon cycle. Although a number of species of cultured bacteria are known to degrade crystalline cellulose, little is known of the polysaccharide hydrolases expressed by cellulose-degrading microbial communities, particularly in the marine environment. Next generation 454 Pyrosequencing was applied to analyze the microbial community that colonizes and degrades insoluble polysaccharides in situ in the Irish Sea. The bioinformatics tool MG-RAST was used to examine the randomly sampled data for taxonomic markers and functional genes, and showed that the community was dominated by members of the Gammaproteobacteria and Bacteroidetes. Furthermore, the identification of 211 gene sequences matched to a custom-made database comprising the members of nine glycoside hydrolase families revealed an extensive repertoire of functional genes predicted to be involved in cellulose utilization. This demonstrates that the use of an in situ cellulose baiting method yielded a marine microbial metagenome considerably enriched in functional genes involved in polysaccharide degradation. The research reported here is the first designed to specifically address the bacterial communities that colonize and degrade cellulose in the marine environment and to evaluate the glycoside hydrolase (cellulase and chitinase gene repertoire of that community, in the absence of the biases associated with PCR-based molecular techniques.

  10. A culture-independent approach to unravel uncultured bacteria and functional genes in a complex microbial community.

    Directory of Open Access Journals (Sweden)

    Yun Wang

    Full Text Available Most microorganisms in nature are uncultured with unknown functionality. Sequence-based metagenomics alone answers 'who/what are there?' but not 'what are they doing and who is doing it and how?'. Function-based metagenomics reveals gene function but is usually limited by the specificity and sensitivity of screening strategies, especially the identification of clones whose functional gene expression has no distinguishable activity or phenotypes. A 'biosensor-based genetic transducer' (BGT technique, which employs a whole-cell biosensor to quantitatively detect expression of inserted genes encoding designated functions, is able to screen for functionality of unknown genes from uncultured microorganisms. In this study, BGT was integrated with Stable isotope probing (SIP-enabled Metagenomics to form a culture-independent SMB toolbox. The utility of this approach was demonstrated in the discovery of a novel functional gene cluster in naphthalene contaminated groundwater. Specifically, metagenomic sequencing of the (13C-DNA fraction obtained by SIP indicated that an uncultured Acidovorax sp. was the dominant key naphthalene degrader in-situ, although three culturable Pseudomonas sp. degraders were also present in the same groundwater. BGT verified the functionality of a new nag2 operon which co-existed with two other nag and two nah operons for naphthalene biodegradation in the same microbial community. Pyrosequencing analysis showed that the nag2 operon was the key functional operon in naphthalene degradation in-situ, and shared homology with both nag operons in Ralstonia sp. U2 and Polaromonas naphthalenivorans CJ2. The SMB toolbox will be useful in providing deep insights into uncultured microorganisms and unravelling their ecological roles in natural environments.

  11. Use of a wiki as an interactive teaching tool in pathology residency education: Experience with a genomics, research, and informatics in pathology course

    Directory of Open Access Journals (Sweden)

    Seung Park

    2012-01-01

    Full Text Available Background: The need for informatics and genomics training in pathology is critical, yet limited resources for such training are available. In this study we sought to critically test the hypothesis that the incorporation of a wiki (a collaborative writing and publication tool with roots in "Web 2.0" in a combined informatics and genomics course could both (1 serve as an interactive, collaborative educational resource and reference and (2 actively engage trainees by requiring the creation and sharing of educational materials. Materials and Methods: A 2-week full-time course at our institution covering genomics, research, and pathology informatics (GRIP was taught by 36 faculty to 18 second- and third-year pathology residents. The course content included didactic lectures and hands-on demonstrations of technology (e.g., whole-slide scanning, telepathology, and statistics software. Attendees were given pre- and posttests. Residents were trained to use wiki technology (MediaWiki and requested to construct a wiki about the GRIP course by writing comprehensive online review articles on assigned lectures. To gauge effectiveness, pretest and posttest scores for our course were compared with scores from the previous 7 years from the predecessor course (limited to informatics given at our institution that did not utilize wikis. Results: Residents constructed 59 peer-reviewed collaborative wiki articles. This group showed a 25% improvement (standard deviation 12% in test scores, which was greater than the 16% delta recorded in the prior 7 years of our predecessor course (P = 0.006. Conclusions: Our use of wiki technology provided a wiki containing high-quality content that will form the basis of future pathology informatics and genomics courses and proved to be an effective teaching tool, as evidenced by the significant rise in our resident posttest scores. Data from this project provide support for the notion that active participation in content creation

  12. The Mouse Genome Database (MGD): from genes to mice--a community resource for mouse biology.

    Science.gov (United States)

    Eppig, Janan T; Bult, Carol J; Kadin, James A; Richardson, Joel E; Blake, Judith A; Anagnostopoulos, A; Baldarelli, R M; Baya, M; Beal, J S; Bello, S M; Boddy, W J; Bradt, D W; Burkart, D L; Butler, N E; Campbell, J; Cassell, M A; Corbani, L E; Cousins, S L; Dahmen, D J; Dene, H; Diehl, A D; Drabkin, H J; Frazer, K S; Frost, P; Glass, L H; Goldsmith, C W; Grant, P L; Lennon-Pierce, M; Lewis, J; Lu, I; Maltais, L J; McAndrews-Hill, M; McClellan, L; Miers, D B; Miller, L A; Ni, L; Ormsby, J E; Qi, D; Reddy, T B K; Reed, D J; Richards-Smith, B; Shaw, D R; Sinclair, R; Smith, C L; Szauter, P; Walker, M B; Walton, D O; Washburn, L L; Witham, I T; Zhu, Y

    2005-01-01

    The Mouse Genome Database (MGD) forms the core of the Mouse Genome Informatics (MGI) system (http://www.informatics.jax.org), a model organism database resource for the laboratory mouse. MGD provides essential integration of experimental knowledge for the mouse system with information annotated from both literature and online sources. MGD curates and presents consensus and experimental data representations of genotype (sequence) through phenotype information, including highly detailed reports about genes and gene products. Primary foci of integration are through representations of relationships among genes, sequences and phenotypes. MGD collaborates with other bioinformatics groups to curate a definitive set of information about the laboratory mouse and to build and implement the data and semantic standards that are essential for comparative genome analysis. Recent improvements in MGD discussed here include the enhancement of phenotype resources, the re-development of the International Mouse Strain Resource, IMSR, the update of mammalian orthology datasets and the electronic publication of classic books in mouse genetics.

  13. English Writing Instruction Model in Wiki Setting%Wiki环境下的大学英语协作教学模式

    Institute of Scientific and Technical Information of China (English)

    鲁艳辉; 曹立

    2014-01-01

    In terms of the application of Wiki in pedagogy, this paper tries to introduce Wiki concept into College English Teaching. Wiki model is collaborative model with a shared environment where online students and teachers can collaboratively participate in the integration and co-creation of knowledge. Using wiki in the teaching demands careful planning, design and ef-fective facilitation. Introducing wiki concept into our teaching aims to improve students' participation, creativity and collabora-tion awareness.%基于Wiki在教育领域的发展,在大学英语教学中引入Wiki教学理念。Wiki教学模式是充分利用信息技术,教师与学生协作构建知识、分享知识,共同参与教学的一种协作式教学。wiki模式的有效开展需要教师精心的设计、不断激发学生兴趣和师生共同构建知识。Wiki教学模式着眼于提高学习者学习的参与性、创造性及协作意识。

  14. Lean mass, muscle strength and gene expression in community dwelling older men: findings from the Hertfordshire Sarcopenia Study (HSS).

    Science.gov (United States)

    Patel, Harnish P; Al-Shanti, Nasser; Davies, Lucy C; Barton, Sheila J; Grounds, Miranda D; Tellam, Ross L; Stewart, Claire E; Cooper, Cyrus; Sayer, Avan Aihie

    2014-10-01

    Sarcopenia is associated with adverse health outcomes. This study investigated whether skeletal muscle gene expression was associated with lean mass and grip strength in community-dwelling older men. Utilising a cross-sectional study design, lean muscle mass and grip strength were measured in 88 men aged 68-76 years. Expression profiles of 44 genes implicated in the cellular regulation of skeletal muscle were determined. Serum was analysed for circulating cytokines TNF (tumour necrosis factor), IL-6 (interleukin 6, IFNG (interferon gamma), IL1R1 (interleukin-1 receptor-1). Relationships between skeletal muscle gene expression, circulating cytokines, lean mass and grip strength were examined. Participant groups with higher and lower values of lean muscle mass (n = 18) and strength (n = 20) were used in the analysis of gene expression fold change. Expression of VDR (vitamin D receptor) [fold change (FC) 0.52, standard error for fold change (SE) ± 0.08, p = 0.01] and IFNG mRNA (FC 0.31; SE ± 0.19, p = 0.01) were lower in those with higher lean mass. Expression of IL-6 (FC 0.43; SE ± 0.13, p = 0.02), TNF (FC 0.52; SE ± 0.10, p = 0.02), IL1R1 (FC 0.63; SE ± 0.09, p = 0.04) and MSTN (myostatin) (FC 0.64; SE ± 0.11, p = 0.04) were lower in those with higher grip strength. No other significant changes were observed. Significant negative correlations between serum IL-6 (R = -0.29, p = 0.005), TNF (R = -0.24, p = 0.017) and grip strength were demonstrated. This novel skeletal muscle gene expression study carried out within a well-characterized epidemiological birth cohort has demonstrated that lower expression of VDR and IFNG is associated with higher lean mass, and lower expression of IL-6, TNF, IL1R1 and myostatin is associated with higher grip strength. These findings are consistent with a role of proinflammatory factors in mediating lower muscle strength in community-dwelling older men.

  15. Expression of acetate permease-like (apl) genes in subsurface communities of Geobacter species under fluctuating acetate concentrations

    Energy Technology Data Exchange (ETDEWEB)

    Elifantz, H.; N' Guessan, L.A.; Mouser, P.J.; Williams, K H.; Wilkins, M J.; Risso, C.; Holmes, D.E.; Long, P.E.; Lovley, D.R.

    2010-03-01

    The addition of acetate to uranium-contaminated aquifers in order to stimulate the growth and activity of Geobacter species that reduce uranium is a promising in situ bioremediation option. Optimizing this bioremediation strategy requires that sufficient acetate be added to promote Geobacter species growth. We hypothesized that under acetate-limiting conditions, subsurface Geobacter species would increase the expression of either putative acetate symporters genes (aplI and aplII). Acetate was added to a uranium-contaminated aquifer (Rifle, CO) in two continuous amendments separated by 5 days of groundwater flush to create changing acetate concentrations. While the expression of aplI in monitoring well D04 (high acetate) weakly correlated with the acetate concentration over time, the transcript levels for this gene were relatively constant in well D08 (low acetate). At the lowest acetate concentrations during the groundwater flush, the transcript levels of aplII were the highest. The expression of aplII decreased 2-10-fold upon acetate reintroduction. However, the overall instability of acetate concentrations throughout the experiment could not support a robust conclusion regarding the role of apl genes in response to acetate limitation under field conditions, in contrast to previous chemostat studies, suggesting that the function of a microbial community cannot be inferred based on lab experiments alone.

  16. Geo-Wiki.Org: The Use of Crowdsourcing to Improve Global Land Cover

    Directory of Open Access Journals (Sweden)

    Florian Kraxner

    2009-08-01

    Full Text Available Global land cover is one of the essential terrestrial baseline datasets available for ecosystem modeling, however uncertainty remains an issue. Tools such as Google Earth offer enormous potential for land cover validation. With an ever increasing amount of very fine spatial resolution images (up to 50 cm × 50 cm available on Google Earth, it is becoming possible for every Internet user (including non remote sensing experts to distinguish land cover features with a high degree of reliability. Such an approach is inexpensive and allows Internet users from any region of the world to get involved in this global validation exercise. The Geo-Wiki Project is a global network of volunteers who wish to help improve the quality of global land cover maps. Since large differences occur between existing global land cover maps, current ecosystem and land-use science lacks crucial accurate data (e.g., to determine the potential of additional agricultural land available to grow crops in Africa, volunteers are asked to review hotspot maps of global land cover disagreement and determine, based on what they actually see in Google Earth and their local knowledge, if the land cover maps are correct or incorrect. Their input is recorded in a database, along with uploaded photos, to be used in the future for the creation of a new and improved hybrid global land cover map.

  17. Perancangan Knowledge Management System Pada IT Bina Nusantara menggunakan Blog, Wiki, Forum dan Document

    Directory of Open Access Journals (Sweden)

    Karto Iskandar

    2014-06-01

    Full Text Available This research purpose is to design a Knowledge Management System (KMS in Bina Nusantara IT to facilitate knowledge sharing and knowledge management dashboard view to see the development of employee knowledge achieved in KMS. The high turnover rate caused the walkout knowledge. The knowledge is not well structured so that employees often have difficulty in searching for knowledge. Methods of the research conducted by the method of Software Development Life Cycle (SDLC, model iterations. The next step is formulating a study literature to find references to these problems. Then do a system design in the form of UML diagrams user interface and database. The results achieved in the form of KMS-based design to support knowledge sharing among IT BINUS employees. The conclusion from this study is that spread knowledge can be identified, stored and reused. Through this system, documentation of knowledge is optimized so that it can be a solution for walkout knowledge. There are a variety of KM applications in the system, such as Blog, Wiki, Forum, and Document.

  18. FoodWiki: Ontology-Driven Mobile Safe Food Consumption System

    Directory of Open Access Journals (Sweden)

    Duygu Çelik

    2015-01-01

    Full Text Available An ontology-driven safe food consumption mobile system is considered. Over 3,000 compounds are being added to processed food, with numerous effects on the food: to add color, stabilize, texturize, preserve, sweeten, thicken, add flavor, soften, emulsify, and so forth. According to World Health Organization, governments have lately focused on legislation to reduce such ingredients or compounds in manufactured foods as they may have side effects causing health risks such as heart disease, cancer, diabetes, allergens, and obesity. By supervising what and how much to eat as well as what not to eat, we can maximize a patient’s life quality through avoidance of unhealthy ingredients. Smart e-health systems with powerful knowledge bases can provide suggestions of appropriate foods to individuals. Next-generation smart knowledgebase systems will not only include traditional syntactic-based search, which limits the utility of the search results, but will also provide semantics for rich searching. In this paper, performance of concept matching of food ingredients is semantic-based, meaning that it runs its own semantic based rule set to infer meaningful results through the proposed Ontology-Driven Mobile Safe Food Consumption System (FoodWiki.

  19. FoodWiki: Ontology-Driven Mobile Safe Food Consumption System.

    Science.gov (United States)

    Çelik, Duygu

    2015-01-01

    An ontology-driven safe food consumption mobile system is considered. Over 3,000 compounds are being added to processed food, with numerous effects on the food: to add color, stabilize, texturize, preserve, sweeten, thicken, add flavor, soften, emulsify, and so forth. According to World Health Organization, governments have lately focused on legislation to reduce such ingredients or compounds in manufactured foods as they may have side effects causing health risks such as heart disease, cancer, diabetes, allergens, and obesity. By supervising what and how much to eat as well as what not to eat, we can maximize a patient's life quality through avoidance of unhealthy ingredients. Smart e-health systems with powerful knowledge bases can provide suggestions of appropriate foods to individuals. Next-generation smart knowledgebase systems will not only include traditional syntactic-based search, which limits the utility of the search results, but will also provide semantics for rich searching. In this paper, performance of concept matching of food ingredients is semantic-based, meaning that it runs its own semantic based rule set to infer meaningful results through the proposed Ontology-Driven Mobile Safe Food Consumption System (FoodWiki).

  20. Genes homologous to glycopeptide resistance vanA are widespread in soil microbial communities

    DEFF Research Database (Denmark)

    Guardabassi, L.; Agersø, Yvonne

    2006-01-01

    The occurrence of D-Ala : D-Lac ligase genes homologous to glycopeptide resistance vanA was studied in samples of agricultural (n=9) and garden (n=3) soil by culture-independent methods. Cloning and sequencing of nested degenerate PCR products obtained from soil DNA revealed the occurrence of D-A...

  1. APOLIPOPROTEIN E GENE POLYMORPHISMS ARE NOT ASSOCIATED WITH DIABETIC RETINOPATHY: THE ATHEROSCLEROSIS RISK IN COMMUNITIES STUDY

    Science.gov (United States)

    PURPOSE: Polymorphism of the apolipoprotein E (APOE) gene has been associated with dyslipidemia and cardiovascular disease. This study examines the association of APOE polymorphisms and diabetic retinopathy. DESIGN: Population-based cross-sectional study. METHODS: We studied 1,398 people aged 49 to ...

  2. Global analysis of gene expression dynamics within the marine microbial community during the VAHINE mesocosm experiment in the southwest Pacific

    Science.gov (United States)

    Pfreundt, Ulrike; Spungin, Dina; Bonnet, Sophie; Berman-Frank, Ilana; Hess, Wolfgang R.

    2016-07-01

    Microbial gene expression was followed for 23 days within a mesocosm (M1) isolating 50 m3 of seawater and in the surrounding waters in the Nouméa lagoon, New Caledonia, in the southwest Pacific as part of the VAriability of vertical and tropHIc transfer of diazotroph derived N in the south wEst Pacific (VAHINE) experiment. The aim of VAHINE was to examine the fate of diazotroph-derived nitrogen (DDN) in a low-nutrient, low-chlorophyll ecosystem. On day 4 of the experiment, the mesocosm was fertilized with phosphate. In the lagoon, gene expression was dominated by the cyanobacterium Synechococcus, closely followed by Alphaproteobacteria. In contrast, drastic changes in the microbial community composition and transcriptional activity were triggered within the mesocosm within the first 4 days, with transcription bursts from different heterotrophic bacteria in rapid succession. The microbial composition and activity of the surrounding lagoon ecosystem appeared more stable, although following similar temporal trends as in M1. We detected significant gene expression from Chromerida in M1, as well as the Nouméa lagoon, suggesting these photoautotrophic alveolates were present in substantial numbers in the open water. Other groups contributing substantially to the metatranscriptome were affiliated with marine Euryarchaeota Candidatus Thalassoarchaea (inside and outside) and Myoviridae bacteriophages likely infecting Synechococcus, specifically inside M1. High transcript abundances for ammonium transporters and glutamine synthetase in many different taxa (e.g., Pelagibacteraceae, Synechococcus, Prochlorococcus, and Rhodobacteraceae) was consistent with the known preference of most bacteria for this nitrogen source. In contrast, Alteromonadaceae highly expressed urease genes; Rhodobacteraceae and Prochlorococcus showed some urease expression, too. Nitrate reductase transcripts were detected on day 10 very prominently in Synechococcus and in Halomonadaceae. Alkaline

  3. Temporal changes of antibiotic-resistance genes and bacterial communities in two contrasting soils treated with cattle manure.

    Science.gov (United States)

    Hu, Hang-Wei; Han, Xue-Mei; Shi, Xiu-Zhen; Wang, Jun-Tao; Han, Li-Li; Chen, Deli; He, Ji-Zheng

    2016-02-01

    The emerging environmental spread of antibiotic-resistance genes (ARGs) and their subsequent acquisition by clinically relevant microorganisms is a major threat to public health. Animal manure has been recognized as an important reservoir of ARGs; however, the dissemination of manure-derived ARGs and the impacts of manure application on the soil resistome remain obscure. Here, we conducted a microcosm study to assess the temporal succession of total bacteria and a broad spectrum of ARGs in two contrasting soils following manure application from cattle that had not been treated with antibiotics. High-capacity quantitative PCR detected 52 unique ARGs across all the samples, with β-lactamase as the most dominant ARG type. Several genes of soil indigenous bacteria conferring resistance to β-lactam, which could not be detected in manure, were found to be highly enriched in manure-treated soils, and the level of enrichment was maintained over the entire course of 140 days. The enriched β-lactam resistance genes had significantly positive relationships with the relative abundance of the integrase intI1 gene, suggesting an increasing mobility potential in manure-treated soils. The changes in ARG patterns were accompanied by a significant effect of cattle manure on the total bacterial community compositions. Our study indicates that even in the absence of selective pressure imposed by agricultural use of antibiotics, manure application could still strongly impact the abundance, diversity and mobility potential of a broad spectrum of soil ARGs. Our findings are important for reliable prediction of ARG behaviors in soil environment and development of appropriate strategies to minimize their dissemination.

  4. Leveraging the power of Web 2.0 tools: a wiki platform as a multimedia teaching and learning environment in dental education.

    Science.gov (United States)

    Salajan, Florin D; Mount, Greg J

    2012-04-01

    This article presents the development and implementation of a wiki-based application for the delivery of educational content in dentistry. The Dental Procedure Education System (DPES) is a new web application that uses SharePoint to combine online collaborative authoring characteristic of wiki spaces with instructional video documentaries. Harnessing the wiki's versatility, DPES offers faculty members an avenue to develop an authoritative source of information for both students, through DPES Pro, and the public at large, through DPES Public. Principles of cognitive theory of multimedia learning, constructivist theory, and collaborative writing were employed in the development of DPES. An authoring protocol, with a clearly defined sequence of steps, was established in order to keep the production of the DPES procedures consistent and predictable. Initial, anecdotal user reports indicate that DPES is well received among dental students and faculty members. Expected outcomes and benefits of DPES use are discussed, and directions for research are proposed.

  5. Phylogeny of intestinal ciliates, including Charonina ventriculi, and comparison of microscopy and 18S rRNA gene pyrosequencing for rumen ciliate community structure analysis.

    Science.gov (United States)

    Kittelmann, Sandra; Devente, Savannah R; Kirk, Michelle R; Seedorf, Henning; Dehority, Burk A; Janssen, Peter H

    2015-04-01

    The development of high-throughput methods, such as the construction of 18S rRNA gene clone or pyrosequencing libraries, has allowed evaluation of ciliate community composition in hundreds of samples from the rumen and other intestinal habitats. However, several genera of mammalian intestinal ciliates have been described based only on morphological features and, to date, have not been identified using molecular methods. Here, we isolated single cells of one of the smallest but widely distributed intestinal ciliates, Charonina ventriculi, and sequenced its 18S rRNA gene. We verified the sequence in a full-cycle rRNA approach using fluorescence in situ hybridization and thereby assigned an 18S rRNA gene sequence to this species previously known only by its morphology. Based on its full-length 18S rRNA gene sequence, Charonina ventriculi was positioned within the phylogeny of intestinal ciliates in the subclass Trichostomatia. The taxonomic framework derived from this phylogeny was used for taxonomic assignment of trichostome ciliate 18S rRNA gene sequence data stemming from high-throughput amplicon pyrosequencing of rumen-derived DNA samples. The 18S rRNA gene-based ciliate community structure was compared to that obtained from microscopic counts using the same samples. Both methods allowed identification of dominant members of the ciliate communities and classification of the rumen ciliate community into one of the types first described by Eadie in 1962. Notably, each method is associated with advantages and disadvantages. Microscopy is a highly accurate method for evaluation of total numbers or relative abundances of different ciliate genera in a sample, while 18S rRNA gene pyrosequencing represents a valuable alternative for comparison of ciliate community structure in a large number of samples from different animals or treatment groups.

  6. Structural Dynamics of Community Gene Expression In a Freshwater Cyanobacterial Bloom Over a Day-Night Cycle

    Science.gov (United States)

    Wang, J.; Fernando, S.; Thompson, J. R.

    2011-12-01

    Cyanobacterial blooms are a major problem in eutrophic lakes and reservoirs, negatively impacting the ecology of the water body through oxygen depletion upon bloom decay and in some cases through production of toxins. Waterborne cyanobacterial toxins pose a public health threat through drinking and recreational exposure. The frequency of harmful cyanobacterial blooms (cyanoHABs) is predicted to increase due to warming regional climates (Paerl et.al, 2011) and increases in non-point source pollution due to urban expansion (Novotny, 2011). CyanoHABs represent complex consortia of cyanobacteria that live in association with diverse assemblages of heterotrophic and anoxygenic photosynthetic bacteria. A better understanding of the structure, function, and interaction between members of the complex microbial communities that support the proliferation of toxigenic cyanobacteria will improve our ability to prevent and control cyanoHABs. Studies of community gene expression, or metatranscriptomics, provide a powerful approach for quantifying changes in both the taxonomic composition (structure) and activity (function) of complex microbial systems in response to dynamic environmental conditions. We have used next-generation Illumina sequencing to characterize the metatranscriptome of a tropical eutrophic drinking water reservoir dominated by the toxigenic cyanobacterium Microcystis aeruginosa over a day/night cycle. Bacterioplankton sampling was carried out at six time points over a 24 hour period to capture variability associated with changes in the balance between phototrophic and heterotrophic activity. Total RNA was extracted and subjected to ribosomal depletion followed by cDNA synthesis and sequencing, generating 493,468 to 678,064 95-101 bp post-quality control reads per sample. Hierarchical Clustering of transcriptional profiles supported sorting of samples into two clusters corresponding to "day" and "night" collection times. Annotation of reads through the MG

  7. Imported anthropogenic bacteria may survive the Antarctic winter and introduce new genes into local bacterial communities

    Directory of Open Access Journals (Sweden)

    Brat Kristian

    2016-03-01

    Full Text Available We studied dynamic changes in anthropogenic bacterial communities at a summer-operated Czech research base (the Mendel Research Station in the Antarctic during 2012 and 2013. We observed an increase in total numbers of detected bacteria between the beginning and the end of each stay in the Antarctic. In the first series of samples, bacteria of Bacillus sp. predominated. Surprisingly, high numbers of Gram-positive cocci and coliforms were found (including opportunistic human pathogens, although the conditions for bacterial life were unfavourable (Antarctic winter. In the second series of samples, coliforms and Gram-positive cocci predominated. Dangerous human pathogens were also detected. Yersinia enterocolitica was identified as serotype O:9. Antibiotic susceptibility testing showed medium-to-high resistance rates to ampicillin, cefalotin, cefuroxime, amoxicillin-clavulanate and gentamicin in Enterobacteriaceae. 16S rRNA sequencing showed high rates of accordance between nucleotide sequences among the tested strains. Three conclusions were drawn: (1 Number of anthropogenic bacteria were able to survive the harsh conditions of the Antarctic winter (inside and outside the polar station. Under certain circumstances (e.g. impaired immunity, the surviving bacteria might pose a health risk to the participants of future expeditions or to other visitors to the base. (2 The bacteria released into the outer environment might have impacts on local ecosystems. (3 New characteristics (e.g. resistance to antibiotics may be introduced into local bacterial communities.

  8. Gene regulation knowledge commons: community action takes care of DNA binding transcription factors.

    Science.gov (United States)

    Tripathi, Sushil; Vercruysse, Steven; Chawla, Konika; Christie, Karen R; Blake, Judith A; Huntley, Rachael P; Orchard, Sandra; Hermjakob, Henning; Thommesen, Liv; Lægreid, Astrid; Kuiper, Martin

    2016-01-01

    A large gap remains between the amount of knowledge in scientific literature and the fraction that gets curated into standardized databases, despite many curation initiatives. Yet the availability of comprehensive knowledge in databases is crucial for exploiting existing background knowledge, both for designing follow-up experiments and for interpreting new experimental data. Structured resources also underpin the computational integration and modeling of regulatory pathways, which further aids our understanding of regulatory dynamics. We argue how cooperation between the scientific community and professional curators can increase the capacity of capturing precise knowledge from literature. We demonstrate this with a project in which we mobilize biological domain experts who curate large amounts of DNA binding transcription factors, and show that they, although new to the field of curation, can make valuable contributions by harvesting reported knowledge from scientific papers. Such community curation can enhance the scientific epistemic process.Database URL: http://www.tfcheckpoint.org. © The Author(s) 2016. Published by Oxford University Press.

  9. Coamplification of eukaryotic DNA with 16S rRNA gene-based PCR primers: possible consequences for population fingerprinting of complex microbial communities.

    Science.gov (United States)

    Huys, Geert; Vanhoutte, Tom; Joossens, Marie; Mahious, Amal S; De Brandt, Evie; Vermeire, Severine; Swings, Jean

    2008-06-01

    The main aim of this study was to evaluate the specificity of three commonly used 16S rRNA gene-based polymerase chain reaction (PCR) primer sets for bacterial community analysis of samples contaminated with eukaryotic DNA. The specificity of primer sets targeting the V3, V3-V5, and V6-V8 hypervariable regions of the 16S rRNA gene was investigated in silico and by community fingerprinting of human and fish intestinal samples. Both in silico and PCR-based analysis revealed cross-reactivity of the V3 and V3-V5 primers with the 18S rRNA gene of human and sturgeon. The consequences of this primer anomaly were illustrated by denaturing gradient gel electrophoresis (DGGE) profiling of microbial communities in human feces and mixed gut of Siberian sturgeon. DGGE profiling indicated that the cross-reactivity of 16S rRNA gene primers with nontarget eukaryotic DNA might lead to an overestimation of bacterial biodiversity. This study has confirmed previous sporadic indications in literature indicating that several commonly applied 16S rRNA gene primer sets lack specificity toward bacteria in the presence of eukaryotic DNA. The phenomenon of cross-reactivity is a potential source of systematic error in all biodiversity studies where no subsequent analysis of individual community amplicons by cloning and sequencing is performed.

  10. Media Art Wiki. Uso de Wikis para la enseñanza interdisciplinar y multimedia del arte de los nuevos medios de comunicación en entornos virtuales de aprendizaje

    Directory of Open Access Journals (Sweden)

    Pau Alsina

    2010-01-01

    Full Text Available Este capítulo expone y analiza una experiencia piloto de uso de Wikis para la enseñanza de las prácticas artísticas vinculadas a los nuevos medios de comunicación digital. El denominado "Media Art Wiki" constituye un recurso para la enseñanza del Arte y la Estética de los nuevos medios en un contexto de enseñanza-aprendizaje virtual como es la Universitat Oberta de Catalunya (UOC. Los objetivos iniciales del proyecto consistieron en generar un entorno dinámico de documentación multimedia de las prácticas de Arte de los nuevos medios, y a su vez, que ese espacio de contenidos abiertos pudiera alimentarse de la acción participativa y colaborativa de los estudiantes de las diferentes asignaturas implicadas, contribuyendo de este modo a un enfoque interdisciplinar de la materia común. El Media Art Wiki pretende innovar dentro del aula virtual en cuatro aspectos diferentes: proceso, formato, estructura y contenidos tratando de responder asimismo a un planteamiento pedagógico, que vincule cada una de las actividades implicadas en el Wiki con varios programas y asignaturas. En este capítulo intentaremos dar cuenta de las implicaciones del uso de este tipo de herramientas en la enseñanza universitaria, estructurando el texto en diferentes apartados que, por un lado, trazan el contexto a partir del cual surgió el proyecto, sus necesidades, objetivos y motivaciones dentro del marco teórico del aprendizaje significativo- y el contexto -modelo de enseñanza-aprendizaje- de la UOC. Por otro lado procedemos a la descripción técnica y de contenido del proyecto, así como el diseño de la estrategia didáctica y de las actividades a desarrollar por los estudiantes a corto y medio plazo. Finalmente exponemos la evaluación de dicha experiencia desde la perspectiva de los docentes y los estudiantes para llegar a plantear nuestras conclusiones y posibilidades de desarrollos de futuro.

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

    Directory of Open Access Journals (Sweden)

    Guy C J Abell

    Full Text Available Advances in microbial ecology research are more often than not limited by the capabilities of available methodologies. Aerobic autotrophic nitrification is one of the most important and well studied microbiological processes in terrestrial and aquatic ecosystems. We have developed and validated a microbial diagnostic microarray based on the ammonia-monooxygenase subunit A (amoA gene, enabling the in-depth analysis of the community structure of bacterial and archaeal ammonia oxidisers. The amoA microarray has been successfully applied to analyse nitrifier diversity in marine, estuarine, soil and wastewater treatment plant environments. The microarray has moderate costs for labour and consumables and enables the analysis of hundreds of environmental DNA or RNA samples per week per person. The array has been thoroughly validated with a range of individual and complex targets (amoA clones and environmental samples, respectively, combined with parallel analysis using traditional sequencing methods. The moderate cost and high throughput of the microarray makes it possible to adequately address broader questions of the ecology of microbial ammonia oxidation requiring high sample numbers and high resolution of the community composition.

  12. Influences of graphene on microbial community and antibiotic resistance genes in mouse gut as determined by high-throughput sequencing.

    Science.gov (United States)

    Xie, Yongchao; Wu, Bing; Zhang, Xu-Xiang; Yin, Jinbao; Mao, Liang; Hu, Maojie

    2016-02-01

    Graphene is a promising candidate as an antibacterial material owning to its bacterial toxicity. However, little information on influence of graphene on gut microbiota is available. In this study, mice were exposed to graphene for 4 weeks, and high-throughput sequencing was applied to characterize the changes in microbial community and antibiotic resistance genes (ARGs) in mouse gut. The results showed that graphene exposure increased biodiversity of gut microbiota, and changed their community. The 1 μg/d graphene exposure had higher influences on the gut microbiota than 10 μg/d and 100 μg/d graphene exposures, which might be due to higher aggregation of high-level graphene. The influence of graphene on gut microbiota might attribute to that graphene could induce oxidative stress and damage of cell membrane integrity. The results were verified by the increase of ratio of Gram-negative bacteria. Outer membrane of Gram-negative bacteria could reduce the membrane damage induced by graphene and make them more tolerance to graphene. Further, we found that graphene exposure significantly increased the abundance and types of ARGs, indicating a potential health risk of graphene. This study firstly provides new insight to the health effects of graphene on gut microbiota.

  13. Making sense of the German Wikipedia community

    Directory of Open Access Journals (Sweden)

    Rikke Frank Jørgensen

    2012-08-01

    Full Text Available This article presents the findings from a qualitative study of the German Wikipedia community, focusing on how people engaged with Wikipedia make sense of norms, collaborative practices and means of regulation within the community. The study highlights the strong focus on the quality of the end-product (the encyclopedia in the German community, stressing that article quality is seen as more important than the wiki-process as such. As the community has grown, an increasing number of rules and mechanisms have been deployed to resolve various issues and conflicts, however the interviewees do not perceive Wikipedia as being bureaucratic, but rather describe it as a “rule-governed anarchy”. The findings suggest that people contribute for a variety of reasons, yet point to reactions from and interactions with fellow Wikipedians as one of the strongest motivational drivers for participation.

  14. 基于WIKI的论文网络协作与发表平台%Online Paper Collaboration and Publish Platform Based on WIKI

    Institute of Scientific and Technical Information of China (English)

    孙彧; 江波; 黄建新; 林满

    2011-01-01

    阐述了WIKI技术的定义和特点,深入研究了运用WIKI技术构建互联网论文协作与发表平台的方法,并对平台进行了需求分析和系统设计.%This paper discusses the definition and features of WIKI, studies the use of WIKI technologies in the papers published and collaboration platform, discusses the needs and system design of the platform.

  15. Abundance of Pathogenic Escherichia coli Virulence-Associated Genes in Well and Borehole Water Used for Domestic Purposes in a Peri-Urban Community of South Africa

    Science.gov (United States)

    Abia, Akebe Luther King; Schaefer, Lisa; Ubomba-Jaswa, Eunice; Le Roux, Wouter

    2017-01-01

    In the absence of pipe-borne water, many people in Africa, especially in rural communities, depend on alternative water sources such as wells, boreholes and rivers for household and personal hygiene. Poor maintenance and nearby pit latrines, however, lead to microbial pollution of these sources. We evaluated the abundance of Escherichia coli and the prevalence of pathogenic E. coli virulence genes in water from wells, boreholes and a river in a South African peri-urban community. Monthly samples were collected between August 2015 and November 2016. In all, 144 water samples were analysed for E. coli using the Colilert 18 system. Virulence genes (eagg, eaeA, stx1, stx2, flichH7, ST, ipaH, ibeA) were investigated using real-time polymerase chain reaction. Mean E. coli counts ranged between 0 and 443.1 Most Probable Number (MPN)/100 mL of water sample. Overall, 99.3% of samples were positive for at least one virulence gene studied, with flicH7 being the most detected gene (81/140; 57.6%) and the stx2 gene the least detected gene (8/140; 5.7%). Both intestinal and extraintestinal pathogenic E. coli genes were detected. The detection of virulence genes in these water sources suggests the presence of potentially pathogenic E. coli strains and is a public health concern. PMID:28335539

  16. Abundance of Pathogenic Escherichia coli Virulence-Associated Genes in Well and Borehole Water Used for Domestic Purposes in a Peri-Urban Community of South Africa

    Directory of Open Access Journals (Sweden)

    Akebe Luther King Abia

    2017-03-01

    Full Text Available In the absence of pipe-borne water, many people in Africa, especially in rural communities, depend on alternative water sources such as wells, boreholes and rivers for household and personal hygiene. Poor maintenance and nearby pit latrines, however, lead to microbial pollution of these sources. We evaluated the abundance of Escherichia coli and the prevalence of pathogenic E. coli virulence genes in water from wells, boreholes and a river in a South African peri-urban community. Monthly samples were collected between August 2015 and November 2016. In all, 144 water samples were analysed for E. coli using the Colilert 18 system. Virulence genes (eagg, eaeA, stx1, stx2, flichH7, ST, ipaH, ibeA were investigated using real-time polymerase chain reaction. Mean E. coli counts ranged between 0 and 443.1 Most Probable Number (MPN/100 mL of water sample. Overall, 99.3% of samples were positive for at least one virulence gene studied, with flicH7 being the most detected gene (81/140; 57.6% and the stx2 gene the least detected gene (8/140; 5.7%. Both intestinal and extraintestinal pathogenic E. coli genes were detected. The detection of virulence genes in these water sources suggests the presence of potentially pathogenic E. coli strains and is a public health concern.

  17. The Impact of ICT Training Through Wikis on In-Service EFL Teachers: Changes in Beliefs, Attitudes, and Competencies

    Directory of Open Access Journals (Sweden)

    Yamith José Fandiño Parra

    2012-12-01

    Full Text Available The development of information and communication technology (ICT invites teachers to abandon traditional roles and act more as mentors, exploring the new media themselves as learners and thus acting as role models for their students (Fitzpatrick & Davies, 2003. For turning students into producers of online content and creating a collaborative learning environment, wikis appear to help foreign language teachers to infuse ICT in their classrooms (Kovacic, Bubas & Zlatovic, 2007. Within this context, results from an action research project carried out in four public schools suggest that beliefs, attitudes, and competencies can be impacted positively when working on the use of new technologies with in-service English teachers.

  18. Wikis, blogs and podcasts: a new generation of Web-based tools for virtual collaborative clinical practice and education.

    Science.gov (United States)

    Boulos, Maged N Kamel; Maramba, Inocencio; Wheeler, Steve

    2006-08-15

    We have witnessed a rapid increase in the use of Web-based 'collaborationware' in recent years. These Web 2.0 applications, particularly wikis, blogs and podcasts, have been increasingly adopted by many online health-related professional and educational services. Because of their ease of use and rapidity of deployment, they offer the opportunity for powerful information sharing and ease of collaboration. Wikis are Web sites that can be edited by anyone who has access to them. The word 'blog' is a contraction of 'Web Log' - an online Web journal that can offer a resource rich multimedia environment. Podcasts are repositories of audio and video materials that can be "pushed" to subscribers, even without user intervention. These audio and video files can be downloaded to portable media players that can be taken anywhere, providing the potential for "anytime, anywhere" learning experiences (mobile learning). Wikis, blogs and podcasts are all relatively easy to use, which partly accounts for their proliferation. The fact that there are many free and Open Source versions of these tools may also be responsible for their explosive growth. Thus it would be relatively easy to implement any or all within a Health Professions' Educational Environment. Paradoxically, some of their disadvantages also relate to their openness and ease of use. With virtually anybody able to alter, edit or otherwise contribute to the collaborative Web pages, it can be problematic to gauge the reliability and accuracy of such resources. While arguably, the very process of collaboration leads to a Darwinian type 'survival of the fittest' content within a Web page, the veracity of these resources can be assured through careful monitoring, moderation, and operation of the collaborationware in a closed and secure digital environment. Empirical research is still needed to build our pedagogic evidence base about the different aspects of these tools in the context of medical/health education. If

  19. Wikis, blogs and podcasts: a new generation of Web-based tools for virtual collaborative clinical practice and education

    Directory of Open Access Journals (Sweden)

    Maramba Inocencio

    2006-08-01

    Full Text Available Abstract Background We have witnessed a rapid increase in the use of Web-based 'collaborationware' in recent years. These Web 2.0 applications, particularly wikis, blogs and podcasts, have been increasingly adopted by many online health-related professional and educational services. Because of their ease of use and rapidity of deployment, they offer the opportunity for powerful information sharing and ease of collaboration. Wikis are Web sites that can be edited by anyone who has access to them. The word 'blog' is a contraction of 'Web Log' – an online Web journal that can offer a resource rich multimedia environment. Podcasts are repositories of audio and video materials that can be "pushed" to subscribers, even without user intervention. These audio and video files can be downloaded to portable media players that can be taken anywhere, providing the potential for "anytime, anywhere" learning experiences (mobile learning. Discussion Wikis, blogs and podcasts are all relatively easy to use, which partly accounts for their proliferation. The fact that there are many free and Open Source versions of these tools may also be responsible for their explosive growth. Thus it would be relatively easy to implement any or all within a Health Professions' Educational Environment. Paradoxically, some of their disadvantages also relate to their openness and ease of use. With virtually anybody able to alter, edit or otherwise contribute to the collaborative Web pages, it can be problematic to gauge the reliability and accuracy of such resources. While arguably, the very process of collaboration leads to a Darwinian type 'survival of the fittest' content within a Web page, the veracity of these resources can be assured through careful monitoring, moderation, and operation of the collaborationware in a closed and secure digital environment. Empirical research is still needed to build our pedagogic evidence base about the different aspects of these tools in

  20. Wiki知识元语义图研究%Semantic Graph of Knowledge Unit on Wiki Platform

    Institute of Scientific and Technical Information of China (English)

    温有奎; 焦玉英

    2009-01-01

    From the perspective of the retrieval model,knowledge retrieval systems focus on the semantics and knowledge organization. Data retrieval and information retrieval organize the data and documents by indexing,while knowledge retrieval is to organize knowledge by linking among knowledge units and knowledge structures. Simultaneously,Wiki systems are becoming more and more popular as facilities for content and knowledge management. A kind of semantic graph creation systems of knowledge unit based on Wiki platform is proposed in the paper. The model of knowledge organizing and knowledge management about Wiki platform,Ontology structure of knowledge units and the model of knowledge units base,the extraction arithmetic of knowledge unit and a semantic Wiki of knowledge units are discussed. A semantic graph system of knowledge unit is implemented.%从检索模型的视角看,知识检索系统的焦点在于语义和知识组织.数据检索和信息检索是通过标引组织数据和文献,而知识检索则是通过链接知识元和知识结构组织知识.与此同时,Wiki越来越成为内容管理和知识管理的一种流行工具.本文提出了一种基于Wiki平台的知识元语义图系统.分析了Wiki平台的知识组织与管理模式,给出了知识元库系统模型,知识元的抽取算法和知识元语义图模型.讨论了Wiki平台的搭建和语义Wiki页面的创建步骤.实现了Wiki网站上的知识元语义图系统.试验表明,基于Wiki平台的知识元语义图对知识交流和思想创新有促进作用.

  1. Abundance of antibiotics, antibiotic resistance genes and bacterial community composition in wastewater effluents from different Romanian hospitals.

    Science.gov (United States)

    Szekeres, Edina; Baricz, Andreea; Chiriac, Cecilia Maria; Farkas, Anca; Opris, Ocsana; Soran, Maria-Loredana; Andrei, Adrian-Stefan; Rudi, Knut; Balcázar, Jose Luis; Dragos, Nicolae; Coman, Cristian

    2017-06-01

    Antimicrobial resistance represents a growing and significant public health threat, which requires a global response to develop effective strategies and mitigate the emergence and spread of this phenomenon in clinical and environmental settings. We investigated, therefore, the occurrence and abundance of several antibiotics and antibiotic resistance genes (ARGs), as well as bacterial community composition in wastewater effluents from different hospitals located in the Cluj County, Romania. Antibiotic concentrations ranged between 3.67 and 53.05 μg L(-1), and the most abundant antibiotic classes were β-lactams, glycopeptides, and trimethoprim. Among the ARGs detected, 14 genes confer resistance to β-lactams, aminoglycosides, chloramphenicol, macrolide-lincosamide-streptogramin B (MLSB) antibiotics, sulfonamides, and tetracyclines. Genes encoding quaternary ammonium resistance and a transposon-related element were also detected. The sulI and qacEΔ1 genes, which confer resistance to sulfonamides and quaternary ammonium, had the highest relative abundance with values ranging from 5.33 × 10(-2) to 1.94 × 10(-1) and 1.94 × 10(-2) to 4.89 × 10(-2) copies/16 rRNA gene copies, respectively. The dominant phyla detected in the hospital wastewater samples were Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. Among selected hospitals, one of them applied an activated sludge and chlorine disinfection process before releasing the effluent to the municipal collector. This conventional wastewater treatment showed moderate removal efficiency of the studied pollutants, with a 55-81% decrease in antibiotic concentrations, 1-3 order of magnitude lower relative abundance of ARGs, but with a slight increase of some potentially pathogenic bacteria. Given this, hospital wastewaters (raw or treated) may contribute to the spread of these emerging pollutants in the receiving environments. To the best of our knowledge, this study quantified for the first time

  2. Promoting Precision Cancer Medicine through a Community-Driven Knowledgebase

    Directory of Open Access Journals (Sweden)

    Nophar Geifman

    2014-12-01

    Full Text Available Increasing efforts are being dedicated towards improving cancer care via personalized medicine. These efforts depend to a large degree on the availability of a knowledge foundation. Unfortunately, existing knowledge linking cancer drugs and potential efficacy biomarkers is in its infancy; and where links are known, they are frequently unstructured and poorly documented. We have developed a new open-access knowledgebase for precision cancer medicine (the PCM Wiki and Knowledgebase. This knowledgebase was constructed using an innovative, two-pronged approach involving a structured knowledgebase at the back-end, and an intuitive knowledge-sharing interface and user-friendly query engine in front. The knowledgebase was seeded with several patient case reports and information was mined via text-mining and literature review by human curators. Using our novel Wiki-based platform to present and share knowledge stored in the PCM knowledgebase, users are able to suggest corrections, propose additions or point to errors in the knowledgebase. The result is a community-driven evolving knowledgebase holding integrated and consolidated knowledge of markers and indications for personalized cancer medicine. We suggest that the PCM Knowledgebase and Wiki could serve as an important tool for the advancement of clinical trials and care in the field of precision cancer medicine.

  3. Spatial and temporal changes of cyanophage communities in paddy field soils as revealed by the capsid assembly protein gene g20.

    Science.gov (United States)

    Wang, Guanghua; Asakawa, Susumu; Kimura, Makoto

    2011-05-01

    Bacteriophages are ubiquitous in various environments. Our previous study revealed the diversity of the cyanophage community in paddy floodwater. In this study, the phylogeny and genetic diversity of cyanophage communities in paddy field soils were reported. The viral capsid assembly protein gene (g20) of cyanophage was amplified with the primers CPS1 and CPS8 from soil DNA extracted during two different sampling times at three sampling sites in Japan. The sequencing results indicated that about 93% of the clones were g20 genes. In total, 70 clones of g20 genes were obtained in this study, of which 69 clones were of cyanophage origin. As evaluated by g20 sequence assemblages in paddy field soils, the unifrac analyses results indicated that cyanophage communities changed among the sampling sites and times and differed from those communities detected in paddy floodwater. The phylogenetic analysis showed that the g20 sequences in paddy field soils were very diverse and distributed into Clusters α, β and ɛ, as well as four newly formed clusters. Within Clusters β and ɛ, four unique subclusters were formed from the g20 clones that were only observed in this study. These findings suggested that the cyanophage communities in paddy field soils are different from those found in freshwater, marine water and paddy floodwater.

  4. Pyrosequencing of mcrA and archaeal 16S rRNA genes reveals diversity and substrate preferences of methanogen communities in anaerobic digesters.

    Science.gov (United States)

    Wilkins, David; Lu, Xiao-Ying; Shen, Zhiyong; Chen, Jiapeng; Lee, Patrick K H

    2015-01-01

    Methanogenic archaea play a key role in biogas-producing anaerobic digestion and yet remain poorly taxonomically characterized. This is in part due to the limitations of low-throughput Sanger sequencing of a single (16S rRNA) gene, which in the past may have undersampled methanogen diversity. In this study, archaeal communities from three sludge digesters in Hong Kong and one wastewater digester in China were examined using high-throughput pyrosequencing of the methyl coenzyme M reductase (mcrA) and 16S rRNA genes. Methanobacteriales, Methanomicrobiales, and Methanosarcinales were detected in each digester, indicating that both hydrogenotrophic and acetoclastic methanogenesis was occurring. Two sludge digesters had similar community structures, likely due to their similar design and feedstock. Taxonomic classification of the mcrA genes suggested that these digesters were dominated by acetoclastic methanogens, particularly Methanosarcinales, while the other digesters were dominated by hydrogenotrophic Methanomicrobiales. The proposed euryarchaeotal order Methanomassiliicoccales and the uncultured WSA2 group were detected with the 16S rRNA gene, and potential mcrA genes for these groups were identified. 16S rRNA gene sequencing also recovered several crenarchaeotal groups potentially involved in the initial anaerobic digestion processes. Overall, the two genes produced different taxonomic profiles for the digesters, while greater methanogen richness was detected using the mcrA gene, supporting the use of this functional gene as a complement to the 16S rRNA gene to better assess methanogen diversity. A significant positive correlation was detected between methane production and the abundance of mcrA transcripts in digesters treating sludge and wastewater samples, supporting the mcrA gene as a biomarker for methane yield.

  5. Characterization of microbial communities found in the human vagina by analysis of terminal restriction fragment length polymorphisms of 16S rRNA genes

    NARCIS (Netherlands)

    Coolen, MJL; Post, E; Davis, CC; Forney, LJ

    2005-01-01

    To define and monitor the structure of microbial communities found in the human vagina, a cultivation-independent approach based on analyses of terminal restriction fragment length polymorphisms (T-RFLP) of 16S rRNA genes was developed and validated. Sixteen bacterial strains commonly found in the h

  6. [Distinctive Features of the Microbial Diversity and the Polyketide Synthase GenesSpectrum in the Community of the Endemic Baikal Sponge Swartschewskia papyracea].

    Science.gov (United States)

    Kaluzhnaya, O V; Itskovich, V B

    2016-01-01

    The diversity of the symbiotic community of the endemic Baikal sponge Swartschewskia papyracea was studied, and an analysis of the polyketide synthases genes spectrum in sponge-associated microorganisms was carried out. Six bacterial phyla were detected in the S. papyracea microbiome, namely, Verrucomicrobia, Cyanobacteria, Actinobacteria, Bacteroidetes, Proteobacteria, and Planctomycetes. Unlike the microbial associations of other freshwater sponges, the community under study was dominated by the Verrucomicrobia (42.1%) and Cyanobacteria (17.5%) phyla, while the proportion of the Proteobacteria was unusually low (9.7%). In the S. papyracea community metagenome, there were identified 18 polyketide synthases genes fragments, the closest homologs of which included the polyketide synthases of the microorganisms belonging to the bacterial phyla Cyanobacteria, Proteobacteria (Betaproteobacteria, Deltaproteobacteria, and Gammaproteobacteria classes), and Acidobacteria and to the eukaryotic algae of the Heterokonta phylum (Eustigmatophyceae class). Polyketide synthase sequences from S. papyracea formed three groups on the phylogenetic tree: a group of hybrid NRPS/PKS complexes, a group of cyanobacterial polyketide synthases, and a group of homologs of the eukaryotic alga Nannochloropsis galiana. Notably, the identified polyketide synthase genes fragments showed only a 57-88% similarity to the sequences in the databases, which implies the presence of genes controlling the synthesis of the novel, still unstudied, polyketide compounds in the S. papyracea community. It was proposed that the habitation conditions of S. papyracea affect the taxonomic composition of the microorganisms associated with the sponge, including the diversity of the producers of secondary metabolites.

  7. Effect of red mud addition on tetracycline and copper resistance genes and microbial community during the full scale swine manure composting.

    Science.gov (United States)

    Wang, Rui; Zhang, Junya; Sui, Qianwen; Wan, Hefeng; Tong, Juan; Chen, Meixue; Wei, Yuansong; Wei, Dongbin

    2016-09-01

    Swine manure has been considered as the reservoir of antibiotic resistance genes (ARGs). Composting is one of the most suitable technologies for treating livestock manures, and red mud was proved to have a positive effect on nitrogen conservation during composting. This study investigated the abundance of eight tetracycline and three copper resistance genes, the bacterial community during the full scale swine manure composting with or without addition of red mud. The results showed that ARGs in swine manure could be effectively removed through composting (reduced by 2.4log copies/g TS), especially during the thermophilic phase (reduced by 1.5log copies/g TS), which the main contributor might be temperature. Additionally, evolution of bacterial community could also have a great influence on ARGs. Although addition of red mud could enhance nitrogen conservation, it obviously hindered removal of ARGs (reduced by 1.7log copies/g TS) and affected shaping of bacterial community during composting.

  8. Microbial communities and functional genes associated with soil arsenic contamination and the rhizosphere of the arsenic-hyperaccumulating plant Pteris vittata L.

    Science.gov (United States)

    Xiong, Jinbo; Wu, Liyou; Tu, Shuxin; Van Nostrand, Joy D; He, Zhili; Zhou, Jizhong; Wang, Gejiao

    2010-11-01

    To understand how microbial communities and functional genes respond to arsenic contamination in the rhizosphere of Pteris vittata, five soil samples with different arsenic contamination levels were collected from the rhizosphere of P. vittata and nonrhizosphere areas and investigated by Biolog, geochemical, and functional gene microarray (GeoChip 3.0) analyses. Biolog analysis revealed that the uncontaminated soil harbored the greatest diversity of sole-carbon utilization abilities and that arsenic contamination decreased the metabolic diversity, while rhizosphere soils had higher metabolic diversities than did the nonrhizosphere soils. GeoChip 3.0 analysis showed low proportions of overlapping genes across the five soil samples (16.52% to 45.75%). The uncontaminated soil had a higher heterogeneity and more unique genes (48.09%) than did the arsenic-contaminated soils. Arsenic resistance, sulfur reduction, phosphorus utilization, and denitrification genes were remarkably distinct between P. vittata rhizosphere and nonrhizosphere soils, which provides evidence for a strong linkage among the level of arsenic contamination, the rhizosphere, and the functional gene distribution. Canonical correspondence analysis (CCA) revealed that arsenic is the main driver in reducing the soil functional gene diversity; however, organic matter and phosphorus also have significant effects on the soil microbial community structure. The results implied that rhizobacteria play an important role during soil arsenic uptake and hyperaccumulation processes of P. vittata.

  9. Highlighting of quorum sensing lux genes and their expression in the hydrothermal vent shrimp Rimicaris exoculata ectosymbiontic community. Possible use as biogeographic markers.

    Science.gov (United States)

    Le Bloa, Simon; Durand, Lucile; Cueff-Gauchard, Valérie; Le Bars, Josiane; Taupin, Laure; Marteau, Charlotte; Bazire, Alexis; Cambon-Bonavita, Marie-Anne

    2017-01-01

    Rimicaris exoculata is a caridean shrimp that dominates the fauna at several hydrothermal vent sites of the Mid-Atlantic Ridge. It has two distinct and stable microbial communities. One of these epibiontic bacterial communities is located in the shrimp gut and has a distribution and role that are poorly understood. The second colonizes its enlarged gill chamber and is involved in host nutrition. It is eliminated after each molt, and has colonization processes reminiscent of those of a biofilm. The presence and expression of genes usually involved in quorum sensing (QS) were then studied. At four sites, Rainbow, TAG, Snake Pit and Logatchev, two lux genes were identified in the R. exoculata epibiontic community at different shrimp molt stages and life stages. RT-PCR experiments highlighted lux gene expression activity at TAG, Snake Pit and Rainbow vent sites. Their potential QS activity and their possible roles in epibiont colonization processes are discussed. Moreover, phylogenetic analysis has shown the presence of three clades for luxS (Epsilonproteobacteria) and four clades for luxR (Gammaproteobacteria) genes, each clade being restricted to a single site. These genes are more divergent than the 16S rRNA one. They could therefore be used as biogeographical genetic markers.

  10. Highlighting of quorum sensing lux genes and their expression in the hydrothermal vent shrimp Rimicaris exoculata ectosymbiontic community. Possible use as biogeographic markers

    Science.gov (United States)

    Le Bloa, Simon; Durand, Lucile; Cueff- Gauchard, Valérie; Le Bars, Josiane; Taupin, Laure; Marteau, Charlotte; Bazire, Alexis

    2017-01-01

    Rimicaris exoculata is a caridean shrimp that dominates the fauna at several hydrothermal vent sites of the Mid-Atlantic Ridge. It has two distinct and stable microbial communities. One of these epibiontic bacterial communities is located in the shrimp gut and has a distribution and role that are poorly understood. The second colonizes its enlarged gill chamber and is involved in host nutrition. It is eliminated after each molt, and has colonization processes reminiscent of those of a biofilm. The presence and expression of genes usually involved in quorum sensing (QS) were then studied. At four sites, Rainbow, TAG, Snake Pit and Logatchev, two lux genes were identified in the R. exoculata epibiontic community at different shrimp molt stages and life stages. RT-PCR experiments highlighted lux gene expression activity at TAG, Snake Pit and Rainbow vent sites. Their potential QS activity and their possible roles in epibiont colonization processes are discussed. Moreover, phylogenetic analysis has shown the presence of three clades for luxS (Epsilonproteobacteria) and four clades for luxR (Gammaproteobacteria) genes, each clade being restricted to a single site. These genes are more divergent than the 16S rRNA one. They could therefore be used as biogeographical genetic markers. PMID:28328982

  11. Occurrence and analysis of irp2 virulence gene in isolates of Klebsiella pneumoniae and Enterobacter spp. from microbiota and hospital and community-acquired infections.

    Science.gov (United States)

    Souza Lopes, Ana Catarina; Rodrigues, Juliana Falcão; Cabral, Adriane Borges; da Silva, Maíra Espíndola; Leal, Nilma Cintra; da Silveira, Vera Magalhães; de Morais Júnior, Marcos Antônio

    2016-07-01

    Eighty-five isolates of Klebsiella pneumoniae and Enterobacter spp., originating from hospital- and community-acquired infections and from oropharyngeal and faecal microbiota from patients in Recife-PE, Brazil, were analyzed regarding the presence of irp2 gene. This is a Yersinia typical gene involved in the synthesis of siderophore yersiniabactin. DNA sequencing confirmed the identity of irp2 gene in five K. pneumoniae, five Enterobacter aerogenes and one Enterobacter amnigenus isolates. To our knowledge in the current literature, this is the first report of the irp2 gene in E. amnigenus, a species considered an unusual human pathogen, and in K. pneumoniae and E. aerogenes isolates from the normal microbiota and from community infections, respectively. Additionally, the analyses of nucleotide and amino acid sequences suggest the irp2 genes derived from isolates used in this study are more closely related to that of Yersinia pestis P.CE882 than to that of Yersinia enterocolitica 8081. These data demonstrated that K. pneumoniae and Enterobacter spp. from normal microbiota and from community- and hospital-acquired infections possess virulence factors important for the establishment of extra-intestinal infections. Copyright © 2016 Elsevier Ltd. All rights reserved.

  12. Comparison of antimicrobial resistance phenotypes and resistance genes in Enterococcus faecalis and Enterococcus faecium from humans in the community, broilers and pigs in Denmark

    DEFF Research Database (Denmark)

    Aarestrup, Frank Møller; Agersø, Yvonne; Gerner-Smidt, P.;

    2000-01-01

    Enterococcus faecalis and E. faecium isolated from humans in the community (98 and 65 isolates), broilers (126 and 122), and pigs (102 and 88) during 1998 were tested for susceptibility to 12 different antimicrobial agents and for the presence of selected genes encoding resistance using PCR...... of the 38 human fecal samples examined using selective enrichment. All vancomycin resistant isolates contained the vanA gene, all chloramphenicol resistant isolates the catpIP501 gene, and all five gentamicin resistant isolates the aac6-aph2 gene. Sixty-one (85%) of 72 erythromycin resistant E. faecalis...... examined and 57 (90%) of 63 erythromycin resistant E. faecium isolates examined contained ermB. Forty (91%) of the kanamycin resistant E. faecalis and 18 (72%) of the kanamycin resistant E. faecium isolates contained aphA3. The tet(M) gene was found in 95% of the tetracycline resistant E. faecalis and E...

  13. Idiopathic neonatal necrotising fasciitis caused by community-acquired MSSA encoding Panton Valentine Leukocidin genes.

    LENUS (Irish Health Repository)

    Dunlop, Rebecca L E

    2012-02-01

    Neonatal necrotising fasciitis is very rare in comparison to the adult presentation of the disease and a Plastic Surgeon may only encounter one such case during his or her career. Often this is initially misdiagnosed and managed as simple cellulitis. It generally affects previously healthy babies, the site is often the lower back area and a history of minor skin trauma may be elicited. The causative organism is usually Streptococcus or polymicrobial, as is the case in the adult population. We present the case of a previously healthy 11-day-old infant with idiopathic, rapidly progressive necrotising fasciitis of the back, cause by Methicillin sensitive Staphylococcus aureus (MSSA) infection. The strain was isolated and found to encode the Panton-Valentine Leukocidin genes, which have been associated with particularly severe necrotising infections in other sites, with high mortality. These strains are the subject of specific treatment and eradication guidance in the UK but awareness of this and the importance of obtaining detailed culture typing is likely to be low amongst Plastic Surgeons.

  14. Changes in 16s RNA Gene Microbial Community Profiling by Concentration of Prokaryotic DNA.

    Science.gov (United States)

    Glassing, Angela; Dowd, Scot E; Galandiuk, Susan; Davis, Brian; Jorden, Jeffrey R; Chiodini, Rodrick J

    2015-12-01

    Microbial metagenomics are hindered in clinical tissue samples as a result of the large relative amount of human DNA in relation to microbial DNA acting as competitive inhibitors of downstream applications. We evaluated the LOOXSTER® Enrichment Kit to separate eukaryotic and prokaryotic DNA in submucosal intestinal tissue samples having a low microbial biomass and to determine the effects of enrichment on 16s rRNA microbiota sequencing. The enrichment kit reduced the amount of human DNA in the samples 40-70% resulting in a 3.5-fold increase in the number of 16s bacterial gene sequences detected on the Illumina MiSeq platform. This increase was accompanied by the detection of 41 additional bacterial genera and 94 tentative species. The additional bacterial taxa detected accounted for as much as 25% of the total bacterial population that significantly altered the relative prevalence and composition of the intestinal microbiota. The ability to reduce the competitive inhibition created by human DNA and the concentration of bacterial DNA may allow metagenomics to be performed on complex tissues containing a low bacterial biomass.

  15. Marine Microbial Gene Abundance and Community Composition in Response to Ocean Acidification and Elevated Temperature in Two Contrasting Coastal Marine Sediments.

    Science.gov (United States)

    Currie, Ashleigh R; Tait, Karen; Parry, Helen; de Francisco-Mora, Beatriz; Hicks, Natalie; Osborn, A Mark; Widdicombe, Steve; Stahl, Henrik

    2017-01-01

    Marine ecosystems are exposed to a range of human-induced climate stressors, in particular changing carbonate chemistry and elevated sea surface temperatures as a consequence of climate change. More research effort is needed to reduce uncertainties about the effects of global-scale warming and acidification for benthic microbial communities, which drive sedimentary biogeochemical cycles. In this research, mesocosm experiments were set up using muddy and sandy coastal sediments to investigate the independent and interactive effects of elevated carbon dioxide concentrations (750 ppm CO2) and elevated temperature (ambient +4°C) on the abundance of taxonomic and functional microbial genes. Specific quantitative PCR primers were used to target archaeal, bacterial, and cyanobacterial/chloroplast 16S rRNA in both sediment types. Nitrogen cycling genes archaeal and bacterial ammonia monooxygenase (amoA) and bacterial nitrite reductase (nirS) were specifically targeted to identify changes in microbial gene abundance and potential impacts on nitrogen cycling. In muddy sediment, microbial gene abundance, including amoA and nirS genes, increased under elevated temperature and reduced under elevated CO2 after 28 days, accompanied by shifts in community composition. In contrast, the combined stressor treatment showed a non-additive effect with lower microbial gene abundance throughout the experiment. The response of microbial communities in the sandy sediment was less pronounced, with the most noticeable response seen in the archaeal gene abundances in response to environmental stressors over time. 16S rRNA genes (amoA and nirS) were lower in abundance in the combined stressor treatments in sandy sediments. Our results indicated that marine benthic microorganisms, especially in muddy sediments, are susceptible to changes in ocean carbonate chemistry and seawater temperature, which ultimately may have an impact upon key benthic biogeochemical cycles.

  16. Marine Microbial Gene Abundance and Community Composition in Response to Ocean Acidification and Elevated Temperature in Two Contrasting Coastal Marine Sediments

    Directory of Open Access Journals (Sweden)

    Ashleigh R. Currie

    2017-08-01

    Full Text Available Marine ecosystems are exposed to a range of human-induced climate stressors, in particular changing carbonate chemistry and elevated sea surface temperatures as a consequence of climate change. More research effort is needed to reduce uncertainties about the effects of global-scale warming and acidification for benthic microbial communities, which drive sedimentary biogeochemical cycles. In this research, mesocosm experiments were set up using muddy and sandy coastal sediments to investigate the independent and interactive effects of elevated carbon dioxide concentrations (750 ppm CO2 and elevated temperature (ambient +4°C on the abundance of taxonomic and functional microbial genes. Specific quantitative PCR primers were used to target archaeal, bacterial, and cyanobacterial/chloroplast 16S rRNA in both sediment types. Nitrogen cycling genes archaeal and bacterial ammonia monooxygenase (amoA and bacterial nitrite reductase (nirS were specifically targeted to identify changes in microbial gene abundance and potential impacts on nitrogen cycling. In muddy sediment, microbial gene abundance, including amoA and nirS genes, increased under elevated temperature and reduced under elevated CO2 after 28 days, accompanied by shifts in community composition. In contrast, the combined stressor treatment showed a non-additive effect with lower microbial gene abundance throughout the experiment. The response of microbial communities in the sandy sediment was less pronounced, with the most noticeable response seen in the archaeal gene abundances in response to environmental stressors over time. 16S rRNA genes (amoA and nirS were lower in abundance in the combined stressor treatments in sandy sediments. Our results indicated that marine benthic microorganisms, especially in muddy sediments, are susceptible to changes in ocean carbonate chemistry and seawater temperature, which ultimately may have an impact upon key benthic biogeochemical cycles.

  17. LACO-Wiki: A land cover validation tool and a new, innovative teaching resource for remote sensing and the geosciences

    Science.gov (United States)

    See, Linda; Perger, Christoph; Dresel, Christopher; Hofer, Martin; Weichselbaum, Juergen; Mondel, Thomas; Steffen, Fritz

    2016-04-01

    The validation of land cover products is an important step in the workflow of generating a land cover map from remotely-sensed imagery. Many students of remote sensing will be given exercises on classifying a land cover map followed by the validation process. Many algorithms exist for classification, embedded within proprietary image processing software or increasingly as open source tools. However, there is little standardization for land cover validation, nor a set of open tools available for implementing this process. The LACO-Wiki tool was developed as a way of filling this gap, bringing together standardized land cover validation methods and workflows into a single portal. This includes the storage and management of land cover maps and validation data; step-by-step instructions to guide users through the validation process; sound sampling designs; an easy-to-use environment for validation sample interpretation; and the generation of accuracy reports based on the validation process. The tool was developed for a range of users including producers of land cover maps, researchers, teachers and students. The use of such a tool could be embedded within the curriculum of remote sensing courses at a university level but is simple enough for use by students aged 13-18. A beta version of the tool is available for testing at: http://www.laco-wiki.net.

  18. Hybridizing Daphnia communities from ten neighbouring lakes: spatio-temporal dynamics, local processes, gene flow and invasiveness.

    Science.gov (United States)

    Yin, Mingbo; Gießler, Sabine; Griebel, Johanna; Wolinska, Justyna

    2014-04-12

    In natural communities of cyclical parthenogens, rapid response to environmental change is enabled by switching between two reproduction modes. While long periods of asexual reproduction allow some clones to outcompete others, and may result in "clonal erosion", sexual reproduction restores genetic variation in such systems. Moreover, sexual reproduction may result in the formation of interspecific hybrids. These hybrids can then reach high abundances, through asexual clonal reproduction. In the present study, we explored genetic variation in water fleas of the genus Daphnia. The focus was on the short-term dynamics within several clonal assemblages from the hybridizing Daphnia longispina complex and the impact of gene flow at small spatial scales. Daphnia individuals belonged either to the parental species D. galeata and D. longispina, or to different hybrid classes, as identified by 15 microsatellite markers. The distribution and genotypic structure of parental species, but not hybrids, corresponded well with the geographical positions of the lakes. Within parental species, the genetic distance among populations of D. galeata was lower than among populations of D. longispina. Moreover, D. galeata dominance was associated with higher phosphorous load. Finally, there was no evidence for clonal erosion. Our results suggest that the contemporary structure of hybridizing Daphnia communities from ten nearby lakes is influenced by colonization events from neighbouring habitats as well as by environmental factors. Unlike the parental species, however, there was little evidence for successful dispersal of hybrids, which seem to be produced locally. Finally, in contrast to temporary Daphnia populations, in which a decrease in clonal diversity was sometimes detectable over a single growing season, the high clonal diversity and lack of clonal erosion observed here might result from repeated hatching of sexually produced offspring. Overall, our study provides insights into

  19. The Effects of Wiki-Based Recursive Process Writing on Chinese Narrative Essays for Chinese as a Second Language (CSL) Students in Singapore

    Science.gov (United States)

    Chin, Chee Kuen; Gong, Cheng; Tay, Boon Pei

    2015-01-01

    This paper reports on the effects of using wiki-based process writing in Singapore's Chinese as a Second Language (CSL) scenarios. A group of 32 Secondary 1 (Seventh Grade) students ("Students") received various forms of online scaffolding at different steps of the writing process over two years. A whole set of teaching materials on 45…

  20. Gowinda: unbiased analysis of gene set enrichment for genome-wide association studies.

    Science.gov (United States)

    Kofler, Robert; Schlötterer, Christian

    2012-08-01

    An analysis of gene set [e.g. Gene Ontology (GO)] enrichment assumes that all genes are sampled independently from each other with the same probability. These assumptions are violated in genome-wide association (GWA) studies since (i) longer genes typically have more single-nucleotide polymorphisms resulting in a higher probability of being sampled and (ii) overlapping genes are sampled in clusters. Herein, we introduce Gowinda, a software specifically designed to test for enrichment of gene sets in GWA studies. We show that GO tests on GWA data could result in a substantial number of false-positive GO terms. Permutation tests implemented in Gowinda eliminate these biases, but maintain sufficient power to detect enrichment of GO terms. Since sufficient resolution for large datasets requires millions of permutations, we use multi-threading to keep computation times reasonable. Gowinda is implemented in Java (v1.6) and freely available on http://code.google.com/p/gowinda/ christian.schloetterer@vetmeduni.ac.at Manual: http://code.google.com/p/gowinda/wiki/Manual. Test data and tutorial: http://code.google.com/p/gowinda/wiki/Tutorial. http://code.google.com/p/gowinda/wiki/VALIDATION.

  1. Characterization of bacterial community associated with phytoplankton bloom in a eutrophic lake in South Norway using 16S rRNA gene amplicon sequence analysis.

    Science.gov (United States)

    Parulekar, Niranjan Nitin; Kolekar, Pandurang; Jenkins, Andrew; Kleiven, Synne; Utkilen, Hans; Johansen, Anette; Sawant, Sangeeta; Kulkarni-Kale, Urmila; Kale, Mohan; Sæbø, Mona

    2017-01-01

    Interactions between different phytoplankton taxa and heterotrophic bacterial communities within aquatic environments can differentially support growth of various heterotrophic bacterial species. In this study, phytoplankton diversity was studied using traditional microscopic techniques and the bacterial communities associated with phytoplankton bloom were studied using High Throughput Sequencing (HTS) analysis of 16S rRNA gene amplicons from the V1-V3 and V3-V4 hypervariable regions. Samples were collected from Lake Akersvannet, a eutrophic lake in South Norway, during the growth season from June to August 2013. Microscopic examination revealed that the phytoplankton community was mostly represented by Cyanobacteria and the dinoflagellate Ceratium hirundinella. The HTS results revealed that Proteobacteria (Alpha, Beta, and Gamma), Bacteriodetes, Cyanobacteria, Actinobacteria and Verrucomicrobia dominated the bacterial community, with varying relative abundances throughout the sampling season. Species level identification of Cyanobacteria showed a mixed population of Aphanizomenon flos-aquae, Microcystis aeruginosa and Woronichinia naegeliana. A significant proportion of the microbial community was composed of unclassified taxa which might represent locally adapted freshwater bacterial groups. Comparison of cyanobacterial species composition from HTS and microscopy revealed quantitative discrepancies, indicating a need for cross validation of results. To our knowledge, this is the first study that uses HTS methods for studying the bacterial community associated with phytoplankton blooms in a Norwegian lake. The study demonstrates the value of considering results from multiple methods when studying bacterial communities.

  2. Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys

    Energy Technology Data Exchange (ETDEWEB)

    Walters, William; Hyde, Embriette R.; Berg-Lyons, Donna; Ackermann, Gail; Humphrey, Greg; Parada, Alma; Gilbert, Jack A.; Jansson, Janet K.; Caporaso, J. Gregory; Fuhrman, Jed A.; Apprill, Amy; Knight, Rob; Bik, Holly

    2015-12-22

    ABSTRACT

    Designing primers for PCR-based taxonomic surveys that amplify a broad range of phylotypes in varied community samples is a difficult challenge, and the comparability of data sets amplified with varied primers requires attention. Here, we examined the performance of modified 16S rRNA gene and internal transcribed spacer (ITS) primers for archaea/bacteria and fungi, respectively, with nonaquatic samples. We moved primer bar codes to the 5′ end, allowing for a range of different 3′ primer pairings, such as the 515f/926r primer pair, which amplifies variable regions 4 and 5 of the 16S rRNA gene. We additionally demonstrated that modifications to the 515f/806r (variable region 4) 16S primer pair, which improves detection ofThaumarchaeotaand clade SAR11 in marine samples, do not degrade performance on taxa already amplified effectively by the original primer set. Alterations to the fungal ITS primers did result in differential but overall improved performance compared to the original primers. In both cases, the improved primers should be widely adopted for amplicon studies.

    ImportanceWe continue to uncover a wealth of information connecting microbes in important ways to human and environmental ecology. As our scientific knowledge and technical abilities improve, the tools used for microbiome surveys can be modified to improve the accuracy of our techniques, ensuring that we can continue to identify groundbreaking connections between microbes and the ecosystems they populate, from ice caps to the human body. It is important to confirm that modifications to these tools do not cause new, detrimental biases that would inhibit the field rather than continue to move it forward. We therefore demonstrated that two recently modified primer pairs that target taxonomically discriminatory regions of bacterial and fungal genomic DNA do not introduce new biases when used on a variety of sample types, from soil to

  3. Analysis of the metatranscriptome of microbial communities of an alkaline hot sulfur spring revealed different gene encoding pathway enzymes associated with energy metabolism.

    Science.gov (United States)

    Tripathy, Swetaleena; Padhi, Soumesh Kumar; Mohanty, Sriprakash; Samanta, Mrinal; Maiti, Nikhil Kumar

    2016-07-01

    Alkaline sulfur hot springs notable for their specialized and complex ecosystem powered by geothermal energy are abundantly rich in different chemotrophic and phototrophic thermophilic microorganisms. Survival and adaptation of these organisms in the extreme environment is specifically related to energy metabolism. To gain a better understanding of survival mechanism of the organisms in these ecosystems, we determined the different gene encoding enzymes associated with anaerobic pathways of energy metabolism by applying the metatranscriptomics approach. The analysis of the microbial population of hot sulfur spring revealed the presence of both aerobic and anaerobic organisms indicating dual mode of lifestyle of the community members. Proteobacteria (28.1 %) was the most dominant community. A total of 988 reads were associated with energy metabolism, out of which 33.7 % of the reads were assigned to nitrogen, sulfur, and methane metabolism based on KEGG classification. The major lineages of hot spring communities were linked with the anaerobic pathways. Different gene encoding enzymes (hao, nir, nar, cysH, cysI, acs) showed the involvement of microbial members in nitrification, denitrification, dissimilatory sulfate reduction, and methane generation. This study enhances our understanding of important gene encoding enzymes involved in energy metabolism, required for the survival and adaptation of microbial communities in the hot spring.

  4. Effect of nitrogen fertilization on methane oxidation, abundance, community structure, and gene expression of methanotrophs in the rice rhizosphere.

    Science.gov (United States)

    Shrestha, Minita; Shrestha, Pravin Malla; Frenzel, Peter; Conrad, Ralf

    2010-12-01

    Nitrogen, one of the limiting factors for the yield of rice, can also have an important function in methane oxidation, thus affecting its global budget. Rice microcosms, planted in the greenhouse, were treated with the N-fertilizers urea (UPK) and ammonium sulfate (APK) or were only treated with phosphorous and potassium (PK). Methane oxidation rates in PK and UPK treatments were similar during most of the rice-growing season, revealing no effect of urea. However, ammonium sulfate strongly suppressed methanogenesis providing an unfavorable environment for methanotrophs in APK treatment. Roots and rhizospheric soil samples, collected from six different growth stages of the rice plant, were analyzed by terminal restriction fragment length polymorphism (T-RFLP) of the pmoA gene. Assignment of abundant T-RFs to cloned pmoA sequences indicated that the populations on roots were dominated by type-I methanotrophs, whereas the populations in rhizospheric soil were dominated by type-II methanotrophs irrespectively of growth stages and fertilizer treatments. Non-metric multidimensional scaling ordination analysis of T-RFLP profiles revealed that the methanotrophic community was significantly (PAPK treatment.

  5. [Characterizing Beijing's Airborne Bacterial Communities in PM2.5 and PM1 Samples During Haze Pollution Episodes Using 16S rRNA Gene Analysis Method].

    Science.gov (United States)

    Wang, Bu-ying; Lang, Ji-dong; Zhang, Li-na; Fang, Jian-huo; Cao, Chen; Hao, Ji-ming; Zhu, Ting; Tian, Geng; Jiang, Jing-kun

    2015-08-01

    During 8th-14th Jan., 2013, severe particulate matter (PM) pollution episodes happened in Beijing. These air pollution events lead to high risks for public health. In addition to various PM chemical compositions, biological components in the air may also impose threaten. Little is known about airborne microbial community in such severe air pollution conditions. PM2.5 and PM10 samples were collected during that 7-day pollution period. The 16S rRNA gene V3 amplification and the MiSeq sequencing were performed for analyzing these samples. It is found that there is no significant difference at phylum level for PM2.5 bacterial communities during that 7-day pollution period both at phylum and at genus level. At genus level, Arthrobacter and Frankia are the major airborne microbes presented in Beijing winter.samples. At genus level, there are 39 common genera (combined by first 50 genera bacterial of the two analysis) between the 16S rRNA gene analysis and those are found by Metagenomic analysis on the same PM samples. Frankia and Paracoccus are relatively more abundant in 16S rRNA gene data, while Kocuria and Geodermatophilus are relatively more abundant in Meta-data. PM10 bacterial communities are similar to those of PM2.5 with some noticeable differences, i.e., at phylum level, more Firmicutes and less Actinobacteria present in PM10 samples than in PM2.5 samples, while at genus level, more Clostridium presents in PM10 samples. The findings in Beijing were compared with three 16S rRNA gene studies in other countries. Although the sampling locations and times are different from each other, compositions of bacterial community are similar for those sampled at the ground atmosphere. Airborne microbial communities near the ground surface are different from those sampled in the upper troposphere.

  6. Mountain pine beetles colonizing historical and naive host trees are associated with a bacterial community highly enriched in genes contributing to terpene metabolism.

    Science.gov (United States)

    Adams, Aaron S; Aylward, Frank O; Adams, Sandye M; Erbilgin, Nadir; Aukema, Brian H; Currie, Cameron R; Suen, Garret; Raffa, Kenneth F

    2013-06-01

    The mountain pine beetle, Dendroctonus ponderosae, is a subcortical herbivore native to western North America that can kill healthy conifers by overcoming host tree defenses, which consist largely of high terpene concentrations. The mechanisms by which these beetles contend with toxic compounds are not well understood. Here, we explore a component of the hypothesis that beetle-associated bacterial symbionts contribute to the ability of D. ponderosae to overcome tree defenses by assisting with terpene detoxification. Such symbionts may facilitate host tree transitions during range expansions currently being driven by climate change. For example, this insect has recently breached the historical geophysical barrier of the Canadian Rocky Mountains, providing access to näive tree hosts and unprecedented connectivity to eastern forests. We use culture-independent techniques to describe the bacterial community associated with D. ponderosae beetles and their galleries from their historical host, Pinus contorta, and their more recent host, hybrid P. contorta-Pinus banksiana. We show that these communities are enriched with genes involved in terpene degradation compared with other plant biomass-processing microbial communities. These pine beetle microbial communities are dominated by members of the genera Pseudomonas, Rahnella, Serratia, and Burkholderia, and the majority of genes involved in terpene degradation belong to these genera. Our work provides the first metagenome of bacterial communities associated with a bark beetle and is consistent with a potential microbial contribution to detoxification of tree defenses needed to survive the subcortical environment.

  7. Gene

    Data.gov (United States)

    U.S. Department of Health & Human Services — Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes,...

  8. WEBQUEST AND WIKI: SEARCH OF INFORMATION IN INTERNET AND DEVELOPMENT OF COMPETENCES IN COLLABORATIVE WEBQUEST Y WIKIS: BÚSQUEDA DE INFORMACIÓN EN RED Y DESARROLLO DE COMPETENCIAS EN COLABORACIÓN

    Directory of Open Access Journals (Sweden)

    Lourdes Villalustre Martínez

    2011-03-01

    Full Text Available In university education is committed to strategies and resources, -that exploit the potential of digital tools-, such as Webquests as supported collaborative research methodologies in the search for information and the use of content on the Internet for conducting projects. Which can be articulated from 2.0 tools like wikis, for its versatility and capacity to generate knowledge collaboratively by creating online content.In the virtual subject of Education in the rural area was designed a collaborative learning activity based on the philosophy of webquests and supported by the use of wikis, - setting up what was called Gameproject - that facilitates access and management information to create a project of socio-educational intervention.After its implementation in several years, 161 students were asked about competences they considered to have developed and consolidated with the proposed collaborative work. The students stressed the skills to research, collection and processing of information, and other more specific competences relating to the future performance of their work. Noted that students without prior experience in virtual training, considered to have consolidated over the powers associated with the use of tools.En la formación universitaria se está apostando por estrategias y recursos didácticos, -que aprovechan las potencialidades de diferentes instrumentos digitales-, como las Webquests en tanto metodologías de investigación colaborativa apoyada en la búsqueda de información y en la utilización de contenidos alojados en Internet para la realización de proyectos. Los cuales pueden articularse a partir de herramientas 2.0 como las wikis, por su gran versatilidad y capacidad para generar conocimiento de forma colaborativa mediante la creación de contenidos on-line.   En la asignatura virtual de Educación en el ámbito rural1 se ha diseñado una actividad formativa en colaboración basada en la filosofía de las webquests y

  9. WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization [v2; ref status: indexed, http://f1000r.es/49l

    Directory of Open Access Journals (Sweden)

    Martina Kutmon

    2014-09-01

    Full Text Available In this paper we present the open-source WikiPathways app for Cytoscape (http://apps.cytoscape.org/apps/wikipathways that can be used to import biological pathways for data visualization and network analysis. WikiPathways is an open, collaborative biological pathway database that provides fully annotated pathway diagrams for manual download or through web services. The WikiPathways app allows users to load pathways in two different views: as an annotated pathway ideal for data visualization and as a simple network to perform computational analysis. An example pathway and dataset are used to demonstrate the functionality of the WikiPathways app and how they can be combined and used together with other apps. More than 3000 downloads in the first 12 months following its release in August 2013 highlight the importance and adoption of the app in the network biology field.

  10. Statistics and Analysis of Wiki-Based Chinese Online-Encyclopedia Cited by Journal Papers%期刊论文引用中文 Wiki 网络百科的统计与分析

    Institute of Scientific and Technical Information of China (English)

    丁玉东; 张春峰; 刘颖

    2013-01-01

    Abstract It counted the amount of the wiki-based Chinese online-encyclopedia cited by journal articles from 2006 to 2012. The number of articles, citation department, subject of the articles, and the journals were analyzed in terms of quantity distribution, also with the citing content and citing motivation of the articles that cited online-encyclopedia entry was analyzed by sampling method. Results showed that the influence of online-encyclopedia in academic activities was gradually rising, more and more scholars cited its concept, digit and con-tent to support their point of views, but no one questioned the contents of the entry when they cited it, which was a phenomenon more ap-parent in the field of social science.%  对2006~2012年间引用 Wiki 模式中文网络百科词条的中文期刊论文数量进行了统计,从论文数量、引用的单位、论文所在的学科、论文所在的期刊等方面分析了数量分布情况,并通过抽样方法分析了学术文献引用网络百科词条的内容和动机。结果标明网络百科在学术活动中的影响力正在逐步攀升,越来越多的学术作者借鉴了其中的概念、数字和内容支撑自己的观点,但没有学者在引用时质疑词条中的内容,这一现象在社会科学领域更为明显。

  11. Vertical Distribution of Bacterial Communities in the Indian Ocean as Revealed by Analyses of 16S rRNA and nasA Genes.

    Science.gov (United States)

    Jiang, Xuexia; Jiao, Nianzhi

    2016-09-01

    Bacteria play an important role in the marine biogeochemical cycles. However, research on the bacterial community structure of the Indian Ocean is scarce, particularly within the vertical dimension. In this study, we investigated the bacterial diversity of the pelagic, mesopelagic and bathypelagic zones of the southwestern Indian Ocean (50.46°E, 37.71°S). The clone libraries constructed by 16S rRNA gene sequence revealed that most phylotypes retrieved from the Indian Ocean were highly divergent from those retrieved from other oceans. Vertical differences were observed based on the analysis of natural bacterial community populations derived from the 16S rRNA gene sequences. Based on the analysis of the nasA gene sequences from GenBank database, a pair of general primers was developed and used to amplify the bacterial nitrate-assimilating populations. Environmental factors play an important role in mediating the bacterial communities in the Indian Ocean revealed by canonical correlation analysis.

  12. Effects of oxytetracycline on archaeal community, and tetracycline resistance genes in anaerobic co-digestion of pig manure and wheat straw.

    Science.gov (United States)

    Wang, Xiaojuan; Pan, Hongjia; Gu, Jie; Qian, Xun; Gao, Hua; Qin, Qingjun

    2016-12-01

    In this study, the effects of different concentrations of oxytetracycline (OTC) on biogas production, archaeal community structure, and the levels of tetracycline resistance genes (TRGs) were investigated in the anaerobic co-digestion products of pig manure and wheat straw. PCR denaturing gradient gel electrophoresis analysis and real-time quantitative polymerase chain reaction (RT-qPCR) (PCR) were used to detect the archaeal community structure and the levels of four TRGs: tet(M), tet(Q), tet(W), and tet(C). The results showed that anaerobic co-digestion with OTC at concentrations of 60, 100, and 140 mg/kg (dry weight of pig manure) reduced the cumulative biogas production levels by 9.9%, 10.4%, and 14.1%, respectively, compared with that produced by the control, which lacked the antibiotic. The addition of OTC substantially modified the structure of the archaeal community. Two orders were identified by phylogenetic analysis, that is, Pseudomonadales and Methanomicrobiales, and the methanogen present during anaerobic co-digestion with OTC may have been resistant to OTC. The abundances of tet(Q) and tet(W) genes increased as the OTC concentration increased, whereas the abundances of tet(M) and tet(C) genes decreased as the OTC concentration increased.

  13. Nutrients, heavy metals and microbial communities co-driven distribution of antibiotic resistance genes in adjacent environment of mariculture.

    Science.gov (United States)

    Zhao, Zelong; Wang, Jing; Han, Ying; Chen, Jingwen; Liu, Guangfei; Lu, Hong; Yan, Bin; Chen, Shiaoshing

    2017-01-01

    With the rapid development of aquaculture, the large amounts of pollutants were discharged into the aquatic environment, where the detected antibiotic resistance genes (ARGs) have drawn increasing attention due to their potential threats to ecological environment and human health. Thus, the impact of mariculture on ARGs was assessed and the underlying mechanism of their propagation was explained. Sediments from eight sampling sites were collected along a mariculture drainage ditch, and the sediment in Yellow River Delta National Park was used as a non-mariculture control. Microbial ARGs qPCR array and illumina sequencing of 16S rRNA gene were applied to examine the changing patterns of ARGs and bacterial communities. Results showed that 18 ARGs (3 fluoroquinolone, 1 aminoglycoside, 3 macrolide-lincosamide-streptogramin B, 2 tetracycline, and 9 beta-lactam resistance genes) were influenced by mariculture, and ARGs abundance and diversity were significantly increased in mariculture sediments (p < 0.05). A remarkable shift in bacterial community structure and composition was also observed. The abundance of most of ARGs were significantly decreased in the estuary samples, implying that seawater had a significant dilution effect on the ARGs emission from the mariculture sites. Partial redundancy analysis showed that nutrients, heavy metals, and bacteria communities might directly and indirectly contribute to ARGs propagation, suggesting that the profile and dissemination of ARGs were driven by the combined effects of multiple factors in mariculture-impacted sites. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. La investigación del discurso escrito en el aprendizaje de idiomas en entornos colaborativos y wikis

    Directory of Open Access Journals (Sweden)

    María Belén Díez-Bedmar

    2010-01-01

    Full Text Available Es bien sabido que el uso de las nuevas tecnologías ha sido instrumental en la promoción del conocimiento digital y del aprendizaje colaborativo del lenguaje. Sin embargo, Bax (2003 ha visto en la comunicación asistida por ordenador un gran potencial en las etapas abierta y de normalización. Aunque un número importante de investigaciones en los últimos años se han dedicado a la comunicación asíncrona por medio de web 1.0, los esfuerzos realizados en la actualidad han comenzado a analizar el uso de herramientas de video síncronas (Jáuregui y Bañados, 2008, blogs (Murray y Hourigan, 2008 y wikis (Lund, 2008. En este artículo presentamos una experiencia colaborativa en línea entre dos Instituciones de Educación Superior en Inglaterra y España (curso académico 2008/2009. Dicha experiencia ofreció a los alumnos la oportunidad de desarrollar su destreza escritora por medio de una serie de actividades de naturaleza digital en las que el wiki estaba integrado de forma natural. Los alumnos ingleses y españoles se embarcaron en la redacción de un folleto turístico de un monumento relevante desde el punto de vista histórico/artístico del otro país de forma colaborativa, ayudando al compañero en la redacción de su folleto y siendo ayudado de la misma manera.

  15. WEBQUEST Y WIKIS: BÚSQUEDA DE INFORMACIÓN EN RED Y DESARROLLO DE COMPETENCIAS EN COLABORACIÓN

    Directory of Open Access Journals (Sweden)

    Lourdes Villalustre Martínez

    2011-04-01

    Full Text Available En la formación universitaria se está apostando por estrategias y recursos didácticos, -que aprovechan las potencialidades de diferentes instrumentos digitales-, como las Webquests en tanto metodologías de investigación colaborativa apoyada en la búsqueda de información y en la utilización de contenidos alojados en Internet para la realización de proyectos. Los cuales pueden articularse a partir de herramientas 2.0 como las wikis, por su gran versatilidad y capacidad para generar conocimiento de forma colaborativa mediante la creación de contenidos on-line.   En la asignatura virtual de Educación en el ámbito rural1 se ha diseñado una actividad formativa en colaboración basada en la filosofía de las webquests y apoyada en el uso de las wikis, - configurando lo que se denominó Gameproject- Del Moral; Villalustre (2007b, que promueve el acceso y gestión de la información para elaborar un proyecto de intervención socio-educativo. Tras su implementación en varios años, se preguntó a 161 estudiantes sobre las competencias que consideraban haber desarrollado y/o consolidado con el trabajo colaborativo planteado. Éstos destacaron mayoritariamente las habilidades para la investigación, la recogida y tratamiento de la información, y otras más específicas vinculadas al futuro desempeño de su actividad profesional. Hay que destacar que los estudiantes sin experiencia previa en cursos de formación virtual consideraron haber consolidado más las competencias vinculadas al uso de herramientas informáticas.

  16. Methopedia - Pedagogical Design Community for European Educators

    DEFF Research Database (Denmark)

    Ryberg, Thomas; Niemczik, Christian; Brenstein, Elke

    2009-01-01

    by drawing on research within learning design and the educational pattern design approach. In particular we focus on exploring designs and descriptions of singular or sequences of learning activities. Furthermore, we discuss some of the tools and concepts under development as part of the work on Methopedia...... use to describe and share their learning designs or learning activities, e.g. what categories would be helpful? How much metadata is relevant and how standardised or flexible the templates should be? We also discuss the theoretical considerations underlying the descriptive model of the templates......The paper will discuss theoretical, methodological and technical aspects of the community based Methopedia wiki (www.methopedia.eu), which has been developed as a part of the EU-funded collaborative research project “Community of Integrated Blended Learning in Europe” (COMBLE; www...

  17. Towards Distributed Citizen Participation: Lessons from WikiLeaks and the Queensland Floods

    Directory of Open Access Journals (Sweden)

    Axel Bruns

    2012-12-01

    Full Text Available This paper examines the rapid and ad hoc development and interactions of participative citizen communities during acute events, using the examples of the 2011 floods in Queensland, Australia, and the global controversy surrounding Wikileaks and its spokesman, Julian Assange. The self-organising community responses to such events which can be observed in these cases bypass or leapfrog, at least temporarily, most organisational or administrative hurdles which may otherwise frustrate the establishment of online communities; they fast-track the processes of community development and structuration. By understanding them as a form of rapid prototyping, e-democracy initiatives can draw important lessons from observing the community activities around such acute events.

  18. Quantitative analysis of dinoflagellates and diatoms community via Miseq sequencing of actin gene and v9 region of 18S rDNA

    Science.gov (United States)

    Guo, Liliang; Sui, Zhenghong; Liu, Yuan

    2016-01-01

    Miseq sequencing and data analysis for the actin gene and v9 region of 18S rDNA of 7 simulated samples consisting of different mixture of dinoflagellates and diatoms were carried out. Not all the species were detectable in all the 18S v9 samples, and sequence percent in all the v9 samples were not consistent with the corresponding cell percent which may suggest that 18S rDNA copy number in different cells of these species differed greatly which result in the large deviation of the amplification. And 18S rDNA amplification of the microalgae was prone to be contaminated by fungus. The amplification of actin gene all was from the dinoflagellates because of its targeted degenerate primers. All the actin sequences of dinoflagellates were detected in the act samples except act4, and sequence percentage of the dinoflagellates in the act samples was not completely consistent with the dinoflagellates percentage of cell samples, but with certain amplification deviations. Indexes of alpha diversity of actin gene sequencing may be better reflection of community structure, and beta diversity analysis could cluster the dinoflagellates samples with identical or similar composition together and was distinguishable with blooming simulating samples at the generic level. Hence, actin gene was more proper than rDNA as the molecular marker for the community analysis of the dinoflagellates. PMID:27721499

  19. Microeukaryotic community and oxygen response in rice field soil revealed using a combined rRNA-gene and rRNA-based approach.

    Science.gov (United States)

    Murase, Jun; Takenouchi, Yuriko; Iwasaki, Kazufumi; Kimura, Makoto

    2014-01-01

    Irrigated rice field soil is subjected to frequent changes in oxygen status due to the water regime by agricultural management. In this study, the community response of microeukaryotes in rice field soil to the oxygen status was explored in a microcosm experiment under defined conditions. Water-saturated soil was incubated under a two-level factorial design of oxygen and organic enrichment with plant residue. The eukaryotic microbial community composition, which was either present or potentially active in the soils, was analyzed using denaturing gradient gel electrophoresis (DGGE) targeting the 18S rRNA gene or reverse-transcribed 18S rRNA. Oxygen availability was a primary factor shaping the microeukaryotic community in both DNA- and RNA-based analyses, revealing a shift within a week of incubation. Plant residue also affected the microeukaryotic community, which was more notable in the active community showing rRNA expression with time. Sequences of amplicons in DGGE bands indicated that protozoa (ciliates, flagellates, and amoebae) were the most prominent microeukaryotes in water-saturated rice field soil both in DNA- and RNA-based analyses. The use of a modified primer for soil protozoa suggested the functional importance of Heterolobosea amoeba in rice field soil, particularly in anoxic soil with organic enrichment.

  20. Molecular analysis of fungal communities and laccase genes in decomposing litter reveals differences among forest types but no impact of nitrogen deposition

    Science.gov (United States)

    Blackwood, C.B.; Waldrop, M.P.; Zak, D.R.; Sinsabaugh, R. L.

    2007-01-01

    The fungal community of the forest floor was examined as the cause of previously reported increases in soil organic matter due to experimental N deposition in ecosystems producing predominantly high-lignin litter, and the opposite response in ecosystems producing low-lignin litter. The mechanism proposed to explain this phenomenon was that white-rot basidiomycetes are more important in the degradation of high-lignin litter than of low-lignin litter, and that their activity is suppressed by N deposition. We found that forest floor mass in the low-lignin sugar-maple dominated system decreased in October due to experimental N deposition, whereas forest floor mass of high-lignin oak-dominated ecosystems was unaffected by N deposition. Increased relative abundance of basidiomycetes in high-lignin forest floor was confirmed by denaturing gradient gel electrophoresis (DGGE) and sequencing. Abundance of basidiomycete laccase genes, encoding an enzyme used by white-rot basidiomycetes in the degradation of lignin, was 5-10 times greater in high-lignin forest floor than in low-lignin forest floor. While the differences between the fungal communities in different ecosystems were consistent with the proposed mechanism, no significant effects of N deposition were detected on DGGE profiles, laccase gene abundance, laccase length heterogeneity profiles, or phenol oxidase activity. Our observations indicate that the previously detected accumulation of soil organic matter in the high-lignin system may be driven by effects of N deposition on organisms in the mineral soil, rather than on organisms residing in the forest floor. However, studies of in situ gene expression and temporal and spatial variability within forest floor communities will be necessary to further relate the ecosystem dynamics of organic carbon to microbial communities and atmospheric N deposition. ?? 2007 The Authors; Journal compilation ?? 2007 Society for Applied Microbiology and Blackwell Publishing Ltd.

  1. Community intelligence in knowledge curation: an application to managing scientific nomenclature.

    Directory of Open Access Journals (Sweden)

    Lin Dai

    Full Text Available Harnessing community intelligence in knowledge curation bears significant promise in dealing with communication and education in the flood of scientific knowledge. As knowledge is accumulated at ever-faster rates, scientific nomenclature, a particular kind of knowledge, is concurrently generated in all kinds of fields. Since nomenclature is a system of terms used to name things in a particular discipline, accurate translation of scientific nomenclature in different languages is of critical importance, not only for communications and collaborations with English-speaking people, but also for knowledge dissemination among people in the non-English-speaking world, particularly young students and researchers. However, it lacks of accuracy and standardization when translating scientific nomenclature from English to other languages, especially for those languages that do not belong to the same language family as English. To address this issue, here we propose for the first time the application of community intelligence in scientific nomenclature management, namely, harnessing collective intelligence for translation of scientific nomenclature from English to other languages. As community intelligence applied to knowledge curation is primarily aided by wiki and Chinese is the native language for about one-fifth of the world's population, we put the proposed application into practice, by developing a wiki-based English-to-Chinese Scientific Nomenclature Dictionary (ESND; http://esnd.big.ac.cn. ESND is a wiki-based, publicly editable and open-content platform, exploiting the whole power of the scientific community in collectively and collaboratively managing scientific nomenclature. Based on community curation, ESND is capable of achieving accurate, standard, and comprehensive scientific nomenclature, demonstrating a valuable application of community intelligence in knowledge curation.

  2. Community analysis of chronic wound bacteria using 16S rRNA gene-based pyrosequencing: impact of diabetes and antibiotics on chronic wound microbiota.

    Directory of Open Access Journals (Sweden)

    Lance B Price

    Full Text Available BACKGROUND: Bacterial colonization is hypothesized to play a pathogenic role in the non-healing state of chronic wounds. We characterized wound bacteria from a cohort of chronic wound patients using a 16S rRNA gene-based pyrosequencing approach and assessed the impact of diabetes and antibiotics on chronic wound microbiota. METHODOLOGY/PRINCIPAL FINDINGS: We prospectively enrolled 24 patients at a referral wound center in Baltimore, MD; sampled patients' wounds by curette; cultured samples under aerobic and anaerobic conditions; and pyrosequenced the 16S rRNA V3 hypervariable region. The 16S rRNA gene-based analyses revealed an average of 10 different bacterial families in wounds--approximately 4 times more than estimated by culture-based analyses. Fastidious anaerobic bacteria belonging to the Clostridiales family XI were among the most prevalent bacteria identified exclusively by 16S rRNA gene-based analyses. Community-scale analyses showed that wound microbiota from antibiotic treated patients were significantly different from untreated patients (p = 0.007 and were characterized by increased Pseudomonadaceae abundance. These analyses also revealed that antibiotic use was associated with decreased Streptococcaceae among diabetics and that Streptococcaceae was more abundant among diabetics as compared to non-diabetics. CONCLUSIONS/SIGNIFICANCE: The 16S rRNA gene-based analyses revealed complex bacterial communities including anaerobic bacteria that may play causative roles in the non-healing state of some chronic wounds. Our data suggest that antimicrobial therapy alters community structure--reducing some bacteria while selecting for others.

  3. Barriers to prostate cancer prevention and community recommended health education strategies in an urban African American community in Jackson, Mississippi.

    Science.gov (United States)

    Ekúndayò, Olúgbémiga T; Tataw, David B

    2013-01-01

    This article describes the use of survey research in collaboration with the African American urban community of Georgetown, Jackson, Mississippi to identify and understand prostate cancer knowledge, resource utilization, and health education strategies considered most effective in reaching the community with prostate cancer prevention messages. The study revealed profound needs in disease identification and resources awareness and utilization. Barriers to utilization were identified by participants to include lack of self-efficacy, low self-esteem, lack of trust in the health care system, limited knowledge of prostate pathology, and limited ability to pay. Participants' recommended strategies for reaching the community with prostate cancer education include traditional and nontraditional strategies. The list of recommendations exclude modern-day outlets such as handheld devices, Twitter, Facebook, blogs, wikis, and other Internet-based outlets. The findings provide a road map for program development and an intervention research agenda custom-tailored to the Georgetown community of Jackson, Mississippi.

  4. La utilización de rúbricas para la evaluación del trabajo colaborativo del alumnado en las wikis

    Directory of Open Access Journals (Sweden)

    María Cristina Santana Quintana

    2013-07-01

    Full Text Available The aim of this article is to address the complex issue of the evaluation of educational activities offered by new technology resources. One of these innovations is related to social software tools, specifically with the use of Wikis as a space for communication and presentation tasks. The establishment of tools such as wikis is causing many teachers to redefine not only the educational aspects of their teaching, but also to delineate consistent assessment criteria. For this reason, it is important to use rubrics as an evaluation method since rubrics enable teachers to qualify students according to some criteria already specified, making the evaluation process more transparent and simple.El objetivo de este artículo es abordar el complejo tema de la evaluación de las actividades pedagógicas que ofrecen los nuevos recursos tecnológicos. Una de estas innovaciones se relaciona con las herramientas de software social, específicamente con el uso de las Wikis como espacio para la comunicación y para la presentación de tareas. El establecimiento de herramientas tales como las wikis está provocando que muchos profesores deban redefinir no sólo los aspectos pedagógicos de su enseñanza, sino también delinear unos criterios de evaluación consistentes. Por esta razón, es importante el uso de las rúbricas como un método de evaluación, ya que éstas permiten calificar de acuerdo con unos criterios ya especificados, haciendo el proceso de evaluación más transparente y simple.

  5. The Songbird Neurogenomics (SoNG Initiative: Community-based tools and strategies for study of brain gene function and evolution

    Directory of Open Access Journals (Sweden)

    Lewin Harris A

    2008-03-01

    Full Text Available Abstract Background Songbirds hold great promise for biomedical, environmental and evolutionary research. A complete draft sequence of the zebra finch genome is imminent, yet a need remains for application of genomic resources within a research community traditionally focused on ethology and neurobiological methods. In response, we developed a core set of genomic tools and a novel collaborative strategy to probe gene expression in diverse songbird species and natural contexts. Results We end-sequenced cDNAs from zebra finch brain and incorporated additional sequences from community sources into a database of 86,784 high quality reads. These assembled into 31,658 non-redundant contigs and singletons, which we annotated via BLAST search of chicken and human databases. The results are publicly available in the ESTIMA:Songbird database. We produced a spotted cDNA microarray with 20,160 addresses representing 17,214 non-redundant products of an estimated 11,500–15,000 genes, validating it by analysis of immediate-early gene (zenk gene activation following song exposure and by demonstrating effective cross hybridization to genomic DNAs of other songbird species in the Passerida Parvorder. Our assembly was also used in the design of the "Lund-zfa" Affymetrix array representing ~22,000 non-redundant sequences. When the two arrays were hybridized to cDNAs from the same set of male and female zebra finch brain samples, both arrays detected a common set of regulated transcripts with a Pearson correlation coefficient of 0.895. To stimulate use of these resources by the songbird research community and to maintain consistent technical standards, we devised a "Community Collaboration" mechanism whereby individual birdsong researchers develop experiments and provide tissues, but a single individual in the community is responsible for all RNA extractions, labelling and microarray hybridizations. Conclusion Immediately, these results set the foundation for a

  6. Diversification of nitrogen fixing bacterial community using nifH gene as a biomarker in different geographical soils of Western Indian Himalayas.

    Science.gov (United States)

    Singh, Chhug; Soni, Ravindra; Jain, Sourabh; Roy, Subhadip; Goel, Reeta

    2010-09-01

    Six soil samples (Pantnagar, Chamoli, Almora, Ranichauri, Pithoragarh and Badrinath) belonging to different geographical locations of Western Himalayas in India, were analyzed to diversify the nitrogen fixing bacterial community using nifH gene biomarker DNA from soil samples were isolated and amplified using nifH gene specific primers. Genomic DNA and PCR amplified products were then individually subjected to restriction digestion with tetra to octacutter enzymes (AluI, MspI, BgIII, XbaI, HindIII, HaeIII, AluI, MspI and PasI. Further restriction pattern was studied by preparing dendograms on the basis of similarity matrix and compared for the nifH community. It was observed that temperate region soils (Ranichauri and Pithoragarh) were negative for nifH marker while subalpine region (Badrinath) and tarai region soils (Pantnagar) documented similar nifH community. Moreover; the direct genomic DNA restriction analysis indicated that subalpine region soil (Badrinath) was most diversified.

  7. El diseño de una Wiki sobre ecoturismo como herramienta para el aprendizaje universitario de turismo en entorno virtual

    Directory of Open Access Journals (Sweden)

    Francesc González Reverté

    2010-01-01

    Full Text Available La experiencia consiste en la creación de una wiki sobre Ecoturismo organizada en torno al trabajo colectivo como objeto de aprendizaje de la evaluación continua para la asignatura de (Ecoturismo. Tiene dos objetivos de innovación: 1 el desarrollo de metodologías docentes aptas para el trabajo colaborativo, y 2 habituar al uso de las herramientas del web 2.0 a estudiantes y a docentes. Las principales aportaciones del proyecto han sido el diseño de una metodología novedosa de trabajo en equipo en entorno de aprendizaje virtual; y la integración de las entradas de la wiki como recurso docente. Las encuestas de satisfacción realizadas entre los estudiantes muestran la excelente acogida del proyecto. Los principales problemas detectados tienen que ver con las dificultades técnicas en la implementación de la wiki así como el exceso de carga docente que ha supuesto.

  8. The Impact of WikiLeaks on Government%试析维基解密对政府管理的影响

    Institute of Scientific and Technical Information of China (English)

    马运瑞; 庞慧敏

    2011-01-01

    维基解密这一新的信息传播方式,必将对当下及未来的政府管理产生重要影响。维基解密会成为全球性的监督政府管理的新形式,一定程度上颠覆了传统的政媒关系,这促使政府在提高对这一类媒体警惕性并加强监管的同时,探索驾驭这类媒体的新途径。在未来政府间关系的处理上,维基解密既可能成为政府间竞争的新工具,也可能使政府间关系发生微妙变化。%WikiLeaks is not merely a news event, but will have an important impact on government management in the future. WikiLeaks will become a new global monitoring form of government, as well as increase the vigilance of different governments to the new media, and cause the government to review the border control. To some extent, it overthrows the traditional relations between government and media, and maybe becomes a new tool among government struggles. As dealing with the new media like WikiLeaks, the intergovernment relations may occur subtle changes.

  9. 语义wiki在词表编制中的应用探讨%The Use of Semantic Wiki as Vocabulary Development Platform

    Institute of Scientific and Technical Information of China (English)

    范炜; 陈圭璋

    2014-01-01

    This paper analyzes traditional vocabulary development bot leneck and introduces the characteristics of semantic wiki, then discusses a semantic wiki way to deploy vocabulary development platform. Final y, it points out that semantic wiki as a technology tool builds a bridge between traditional vocabulary research and current semantic web applications, taking the traditional vocabulary in lower costs and faster way into the current information environment and thus vocabularies play a dual role as organization tool and terminology resources.%通过分析传统词表的发展瓶颈和语义wiki的特征,讨论了语义wiki用作词表技术平台的可行性与具体实现思路。最后指出语义wiki作为一种技术手段,它为传统词表研究与当前的语义网应用搭建了一个互通的桥梁,使得传统词表能够以较低的成本和较快的方式融入到当前的信息环境中来,从而发挥其作为组织工具和术语资源的双重作用。

  10. Prevalence of Panton-Valentine leukocidin genes in community-associated methicillin-resistant Staphylococcus aureus in the district of Pomoravlje

    Directory of Open Access Journals (Sweden)

    Petrović-Jeremić Ljiljana

    2016-01-01

    Full Text Available Background/Aim. Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA strains appear to have rapidly disseminated among population in the community without established risk factors for MRSA worldwide. Panton-Valentine leukocidin (PVL is a cytolytic toxin, encoded by the lukF-PV and lukF-PV genes. PVL may be the key toxin responsible for enhanced virulence of CA-MRSA. The aim of this study was to detect the genes encoding PVL in CA-MRSA isolates from healthy people from the District of Pomoravlje. Methods. We took throat and nose swabs from healthy, employed persons with mandatory sanitary examinations and analyzed the presence of MRSA, between January 2011 and December 2012 in the District of Pomoravlje. Susceptibility of isolated strains to cefoxitin was investigated by using disc diffusion according to the recommendation of CLSI (Clinical Laboratory Standard Institute, and by E test. The presence of penicillin-binding protein 2a (PBP2a in Staphylococci was detected using latex agglutination Slidex ®MRSA Detection test. The gold standard, polymerase chain reaction (PCR assay, was used for detection of mecA gene and PVL gene, and typing of SCCmec region. Results. Our investigation showed that staphylococcal carrier state was present in 2.58% of 52,910 throat and nasal swabs, and in 50 of them (3.67% MRSA was isolated. Among these MRSA, 2 (4% isolates were PVL-positive. Conclusion. The prevalence of CAMRSA and the presence of PVL gene among healthy, employed population in the District of Pomoravlje were low. The values obtained in this study show that, our region is not significantly different from the other parts of our country, nor from the other European countries.

  11. Epidemiological features, resistance genes, and clones among community-onset methicillin-resistant Staphylococcus aureus (CO-MRSA) isolates detected in northern Spain.

    Science.gov (United States)

    González-Domínguez, María; Seral, Cristina; Sáenz, Yolanda; Salvo, Soledad; Gude, María José; Porres-Osante, Nerea; Torres, Carmen; Castillo, Francisco Javier

    2012-12-01

    Twenty-nine community-onset methicillin-resistant Staphylococcus aureus (CO-MRSA) isolates were prospectively selected according to epidemiological criteria among 374 MRSA isolates collected in our laboratory during 2009-2010 in order to determine which community-associated MRSA (CA-MRSA) and healthcare-associated MRSA (HA-MRSA) clones are circulating in the community in northern Spain. PVL genes were detected in 5 strains (17.2%) that belonged to SCCmec type IV or V and to the agr group I (ST8 and ST2050), agr group II (ST121), and agr group III (ST30 and ST852). These strains were isolated from patients with different clinical manifestations such as urinary tract infection, abscess, or pneumonia, and most of them belonged to emergency department patients with no history of visits to General Practitioners (GPs) in the year before the isolation. We considered that the prevalence of CA-MRSA in community-onset isolates was low (17.2%). A high proportion of the CO-MRSA strains (58.6%) were ST125-MRSA-IVc (CC5), responsible for most of the infections caused by HA-MRSA strains in Spain. This endemic clone is also circulating in the community of northern Spain as we could demonstrate in this study. Antimicrobial resistance was found in spa type t067 isolates linked to the presence of ant(4')-Ia and msr(A). Most of the CO-MRSA isolates in this study corresponded to spa types more associated to the hospital environment, suggesting the interchange of genetic lineages of MRSA among community and hospital niches.

  12. Evidence of association between Val66Met polymorphism at BDNF gene and anxiety disorders in a community sample of children and adolescents.

    Science.gov (United States)

    Tocchetto, Andréa; Salum, Giovanni A; Blaya, Carolina; Teche, Stefania; Isolan, Luciano; Bortoluzzi, Andressa; Rebelo E Silva, Rafael; Becker, Juliana A; Bianchin, Marino M; Rohde, Luis Augusto; Leistner-Segal, Sandra; Manfro, Gisele G

    2011-09-20

    Different lines of evidence support BDNF as a candidate gene in mood and anxiety modulation. More recently, the Met allele of the BDNF Val66Met polymorphism has been implicated in anxiety in animal models and anxiety-traits in humans. The aim of this study is to evaluate the a priori hypothesis that the association between anxiety disorders and Val66Met polymorphism at the BDNF gene would be replicated in a community sample of children and adolescents. 240 subjects from a total sample of 2457 children and adolescents aged 10-17 years from the public schools in the catchment area of the primary care unit of a university hospital participated in this case-control study and were assessed for psychopathology using the K-SADS-PL. A sample of saliva was collected for DNA analysis of Val66Met polymorphism. BDNF was the single gene evaluated in this sample. We found a significant association between carrying one copy of the Met allele and higher chance of anxiety disorders in children and adolescents. The association remained positive even after the adjustment for potential confounders (228 subjects; OR=3.53 (CI95% 1.77-7.06; p<0.001)). Our results support the a priori hypothesis of an association between anxiety and the polymorphism Val66Met. To our knowledge, this is the first study documenting a potential role of this polymorphism in a community sample of anxious children and adolescents.

  13. Presence or Absence of mlr Genes and Nutrient Concentrations Co-Determine the Microcystin Biodegradation Efficiency of a Natural Bacterial Community.

    Science.gov (United States)

    Lezcano, María Ángeles; Morón-López, Jesús; Agha, Ramsy; López-Heras, Isabel; Nozal, Leonor; Quesada, Antonio; El-Shehawy, Rehab

    2016-11-03

    The microcystin biodegradation potential of a natural bacterial community coexisting with a toxic cyanobacterial bloom was investigated in a water reservoir from central Spain. The biodegradation capacity was confirmed in all samples during the bloom and an increase of mlrA gene copies was found with increasing microcystin concentrations. Among the 24 microcystin degrading strains isolated from the bacterial community, only 28% showed presence of mlrA gene, strongly supporting the existence and abundance of alternative microcystin degradation pathways in nature. In vitro degradation assays with both mlr⁺ and mlr(-) bacterial genotypes (with presence and absence of the complete mlr gene cluster, respectively) were performed with four isolated strains (Sphingopyxis sp. IM-1, IM-2 and IM-3; Paucibacter toxinivorans IM-4) and two bacterial degraders from the culture collection (Sphingosinicella microcystinivorans Y2; Paucibacter toxinivorans 2C20). Differences in microcystin degradation efficiencies between genotypes were found under different total organic carbon and total nitrogen concentrations. While mlr⁺ strains significantly improved microcystin degradation rates when exposed to other carbon and nitrogen sources, mlr(-) strains showed lower degradation efficiencies. This suggests that the presence of alternative carbon and nitrogen sources possibly competes with microcystins and impairs putative non-mlr microcystin degradation pathways. Considering the abundance of the mlr(-) bacterial population and the increasing frequency of eutrophic conditions in aquatic systems, further research on the diversity of this population and the characterization and conditions affecting non-mlr degradation pathways deserves special attention.

  14. Presence or Absence of mlr Genes and Nutrient Concentrations Co-Determine the Microcystin Biodegradation Efficiency of a Natural Bacterial Community

    Directory of Open Access Journals (Sweden)

    María Ángeles Lezcano

    2016-11-01

    Full Text Available The microcystin biodegradation potential of a natural bacterial community coexisting with a toxic cyanobacterial bloom was investigated in a water reservoir from central Spain. The biodegradation capacity was confirmed in all samples during the bloom and an increase of mlrA gene copies was found with increasing microcystin concentrations. Among the 24 microcystin degrading strains isolated from the bacterial community, only 28% showed presence of mlrA gene, strongly supporting the existence and abundance of alternative microcystin degradation pathways in nature. In vitro degradation assays with both mlr+ and mlr− bacterial genotypes (with presence and absence of the complete mlr gene cluster, respectively were performed with four isolated strains (Sphingopyxis sp. IM-1, IM-2 and IM-3; Paucibacter toxinivorans IM-4 and two bacterial degraders from the culture collection (Sphingosinicella microcystinivorans Y2; Paucibacter toxinivorans 2C20. Differences in microcystin degradation efficiencies between genotypes were found under different total organic carbon and total nitrogen concentrations. While mlr+ strains significantly improved microcystin degradation rates when exposed to other carbon and nitrogen sources, mlr− strains showed lower degradation efficiencies. This suggests that the presence of alternative carbon and nitrogen sources possibly competes with microcystins and impairs putative non-mlr microcystin degradation pathways. Considering the abundance of the mlr− bacterial population and the increasing frequency of eutrophic conditions in aquatic systems, further research on the diversity of this population and the characterization and conditions affecting non-mlr degradation pathways deserves special attention.

  15. Class 1 Integrons Potentially Predating the Association with Tn402-Like Transposition Genes Are Present in a Sediment Microbial Community

    DEFF Research Database (Denmark)

    Stokes, Harold W.; Nesbø, Camilla L.; Holley, Marita;

    2006-01-01

    Integrons are genetic elements that contribute to lateral gene transfer in bacteria as a consequence of possessing a site-specific recombination system. This system facilitates the spread of genes when they are part of mobile cassettes. Most integrons are contained within chromosomes and are conf......Integrons are genetic elements that contribute to lateral gene transfer in bacteria as a consequence of possessing a site-specific recombination system. This system facilitates the spread of genes when they are part of mobile cassettes. Most integrons are contained within chromosomes...

  16. Comparison of eukaryotic phytobenthic community composition in a polluted river by partial 18S rRNA gene cloning and sequencing.

    Science.gov (United States)

    Dorigo, U; Bérard, A; Humbert, J F

    2002-11-01

    We compared the species composition in phytobenthic communities at different sampling sites in a small French river presenting polluted and unpolluted areas. For each sampling point, the total DNA was extracted and used to construct an 18S rRNA gene clone library after PCR amplification of a ca 400 bp fragment. Phytobenthic community composition was estimated by random sequencing of several clones per library. Most of the sequences corresponded to the Bacillariophyceae and Chlorophyceae groups. By combining phylogenetic and correspondence analyses, we showed that our molecular approach is able to estimate and compare the species composition at different sampling sites in order to assess the environmental impact of xenobiotics on phytobenthic communities. Changes in species composition of these communities were found, but no evident decrease in the diversity. We discuss the significance of these changes with regard to the existing level of pollution and their impact on the functionality of the ecosystem. Our findings suggest that it is now possible to use faster molecular methods (DGGE, ARISA.) to test large numbers of samples in the context of ecotoxicological studies, and thus to assess the impact of pollution in an aquatic ecosystem.

  17. The structure of bacterial communities in the western Arctic Ocean as revealed by pyrosequencing of 16S rRNA genes.

    Science.gov (United States)

    Kirchman, David L; Cottrell, Matthew T; Lovejoy, Connie

    2010-05-01

    Bacterial communities in the surface layer of the oceans consist of a few abundant phylotypes and many rare ones, most with unknown ecological functions and unclear roles in biogeochemical processes. To test hypotheses about relationships between abundant and rare phylotypes, we examined bacterial communities in the western Arctic Ocean using pyrosequence data of the V6 region of the 16S rRNA gene. Samples were collected from various locations in the Chukchi Sea, the Beaufort Sea and Franklin Bay in summer and winter. We found that bacterial communities differed between summer and winter at a few locations, but overall there was no significant difference between the two seasons in spite of large differences in biogeochemical properties. The sequence data suggested that abundant phylotypes remained abundant while rare phylotypes remained rare between the two seasons and among the Arctic regions examined here, arguing against the 'seed bank' hypothesis. Phylotype richness was calculated for various bacterial groups defined by sequence similarity or by phylogeny (phyla and proteobacterial classes). Abundant bacterial groups had higher within-group diversity than rare groups, suggesting that the ecological success of a bacterial lineage depends on diversity rather than on the dominance of a few phylotypes. In these Arctic waters, in spite of dramatic variation in several biogeochemical properties, bacterial community structure was remarkably stable over time and among regions, and any variation was due to the abundant phylotypes rather than rare ones.

  18. Physical factors correlate to microbial community structure and nitrogen cycling gene abundance in a nitrate fed eutrophic lagoon

    OpenAIRE

    Matthew Paul Highton; Stéphanie Roosa; Josie Crawshaw; Marc Schallenberg; Sergio E. Morales

    2016-01-01

    Nitrogenous run-off from farmed pastures contributes to the eutrophication of Lake Ellesmere, a large shallow lagoon/lake on the east coast of New Zealand. Tributaries periodically deliver high loads of nitrate to the lake which likely affect microbial communities therein. We hypothesized that a nutrient gradient would form from the potential sources (tributaries) creating a disturbance resulting in changes in microbial community structure. To test this we first determined the existence of su...

  19. Who Possesses Drug Resistance Genes in the Aquatic Environment? : Sulfamethoxazole (SMX Resistance Genes among the Bacterial Community in Water Environment of Metro-Manila, Philippines

    Directory of Open Access Journals (Sweden)

    Satoru eSuzuki

    2013-04-01

    Full Text Available Recent evidence has shown that antibiotic resistant bacteria (ARB and antibiotic resistance genes (ARG are ubiquitous in natural environments, including sites considered pristine. To understand the origin of ARGs and their dynamics, we must first define their actual presence in the natural bacterial assemblage. Here we found varying distribution profiles of sul genes in colony forming bacterial assemblages and natural bacterial assemblages. Our monitoring for antibiotic contamination revealed that sulfamethoxazole (SMX is a major contaminant in aquatic environments of Metro-Manila, which would have been derived from human and animal use, and subsequently decreased through the process of outflow from source to the sea. The SMX-resistant bacterial rate evaluated by the colony forming unit showed 10 to 86 % of the total colony numbers showed higher rates from freshwater sites compared to marine sites. When sul genes were quantified by qPCR, colony-forming bacteria conveyed sul1 and sul2 genes in freshwater and seawater (10-5-10-2 copy/16S but not sul3. Among the natural bacterial assemblage, all sul1, sul2 and sul3 were detected (10-5-10-3 copy/16S, whereas all sul genes were at an almost non-detectable level in the freshwater assemblage. This study suggests that sul1 and sul2 are main sul genes in culturable bacteria, whereas sul3 is conveyed by non-culturable bacteria in the sea. As a result marine bacteria possess sul1, sul2 and sul3 genes in the marine environment.

  20. Antimicrobial susceptibility, risk factors and prevalence of bla cefotaximase, temoneira, and sulfhydryl variable genes among Escherichia coli in community-acquired pediatric urinary tract infection.

    Science.gov (United States)

    Nisha, Kallyadan V; Veena, Shetty A; Rathika, Shenoy D; Vijaya, Shenoy M; Avinash, Shetty K

    2017-01-01

    The emergence of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli has become an important challenge among pediatric patients with community-acquired urinary tract infection (UTI). The aim of this study was to assess the antimicrobial susceptibility patterns, associated risk factors and to survey the frequency of bla cefotaximase (CTX-M), bla temoneira (TEM), and bla sulfhydryl variable (SHV) genotypes in ESBL-producing E. coli isolated from children with community-acquired UTI. This was a prospective study conducted from November 2012 to March 2016 in a tertiary care center. E. coli isolated in urine cultures from children aged ≤18 years was identified and confirmed for ESBL production. ESBL-positive strains were screened for ESBL encoding genes. Chi-square test and Fisher's exact test were used to compare the difference in antibiotic susceptibility with respect to ESBL positive and negative, and binary logistic regression was used to identify the risk factors associated with ESBL production. Among 523 E. coli isolates, 196 (37.5%) were ESBL positive, >90% were resistant to cephalosporins, and 56% were resistant to fluoroquinolones. Least resistance was observed for imipenem, netilmicin, and nitrofurantoin (2%, 8.6%, 15.3%). Association between ESBL production and drug resistance was significant for ceftazidime (P community-acquired pediatric UTI carries more than one type of beta-lactamase coding genes correlating their increased antibiotic resistance. Aggressive infection control policy, routine screening for detecting ESBL isolates in clinical samples, and antimicrobial stewardship are the keys to prevent their dissemination in community settings.

  1. The Diversity of Sulfide Oxidation and Sulfate Reduction Genes Expressed by the Bacterial Communities of the Cariaco Basin, Venezuela.

    Science.gov (United States)

    Rodriguez-Mora, Maria J; Edgcomb, Virginia P; Taylor, Craig; Scranton, Mary I; Taylor, Gordon T; Chistoserdov, Andrei Y

    2016-01-01

    Qualitative expression of dissimilative sulfite reductase (dsrA), a key gene in sulfate reduction, and sulfide:quinone oxidoreductase (sqr), a key gene in sulfide oxidation was investigated. Neither of the two could be amplified from mRNA retrieved with Niskin bottles but were amplified from mRNA retrieved by the Deep SID. The sqr and sqr-like genes retrieved from the Cariaco Basin were related to the sqr genes from a Bradyrhizobium sp., Methylomicrobium alcaliphilum, Sulfurovum sp. NBC37-1, Sulfurimonas autotrophica, Thiorhodospira sibirica and Chlorobium tepidum. The dsrA gene sequences obtained from the redoxcline of the Cariaco Basin belonged to chemoorganotrophic and chemoautotrophic sulfate and sulfur reducers belonging to the class Deltaproteobacteria (phylum Proteobacteria) and the order Clostridiales (phylum Firmicutes).

  2. A case of familial transmission of community-acquired methicillin-resistant Staphylococcus aureus carrying the Inu(A) gene in Santa Fe city, Argentina.

    Science.gov (United States)

    Méndez, Emilce de Los A; Roldán, María L; Baroni, María R; Mendosa, María A; Cristóbal, Sabrina A; Virgolini, Stella M; Faccone, Diego

    2012-01-01

    Community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) is increasingly recognized as an important pathogen causing skin and soft tissue infections as well as necrotizing pneumonia. We describe a case of familial transmission of CA-MRSA between a 6-month-old boy and his mother in Santa Fe City, Argentina. Both isolates showed an identical antimicrobial susceptibility profile, carried type IV SCCmec and harboured the pvl and the lnu(A) genes. Isolates showed indistinguishable SmaI-PFGE patterns confirming their genetic relationship. These results corroborate the intrafamilial transmission of CA-MRSA and might associate this strain with the repetitive events of furunculosis within the family.

  3. IL-8 CHEMOTACTIC FACTOR IN PATIENTS WITH COMMUNITY-ACQUIRED PNEUMONIA AND FEATURES OF IL-8 GENE POLYMORPHISM (251 T/А

    Directory of Open Access Journals (Sweden)

    L. F. Aznabaeva

    2010-01-01

    Full Text Available Fifty-four patients with different clinical course (acute and protracted forms of community-acquired pneumonia (CAP, were studied for interleukin-8 (IL-8 contents in blood serum and its production levels (spontaneous and PHA-stimulated, depending on the IL-8 gene polymorphism at the 251 T → A locus. Employing the data about immunogenetic differences, we have shown some associations between IL-8 production, depending on clinical outcome (adequate responders vs poor response to medication in acute pneumonia. Both in acute and chronic forms of pneumonia, poor response to therapy was associated with decreased reserve capacity of IL-8 production, and a downward trend of cytokine concentration in blood serum. It was revealed that the CAP patients with poor response to treatment exhibit deficient production of IL-8 associated with homozygous AA genotype at the -251 T/A locus of IL-8 gene.

  4. Antibiotic Resistance Genes and Correlations with Microbial Community and Metal Resistance Genes in Full-Scale Biogas Reactors As Revealed by Metagenomic Analysis

    DEFF Research Database (Denmark)

    Luo, Gang; Li, Bing; Li, Li-Guan

    2017-01-01

    Digested residues from biogas plants are often used as biofertilizers for agricultural crops cultivation. The antibiotic resistance genes (ARGs) in digested residues pose a high risk to public health due to their potential spread to the disease-causing microorganisms and thus reduce the susceptib......Digested residues from biogas plants are often used as biofertilizers for agricultural crops cultivation. The antibiotic resistance genes (ARGs) in digested residues pose a high risk to public health due to their potential spread to the disease-causing microorganisms and thus reduce...

  5. Characterization of the airborne bacteria community at different distances from the rotating brushes in a wastewater treatment plant by 16S rRNA gene clone libraries

    Institute of Scientific and Technical Information of China (English)

    Yunping Han; Lin Li; Junxin Liu

    2013-01-01

    Biological risks of bioaerosols emitted from wastewater treatment processes have attracted wide attention in the recent years.However,the culture-based analysis method has been mostly adopted for detecting the bacterial community in bioaerosols,which may result in the underestimation of total microorganism concentration as not all microorganisms are cultivable.In this study,oligonucleotide fingerprinting of 16S rRNA genes was applied to reveal the composition and structure of the bacterial community in bioaerosols from an Orbal oxidation ditch in a Beijing wastewater treatment plant (WWTP).Bioaerosols were collected at different distances from the aerosol source,rotating brushes,and the sampling height was 1.5 m which is the common respiratory height of a human being.The bacterial communities of bioaerosols were diverse,and the lowest bacterial diversity was found at the sampling site just after the rotating brush rotating brush.A large proportion of bacteria in bioaerosols were affiliated with Proteobacteria and Bacteroidetes.Numerous bacteria present in the bioaerosols also emerged in water,indicating that the bacterial community in the bioaerosols was related to that of the aerosols' sources.The forced aeration of rotating brushes brought about observably distinct bacterial communities between sampling sites situated before and after the rotating brush.Isolation sources of closest relatives in bioaerosols done libraries were associated with the aqueous environment in the WWTP.Common potential pathogens in bioaerosols as well as those not reported in previous research were also analyzed in this study.Measures should be adopted to reduce the emission of bioaerosols and prevent their exposure to workers.

  6. Chasing the Origin of Viruses: Capsid-Forming Genes as a Life-Saving Preadaptation within a Community of Early Replicators.

    Science.gov (United States)

    Jalasvuori, Matti; Mattila, Sari; Hoikkala, Ville

    2015-01-01

    Virus capsids mediate the transfer of viral genetic information from one cell to another, thus the origin of the first viruses arguably coincides with the origin of the viral capsid. Capsid genes are evolutionarily ancient and their emergence potentially predated even the origin of first free-living cells. But does the origin of the capsid coincide with the origin of viruses, or is it possible that capsid-like functionalities emerged before the appearance of true viral entities? We set to investigate this question by using a computational simulator comprising primitive replicators and replication parasites within a compartment matrix. We observe that systems with no horizontal gene transfer between compartments collapse due to the rapidly emerging replication parasites. However, introduction of capsid-like genes that induce the movement of randomly selected genes from one compartment to another rescues life by providing the non-parasitic replicators a mean to escape their current compartments before the emergence of replication parasites. Capsid-forming genes can mediate the establishment of a stable meta-population where parasites cause only local tragedies but cannot overtake the whole community. The long-term survival of replicators is dependent on the frequency of horizontal transfer events, as systems with either too much or too little genetic exchange are doomed to succumb to replication-parasites. This study provides a possible scenario for explaining the origin of viral capsids before the emergence of genuine viruses: in the absence of other means of horizontal gene transfer between compartments, evolution of capsid-like functionalities may have been necessary for early life to prevail.

  7. Evolution properties of the community members for dynamic networks

    Science.gov (United States)

    Yang, Kai; Guo, Qiang; Li, Sheng-Nan; Han, Jing-Ti; Liu, Jian-Guo

    2017-03-01

    The collective behaviors of community members for dynamic social networks are significant for understanding evolution features of communities. In this Letter, we empirically investigate the evolution properties of the new community members for dynamic networks. Firstly, we separate data sets into different slices, and analyze the statistical properties of new members as well as communities they joined in for these data sets. Then we introduce a parameter φ to describe community evolution between different slices and investigate the dynamic community properties of the new community members. The empirical analyses for the Facebook, APS, Enron and Wiki data sets indicate that both the number of new members and joint communities increase, the ratio declines rapidly and then becomes stable over time, and most of the new members will join in the small size communities that is s ≤ 10. Furthermore, the proportion of new members in existed communities decreases firstly and then becomes stable and relatively small for these data sets. Our work may be helpful for deeply understanding the evolution properties of community members for social networks.

  8. Students’ perceptions about the use of wiki. analysis of an experience of collaborative learning at the University of Girona

    Directory of Open Access Journals (Sweden)

    Albert Ruda González

    2013-02-01

    Full Text Available 0 0 1 47 260 USAL 2 1 306 14.0 Normal 0 21 false false false ES JA X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Tabla normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin-top:0cm; mso-para-margin-right:0cm; mso-para-margin-bottom:10.0pt; mso-para-margin-left:0cm; line-height:115%; mso-pagination:widow-orphan; font-size:11.0pt; font-family:Calibri; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-ansi-language:ES; mso-fareast-language:EN-US;} This paper focuses on frustration experienced by law students as a result of using wikis to carry out a group investigation assignment at an on-site university. The reasons which may have contributed to such a negative response by the students are explored and some proposals for improvement are presented.

  9. Wiki, tekster og arbeidsmåter i morgendagens engelskfag: et eksempel fra lærerutdanninga

    Directory of Open Access Journals (Sweden)

    Hilde Brox

    2014-09-01

    Full Text Available Artikkelen diskuterer hvordan wiki kan brukes i engelskundervisning for å la nye og tradisjonelle tekster møtes i digital dialogisk interaksjon. Med utgangpunkt i begrepene multimodalitet, hypertekstualitet og prosessualitet, tre egenskaper som i følge Ture Schwebs (2006 skiller digitale tekster fra analoge, diskuterer artikkelen et eksempel fra et undervisningopplegg for lærerstudenter. Basert på et bilde skapte studentene et felles nettsted og en kollektiv, fiktiv, men realistisk historie. Historien dannet så i neste omgang en ramme for produksjon av tekster i ulike modaliteter og sjangre. Bildet etablerte en bestemt historisk og kulturell kontekst som studentene aktivt måtte utforske for å skape sine tekster. Wikiens funksjonaliteter åpnet opp for samskriving, utvikling av ferdigheter for å tolke og skape tekster med sammensatte modaliteter, utnyttelse av hypertekstens struktur og samarbeid om tekstskaping som prosess på tvers av tid og rom. Dette er kunnskaper og ferdigheter framtidige lærere vil trenge.

  10. Challenges to Freedom of Expression in the Digital World: Lessons from WikiLeaks and the Arab Spring

    Directory of Open Access Journals (Sweden)

    Arne HINTZ

    2012-01-01

    Full Text Available Two recent developments – the WikiLeaks releases and the Arab Spring – have demonstrated the capacities of individuals and movements in advancing free expression, transparency and social change through the use of online and social media. However they have also highlighted new sets of challenges and threats that interfere with, and restrict, such media uses. In this article I will present an analytical framework for understanding and investigating these contemporary restrictions to freedom of expression, based on the dimensions of information control, access to infrastructure, critical resources and applications, surveillance, and physical repression. The model takes into account current trends such as the use of intermediaries in control regimes, and provides a global perspective that incorporates restrictions in both East and West. Further, I will outline how free expression advocates and civil society campaigns, such as the Icelandic Modern Media Initiative (IMMI, have contested these practices, and discuss whether their agendas confirm the issue areas highlighted above. The restrictions to, and the advocacy for, free online communication demonstrate some of the key struggles and contestations on freedom of expression in the current digital media environment, the strategic points of intervention by different actors (states, businesses, and civil society, and the requirements for “modern freedom of expression”.

  11. Complex Network Property Analysis of Wiki Network%Wiki网复杂网络特性分析

    Institute of Scientific and Technical Information of China (English)

    刘智洋; 刘鲁

    2011-01-01

    以Wiki网络百度百科为研究对象,采用实证研究方法,收集百度百科184470条词条映射为复杂网络.通过计算该网络的节点度分布、平均距离、簇系数,得出以知识主题为节点的知识协作网络具有无标度和小世界特征.与现有复杂网络演化模型以及万维网、Internet科研协作网的实证研究结果进行对比,初步揭示知识协作网络的演化规律.%This paper adopts empirical research method, with Wiki network baidu-baike for research object, 184 470 topics are collected and mapped into complex network. By calculating the node degree distribution, the average path length and the clustering coefficient of the network, it is got that the knowledge cooperation network with knowledge topic has the features of scale free and small world. In comparison of the existing evolving mode for complex network with the result demonstrated by empirical research on World Wide Web, Internet and Science collaboration graph, the evolving rule is initially revealed for the knowledge cooperation network.

  12. 23S rRNA gene-based enterococci community signatures in Lake Pontchartrain, Louisiana, USA, following urban runoff inputs after Hurricane Katrina.

    Science.gov (United States)

    Bae, Hee-Sung; Hou, Aixin

    2013-02-01

    Little is known about the impacts of fecal polluted urban runoff inputs on the structure of enterococci communities in estuarine waters. This study employed a 23S rRNA gene-based polymerase chain reaction (PCR) assay with newly designed genus-specific primers, Ent127F-Ent907R, to determine the possible impacts of Hurricane Katrina floodwaters via the 17th Street Canal discharge on the community structure of enterococci in Lake Pontchartrain. A total of 94 phylotypes were identified through the restriction fragment length polymorphism (RFLP) screening of 494 clones while only 8 phylotypes occurred among 88 cultivated isolates. Sequence analyses of representative phylotypes and their temporal and spatial distribution in the lake and the canal indicated the Katrina floodwater input introduced a large portion of Enterococcus flavescens, Enterococcus casseliflavus, and Enterococcus dispar into the lake; typical fecal groups Enterococcus faecium, Enterococcus durans, Enterococcus hirae, and Enterococcus mundtii were detected primarily in the floodwater-impacted waters. This study provides a global picture of enterococci in estuarine waters impacted by Hurricane Katrina-derived urban runoff. It also demonstrates the culture-independent PCR approach using 23S rRNA gene as a molecular marker could be a good alternative in ecological studies of enterococci in natural environments to overcome the limitation of conventional cultivation methods.

  13. Bacterial communities in chitin-amended soil as revealed by 16S rRNA gene based pyrosequencing

    NARCIS (Netherlands)

    Cretoiu, Mariana Silvia; Kielak, Anna Maria; Schluter, Andreas; van Elsas, Jan Dirk

    2014-01-01

    Chitin and its derivatives are natural biopolymers that are often used as compounds for the control of soilborne plant pathogens. In spite of recent advances in agricultural practices involving chitin amendments, the microbial communities in chitin-amended soils remain poorly known. The objectives o

  14. Effects of manure and mineral fertilization strategies on soil antibiotic resistance gene levels and microbial community in a paddy-upland rotation system.

    Science.gov (United States)

    Lin, Hui; Sun, Wanchun; Zhang, Zulin; Chapman, Stephen J; Freitag, Thomas E; Fu, Jianrong; Zhang, Xin; Ma, Junwei

    2016-04-01

    This work investigated the responses of antibiotic resistance genes (ARGs) and the soil microbial community in a paddy-upland rotation system to mineral fertilizer (NPK) and different application dosages of manure combined with NPK. The occurrence of five tetracycline ARGs (tetA, tetB, tetC, tetG and tetW), two sulfonamide ARGs (sul1 and sul2) and one genetic element (IntI1) was quantified. NPK application showed only slight or no impact on soil ARGs abundances compared with the control without fertilizer. Soil ARGs abundances could be increased by manure-NPK application but was related to manure dosage (2250-9000 kg ha(-1)). Principal component analysis (PCA) showed that the soil ARG profile of the treatment with 9000 kg ha(-1) manure separated clearly from the other treatments; the ARGs that contributed most to the discrimination of this treatment were tetA, tetG, tetW, sul1, sul2 and IntI1. Community level physiological profile (CLPP) analysis showed that increasing manure dosage from 4500 kg ha(-1) to 9000 kg ha(-1) induced a sharp increase in almost all of the detected ARGs but would not change the microbial community at large. However, 9000 kg ha(-1) manure application produced a decline in soil microbial activity. Determination of antibiotics and heavy metals in soils suggested that the observed bloom of soil ARGs might associate closely with the accumulation of copper and zinc in soil.

  15. Culture-Independent Identification of Manganese-Oxidizing Genes from Deep-Sea Hydrothermal Vent Chemoautotrophic Ferromanganese Microbial Communities Using a Metagenomic Approach

    Science.gov (United States)

    Davis, R.; Tebo, B. M.

    2013-12-01

    Microbial activity has long been recognized as being important to the fate of manganese (Mn) in hydrothermal systems, yet we know very little about the organisms that catalyze Mn oxidation, the mechanisms by which Mn is oxidized or the physiological function that Mn oxidation serves in these hydrothermal systems. Hydrothermal vents with thick ferromanganese microbial mats and Mn oxide-coated rocks observed throughout the Pacific Ring of Fire are ideal models to study the mechanisms of microbial Mn oxidation, as well as primary productivity in these metal-cycling ecosystems. We sampled ferromanganese microbial mats from Vai Lili Vent Field (Tmax=43°C) located on the Eastern Lau Spreading Center and Mn oxide-encrusted rhyolytic pumice (4°C) from Niua South Seamount on the Tonga Volcanic Arc. Metagenomic libraries were constructed and assembled from these samples and key genes known to be involved in Mn oxidation and carbon fixation pathways were identified in the reconstructed genomes. The Vai Lili metagenome assembled to form 121,157 contiguous sequences (contigs) greater than 1000bp in length, with an N50 of 8,261bp and a total metagenome size of 593 Mbp. Contigs were binned using an emergent self-organizing map of tetranucleotide frequencies. Putative homologs of the multicopper Mn-oxidase MnxG were found in the metagenome that were related to both the Pseudomonas-like and Bacillus-like forms of the enzyme. The bins containing the Pseudomonas-like mnxG genes are most closely related to uncultured Deltaproteobacteria and Chloroflexi. The Deltaproteobacteria bin appears to be an obligate anaerobe with possible chemoautotrophic metabolisms, while the Chloroflexi appears to be a heterotrophic organism. The metagenome from the Mn-stained pumice was assembled into 122,092 contigs greater than 1000bp in length with an N50 of 7635 and a metagenome size of 385 Mbp. Both forms of mnxG genes are present in this metagenome as well as the genes encoding the putative Mn

  16. Effects of gene-augmentation on the formation, characteristics and microbial community of 2,4-dichlorophenoxyacetic acid degrading aerobic microbial granules

    Energy Technology Data Exchange (ETDEWEB)

    Quan, Xiang-chun, E-mail: xchquan@yahoo.com.cn [Key Laboratory of Water and Sediment Sciences of Ministry of Education/State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875 (China); Ma, Jing-yun; Xiong, Wei-cong; Yang, Zhi-feng [Key Laboratory of Water and Sediment Sciences of Ministry of Education/State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875 (China)

    2011-11-30

    Highlights: Black-Right-Pointing-Pointer The first study to cultivate aerobic granules capable of utilizing 2,4-D as the sole carbon source. Black-Right-Pointing-Pointer Granules cultivated through gene-augmentation were first compared systematically with the control on granule formation, degradation kinetics, morphology, and microbial community. Black-Right-Pointing-Pointer The first report on the fate of transconjugats in the granules during long term operation after bioaugmentation. Black-Right-Pointing-Pointer The first study to isolate in dominant bacteria in 2,4-D degrading microbial granules. - Abstract: Development of 2,4-dichlorophenoxyacetic acid (2,4-D) degrading aerobic granular sludge was conducted in two sequencing batch reactors (SBR) with one bioaugmented with a plasmid pJP4 donor strain Pseudomonas putida SM1443 and the other as a control. Half-matured aerobic granules pre-grown on glucose were used as the starting seeds and a two-stage operation strategy was applied. Granules capable of utilizing 2,4-D (about 500 mg/L) as the sole carbon source was successfully cultivated in both reactors. Gene-augmentation resulted in the enhancement of 2,4-D degradation rates by the percentage of 65-135% for the granules on Day 18, and 6-24% for the granules on Day 105. Transconjugants receiving plasmid pJP4 were established in the granule microbial community after bioaugmentation and persisted till the end of operation. Compared with the control granules, the granules in the bioaugmented reactor demonstrated a better settling ability, larger size, more abundant microbial diversity and stronger tolerance to 2,4-D. The finally obtained granules in the bioaugmented and control reactor had a granule size of around 600 {mu}m and 500 {mu}m, a Shannon-Weaver diversity index (H) of 0.96 and 0.55, respectively. A shift in microbial community was found during the granulation process.

  17. Interaction of FKBP5 Gene Variants and Adverse Life Events in Predicting Depression Onset: Results From a 10-Year Prospective Community Study

    Science.gov (United States)

    Zimmermann, Petra; Brückl, Tanja; Nocon, Agnes; Pfister, Hildegard; Binder, Elisabeth B.; Uhr, Manfred; Lieb, Roselind; Moffitt, Terrie E.; Caspi, Avshalom; Holsboer, Florian; Ising, Marcus

    2013-01-01

    Objective The binding protein FKBP5 is an important modulator of the function of the glucocorticoid receptor, the main receptor of the stress horm one system. This turns the FKBP5 gene into a key candidate for gene-environment interactions, which are considered critical for pathogenesis of stress-related disorders. The authors explored gene-environment interactions between FKBP5 gene variants and adverse life events in predicting the first occurrence of a major depressive episode. Method The analyses were based on 884 Caucasians in a 10-year prospective community study. At baseline, they were 14–24 years old and did not fulfill criteria for a major depressive episode. The DSM-IV-based Munich Composite International Diagnostic Interview was used to assess adverse life events preceding baseline and major depressive episodes during follow-up. On the basis of previous findings, five single-nucleotide polymorphisms (SNPs) within the FKBP5 gene were selected for genotyping. Results While the authors did not observe genetic main effects, they found interactions between the five SNPs and traumatic (but not separation) events, with the strongest effect for severe trauma. The effect of trauma on incident major depressive episodes was evident among subjects homozygous for the minor alleles but not subjects with other genotypes. The findings were replicated in the U.K. Environmental Risk Longitudinal Twin Study. Conclusions These hypothesis-driven results suggest that an interaction between FKBP5 genotype and trauma is involved in the onset of depression. Subjects homozygous for the minor alleles of the investigated FKBP5 SNPs seem to be particularly sensitive to effects of trauma exposure in terms of triggering depression onset. PMID:21865530

  18. Influence of heterogeneous ammonium availability on bacterial community structure and the expression of nitrogen fixation and ammonium transporter genes during in situ bioremediation of uranium-contaminated groundwater

    Energy Technology Data Exchange (ETDEWEB)

    Mouser, P.J.; N' Guessan, A.L.; Elifantz, H.; Holmes, D.E.; Williams, K.H.; Wilkins, M.J.; Long, P.E.; Lovley, D.R.

    2009-04-01

    The impact of ammonium availability on microbial community structure and the physiological status and activity of Geobacter species during in situ bioremediation of uranium-contaminated groundwater was evaluated. Ammonium concentrations varied by as much as two orders of magnitude (<4 to 400 {micro}M) across the study site. Analysis of 16S rRNA gene sequences suggested that ammonium influenced the composition of the microbial community prior to acetate addition with Rhodoferax species predominating over Geobacter species at the site with the highest ammonium, and Dechloromonas species dominating at sites with lowest ammonium. However, once acetate was added, and dissimilatory metal reduction was stimulated, Geobacter species became the predominant organisms at all locations. Rates of U(VI) reduction appeared to be more related to the concentration of acetate that was delivered to each location rather than the amount of ammonium available in the groundwater. In situ mRNA transcript abundance of the nitrogen fixation gene, nifD, and the ammonium importer gene, amtB, in Geobacter species indicated that ammonium was the primary source of nitrogen during in situ uranium reduction, and that the abundance of amtB transcripts was inversely correlated to ammonium levels across all sites examined. These results suggest that nifD and amtB expression by subsurface Geobacter species are closely regulated in response to ammonium availability to ensure an adequate supply of nitrogen while conserving cell resources. Thus, quantifying nifD and amtB expression appears to be a useful approach for monitoring the nitrogen-related physiological status of Geobacter species in subsurface environments during bioremediation. This study also emphasizes the need for more detailed analysis of geochemical/physiological interactions at the field scale, in order to adequately model subsurface microbial processes.

  19. Evaluation of 16S rRNA Gene Primer Pairs for Monitoring Microbial Community Structures Showed High Reproducibility within and Low Comparability between Datasets Generated with Multiple Archaeal and Bacterial Primer Pairs.

    Science.gov (United States)

    Fischer, Martin A; Güllert, Simon; Neulinger, Sven C; Streit, Wolfgang R; Schmitz, Ruth A

    2016-01-01

    The application of next-generation sequencing technology in microbial community analysis increased our knowledge and understanding of the complexity and diversity of a variety of ecosystems. In contrast to Bacteria, the archaeal domain was often not particularly addressed in the analysis of microbial communities. Consequently, established primers specifically amplifying the archaeal 16S ribosomal gene region are scarce compared to the variety of primers targeting bacterial sequences. In this study, we aimed to validate archaeal primers suitable for high throughput next generation sequencing. Three archaeal 16S primer pairs as well as two bacterial and one general microbial 16S primer pairs were comprehensively tested by in-silico evaluation and performing an experimental analysis of a complex microbial community of a biogas reactor. The results obtained clearly demonstrate that comparability of community profiles established using different primer pairs is difficult. 16S rRNA gene data derived from a shotgun metagenome of the same reactor sample added an additional perspective on the community structure. Furthermore, in-silico evaluation of primers, especially those for amplification of archaeal 16S rRNA gene regions, does not necessarily reflect the results obtained in experimental approaches. In the latter, archaeal primer pair ArchV34 showed the highest similarity to the archaeal community structure compared to observed by the metagenomic approach and thus appears to be the appropriate for analyzing archaeal communities in biogas reactors. However, a disadvantage of this primer pair was its low specificity for the archaeal domain in the experimental application leading to high amounts of bacterial sequences within the dataset. Overall our results indicate a rather limited comparability between community structures investigated and determined using different primer pairs as well as between metagenome and 16S rRNA gene amplicon based community structure analysis

  20. Building Practice on Personal Knowledge Management System Based on Semantic Wiki%基于语义Wild的个人知识管理系统构建实践

    Institute of Scientific and Technical Information of China (English)

    晏凌; 张淑君

    2012-01-01

    在分析语义Wiki对于个人知识管理的意义及研究基于语义Wiki的个人知识管理系统体系结构的基础上,构建基于Platypus Wiki的个人知识管理系统,以期通过实践,使基于语义Wiki的个人知识管理能够得到广泛应用。%After analyzing the significance of semantic Wiki in managing personal knowledge and researching the personal knowledge management system architecture based on semantic Wiki, the authors practice building a personal knowledge management system based on the Platypus Wiki to make it widely used.