VISIBIOweb: visualization and layout services for BioPAX pathway models

PubMed Central

Dilek, Alptug; Belviranli, Mehmet E.; Dogrusoz, Ugur

2010-01-01

With recent advancements in techniques for cellular data acquisition, information on cellular processes has been increasing at a dramatic rate. Visualization is critical to analyzing and interpreting complex information; representing cellular processes or pathways is no exception. VISIBIOweb is a free, open-source, web-based pathway visualization and layout service for pathway models in BioPAX format. With VISIBIOweb, one can obtain well-laid-out views of pathway models using the standard notation of the Systems Biology Graphical Notation (SBGN), and can embed such views within one's web pages as desired. Pathway views may be navigated using zoom and scroll tools; pathway object properties, including any external database references available in the data, may be inspected interactively. The automatic layout component of VISIBIOweb may also be accessed programmatically from other tools using Hypertext Transfer Protocol (HTTP). The web site is free and open to all users and there is no login requirement. It is available at: http://visibioweb.patika.org. PMID:20460470

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

DOE PAGES

King, Zachary A.; Drager, Andreas; Ebrahim, Ali; ...

2015-08-27

Escher is a web application for visualizing data on biological pathways. Three key features make Escher a uniquely effective tool for pathway visualization. First, users can rapidly design new pathway maps. Escher provides pathway suggestions based on user data and genome-scale models, so users can draw pathways in a semi-automated way. Second, users can visualize data related to genes or proteins on the associated reactions and pathways, using rules that define which enzymes catalyze each reaction. Thus, users can identify trends in common genomic data types (e.g. RNA-Seq, proteomics, ChIP)—in conjunction with metabolite- and reaction-oriented data types (e.g. metabolomics, fluxomics).more » Third, Escher harnesses the strengths of web technologies (SVG, D3, developer tools) so that visualizations can be rapidly adapted, extended, shared, and embedded. This paper provides examples of each of these features and explains how the development approach used for Escher can be used to guide the development of future visualization tools.« less

Ontology-Based Concept Map for Planning a Personalised Learning Path

ERIC Educational Resources Information Center

Chen, Chih-Ming

2009-01-01

Developing personalised web-based learning systems has been an important research issue in e-learning because no fixed learning pathway will be appropriate for all learners. However, most current web-based learning platforms with personalised curriculum sequencing tend to emphasise the learner preferences and interests in relation to personalised…

Pathway Distiller - multisource biological pathway consolidation

PubMed Central

2012-01-01

Background One method to understand and evaluate an experiment that produces a large set of genes, such as a gene expression microarray analysis, is to identify overrepresentation or enrichment for biological pathways. Because pathways are able to functionally describe the set of genes, much effort has been made to collect curated biological pathways into publicly accessible databases. When combining disparate databases, highly related or redundant pathways exist, making their consolidation into pathway concepts essential. This will facilitate unbiased, comprehensive yet streamlined analysis of experiments that result in large gene sets. Methods After gene set enrichment finds representative pathways for large gene sets, pathways are consolidated into representative pathway concepts. Three complementary, but different methods of pathway consolidation are explored. Enrichment Consolidation combines the set of the pathways enriched for the signature gene list through iterative combining of enriched pathways with other pathways with similar signature gene sets; Weighted Consolidation utilizes a Protein-Protein Interaction network based gene-weighting approach that finds clusters of both enriched and non-enriched pathways limited to the experiments' resultant gene list; and finally the de novo Consolidation method uses several measurements of pathway similarity, that finds static pathway clusters independent of any given experiment. Results We demonstrate that the three consolidation methods provide unified yet different functional insights of a resultant gene set derived from a genome-wide profiling experiment. Results from the methods are presented, demonstrating their applications in biological studies and comparing with a pathway web-based framework that also combines several pathway databases. Additionally a web-based consolidation framework that encompasses all three methods discussed in this paper, Pathway Distiller (http://cbbiweb.uthscsa.edu/PathwayDistiller), is established to allow researchers access to the methods and example microarray data described in this manuscript, and the ability to analyze their own gene list by using our unique consolidation methods. Conclusions By combining several pathway systems, implementing different, but complementary pathway consolidation methods, and providing a user-friendly web-accessible tool, we have enabled users the ability to extract functional explanations of their genome wide experiments. PMID:23134636

Pathway Distiller - multisource biological pathway consolidation.

PubMed

Doderer, Mark S; Anguiano, Zachry; Suresh, Uthra; Dashnamoorthy, Ravi; Bishop, Alexander J R; Chen, Yidong

2012-01-01

One method to understand and evaluate an experiment that produces a large set of genes, such as a gene expression microarray analysis, is to identify overrepresentation or enrichment for biological pathways. Because pathways are able to functionally describe the set of genes, much effort has been made to collect curated biological pathways into publicly accessible databases. When combining disparate databases, highly related or redundant pathways exist, making their consolidation into pathway concepts essential. This will facilitate unbiased, comprehensive yet streamlined analysis of experiments that result in large gene sets. After gene set enrichment finds representative pathways for large gene sets, pathways are consolidated into representative pathway concepts. Three complementary, but different methods of pathway consolidation are explored. Enrichment Consolidation combines the set of the pathways enriched for the signature gene list through iterative combining of enriched pathways with other pathways with similar signature gene sets; Weighted Consolidation utilizes a Protein-Protein Interaction network based gene-weighting approach that finds clusters of both enriched and non-enriched pathways limited to the experiments' resultant gene list; and finally the de novo Consolidation method uses several measurements of pathway similarity, that finds static pathway clusters independent of any given experiment. We demonstrate that the three consolidation methods provide unified yet different functional insights of a resultant gene set derived from a genome-wide profiling experiment. Results from the methods are presented, demonstrating their applications in biological studies and comparing with a pathway web-based framework that also combines several pathway databases. Additionally a web-based consolidation framework that encompasses all three methods discussed in this paper, Pathway Distiller (http://cbbiweb.uthscsa.edu/PathwayDistiller), is established to allow researchers access to the methods and example microarray data described in this manuscript, and the ability to analyze their own gene list by using our unique consolidation methods. By combining several pathway systems, implementing different, but complementary pathway consolidation methods, and providing a user-friendly web-accessible tool, we have enabled users the ability to extract functional explanations of their genome wide experiments.

PaintOmics 3: a web resource for the pathway analysis and visualization of multi-omics data.

PubMed

Hernández-de-Diego, Rafael; Tarazona, Sonia; Martínez-Mira, Carlos; Balzano-Nogueira, Leandro; Furió-Tarí, Pedro; Pappas, Georgios J; Conesa, Ana

2018-05-25

The increasing availability of multi-omic platforms poses new challenges to data analysis. Joint visualization of multi-omics data is instrumental in better understanding interconnections across molecular layers and in fully utilizing the multi-omic resources available to make biological discoveries. We present here PaintOmics 3, a web-based resource for the integrated visualization of multiple omic data types onto KEGG pathway diagrams. PaintOmics 3 combines server-end capabilities for data analysis with the potential of modern web resources for data visualization, providing researchers with a powerful framework for interactive exploration of their multi-omics information. Unlike other visualization tools, PaintOmics 3 covers a comprehensive pathway analysis workflow, including automatic feature name/identifier conversion, multi-layered feature matching, pathway enrichment, network analysis, interactive heatmaps, trend charts, and more. It accepts a wide variety of omic types, including transcriptomics, proteomics and metabolomics, as well as region-based approaches such as ATAC-seq or ChIP-seq data. The tool is freely available at www.paintomics.org.

Large-scale Scanning Transmission Electron Microscopy (Nanotomy) of Healthy and Injured Zebrafish Brain.

PubMed

Kuipers, Jeroen; Kalicharan, Ruby D; Wolters, Anouk H G; van Ham, Tjakko J; Giepmans, Ben N G

2016-05-25

Large-scale 2D electron microscopy (EM), or nanotomy, is the tissue-wide application of nanoscale resolution electron microscopy. Others and we previously applied large scale EM to human skin pancreatic islets, tissue culture and whole zebrafish larvae(1-7). Here we describe a universally applicable method for tissue-scale scanning EM for unbiased detection of sub-cellular and molecular features. Nanotomy was applied to investigate the healthy and a neurodegenerative zebrafish brain. Our method is based on standardized EM sample preparation protocols: Fixation with glutaraldehyde and osmium, followed by epoxy-resin embedding, ultrathin sectioning and mounting of ultrathin-sections on one-hole grids, followed by post staining with uranyl and lead. Large-scale 2D EM mosaic images are acquired using a scanning EM connected to an external large area scan generator using scanning transmission EM (STEM). Large scale EM images are typically ~ 5 - 50 G pixels in size, and best viewed using zoomable HTML files, which can be opened in any web browser, similar to online geographical HTML maps. This method can be applied to (human) tissue, cross sections of whole animals as well as tissue culture(1-5). Here, zebrafish brains were analyzed in a non-invasive neuronal ablation model. We visualize within a single dataset tissue, cellular and subcellular changes which can be quantified in various cell types including neurons and microglia, the brain's macrophages. In addition, nanotomy facilitates the correlation of EM with light microscopy (CLEM)(8) on the same tissue, as large surface areas previously imaged using fluorescent microscopy, can subsequently be subjected to large area EM, resulting in the nano-anatomy (nanotomy) of tissues. In all, nanotomy allows unbiased detection of features at EM level in a tissue-wide quantifiable manner.

Large-scale Scanning Transmission Electron Microscopy (Nanotomy) of Healthy and Injured Zebrafish Brain

PubMed Central

Kuipers, Jeroen; Kalicharan, Ruby D.; Wolters, Anouk H. G.

2016-01-01

Large-scale 2D electron microscopy (EM), or nanotomy, is the tissue-wide application of nanoscale resolution electron microscopy. Others and we previously applied large scale EM to human skin pancreatic islets, tissue culture and whole zebrafish larvae1-7. Here we describe a universally applicable method for tissue-scale scanning EM for unbiased detection of sub-cellular and molecular features. Nanotomy was applied to investigate the healthy and a neurodegenerative zebrafish brain. Our method is based on standardized EM sample preparation protocols: Fixation with glutaraldehyde and osmium, followed by epoxy-resin embedding, ultrathin sectioning and mounting of ultrathin-sections on one-hole grids, followed by post staining with uranyl and lead. Large-scale 2D EM mosaic images are acquired using a scanning EM connected to an external large area scan generator using scanning transmission EM (STEM). Large scale EM images are typically ~ 5 - 50 G pixels in size, and best viewed using zoomable HTML files, which can be opened in any web browser, similar to online geographical HTML maps. This method can be applied to (human) tissue, cross sections of whole animals as well as tissue culture1-5. Here, zebrafish brains were analyzed in a non-invasive neuronal ablation model. We visualize within a single dataset tissue, cellular and subcellular changes which can be quantified in various cell types including neurons and microglia, the brain's macrophages. In addition, nanotomy facilitates the correlation of EM with light microscopy (CLEM)8 on the same tissue, as large surface areas previously imaged using fluorescent microscopy, can subsequently be subjected to large area EM, resulting in the nano-anatomy (nanotomy) of tissues. In all, nanotomy allows unbiased detection of features at EM level in a tissue-wide quantifiable manner. PMID:27285162

Web-based metabolic network visualization with a zooming user interface

PubMed Central

2011-01-01

Background Displaying complex metabolic-map diagrams, for Web browsers, and allowing users to interact with them for querying and overlaying expression data over them is challenging. Description We present a Web-based metabolic-map diagram, which can be interactively explored by the user, called the Cellular Overview. The main characteristic of this application is the zooming user interface enabling the user to focus on appropriate granularities of the network at will. Various searching commands are available to visually highlight sets of reactions, pathways, enzymes, metabolites, and so on. Expression data from single or multiple experiments can be overlaid on the diagram, which we call the Omics Viewer capability. The application provides Web services to highlight the diagram and to invoke the Omics Viewer. This application is entirely written in JavaScript for the client browsers and connect to a Pathway Tools Web server to retrieve data and diagrams. It uses the OpenLayers library to display tiled diagrams. Conclusions This new online tool is capable of displaying large and complex metabolic-map diagrams in a very interactive manner. This application is available as part of the Pathway Tools software that powers multiple metabolic databases including Biocyc.org: The Cellular Overview is accessible under the Tools menu. PMID:21595965

NemaPath: online exploration of KEGG-based metabolic pathways for nematodes

PubMed Central

Wylie, Todd; Martin, John; Abubucker, Sahar; Yin, Yong; Messina, David; Wang, Zhengyuan; McCarter, James P; Mitreva, Makedonka

2008-01-01

Background Nematode.net is a web-accessible resource for investigating gene sequences from parasitic and free-living nematode genomes. Beyond the well-characterized model nematode C. elegans, over 500,000 expressed sequence tags (ESTs) and nearly 600,000 genome survey sequences (GSSs) have been generated from 36 nematode species as part of the Parasitic Nematode Genomics Program undertaken by the Genome Center at Washington University School of Medicine. However, these sequencing data are not present in most publicly available protein databases, which only include sequences in Swiss-Prot. Swiss-Prot, in turn, relies on GenBank/Embl/DDJP for predicted proteins from complete genomes or full-length proteins. Description Here we present the NemaPath pathway server, a web-based pathway-level visualization tool for navigating putative metabolic pathways for over 30 nematode species, including 27 parasites. The NemaPath approach consists of two parts: 1) a backend tool to align and evaluate nematode genomic sequences (curated EST contigs) against the annotated Kyoto Encyclopedia of Genes and Genomes (KEGG) protein database; 2) a web viewing application that displays annotated KEGG pathway maps based on desired confidence levels of primary sequence similarity as defined by a user. NemaPath also provides cross-referenced access to nematode genome information provided by other tools available on Nematode.net, including: detailed NemaGene EST cluster information; putative translations; GBrowse EST cluster views; links from nematode data to external databases for corresponding synonymous C. elegans counterparts, subject matches in KEGG's gene database, and also KEGG Ontology (KO) identification. Conclusion The NemaPath server hosts metabolic pathway mappings for 30 nematode species and is available on the World Wide Web at . The nematode source sequences used for the metabolic pathway mappings are available via FTP , as provided by the Genome Center at Washington University School of Medicine. PMID:18983679

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

PubMed Central

Waagmeester, Andra; Pico, Alexander R.

2016-01-01

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. PMID:27336457

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

PubMed

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.

Plant MetGenMAP: an integrative analysis system for plant systems biology

USDA-ARS?s Scientific Manuscript database

We have developed a web-based system, Plant MetGenMAP, which can identify significantly altered biochemical pathways and highly affected biological processes, predict functional roles of pathway genes, and potential pathway-related regulatory motifs from transcript and metabolite profile datasets. P...

Influence of plankton mercury dynamics and trophic pathways on mercury concentrations of top predator fish of a mining-impacted reservoir

USGS Publications Warehouse

Stewart, A.R.; Saiki, M.K.; Kuwabara, J.S.; Alpers, Charles N.; Marvin-DiPasquale, M.; Krabbenhoft, D.P.

2008-01-01

Physical and biogeochemical characteristics of the aquatic environment that affect growth dynamics of phytoplankton and the zooplankton communities that depend on them may also affect uptake of methylmercury (MeHg) into the pelagic food web of oligotrophic reservoirs. We evaluated changes in the quality and quantity of suspended particulate material, zooplankton taxonomy, and MeHg concentrations coincident with seasonal changes in water storage of a mining-impacted reservoir in northern California, USA. MeHg concentrations in bulk zooplankton increased from 4 ng??g-1 at low water to 77 ?? 6.1 ng??g-1 at high water and were positively correlated with cladoceran biomass (r = 0.66) and negatively correlated with rotifer biomass (r = -0.65). Stable isotope analysis revealed overall higher MeHg concentrations in the pelagic-based food web relative to the benthic-based food web. Statistically similar patterns of trophic enrichment of MeHg (slopes) for the pelagic and benthic food webs and slightly higher MeHg concentrations in zooplankton than in benthic invertebrates suggest that the difference in MeHg bioaccumulation among trophic pathways is set at the base of the food webs. These results suggest an important role for plankton dynamics in driving the MeHg content of zooplankton and ultimately MeHg bioaccumulation in top predators in pelagic-based food webs. ?? 2008 NRC.

Graphite Web: web tool for gene set analysis exploiting pathway topology

PubMed Central

Sales, Gabriele; Calura, Enrica; Martini, Paolo; Romualdi, Chiara

2013-01-01

Graphite web is a novel web tool for pathway analyses and network visualization for gene expression data of both microarray and RNA-seq experiments. Several pathway analyses have been proposed either in the univariate or in the global and multivariate context to tackle the complexity and the interpretation of expression results. These methods can be further divided into ‘topological’ and ‘non-topological’ methods according to their ability to gain power from pathway topology. Biological pathways are, in fact, not only gene lists but can be represented through a network where genes and connections are, respectively, nodes and edges. To this day, the most used approaches are non-topological and univariate although they miss the relationship among genes. On the contrary, topological and multivariate approaches are more powerful, but difficult to be used by researchers without bioinformatic skills. Here we present Graphite web, the first public web server for pathway analysis on gene expression data that combines topological and multivariate pathway analyses with an efficient system of interactive network visualizations for easy results interpretation. Specifically, Graphite web implements five different gene set analyses on three model organisms and two pathway databases. Graphite Web is freely available at http://graphiteweb.bio.unipd.it/. PMID:23666626

Communication of Career Pathways Through Associate Degree Program Web Sites: A Baseline Assessment.

PubMed

Becker, Ellen A; Vargas, Jenny

2018-05-08

The American Association for Respiratory Care sponsored a series of conferences that addressed the competency of the future workforce of respiratory therapists (RTs). Based upon the findings from those conferences, several initiatives emerged that support RTs earning a baccalaureate (or bachelor's) degree. The objective of this study was to identify the ways that associate degree programs communicate career pathways toward a baccalaureate degree through their Web sites. This cross-sectional observational study used a random sample of 100 of the 362 associate degree programs approved by the Commission on Accreditation for Respiratory Care. Data were collected from 3 specific categories: demographic data, baccalaureate completion information, and the Web page location for the program. The presence of statements related to any pathway toward a bachelor's degree, transfer credits, articulation agreements, and links for baccalaureate completion were recorded. The descriptive statistics in this study were reported as total numbers and percentages. Of the 100 programs in the random sample, only 89 were included in the study. Only 39 (44%) programs had links on their program Web site that had any content related to bachelor's degrees, 16 (18%) identified college transfer courses toward a bachelor's degree, and 26 (29%) programs included baccalaureate articulation agreements on their Web site. A minority of associate degree programs communicated career pathway information to their prospective and current students through program Web sites. An informative Web site would make the path more transparent for entry-level students to meet their future educational needs as their careers progress. Copyright © 2018 by Daedalus Enterprises.

Reactome diagram viewer: data structures and strategies to boost performance.

PubMed

Fabregat, Antonio; Sidiropoulos, Konstantinos; Viteri, Guilherme; Marin-Garcia, Pablo; Ping, Peipei; Stein, Lincoln; D'Eustachio, Peter; Hermjakob, Henning

2018-04-01

Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. For web-based pathway visualization, Reactome uses a custom pathway diagram viewer that has been evolved over the past years. Here, we present comprehensive enhancements in usability and performance based on extensive usability testing sessions and technology developments, aiming to optimize the viewer towards the needs of the community. The pathway diagram viewer version 3 achieves consistently better performance, loading and rendering of 97% of the diagrams in Reactome in less than 1 s. Combining the multi-layer html5 canvas strategy with a space partitioning data structure minimizes CPU workload, enabling the introduction of new features that further enhance user experience. Through the use of highly optimized data structures and algorithms, Reactome has boosted the performance and usability of the new pathway diagram viewer, providing a robust, scalable and easy-to-integrate solution to pathway visualization. As graph-based visualization of complex data is a frequent challenge in bioinformatics, many of the individual strategies presented here are applicable to a wide range of web-based bioinformatics resources. Reactome is available online at: https://reactome.org. The diagram viewer is part of the Reactome pathway browser (https://reactome.org/PathwayBrowser/) and also available as a stand-alone widget at: https://reactome.org/dev/diagram/. The source code is freely available at: https://github.com/reactome-pwp/diagram. fabregat@ebi.ac.uk or hhe@ebi.ac.uk. Supplementary data are available at Bioinformatics online.

TabPath: interactive tables for metabolic pathway analysis.

PubMed

Moraes, Lauro Ângelo Gonçalves de; Felestrino, Érica Barbosa; Assis, Renata de Almeida Barbosa; Matos, Diogo; Lima, Joubert de Castro; Lima, Leandro de Araújo; Almeida, Nalvo Franco; Setubal, João Carlos; Garcia, Camila Carrião Machado; Moreira, Leandro Marcio

2018-03-15

Information about metabolic pathways in a comparative context is one of the most powerful tool to help the understanding of genome-based differences in phenotypes among organisms. Although several platforms exist that provide a wealth of information on metabolic pathways of diverse organisms, the comparison among organisms using metabolic pathways is still a difficult task. We present TabPath (Tables for Metabolic Pathway), a web-based tool to facilitate comparison of metabolic pathways in genomes based on KEGG. From a selection of pathways and genomes of interest on the menu, TabPath generates user-friendly tables that facilitate analysis of variations in metabolism among the selected organisms. TabPath is available at http://200.239.132.160:8686. lmmorei@gmail.com.

Trophic groups and modules: two levels of group detection in food webs

PubMed Central

Gauzens, Benoit; Thébault, Elisa; Lacroix, Gérard; Legendre, Stéphane

2015-01-01

Within food webs, species can be partitioned into groups according to various criteria. Two notions have received particular attention: trophic groups (TGs), which have been used for decades in the ecological literature, and more recently, modules. The relationship between these two group concepts remains unknown in empirical food webs. While recent developments in network theory have led to efficient methods for detecting modules in food webs, the determination of TGs (groups of species that are functionally similar) is largely based on subjective expert knowledge. We develop a novel algorithm for TG detection. We apply this method to empirical food webs and show that aggregation into TGs allows for the simplification of food webs while preserving their information content. Furthermore, we reveal a two-level hierarchical structure where modules partition food webs into large bottom–top trophic pathways, whereas TGs further partition these pathways into groups of species with similar trophic connections. This provides new perspectives for the study of dynamical and functional consequences of food-web structure, bridging topological and dynamical analysis. TGs have a clear ecological meaning and are found to provide a trade-off between network complexity and information loss. PMID:25878127

MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions.

PubMed

Hayashi, Takanori; Matsuzaki, Yuri; Yanagisawa, Keisuke; Ohue, Masahito; Akiyama, Yutaka

2018-05-08

Protein-protein interactions (PPIs) play several roles in living cells, and computational PPI prediction is a major focus of many researchers. The three-dimensional (3D) structure and binding surface are important for the design of PPI inhibitors. Therefore, rigid body protein-protein docking calculations for two protein structures are expected to allow elucidation of PPIs different from known complexes in terms of 3D structures because known PPI information is not explicitly required. We have developed rapid PPI prediction software based on protein-protein docking, called MEGADOCK. In order to fully utilize the benefits of computational PPI predictions, it is necessary to construct a comprehensive database to gather prediction results and their predicted 3D complex structures and to make them easily accessible. Although several databases exist that provide predicted PPIs, the previous databases do not contain a sufficient number of entries for the purpose of discovering novel PPIs. In this study, we constructed an integrated database of MEGADOCK PPI predictions, named MEGADOCK-Web. MEGADOCK-Web provides more than 10 times the number of PPI predictions than previous databases and enables users to conduct PPI predictions that cannot be found in conventional PPI prediction databases. In MEGADOCK-Web, there are 7528 protein chains and 28,331,628 predicted PPIs from all possible combinations of those proteins. Each protein structure is annotated with PDB ID, chain ID, UniProt AC, related KEGG pathway IDs, and known PPI pairs. Additionally, MEGADOCK-Web provides four powerful functions: 1) searching precalculated PPI predictions, 2) providing annotations for each predicted protein pair with an experimentally known PPI, 3) visualizing candidates that may interact with the query protein on biochemical pathways, and 4) visualizing predicted complex structures through a 3D molecular viewer. MEGADOCK-Web provides a huge amount of comprehensive PPI predictions based on docking calculations with biochemical pathways and enables users to easily and quickly assess PPI feasibilities by archiving PPI predictions. MEGADOCK-Web also promotes the discovery of new PPIs and protein functions and is freely available for use at http://www.bi.cs.titech.ac.jp/megadock-web/ .

Nutrient enrichment reduces constraints on material flows in a detritus-based food web

Treesearch

Wyatt F. Cross; Bruce Wallace; Amy D. Rosemond

2007-01-01

Most aquatic and terrestrial ecosystems are experiencing increased nutrient availability, which is affecting their structure and function. By altering community composition and productivity of consumers, enrichment can indirectly cause changes in the pathways and magnitude of material flows in food webs. These changes, in turn, have major consequences for material...

User Interface Requirements for Web-Based Integrated Care Pathways: Evidence from the Evaluation of an Online Care Pathway Investigation Tool.

PubMed

Balatsoukas, Panos; Williams, Richard; Davies, Colin; Ainsworth, John; Buchan, Iain

2015-11-01

Integrated care pathways (ICPs) define a chronological sequence of steps, most commonly diagnostic or treatment, to be followed in providing care for patients. Care pathways help to ensure quality standards are met and to reduce variation in practice. Although research on the computerisation of ICP progresses, there is still little knowledge on what are the requirements for designing user-friendly and usable electronic care pathways, or how users (normally health care professionals) interact with interfaces that support design, analysis and visualisation of ICPs. The purpose of the study reported in this paper was to address this gap by evaluating the usability of a novel web-based tool called COCPIT (Collaborative Online Care Pathway Investigation Tool). COCPIT supports the design, analysis and visualisation of ICPs at the population level. In order to address the aim of this study, an evaluation methodology was designed based on heuristic evaluations and a mixed method usability test. The results showed that modular visualisation and direct manipulation of information related to the design and analysis of ICPs is useful for engaging and stimulating users. However, designers should pay attention to issues related to the visibility of the system status and the match between the system and the real world, especially in relation to the display of statistical information about care pathways and the editing of clinical information within a care pathway. The paper concludes with recommendations for interface design.

The Role of Web-Based Health Information in Help-Seeking Behavior Prior to a Diagnosis of Lung Cancer: A Mixed-Methods Study

PubMed Central

Jay, Caroline; Harper, Simon; Todd, Chris

2017-01-01

Background Delays to diagnosis in lung cancer can lead to reduced chance of survival, and patients often wait for several months before presenting symptoms. The time between first symptom recognition until diagnosis has been theorized into three intervals: symptom appraisal, help-seeking, and diagnostic interval (here: “pathway to diagnosis”). Interventions are needed to reduce delays to diagnosis in lung cancer. The Web has become an important lay health information source and could potentially play a role in this pathway to diagnosis. Objective Our overall aim was to gain a preliminary insight into whether Web-based information plays a role in the pathway to diagnosis in lung cancer in order to assess whether it may be possible to leverage this information source to reduce delays to diagnosis. Methods Patients diagnosed with lung cancer in the 6 months before study entry completed a survey about whether (and how, if yes) they had used the Web to appraise their condition prior to diagnosis. Based on survey responses, we purposively sampled patients and their next-of-kin for semistructured interviews (24 interviews; 33 participants). Interview data were analyzed qualitatively using Framework Analysis in the context of the pathway to diagnosis model. Results A total of 113 patients completed the survey (age: mean 67.0, SD 8.8 years). In all, 20.4% (23/113) reported they or next-of-kin had researched their condition online before the diagnosis. The majority of searches (20/23, 87.0%) were conducted by or with the help of next-of-kin. Interview results suggest that patients and next-of-kin perceived an impact of the information found online on all three intervals in the time to diagnosis. In the appraisal interval, participants used online information to evaluate symptoms and possible causes. In the help-seeking interval, the Web was used to inform the decision of whether to present to health services. In the diagnostic interval, it was used to evaluate health care professionals’ advice, to support requests for further investigation of symptoms, and to understand medical jargon. Within this interval, we identified two distinct subintervals (before/after relevant diagnostic tests were initiated), in which the Web reportedly played different roles. Conclusions Because only 20.4% of the sample reported prediagnosis Web searches, it seems the role of the Web before diagnosis of lung cancer is at present still limited, but this proportion is likely to increase in the future, when barriers such as unfamiliarity with technology and unwillingness to be informed about one’s own health are likely to decrease. Participants’ perceptions suggest that the Web can have an impact on all three intervals in the pathway to diagnosis. Thus, the Web may hold the potential to reduce delays in the diagnostic process, and this should be explored in future research and interventions. Our results also suggest a division of the diagnostic interval into two subintervals may be useful. PMID:28596146

The Role of Web-Based Health Information in Help-Seeking Behavior Prior to a Diagnosis of Lung Cancer: A Mixed-Methods Study.

PubMed

Mueller, Julia; Jay, Caroline; Harper, Simon; Todd, Chris

2017-06-08

Delays to diagnosis in lung cancer can lead to reduced chance of survival, and patients often wait for several months before presenting symptoms. The time between first symptom recognition until diagnosis has been theorized into three intervals: symptom appraisal, help-seeking, and diagnostic interval (here: "pathway to diagnosis"). Interventions are needed to reduce delays to diagnosis in lung cancer. The Web has become an important lay health information source and could potentially play a role in this pathway to diagnosis. Our overall aim was to gain a preliminary insight into whether Web-based information plays a role in the pathway to diagnosis in lung cancer in order to assess whether it may be possible to leverage this information source to reduce delays to diagnosis. Patients diagnosed with lung cancer in the 6 months before study entry completed a survey about whether (and how, if yes) they had used the Web to appraise their condition prior to diagnosis. Based on survey responses, we purposively sampled patients and their next-of-kin for semistructured interviews (24 interviews; 33 participants). Interview data were analyzed qualitatively using Framework Analysis in the context of the pathway to diagnosis model. A total of 113 patients completed the survey (age: mean 67.0, SD 8.8 years). In all, 20.4% (23/113) reported they or next-of-kin had researched their condition online before the diagnosis. The majority of searches (20/23, 87.0%) were conducted by or with the help of next-of-kin. Interview results suggest that patients and next-of-kin perceived an impact of the information found online on all three intervals in the time to diagnosis. In the appraisal interval, participants used online information to evaluate symptoms and possible causes. In the help-seeking interval, the Web was used to inform the decision of whether to present to health services. In the diagnostic interval, it was used to evaluate health care professionals' advice, to support requests for further investigation of symptoms, and to understand medical jargon. Within this interval, we identified two distinct subintervals (before/after relevant diagnostic tests were initiated), in which the Web reportedly played different roles. Because only 20.4% of the sample reported prediagnosis Web searches, it seems the role of the Web before diagnosis of lung cancer is at present still limited, but this proportion is likely to increase in the future, when barriers such as unfamiliarity with technology and unwillingness to be informed about one's own health are likely to decrease. Participants' perceptions suggest that the Web can have an impact on all three intervals in the pathway to diagnosis. Thus, the Web may hold the potential to reduce delays in the diagnostic process, and this should be explored in future research and interventions. Our results also suggest a division of the diagnostic interval into two subintervals may be useful. ©Julia Mueller, Caroline Jay, Simon Harper, Chris Todd. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 08.06.2017.

Drug-Path: a database for drug-induced pathways

PubMed Central

Zeng, Hui; Cui, Qinghua

2015-01-01

Some databases for drug-associated pathways have been built and are publicly available. However, the pathways curated in most of these databases are drug-action or drug-metabolism pathways. In recent years, high-throughput technologies such as microarray and RNA-sequencing have produced lots of drug-induced gene expression profiles. Interestingly, drug-induced gene expression profile frequently show distinct patterns, indicating that drugs normally induce the activation or repression of distinct pathways. Therefore, these pathways contribute to study the mechanisms of drugs and drug-repurposing. Here, we present Drug-Path, a database of drug-induced pathways, which was generated by KEGG pathway enrichment analysis for drug-induced upregulated genes and downregulated genes based on drug-induced gene expression datasets in Connectivity Map. Drug-Path provides user-friendly interfaces to retrieve, visualize and download the drug-induced pathway data in the database. In addition, the genes deregulated by a given drug are highlighted in the pathways. All data were organized using SQLite. The web site was implemented using Django, a Python web framework. Finally, we believe that this database will be useful for related researches. Database URL: http://www.cuilab.cn/drugpath PMID:26130661

Drug-Path: a database for drug-induced pathways.

PubMed

Zeng, Hui; Qiu, Chengxiang; Cui, Qinghua

2015-01-01

Some databases for drug-associated pathways have been built and are publicly available. However, the pathways curated in most of these databases are drug-action or drug-metabolism pathways. In recent years, high-throughput technologies such as microarray and RNA-sequencing have produced lots of drug-induced gene expression profiles. Interestingly, drug-induced gene expression profile frequently show distinct patterns, indicating that drugs normally induce the activation or repression of distinct pathways. Therefore, these pathways contribute to study the mechanisms of drugs and drug-repurposing. Here, we present Drug-Path, a database of drug-induced pathways, which was generated by KEGG pathway enrichment analysis for drug-induced upregulated genes and downregulated genes based on drug-induced gene expression datasets in Connectivity Map. Drug-Path provides user-friendly interfaces to retrieve, visualize and download the drug-induced pathway data in the database. In addition, the genes deregulated by a given drug are highlighted in the pathways. All data were organized using SQLite. The web site was implemented using Django, a Python web framework. Finally, we believe that this database will be useful for related researches. © The Author(s) 2015. Published by Oxford University Press.

Trophic groups and modules: two levels of group detection in food webs.

PubMed

Gauzens, Benoit; Thébault, Elisa; Lacroix, Gérard; Legendre, Stéphane

2015-05-06

Within food webs, species can be partitioned into groups according to various criteria. Two notions have received particular attention: trophic groups (TGs), which have been used for decades in the ecological literature, and more recently, modules. The relationship between these two group concepts remains unknown in empirical food webs. While recent developments in network theory have led to efficient methods for detecting modules in food webs, the determination of TGs (groups of species that are functionally similar) is largely based on subjective expert knowledge. We develop a novel algorithm for TG detection. We apply this method to empirical food webs and show that aggregation into TGs allows for the simplification of food webs while preserving their information content. Furthermore, we reveal a two-level hierarchical structure where modules partition food webs into large bottom-top trophic pathways, whereas TGs further partition these pathways into groups of species with similar trophic connections. This provides new perspectives for the study of dynamical and functional consequences of food-web structure, bridging topological and dynamical analysis. TGs have a clear ecological meaning and are found to provide a trade-off between network complexity and information loss. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Caryoscope: An Open Source Java application for viewing microarray data in a genomic context

PubMed Central

Awad, Ihab AB; Rees, Christian A; Hernandez-Boussard, Tina; Ball, Catherine A; Sherlock, Gavin

2004-01-01

Background Microarray-based comparative genome hybridization experiments generate data that can be mapped onto the genome. These data are interpreted more easily when represented graphically in a genomic context. Results We have developed Caryoscope, which is an open source Java application for visualizing microarray data from array comparative genome hybridization experiments in a genomic context. Caryoscope can read General Feature Format files (GFF files), as well as comma- and tab-delimited files, that define the genomic positions of the microarray reporters for which data are obtained. The microarray data can be browsed using an interactive, zoomable interface, which helps users identify regions of chromosomal deletion or amplification. The graphical representation of the data can be exported in a number of graphic formats, including publication-quality formats such as PostScript. Conclusion Caryoscope is a useful tool that can aid in the visualization, exploration and interpretation of microarray data in a genomic context. PMID:15488149

Payao: a community platform for SBML pathway model curation

PubMed Central

Matsuoka, Yukiko; Ghosh, Samik; Kikuchi, Norihiro; Kitano, Hiroaki

2010-01-01

Summary: Payao is a community-based, collaborative web service platform for gene-regulatory and biochemical pathway model curation. The system combines Web 2.0 technologies and online model visualization functions to enable a collaborative community to annotate and curate biological models. Payao reads the models in Systems Biology Markup Language format, displays them with CellDesigner, a process diagram editor, which complies with the Systems Biology Graphical Notation, and provides an interface for model enrichment (adding tags and comments to the models) for the access-controlled community members. Availability and implementation: Freely available for model curation service at http://www.payaologue.org. Web site implemented in Seaser Framework 2.0 with S2Flex2, MySQL 5.0 and Tomcat 5.5, with all major browsers supported. Contact: kitano@sbi.jp PMID:20371497

FMM: a web server for metabolic pathway reconstruction and comparative analysis.

PubMed

Chou, Chih-Hung; Chang, Wen-Chi; Chiu, Chih-Min; Huang, Chih-Chang; Huang, Hsien-Da

2009-07-01

Synthetic Biology, a multidisciplinary field, is growing rapidly. Improving the understanding of biological systems through mimicry and producing bio-orthogonal systems with new functions are two complementary pursuits in this field. A web server called FMM (From Metabolite to Metabolite) was developed for this purpose. FMM can reconstruct metabolic pathways form one metabolite to another metabolite among different species, based mainly on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and other integrated biological databases. Novel presentation for connecting different KEGG maps is newly provided. Both local and global graphical views of the metabolic pathways are designed. FMM has many applications in Synthetic Biology and Metabolic Engineering. For example, the reconstruction of metabolic pathways to produce valuable metabolites or secondary metabolites in bacteria or yeast is a promising strategy for drug production. FMM provides a highly effective way to elucidate the genes from which species should be cloned into those microorganisms based on FMM pathway comparative analysis. Consequently, FMM is an effective tool for applications in synthetic biology to produce both drugs and biofuels. This novel and innovative resource is now freely available at http://FMM.mbc.nctu.edu.tw/.

Tag Clouds as a Pathway to Improved Pedagogical Efficacy in Information Systems Courses: A Baseline Study Involving Web 2.0 Technologies

ERIC Educational Resources Information Center

Conn, Samuel S.; English, John; Scheffler, Fred; Hall, Simin

2011-01-01

Various Web 2.0 technologies can be used to support pedagogy. Examples include wikis, blogs, and social media including forum discussions. Online class forum discussions involving electronic text can result in robust strings of data containing meta-knowledge, inherent meaning, themes and patterns. Based on instructional design, learning outcomes…

NaviCell Web Service for network-based data visualization.

PubMed

Bonnet, Eric; Viara, Eric; Kuperstein, Inna; Calzone, Laurence; Cohen, David P A; Barillot, Emmanuel; Zinovyev, Andrei

2015-07-01

Data visualization is an essential element of biological research, required for obtaining insights and formulating new hypotheses on mechanisms of health and disease. NaviCell Web Service is a tool for network-based visualization of 'omics' data which implements several data visual representation methods and utilities for combining them together. NaviCell Web Service uses Google Maps and semantic zooming to browse large biological network maps, represented in various formats, together with different types of the molecular data mapped on top of them. For achieving this, the tool provides standard heatmaps, barplots and glyphs as well as the novel map staining technique for grasping large-scale trends in numerical values (such as whole transcriptome) projected onto a pathway map. The web service provides a server mode, which allows automating visualization tasks and retrieving data from maps via RESTful (standard HTTP) calls. Bindings to different programming languages are provided (Python and R). We illustrate the purpose of the tool with several case studies using pathway maps created by different research groups, in which data visualization provides new insights into molecular mechanisms involved in systemic diseases such as cancer and neurodegenerative diseases. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

NaviCell Web Service for network-based data visualization

PubMed Central

Bonnet, Eric; Viara, Eric; Kuperstein, Inna; Calzone, Laurence; Cohen, David P. A.; Barillot, Emmanuel; Zinovyev, Andrei

2015-01-01

Data visualization is an essential element of biological research, required for obtaining insights and formulating new hypotheses on mechanisms of health and disease. NaviCell Web Service is a tool for network-based visualization of ‘omics’ data which implements several data visual representation methods and utilities for combining them together. NaviCell Web Service uses Google Maps and semantic zooming to browse large biological network maps, represented in various formats, together with different types of the molecular data mapped on top of them. For achieving this, the tool provides standard heatmaps, barplots and glyphs as well as the novel map staining technique for grasping large-scale trends in numerical values (such as whole transcriptome) projected onto a pathway map. The web service provides a server mode, which allows automating visualization tasks and retrieving data from maps via RESTful (standard HTTP) calls. Bindings to different programming languages are provided (Python and R). We illustrate the purpose of the tool with several case studies using pathway maps created by different research groups, in which data visualization provides new insights into molecular mechanisms involved in systemic diseases such as cancer and neurodegenerative diseases. PMID:25958393

A Web Tool for Generating High Quality Machine-readable Biological Pathways.

PubMed

Ramirez-Gaona, Miguel; Marcu, Ana; Pon, Allison; Grant, Jason; Wu, Anthony; Wishart, David S

2017-02-08

PathWhiz is a web server built to facilitate the creation of colorful, interactive, visually pleasing pathway diagrams that are rich in biological information. The pathways generated by this online application are machine-readable and fully compatible with essentially all web-browsers and computer operating systems. It uses a specially developed, web-enabled pathway drawing interface that permits the selection and placement of different combinations of pre-drawn biological or biochemical entities to depict reactions, interactions, transport processes and binding events. This palette of entities consists of chemical compounds, proteins, nucleic acids, cellular membranes, subcellular structures, tissues, and organs. All of the visual elements in it can be interactively adjusted and customized. Furthermore, because this tool is a web server, all pathways and pathway elements are publicly accessible. This kind of pathway "crowd sourcing" means that PathWhiz already contains a large and rapidly growing collection of previously drawn pathways and pathway elements. Here we describe a protocol for the quick and easy creation of new pathways and the alteration of existing pathways. To further facilitate pathway editing and creation, the tool contains replication and propagation functions. The replication function allows existing pathways to be used as templates to create or edit new pathways. The propagation function allows one to take an existing pathway and automatically propagate it across different species. Pathways created with this tool can be "re-styled" into different formats (KEGG-like or text-book like), colored with different backgrounds, exported to BioPAX, SBGN-ML, SBML, or PWML data exchange formats, and downloaded as PNG or SVG images. The pathways can easily be incorporated into online databases, integrated into presentations, posters or publications, or used exclusively for online visualization and exploration. This protocol has been successfully applied to generate over 2,000 pathway diagrams, which are now found in many online databases including HMDB, DrugBank, SMPDB, and ECMDB.

A novel dysregulated pathway-identification analysis based on global influence of within-pathway effects and crosstalk between pathways

PubMed Central

Han, Junwei; Li, Chunquan; Yang, Haixiu; Xu, Yanjun; Zhang, Chunlong; Ma, Jiquan; Shi, Xinrui; Liu, Wei; Shang, Desi; Yao, Qianlan; Zhang, Yunpeng; Su, Fei; Feng, Li; Li, Xia

2015-01-01

Identifying dysregulated pathways from high-throughput experimental data in order to infer underlying biological insights is an important task. Current pathway-identification methods focus on single pathways in isolation; however, consideration of crosstalk between pathways could improve our understanding of alterations in biological states. We propose a novel method of pathway analysis based on global influence (PAGI) to identify dysregulated pathways, by considering both within-pathway effects and crosstalk between pathways. We constructed a global gene–gene network based on the relationships among genes extracted from a pathway database. We then evaluated the extent of differential expression for each gene, and mapped them to the global network. The random walk with restart algorithm was used to calculate the extent of genes affected by global influence. Finally, we used cumulative distribution functions to determine the significance values of the dysregulated pathways. We applied the PAGI method to five cancer microarray datasets, and compared our results with gene set enrichment analysis and five other methods. Based on these analyses, we demonstrated that PAGI can effectively identify dysregulated pathways associated with cancer, with strong reproducibility and robustness. We implemented PAGI using the freely available R-based and Web-based tools (http://bioinfo.hrbmu.edu.cn/PAGI). PMID:25551156

Adaptable Learning Pathway Generation with Ant Colony Optimization

ERIC Educational Resources Information Center

Wong, Lung-Hsiang; Looi, Chee-Kit

2009-01-01

One of the new major directions in research on web-based educational systems is the notion of adaptability: the educational system adapts itself to the learning profile, preferences and ability of the student. In this paper, we look into the issues of providing adaptability with respect to learning pathways. We explore the state of the art with…

CalFitter: a web server for analysis of protein thermal denaturation data.

PubMed

Mazurenko, Stanislav; Stourac, Jan; Kunka, Antonin; Nedeljkovic, Sava; Bednar, David; Prokop, Zbynek; Damborsky, Jiri

2018-05-14

Despite significant advances in the understanding of protein structure-function relationships, revealing protein folding pathways still poses a challenge due to a limited number of relevant experimental tools. Widely-used experimental techniques, such as calorimetry or spectroscopy, critically depend on a proper data analysis. Currently, there are only separate data analysis tools available for each type of experiment with a limited model selection. To address this problem, we have developed the CalFitter web server to be a unified platform for comprehensive data fitting and analysis of protein thermal denaturation data. The server allows simultaneous global data fitting using any combination of input data types and offers 12 protein unfolding pathway models for selection, including irreversible transitions often missing from other tools. The data fitting produces optimal parameter values, their confidence intervals, and statistical information to define unfolding pathways. The server provides an interactive and easy-to-use interface that allows users to directly analyse input datasets and simulate modelled output based on the model parameters. CalFitter web server is available free at https://loschmidt.chemi.muni.cz/calfitter/.

The GB/3D Type Fossils Online Web Portal

NASA Astrophysics Data System (ADS)

McCormick, T.; Howe, M. P.

2013-12-01

Fossils are the remains of once-living organisms that existed and played out their lives in 3-dimensional environments. The information content provided by a 3d representation of a fossil is much greater than that provided by a traditional photograph, and can grab the attention and imagination of the younger and older general public alike. The British Geological Survey has been leading a consortium of UK natural history museums including the Oxford University Museum of Natural History, the Sedgwick Museum Cambridge, the National Museum of Wales Cardiff, and a number of smaller regional British museums to construct a web portal giving access to metadata, high resolution images and interactive 3d models of type fossils from the UK. The web portal at www.3d-fossils.ac.uk was officially launched in August 2013. It can be used to discover metadata describing the provenance, taxonomy, and stratigraphy of the specimens. Zoom-able high resolution digital photographs are available, including for many specimens ';anaglyph' stereo images that can be viewed in 3d using red-cyan stereo spectacles. For many of the specimens interactive 3d models were generated by scanning with portable ';NextEngine 3D HD' 3d scanners. These models can be downloaded in zipped .OBJ and .PLY format from the web portal, or may be viewed and manipulated directly in certain web browsers. The images and scans may be freely downloaded subject to a Creative Commons Attribution ShareAlike Non-Commercial license. There is a simple application programming interface (API) allowing metadata to be downloaded, with links to the images and models, in a standardised format for use in data mash-ups and third party applications. The web portal also hosts ';open educational resources' explaining the process of fossilization and the importance of type specimens in taxonomy, as well as providing introductions to the most important fossil groups. We have experimented with using a 3d printer to create replicas of the fossils which can be used in education and public outreach. The audience for the web portal includes both professional paleontologists and the general public. The professional paleontologist can use the portal to discover the whereabouts of the type material for a taxon they are studying, and can use the pictures and 3d models to assess the completeness and preservation quality of the material. This may reduce or negate the need to send specimens (which are often fragile and always irreplaceable) to researchers through the post, or for researchers to make possibly long, expensive and environmentally damaging journeys to visit far-off collections. We hope that the pictures and 3d models will help to stimulate public interest in paleontology and natural history. The ability to digitally image and scan specimens in 3d enables institutions to have an archive record in case specimens are lost or destroyed by accident or warfare. Recent events in Cairo and Baghdad remind us that museum collections are vulnerable to civil and military strife.

cPath: open source software for collecting, storing, and querying biological pathways.

PubMed

Cerami, Ethan G; Bader, Gary D; Gross, Benjamin E; Sander, Chris

2006-11-13

Biological pathways, including metabolic pathways, protein interaction networks, signal transduction pathways, and gene regulatory networks, are currently represented in over 220 diverse databases. These data are crucial for the study of specific biological processes, including human diseases. Standard exchange formats for pathway information, such as BioPAX, CellML, SBML and PSI-MI, enable convenient collection of this data for biological research, but mechanisms for common storage and communication are required. We have developed cPath, an open source database and web application for collecting, storing, and querying biological pathway data. cPath makes it easy to aggregate custom pathway data sets available in standard exchange formats from multiple databases, present pathway data to biologists via a customizable web interface, and export pathway data via a web service to third-party software, such as Cytoscape, for visualization and analysis. cPath is software only, and does not include new pathway information. Key features include: a built-in identifier mapping service for linking identical interactors and linking to external resources; built-in support for PSI-MI and BioPAX standard pathway exchange formats; a web service interface for searching and retrieving pathway data sets; and thorough documentation. The cPath software is freely available under the LGPL open source license for academic and commercial use. cPath is a robust, scalable, modular, professional-grade software platform for collecting, storing, and querying biological pathways. It can serve as the core data handling component in information systems for pathway visualization, analysis and modeling.

Methods and approaches in the topology-based analysis of biological pathways

PubMed Central

Mitrea, Cristina; Taghavi, Zeinab; Bokanizad, Behzad; Hanoudi, Samer; Tagett, Rebecca; Donato, Michele; Voichiţa, Călin; Drăghici, Sorin

2013-01-01

The goal of pathway analysis is to identify the pathways significantly impacted in a given phenotype. Many current methods are based on algorithms that consider pathways as simple gene lists, dramatically under-utilizing the knowledge that such pathways are meant to capture. During the past few years, a plethora of methods claiming to incorporate various aspects of the pathway topology have been proposed. These topology-based methods, sometimes referred to as “third generation,” have the potential to better model the phenomena described by pathways. Although there is now a large variety of approaches used for this purpose, no review is currently available to offer guidance for potential users and developers. This review covers 22 such topology-based pathway analysis methods published in the last decade. We compare these methods based on: type of pathways analyzed (e.g., signaling or metabolic), input (subset of genes, all genes, fold changes, gene p-values, etc.), mathematical models, pathway scoring approaches, output (one or more pathway scores, p-values, etc.) and implementation (web-based, standalone, etc.). We identify and discuss challenges, arising both in methodology and in pathway representation, including inconsistent terminology, different data formats, lack of meaningful benchmarks, and the lack of tissue and condition specificity. PMID:24133454

PATIKAweb: a Web interface for analyzing biological pathways through advanced querying and visualization.

PubMed

Dogrusoz, U; Erson, E Z; Giral, E; Demir, E; Babur, O; Cetintas, A; Colak, R

2006-02-01

Patikaweb provides a Web interface for retrieving and analyzing biological pathways in the Patika database, which contains data integrated from various prominent public pathway databases. It features a user-friendly interface, dynamic visualization and automated layout, advanced graph-theoretic queries for extracting biologically important phenomena, local persistence capability and exporting facilities to various pathway exchange formats.

WEbcoli: an interactive and asynchronous web application for in silico design and analysis of genome-scale E.coli model.

PubMed

Jung, Tae-Sung; Yeo, Hock Chuan; Reddy, Satty G; Cho, Wan-Sup; Lee, Dong-Yup

2009-11-01

WEbcoli is a WEb application for in silico designing, analyzing and engineering Escherichia coli metabolism. It is devised and implemented using advanced web technologies, thereby leading to enhanced usability and dynamic web accessibility. As a main feature, the WEbcoli system provides a user-friendly rich web interface, allowing users to virtually design and synthesize mutant strains derived from the genome-scale wild-type E.coli model and to customize pathways of interest through a graph editor. In addition, constraints-based flux analysis can be conducted for quantifying metabolic fluxes and charactering the physiological and metabolic states under various genetic and/or environmental conditions. WEbcoli is freely accessible at http://webcoli.org. cheld@nus.edu.sg.

Soybean Knowledge Base (SoyKB): a Web Resource for Soybean Translational Genomics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Joshi, Trupti; Patil, Kapil; Fitzpatrick, Michael R.

2012-01-17

Background: Soybean Knowledge Base (SoyKB) is a comprehensive all-inclusive web resource for soybean translational genomics. SoyKB is designed to handle the management and integration of soybean genomics, transcriptomics, proteomics and metabolomics data along with annotation of gene function and biological pathway. It contains information on four entities, namely genes, microRNAs, metabolites and single nucleotide polymorphisms (SNPs). Methods: SoyKB has many useful tools such as Affymetrix probe ID search, gene family search, multiple gene/ metabolite search supporting co-expression analysis, and protein 3D structure viewer as well as download and upload capacity for experimental data and annotations. It has four tiers ofmore » registration, which control different levels of access to public and private data. It allows users of certain levels to share their expertise by adding comments to the data. It has a user-friendly web interface together with genome browser and pathway viewer, which display data in an intuitive manner to the soybean researchers, producers and consumers. Conclusions: SoyKB addresses the increasing need of the soybean research community to have a one-stop-shop functional and translational omics web resource for information retrieval and analysis in a user-friendly way. SoyKB can be publicly accessed at http://soykb.org/.« less

PathMAPA: a tool for displaying gene expression and performing statistical tests on metabolic pathways at multiple levels for Arabidopsis.

PubMed

Pan, Deyun; Sun, Ning; Cheung, Kei-Hoi; Guan, Zhong; Ma, Ligeng; Holford, Matthew; Deng, Xingwang; Zhao, Hongyu

2003-11-07

To date, many genomic and pathway-related tools and databases have been developed to analyze microarray data. In published web-based applications to date, however, complex pathways have been displayed with static image files that may not be up-to-date or are time-consuming to rebuild. In addition, gene expression analyses focus on individual probes and genes with little or no consideration of pathways. These approaches reveal little information about pathways that are key to a full understanding of the building blocks of biological systems. Therefore, there is a need to provide useful tools that can generate pathways without manually building images and allow gene expression data to be integrated and analyzed at pathway levels for such experimental organisms as Arabidopsis. We have developed PathMAPA, a web-based application written in Java that can be easily accessed over the Internet. An Oracle database is used to store, query, and manipulate the large amounts of data that are involved. PathMAPA allows its users to (i) upload and populate microarray data into a database; (ii) integrate gene expression with enzymes of the pathways; (iii) generate pathway diagrams without building image files manually; (iv) visualize gene expressions for each pathway at enzyme, locus, and probe levels; and (v) perform statistical tests at pathway, enzyme and gene levels. PathMAPA can be used to examine Arabidopsis thaliana gene expression patterns associated with metabolic pathways. PathMAPA provides two unique features for the gene expression analysis of Arabidopsis thaliana: (i) automatic generation of pathways associated with gene expression and (ii) statistical tests at pathway level. The first feature allows for the periodical updating of genomic data for pathways, while the second feature can provide insight into how treatments affect relevant pathways for the selected experiment(s).

PathMAPA: a tool for displaying gene expression and performing statistical tests on metabolic pathways at multiple levels for Arabidopsis

PubMed Central

Pan, Deyun; Sun, Ning; Cheung, Kei-Hoi; Guan, Zhong; Ma, Ligeng; Holford, Matthew; Deng, Xingwang; Zhao, Hongyu

2003-01-01

Background To date, many genomic and pathway-related tools and databases have been developed to analyze microarray data. In published web-based applications to date, however, complex pathways have been displayed with static image files that may not be up-to-date or are time-consuming to rebuild. In addition, gene expression analyses focus on individual probes and genes with little or no consideration of pathways. These approaches reveal little information about pathways that are key to a full understanding of the building blocks of biological systems. Therefore, there is a need to provide useful tools that can generate pathways without manually building images and allow gene expression data to be integrated and analyzed at pathway levels for such experimental organisms as Arabidopsis. Results We have developed PathMAPA, a web-based application written in Java that can be easily accessed over the Internet. An Oracle database is used to store, query, and manipulate the large amounts of data that are involved. PathMAPA allows its users to (i) upload and populate microarray data into a database; (ii) integrate gene expression with enzymes of the pathways; (iii) generate pathway diagrams without building image files manually; (iv) visualize gene expressions for each pathway at enzyme, locus, and probe levels; and (v) perform statistical tests at pathway, enzyme and gene levels. PathMAPA can be used to examine Arabidopsis thaliana gene expression patterns associated with metabolic pathways. Conclusion PathMAPA provides two unique features for the gene expression analysis of Arabidopsis thaliana: (i) automatic generation of pathways associated with gene expression and (ii) statistical tests at pathway level. The first feature allows for the periodical updating of genomic data for pathways, while the second feature can provide insight into how treatments affect relevant pathways for the selected experiment(s). PMID:14604444

Web-based applications for building, managing and analysing kinetic models of biological systems.

PubMed

Lee, Dong-Yup; Saha, Rajib; Yusufi, Faraaz Noor Khan; Park, Wonjun; Karimi, Iftekhar A

2009-01-01

Mathematical modelling and computational analysis play an essential role in improving our capability to elucidate the functions and characteristics of complex biological systems such as metabolic, regulatory and cell signalling pathways. The modelling and concomitant simulation render it possible to predict the cellular behaviour of systems under various genetically and/or environmentally perturbed conditions. This motivates systems biologists/bioengineers/bioinformaticians to develop new tools and applications, allowing non-experts to easily conduct such modelling and analysis. However, among a multitude of systems biology tools developed to date, only a handful of projects have adopted a web-based approach to kinetic modelling. In this report, we evaluate the capabilities and characteristics of current web-based tools in systems biology and identify desirable features, limitations and bottlenecks for further improvements in terms of usability and functionality. A short discussion on software architecture issues involved in web-based applications and the approaches taken by existing tools is included for those interested in developing their own simulation applications.

cPath: open source software for collecting, storing, and querying biological pathways

PubMed Central

Cerami, Ethan G; Bader, Gary D; Gross, Benjamin E; Sander, Chris

2006-01-01

Background Biological pathways, including metabolic pathways, protein interaction networks, signal transduction pathways, and gene regulatory networks, are currently represented in over 220 diverse databases. These data are crucial for the study of specific biological processes, including human diseases. Standard exchange formats for pathway information, such as BioPAX, CellML, SBML and PSI-MI, enable convenient collection of this data for biological research, but mechanisms for common storage and communication are required. Results We have developed cPath, an open source database and web application for collecting, storing, and querying biological pathway data. cPath makes it easy to aggregate custom pathway data sets available in standard exchange formats from multiple databases, present pathway data to biologists via a customizable web interface, and export pathway data via a web service to third-party software, such as Cytoscape, for visualization and analysis. cPath is software only, and does not include new pathway information. Key features include: a built-in identifier mapping service for linking identical interactors and linking to external resources; built-in support for PSI-MI and BioPAX standard pathway exchange formats; a web service interface for searching and retrieving pathway data sets; and thorough documentation. The cPath software is freely available under the LGPL open source license for academic and commercial use. Conclusion cPath is a robust, scalable, modular, professional-grade software platform for collecting, storing, and querying biological pathways. It can serve as the core data handling component in information systems for pathway visualization, analysis and modeling. PMID:17101041

Nutrients stimulate leaf breakdown rates and detritivore biomass: bottom-up effects via heterotrophic pathways.

Treesearch

Jennifer L. Greenwood; Amy D. Rosemond; J. Bruce Wallace; Wyatt F. Cross; Holly S. Weyers

2009-01-01

Most nutrient enrichment studies in aquatic systems have focused on autotrophic food webs in systems where primary producers dominate the resource base. We tested the heterotrophic response to long-...

Simple rules describe bottom-up and top-down control in food webs with alternative energy pathways.

PubMed

Wollrab, Sabine; Diehl, Sebastian; De Roos, André M

2012-09-01

Many human influences on the world's ecosystems have their largest direct impacts at either the top or the bottom of the food web. To predict their ecosystem-wide consequences we must understand how these impacts propagate. A long-standing, but so far elusive, problem in this endeavour is how to reduce food web complexity to a mathematically tractable, but empirically relevant system. Simplification to main energy channels linking primary producers to top consumers has been recently advocated. Following this approach, we propose a general framework for the analysis of bottom-up and top-down forcing of ecosystems by reducing food webs to two energy pathways originating from a limiting resource shared by competing guilds of primary producers (e.g. edible vs. defended plants). Exploring dynamical models of such webs we find that their equilibrium responses to nutrient enrichment and top consumer harvesting are determined by only two easily measurable topological properties: the lengths of the component food chains (odd-odd, odd-even, or even-even) and presence vs. absence of a generalist top consumer reconnecting the two pathways (yielding looped vs. branched webs). Many results generalise to other looped or branched web structures and the model can be easily adapted to include a detrital pathway. © 2012 Blackwell Publishing Ltd/CNRS.

Population Dynamics and Diversity of Synechococcus on the New England Shelf

DTIC Science & Technology

2014-09-01

pathway through which bacteria enter the marine food web. It is important to understand how Synechococcus is lost from marine systems. The carbon fixed...potential to work its way through the food chain; if lysed, heterotrophic bacteria will most likely remineralize the carbon. Predators and viruses are...mediate global biogeochemical cycles, and form the base of marine food webs. It is vital that we understand the factors that govern their abundance, the

GeneMesh: a web-based microarray analysis tool for relating differentially expressed genes to MeSH terms.

PubMed

Jani, Saurin D; Argraves, Gary L; Barth, Jeremy L; Argraves, W Scott

2010-04-01

An important objective of DNA microarray-based gene expression experimentation is determining inter-relationships that exist between differentially expressed genes and biological processes, molecular functions, cellular components, signaling pathways, physiologic processes and diseases. Here we describe GeneMesh, a web-based program that facilitates analysis of DNA microarray gene expression data. GeneMesh relates genes in a query set to categories available in the Medical Subject Headings (MeSH) hierarchical index. The interface enables hypothesis driven relational analysis to a specific MeSH subcategory (e.g., Cardiovascular System, Genetic Processes, Immune System Diseases etc.) or unbiased relational analysis to broader MeSH categories (e.g., Anatomy, Biological Sciences, Disease etc.). Genes found associated with a given MeSH category are dynamically linked to facilitate tabular and graphical depiction of Entrez Gene information, Gene Ontology information, KEGG metabolic pathway diagrams and intermolecular interaction information. Expression intensity values of groups of genes that cluster in relation to a given MeSH category, gene ontology or pathway can be displayed as heat maps of Z score-normalized values. GeneMesh operates on gene expression data derived from a number of commercial microarray platforms including Affymetrix, Agilent and Illumina. GeneMesh is a versatile web-based tool for testing and developing new hypotheses through relating genes in a query set (e.g., differentially expressed genes from a DNA microarray experiment) to descriptors making up the hierarchical structure of the National Library of Medicine controlled vocabulary thesaurus, MeSH. The system further enhances the discovery process by providing links between sets of genes associated with a given MeSH category to a rich set of html linked tabular and graphic information including Entrez Gene summaries, gene ontologies, intermolecular interactions, overlays of genes onto KEGG pathway diagrams and heatmaps of expression intensity values. GeneMesh is freely available online at http://proteogenomics.musc.edu/genemesh/.

A New Pathway: Video-Based Professional Development in Geography

ERIC Educational Resources Information Center

Boehm, Richard G.; Brysch, Carmen P.; Mohan, Audrey; Backler, Alan

2012-01-01

The Gilbert M. Grosvenor Center for Geographic Education, in partnership with the Agency for Instructional Technology, and the National Geographic Education Foundation have embarked on the production of a twenty-two-program, Web-based professional development series for teachers of geography, social studies, and environmental science, titled…

Integrated pathway-based transcription regulation network mining and visualization based on gene expression profiles.

PubMed

Kibinge, Nelson; Ono, Naoaki; Horie, Masafumi; Sato, Tetsuo; Sugiura, Tadao; Altaf-Ul-Amin, Md; Saito, Akira; Kanaya, Shigehiko

2016-06-01

Conventionally, workflows examining transcription regulation networks from gene expression data involve distinct analytical steps. There is a need for pipelines that unify data mining and inference deduction into a singular framework to enhance interpretation and hypotheses generation. We propose a workflow that merges network construction with gene expression data mining focusing on regulation processes in the context of transcription factor driven gene regulation. The pipeline implements pathway-based modularization of expression profiles into functional units to improve biological interpretation. The integrated workflow was implemented as a web application software (TransReguloNet) with functions that enable pathway visualization and comparison of transcription factor activity between sample conditions defined in the experimental design. The pipeline merges differential expression, network construction, pathway-based abstraction, clustering and visualization. The framework was applied in analysis of actual expression datasets related to lung, breast and prostrate cancer. Copyright © 2016 Elsevier Inc. All rights reserved.

Food web of the intertidal rocky shore of the west Portuguese coast - Determined by stable isotope analysis.

PubMed

Vinagre, Catarina; Mendonça, Vanessa; Narciso, Luís; Madeira, Carolina

2015-09-01

The characterization of food web structure, energy pathways and trophic linkages is essential for the understanding of ecosystem functioning. Isotopic analysis was performed on food web components of the rocky intertidal ecosystem in four sites along the Portuguese west coast. The aim was to 1) determine the general food web structure, 2) estimate the trophic level of the dominant organisms and 3) track the incorporation of organic carbon of different origins in the diet of the top consumers. In this food web, fish are top consumers, followed by shrimp. Anemones and gastropods are intermediate consumers, while bivalves and zooplankton are primary consumers. Macroalgae Bifurcaria bifurcata, Ulva lactuca, Fucus vesiculosus, Codium sp. and phytoplankton are the dominant producers. Two energy pathways were identified, pelagic and benthic. Reliance on the benthic energy pathway was high for many of the consumers but not as high as previously observed in subtidal coastal food webs. The maximum TL was 3.3, which is indicative of a relatively short food web. It is argued that the diet of top consumers relies directly on low levels of the food web to a considerable extent, instead of on intermediate levels, which shortens the trophic length of the food web. Copyright © 2015 Elsevier Ltd. All rights reserved.

IntegromeDB: an integrated system and biological search engine.

PubMed

Baitaluk, Michael; Kozhenkov, Sergey; Dubinina, Yulia; Ponomarenko, Julia

2012-01-19

With the growth of biological data in volume and heterogeneity, web search engines become key tools for researchers. However, general-purpose search engines are not specialized for the search of biological data. Here, we present an approach at developing a biological web search engine based on the Semantic Web technologies and demonstrate its implementation for retrieving gene- and protein-centered knowledge. The engine is available at http://www.integromedb.org. The IntegromeDB search engine allows scanning data on gene regulation, gene expression, protein-protein interactions, pathways, metagenomics, mutations, diseases, and other gene- and protein-related data that are automatically retrieved from publicly available databases and web pages using biological ontologies. To perfect the resource design and usability, we welcome and encourage community feedback.

Lynx web services for annotations and systems analysis of multi-gene disorders.

PubMed

Sulakhe, Dinanath; Taylor, Andrew; Balasubramanian, Sandhya; Feng, Bo; Xie, Bingqing; Börnigen, Daniela; Dave, Utpal J; Foster, Ian T; Gilliam, T Conrad; Maltsev, Natalia

2014-07-01

Lynx is a web-based integrated systems biology platform that supports annotation and analysis of experimental data and generation of weighted hypotheses on molecular mechanisms contributing to human phenotypes and disorders of interest. Lynx has integrated multiple classes of biomedical data (genomic, proteomic, pathways, phenotypic, toxicogenomic, contextual and others) from various public databases as well as manually curated data from our group and collaborators (LynxKB). Lynx provides tools for gene list enrichment analysis using multiple functional annotations and network-based gene prioritization. Lynx provides access to the integrated database and the analytical tools via REST based Web Services (http://lynx.ci.uchicago.edu/webservices.html). This comprises data retrieval services for specific functional annotations, services to search across the complete LynxKB (powered by Lucene), and services to access the analytical tools built within the Lynx platform. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

An event database for rotational seismology

NASA Astrophysics Data System (ADS)

Salvermoser, Johannes; Hadziioannou, Celine; Hable, Sarah; Chow, Bryant; Krischer, Lion; Wassermann, Joachim; Igel, Heiner

2016-04-01

The ring laser sensor (G-ring) located at Wettzell, Germany, routinely observes earthquake-induced rotational ground motions around a vertical axis since its installation in 2003. Here we present results from a recently installed event database which is the first that will provide ring laser event data in an open access format. Based on the GCMT event catalogue and some search criteria, seismograms from the ring laser and the collocated broadband seismometer are extracted and processed. The ObsPy-based processing scheme generates plots showing waveform fits between rotation rate and transverse acceleration and extracts characteristic wavefield parameters such as peak ground motions, noise levels, Love wave phase velocities and waveform coherence. For each event, these parameters are stored in a text file (json dictionary) which is easily readable and accessible on the website. The database contains >10000 events starting in 2007 (Mw>4.5). It is updated daily and therefore provides recent events at a time lag of max. 24 hours. The user interface allows to filter events for epoch, magnitude, and source area, whereupon the events are displayed on a zoomable world map. We investigate how well the rotational motions are compatible with the expectations from the surface wave magnitude scale. In addition, the website offers some python source code examples for downloading and processing the openly accessible waveforms.

IntegromeDB: an integrated system and biological search engine

PubMed Central

2012-01-01

Background With the growth of biological data in volume and heterogeneity, web search engines become key tools for researchers. However, general-purpose search engines are not specialized for the search of biological data. Description Here, we present an approach at developing a biological web search engine based on the Semantic Web technologies and demonstrate its implementation for retrieving gene- and protein-centered knowledge. The engine is available at http://www.integromedb.org. Conclusions The IntegromeDB search engine allows scanning data on gene regulation, gene expression, protein-protein interactions, pathways, metagenomics, mutations, diseases, and other gene- and protein-related data that are automatically retrieved from publicly available databases and web pages using biological ontologies. To perfect the resource design and usability, we welcome and encourage community feedback. PMID:22260095

Pathway enrichment analysis approach based on topological structure and updated annotation of pathway.

PubMed

Yang, Qian; Wang, Shuyuan; Dai, Enyu; Zhou, Shunheng; Liu, Dianming; Liu, Haizhou; Meng, Qianqian; Jiang, Bin; Jiang, Wei

2017-08-16

Pathway enrichment analysis has been widely used to identify cancer risk pathways, and contributes to elucidating the mechanism of tumorigenesis. However, most of the existing approaches use the outdated pathway information and neglect the complex gene interactions in pathway. Here, we first reviewed the existing widely used pathway enrichment analysis approaches briefly, and then, we proposed a novel topology-based pathway enrichment analysis (TPEA) method, which integrated topological properties and global upstream/downstream positions of genes in pathways. We compared TPEA with four widely used pathway enrichment analysis tools, including database for annotation, visualization and integrated discovery (DAVID), gene set enrichment analysis (GSEA), centrality-based pathway enrichment (CePa) and signaling pathway impact analysis (SPIA), through analyzing six gene expression profiles of three tumor types (colorectal cancer, thyroid cancer and endometrial cancer). As a result, we identified several well-known cancer risk pathways that could not be obtained by the existing tools, and the results of TPEA were more stable than that of the other tools in analyzing different data sets of the same cancer. Ultimately, we developed an R package to implement TPEA, which could online update KEGG pathway information and is available at the Comprehensive R Archive Network (CRAN): https://cran.r-project.org/web/packages/TPEA/. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Incorporating food web dynamics into ecological restoration: A modeling approach for river ecosystems

USGS Publications Warehouse

Bellmore, J. Ryan; Benjamin, Joseph R.; Newsom, Michael; Bountry, Jennifer A.; Dombroski, Daniel

2017-01-01

Restoration is frequently aimed at the recovery of target species, but also influences the larger food web in which these species participate. Effects of restoration on this broader network of organisms can influence target species both directly and indirectly via changes in energy flow through food webs. To help incorporate these complexities into river restoration planning we constructed a model that links river food web dynamics to in-stream physical habitat and riparian vegetation conditions. We present an application of the model to the Methow River, Washington (USA), a location of on-going restoration aimed at recovering salmon. Three restoration strategies were simulated: riparian vegetation restoration, nutrient augmentation via salmon carcass addition, and side-channel reconnection. We also added populations of nonnative aquatic snails and fish to the modeled food web to explore how changes in food web structure mediate responses to restoration. Simulations suggest that side-channel reconnection may be a better strategy than carcass addition and vegetation planting for improving conditions for salmon in this river segment. However, modeled responses were strongly sensitive to changes in the structure of the food web. The addition of nonnative snails and fish modified pathways of energy through the food web, which negated restoration improvements. This finding illustrates that forecasting responses to restoration may require accounting for the structure of food webs, and that changes in this structure—as might be expected with the spread of invasive species—could compromise restoration outcomes. Unlike habitat-based approaches to restoration assessment that focus on the direct effects of physical habitat conditions on single species of interest, our approach dynamically links the success of target organisms to the success of competitors, predators, and prey. By elucidating the direct and indirect pathways by which restoration affects target species, dynamic food web models can improve restoration planning by fostering a deeper understanding of system connectedness and dynamics.

web cellHTS2: a web-application for the analysis of high-throughput screening data.

PubMed

Pelz, Oliver; Gilsdorf, Moritz; Boutros, Michael

2010-04-12

The analysis of high-throughput screening data sets is an expanding field in bioinformatics. High-throughput screens by RNAi generate large primary data sets which need to be analyzed and annotated to identify relevant phenotypic hits. Large-scale RNAi screens are frequently used to identify novel factors that influence a broad range of cellular processes, including signaling pathway activity, cell proliferation, and host cell infection. Here, we present a web-based application utility for the end-to-end analysis of large cell-based screening experiments by cellHTS2. The software guides the user through the configuration steps that are required for the analysis of single or multi-channel experiments. The web-application provides options for various standardization and normalization methods, annotation of data sets and a comprehensive HTML report of the screening data analysis, including a ranked hit list. Sessions can be saved and restored for later re-analysis. The web frontend for the cellHTS2 R/Bioconductor package interacts with it through an R-server implementation that enables highly parallel analysis of screening data sets. web cellHTS2 further provides a file import and configuration module for common file formats. The implemented web-application facilitates the analysis of high-throughput data sets and provides a user-friendly interface. web cellHTS2 is accessible online at http://web-cellHTS2.dkfz.de. A standalone version as a virtual appliance and source code for platforms supporting Java 1.5.0 can be downloaded from the web cellHTS2 page. web cellHTS2 is freely distributed under GPL.

An ontology-driven semantic mash-up of gene and biological pathway information: Application to the domain of nicotine dependence

PubMed Central

Sahoo, Satya S.; Bodenreider, Olivier; Rutter, Joni L.; Skinner, Karen J.; Sheth, Amit P.

2008-01-01

Objectives This paper illustrates how Semantic Web technologies (especially RDF, OWL, and SPARQL) can support information integration and make it easy to create semantic mashups (semantically integrated resources). In the context of understanding the genetic basis of nicotine dependence, we integrate gene and pathway information and show how three complex biological queries can be answered by the integrated knowledge base. Methods We use an ontology-driven approach to integrate two gene resources (Entrez Gene and HomoloGene) and three pathway resources (KEGG, Reactome and BioCyc), for five organisms, including humans. We created the Entrez Knowledge Model (EKoM), an information model in OWL for the gene resources, and integrated it with the extant BioPAX ontology designed for pathway resources. The integrated schema is populated with data from the pathway resources, publicly available in BioPAX-compatible format, and gene resources for which a population procedure was created. The SPARQL query language is used to formulate queries over the integrated knowledge base to answer the three biological queries. Results Simple SPARQL queries could easily identify hub genes, i.e., those genes whose gene products participate in many pathways or interact with many other gene products. The identification of the genes expressed in the brain turned out to be more difficult, due to the lack of a common identification scheme for proteins. Conclusion Semantic Web technologies provide a valid framework for information integration in the life sciences. Ontology-driven integration represents a flexible, sustainable and extensible solution to the integration of large volumes of information. Additional resources, which enable the creation of mappings between information sources, are required to compensate for heterogeneity across namespaces. Resource page http://knoesis.wright.edu/research/lifesci/integration/structured_data/JBI-2008/ PMID:18395495

An ontology-driven semantic mashup of gene and biological pathway information: application to the domain of nicotine dependence.

PubMed

Sahoo, Satya S; Bodenreider, Olivier; Rutter, Joni L; Skinner, Karen J; Sheth, Amit P

2008-10-01

This paper illustrates how Semantic Web technologies (especially RDF, OWL, and SPARQL) can support information integration and make it easy to create semantic mashups (semantically integrated resources). In the context of understanding the genetic basis of nicotine dependence, we integrate gene and pathway information and show how three complex biological queries can be answered by the integrated knowledge base. We use an ontology-driven approach to integrate two gene resources (Entrez Gene and HomoloGene) and three pathway resources (KEGG, Reactome and BioCyc), for five organisms, including humans. We created the Entrez Knowledge Model (EKoM), an information model in OWL for the gene resources, and integrated it with the extant BioPAX ontology designed for pathway resources. The integrated schema is populated with data from the pathway resources, publicly available in BioPAX-compatible format, and gene resources for which a population procedure was created. The SPARQL query language is used to formulate queries over the integrated knowledge base to answer the three biological queries. Simple SPARQL queries could easily identify hub genes, i.e., those genes whose gene products participate in many pathways or interact with many other gene products. The identification of the genes expressed in the brain turned out to be more difficult, due to the lack of a common identification scheme for proteins. Semantic Web technologies provide a valid framework for information integration in the life sciences. Ontology-driven integration represents a flexible, sustainable and extensible solution to the integration of large volumes of information. Additional resources, which enable the creation of mappings between information sources, are required to compensate for heterogeneity across namespaces. RESOURCE PAGE: http://knoesis.wright.edu/research/lifesci/integration/structured_data/JBI-2008/

Organization and integration of biomedical knowledge with concept maps for key peroxisomal pathways.

PubMed

Willemsen, A M; Jansen, G A; Komen, J C; van Hooff, S; Waterham, H R; Brites, P M T; Wanders, R J A; van Kampen, A H C

2008-08-15

One important area of clinical genomics research involves the elucidation of molecular mechanisms underlying (complex) disorders which eventually may lead to new diagnostic or drug targets. To further advance this area of clinical genomics one of the main challenges is the acquisition and integration of data, information and expert knowledge for specific biomedical domains and diseases. Currently the required information is not very well organized but scattered over biological and biomedical databases, basic text books, scientific literature and experts' minds and may be highly specific, heterogeneous, complex and voluminous. We present a new framework to construct knowledge bases with concept maps for presentation of information and the web ontology language OWL for the representation of information. We demonstrate this framework through the construction of a peroxisomal knowledge base, which focuses on four key peroxisomal pathways and several related genetic disorders. All 155 concept maps in our knowledge base are linked to at least one other concept map, which allows the visualization of one big network of related pieces of information. The peroxisome knowledge base is available from www.bioinformaticslaboratory.nl (Support-->Web applications). Supplementary data is available from www.bioinformaticslaboratory.nl (Research-->Output--> Publications--> KB_SuppInfo)

The Reactome pathway knowledgebase

PubMed Central

Croft, David; Mundo, Antonio Fabregat; Haw, Robin; Milacic, Marija; Weiser, Joel; Wu, Guanming; Caudy, Michael; Garapati, Phani; Gillespie, Marc; Kamdar, Maulik R.; Jassal, Bijay; Jupe, Steven; Matthews, Lisa; May, Bruce; Palatnik, Stanislav; Rothfels, Karen; Shamovsky, Veronica; Song, Heeyeon; Williams, Mark; Birney, Ewan; Hermjakob, Henning; Stein, Lincoln; D'Eustachio, Peter

2014-01-01

Reactome (http://www.reactome.org) is a manually curated open-source open-data resource of human pathways and reactions. The current version 46 describes 7088 human proteins (34% of the predicted human proteome), participating in 6744 reactions based on data extracted from 15 107 research publications with PubMed links. The Reactome Web site and analysis tool set have been completely redesigned to increase speed, flexibility and user friendliness. The data model has been extended to support annotation of disease processes due to infectious agents and to mutation. PMID:24243840

The Reactome pathway knowledgebase.

PubMed

Croft, David; Mundo, Antonio Fabregat; Haw, Robin; Milacic, Marija; Weiser, Joel; Wu, Guanming; Caudy, Michael; Garapati, Phani; Gillespie, Marc; Kamdar, Maulik R; Jassal, Bijay; Jupe, Steven; Matthews, Lisa; May, Bruce; Palatnik, Stanislav; Rothfels, Karen; Shamovsky, Veronica; Song, Heeyeon; Williams, Mark; Birney, Ewan; Hermjakob, Henning; Stein, Lincoln; D'Eustachio, Peter

2014-01-01

Reactome (http://www.reactome.org) is a manually curated open-source open-data resource of human pathways and reactions. The current version 46 describes 7088 human proteins (34% of the predicted human proteome), participating in 6744 reactions based on data extracted from 15 107 research publications with PubMed links. The Reactome Web site and analysis tool set have been completely redesigned to increase speed, flexibility and user friendliness. The data model has been extended to support annotation of disease processes due to infectious agents and to mutation.

Use of the Chemical Transformation Simulator as a Parameterization Tool for Modeling the Environmental Fate of Organic Chemicals and their Transformation Products

EPA Science Inventory

A Chemical Transformation Simulator is a web-based system for predicting transformation pathways and physicochemical properties of organic chemicals. Role in Environmental Modeling • Screening tool for identifying likely transformation products in the environment • Parameteri...

River food webs: an integrative approach to bottom-up flow webs, top-down impact webs, and trophic position.

PubMed

Benke, Arthur C

2018-03-31

The majority of food web studies are based on connectivity, top-down impacts, bottom-up flows, or trophic position (TP), and ecologists have argued for decades which is best. Rarely have any two been considered simultaneously. The present study uses a procedure that integrates the last three approaches based on taxon-specific secondary production and gut analyses. Ingestion flows are quantified to create a flow web and the same data are used to quantify TP for all taxa. An individual predator's impacts also are estimated using the ratio of its ingestion (I) of each prey to prey production (P) to create an I/P web. This procedure was applied to 41 invertebrate taxa inhabiting submerged woody habitat in a southeastern U.S. river. A complex flow web starting with five basal food resources had 462 flows >1 mg·m -2 ·yr -1 , providing far more information than a connectivity web. Total flows from basal resources to primary consumers/omnivores were dominated by allochthonous amorphous detritus and ranged from 1 to >50,000 mg·m -2 ·yr -1 . Most predator-prey flows were much lower (<50 mg·m -2 ·yr -1 ), but some were >1,000  mg·m -2 ·yr -1 . The I/P web showed that 83% of individual predator impacts were weak (<10%), whereas total predator impacts were often strong (e.g., 35% of prey sustained an impact >90%). Quantitative estimates of TP ranged from 2 to 3.7, contrasting sharply with seven integer-based trophic levels based on longest feeding chain. Traditional omnivores (TP = 2.4-2.9) played an important role by consuming more prey and exerting higher impacts on primary consumers than strict predators (TP ≥ 3). This study illustrates how simultaneous quantification of flow pathways, predator impacts, and TP together provide an integrated characterization of natural food webs. © 2018 by the Ecological Society of America.

Web-based hybrid-dimensional Visualization and Exploration of Cytological Localization Scenarios.

PubMed

Kovanci, Gökhan; Ghaffar, Mehmood; Sommer, Björn

2016-12-21

The CELLmicrocosmos 4.2 PathwayIntegration (CmPI) is a tool which provides hybrid-dimensional visualization and analysis of intracellular protein and gene localizations in the context of a virtual 3D environment. This tool is developed based on Java/Java3D/JOGL and provides a standalone application compatible to all relevant operating systems. However, it requires Java and the local installation of the software. Here we present the prototype of an alternative web-based visualization approach, using Three.js and D3.js. In this way it is possible to visualize and explore CmPI-generated localization scenarios including networks mapped to 3D cell components by just providing a URL to a collaboration partner. This publication describes the integration of the different technologies – Three.js, D3.js and PHP – as well as an application case: a localization scenario of the citrate cycle. The CmPI web viewer is available at: http://CmPIweb.CELLmicrocosmos.org.

Web-based hybrid-dimensional Visualization and Exploration of Cytological Localization Scenarios.

PubMed

Kovanci, Gökhan; Ghaffar, Mehmood; Sommer, Björn

2016-10-01

The CELLmicrocosmos 4.2 PathwayIntegration (CmPI) is a tool which provides hybriddimensional visualization and analysis of intracellular protein and gene localizations in the context of a virtual 3D environment. This tool is developed based on Java/Java3D/JOGL and provides a standalone application compatible to all relevant operating systems. However, it requires Java and the local installation of the software. Here we present the prototype of an alternative web-based visualization approach, using Three.js and D3.js. In this way it is possible to visualize and explore CmPI-generated localization scenarios including networks mapped to 3D cell components by just providing a URL to a collaboration partner. This publication describes the integration of the different technologies - Three.js, D3.js and PHP - as well as an application case: a localization scenario of the citrate cycle. The CmPI web viewer is available at: http://CmPIweb.CELLmicrocosmos.org.

Spatial variations in food web structures with alternative stable states: evidence from stable isotope analysis in a large eutrophic lake

NASA Astrophysics Data System (ADS)

Li, Yunkai; Zhang, Yuying; Xu, Jun; Zhang, Shuo

2018-03-01

Food web structures are well known to vary widely among ecosystems. Moreover, many food web studies of lakes have generally attempted to characterize the overall food web structure and have largely ignored internal spatial and environmental variations. In this study, we hypothesize that there is a high degree of spatial heterogeneity within an ecosystem and such heterogeneity may lead to strong variations in environmental conditions and resource availability, in turn resulting in different trophic pathways. Stable carbon and nitrogen isotopes were employed for the whole food web to describe the structure of the food web in different sub-basins within Taihu Lake. This lake is a large eutrophic freshwater lake that has been intensively managed and highly influenced by human activities for more than 50 years. The results show significant isotopic differences between basins with different environmental characteristics. Such differences likely result from isotopic baseline differences combining with a shift in food web structure. Both are related to local spatial heterogeneity in nutrient loading in waters. Such variation should be explicitly considered in future food web studies and ecosystem-based management in this lake ecosystem.

Detecting Disease Specific Pathway Substructures through an Integrated Systems Biology Approach

PubMed Central

Alaimo, Salvatore; Marceca, Gioacchino Paolo; Ferro, Alfredo; Pulvirenti, Alfredo

2017-01-01

In the era of network medicine, pathway analysis methods play a central role in the prediction of phenotype from high throughput experiments. In this paper, we present a network-based systems biology approach capable of extracting disease-perturbed subpathways within pathway networks in connection with expression data taken from The Cancer Genome Atlas (TCGA). Our system extends pathways with missing regulatory elements, such as microRNAs, and their interactions with genes. The framework enables the extraction, visualization, and analysis of statistically significant disease-specific subpathways through an easy to use web interface. Our analysis shows that the methodology is able to fill the gap in current techniques, allowing a more comprehensive analysis of the phenomena underlying disease states. PMID:29657291

Diet and habitat use influence Hg and Cd transfer to fish and consequent biomagnification in a highly contaminated area: Augusta Bay (Mediterranean Sea).

PubMed

Signa, Geraldina; Mazzola, Antonio; Tramati, Cecilia Doriana; Vizzini, Salvatrice

2017-11-01

Total mercury (T-Hg) and cadmium (Cd) were measured in twenty species of fish to study their bioaccumulation patterns and trophodynamics in the Augusta Bay food web. Adult and juvenile fish were caught in 2012 in Priolo Bay, south of the Augusta harbour (Central Mediterranean Sea), which is known for the high trace element and polycyclic aromatic hydrocarbon contamination level. T-Hg concentration was found to significantly increase along δ 15 N and from pelagic to benthic sedentary fish, revealing a marked influence of trophic position and habitat use (sensu Harmelin 1987) on T-Hg accumulation within ichthyofauna. Cd showed the opposite pattern, in line with the higher trace element (TE) excretion rates of high trophic level fish and the lower level of Cd environmental contamination. Trophic pathways were first characterised in the Priolo Bay food web using carbon and nitrogen stable isotopes (δ 13 C, δ 15 N) and a single main trophic pathway characterised the Priolo Bay food web. Biomagnification was then assessed, including basal sources (surface sediment, macroalgae), zooplankton, benthic invertebrates and fish. T-Hg and Cd were found to biomagnify and biodilute respectively based on the significant linear regressions between log[T-Hg] and log[Cd] vs. δ 15 N of sources and consumers and the trophic magnification factors (TMFs) of 1.22 and 0.83 respectively. Interestingly, different Cd behaviour was found considering only the benthic pathway which leads to the predatory gastropod Hexaplex trunculus. The positive slope and the higher TMF indicated active biomagnification in this benthic food web due to the high bioaccumulation efficiency of this benthic predator. Our findings provide new evidences about the role of Priolo sediments as a sources of pollutants for the food web, representing a threat to fish and, by domino effect, to humans. Copyright © 2017 Elsevier Ltd. All rights reserved.

Visualizing Ecosystem Energy Flow in Complex Food Web Networks: A Comparison of Three Alaskan Large Marine Ecosystems

NASA Astrophysics Data System (ADS)

Kearney, K.; Aydin, K.

2016-02-01

Oceanic food webs are often depicted as network graphs, with the major organisms or functional groups displayed as nodes and the fluxes of between them as the edges. However, the large number of nodes and edges and high connectance of many management-oriented food webs coupled with graph layout algorithms poorly-suited to certain desired characteristics of food web visualizations often lead to hopelessly tangled diagrams that convey little information other than, "It's complex." Here, I combine several new graph visualization techniques- including a new node layout alorithm based on a trophic similarity (quantification of shared predator and prey) and trophic level, divided edge bundling for edge routing, and intelligent automated placement of labels- to create a much clearer visualization of the important fluxes through a food web. The technique will be used to highlight the differences in energy flow within three Alaskan Large Marine Ecosystems (the Bering Sea, Gulf of Alaska, and Aleutian Islands) that include very similar functional groups but unique energy pathways.

A visual identification key utilizing both gestalt and analytic approaches to identification of Carices present in North America (Plantae, Cyperaceae)

PubMed Central

2013-01-01

Abstract Images are a critical part of the identification process because they enable direct, immediate and relatively unmediated comparisons between a specimen being identified and one or more reference specimens. The Carices Interactive Visual Identification Key (CIVIK) is a novel tool for identification of North American Carex species, the largest vascular plant genus in North America, and two less numerous closely-related genera, Cymophyllus and Kobresia. CIVIK incorporates 1288 high-resolution tiled image sets that allow users to zoom in to view minute structures that are crucial at times for identification in these genera. Morphological data are derived from the earlier Carex Interactive Identification Key (CIIK) which in turn used data from the Flora of North America treatments. In this new iteration, images can be viewed in a grid or histogram format, allowing multiple representations of data. In both formats the images are fully zoomable. PMID:24723777

Design of a Day/Night Lunar Rover

NASA Astrophysics Data System (ADS)

Berkelman, Peter; Easudes, Jesse; Martin, Martin C.; Rollins, Eric; Silberman, Jack; Chen, Mei; Hancock, John; Mor, Andrew B.; Sharf, Alex; Warren, Tom; Bapna, Deepak

1995-06-01

The pair of lunar rovers discussed in this report will return video and state data to various ventures, including theme park and marketing concerns, science agencies, and educational institutions. The greatest challenge accepted by the design team was to enable operations throughout the extremely cold and dark lunar night, an unprecedented goal in planetary exploration. This is achieved through the use of the emerging technology of Alkali Metal Thermal to Electric Converters (AMTEC), provided with heat from a innovative beta-decay heat source, Krypton-85 gas. Although previous space missions have returned still images, our design will convey panoramic video from a ring of cameras around the rover. A six-wheel rocker bogie mechanism is implemented to propel the rover. The rovers will also provide the ability to safeguard their operation to allow untrained members of the general public to drive the vehicle. Additionally, scientific exploration and educational outreach will be supported with a user operable, steerable and zoomable camera.

Hierarchical automated clustering of cloud point set by ellipsoidal skeleton: application to organ geometric modeling from CT-scan images

NASA Astrophysics Data System (ADS)

Banegas, Frederic; Michelucci, Dominique; Roelens, Marc; Jaeger, Marc

1999-05-01

We present a robust method for automatically constructing an ellipsoidal skeleton (e-skeleton) from a set of 3D points taken from NMR or TDM images. To ensure steadiness and accuracy, all points of the objects are taken into account, including the inner ones, which is different from the existing techniques. This skeleton will be essentially useful for object characterization, for comparisons between various measurements and as a basis for deformable models. It also provides good initial guess for surface reconstruction algorithms. On output of the entire process, we obtain an analytical description of the chosen entity, semantically zoomable (local features only or reconstructed surfaces), with any level of detail (LOD) by discretization step control in voxel or polygon format. This capability allows us to handle objects at interactive frame rates once the e-skeleton is computed. Each e-skeleton is stored as a multiscale CSG implicit tree.

Metabolome searcher: a high throughput tool for metabolite identification and metabolic pathway mapping directly from mass spectrometry and using genome restriction.

PubMed

Dhanasekaran, A Ranjitha; Pearson, Jon L; Ganesan, Balasubramanian; Weimer, Bart C

2015-02-25

Mass spectrometric analysis of microbial metabolism provides a long list of possible compounds. Restricting the identification of the possible compounds to those produced by the specific organism would benefit the identification process. Currently, identification of mass spectrometry (MS) data is commonly done using empirically derived compound databases. Unfortunately, most databases contain relatively few compounds, leaving long lists of unidentified molecules. Incorporating genome-encoded metabolism enables MS output identification that may not be included in databases. Using an organism's genome as a database restricts metabolite identification to only those compounds that the organism can produce. To address the challenge of metabolomic analysis from MS data, a web-based application to directly search genome-constructed metabolic databases was developed. The user query returns a genome-restricted list of possible compound identifications along with the putative metabolic pathways based on the name, formula, SMILES structure, and the compound mass as defined by the user. Multiple queries can be done simultaneously by submitting a text file created by the user or obtained from the MS analysis software. The user can also provide parameters specific to the experiment's MS analysis conditions, such as mass deviation, adducts, and detection mode during the query so as to provide additional levels of evidence to produce the tentative identification. The query results are provided as an HTML page and downloadable text file of possible compounds that are restricted to a specific genome. Hyperlinks provided in the HTML file connect the user to the curated metabolic databases housed in ProCyc, a Pathway Tools platform, as well as the KEGG Pathway database for visualization and metabolic pathway analysis. Metabolome Searcher, a web-based tool, facilitates putative compound identification of MS output based on genome-restricted metabolic capability. This enables researchers to rapidly extend the possible identifications of large data sets for metabolites that are not in compound databases. Putative compound names with their associated metabolic pathways from metabolomics data sets are returned to the user for additional biological interpretation and visualization. This novel approach enables compound identification by restricting the possible masses to those encoded in the genome.

Defining ecospace of Arctic marine food webs using a novel quantitative approach

NASA Astrophysics Data System (ADS)

Gale, M.; Loseto, L. L.

2011-12-01

The Arctic is currently facing unprecedented change with developmental, physical and climatological changes. Food webs within the marine Arctic environment are highly susceptible to anthropogenic stressors and have thus far been understudied. Stable isotopes, in conjunction with a novel set of metrics, may provide a framework that allows us to understand which areas of the Arctic are most vulnerable to change. The objective of this study was to use linear distance metrics applied to stable isotopes to a) define and quantify four Arctic marine food webs in ecospace; b) enable quantifiable comparisons among the four food webs and with other ecosystems; and, c) evaluate vulnerability of the four food webs to anthropogenic stressors such as climate change. The areas studied were Hudson Bay, Beaufort Sea, Lancaster Sound and North Water Polynya. Each region was selected based on the abundance of previous research and published and available stable isotope data in peer-review literature. We selected species to cover trophic levels ranging from particulate matter to polar bears with consideration of pelagic, benthic and ice-associated energy pathways. We interpret higher diversity in baseline carbon energy as signifying higher stability in food web structure. Based on this, the Beaufort Sea food web had the highest stability; the Beaufort Sea food web occupied the largest isotopic niche space and was supported by multiple carbon sources. Areas with top-down control system, such as Lancaster Sound and North Water Polynya, would be the first to experience an increase in trophic redundancy and possible hardships from external stressors, as they have fewer basal carbon sources and greater numbers of mid-high level consumers. We conclude that a diverse carbon energy based ecosystem such as the Beaufort Sea and Hudson Bay regions are more resilient to change than a top down control system.

Co-LncRNA: investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data

PubMed Central

Zhao, Zheng; Bai, Jing; Wu, Aiwei; Wang, Yuan; Zhang, Jinwen; Wang, Zishan; Li, Yongsheng; Xu, Juan; Li, Xia

2015-01-01

Long non-coding RNAs (lncRNAs) are emerging as key regulators of diverse biological processes and diseases. However, the combinatorial effects of these molecules in a specific biological function are poorly understood. Identifying co-expressed protein-coding genes of lncRNAs would provide ample insight into lncRNA functions. To facilitate such an effort, we have developed Co-LncRNA, which is a web-based computational tool that allows users to identify GO annotations and KEGG pathways that may be affected by co-expressed protein-coding genes of a single or multiple lncRNAs. LncRNA co-expressed protein-coding genes were first identified in publicly available human RNA-Seq datasets, including 241 datasets across 6560 total individuals representing 28 tissue types/cell lines. Then, the lncRNA combinatorial effects in a given GO annotations or KEGG pathways are taken into account by the simultaneous analysis of multiple lncRNAs in user-selected individual or multiple datasets, which is realized by enrichment analysis. In addition, this software provides a graphical overview of pathways that are modulated by lncRNAs, as well as a specific tool to display the relevant networks between lncRNAs and their co-expressed protein-coding genes. Co-LncRNA also supports users in uploading their own lncRNA and protein-coding gene expression profiles to investigate the lncRNA combinatorial effects. It will be continuously updated with more human RNA-Seq datasets on an annual basis. Taken together, Co-LncRNA provides a web-based application for investigating lncRNA combinatorial effects, which could shed light on their biological roles and could be a valuable resource for this community. Database URL: http://www.bio-bigdata.com/Co-LncRNA/ PMID:26363020

PathScore: a web tool for identifying altered pathways in cancer data.

PubMed

Gaffney, Stephen G; Townsend, Jeffrey P

2016-12-01

PathScore quantifies the level of enrichment of somatic mutations within curated pathways, applying a novel approach that identifies pathways enriched across patients. The application provides several user-friendly, interactive graphic interfaces for data exploration, including tools for comparing pathway effect sizes, significance, gene-set overlap and enrichment differences between projects. Web application available at pathscore.publichealth.yale.edu. Site implemented in Python and MySQL, with all major browsers supported. Source code available at: github.com/sggaffney/pathscore with a GPLv3 license. stephen.gaffney@yale.edu. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Species- and habitat-specific bioaccumulation of total mercury and methylmercury in the food web of a deep oligotrophic lake.

PubMed

Arcagni, Marina; Juncos, Romina; Rizzo, Andrea; Pavlin, Majda; Fajon, Vesna; Arribére, María A; Horvat, Milena; Ribeiro Guevara, Sergio

2018-01-15

Niche segregation between introduced and native fish in Lake Nahuel Huapi, a deep oligotrophic lake in Northwest Patagonia (Argentina), occurs through the consumption of different prey. Therefore, in this work we analyzed total mercury [THg] and methylmercury [MeHg] concentrations in top predator fish and in their main prey to test whether their feeding habits influence [Hg]. Results indicate that [THg] and [MeHg] varied by foraging habitat and they increased with greater percentage of benthic diet and decreased with pelagic diet in Lake Nahuel Huapi. This is consistent with the fact that the native creole perch, a mostly benthivorous feeder, which shares the highest trophic level of the food web with introduced salmonids, had higher [THg] and [MeHg] than the more pelagic feeder rainbow trout and bentho-pelagic feeder brown trout. This differential THg and MeHg bioaccumulation observed in native and introduced fish provides evidence to the hypothesis that there are two main Hg transfer pathways from the base of the food web to top predators: a pelagic pathway where Hg is transferred from water, through plankton (with Hg in inorganic species mostly), forage fish to salmonids, and a benthic pathway, as Hg is transferred from the sediments (where Hg methylation occurs mostly), through crayfish (with higher [MeHg] than plankton), to native fish, leading to one fold higher [Hg]. Copyright © 2017 Elsevier B.V. All rights reserved.

JEdI: A New Pathway to Success for Our Forgotten Youth

ERIC Educational Resources Information Center

Kohler, Patty; Reese, Jacque

2008-01-01

For the last several years ago, Arkansas has served incarcerated juveniles in facilities of 485 beds through fourteen juvenile detention centers located in rural as well as urban areas throughout the state. Six years ago a web-based educational program was piloted in one of the juvenile detention centers in northwest Arkansas. The program was…

Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases.

PubMed

Berger, Seth I; Posner, Jeremy M; Ma'ayan, Avi

2007-10-04

In recent years, mammalian protein-protein interaction network databases have been developed. The interactions in these databases are either extracted manually from low-throughput experimental biomedical research literature, extracted automatically from literature using techniques such as natural language processing (NLP), generated experimentally using high-throughput methods such as yeast-2-hybrid screens, or interactions are predicted using an assortment of computational approaches. Genes or proteins identified as significantly changing in proteomic experiments, or identified as susceptibility disease genes in genomic studies, can be placed in the context of protein interaction networks in order to assign these genes and proteins to pathways and protein complexes. Genes2Networks is a software system that integrates the content of ten mammalian interaction network datasets. Filtering techniques to prune low-confidence interactions were implemented. Genes2Networks is delivered as a web-based service using AJAX. The system can be used to extract relevant subnetworks created from "seed" lists of human Entrez gene symbols. The output includes a dynamic linkable three color web-based network map, with a statistical analysis report that identifies significant intermediate nodes used to connect the seed list. Genes2Networks is powerful web-based software that can help experimental biologists to interpret lists of genes and proteins such as those commonly produced through genomic and proteomic experiments, as well as lists of genes and proteins associated with disease processes. This system can be used to find relationships between genes and proteins from seed lists, and predict additional genes or proteins that may play key roles in common pathways or protein complexes.

LENS: web-based lens for enrichment and network studies of human proteins

PubMed Central

2015-01-01

Background Network analysis is a common approach for the study of genetic view of diseases and biological pathways. Typically, when a set of genes are identified to be of interest in relation to a disease, say through a genome wide association study (GWAS) or a different gene expression study, these genes are typically analyzed in the context of their protein-protein interaction (PPI) networks. Further analysis is carried out to compute the enrichment of known pathways and disease-associations in the network. Having tools for such analysis at the fingertips of biologists without the requirement for computer programming or curation of data would accelerate the characterization of genes of interest. Currently available tools do not integrate network and enrichment analysis and their visualizations, and most of them present results in formats not most conducive to human cognition. Results We developed the tool Lens for Enrichment and Network Studies of human proteins (LENS) that performs network and pathway and diseases enrichment analyses on genes of interest to users. The tool creates a visualization of the network, provides easy to read statistics on network connectivity, and displays Venn diagrams with statistical significance values of the network's association with drugs, diseases, pathways, and GWASs. We used the tool to analyze gene sets related to craniofacial development, autism, and schizophrenia. Conclusion LENS is a web-based tool that does not require and download or plugins to use. The tool is free and does not require login for use, and is available at http://severus.dbmi.pitt.edu/LENS. PMID:26680011

CoNVaQ: a web tool for copy number variation-based association studies.

PubMed

Larsen, Simon Jonas; do Canto, Luisa Matos; Rogatto, Silvia Regina; Baumbach, Jan

2018-05-18

Copy number variations (CNVs) are large segments of the genome that are duplicated or deleted. Structural variations in the genome have been linked to many complex diseases. Similar to how genome-wide association studies (GWAS) have helped discover single-nucleotide polymorphisms linked to disease phenotypes, the extension of GWAS to CNVs has aided the discovery of structural variants associated with human traits and diseases. We present CoNVaQ, an easy-to-use web-based tool for CNV-based association studies. The web service allows users to upload two sets of CNV segments and search for genomic regions where the occurrence of CNVs is significantly associated with the phenotype. CoNVaQ provides two models: a simple statistical model using Fisher's exact test and a novel query-based model matching regions to user-defined queries. For each region, the method computes a global q-value statistic by repeated permutation of samples among the populations. We demonstrate our platform by using it to analyze a data set of HPV-positive and HPV-negative penile cancer patients. CoNVaQ provides a simple workflow for performing CNV-based association studies. It is made available as a web platform in order to provide a user-friendly workflow for biologists and clinicians to carry out CNV data analysis without installing any software. Through the web interface, users are also able to analyze their results to find overrepresented GO terms and pathways. In addition, our method is also available as a package for the R programming language. CoNVaQ is available at https://convaq.compbio.sdu.dk .

Web-based resources for mass-spectrometry-based metabolomics: a user's guide.

PubMed

Tohge, Takayuki; Fernie, Alisdair R

2009-03-01

In recent years, a plethora of web-based tools aimed at supporting mass-spectrometry-based metabolite profiling and metabolomics applications have appeared. Given the huge hurdles presented by the chemical diversity and dynamic range of the metabolites present in the plant kingdom, profiling the levels of a broad range of metabolites is highly challenging. Given the scale and costs involved in defining the plant metabolome, it is imperative that data are effectively shared between laboratories pursuing this goal. However, ensuring accurate comparison of samples run on the same machine within the same laboratory, let alone cross-machine and cross-laboratory comparisons, requires both careful experimentation and data interpretation. In this review, we present an overview of currently available software that aids either in peak identification or in the related field of peak alignment as well as those with utility in defining structural information of compounds and metabolic pathways.

Observed and modeled pathways of the Iceland Scotland Overflow Water in the eastern North Atlantic

NASA Astrophysics Data System (ADS)

Zou, Sijia; Lozier, Susan; Zenk, Walter; Bower, Amy; Johns, William

2017-12-01

The spreading of Iceland Scotland Overflow Water (ISOW) in the eastern North Atlantic has largely been studied in an Eulerian frame using numerical models or with observations limited to a few locations. No study to date has provided a comprehensive description of the ISOW spreading pathways from both Eulerian and Lagrangian perspectives. In this paper, we use a combination of previously unreported current meter data, hydrographic data, RAFOS float data, and a high resolution (1/12°) numerical ocean model to study the spreading pathways of ISOW from both of these perspectives. We identify three ISOW transport cores in the central Iceland Basin (∼59°N), with the major core along the eastern boundary of the Reykjanes Ridge (RR) and the other two in the basin interior. Based on trajectories of observed and/or numerical floats seeded along 59°N, we also describe the ISOW spreading pathways and quantify their relative importance. Within 10 years, 7-11% of ISOW from 59°N escapes into the Irminger Sea via gaps in the RR north of the Charlie Gibbs Fracture Zone (CGFZ); the water that moves through these gaps principally originates from the shallower ISOW layer along the RR eastern boundary. 10-13% travels further southward until the CGFZ, where it crosses westward into the western subpolar gyre. 18-21% of ISOW spreads southward along the eastern flank of the Mid-Atlantic Ridge into the Western European Basin (WEB). Most of the remaining water stays in the Iceland Basin over the 10-year period. A model-based investigation provides a first look at the temporal variability of these ISOW pathways. We find that the fraction of southward water exported into the WEB is anti-correlated with the export through the CGFZ, a result assumed to reflect these pathways' interactions with the North Atlantic Current in magnitude and/or position shift.

SPV: a JavaScript Signaling Pathway Visualizer.

PubMed

Calderone, Alberto; Cesareni, Gianni

2018-03-24

The visualization of molecular interactions annotated in web resources is useful to offer to users such information in a clear intuitive layout. These interactions are frequently represented as binary interactions that are laid out in free space where, different entities, cellular compartments and interaction types are hardly distinguishable. SPV (Signaling Pathway Visualizer) is a free open source JavaScript library which offers a series of pre-defined elements, compartments and interaction types meant to facilitate the representation of signaling pathways consisting of causal interactions without neglecting simple protein-protein interaction networks. freely available under Apache version 2 license; Source code: https://github.com/Sinnefa/SPV_Signaling_Pathway_Visualizer_v1.0. Language: JavaScript; Web technology: Scalable Vector Graphics; Libraries: D3.js. sinnefa@gmail.com.

COMAN: a web server for comprehensive metatranscriptomics analysis.

PubMed

Ni, Yueqiong; Li, Jun; Panagiotou, Gianni

2016-08-11

Microbiota-oriented studies based on metagenomic or metatranscriptomic sequencing have revolutionised our understanding on microbial ecology and the roles of both clinical and environmental microbes. The analysis of massive metatranscriptomic data requires extensive computational resources, a collection of bioinformatics tools and expertise in programming. We developed COMAN (Comprehensive Metatranscriptomics Analysis), a web-based tool dedicated to automatically and comprehensively analysing metatranscriptomic data. COMAN pipeline includes quality control of raw reads, removal of reads derived from non-coding RNA, followed by functional annotation, comparative statistical analysis, pathway enrichment analysis, co-expression network analysis and high-quality visualisation. The essential data generated by COMAN are also provided in tabular format for additional analysis and integration with other software. The web server has an easy-to-use interface and detailed instructions, and is freely available at http://sbb.hku.hk/COMAN/ CONCLUSIONS: COMAN is an integrated web server dedicated to comprehensive functional analysis of metatranscriptomic data, translating massive amount of reads to data tables and high-standard figures. It is expected to facilitate the researchers with less expertise in bioinformatics in answering microbiota-related biological questions and to increase the accessibility and interpretation of microbiota RNA-Seq data.

Operational integration in primary health care: patient encounters and workflows.

PubMed

Sifaki-Pistolla, Dimitra; Chatzea, Vasiliki-Eirini; Markaki, Adelais; Kritikos, Kyriakos; Petelos, Elena; Lionis, Christos

2017-11-29

Despite several countrywide attempts to strengthen and standardise the primary healthcare (PHC) system, Greece is still lacking a sustainable, policy-based model of integrated services. The aim of our study was to identify operational integration levels through existing patient care pathways and to recommend an alternative PHC model for optimum integration. The study was part of a large state-funded project, which included 22 randomly selected PHC units located across two health regions of Greece. Dimensions of operational integration in PHC were selected based on the work of Kringos and colleagues. A five-point Likert-type scale, coupled with an algorithm, was used to capture and transform theoretical framework features into measurable attributes. PHC services were grouped under the main categories of chronic care, urgent/acute care, preventive care, and home care. A web-based platform was used to assess patient pathways, evaluate integration levels and propose improvement actions. Analysis relied on a comparison of actual pathways versus optimal, the latter ones having been identified through literature review. Overall integration varied among units. The majority (57%) of units corresponded to a basic level. Integration by type of PHC service ranged as follows: basic (86%) or poor (14%) for chronic care units, poor (78%) or basic (22%) for urgent/acute care units, basic (50%) for preventive care units, and partial or basic (50%) for home care units. The actual pathways across all four categories of PHC services differed from those captured in the optimum integration model. Certain similarities were observed in the operational flows between chronic care management and urgent/acute care management. Such similarities were present at the highest level of abstraction, but also in common steps along the operational flows. Existing patient care pathways were mapped and analysed, and recommendations for an optimum integration PHC model were made. The developed web platform, based on a strong theoretical framework, can serve as a robust integration evaluation tool. This could be a first step towards restructuring and improving PHC services within a financially restrained environment.

PrePhyloPro: phylogenetic profile-based prediction of whole proteome linkages

PubMed Central

Niu, Yulong; Liu, Chengcheng; Moghimyfiroozabad, Shayan; Yang, Yi

2017-01-01

Direct and indirect functional links between proteins as well as their interactions as part of larger protein complexes or common signaling pathways may be predicted by analyzing the correlation of their evolutionary patterns. Based on phylogenetic profiling, here we present a highly scalable and time-efficient computational framework for predicting linkages within the whole human proteome. We have validated this method through analysis of 3,697 human pathways and molecular complexes and a comparison of our results with the prediction outcomes of previously published co-occurrency model-based and normalization methods. Here we also introduce PrePhyloPro, a web-based software that uses our method for accurately predicting proteome-wide linkages. We present data on interactions of human mitochondrial proteins, verifying the performance of this software. PrePhyloPro is freely available at http://prephylopro.org/phyloprofile/. PMID:28875072

Development of a multichemical food web model: application to PBDEs in Lake Ellasjoen, Bear Island, Norway.

PubMed

Gandhi, Nilima; Bhavsar, Satyendra P; Gewurtz, Sarah B; Diamond, Miriam L; Evenset, Anita; Christensen, Guttorm N; Gregor, Dennis

2006-08-01

A multichemical food web model has been developed to estimate the biomagnification of interconverting chemicals in aquatic food webs. We extended a fugacity-based food web model for single chemicals to account for reversible and irreversible biotransformation among a parent chemical and transformation products, by simultaneously solving mass balance equations of the chemicals using a matrix solution. The model can be applied to any number of chemicals and organisms or taxonomic groups in a food web. The model was illustratively applied to four PBDE congeners, BDE-47, -99, -100, and -153, in the food web of Lake Ellasjøen, Bear Island, Norway. In Ellasjøen arctic char (Salvelinus alpinus), the multichemical model estimated PBDE biotransformation from higher to lower brominated congeners and improved the correspondence between estimated and measured concentrations in comparison to estimates from the single-chemical food web model. The underestimation of BDE-47, even after considering bioformation due to biotransformation of the otherthree congeners, suggests its formation from additional biotransformation pathways not considered in this application. The model estimates approximate values for congener-specific biotransformation half-lives of 5.7,0.8,1.14, and 0.45 years for BDE-47, -99, -100, and -153, respectively, in large arctic char (S. alpinus) of Lake Ellasjøen.

Mixotrophy and intraguild predation - dynamic consequences of shifts between food web motifs

NASA Astrophysics Data System (ADS)

Karnatak, Rajat; Wollrab, Sabine

2017-06-01

Mixotrophy is ubiquitous in microbial communities of aquatic systems with many flagellates being able to use autotroph as well as heterotroph pathways for energy acquisition. The usage of one over the other pathway is associated with resource availability and the coupling of alternative pathways has strong implications for system stability. We investigated the impact of dominance of different energy pathways related to relative resource availability on system dynamics in the setting of a tritrophic food web motif. This motif consists of a mixotroph feeding on a purely autotroph species while competing for a shared resource. In addition, the autotroph can use an additional exclusive food source. By changing the relative abundance of shared vs. exclusive food source, we shift the food web motif from an intraguild predation motif to a food chain motif. We analyzed the dependence of system dynamics on absolute and relative resource availability. In general, the system exhibits a transition from stable to oscillatory dynamics with increasing nutrient availability. However, this transition occurs at a much lower nutrient level for the food chain in comparison to the intraguild predation motif. A similar transition is also observed with variations in the relative abundance of food sources for a range of nutrient levels. We expect this shift in food web motifs to occur frequently in microbial communities and therefore the results from our study are highly relevant for natural systems.

Pathways of Sleep, Affect, and Stress Constellations during the First Year of College: Transition Difficulties of Emerging Adults

ERIC Educational Resources Information Center

Ari, Lilac Lev; Shulman, Shmuel

2012-01-01

One hundred and fifty Israeli first-year college students were assessed twice: during the first semester following the commencement of their undergraduate studies and toward the end of the second semester. At each semester, participants completed web-based daily diaries for seven consecutive days assessing daily sleep, affective mood, stress, and…

Mining and integration of pathway diagrams from imaging data.

PubMed

Kozhenkov, Sergey; Baitaluk, Michael

2012-03-01

Pathway diagrams from PubMed and World Wide Web (WWW) contain valuable highly curated information difficult to reach without tools specifically designed and customized for the biological semantics and high-content density of the images. There is currently no search engine or tool that can analyze pathway images, extract their pathway components (molecules, genes, proteins, organelles, cells, organs, etc.) and indicate their relationships. Here, we describe a resource of pathway diagrams retrieved from article and web-page images through optical character recognition, in conjunction with data mining and data integration methods. The recognized pathways are integrated into the BiologicalNetworks research environment linking them to a wealth of data available in the BiologicalNetworks' knowledgebase, which integrates data from >100 public data sources and the biomedical literature. Multiple search and analytical tools are available that allow the recognized cellular pathways, molecular networks and cell/tissue/organ diagrams to be studied in the context of integrated knowledge, experimental data and the literature. BiologicalNetworks software and the pathway repository are freely available at www.biologicalnetworks.org. Supplementary data are available at Bioinformatics online.

Sealife: a semantic grid browser for the life sciences applied to the study of infectious diseases.

PubMed

Schroeder, Michael; Burger, Albert; Kostkova, Patty; Stevens, Robert; Habermann, Bianca; Dieng-Kuntz, Rose

2006-01-01

The objective of Sealife is the conception and realisation of a semantic Grid browser for the life sciences, which will link the existing Web to the currently emerging eScience infrastructure. The SeaLife Browser will allow users to automatically link a host of Web servers and Web/Grid services to the Web content he/she is visiting. This will be accomplished using eScience's growing number of Web/Grid Services and its XML-based standards and ontologies. The browser will identify terms in the pages being browsed through the background knowledge held in ontologies. Through the use of Semantic Hyperlinks, which link identified ontology terms to servers and services, the SeaLife Browser will offer a new dimension of context-based information integration. In this paper, we give an overview over the different components of the browser and their interplay. This SeaLife Browser will be demonstrated within three application scenarios in evidence-based medicine, literature & patent mining, and molecular biology, all relating to the study of infectious diseases. The three applications vertically integrate the molecule/cell, the tissue/organ and the patient/population level by covering the analysis of high-throughput screening data for endocytosis (the molecular entry pathway into the cell), the expression of proteins in the spatial context of tissue and organs, and a high-level library on infectious diseases designed for clinicians and their patients. For more information see http://www.biote.ctu-dresden.de/sealife.

Mercury and selenium in the food web of Lake Nahuel Huapi, Patagonia, Argentina.

PubMed

Arcagni, Marina; Rizzo, Andrea; Juncos, Romina; Pavlin, Majda; Campbell, Linda M; Arribére, María A; Horvat, Milena; Ribeiro Guevara, Sergio

2017-01-01

Despite located far from point sources of Hg pollution, high concentrations were recorded in plankton from the deep oligotrophic Lake Nahuel Huapi, located in North Patagonia. Native and introduced top predator fish with differing feeding habits are a valuable economic resource to the region. Hence, Hg and Se trophic interactions and pathways to these fish were assessed in the food web of this lake at three sites, using stable nitrogen and carbon isotopes. As expected based on the high THg in plankton, mercury did not biomagnify in the food web of Lake Nahuel Huapi, as most of the THg in plankton is in the inorganic form. As was observed in other aquatic systems, Se did not biomagnify either. When trophic pathways to top predator fish were analyzed, they showed that THg biomagnified in the food chains of native fish but biodiluted in the food chains of introduced salmonids. A more benthic diet, typical of native fish, resulted in higher [THg] bioaccumulation than a more pelagic or mixed diet, as in the case of introduced fish. Se:THg molar ratios were higher than 1 in all the fish species, indicating that Se might be offering a natural protection against Hg toxicity. Copyright © 2016 Elsevier Ltd. All rights reserved.

NMSim web server: integrated approach for normal mode-based geometric simulations of biologically relevant conformational transitions in proteins.

PubMed

Krüger, Dennis M; Ahmed, Aqeel; Gohlke, Holger

2012-07-01

The NMSim web server implements a three-step approach for multiscale modeling of protein conformational changes. First, the protein structure is coarse-grained using the FIRST software. Second, a rigid cluster normal-mode analysis provides low-frequency normal modes. Third, these modes are used to extend the recently introduced idea of constrained geometric simulations by biasing backbone motions of the protein, whereas side chain motions are biased toward favorable rotamer states (NMSim). The generated structures are iteratively corrected regarding steric clashes and stereochemical constraint violations. The approach allows performing three simulation types: unbiased exploration of conformational space; pathway generation by a targeted simulation; and radius of gyration-guided simulation. On a data set of proteins with experimentally observed conformational changes, the NMSim approach has been shown to be a computationally efficient alternative to molecular dynamics simulations for conformational sampling of proteins. The generated conformations and pathways of conformational transitions can serve as input to docking approaches or more sophisticated sampling techniques. The web server output is a trajectory of generated conformations, Jmol representations of the coarse-graining and a subset of the trajectory and data plots of structural analyses. The NMSim webserver, accessible at http://www.nmsim.de, is free and open to all users with no login requirement.

NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps

PubMed Central

2013-01-01

Background Molecular biology knowledge can be formalized and systematically represented in a computer-readable form as a comprehensive map of molecular interactions. There exist an increasing number of maps of molecular interactions containing detailed and step-wise description of various cell mechanisms. It is difficult to explore these large maps, to organize discussion of their content and to maintain them. Several efforts were recently made to combine these capabilities together in one environment, and NaviCell is one of them. Results NaviCell is a web-based environment for exploiting large maps of molecular interactions, created in CellDesigner, allowing their easy exploration, curation and maintenance. It is characterized by a combination of three essential features: (1) efficient map browsing based on Google Maps; (2) semantic zooming for viewing different levels of details or of abstraction of the map and (3) integrated web-based blog for collecting community feedback. NaviCell can be easily used by experts in the field of molecular biology for studying molecular entities of interest in the context of signaling pathways and crosstalk between pathways within a global signaling network. NaviCell allows both exploration of detailed molecular mechanisms represented on the map and a more abstract view of the map up to a top-level modular representation. NaviCell greatly facilitates curation, maintenance and updating the comprehensive maps of molecular interactions in an interactive and user-friendly fashion due to an imbedded blogging system. Conclusions NaviCell provides user-friendly exploration of large-scale maps of molecular interactions, thanks to Google Maps and WordPress interfaces, with which many users are already familiar. Semantic zooming which is used for navigating geographical maps is adopted for molecular maps in NaviCell, making any level of visualization readable. In addition, NaviCell provides a framework for community-based curation of maps. PMID:24099179

NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps.

PubMed

Kuperstein, Inna; Cohen, David P A; Pook, Stuart; Viara, Eric; Calzone, Laurence; Barillot, Emmanuel; Zinovyev, Andrei

2013-10-07

Molecular biology knowledge can be formalized and systematically represented in a computer-readable form as a comprehensive map of molecular interactions. There exist an increasing number of maps of molecular interactions containing detailed and step-wise description of various cell mechanisms. It is difficult to explore these large maps, to organize discussion of their content and to maintain them. Several efforts were recently made to combine these capabilities together in one environment, and NaviCell is one of them. NaviCell is a web-based environment for exploiting large maps of molecular interactions, created in CellDesigner, allowing their easy exploration, curation and maintenance. It is characterized by a combination of three essential features: (1) efficient map browsing based on Google Maps; (2) semantic zooming for viewing different levels of details or of abstraction of the map and (3) integrated web-based blog for collecting community feedback. NaviCell can be easily used by experts in the field of molecular biology for studying molecular entities of interest in the context of signaling pathways and crosstalk between pathways within a global signaling network. NaviCell allows both exploration of detailed molecular mechanisms represented on the map and a more abstract view of the map up to a top-level modular representation. NaviCell greatly facilitates curation, maintenance and updating the comprehensive maps of molecular interactions in an interactive and user-friendly fashion due to an imbedded blogging system. NaviCell provides user-friendly exploration of large-scale maps of molecular interactions, thanks to Google Maps and WordPress interfaces, with which many users are already familiar. Semantic zooming which is used for navigating geographical maps is adopted for molecular maps in NaviCell, making any level of visualization readable. In addition, NaviCell provides a framework for community-based curation of maps.

Computational knowledge integration in biopharmaceutical research.

PubMed

Ficenec, David; Osborne, Mark; Pradines, Joel; Richards, Dan; Felciano, Ramon; Cho, Raymond J; Chen, Richard O; Liefeld, Ted; Owen, James; Ruttenberg, Alan; Reich, Christian; Horvath, Joseph; Clark, Tim

2003-09-01

An initiative to increase biopharmaceutical research productivity by capturing, sharing and computationally integrating proprietary scientific discoveries with public knowledge is described. This initiative involves both organisational process change and multiple interoperating software systems. The software components rely on mutually supporting integration techniques. These include a richly structured ontology, statistical analysis of experimental data against stored conclusions, natural language processing of public literature, secure document repositories with lightweight metadata, web services integration, enterprise web portals and relational databases. This approach has already begun to increase scientific productivity in our enterprise by creating an organisational memory (OM) of internal research findings, accessible on the web. Through bringing together these components it has also been possible to construct a very large and expanding repository of biological pathway information linked to this repository of findings which is extremely useful in analysis of DNA microarray data. This repository, in turn, enables our research paradigm to be shifted towards more comprehensive systems-based understandings of drug action.

Very-high-resolution time-lapse photography for plant and ecosystems research.

PubMed

Nichols, Mary H; Steven, Janet C; Sargent, Randy; Dille, Paul; Schapiro, Joshua

2013-09-01

Traditional photography is a compromise between image detail and area covered. We report a new method for creating time-lapse sequences of very-high-resolution photographs to produce zoomable images that facilitate observation across a range of spatial and temporal scales. • A robotic camera mount and software were used to capture images of the growth and movement in Brassica rapa every 15 s in the laboratory. The resultant time-lapse sequence (http://timemachine.gigapan.org/wiki/Plant_Growth) captures growth detail such as circumnutation. A modified, solar-powered system was deployed at a remote field site in southern Arizona. Images were collected every 2 h over a 3-mo period to capture the response of vegetation to monsoon season rainfall (http://timemachine.gigapan.org/wiki/Arizona_Grasslands). • A technique for observing time sequences of both individual plant and ecosystem response at a range of spatial scales is available for use in the laboratory and in the field.

Very-high-resolution time-lapse photography for plant and ecosystems research1

PubMed Central

Nichols, Mary H.; Steven, Janet C.; Sargent, Randy; Dille, Paul; Schapiro, Joshua

2013-01-01

• Premise of the study: Traditional photography is a compromise between image detail and area covered. We report a new method for creating time-lapse sequences of very-high-resolution photographs to produce zoomable images that facilitate observation across a range of spatial and temporal scales. • Methods and Results: A robotic camera mount and software were used to capture images of the growth and movement in Brassica rapa every 15 s in the laboratory. The resultant time-lapse sequence (http://timemachine.gigapan.org/wiki/Plant_Growth) captures growth detail such as circumnutation. A modified, solar-powered system was deployed at a remote field site in southern Arizona. Images were collected every 2 h over a 3-mo period to capture the response of vegetation to monsoon season rainfall (http://timemachine.gigapan.org/wiki/Arizona_Grasslands). • Conclusions: A technique for observing time sequences of both individual plant and ecosystem response at a range of spatial scales is available for use in the laboratory and in the field. PMID:25202588

Lifemap: Exploring the Entire Tree of Life.

PubMed

de Vienne, Damien M

2016-12-01

The Tree of Life (ToL) is meant to be a unique representation of the evolutionary relationships between all species on earth. Huge efforts are made to assemble such a large tree, helped by the decrease of sequencing costs and improved methods to reconstruct and combine phylogenies, but no tool exists today to explore the ToL in its entirety in a satisfying manner. By combining methods used in modern cartography, such as OpenStreetMap, with a new way of representing tree-like structures, I created Lifemap, a tool allowing the exploration of a complete representation of the ToL (between 800,000 and 2.2 million species depending on the data source) in a zoomable interface. A server version of Lifemap also allows users to visualize their own trees. This should help researchers in ecology and evolutionary biology in their everyday work, but may also permit the diffusion to a broader audience of our current knowledge of the evolutionary relationships linking all organisms.

Impact of a Web-based worksite health promotion program on absenteeism.

PubMed

Niessen, Maurice A J; Kraaijenhagen, Roderik A; Dijkgraaf, Marcel G W; Van Pelt, Danielle; Van Kalken, Coen K; Peek, Niels

2012-04-01

To evaluate the effect of participation in a comprehensive, Web-based worksite health promotion program on absenteeism. Study population consists of Dutch workers employed at a large financial services company. Linear regression was used to assess the impact of program attendance on the difference between baseline and follow-up absenteeism rates, controlling for gender, age, job level, years of employment, and noncompletion of the program. Data from 20,797 individuals were analyzed; 3826 individuals enrolled in the program during the study period. A 20.3% reduction in absenteeism was shown among program attendees compared with nonparticipants during a median follow-up period of 23.3 months. Participating in the worksite health promotion program led to an immediate reduction in absenteeism. Improved psychological well-being, increased exercise, and weight reduction are possible pathways toward this reduction.

Co-LncRNA: investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data.

PubMed

Zhao, Zheng; Bai, Jing; Wu, Aiwei; Wang, Yuan; Zhang, Jinwen; Wang, Zishan; Li, Yongsheng; Xu, Juan; Li, Xia

2015-01-01

Long non-coding RNAs (lncRNAs) are emerging as key regulators of diverse biological processes and diseases. However, the combinatorial effects of these molecules in a specific biological function are poorly understood. Identifying co-expressed protein-coding genes of lncRNAs would provide ample insight into lncRNA functions. To facilitate such an effort, we have developed Co-LncRNA, which is a web-based computational tool that allows users to identify GO annotations and KEGG pathways that may be affected by co-expressed protein-coding genes of a single or multiple lncRNAs. LncRNA co-expressed protein-coding genes were first identified in publicly available human RNA-Seq datasets, including 241 datasets across 6560 total individuals representing 28 tissue types/cell lines. Then, the lncRNA combinatorial effects in a given GO annotations or KEGG pathways are taken into account by the simultaneous analysis of multiple lncRNAs in user-selected individual or multiple datasets, which is realized by enrichment analysis. In addition, this software provides a graphical overview of pathways that are modulated by lncRNAs, as well as a specific tool to display the relevant networks between lncRNAs and their co-expressed protein-coding genes. Co-LncRNA also supports users in uploading their own lncRNA and protein-coding gene expression profiles to investigate the lncRNA combinatorial effects. It will be continuously updated with more human RNA-Seq datasets on an annual basis. Taken together, Co-LncRNA provides a web-based application for investigating lncRNA combinatorial effects, which could shed light on their biological roles and could be a valuable resource for this community. Database URL: http://www.bio-bigdata.com/Co-LncRNA/. © The Author(s) 2015. Published by Oxford University Press.

Tox21 Enricher: Web-based Chemical/Biological Functional Annotation Analysis Tool Based on Tox21 Toxicity Screening Platform.

PubMed

Hur, Junguk; Danes, Larson; Hsieh, Jui-Hua; McGregor, Brett; Krout, Dakota; Auerbach, Scott

2018-05-01

The US Toxicology Testing in the 21st Century (Tox21) program was established to develop more efficient and human-relevant toxicity assessment methods. The Tox21 program screens >10,000 chemicals using quantitative high-throughput screening (qHTS) of assays that measure effects on toxicity pathways. To date, more than 70 assays have yielded >12 million concentration-response curves. The patterns of activity across assays can be used to define similarity between chemicals. Assuming chemicals with similar activity profiles have similar toxicological properties, we may infer toxicological properties based on its neighbourhood. One approach to inference is chemical/biological annotation enrichment analysis. Here, we present Tox21 Enricher, a web-based chemical annotation enrichment tool for the Tox21 toxicity screening platform. Tox21 Enricher identifies over-represented chemical/biological annotations among lists of chemicals (neighbourhoods), facilitating the identification of the toxicological properties and mechanisms in the chemical set. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Global opportunities on 239 general surgery residency Web sites.

PubMed

Wackerbarth, Joel J; Campbell, Timothy D; Wren, Sherry; Price, Raymond R; Maier, Ronald V; Numann, Patricia; Kushner, Adam L

2015-09-01

Many general surgical residency programs lack a formal international component. We hypothesized that most surgery programs do not have international training or do not provide the information to prospective applicants regarding electives or programs in an easily accessible manner via Web-based resources. Individual general surgery program Web sites and the American College of Surgeons residency tool were used to identify 239 residencies. The homepages were examined for specific mention of international or global health programs. Ease of access was also considered. Global surgery specific pages or centers were noted. Programs were assessed for length of rotation, presence of research component, and mention of benefits to residents and respective institution. Of 239 programs, 24 (10%) mentioned international experiences on their home page and 42 (18%) contained information about global surgery. Of those with information available, 69% were easily accessible. Academic programs were more likely than independent programs to have information about international opportunities on their home page (13.7% versus 4.0%, P = 0.006) and more likely to have a dedicated program or pathway Web site (18.8% versus 2.0%, P < 0.0001). Half of the residencies with global surgery information did not have length of rotation available. Research was only mentioned by 29% of the Web sites. Benefits to high-income country residents were discussed more than benefits to low- and middle-income country residents (57% versus 17%). General surgery residency programs do not effectively communicate international opportunities for prospective residents through Web-based resources and should seriously consider integrating international options into their curriculum and better present them on department Web sites. Copyright © 2015 Elsevier Inc. All rights reserved.

A Powerful Procedure for Pathway-Based Meta-analysis Using Summary Statistics Identifies 43 Pathways Associated with Type II Diabetes in European Populations.

PubMed

Zhang, Han; Wheeler, William; Hyland, Paula L; Yang, Yifan; Shi, Jianxin; Chatterjee, Nilanjan; Yu, Kai

2016-06-01

Meta-analysis of multiple genome-wide association studies (GWAS) has become an effective approach for detecting single nucleotide polymorphism (SNP) associations with complex traits. However, it is difficult to integrate the readily accessible SNP-level summary statistics from a meta-analysis into more powerful multi-marker testing procedures, which generally require individual-level genetic data. We developed a general procedure called Summary based Adaptive Rank Truncated Product (sARTP) for conducting gene and pathway meta-analysis that uses only SNP-level summary statistics in combination with genotype correlation estimated from a panel of individual-level genetic data. We demonstrated the validity and power advantage of sARTP through empirical and simulated data. We conducted a comprehensive pathway-based meta-analysis with sARTP on type 2 diabetes (T2D) by integrating SNP-level summary statistics from two large studies consisting of 19,809 T2D cases and 111,181 controls with European ancestry. Among 4,713 candidate pathways from which genes in neighborhoods of 170 GWAS established T2D loci were excluded, we detected 43 T2D globally significant pathways (with Bonferroni corrected p-values < 0.05), which included the insulin signaling pathway and T2D pathway defined by KEGG, as well as the pathways defined according to specific gene expression patterns on pancreatic adenocarcinoma, hepatocellular carcinoma, and bladder carcinoma. Using summary data from 8 eastern Asian T2D GWAS with 6,952 cases and 11,865 controls, we showed 7 out of the 43 pathways identified in European populations remained to be significant in eastern Asians at the false discovery rate of 0.1. We created an R package and a web-based tool for sARTP with the capability to analyze pathways with thousands of genes and tens of thousands of SNPs.

A Powerful Procedure for Pathway-Based Meta-analysis Using Summary Statistics Identifies 43 Pathways Associated with Type II Diabetes in European Populations

PubMed Central

Zhang, Han; Wheeler, William; Hyland, Paula L.; Yang, Yifan; Shi, Jianxin; Chatterjee, Nilanjan; Yu, Kai

2016-01-01

Meta-analysis of multiple genome-wide association studies (GWAS) has become an effective approach for detecting single nucleotide polymorphism (SNP) associations with complex traits. However, it is difficult to integrate the readily accessible SNP-level summary statistics from a meta-analysis into more powerful multi-marker testing procedures, which generally require individual-level genetic data. We developed a general procedure called Summary based Adaptive Rank Truncated Product (sARTP) for conducting gene and pathway meta-analysis that uses only SNP-level summary statistics in combination with genotype correlation estimated from a panel of individual-level genetic data. We demonstrated the validity and power advantage of sARTP through empirical and simulated data. We conducted a comprehensive pathway-based meta-analysis with sARTP on type 2 diabetes (T2D) by integrating SNP-level summary statistics from two large studies consisting of 19,809 T2D cases and 111,181 controls with European ancestry. Among 4,713 candidate pathways from which genes in neighborhoods of 170 GWAS established T2D loci were excluded, we detected 43 T2D globally significant pathways (with Bonferroni corrected p-values < 0.05), which included the insulin signaling pathway and T2D pathway defined by KEGG, as well as the pathways defined according to specific gene expression patterns on pancreatic adenocarcinoma, hepatocellular carcinoma, and bladder carcinoma. Using summary data from 8 eastern Asian T2D GWAS with 6,952 cases and 11,865 controls, we showed 7 out of the 43 pathways identified in European populations remained to be significant in eastern Asians at the false discovery rate of 0.1. We created an R package and a web-based tool for sARTP with the capability to analyze pathways with thousands of genes and tens of thousands of SNPs. PMID:27362418

Trends in hospital librarianship and hospital library services: 1989 to 2006.

PubMed

Thibodeau, Patricia L; Funk, Carla J

2009-10-01

The research studied the status of hospital librarians and library services to better inform the Medical Library Association's advocacy activities. The Vital Pathways Survey Subcommittee of the Task Force on Vital Pathways for Hospital Librarians distributed a web-based survey to hospital librarians and academic health sciences library directors. The survey results were compared to data collected in a 1989 survey of hospital libraries by the American Hospital Association in order to identify any trends in hospital libraries, roles of librarians, and library services. A web-based hospital library report form based on the survey questions was also developed to more quickly identify changes in the status of hospital libraries on an ongoing basis. The greatest change in library services between 1989 and 2005/06 was in the area of access to information, with 40% more of the respondents providing access to commercial online services, 100% more providing access to Internet resources, and 28% more providing training in database searching and use of information resources. Twenty-nine percent (n = 587) of the 2005/06 respondents reported a decrease in staff over the last 5 years. Survey data support reported trends of consolidation of hospitals and hospital libraries and additions of new services. These services have likely required librarians to acquire new skills. It is hoped that future surveys will be undertaken to continue to study these trends.

Trends in hospital librarianship and hospital library services: 1989 to 2006

PubMed Central

Thibodeau, Patricia L.; Funk, Carla J.

2009-01-01

Objective: The research studied the status of hospital librarians and library services to better inform the Medical Library Association's advocacy activities. Methods: The Vital Pathways Survey Subcommittee of the Task Force on Vital Pathways for Hospital Librarians distributed a web-based survey to hospital librarians and academic health sciences library directors. The survey results were compared to data collected in a 1989 survey of hospital libraries by the American Hospital Association in order to identify any trends in hospital libraries, roles of librarians, and library services. A web-based hospital library report form based on the survey questions was also developed to more quickly identify changes in the status of hospital libraries on an ongoing basis. Results: The greatest change in library services between 1989 and 2005/06 was in the area of access to information, with 40% more of the respondents providing access to commercial online services, 100% more providing access to Internet resources, and 28% more providing training in database searching and use of information resources. Twenty-nine percent (n = 587) of the 2005/06 respondents reported a decrease in staff over the last 5 years. Conclusions: Survey data support reported trends of consolidation of hospitals and hospital libraries and additions of new services. These services have likely required librarians to acquire new skills. It is hoped that future surveys will be undertaken to continue to study these trends. PMID:19851491

The importance of nature's invisible fabric: food web structure mediates modeled responses to river restoration

NASA Astrophysics Data System (ADS)

Bellmore, R.; Benjamin, J.; Newsom, M.; Bountry, J.; Dombroski, D.

2016-12-01

Restoration is frequently aimed at the recovery of target species, but also influences the larger food web in which these species participate. Effects of restoration on this broader network of organisms can influence target species both directly and indirectly via changes in energy flow through food webs. To help incorporate these complexities into river restoration planning we constructed a food web model that links river food web dynamics to in-stream physical habitat and riparian vegetation conditions. We present an application of this model to the Methow River, Washington (USA), a location of on-going restoration aimed at recovering salmon. Three restoration strategies were simulated: riparian vegetation restoration, nutrient augmentation via salmon carcass addition, and floodplain reconnection. To explore how food web structure mediates responses to these actions, we modified the food web by adding populations of invasive aquatic snails and nonnative fish. Simulations suggest that floodplain reconnection may be a better strategy than carcass addition and vegetation planting for improving conditions for salmon in this river segment. However, modeled responses were strongly sensitive to changes in the structure of the food web. The addition of invasive snails and nonnative fishes modified pathways of energy through the food web, which negated restoration improvements. This finding illustrates that forecasting responses to restoration may require accounting for the structure of food webs, and that changes in this structure—as might be expected with the spread of invasive species—could compromise restoration outcomes. By elucidating the direct and indirect pathways by which restoration affects target species, dynamic food web models can improve restoration planning by fostering a deeper understanding of system connectedness and dynamics.

MelanomaDB: A Web Tool for Integrative Analysis of Melanoma Genomic Information to Identify Disease-Associated Molecular Pathways

PubMed Central

Trevarton, Alexander J.; Mann, Michael B.; Knapp, Christoph; Araki, Hiromitsu; Wren, Jonathan D.; Stones-Havas, Steven; Black, Michael A.; Print, Cristin G.

2013-01-01

Despite on-going research, metastatic melanoma survival rates remain low and treatment options are limited. Researchers can now access a rapidly growing amount of molecular and clinical information about melanoma. This information is becoming difficult to assemble and interpret due to its dispersed nature, yet as it grows it becomes increasingly valuable for understanding melanoma. Integration of this information into a comprehensive resource to aid rational experimental design and patient stratification is needed. As an initial step in this direction, we have assembled a web-accessible melanoma database, MelanomaDB, which incorporates clinical and molecular data from publically available sources, which will be regularly updated as new information becomes available. This database allows complex links to be drawn between many different aspects of melanoma biology: genetic changes (e.g., mutations) in individual melanomas revealed by DNA sequencing, associations between gene expression and patient survival, data concerning drug targets, biomarkers, druggability, and clinical trials, as well as our own statistical analysis of relationships between molecular pathways and clinical parameters that have been produced using these data sets. The database is freely available at http://genesetdb.auckland.ac.nz/melanomadb/about.html. A subset of the information in the database can also be accessed through a freely available web application in the Illumina genomic cloud computing platform BaseSpace at http://www.biomatters.com/apps/melanoma-profiler-for-research. The MelanomaDB database illustrates dysregulation of specific signaling pathways across 310 exome-sequenced melanomas and in individual tumors and identifies the distribution of somatic variants in melanoma. We suggest that MelanomaDB can provide a context in which to interpret the tumor molecular profiles of individual melanoma patients relative to biological information and available drug therapies. PMID:23875173

TimeXNet Web: Identifying cellular response networks from diverse omics time-course data.

PubMed

Tan, Phit Ling; López, Yosvany; Nakai, Kenta; Patil, Ashwini

2018-05-14

Condition-specific time-course omics profiles are frequently used to study cellular response to stimuli and identify associated signaling pathways. However, few online tools allow users to analyze multiple types of high-throughput time-course data. TimeXNet Web is a web server that extracts a time-dependent gene/protein response network from time-course transcriptomic, proteomic or phospho-proteomic data, and an input interaction network. It classifies the given genes/proteins into time-dependent groups based on the time of their highest activity and identifies the most probable paths connecting genes/proteins in consecutive groups. The response sub-network is enriched in activated genes/proteins and contains novel regulators that do not show any observable change in the input data. Users can view the resultant response network and analyze it for functional enrichment. TimeXNet Web supports the analysis of high-throughput data from multiple species by providing high quality, weighted protein-protein interaction networks for 12 model organisms. http://txnet.hgc.jp/. ashwini@hgc.jp. Supplementary data are available at Bioinformatics online.

An indicator-based evaluation of Black Sea food web dynamics during 1960-2000

NASA Astrophysics Data System (ADS)

Akoglu, Ekin; Salihoglu, Baris; Libralato, Simone; Oguz, Temel; Solidoro, Cosimo

2014-06-01

Four Ecopath mass-balance models were implemented for evaluating the structure and function of the Black Sea ecosystem using several ecological indicators during four distinctive periods (1960s, 1980-1987, 1988-1994 and 1995-2000). The results exemplify how the Black Sea ecosystem structure started to change after the 1960s as a result of a series of trophic transformations, i.e., shifts in the energy flow pathways through the food web. These transformations were initiated by anthropogenic factors, such as eutrophication and overfishing, that led to the transfer of large quantities of energy to the trophic dead-end species, which had no natural predators in the ecosystem, i.e., jellyfish whose biomass increased from 0.03 g C m- 2 in 1960-1969 to 0.933 g C m- 2 in 1988-1994. Concurrently, an alternative short pathway for energy transfer was formed that converted significant amounts of system production back to detritus. This decreased the transfer efficiency of energy flow from the primary producers to the higher trophic levels from 9% in the 1960s to 3% between 1980 and 1987. We conclude that the anchovy stock collapse and successful establishment of the alien comb-jelly Mnemiopsis in 1989 were rooted in the trophic interactions in the food web, all of which were exacerbated because of the long-term establishment of a combination of anthropogenic stressors.

A user-friendly mathematical modelling web interface to assist local decision making in the fight against drug-resistant tuberculosis.

PubMed

Ragonnet, Romain; Trauer, James M; Denholm, Justin T; Marais, Ben J; McBryde, Emma S

2017-05-30

Multidrug-resistant and rifampicin-resistant tuberculosis (MDR/RR-TB) represent an important challenge for global tuberculosis (TB) control. The high rates of MDR/RR-TB observed among re-treatment cases can arise from diverse pathways: de novo amplification during initial treatment, inappropriate treatment of undiagnosed MDR/RR-TB, relapse despite appropriate treatment, or reinfection with MDR/RR-TB. Mathematical modelling allows quantification of the contribution made by these pathways in different settings. This information provides valuable insights for TB policy-makers, allowing better contextualised solutions. However, mathematical modelling outputs need to consider local data and be easily accessible to decision makers in order to improve their usefulness. We present a user-friendly web-based modelling interface, which can be used by people without technical knowledge. Users can input their own parameter values and produce estimates for their specific setting. This innovative tool provides easy access to mathematical modelling outputs that are highly relevant to national TB control programs. In future, the same approach could be applied to a variety of modelling applications, enhancing local decision making.

Using Answer Set Programming to Integrate RNA Expression with Signalling Pathway Information to Infer How Mutations Affect Ageing

PubMed Central

Papatheodorou, Irene; Ziehm, Matthias; Wieser, Daniela; Alic, Nazif; Partridge, Linda; Thornton, Janet M.

2012-01-01

A challenge of systems biology is to integrate incomplete knowledge on pathways with existing experimental data sets and relate these to measured phenotypes. Research on ageing often generates such incomplete data, creating difficulties in integrating RNA expression with information about biological processes and the phenotypes of ageing, including longevity. Here, we develop a logic-based method that employs Answer Set Programming, and use it to infer signalling effects of genetic perturbations, based on a model of the insulin signalling pathway. We apply our method to RNA expression data from Drosophila mutants in the insulin pathway that alter lifespan, in a foxo dependent fashion. We use this information to deduce how the pathway influences lifespan in the mutant animals. We also develop a method for inferring the largest common sub-paths within each of our signalling predictions. Our comparisons reveal consistent homeostatic mechanisms across both long- and short-lived mutants. The transcriptional changes observed in each mutation usually provide negative feedback to signalling predicted for that mutation. We also identify an S6K-mediated feedback in two long-lived mutants that suggests a crosstalk between these pathways in mutants of the insulin pathway, in vivo. By formulating the problem as a logic-based theory in a qualitative fashion, we are able to use the efficient search facilities of Answer Set Programming, allowing us to explore larger pathways, combine molecular changes with pathways and phenotype and infer effects on signalling in in vivo, whole-organism, mutants, where direct signalling stimulation assays are difficult to perform. Our methods are available in the web-service NetEffects: http://www.ebi.ac.uk/thornton-srv/software/NetEffects. PMID:23251396

Using answer set programming to integrate RNA expression with signalling pathway information to infer how mutations affect ageing.

PubMed

Papatheodorou, Irene; Ziehm, Matthias; Wieser, Daniela; Alic, Nazif; Partridge, Linda; Thornton, Janet M

2012-01-01

A challenge of systems biology is to integrate incomplete knowledge on pathways with existing experimental data sets and relate these to measured phenotypes. Research on ageing often generates such incomplete data, creating difficulties in integrating RNA expression with information about biological processes and the phenotypes of ageing, including longevity. Here, we develop a logic-based method that employs Answer Set Programming, and use it to infer signalling effects of genetic perturbations, based on a model of the insulin signalling pathway. We apply our method to RNA expression data from Drosophila mutants in the insulin pathway that alter lifespan, in a foxo dependent fashion. We use this information to deduce how the pathway influences lifespan in the mutant animals. We also develop a method for inferring the largest common sub-paths within each of our signalling predictions. Our comparisons reveal consistent homeostatic mechanisms across both long- and short-lived mutants. The transcriptional changes observed in each mutation usually provide negative feedback to signalling predicted for that mutation. We also identify an S6K-mediated feedback in two long-lived mutants that suggests a crosstalk between these pathways in mutants of the insulin pathway, in vivo. By formulating the problem as a logic-based theory in a qualitative fashion, we are able to use the efficient search facilities of Answer Set Programming, allowing us to explore larger pathways, combine molecular changes with pathways and phenotype and infer effects on signalling in in vivo, whole-organism, mutants, where direct signalling stimulation assays are difficult to perform. Our methods are available in the web-service NetEffects: http://www.ebi.ac.uk/thornton-srv/software/NetEffects.

Stable Isotope Tracers of Process in Great Lakes Food Webs

EPA Science Inventory

Stable isotope analyses of biota are now commonly used to discern trophic pathways between consumers and their foods. However, those same isotope data also hold information about processes that influence the physicochemical setting of food webs as well as biological processes ope...

Guano-Derived Nutrient Subsidies Drive Food Web Structure in Coastal Ponds.

PubMed

Vizzini, Salvatrice; Signa, Geraldina; Mazzola, Antonio

2016-01-01

A stable isotope study was carried out seasonally in three coastal ponds (Marinello system, Italy) affected by different gull guano input to investigate the effect of nutrient subsidies on food web structure and dynamics. A marked 15N enrichment occurred in the pond receiving the highest guano input, indicating that gull-derived fertilization (guanotrophication) had a strong localised effect and flowed across trophic levels. The main food web response to guanotrophication was an overall erosion of the benthic pathway in favour of the planktonic. Subsidized primary consumers, mostly deposit feeders, switched their diet according to organic matter source availability. Secondary consumers and, in particular, fish from the guanotrophic pond, acted as couplers of planktonic and benthic pathways and showed an omnivorous trophic behaviour. Food web structure showed substantial variability among ponds and a marked seasonality in the subsidized one: an overall simplification was evident only in summer when guano input maximises its trophic effects, while higher trophic diversity and complexity resulted when guano input was low to moderate.

Guano-Derived Nutrient Subsidies Drive Food Web Structure in Coastal Ponds

PubMed Central

Vizzini, Salvatrice; Signa, Geraldina; Mazzola, Antonio

2016-01-01

A stable isotope study was carried out seasonally in three coastal ponds (Marinello system, Italy) affected by different gull guano input to investigate the effect of nutrient subsidies on food web structure and dynamics. A marked 15N enrichment occurred in the pond receiving the highest guano input, indicating that gull-derived fertilization (guanotrophication) had a strong localised effect and flowed across trophic levels. The main food web response to guanotrophication was an overall erosion of the benthic pathway in favour of the planktonic. Subsidized primary consumers, mostly deposit feeders, switched their diet according to organic matter source availability. Secondary consumers and, in particular, fish from the guanotrophic pond, acted as couplers of planktonic and benthic pathways and showed an omnivorous trophic behaviour. Food web structure showed substantial variability among ponds and a marked seasonality in the subsidized one: an overall simplification was evident only in summer when guano input maximises its trophic effects, while higher trophic diversity and complexity resulted when guano input was low to moderate. PMID:26953794

Interactive effects of fire and large herbivores on web-building spiders.

PubMed

Foster, C N; Barton, P S; Wood, J T; Lindenmayer, D B

2015-09-01

Altered disturbance regimes are a major driver of biodiversity loss worldwide. Maintaining or re-creating natural disturbance regimes is therefore the focus of many conservation programmes. A key challenge, however, is to understand how co-occurring disturbances interact to affect biodiversity. We experimentally tested for the interactive effects of prescribed fire and large macropod herbivores on the web-building spider assemblage of a eucalypt forest understorey and investigated the role of vegetation in mediating these effects using path analysis. Fire had strong negative effects on the density of web-building spiders, which were partly mediated by effects on vegetation structure, while negative effects of large herbivores on web density were not related to changes in vegetation. Fire amplified the effects of large herbivores on spiders, both via vegetation-mediated pathways and by increasing herbivore activity. The importance of vegetation-mediated pathways and fire-herbivore interactions differed for web density and richness and also differed between web types. Our results demonstrate that for some groups of web-building spiders, the effects of co-occurring disturbance drivers may be mostly additive, whereas for other groups, interactions between drivers can amplify disturbance effects. In our study system, the use of prescribed fire in the presence of high densities of herbivores could lead to reduced densities and altered composition of web-building spiders, with potential cascading effects through the arthropod food web. Our study highlights the importance of considering both the independent and interactive effects of disturbances, as well as the mechanisms driving their effects, in the management of disturbance regimes.

The CASPER Virtual Physics Circus

NASA Astrophysics Data System (ADS)

Carmona-Reyes, Jorge; Harris, Brandon; Chen, Mudi; Matthews, Lorin; Hyde, Truell

2013-10-01

CASPER's Virtual Physics Circus (VPC) is based on the long-running CASPER Physics Circus and is the most recent component in CASPER's ``Seamless Pathway'' educational outreach initiative. The VPC was developed by an interdisciplinary group of physicists, web-designers and educators and employs both web and video game environments to provide students and teachers with engaging, fast-paced educational activities. Access to an integrated curriculum and video library, aligned to both the TEKS (Texas Essentials Knowledge and Skill) and the National Science and Mathematics Standards, is also part of the VPC package. In this talk an initial beta-test of the VPC, conducted for a central Texas independent school district, will be discussed. Future plans for both expansion and translation into Spanish will also be discussed.

ICSNPathway: identify candidate causal SNPs and pathways from genome-wide association study by one analytical framework.

PubMed

Zhang, Kunlin; Chang, Suhua; Cui, Sijia; Guo, Liyuan; Zhang, Liuyan; Wang, Jing

2011-07-01

Genome-wide association study (GWAS) is widely utilized to identify genes involved in human complex disease or some other trait. One key challenge for GWAS data interpretation is to identify causal SNPs and provide profound evidence on how they affect the trait. Currently, researches are focusing on identification of candidate causal variants from the most significant SNPs of GWAS, while there is lack of support on biological mechanisms as represented by pathways. Although pathway-based analysis (PBA) has been designed to identify disease-related pathways by analyzing the full list of SNPs from GWAS, it does not emphasize on interpreting causal SNPs. To our knowledge, so far there is no web server available to solve the challenge for GWAS data interpretation within one analytical framework. ICSNPathway is developed to identify candidate causal SNPs and their corresponding candidate causal pathways from GWAS by integrating linkage disequilibrium (LD) analysis, functional SNP annotation and PBA. ICSNPathway provides a feasible solution to bridge the gap between GWAS and disease mechanism study by generating hypothesis of SNP → gene → pathway(s). The ICSNPathway server is freely available at http://icsnpathway.psych.ac.cn/.

An interactive web-based application for Comprehensive Analysis of RNAi-screen Data.

PubMed

Dutta, Bhaskar; Azhir, Alaleh; Merino, Louis-Henri; Guo, Yongjian; Revanur, Swetha; Madhamshettiwar, Piyush B; Germain, Ronald N; Smith, Jennifer A; Simpson, Kaylene J; Martin, Scott E; Buehler, Eugen; Beuhler, Eugen; Fraser, Iain D C

2016-02-23

RNAi screens are widely used in functional genomics. Although the screen data can be susceptible to a number of experimental biases, many of these can be corrected by computational analysis. For this purpose, here we have developed a web-based platform for integrated analysis and visualization of RNAi screen data named CARD (for Comprehensive Analysis of RNAi Data; available at https://card.niaid.nih.gov). CARD allows the user to seamlessly carry out sequential steps in a rigorous data analysis workflow, including normalization, off-target analysis, integration of gene expression data, optimal thresholds for hit selection and network/pathway analysis. To evaluate the utility of CARD, we describe analysis of three genome-scale siRNA screens and demonstrate: (i) a significant increase both in selection of subsequently validated hits and in rejection of false positives, (ii) an increased overlap of hits from independent screens of the same biology and (iii) insight to microRNA (miRNA) activity based on siRNA seed enrichment.

An interactive web-based application for Comprehensive Analysis of RNAi-screen Data

PubMed Central

Dutta, Bhaskar; Azhir, Alaleh; Merino, Louis-Henri; Guo, Yongjian; Revanur, Swetha; Madhamshettiwar, Piyush B.; Germain, Ronald N.; Smith, Jennifer A.; Simpson, Kaylene J.; Martin, Scott E.; Beuhler, Eugen; Fraser, Iain D. C.

2016-01-01

RNAi screens are widely used in functional genomics. Although the screen data can be susceptible to a number of experimental biases, many of these can be corrected by computational analysis. For this purpose, here we have developed a web-based platform for integrated analysis and visualization of RNAi screen data named CARD (for Comprehensive Analysis of RNAi Data; available at https://card.niaid.nih.gov). CARD allows the user to seamlessly carry out sequential steps in a rigorous data analysis workflow, including normalization, off-target analysis, integration of gene expression data, optimal thresholds for hit selection and network/pathway analysis. To evaluate the utility of CARD, we describe analysis of three genome-scale siRNA screens and demonstrate: (i) a significant increase both in selection of subsequently validated hits and in rejection of false positives, (ii) an increased overlap of hits from independent screens of the same biology and (iii) insight to microRNA (miRNA) activity based on siRNA seed enrichment. PMID:26902267

Impact of nitrogen deposition on forest and lake food webs in nitrogen-limited environments.

PubMed

Meunier, Cédric L; Gundale, Michael J; Sánchez, Irene S; Liess, Antonia

2016-01-01

Increased reactive nitrogen (Nr ) deposition has raised the amount of N available to organisms and has greatly altered the transfer of energy through food webs, with major consequences for trophic dynamics. The aim of this review was to: (i) clarify the direct and indirect effects of Nr deposition on forest and lake food webs in N-limited biomes, (ii) compare and contrast how aquatic and terrestrial systems respond to increased Nr deposition, and (iii) identify how the nutrient pathways within and between ecosystems change in response to Nr deposition. We present that Nr deposition releases primary producers from N limitation in both forest and lake ecosystems and raises plants' N content which in turn benefits herbivores with high N requirements. Such trophic effects are coupled with a general decrease in biodiversity caused by different N-use efficiencies; slow-growing species with low rates of N turnover are replaced by fast-growing species with high rates of N turnover. In contrast, Nr deposition diminishes below-ground production in forests, due to a range of mechanisms that reduce microbial biomass, and decreases lake benthic productivity by switching herbivore growth from N to phosphorus (P) limitation, and by intensifying P limitation of benthic fish. The flow of nutrients between ecosystems is expected to change with increasing Nr deposition. Due to higher litter production and more intense precipitation, more terrestrial matter will enter lakes. This will benefit bacteria and will in turn boost the microbial food web. Additionally, Nr deposition promotes emergent insects, which subsidize the terrestrial food web as prey for insectivores or by dying and decomposing on land. So far, most studies have examined Nr -deposition effects on the food web base, whereas our review highlights that changes at the base of food webs substantially impact higher trophic levels and therefore food web structure and functioning. © 2015 John Wiley & Sons Ltd.

Genomic Enzymology: Web Tools for Leveraging Protein Family Sequence-Function Space and Genome Context to Discover Novel Functions.

PubMed

Gerlt, John A

2017-08-22

The exponentially increasing number of protein and nucleic acid sequences provides opportunities to discover novel enzymes, metabolic pathways, and metabolites/natural products, thereby adding to our knowledge of biochemistry and biology. The challenge has evolved from generating sequence information to mining the databases to integrating and leveraging the available information, i.e., the availability of "genomic enzymology" web tools. Web tools that allow identification of biosynthetic gene clusters are widely used by the natural products/synthetic biology community, thereby facilitating the discovery of novel natural products and the enzymes responsible for their biosynthesis. However, many novel enzymes with interesting mechanisms participate in uncharacterized small-molecule metabolic pathways; their discovery and functional characterization also can be accomplished by leveraging information in protein and nucleic acid databases. This Perspective focuses on two genomic enzymology web tools that assist the discovery novel metabolic pathways: (1) Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST) for generating sequence similarity networks to visualize and analyze sequence-function space in protein families and (2) Enzyme Function Initiative-Genome Neighborhood Tool (EFI-GNT) for generating genome neighborhood networks to visualize and analyze the genome context in microbial and fungal genomes. Both tools have been adapted to other applications to facilitate target selection for enzyme discovery and functional characterization. As the natural products community has demonstrated, the enzymology community needs to embrace the essential role of web tools that allow the protein and genome sequence databases to be leveraged for novel insights into enzymological problems.

Benthic and Pelagic Pathways of Methylmercury Bioaccumulation in Estuarine Food Webs of the Northeast United States

PubMed Central

Chen, Celia Y.; Borsuk, Mark E.; Bugge, Deenie M.; Hollweg, Terill; Balcom, Prentiss H.; Ward, Darren M.; Williams, Jason; Mason, Robert P.

2014-01-01

Methylmercury (MeHg) is a contaminant of global concern that bioaccumulates and bioamagnifies in marine food webs. Lower trophic level fauna are important conduits of MeHg from sediment and water to estuarine and coastal fish harvested for human consumption. However, the sources and pathways of MeHg to these coastal fisheries are poorly known particularly the potential for transfer of MeHg from the sediment to biotic compartments. Across a broad gradient of human land impacts, we analyzed MeHg concentrations in food webs at ten estuarine sites in the Northeast US (from the Hackensack Meadowlands, NJ to the Gulf of Maine). MeHg concentrations in water column particulate material, but not in sediments, were predictive of MeHg concentrations in fish (killifish and Atlantic silversides). Moreover, MeHg concentrations were higher in pelagic fauna than in benthic-feeding fauna suggesting that MeHg delivery to the water column from methylation sites from within or outside of the estuary may be an important driver of MeHg bioaccumulation in estuarine pelagic food webs. In contrast, bulk sediment MeHg concentrations were only predictive of concentrations of MeHg in the infaunal worms. Our results across a broad gradient of sites demonstrate that the pathways of MeHg to lower trophic level estuarine organisms are distinctly different between benthic deposit feeders and forage fish. Thus, even in systems with contaminated sediments, transfer of MeHg into estuarine food webs maybe driven more by the efficiency of processes that determine MeHg input and bioavailability in the water column. PMID:24558491

Genomic Enzymology: Web Tools for Leveraging Protein Family Sequence–Function Space and Genome Context to Discover Novel Functions

PubMed Central

2017-01-01

The exponentially increasing number of protein and nucleic acid sequences provides opportunities to discover novel enzymes, metabolic pathways, and metabolites/natural products, thereby adding to our knowledge of biochemistry and biology. The challenge has evolved from generating sequence information to mining the databases to integrating and leveraging the available information, i.e., the availability of “genomic enzymology” web tools. Web tools that allow identification of biosynthetic gene clusters are widely used by the natural products/synthetic biology community, thereby facilitating the discovery of novel natural products and the enzymes responsible for their biosynthesis. However, many novel enzymes with interesting mechanisms participate in uncharacterized small-molecule metabolic pathways; their discovery and functional characterization also can be accomplished by leveraging information in protein and nucleic acid databases. This Perspective focuses on two genomic enzymology web tools that assist the discovery novel metabolic pathways: (1) Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST) for generating sequence similarity networks to visualize and analyze sequence–function space in protein families and (2) Enzyme Function Initiative-Genome Neighborhood Tool (EFI-GNT) for generating genome neighborhood networks to visualize and analyze the genome context in microbial and fungal genomes. Both tools have been adapted to other applications to facilitate target selection for enzyme discovery and functional characterization. As the natural products community has demonstrated, the enzymology community needs to embrace the essential role of web tools that allow the protein and genome sequence databases to be leveraged for novel insights into enzymological problems. PMID:28826221

Food web structure in exotic and native mangroves: A Hawaii-Puerto Rico comparison

USGS Publications Warehouse

Demopoulos, A.W.J.; Fry, B.; Smith, C.R.

2007-01-01

Plant invasions can fundamentally alter detrital inputs and the structure of detritus-based food webs. We examined the detrital pathways in mangrove food webs in native (Puerto Rican) and introduced (Hawaiian) Rhizophora mangle forests using a dual isotope approach and a mixing model. Based on trophic-level fractionation of 0-1??? for ?? 13C and 2-3??? for ?? 15N, among the invertebrates, only nematodes, oligochaetes, and nereid polychaetes from native mangroves exhibited stable isotopes consistent with a mangrove-derived diet. Certain fauna, in particular tubificid oligochaetes, had ?? 13C values consistent with the consumption of mangrove leaves, but they were depleted in 15N, suggesting their primary nitrogen source was low in 15N, and was possibly N 2-fixing bacteria. In introduced mangroves, all feeding groups appeared to rely heavily on non-mangrove sources, especially phytoplankton inputs. Mixing model results and discriminant analysis showed clear separation of introduced and native mangrove sites based on differential food source utilization within feeding groups, with stronger and more diverse use of benthic foods observed in native forests. Observed differences between native and invasive mangrove food webs may be due to Hawaiian detritivores being poorly adapted to utilizing the tannin-rich, nitrogen-poor mangrove detritus. In addition, differential utilization of mangrove detritus between native and introduced mangroves may be a consequence of forest age. We postulate that increasing mangrove forest age may promote diversification of bacterial food webs important in N and S cycling. Our results also suggest a potentially important role for sulfur bacteria in supporting the most abundant infaunal consumers, nematodes, in the most mature systems. ?? 2007 Springer-Verlag.

Genomic Target Database (GTD): A database of potential targets in human pathogenic bacteria

PubMed Central

Barh, Debmalya; Kumar, Anil; Misra, Amarendra Narayana

2009-01-01

A Genomic Target Database (GTD) has been developed having putative genomic drug targets for human bacterial pathogens. The selected pathogens are either drug resistant or vaccines are yet to be developed against them. The drug targets have been identified using subtractive genomics approaches and these are subsequently classified into Drug targets in pathogen specific unique metabolic pathways,Drug targets in host-pathogen common metabolic pathways, andMembrane localized drug targets. HTML code is used to link each target to its various properties and other available public resources. Essential resources and tools for subtractive genomic analysis, sub-cellular localization, vaccine and drug designing are also mentioned. To the best of authors knowledge, no such database (DB) is presently available that has listed metabolic pathways and membrane specific genomic drug targets based on subtractive genomics. Listed targets in GTD are readily available resource in developing drug and vaccine against the respective pathogen, its subtypes, and other family members. Currently GTD contains 58 drug targets for four pathogens. Shortly, drug targets for six more pathogens will be listed. Availability GTD is available at IIOAB website http://www.iioab.webs.com/GTD.htm. It can also be accessed at http://www.iioabdgd.webs.com.GTD is free for academic research and non-commercial use only. Commercial use is strictly prohibited without prior permission from IIOAB. PMID:20011153

EDdb: a web resource for eating disorder and its application to identify an extended adipocytokine signaling pathway related to eating disorder.

PubMed

Zhao, Min; Li, XiaoMo; Qu, Hong

2013-12-01

Eating disorder is a group of physiological and psychological disorders affecting approximately 1% of the female population worldwide. Although the genetic epidemiology of eating disorder is becoming increasingly clear with accumulated studies, the underlying molecular mechanisms are still unclear. Recently, integration of various high-throughput data expanded the range of candidate genes and started to generate hypotheses for understanding potential pathogenesis in complex diseases. This article presents EDdb (Eating Disorder database), the first evidence-based gene resource for eating disorder. Fifty-nine experimentally validated genes from the literature in relation to eating disorder were collected as the core dataset. Another four datasets with 2824 candidate genes across 601 genome regions were expanded based on the core dataset using different criteria (e.g., protein-protein interactions, shared cytobands, and related complex diseases). Based on human protein-protein interaction data, we reconstructed a potential molecular sub-network related to eating disorder. Furthermore, with an integrative pathway enrichment analysis of genes in EDdb, we identified an extended adipocytokine signaling pathway in eating disorder. Three genes in EDdb (ADIPO (adiponectin), TNF (tumor necrosis factor) and NR3C1 (nuclear receptor subfamily 3, group C, member 1)) link the KEGG (Kyoto Encyclopedia of Genes and Genomes) "adipocytokine signaling pathway" with the BioCarta "visceral fat deposits and the metabolic syndrome" pathway to form a joint pathway. In total, the joint pathway contains 43 genes, among which 39 genes are related to eating disorder. As the first comprehensive gene resource for eating disorder, EDdb ( http://eddb.cbi.pku.edu.cn ) enables the exploration of gene-disease relationships and cross-talk mechanisms between related disorders. Through pathway statistical studies, we revealed that abnormal body weight caused by eating disorder and obesity may both be related to dysregulation of the novel joint pathway of adipocytokine signaling. In addition, this joint pathway may be the common pathway for body weight regulation in complex human diseases related to unhealthy lifestyle.

Columba: an integrated database of proteins, structures, and annotations.

PubMed

Trissl, Silke; Rother, Kristian; Müller, Heiko; Steinke, Thomas; Koch, Ina; Preissner, Robert; Frömmel, Cornelius; Leser, Ulf

2005-03-31

Structural and functional research often requires the computation of sets of protein structures based on certain properties of the proteins, such as sequence features, fold classification, or functional annotation. Compiling such sets using current web resources is tedious because the necessary data are spread over many different databases. To facilitate this task, we have created COLUMBA, an integrated database of annotations of protein structures. COLUMBA currently integrates twelve different databases, including PDB, KEGG, Swiss-Prot, CATH, SCOP, the Gene Ontology, and ENZYME. The database can be searched using either keyword search or data source-specific web forms. Users can thus quickly select and download PDB entries that, for instance, participate in a particular pathway, are classified as containing a certain CATH architecture, are annotated as having a certain molecular function in the Gene Ontology, and whose structures have a resolution under a defined threshold. The results of queries are provided in both machine-readable extensible markup language and human-readable format. The structures themselves can be viewed interactively on the web. The COLUMBA database facilitates the creation of protein structure data sets for many structure-based studies. It allows to combine queries on a number of structure-related databases not covered by other projects at present. Thus, information on both many and few protein structures can be used efficiently. The web interface for COLUMBA is available at http://www.columba-db.de.

Perfluoroalkyl Acids (PFAAs) and Selected Precursors in the Baltic Sea Environment: Do Precursors Play a Role in Food Web Accumulation of PFAAs?

PubMed

Gebbink, Wouter A; Bignert, Anders; Berger, Urs

2016-06-21

The present study examined the presence of perfluoroalkyl acids (PFAAs) and selected precursors in the Baltic Sea abiotic environment and guillemot food web, and investigated the relative importance of precursors in food web accumulation of PFAAs. Sediment, water, zooplankton, herring, sprat, and guillemot eggs were analyzed for perfluoroalkane sulfonic acids (PFSAs; C4,6,8,10) and perfluoroalkyl carboxylic acids (PFCAs; C6-15) along with six perfluoro-octane sulfonic acid (PFOS) precursors and 11 polyfluoroalkyl phosphoric acid diesters (diPAPs). FOSA, FOSAA and its methyl and ethyl derivatives (Me- and EtFOSAA), and 6:2/6:2 diPAP were detected in sediment and water. While FOSA and the three FOSAAs were detected in all biota, a total of nine diPAPs were only detected in zooplankton. Concentrations of PFOS precursors and diPAPs exceeded PFOS and PFCA concentrations, respectively, in zooplankton, but not in fish and guillemot eggs. Although PFOS precursors were present at all trophic levels, they appear to play a minor role in food web accumulation of PFOS based on PFOS precursor/PFOS ratios and PFOS and FOSA isomer patterns. The PFCA pattern in fish could not be explained by the intake pattern based on PFCAs and analyzed precursors, that is, diPAPs. Exposure to additional precursors might therefore be a dominant exposure pathway compared to direct PFCA exposure for fish.

PyPathway: Python Package for Biological Network Analysis and Visualization.

PubMed

Xu, Yang; Luo, Xiao-Chun

2018-05-01

Life science studies represent one of the biggest generators of large data sets, mainly because of rapid sequencing technological advances. Biological networks including interactive networks and human curated pathways are essential to understand these high-throughput data sets. Biological network analysis offers a method to explore systematically not only the molecular complexity of a particular disease but also the molecular relationships among apparently distinct phenotypes. Currently, several packages for Python community have been developed, such as BioPython and Goatools. However, tools to perform comprehensive network analysis and visualization are still needed. Here, we have developed PyPathway, an extensible free and open source Python package for functional enrichment analysis, network modeling, and network visualization. The network process module supports various interaction network and pathway databases such as Reactome, WikiPathway, STRING, and BioGRID. The network analysis module implements overrepresentation analysis, gene set enrichment analysis, network-based enrichment, and de novo network modeling. Finally, the visualization and data publishing modules enable users to share their analysis by using an easy web application. For package availability, see the first Reference.

Following the flow of ornithogenic nutrients through the Arctic marine coastal food webs

NASA Astrophysics Data System (ADS)

Zmudczyńska-Skarbek, Katarzyna; Balazy, Piotr

2017-04-01

Arctic colonial seabirds are recognized as effective fertilizers of terrestrial ecosystems by delivering marine-origin nutrients to the vicinities of their nesting sites. A proportion of this ornithogenic matter is then thought to return to the sea and, concentrated within a smaller area, locally provides additional nutrients for the nearshore marine communities. The aim of this study was to assess the presence and impact of local ornithogenic enrichment on two important elements of the Arctic coastal food web: (1) the planktonic pathway originating in the surface water, and (2) the benthic pathway based on benthic primary production. We sampled two areas in Isfjorden (Spitsbergen): one located below a coastal mixed breeding colony of guillemots and kittiwakes, and a control area not influenced by the colony. Slightly higher nitrogen stable isotope ratios (δ15N) were found in particulate organic matter suspended in the surface water (POM), sedimentary organic matter (SOM) from outside the zone of dense kelp forest, and the predatory/scavenging whelks Buccinum sp. collected below the seabird colony (the components recognized as following the planktonic path). In contrast, no ornithogenic isotopic enrichment was detected in the herbivorous gastropod Margarites helicinus or in SOM from the kelp zone (benthic path). The data are compatible with those obtained from the same location a year before, showing δ15N enrichment in predatory/scavenging hermit crabs Pagurus pubescens below the seabird, and no such changes in kelps Saccharina latissima or their presumed consumers, sea urchins Strongylocentrotus droebachiensis (Zmudczyńska-Skarbek et al., 2015a). The results suggest that, in the conditions of periodic, short-term pulses of ornithogenic nutrient inputs to the local marine environment, which typify the short High Arctic summer, planktonic organisms are the initial organisms to incorporate these nutrients before transfer to the benthic food web via pelagic-benthic coupling. However, the supply of ornithogenic resources alone is insufficient to support benthic producers and the trophic pathways based on them. Overall, the ornithogenic subsidies are not a major nutrient source for marine organisms from below the seabird colony.

SpirPro: A Spirulina proteome database and web-based tools for the analysis of protein-protein interactions at the metabolic level in Spirulina (Arthrospira) platensis C1.

PubMed

Senachak, Jittisak; Cheevadhanarak, Supapon; Hongsthong, Apiradee

2015-07-29

Spirulina (Arthrospira) platensis is the only cyanobacterium that in addition to being studied at the molecular level and subjected to gene manipulation, can also be mass cultivated in outdoor ponds for commercial use as a food supplement. Thus, encountering environmental changes, including temperature stresses, is common during the mass production of Spirulina. The use of cyanobacteria as an experimental platform, especially for photosynthetic gene manipulation in plants and bacteria, is becoming increasingly important. Understanding the mechanisms and protein-protein interaction networks that underlie low- and high-temperature responses is relevant to Spirulina mass production. To accomplish this goal, high-throughput techniques such as OMICs analyses are used. Thus, large datasets must be collected, managed and subjected to information extraction. Therefore, databases including (i) proteomic analysis and protein-protein interaction (PPI) data and (ii) domain/motif visualization tools are required for potential use in temperature response models for plant chloroplasts and photosynthetic bacteria. A web-based repository was developed including an embedded database, SpirPro, and tools for network visualization. Proteome data were analyzed integrated with protein-protein interactions and/or metabolic pathways from KEGG. The repository provides various information, ranging from raw data (2D-gel images) to associated results, such as data from interaction and/or pathway analyses. This integration allows in silico analyses of protein-protein interactions affected at the metabolic level and, particularly, analyses of interactions between and within the affected metabolic pathways under temperature stresses for comparative proteomic analysis. The developed tool, which is coded in HTML with CSS/JavaScript and depicted in Scalable Vector Graphics (SVG), is designed for interactive analysis and exploration of the constructed network. SpirPro is publicly available on the web at http://spirpro.sbi.kmutt.ac.th . SpirPro is an analysis platform containing an integrated proteome and PPI database that provides the most comprehensive data on this cyanobacterium at the systematic level. As an integrated database, SpirPro can be applied in various analyses, such as temperature stress response networking analysis in cyanobacterial models and interacting domain-domain analysis between proteins of interest.

A Pyramid Scheme for Constructing Geologic Maps on Geobrowsers

NASA Astrophysics Data System (ADS)

Whitmeyer, S. J.; de Paor, D. G.; Daniels, J.; Jeremy, N.; Michael, R.; Santangelo, B.

2008-12-01

Hundreds of geologic maps have been draped onto Google Earth (GE) using the ground overlay tag of Keyhole Markup Language (KML) and dozens have been published on academic and survey web pages as downloadable KML or KMZ (zipped KML) files. The vast majority of these are small KML docs that link to single, large - often very large - image files (jpegs, tiffs, etc.) Files that exceed 50 MB in size defeat the purpose of GE as an interactive and responsive, and therefore fast, virtual terrain medium. KML supports super-overlays (a.k.a. image pyramids), which break large graphic files into manageable tiles that load only when they are in the visible region at a sufficient level of detail (LOD), and several automatic tile-generating applications have been written. The process of exporting map data from applications such as ArcGIS® to KML format is becoming more manageable but still poses challenges. Complications arise, for example, because of differences between grid-north at a point on a map and true north at the equivalent location on the virtual globe. In our recent field season, we devised ways of overcoming many of these obstacles in order to generate responsive, panable, zoomable geologic maps in which data is layered in a pyramid structure similar to the image pyramid used for default GE terrain. The structure of our KML code for each level of the pyramid is self-similar: (i) check whether the current tile is in the visible region, (ii) if so, render the current overlay, (iii) add the current data level, and (iv) using four network links, check the visibility and LOD of four nested tiles. By using this pyramid structure we provide the user with access to geologic and map data at multiple levels of observation. For example, when the viewpoint is distant, regional structures and stratigraphy (e.g. lithological groups and terrane boundaries) are visible. As the user zooms to lower elevations, formations and ultimately individual outcrops come into focus. The pyramid structure is ideally suited to geologic data which tends to be unevenly exposed across the earth's surface.

Mergeomics: a web server for identifying pathological pathways, networks, and key regulators via multidimensional data integration.

PubMed

Arneson, Douglas; Bhattacharya, Anindya; Shu, Le; Mäkinen, Ville-Petteri; Yang, Xia

2016-09-09

Human diseases are commonly the result of multidimensional changes at molecular, cellular, and systemic levels. Recent advances in genomic technologies have enabled an outpour of omics datasets that capture these changes. However, separate analyses of these various data only provide fragmented understanding and do not capture the holistic view of disease mechanisms. To meet the urgent needs for tools that effectively integrate multiple types of omics data to derive biological insights, we have developed Mergeomics, a computational pipeline that integrates multidimensional disease association data with functional genomics and molecular networks to retrieve biological pathways, gene networks, and central regulators critical for disease development. To make the Mergeomics pipeline available to a wider research community, we have implemented an online, user-friendly web server ( http://mergeomics. idre.ucla.edu/ ). The web server features a modular implementation of the Mergeomics pipeline with detailed tutorials. Additionally, it provides curated genomic resources including tissue-specific expression quantitative trait loci, ENCODE functional annotations, biological pathways, and molecular networks, and offers interactive visualization of analytical results. Multiple computational tools including Marker Dependency Filtering (MDF), Marker Set Enrichment Analysis (MSEA), Meta-MSEA, and Weighted Key Driver Analysis (wKDA) can be used separately or in flexible combinations. User-defined summary-level genomic association datasets (e.g., genetic, transcriptomic, epigenomic) related to a particular disease or phenotype can be uploaded and computed real-time to yield biologically interpretable results, which can be viewed online and downloaded for later use. Our Mergeomics web server offers researchers flexible and user-friendly tools to facilitate integration of multidimensional data into holistic views of disease mechanisms in the form of tissue-specific key regulators, biological pathways, and gene networks.

The Human EST Ontology Explorer: a tissue-oriented visualization system for ontologies distribution in human EST collections.

PubMed

Merelli, Ivan; Caprera, Andrea; Stella, Alessandra; Del Corvo, Marcello; Milanesi, Luciano; Lazzari, Barbara

2009-10-15

The NCBI dbEST currently contains more than eight million human Expressed Sequenced Tags (ESTs). This wide collection represents an important source of information for gene expression studies, provided it can be inspected according to biologically relevant criteria. EST data can be browsed using different dedicated web resources, which allow to investigate library specific gene expression levels and to make comparisons among libraries, highlighting significant differences in gene expression. Nonetheless, no tool is available to examine distributions of quantitative EST collections in Gene Ontology (GO) categories, nor to retrieve information concerning library-dependent EST involvement in metabolic pathways. In this work we present the Human EST Ontology Explorer (HEOE) http://www.itb.cnr.it/ptp/human_est_explorer, a web facility for comparison of expression levels among libraries from several healthy and diseased tissues. The HEOE provides library-dependent statistics on the distribution of sequences in the GO Direct Acyclic Graph (DAG) that can be browsed at each GO hierarchical level. The tool is based on large-scale BLAST annotation of EST sequences. Due to the huge number of input sequences, this BLAST analysis was performed with the aid of grid computing technology, which is particularly suitable to address data parallel task. Relying on the achieved annotation, library-specific distributions of ESTs in the GO Graph were inferred. A pathway-based search interface was also implemented, for a quick evaluation of the representation of libraries in metabolic pathways. EST processing steps were integrated in a semi-automatic procedure that relies on Perl scripts and stores results in a MySQL database. A PHP-based web interface offers the possibility to simultaneously visualize, retrieve and compare data from the different libraries. Statistically significant differences in GO categories among user selected libraries can also be computed. The HEOE provides an alternative and complementary way to inspect EST expression levels with respect to approaches currently offered by other resources. Furthermore, BLAST computation on the whole human EST dataset was a suitable test of grid scalability in the context of large-scale bioinformatics analysis. The HEOE currently comprises sequence analysis from 70 non-normalized libraries, representing a comprehensive overview on healthy and unhealthy tissues. As the analysis procedure can be easily applied to other libraries, the number of represented tissues is intended to increase.

eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks.

PubMed

Clarke, Daniel J B; Kuleshov, Maxim V; Schilder, Brian M; Torre, Denis; Duffy, Mary E; Keenan, Alexandra B; Lachmann, Alexander; Feldmann, Axel S; Gundersen, Gregory W; Silverstein, Moshe C; Wang, Zichen; Ma'ayan, Avi

2018-05-25

While gene expression data at the mRNA level can be globally and accurately measured, profiling the activity of cell signaling pathways is currently much more difficult. eXpression2Kinases (X2K) computationally predicts involvement of upstream cell signaling pathways, given a signature of differentially expressed genes. X2K first computes enrichment for transcription factors likely to regulate the expression of the differentially expressed genes. The next step of X2K connects these enriched transcription factors through known protein-protein interactions (PPIs) to construct a subnetwork. The final step performs kinase enrichment analysis on the members of the subnetwork. X2K Web is a new implementation of the original eXpression2Kinases algorithm with important enhancements. X2K Web includes many new transcription factor and kinase libraries, and PPI networks. For demonstration, thousands of gene expression signatures induced by kinase inhibitors, applied to six breast cancer cell lines, are provided for fetching directly into X2K Web. The results are displayed as interactive downloadable vector graphic network images and bar graphs. Benchmarking various settings via random permutations enabled the identification of an optimal set of parameters to be used as the default settings in X2K Web. X2K Web is freely available from http://X2K.cloud.

iCOSSY: An Online Tool for Context-Specific Subnetwork Discovery from Gene Expression Data

PubMed Central

Saha, Ashis; Jeon, Minji; Tan, Aik Choon; Kang, Jaewoo

2015-01-01

Pathway analyses help reveal underlying molecular mechanisms of complex biological phenotypes. Biologists tend to perform multiple pathway analyses on the same dataset, as there is no single answer. It is often inefficient for them to implement and/or install all the algorithms by themselves. Online tools can help the community in this regard. Here we present an online gene expression analytical tool called iCOSSY which implements a novel pathway-based COntext-specific Subnetwork discoverY (COSSY) algorithm. iCOSSY also includes a few modifications of COSSY to increase its reliability and interpretability. Users can upload their gene expression datasets, and discover important subnetworks of closely interacting molecules to differentiate between two phenotypes (context). They can also interactively visualize the resulting subnetworks. iCOSSY is a web server that finds subnetworks that are differentially expressed in two phenotypes. Users can visualize the subnetworks to understand the biology of the difference. PMID:26147457

Tracing salmon-derived nutrients and contaminants in freshwater food webs across a pronounced spawner density gradient.

PubMed

Gregory-Eaves, Irene; Demers, J Marc J; Kimpe, Lynda; Krümmel, Eva M; Macdonald, Robie W; Finney, Bruce P; Blais, Jules M

2007-06-01

Many have demonstrated that anadromous Pacific salmon are significant vectors of nutrients from the ocean to freshwaters. Recently. however, it has been recognized that salmon spawners also input significant quantities of contaminants. The objectives of this paper are to delineate the extent to which salmon-derived nutrients are integrated into the freshwater food web using delta(15)N and delta(13)C and to assess the influence of the salmon pathway in the accumulation of contaminants in rainbow trout (Oncorhynchus mykiss). We found that the delta(15)N and delta(13)C of food web components were related positively and significantly to sockeye salmon (Oncorhynchus nerka) spawner density. Contaminant concentrations in rainbow trout also positively and significantly were related to sockeye salmon spawner density. These data suggest that the anadromous salmon nutrient and contaminant pathways are related and significantly impact the contaminant burden of resident fish.

Web-based telemonitoring and delivery of caregiver support for patients with Parkinson disease after deep brain stimulation: protocol.

PubMed

Marceglia, Sara; Rossi, Elena; Rosa, Manuela; Cogiamanian, Filippo; Rossi, Lorenzo; Bertolasi, Laura; Vogrig, Alberto; Pinciroli, Francesco; Barbieri, Sergio; Priori, Alberto

2015-03-06

The increasing number of patients, the high costs of management, and the chronic progress of the disease that prevents patients from performing even simple daily activities make Parkinson disease (PD) a complex pathology with a high impact on society. In particular, patients implanted with deep brain stimulation (DBS) electrodes face a highly fragile stabilization period, requiring specific support at home. However, DBS patients are followed usually by untrained personnel (caregivers or family), without specific care pathways and supporting systems. This projects aims to (1) create a reference consensus guideline and a shared requirements set for the homecare and monitoring of DBS patients, (2) define a set of biomarkers that provides alarms to caregivers for continuous home monitoring, and (3) implement an information system architecture allowing communication between health care professionals and caregivers and improving the quality of care for DBS patients. The definitions of the consensus care pathway and of caregiver needs will be obtained by analyzing the current practices for patient follow-up through focus groups and structured interviews involving health care professionals, patients, and caregivers. The results of this analysis will be represented in a formal graphical model of the process of DBS patient care at home. To define the neurophysiological biomarkers to be used to raise alarms during the monitoring process, neurosignals will be acquired from DBS electrodes through a new experimental system that records while DBS is turned ON and transmits signals by radiofrequency. Motor, cognitive, and behavioral protocols will be used to study possible feedback/alarms to be provided by the system. Finally, a set of mobile apps to support the caregiver at home in managing and monitoring the patient will be developed and tested in the community of caregivers that participated in the focus groups. The set of developed apps will be connected to the already existing WebBioBank Web-based platform allowing health care professionals to manage patient electronic health records and neurophysiological signals. New modules in the WebBioBank platform will be implemented to allow integration and data exchange with mobile health apps. The results of this project will provide a novel approach to long-term evaluation of patients with chronic, severe conditions in the homecare environment, based on caregiver empowerment and tailored applications developed according to consensus care pathways established by clinicians. The creation of a direct communication channel between health care professionals and caregivers can benefit large communities of patients and would represent a scalable experience in integrating data and information coming from a clinical setting to those in home monitoring.

Web-Based Telemonitoring and Delivery of Caregiver Support for Patients With Parkinson Disease After Deep Brain Stimulation: Protocol

PubMed Central

Rossi, Elena; Rosa, Manuela; Cogiamanian, Filippo; Rossi, Lorenzo; Bertolasi, Laura; Vogrig, Alberto; Pinciroli, Francesco; Barbieri, Sergio; Priori, Alberto

2015-01-01

Background The increasing number of patients, the high costs of management, and the chronic progress of the disease that prevents patients from performing even simple daily activities make Parkinson disease (PD) a complex pathology with a high impact on society. In particular, patients implanted with deep brain stimulation (DBS) electrodes face a highly fragile stabilization period, requiring specific support at home. However, DBS patients are followed usually by untrained personnel (caregivers or family), without specific care pathways and supporting systems. Objective This projects aims to (1) create a reference consensus guideline and a shared requirements set for the homecare and monitoring of DBS patients, (2) define a set of biomarkers that provides alarms to caregivers for continuous home monitoring, and (3) implement an information system architecture allowing communication between health care professionals and caregivers and improving the quality of care for DBS patients. Methods The definitions of the consensus care pathway and of caregiver needs will be obtained by analyzing the current practices for patient follow-up through focus groups and structured interviews involving health care professionals, patients, and caregivers. The results of this analysis will be represented in a formal graphical model of the process of DBS patient care at home. To define the neurophysiological biomarkers to be used to raise alarms during the monitoring process, neurosignals will be acquired from DBS electrodes through a new experimental system that records while DBS is turned ON and transmits signals by radiofrequency. Motor, cognitive, and behavioral protocols will be used to study possible feedback/alarms to be provided by the system. Finally, a set of mobile apps to support the caregiver at home in managing and monitoring the patient will be developed and tested in the community of caregivers that participated in the focus groups. The set of developed apps will be connected to the already existing WebBioBank Web-based platform allowing health care professionals to manage patient electronic health records and neurophysiological signals. New modules in the WebBioBank platform will be implemented to allow integration and data exchange with mobile health apps. Results The results of this project will provide a novel approach to long-term evaluation of patients with chronic, severe conditions in the homecare environment, based on caregiver empowerment and tailored applications developed according to consensus care pathways established by clinicians. Conclusions The creation of a direct communication channel between health care professionals and caregivers can benefit large communities of patients and would represent a scalable experience in integrating data and information coming from a clinical setting to those in home monitoring. PMID:25803512

GeNets: a unified web platform for network-based genomic analyses.

PubMed

Li, Taibo; Kim, April; Rosenbluh, Joseph; Horn, Heiko; Greenfeld, Liraz; An, David; Zimmer, Andrew; Liberzon, Arthur; Bistline, Jon; Natoli, Ted; Li, Yang; Tsherniak, Aviad; Narayan, Rajiv; Subramanian, Aravind; Liefeld, Ted; Wong, Bang; Thompson, Dawn; Calvo, Sarah; Carr, Steve; Boehm, Jesse; Jaffe, Jake; Mesirov, Jill; Hacohen, Nir; Regev, Aviv; Lage, Kasper

2018-06-18

Functional genomics networks are widely used to identify unexpected pathway relationships in large genomic datasets. However, it is challenging to compare the signal-to-noise ratios of different networks and to identify the optimal network with which to interpret a particular genetic dataset. We present GeNets, a platform in which users can train a machine-learning model (Quack) to carry out these comparisons and execute, store, and share analyses of genetic and RNA-sequencing datasets.

ChemiRs: a web application for microRNAs and chemicals.

PubMed

Su, Emily Chia-Yu; Chen, Yu-Sing; Tien, Yun-Cheng; Liu, Jeff; Ho, Bing-Ching; Yu, Sung-Liang; Singh, Sher

2016-04-18

MicroRNAs (miRNAs) are about 22 nucleotides, non-coding RNAs that affect various cellular functions, and play a regulatory role in different organisms including human. Until now, more than 2500 mature miRNAs in human have been discovered and registered, but still lack of information or algorithms to reveal the relations among miRNAs, environmental chemicals and human health. Chemicals in environment affect our health and daily life, and some of them can lead to diseases by inferring biological pathways. We develop a creditable online web server, ChemiRs, for predicting interactions and relations among miRNAs, chemicals and pathways. The database not only compares gene lists affected by chemicals and miRNAs, but also incorporates curated pathways to identify possible interactions. Here, we manually retrieved associations of miRNAs and chemicals from biomedical literature. We developed an online system, ChemiRs, which contains miRNAs, diseases, Medical Subject Heading (MeSH) terms, chemicals, genes, pathways and PubMed IDs. We connected each miRNA to miRBase, and every current gene symbol to HUGO Gene Nomenclature Committee (HGNC) for genome annotation. Human pathway information is also provided from KEGG and REACTOME databases. Information about Gene Ontology (GO) is queried from GO Online SQL Environment (GOOSE). With a user-friendly interface, the web application is easy to use. Multiple query results can be easily integrated and exported as report documents in PDF format. Association analysis of miRNAs and chemicals can help us understand the pathogenesis of chemical components. ChemiRs is freely available for public use at http://omics.biol.ntnu.edu.tw/ChemiRs .

Efficient exploration of pan-cancer networks by generalized covariance selection and interactive web content

PubMed Central

Kling, Teresia; Johansson, Patrik; Sanchez, José; Marinescu, Voichita D.; Jörnsten, Rebecka; Nelander, Sven

2015-01-01

Statistical network modeling techniques are increasingly important tools to analyze cancer genomics data. However, current tools and resources are not designed to work across multiple diagnoses and technical platforms, thus limiting their applicability to comprehensive pan-cancer datasets such as The Cancer Genome Atlas (TCGA). To address this, we describe a new data driven modeling method, based on generalized Sparse Inverse Covariance Selection (SICS). The method integrates genetic, epigenetic and transcriptional data from multiple cancers, to define links that are present in multiple cancers, a subset of cancers, or a single cancer. It is shown to be statistically robust and effective at detecting direct pathway links in data from TCGA. To facilitate interpretation of the results, we introduce a publicly accessible tool (cancerlandscapes.org), in which the derived networks are explored as interactive web content, linked to several pathway and pharmacological databases. To evaluate the performance of the method, we constructed a model for eight TCGA cancers, using data from 3900 patients. The model rediscovered known mechanisms and contained interesting predictions. Possible applications include prediction of regulatory relationships, comparison of network modules across multiple forms of cancer and identification of drug targets. PMID:25953855

A high-level language for rule-based modelling.

PubMed

Pedersen, Michael; Phillips, Andrew; Plotkin, Gordon D

2015-01-01

Rule-based languages such as Kappa excel in their support for handling the combinatorial complexities prevalent in many biological systems, including signalling pathways. But Kappa provides little structure for organising rules, and large models can therefore be hard to read and maintain. This paper introduces a high-level, modular extension of Kappa called LBS-κ. We demonstrate the constructs of the language through examples and three case studies: a chemotaxis switch ring, a MAPK cascade, and an insulin signalling pathway. We then provide a formal definition of LBS-κ through an abstract syntax and a translation to plain Kappa. The translation is implemented in a compiler tool which is available as a web application. We finally demonstrate how to increase the expressivity of LBS-κ through embedded scripts in a general-purpose programming language, a technique which we view as generally applicable to other domain specific languages.

A High-Level Language for Rule-Based Modelling

PubMed Central

Pedersen, Michael; Phillips, Andrew; Plotkin, Gordon D.

2015-01-01

Rule-based languages such as Kappa excel in their support for handling the combinatorial complexities prevalent in many biological systems, including signalling pathways. But Kappa provides little structure for organising rules, and large models can therefore be hard to read and maintain. This paper introduces a high-level, modular extension of Kappa called LBS-κ. We demonstrate the constructs of the language through examples and three case studies: a chemotaxis switch ring, a MAPK cascade, and an insulin signalling pathway. We then provide a formal definition of LBS-κ through an abstract syntax and a translation to plain Kappa. The translation is implemented in a compiler tool which is available as a web application. We finally demonstrate how to increase the expressivity of LBS-κ through embedded scripts in a general-purpose programming language, a technique which we view as generally applicable to other domain specific languages. PMID:26043208

A guide for building biological pathways along with two case studies: hair and breast development.

PubMed

Trindade, Daniel; Orsine, Lissur A; Barbosa-Silva, Adriano; Donnard, Elisa R; Ortega, J Miguel

2015-03-01

Genomic information is being underlined in the format of biological pathways. Building these biological pathways is an ongoing demand and benefits from methods for extracting information from biomedical literature with the aid of text-mining tools. Here we hopefully guide you in the attempt of building a customized pathway or chart representation of a system. Our manual is based on a group of software designed to look at biointeractions in a set of abstracts retrieved from PubMed. However, they aim to support the work of someone with biological background, who does not need to be an expert on the subject and will play the role of manual curator while designing the representation of the system, the pathway. We therefore illustrate with two challenging case studies: hair and breast development. They were chosen for focusing on recent acquisitions of human evolution. We produced sub-pathways for each study, representing different phases of development. Differently from most charts present in current databases, we present detailed descriptions, which will additionally guide PESCADOR users along the process. The implementation as a web interface makes PESCADOR a unique tool for guiding the user along the biointeractions, which will constitute a novel pathway. Copyright © 2014 Elsevier Inc. All rights reserved.

Food-web dynamics in a large river discontinuum

USGS Publications Warehouse

Cross, Wyatt F.; Baxter, Colden V.; Rosi-Marshall, Emma J.; Hall, Robert O.; Kennedy, Theodore A.; Donner, Kevin C.; Kelly, Holly A. Wellard; Seegert, Sarah E.Z.; Behn, Kathrine E.; Yard, Michael D.

2013-01-01

Nearly all ecosystems have been altered by human activities, and most communities are now composed of interacting species that have not co-evolved. These changes may modify species interactions, energy and material flows, and food-web stability. Although structural changes to ecosystems have been widely reported, few studies have linked such changes to dynamic food-web attributes and patterns of energy flow. Moreover, there have been few tests of food-web stability theory in highly disturbed and intensely managed freshwater ecosystems. Such synthetic approaches are needed for predicting the future trajectory of ecosystems, including how they may respond to natural or anthropogenic perturbations. We constructed flow food webs at six locations along a 386-km segment of the Colorado River in Grand Canyon (Arizona, USA) for three years. We characterized food-web structure and production, trophic basis of production, energy efficiencies, and interaction-strength distributions across a spatial gradient of perturbation (i.e., distance from Glen Canyon Dam), as well as before and after an experimental flood. We found strong longitudinal patterns in food-web characteristics that strongly correlated with the spatial position of large tributaries. Above tributaries, food webs were dominated by nonnative New Zealand mudsnails (62% of production) and nonnative rainbow trout (100% of fish production). The simple structure of these food webs led to few dominant energy pathways (diatoms to few invertebrate taxa to rainbow trout), large energy inefficiencies (i.e., Below large tributaries, invertebrate production declined ∼18-fold, while fish production remained similar to upstream sites and comprised predominately native taxa (80–100% of production). Sites below large tributaries had increasingly reticulate and detritus-based food webs with a higher prevalence of omnivory, as well as interaction strength distributions more typical of theoretically stable food webs (i.e., nearly twofold higher proportion of weak interactions). Consistent with theory, downstream food webs were less responsive to the experimental flood than sites closest to the dam. We show how human-induced shifts to food-web structure can affect energy flow and interaction strengths, and we show that these changes have consequences for food-web function and response to perturbations.

Looking for Cancer Clues in Publicly Accessible Databases

PubMed Central

Lemkin, Peter F.; Smythers, Gary W.; Munroe, David J.

2004-01-01

What started out as a mere attempt to tentatively identify proteins in experimental cancer-related 2D-PAGE maps developed into VIRTUAL2D, a web-accessible repository for theoretical pI/MW charts for 92 organisms. Using publicly available expression data, we developed a collection of tissue-specific plots based on differential gene expression between normal and diseased states. We use this comparative cancer proteomics knowledge base, known as the tissue molecular anatomy project (TMAP), to uncover threads of cancer markers common to several types of cancer and to relate this information to established biological pathways. PMID:18629065

Looking for cancer clues in publicly accessible databases.

PubMed

Medjahed, Djamel; Lemkin, Peter F; Smythers, Gary W; Munroe, David J

2004-01-01

What started out as a mere attempt to tentatively identify proteins in experimental cancer-related 2D-PAGE maps developed into VIRTUAL2D, a web-accessible repository for theoretical pI/MW charts for 92 organisms. Using publicly available expression data, we developed a collection of tissue-specific plots based on differential gene expression between normal and diseased states. We use this comparative cancer proteomics knowledge base, known as the tissue molecular anatomy project (TMAP), to uncover threads of cancer markers common to several types of cancer and to relate this information to established biological pathways.

Interleukins and their signaling pathways in the Reactome biological pathway database.

PubMed

Jupe, Steve; Ray, Keith; Roca, Corina Duenas; Varusai, Thawfeek; Shamovsky, Veronica; Stein, Lincoln; D'Eustachio, Peter; Hermjakob, Henning

2018-04-01

There is a wealth of biological pathway information available in the scientific literature, but it is spread across many thousands of publications. Alongside publications that contain definitive experimental discoveries are many others that have been dismissed as spurious, found to be irreproducible, or are contradicted by later results and consequently now considered controversial. Many descriptions and images of pathways are incomplete stylized representations that assume the reader is an expert and familiar with the established details of the process, which are consequently not fully explained. Pathway representations in publications frequently do not represent a complete, detailed, and unambiguous description of the molecules involved; their precise posttranslational state; or a full account of the molecular events they undergo while participating in a process. Although this might be sufficient to be interpreted by an expert reader, the lack of detail makes such pathways less useful and difficult to understand for anyone unfamiliar with the area and of limited use as the basis for computational models. Reactome was established as a freely accessible knowledge base of human biological pathways. It is manually populated with interconnected molecular events that fully detail the molecular participants linked to published experimental data and background material by using a formal and open data structure that facilitates computational reuse. These data are accessible on a Web site in the form of pathway diagrams that have descriptive summaries and annotations and as downloadable data sets in several formats that can be reused with other computational tools. The entire database and all supporting software can be downloaded and reused under a Creative Commons license. Pathways are authored by expert biologists who work with Reactome curators and editorial staff to represent the consensus in the field. Pathways are represented as interactive diagrams that include as much molecular detail as possible and are linked to literature citations that contain supporting experimental details. All newly created events undergo a peer-review process before they are added to the database and made available on the associated Web site. New content is added quarterly. The 63rd release of Reactome in December 2017 contains 10,996 human proteins participating in 11,426 events in 2,179 pathways. In addition, analytic tools allow data set submission for the identification and visualization of pathway enrichment and representation of expression profiles as an overlay on Reactome pathways. Protein-protein and compound-protein interactions from several sources, including custom user data sets, can be added to extend pathways. Pathway diagrams and analytic result displays can be downloaded as editable images, human-readable reports, and files in several standard formats that are suitable for computational reuse. Reactome content is available programmatically through a REpresentational State Transfer (REST)-based content service and as a Neo4J graph database. Signaling pathways for IL-1 to IL-38 are hierarchically classified within the pathway "signaling by interleukins." The classification used is largely derived from Akdis et al. The addition to Reactome of a complete set of the known human interleukins, their receptors, and established signaling pathways linked to annotations of relevant aspects of immune function provides a significant computationally accessible resource of information about this important family. This information can be extended easily as new discoveries become accepted as the consensus in the field. A key aim for the future is to increase coverage of gene expression changes induced by interleukin signaling. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Structural optimization of 3D-printed synthetic spider webs for high strength

NASA Astrophysics Data System (ADS)

Qin, Zhao; Compton, Brett G.; Lewis, Jennifer A.; Buehler, Markus J.

2015-05-01

Spiders spin intricate webs that serve as sophisticated prey-trapping architectures that simultaneously exhibit high strength, elasticity and graceful failure. To determine how web mechanics are controlled by their topological design and material distribution, here we create spider-web mimics composed of elastomeric filaments. Specifically, computational modelling and microscale 3D printing are combined to investigate the mechanical response of elastomeric webs under multiple loading conditions. We find the existence of an asymptotic prey size that leads to a saturated web strength. We identify pathways to design elastomeric material structures with maximum strength, low density and adaptability. We show that the loading type dictates the optimal material distribution, that is, a homogeneous distribution is better for localized loading, while stronger radial threads with weaker spiral threads is better for distributed loading. Our observations reveal that the material distribution within spider webs is dictated by the loading condition, shedding light on their observed architectural variations.

Structural optimization of 3D-printed synthetic spider webs for high strength.

PubMed

Qin, Zhao; Compton, Brett G; Lewis, Jennifer A; Buehler, Markus J

2015-05-15

Spiders spin intricate webs that serve as sophisticated prey-trapping architectures that simultaneously exhibit high strength, elasticity and graceful failure. To determine how web mechanics are controlled by their topological design and material distribution, here we create spider-web mimics composed of elastomeric filaments. Specifically, computational modelling and microscale 3D printing are combined to investigate the mechanical response of elastomeric webs under multiple loading conditions. We find the existence of an asymptotic prey size that leads to a saturated web strength. We identify pathways to design elastomeric material structures with maximum strength, low density and adaptability. We show that the loading type dictates the optimal material distribution, that is, a homogeneous distribution is better for localized loading, while stronger radial threads with weaker spiral threads is better for distributed loading. Our observations reveal that the material distribution within spider webs is dictated by the loading condition, shedding light on their observed architectural variations.

Developing a semantic web model for medical differential diagnosis recommendation.

PubMed

Mohammed, Osama; Benlamri, Rachid

2014-10-01

In this paper we describe a novel model for differential diagnosis designed to make recommendations by utilizing semantic web technologies. The model is a response to a number of requirements, ranging from incorporating essential clinical diagnostic semantics to the integration of data mining for the process of identifying candidate diseases that best explain a set of clinical features. We introduce two major components, which we find essential to the construction of an integral differential diagnosis recommendation model: the evidence-based recommender component and the proximity-based recommender component. Both approaches are driven by disease diagnosis ontologies designed specifically to enable the process of generating diagnostic recommendations. These ontologies are the disease symptom ontology and the patient ontology. The evidence-based diagnosis process develops dynamic rules based on standardized clinical pathways. The proximity-based component employs data mining to provide clinicians with diagnosis predictions, as well as generates new diagnosis rules from provided training datasets. This article describes the integration between these two components along with the developed diagnosis ontologies to form a novel medical differential diagnosis recommendation model. This article also provides test cases from the implementation of the overall model, which shows quite promising diagnostic recommendation results.

Food web dynamics affect Northeast Arctic cod recruitment.

PubMed

Hjermann, Dag Ø; Bogstad, Bjarte; Eikeset, Anne Maria; Ottersen, Geir; Gjøsaeter, Harald; Stenseth, Nils Chr

2007-03-07

Proper management of ecosystems requires an understanding of both the species interactions as well as the effect of climate variation. However, a common problem is that the available time-series are of different lengths. Here, we present a general approach for studying the dynamic structure of such interactions. Specifically, we analyse the recruitment of the world's largest cod stock, the Northeast Arctic cod. Studies based on data starting in the 1970-1980s indicate that this stock is affected by temperature through a variety of pathways. However, the value of such studies is somewhat limited by the fact that they are based on a quite specific ecological and climatic situation. Recently, this stock has consisted of fairly young fish and the spawning stock has consisted of relatively few age groups. In this study, we develop a model for the effect of capelin (the cod's main prey) and herring on cod recruitment since 1973. Based on this model, we analyse data on cod, herring and temperature going back to 1921 and find that food-web effects explain a significant part of the cod recruitment variation back to around 1950.

PathJam: a new service for integrating biological pathway information.

PubMed

Glez-Peña, Daniel; Reboiro-Jato, Miguel; Domínguez, Rubén; Gómez-López, Gonzalo; Pisano, David G; Fdez-Riverola, Florentino

2010-10-28

Biological pathways are crucial to much of the scientific research today including the study of specific biological processes related with human diseases. PathJam is a new comprehensive and freely accessible web-server application integrating scattered human pathway annotation from several public sources. The tool has been designed for both (i) being intuitive for wet-lab users providing statistical enrichment analysis of pathway annotations and (ii) giving support to the development of new integrative pathway applications. PathJam’s unique features and advantages include interactive graphs linking pathways and genes of interest, downloadable results in fully compatible formats, GSEA compatible output files and a standardized RESTful API.

Protein Sequence Annotation Tool (PSAT): A centralized web-based meta-server for high-throughput sequence annotations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leung, Elo; Huang, Amy; Cadag, Eithon

In this study, we introduce the Protein Sequence Annotation Tool (PSAT), a web-based, sequence annotation meta-server for performing integrated, high-throughput, genome-wide sequence analyses. Our goals in building PSAT were to (1) create an extensible platform for integration of multiple sequence-based bioinformatics tools, (2) enable functional annotations and enzyme predictions over large input protein fasta data sets, and (3) provide a web interface for convenient execution of the tools. In this paper, we demonstrate the utility of PSAT by annotating the predicted peptide gene products of Herbaspirillum sp. strain RV1423, importing the results of PSAT into EC2KEGG, and using the resultingmore » functional comparisons to identify a putative catabolic pathway, thereby distinguishing RV1423 from a well annotated Herbaspirillum species. This analysis demonstrates that high-throughput enzyme predictions, provided by PSAT processing, can be used to identify metabolic potential in an otherwise poorly annotated genome. Lastly, PSAT is a meta server that combines the results from several sequence-based annotation and function prediction codes, and is available at http://psat.llnl.gov/psat/. PSAT stands apart from other sequencebased genome annotation systems in providing a high-throughput platform for rapid de novo enzyme predictions and sequence annotations over large input protein sequence data sets in FASTA. PSAT is most appropriately applied in annotation of large protein FASTA sets that may or may not be associated with a single genome.« less

Protein Sequence Annotation Tool (PSAT): A centralized web-based meta-server for high-throughput sequence annotations

DOE PAGES

Leung, Elo; Huang, Amy; Cadag, Eithon; ...

2016-01-20

In this study, we introduce the Protein Sequence Annotation Tool (PSAT), a web-based, sequence annotation meta-server for performing integrated, high-throughput, genome-wide sequence analyses. Our goals in building PSAT were to (1) create an extensible platform for integration of multiple sequence-based bioinformatics tools, (2) enable functional annotations and enzyme predictions over large input protein fasta data sets, and (3) provide a web interface for convenient execution of the tools. In this paper, we demonstrate the utility of PSAT by annotating the predicted peptide gene products of Herbaspirillum sp. strain RV1423, importing the results of PSAT into EC2KEGG, and using the resultingmore » functional comparisons to identify a putative catabolic pathway, thereby distinguishing RV1423 from a well annotated Herbaspirillum species. This analysis demonstrates that high-throughput enzyme predictions, provided by PSAT processing, can be used to identify metabolic potential in an otherwise poorly annotated genome. Lastly, PSAT is a meta server that combines the results from several sequence-based annotation and function prediction codes, and is available at http://psat.llnl.gov/psat/. PSAT stands apart from other sequencebased genome annotation systems in providing a high-throughput platform for rapid de novo enzyme predictions and sequence annotations over large input protein sequence data sets in FASTA. PSAT is most appropriately applied in annotation of large protein FASTA sets that may or may not be associated with a single genome.« less

Semantics based approach for analyzing disease-target associations.

PubMed

Kaalia, Rama; Ghosh, Indira

2016-08-01

A complex disease is caused by heterogeneous biological interactions between genes and their products along with the influence of environmental factors. There have been many attempts for understanding the cause of these diseases using experimental, statistical and computational methods. In the present work the objective is to address the challenge of representation and integration of information from heterogeneous biomedical aspects of a complex disease using semantics based approach. Semantic web technology is used to design Disease Association Ontology (DAO-db) for representation and integration of disease associated information with diabetes as the case study. The functional associations of disease genes are integrated using RDF graphs of DAO-db. Three semantic web based scoring algorithms (PageRank, HITS (Hyperlink Induced Topic Search) and HITS with semantic weights) are used to score the gene nodes on the basis of their functional interactions in the graph. Disease Association Ontology for Diabetes (DAO-db) provides a standard ontology-driven platform for describing genes, proteins, pathways involved in diabetes and for integrating functional associations from various interaction levels (gene-disease, gene-pathway, gene-function, gene-cellular component and protein-protein interactions). An automatic instance loader module is also developed in present work that helps in adding instances to DAO-db on a large scale. Our ontology provides a framework for querying and analyzing the disease associated information in the form of RDF graphs. The above developed methodology is used to predict novel potential targets involved in diabetes disease from the long list of loose (statistically associated) gene-disease associations. Copyright © 2016 Elsevier Inc. All rights reserved.

Creating personalised clinical pathways by semantic interoperability with electronic health records.

PubMed

Wang, Hua-Qiong; Li, Jing-Song; Zhang, Yi-Fan; Suzuki, Muneou; Araki, Kenji

2013-06-01

There is a growing realisation that clinical pathways (CPs) are vital for improving the treatment quality of healthcare organisations. However, treatment personalisation is one of the main challenges when implementing CPs, and the inadequate dynamic adaptability restricts the practicality of CPs. The purpose of this study is to improve the practicality of CPs using semantic interoperability between knowledge-based CPs and semantic electronic health records (EHRs). Simple protocol and resource description framework query language is used to gather patient information from semantic EHRs. The gathered patient information is entered into the CP ontology represented by web ontology language. Then, after reasoning over rules described by semantic web rule language in the Jena semantic framework, we adjust the standardised CPs to meet different patients' practical needs. A CP for acute appendicitis is used as an example to illustrate how to achieve CP customisation based on the semantic interoperability between knowledge-based CPs and semantic EHRs. A personalised care plan is generated by comprehensively analysing the patient's personal allergy history and past medical history, which are stored in semantic EHRs. Additionally, by monitoring the patient's clinical information, an exception is recorded and handled during CP execution. According to execution results of the actual example, the solutions we present are shown to be technically feasible. This study contributes towards improving the clinical personalised practicality of standardised CPs. In addition, this study establishes the foundation for future work on the research and development of an independent CP system. Copyright © 2013 Elsevier B.V. All rights reserved.

Evolution of branched regulatory genetic pathways: directional selection on pleiotropic loci accelerates developmental system drift.

PubMed

Johnson, Norman A; Porter, Adam H

2007-01-01

Developmental systems are regulated by a web of interacting loci. One common and useful approach in studying the evolution of development is to focus on classes of interacting elements within these systems. Here, we use individual-based simulations to study the evolution of traits controlled by branched developmental pathways involving three loci, where one locus regulates two different traits. We examined the system under a variety of selective regimes. In the case where one branch was under stabilizing selection and the other under directional selection, we observed "developmental system drift": the trait under stabilizing selection showed little phenotypic change even though the loci underlying that trait showed considerable evolutionary divergence. This occurs because the pleiotropic locus responds to directional selection and compensatory mutants are then favored in the pathway under stabilizing selection. Though developmental system drift may be caused by other mechanisms, it seems likely that it is accelerated by the same underlying genetic mechanism as that producing the Dobzhansky-Muller incompatibilities that lead to speciation in both linear and branched pathways. We also discuss predictions of our model for developmental system drift and how different selective regimes affect probabilities of speciation in the branched pathway system.

PASMet: a web-based platform for prediction, modelling and analyses of metabolic systems

PubMed Central

Sriyudthsak, Kansuporn; Mejia, Ramon Francisco; Arita, Masanori; Hirai, Masami Yokota

2016-01-01

PASMet (Prediction, Analysis and Simulation of Metabolic networks) is a web-based platform for proposing and verifying mathematical models to understand the dynamics of metabolism. The advantages of PASMet include user-friendliness and accessibility, which enable biologists and biochemists to easily perform mathematical modelling. PASMet offers a series of user-functions to handle the time-series data of metabolite concentrations. The functions are organised into four steps: (i) Prediction of a probable metabolic pathway and its regulation; (ii) Construction of mathematical models; (iii) Simulation of metabolic behaviours; and (iv) Analysis of metabolic system characteristics. Each function contains various statistical and mathematical methods that can be used independently. Users who may not have enough knowledge of computing or programming can easily and quickly analyse their local data without software downloads, updates or installations. Users only need to upload their files in comma-separated values (CSV) format or enter their model equations directly into the website. Once the time-series data or mathematical equations are uploaded, PASMet automatically performs computation on server-side. Then, users can interactively view their results and directly download them to their local computers. PASMet is freely available with no login requirement at http://pasmet.riken.jp/ from major web browsers on Windows, Mac and Linux operating systems. PMID:27174940

Does upwelling intensity influence feeding habits and trophic position of planktivorous fish?

NASA Astrophysics Data System (ADS)

Lopez-Lopez, Lucia; Preciado, Izaskun; Muñoz, Isabel; Decima, Moira; Molinero, Juan Carlos; Tel, Elena

2017-04-01

Food web configuration is shaped by many factors, including primary production patterns and oceanographic features, such as upwelling events. In this study, we investigate variability in the trophic position, food web interlinks and energy pathways of four planktivorous demersal fish in the Southern Bay of Biscay- NE Atlantic. The study area is exposed to upwelling events of varying intensity and shows a significant spatial gradient along the coast. The two sampling years were characterized by markedly different conditions, with weak summer upwelling in 2012 and an intense upwelling season in 2013. We used a complementary approach based on stomach content analysis (SCA) and stable isotope analysis (SIA) to test the effects of upwelling intensity and persistence on the food-web. In particular we investigated whether different intensities shift the main flow of energy between the pelagic and benthic energy pathways. We found conspicuous interannual changes in the isotopic POM, whose δ15N was 2.5‰ lower during the productive 2013 season. Interannual changes in the isotopic signature of the fish species were also detected, although their values did not mirror variability at the basal level. The SCA results did not match the isotopic changes, which likely reflected dietary adjustments of the species during summer. The upwelling intensity gradient along the coast did not affect the nitrogen isotopic ratio of any group, however there was a significant effect of such gradient on the carbon isotopic ratio of the fish and euphausiid species. This effect was likely related to the higher primary production associated with intense upwelling conditions.

[Web-based electronic patient record as an instrument for quality assurance within an integrated care concept].

PubMed

Händel, A; Jünemann, A G M; Prokosch, H-U; Beyer, A; Ganslandt, T; Grolik, R; Klein, A; Mrosek, A; Michelson, G; Kruse, F E

2009-03-01

A prerequisite for integrated care programmes is the implementation of a communication network meeting quality assurance standards. Against this background the main objective of the integrated care project between the University Eye Hospital Erlangen and the health insurance company AOK Bayern was to evaluate the potential and the acceptance of a web-based electronic patient record in the context of cataract and retinal surgery. Standardised modules for capturing pre-, intra- and post-operative data on the basis of clinical pathway guidelines for cataract- and retinal surgery have been developed. There are 6 data sets recorded per patient (1 pre-operative, 1 operative, 4-6 post-operative). For data collection, a web-based communication system (Soarian Integrated Care) has been chosen which meets the high requirements in data security, as well as being easy to handle. This teleconsultation system and the embedded electronic patient record are independent of the software used by respective offices and hospitals. Data transmission and storage were carried out in real-time. At present, 101 private ophthalmologists are taking part in the IGV contract with the University Eye Hospital Erlangen. This corresponds to 52% of all private ophthalmologists in the region. During the period from January 1st 2006 to December 31st 2006, 1844 patients were entered. Complete documentation was achieved in 1390 (75%) of all surgical procedures. For evaluation of this data, a multidimensional report and analysis tool (Cognos) was used. The deviation from target refraction as one quality indicator was in the mean 0.09 diopter. The web-based patient record used in this project was highly accepted by the private ophthalmologists. However there are still general concerns against the exchange of medical data via the internet. Nevertheless, the web-based patient record is an essential tool for a functional integration between the ambulatory and stationary health-care units. In addition to the telemedicine functions of the system, we achieved the export of the data to a data warehouse system in order to provide a flexible and powerful tool for quality assurance analysis and reporting.

Fungal-to-bacterial dominance of soil detrital food-webs: Consequences for biogeochemistry

NASA Astrophysics Data System (ADS)

Rousk, Johannes; Frey, Serita

2015-04-01

Resolving fungal and bacterial groups within the microbial decomposer community is thought to capture disparate microbial life strategies, associating bacteria with an r-selected strategy for carbon (C) and nutrient use, and fungi with a K-selected strategy. Additionally, food-web models have established a widely held belief that the bacterial decomposer pathway in soil supports high turnover rates of easily available substrates, while the slower fungal pathway supports the decomposition of more complex organic material, thus characterising the biogeochemistry of the ecosystem. Three field-experiments to generate gradients of SOC-quality were assessed. (1) the Detritus Input, Removal, and Trenching - DIRT - experiment in a temperate forest in mixed hardwood stands at Harvard Forest LTER, US. There, experimentally adjusted litter input and root input had affected the SOC quality during 23 years. (2) field-application of 14-C labelled glucose to grassland soils, sampled over the course of 13 months to generate an age-gradient of SOM (1 day - 13 months). (3) The Park Grass Experiment at Rothamsted, UK, where 150-years continuous N-fertilisation (0, 50, 100, 150 kg N ha-1 y-1) has affected the quality of SOM in grassland soils. A combination of carbon stable and radio isotope studies, fungal and bacterial growth and biomass measurements, and C and N mineralisation (15N pool dilution) assays were used to investigate how SOC-quality influenced fungal and bacterial food-web pathways and the implications this had for C and nutrient turnover. There was no support that decomposer food-webs dominated by bacteria support high turnover rates of easily available substrates, while slower fungal-dominated decomposition pathways support the decomposition of more complex organic material. Rather, an association between high quality SOC and fungi emerges from the results. This suggests that we need to revise our basic understanding for soil microbial communities and the processes they regulate in soil.

Ecological Network Indicators of Ecosystem Status and Change in the Baltic Sea

PubMed Central

Tomczak, Maciej T.; Heymans, Johanna J.; Yletyinen, Johanna; Niiranen, Susa; Otto, Saskia A.; Blenckner, Thorsten

2013-01-01

Several marine ecosystems under anthropogenic pressure have experienced shifts from one ecological state to another. In the central Baltic Sea, the regime shift of the 1980s has been associated with food-web reorganization and redirection of energy flow pathways. These long-term dynamics from 1974 to 2006 have been simulated here using a food-web model forced by climate and fishing. Ecological network analysis was performed to calculate indices of ecosystem change. The model replicated the regime shift. The analyses of indicators suggested that the system’s resilience was higher prior to 1988 and lower thereafter. The ecosystem topology also changed from a web-like structure to a linearized food-web. PMID:24116045

gene2drug: a computational tool for pathway-based rational drug repositioning.

PubMed

Napolitano, Francesco; Carrella, Diego; Mandriani, Barbara; Pisonero-Vaquero, Sandra; Sirci, Francesco; Medina, Diego L; Brunetti-Pierri, Nicola; di Bernardo, Diego

2018-05-01

Drug repositioning has been proposed as an effective shortcut to drug discovery. The availability of large collections of transcriptional responses to drugs enables computational approaches to drug repositioning directly based on measured molecular effects. We introduce a novel computational methodology for rational drug repositioning, which exploits the transcriptional responses following treatment with small molecule. Specifically, given a therapeutic target gene, a prioritization of potential effective drugs is obtained by assessing their impact on the transcription of genes in the pathway(s) including the target. We performed in silico validation and comparison with a state-of-art technique based on similar principles. We next performed experimental validation in two different real-case drug repositioning scenarios: (i) upregulation of the glutamate-pyruvate transaminase (GPT), which has been shown to induce reduction of oxalate levels in a mouse model of primary hyperoxaluria, and (ii) activation of the transcription factor TFEB, a master regulator of lysosomal biogenesis and autophagy, whose modulation may be beneficial in neurodegenerative disorders. A web tool for Gene2drug is freely available at http://gene2drug.tigem.it. An R package is under development and can be obtained from https://github.com/franapoli/gep2pep. dibernardo@tigem.it. Supplementary data are available at Bioinformatics online.

MetaMapR: pathway independent metabolomic network analysis incorporating unknowns.

PubMed

Grapov, Dmitry; Wanichthanarak, Kwanjeera; Fiehn, Oliver

2015-08-15

Metabolic network mapping is a widely used approach for integration of metabolomic experimental results with biological domain knowledge. However, current approaches can be limited by biochemical domain or pathway knowledge which results in sparse disconnected graphs for real world metabolomic experiments. MetaMapR integrates enzymatic transformations with metabolite structural similarity, mass spectral similarity and empirical associations to generate richly connected metabolic networks. This open source, web-based or desktop software, written in the R programming language, leverages KEGG and PubChem databases to derive associations between metabolites even in cases where biochemical domain or molecular annotations are unknown. Network calculation is enhanced through an interface to the Chemical Translation System, which allows metabolite identifier translation between >200 common biochemical databases. Analysis results are presented as interactive visualizations or can be exported as high-quality graphics and numerical tables which can be imported into common network analysis and visualization tools. Freely available at http://dgrapov.github.io/MetaMapR/. Requires R and a modern web browser. Installation instructions, tutorials and application examples are available at http://dgrapov.github.io/MetaMapR/. ofiehn@ucdavis.edu. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Structural optimization of 3D-printed synthetic spider webs for high strength

PubMed Central

Qin, Zhao; Compton, Brett G.; Lewis, Jennifer A.; Buehler, Markus J.

2015-01-01

Spiders spin intricate webs that serve as sophisticated prey-trapping architectures that simultaneously exhibit high strength, elasticity and graceful failure. To determine how web mechanics are controlled by their topological design and material distribution, here we create spider-web mimics composed of elastomeric filaments. Specifically, computational modelling and microscale 3D printing are combined to investigate the mechanical response of elastomeric webs under multiple loading conditions. We find the existence of an asymptotic prey size that leads to a saturated web strength. We identify pathways to design elastomeric material structures with maximum strength, low density and adaptability. We show that the loading type dictates the optimal material distribution, that is, a homogeneous distribution is better for localized loading, while stronger radial threads with weaker spiral threads is better for distributed loading. Our observations reveal that the material distribution within spider webs is dictated by the loading condition, shedding light on their observed architectural variations. PMID:25975372

Discriminating response groups in metabolic and regulatory pathway networks.

PubMed

Van Hemert, John L; Dickerson, Julie A

2012-04-01

Analysis of omics experiments generates lists of entities (genes, metabolites, etc.) selected based on specific behavior, such as changes in response to stress or other signals. Functional interpretation of these lists often uses category enrichment tests using functional annotations like Gene Ontology terms and pathway membership. This approach does not consider the connected structure of biochemical pathways or the causal directionality of events. The Omics Response Group (ORG) method, described in this work, interprets omics lists in the context of metabolic pathway and regulatory networks using a statistical model for flow within the networks. Statistical results for all response groups are visualized in a novel Pathway Flow plot. The statistical tests are based on the Erlang distribution model under the assumption of independent and identically Exponential-distributed random walk flows through pathways. As a proof of concept, we applied our method to an Escherichia coli transcriptomics dataset where we confirmed common knowledge of the E.coli transcriptional response to Lipid A deprivation. The main response is related to osmotic stress, and we were also able to detect novel responses that are supported by the literature. We also applied our method to an Arabidopsis thaliana expression dataset from an abscisic acid study. In both cases, conventional pathway enrichment tests detected nothing, while our approach discovered biological processes beyond the original studies. We created a prototype for an interactive ORG web tool at http://ecoserver.vrac.iastate.edu/pathwayflow (source code is available from https://subversion.vrac.iastate.edu/Subversion/jlv/public/jlv/pathwayflow). The prototype is described along with additional figures and tables in Supplementary Material. julied@iastate.edu Supplementary data are available at Bioinformatics online.

MESSI: metabolic engineering target selection and best strain identification tool.

PubMed

Kang, Kang; Li, Jun; Lim, Boon Leong; Panagiotou, Gianni

2015-01-01

Metabolic engineering and synthetic biology are synergistically related fields for manipulating target pathways and designing microorganisms that can act as chemical factories. Saccharomyces cerevisiae's ideal bioprocessing traits make yeast a very attractive chemical factory for production of fuels, pharmaceuticals, nutraceuticals as well as a wide range of chemicals. However, future attempts of engineering S. cerevisiae's metabolism using synthetic biology need to move towards more integrative models that incorporate the high connectivity of metabolic pathways and regulatory processes and the interactions in genetic elements across those pathways and processes. To contribute in this direction, we have developed Metabolic Engineering target Selection and best Strain Identification tool (MESSI), a web server for predicting efficient chassis and regulatory components for yeast bio-based production. The server provides an integrative platform for users to analyse ready-to-use public high-throughput metabolomic data, which are transformed to metabolic pathway activities for identifying the most efficient S. cerevisiae strain for the production of a compound of interest. As input MESSI accepts metabolite KEGG IDs or pathway names. MESSI outputs a ranked list of S. cerevisiae strains based on aggregation algorithms. Furthermore, through a genome-wide association study of the metabolic pathway activities with the strains' natural variation, MESSI prioritizes genes and small variants as potential regulatory points and promising metabolic engineering targets. Users can choose various parameters in the whole process such as (i) weight and expectation of each metabolic pathway activity in the final ranking of the strains, (ii) Weighted AddScore Fuse or Weighted Borda Fuse aggregation algorithm, (iii) type of variants to be included, (iv) variant sets in different biological levels.Database URL: http://sbb.hku.hk/MESSI/. © The Author(s) 2015. Published by Oxford University Press.

Serum metabolomics differentiating pancreatic cancer from new-onset diabetes

PubMed Central

He, Xiangyi; Zhong, Jie; Wang, Shuwei; Zhou, Yufen; Wang, Lei; Zhang, Yongping; Yuan, Yaozong

2017-01-01

To establish a screening strategy for pancreatic cancer (PC) based on new-onset diabetic mellitus (NO-DM), serum metabolomics analysis and a search for the metabolic pathways associated with PC related DM were performed. Serum samples from patients with NO-DM (n = 30) and patients with pancreatic cancer and NO-DM were examined by liquid chromatography-mass spectrometry. Data were analyzed using principal components analysis (PCA) and orthogonal projection to latent structures (OPLS) of the most significant metabolites. The diagnostic model was constructed using logistic regression analysis. Metabolic pathways were analyzed using the web-based tool MetPA. PC patients with NO-DM were older and had a lower BMI and shorter duration of DM than those with NO-DM. The metabolomic profiles of patients with PC and NO-DM were significantly different from those of patients with NO-DM in the PCA and OPLS models. Sixty two differential metabolites were identified by the OPLS model. The logistic regression model using a panel of two metabolites including N_Succinyl_L_diaminopimelic_acid and PE (18:2) had high sensitivity (93.3%) and specificity (93.1%) for PC. The top three metabolic pathways associated with PC related DM were valine, leucine and isoleucine biosynthesis and degradation, primary bile acid biosynthesis, and sphingolipid metabolism. In conclusion, screening for PC based on NO-DM using serum metabolomics in combination with clinic characteristics and CA19-9 is a potential useful strategy. Several metabolic pathways differed between PC related DM and type 2 DM. PMID:28418859

Food web pathway determines how selenium affects aquatic ecosystems: A San francisco Bay case study

USGS Publications Warehouse

Stewart, A.R.; Luoma, S.N.; Schlekat, C.E.; Doblin, M.A.; Hieb, K.A.

2004-01-01

Chemical contaminants disrupt ecosystems, but specific effects may be under-appreciated when poorly known processes such as uptake mechanisms, uptake via diet, food preferences, and food web dynamics are influential. Here we show that a combination of food web structure and the physiology of trace element accumulation explain why some species in San Francisco Bay are threatened by a relatively low level of selenium contamination and some are not. Bivalves and crustacean Zooplankton form the base of two dominant food webs in estuaries. The dominant bivalve Potamocorbula amurensis has a 10-fold slower rate constant of loss for selenium than do common crustaceans such as copepods and the mysid Neomysis mercedis (rate constant of loss, ke = 0.025, 0.155, and 0.25 d-1, respectively). The result is much higher selenium concentrations in the bivalve than in the crustaceans. Stable isotope analyses show that this difference is propagated up the respective food webs in San Francisco Bay. Several predators of bivalves have tissue concentrations of selenium that exceed thresholds thought to be associated with teratogenesis or reproductive failure (liver Se > 15 ??g g-1 dry weight). Deformities typical of selenium-induced teratogenesis were observed in one of these species. Concentrations of selenium in tissues of predators of Zooplankton are less than the thresholds. Basic physiological and ecological processes can drive wide differences in exposure and effects among species, but such processes are rarely considered in traditional evaluations of contaminant impacts.

Pathways of CH3Hg and Hg Ingestion in Benthic Organisms: An Enriched Isotope Approach

PubMed Central

2015-01-01

Mercury is a widespread contaminant in marine food webs, and identifying uptake pathways of mercury species, CH3Hg+ and Hg2+, into low trophic level organisms is important to understanding its entry into marine food webs. Enriched stable isotope tracers were used to study benthic vs. pelagic pathways of CH3Hg+ and Hg2+ uptake via food to the infaunal estuarine amphipod, Leptocheirus plumulosus. Algal cells differentially labeled with isotopically enriched CH3Hg+ or Hg2+ were added simultaneously to the sediment and water column of microcosms, and Hg species were monitored in amphipods and in sediment and water compartments. Methylation of Hg2+ occurred during the course of the experiment, enhancing the uptake of Hg2+ spikes. Trophic transfer of Hg from algae added to the water column was determined to be the major uptake route for amphipods, suggesting inputs of contaminated organic matter from the pelagic zone are important to mercury bioaccumulation even in organisms living in sediments. PMID:24678910

Pathways of CH3Hg and Hg ingestion in benthic organisms: an enriched isotope approach.

PubMed

Taylor, Vivien F; Bugge, Deenie; Jackson, Brian P; Chen, Celia Y

2014-05-06

Mercury is a widespread contaminant in marine food webs, and identifying uptake pathways of mercury species, CH3Hg(+) and Hg(2+), into low trophic level organisms is important to understanding its entry into marine food webs. Enriched stable isotope tracers were used to study benthic vs. pelagic pathways of CH3Hg(+) and Hg(2+) uptake via food to the infaunal estuarine amphipod, Leptocheirus plumulosus. Algal cells differentially labeled with isotopically enriched CH3Hg(+) or Hg(2+) were added simultaneously to the sediment and water column of microcosms, and Hg species were monitored in amphipods and in sediment and water compartments. Methylation of Hg(2+) occurred during the course of the experiment, enhancing the uptake of Hg(2+) spikes. Trophic transfer of Hg from algae added to the water column was determined to be the major uptake route for amphipods, suggesting inputs of contaminated organic matter from the pelagic zone are important to mercury bioaccumulation even in organisms living in sediments.

EcoCyc: a comprehensive database resource for Escherichia coli

PubMed Central

Keseler, Ingrid M.; Collado-Vides, Julio; Gama-Castro, Socorro; Ingraham, John; Paley, Suzanne; Paulsen, Ian T.; Peralta-Gil, Martín; Karp, Peter D.

2005-01-01

The EcoCyc database (http://EcoCyc.org/) is a comprehensive source of information on the biology of the prototypical model organism Escherichia coli K12. The mission for EcoCyc is to contain both computable descriptions of, and detailed comments describing, all genes, proteins, pathways and molecular interactions in E.coli. Through ongoing manual curation, extensive information such as summary comments, regulatory information, literature citations and evidence types has been extracted from 8862 publications and added to Version 8.5 of the EcoCyc database. The EcoCyc database can be accessed through a World Wide Web interface, while the downloadable Pathway Tools software and data files enable computational exploration of the data and provide enhanced querying capabilities that web interfaces cannot support. For example, EcoCyc contains carefully curated information that can be used as training sets for bioinformatics prediction of entities such as promoters, operons, genetic networks, transcription factor binding sites, metabolic pathways, functionally related genes, protein complexes and protein–ligand interactions. PMID:15608210

Ontology-oriented retrieval of putative microRNAs in Vitis vinifera via GrapeMiRNA: a web database of de novo predicted grape microRNAs.

PubMed

Lazzari, Barbara; Caprera, Andrea; Cestaro, Alessandro; Merelli, Ivan; Del Corvo, Marcello; Fontana, Paolo; Milanesi, Luciano; Velasco, Riccardo; Stella, Alessandra

2009-06-29

Two complete genome sequences are available for Vitis vinifera Pinot noir. Based on the sequence and gene predictions produced by the IASMA, we performed an in silico detection of putative microRNA genes and of their targets, and collected the most reliable microRNA predictions in a web database. The application is available at http://www.itb.cnr.it/ptp/grapemirna/. The program FindMiRNA was used to detect putative microRNA genes in the grape genome. A very high number of predictions was retrieved, calling for validation. Nine parameters were calculated and, based on the grape microRNAs dataset available at miRBase, thresholds were defined and applied to FindMiRNA predictions having targets in gene exons. In the resulting subset, predictions were ranked according to precursor positions and sequence similarity, and to target identity. To further validate FindMiRNA predictions, comparisons to the Arabidopsis genome, to the grape Genoscope genome, and to the grape EST collection were performed. Results were stored in a MySQL database and a web interface was prepared to query the database and retrieve predictions of interest. The GrapeMiRNA database encompasses 5,778 microRNA predictions spanning the whole grape genome. Predictions are integrated with information that can be of use in selection procedures. Tools added in the web interface also allow to inspect predictions according to gene ontology classes and metabolic pathways of targets. The GrapeMiRNA database can be of help in selecting candidate microRNA genes to be validated.

MetExploreViz: web component for interactive metabolic network visualization.

PubMed

Chazalviel, Maxime; Frainay, Clément; Poupin, Nathalie; Vinson, Florence; Merlet, Benjamin; Gloaguen, Yoann; Cottret, Ludovic; Jourdan, Fabien

2017-09-15

MetExploreViz is an open source web component that can be easily embedded in any web site. It provides features dedicated to the visualization of metabolic networks and pathways and thus offers a flexible solution to analyze omics data in a biochemical context. Documentation and link to GIT code repository (GPL 3.0 license)are available at this URL: http://metexplore.toulouse.inra.fr/metexploreViz/doc /. Tutorial is available at this URL. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Developing a kidney and urinary pathway knowledge base

PubMed Central

2011-01-01

Background Chronic renal disease is a global health problem. The identification of suitable biomarkers could facilitate early detection and diagnosis and allow better understanding of the underlying pathology. One of the challenges in meeting this goal is the necessary integration of experimental results from multiple biological levels for further analysis by data mining. Data integration in the life science is still a struggle, and many groups are looking to the benefits promised by the Semantic Web for data integration. Results We present a Semantic Web approach to developing a knowledge base that integrates data from high-throughput experiments on kidney and urine. A specialised KUP ontology is used to tie the various layers together, whilst background knowledge from external databases is incorporated by conversion into RDF. Using SPARQL as a query mechanism, we are able to query for proteins expressed in urine and place these back into the context of genes expressed in regions of the kidney. Conclusions The KUPKB gives KUP biologists the means to ask queries across many resources in order to aggregate knowledge that is necessary for answering biological questions. The Semantic Web technologies we use, together with the background knowledge from the domain’s ontologies, allows both rapid conversion and integration of this knowledge base. The KUPKB is still relatively small, but questions remain about scalability, maintenance and availability of the knowledge itself. Availability The KUPKB may be accessed via http://www.e-lico.eu/kupkb. PMID:21624162

Cost and Survival Analysis Before and After Implementation of Dana-Farber Clinical Pathways for Patients With Stage IV Non-Small-Cell Lung Cancer.

PubMed

Jackman, David M; Zhang, Yichen; Dalby, Carole; Nguyen, Tom; Nagle, Julia; Lydon, Christine A; Rabin, Michael S; McNiff, Kristen K; Fraile, Belen; Jacobson, Joseph O

2017-04-01

Increasing costs and medical complexity are significant challenges in modern oncology. We explored the use of clinical pathways to support clinical decision making and manage resources prospectively across our network. We created customized lung cancer pathways and partnered with a commercial vendor to provide a Web-based platform for real-time decision support and post-treatment data aggregation. Dana-Farber Cancer Institute (DFCI) Pathways for non-small cell lung cancer (NSCLC) were introduced in January 2014. We identified all DFCI patients who were diagnosed and treated for stage IV NSCLC in 2012 (before pathways) and 2014 (after pathways). Costs of care were determined for 1 year from the time of diagnosis. Pre- and postpathway cohorts included 160 and 210 patients with stage IV NSCLC, respectively. The prepathway group had more women but was otherwise similarly matched for demographic and tumor characteristics. The total 12-month cost of care (adjusted for age, sex, race, distance to DFCI, clinical trial enrollment, and EGFR and ALK status) demonstrated a $15,013 savings after the implementation of pathways ($67,050 before pathways v $52,037 after pathways). Antineoplastics were the largest source of cost savings. Clinical outcomes were not compromised, with similar median overall survival times (10.7 months before v 11.2 months after pathways; P = .08). After introduction of a clinical pathway in metastatic NSCLC, cost of care decreased significantly, with no compromise in survival. In an era where comparative outcomes analysis and value assessment are increasingly important, the implementation of clinical pathways may provide a means to coalesce and disseminate institutional expertise and track and learn from care decisions.

Prioritizing biological pathways by recognizing context in time-series gene expression data.

PubMed

Lee, Jusang; Jo, Kyuri; Lee, Sunwon; Kang, Jaewoo; Kim, Sun

2016-12-23

The primary goal of pathway analysis using transcriptome data is to find significantly perturbed pathways. However, pathway analysis is not always successful in identifying pathways that are truly relevant to the context under study. A major reason for this difficulty is that a single gene is involved in multiple pathways. In the KEGG pathway database, there are 146 genes, each of which is involved in more than 20 pathways. Thus activation of even a single gene will result in activation of many pathways. This complex relationship often makes the pathway analysis very difficult. While we need much more powerful pathway analysis methods, a readily available alternative way is to incorporate the literature information. In this study, we propose a novel approach for prioritizing pathways by combining results from both pathway analysis tools and literature information. The basic idea is as follows. Whenever there are enough articles that provide evidence on which pathways are relevant to the context, we can be assured that the pathways are indeed related to the context, which is termed as relevance in this paper. However, if there are few or no articles reported, then we should rely on the results from the pathway analysis tools, which is termed as significance in this paper. We realized this concept as an algorithm by introducing Context Score and Impact Score and then combining the two into a single score. Our method ranked truly relevant pathways significantly higher than existing pathway analysis tools in experiments with two data sets. Our novel framework was implemented as ContextTRAP by utilizing two existing tools, TRAP and BEST. ContextTRAP will be a useful tool for the pathway based analysis of gene expression data since the user can specify the context of the biological experiment in a set of keywords. The web version of ContextTRAP is available at http://biohealth.snu.ac.kr/software/contextTRAP .

An editor for pathway drawing and data visualization in the Biopathways Workbench.

PubMed

Byrnes, Robert W; Cotter, Dawn; Maer, Andreia; Li, Joshua; Nadeau, David; Subramaniam, Shankar

2009-10-02

Pathway models serve as the basis for much of systems biology. They are often built using programs designed for the purpose. Constructing new models generally requires simultaneous access to experimental data of diverse types, to databases of well-characterized biological compounds and molecular intermediates, and to reference model pathways. However, few if any software applications provide all such capabilities within a single user interface. The Pathway Editor is a program written in the Java programming language that allows de-novo pathway creation and downloading of LIPID MAPS (Lipid Metabolites and Pathways Strategy) and KEGG lipid metabolic pathways, and of measured time-dependent changes to lipid components of metabolism. Accessed through Java Web Start, the program downloads pathways from the LIPID MAPS Pathway database (Pathway) as well as from the LIPID MAPS web server http://www.lipidmaps.org. Data arises from metabolomic (lipidomic), microarray, and protein array experiments performed by the LIPID MAPS consortium of laboratories and is arranged by experiment. Facility is provided to create, connect, and annotate nodes and processes on a drawing panel with reference to database objects and time course data. Node and interaction layout as well as data display may be configured in pathway diagrams as desired. Users may extend diagrams, and may also read and write data and non-lipidomic KEGG pathways to and from files. Pathway diagrams in XML format, containing database identifiers referencing specific compounds and experiments, can be saved to a local file for subsequent use. The program is built upon a library of classes, referred to as the Biopathways Workbench, that convert between different file formats and database objects. An example of this feature is provided in the form of read/construct/write access to models in SBML (Systems Biology Markup Language) contained in the local file system. Inclusion of access to multiple experimental data types and of pathway diagrams within a single interface, automatic updating through connectivity to an online database, and a focus on annotation, including reference to standardized lipid nomenclature as well as common lipid names, supports the view that the Pathway Editor represents a significant, practicable contribution to current pathway modeling tools.

DIANA-microT web server: elucidating microRNA functions through target prediction.

PubMed

Maragkakis, M; Reczko, M; Simossis, V A; Alexiou, P; Papadopoulos, G L; Dalamagas, T; Giannopoulos, G; Goumas, G; Koukis, E; Kourtis, K; Vergoulis, T; Koziris, N; Sellis, T; Tsanakas, P; Hatzigeorgiou, A G

2009-07-01

Computational microRNA (miRNA) target prediction is one of the key means for deciphering the role of miRNAs in development and disease. Here, we present the DIANA-microT web server as the user interface to the DIANA-microT 3.0 miRNA target prediction algorithm. The web server provides extensive information for predicted miRNA:target gene interactions with a user-friendly interface, providing extensive connectivity to online biological resources. Target gene and miRNA functions may be elucidated through automated bibliographic searches and functional information is accessible through Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The web server offers links to nomenclature, sequence and protein databases, and users are facilitated by being able to search for targeted genes using different nomenclatures or functional features, such as the genes possible involvement in biological pathways. The target prediction algorithm supports parameters calculated individually for each miRNA:target gene interaction and provides a signal-to-noise ratio and a precision score that helps in the evaluation of the significance of the predicted results. Using a set of miRNA targets recently identified through the pSILAC method, the performance of several computational target prediction programs was assessed. DIANA-microT 3.0 achieved there with 66% the highest ratio of correctly predicted targets over all predicted targets. The DIANA-microT web server is freely available at www.microrna.gr/microT.

A comprehensive map of the influenza A virus replication cycle

PubMed Central

2013-01-01

Background Influenza is a common infectious disease caused by influenza viruses. Annual epidemics cause severe illnesses, deaths, and economic loss around the world. To better defend against influenza viral infection, it is essential to understand its mechanisms and associated host responses. Many studies have been conducted to elucidate these mechanisms, however, the overall picture remains incompletely understood. A systematic understanding of influenza viral infection in host cells is needed to facilitate the identification of influential host response mechanisms and potential drug targets. Description We constructed a comprehensive map of the influenza A virus (‘IAV’) life cycle (‘FluMap’) by undertaking a literature-based, manual curation approach. Based on information obtained from publicly available pathway databases, updated with literature-based information and input from expert virologists and immunologists, FluMap is currently composed of 960 factors (i.e., proteins, mRNAs etc.) and 456 reactions, and is annotated with ~500 papers and curation comments. In addition to detailing the type of molecular interactions, isolate/strain specific data are also available. The FluMap was built with the pathway editor CellDesigner in standard SBML (Systems Biology Markup Language) format and visualized as an SBGN (Systems Biology Graphical Notation) diagram. It is also available as a web service (online map) based on the iPathways+ system to enable community discussion by influenza researchers. We also demonstrate computational network analyses to identify targets using the FluMap. Conclusion The FluMap is a comprehensive pathway map that can serve as a graphically presented knowledge-base and as a platform to analyze functional interactions between IAV and host factors. Publicly available webtools will allow continuous updating to ensure the most reliable representation of the host-virus interaction network. The FluMap is available at http://www.influenza-x.org/flumap/. PMID:24088197

STEP-TRAMM - A modeling interface for simulating localized rainfall induced shallow landslides and debris flow runout pathways

NASA Astrophysics Data System (ADS)

von Ruette, Jonas; Lehmann, Peter; Fan, Linfeng; Bickel, Samuel; Or, Dani

2017-04-01

Landslides and subsequent debris-flows initiated by rainfall represent a ubiquitous natural hazard in steep mountainous regions. We integrated a landslide hydro-mechanical triggering model and associated debris flow runout pathways with a graphical user interface (GUI) to represent these natural hazards in a wide range of catchments over the globe. The STEP-TRAMM GUI provides process-based locations and sizes of landslides patterns using digital elevation models (DEM) from SRTM database (30 m resolution) linked with soil maps from global database SoilGrids (250 m resolution) and satellite based information on rainfall statistics for the selected region. In a preprocessing step STEP-TRAMM models soil depth distribution and complements soil information that jointly capture key hydrological and mechanical properties relevant to local soil failure representation. In the presentation we will discuss feature of this publicly available platform and compare landslide and debris flow patterns for different regions considering representative intense rainfall events. Model outcomes will be compared for different spatial and temporal resolutions to test applicability of web-based information on elevation and rainfall for hazard assessment.

Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format.

PubMed

Webb, Ryan L; Ma'ayan, Avi

2011-03-21

The World Wide Web plays a critical role in enabling molecular, cell, systems and computational biologists to exchange, search, visualize, integrate, and analyze experimental data. Such efforts can be further enhanced through the development of semantic web concepts. The semantic web idea is to enable machines to understand data through the development of protocol free data exchange formats such as Resource Description Framework (RDF) and the Web Ontology Language (OWL). These standards provide formal descriptors of objects, object properties and their relationships within a specific knowledge domain. However, the overhead of converting datasets typically stored in data tables such as Excel, text or PDF into RDF or OWL formats is not trivial for non-specialists and as such produces a barrier to seamless data exchange between researchers, databases and analysis tools. This problem is particularly of importance in the field of network systems biology where biochemical interactions between genes and their protein products are abstracted to networks. For the purpose of converting biochemical interactions into the BioPAX format, which is the leading standard developed by the computational systems biology community, we developed an open-source command line tool that takes as input tabular data describing different types of molecular biochemical interactions. The tool converts such interactions into the BioPAX level 3 OWL format. We used the tool to convert several existing and new mammalian networks of protein interactions, signalling pathways, and transcriptional regulatory networks into BioPAX. Some of these networks were deposited into PathwayCommons, a repository for consolidating and organizing biochemical networks. The software tool Sig2BioPAX is a resource that enables experimental and computational systems biologists to contribute their identified networks and pathways of molecular interactions for integration and reuse with the rest of the research community.

Effects of differential habitat warming on complex communities.

PubMed

Tunney, Tyler D; McCann, Kevin S; Lester, Nigel P; Shuter, Brian J

2014-06-03

Food webs unfold across a mosaic of micro and macro habitats, with each habitat coupled by mobile consumers that behave in response to local environmental conditions. Despite this fundamental characteristic of nature, research on how climate change will affect whole ecosystems has overlooked (i) that climate warming will generally affect habitats differently and (ii) that mobile consumers may respond to this differential change in a manner that may fundamentally alter the energy pathways that sustain ecosystems. This reasoning suggests a powerful, but largely unexplored, avenue for studying the impacts of climate change on ecosystem functioning. Here, we use lake ecosystems to show that predictable behavioral adjustments to local temperature differentials govern a fundamental structural shift across 54 food webs. Data show that the trophic pathways from basal resources to a cold-adapted predator shift toward greater reliance on a cold-water refuge habitat, and food chain length increases, as air temperatures rise. Notably, cold-adapted predator behavior may substantially drive this decoupling effect across the climatic range in our study independent of warmer-adapted species responses (for example, changes in near-shore species abundance and predator absence). Such modifications reflect a flexible food web architecture that requires more attention from climate change research. The trophic pathway restructuring documented here is expected to alter biomass accumulation, through the regulation of energy fluxes to predators, and thus potentially threatens ecosystem sustainability in times of rapid environmental change.

Web-based interventions for menopause: A systematic integrated literature review.

PubMed

Im, Eun-Ok; Lee, Yaelim; Chee, Eunice; Chee, Wonshik

2017-01-01

Advances in computer and Internet technologies have allowed health care providers to develop, use, and test various types of Web-based interventions for their practice and research. Indeed, an increasing number of Web-based interventions have recently been developed and tested in health care fields. Despite the great potential for Web-based interventions to improve practice and research, little is known about the current status of Web-based interventions, especially those related to menopause. To identify the current status of Web-based interventions used in the field of menopause, a literature review was conducted using multiple databases, with the keywords "online," "Internet," "Web," "intervention," and "menopause." Using these keywords, a total of 18 eligible articles were analyzed to identify the current status of Web-based interventions for menopause. Six themes reflecting the current status of Web-based interventions for menopause were identified: (a) there existed few Web-based intervention studies on menopause; (b) Web-based decision support systems were mainly used; (c) there was a lack of detail on the interventions; (d) there was a lack of guidance on the use of Web-based interventions; (e) counselling was frequently combined with Web-based interventions; and (f) the pros and cons were similar to those of Web-based methods in general. Based on these findings, directions for future Web-based interventions for menopause are provided. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Exploring of the molecular mechanism of rhinitis via bioinformatics methods

PubMed Central

Song, Yufen; Yan, Zhaohui

2018-01-01

The aim of this study was to analyze gene expression profiles for exploring the function and regulatory network of differentially expressed genes (DEGs) in pathogenesis of rhinitis by a bioinformatics method. The gene expression profile of GSE43523 was downloaded from the Gene Expression Omnibus database. The dataset contained 7 seasonal allergic rhinitis samples and 5 non-allergic normal samples. DEGs between rhinitis samples and normal samples were identified via the limma package of R. The webGestal database was used to identify enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of the DEGs. The differentially co-expressed pairs of the DEGs were identified via the DCGL package in R, and the differential co-expression network was constructed based on these pairs. A protein-protein interaction (PPI) network of the DEGs was constructed based on the Search Tool for the Retrieval of Interacting Genes database. A total of 263 DEGs were identified in rhinitis samples compared with normal samples, including 125 downregulated ones and 138 upregulated ones. The DEGs were enriched in 7 KEGG pathways. 308 differential co-expression gene pairs were obtained. A differential co-expression network was constructed, containing 212 nodes. In total, 148 PPI pairs of the DEGs were identified, and a PPI network was constructed based on these pairs. Bioinformatics methods could help us identify significant genes and pathways related to the pathogenesis of rhinitis. Steroid biosynthesis pathway and metabolic pathways might play important roles in the development of allergic rhinitis (AR). Genes such as CDC42 effector protein 5, solute carrier family 39 member A11 and PR/SET domain 10 might be also associated with the pathogenesis of AR, which provided references for the molecular mechanisms of AR. PMID:29257233

Metabolic Biomarkers and Neurodegeneration: A Pathway Enrichment Analysis of Alzheimer's Disease, Parkinson's Disease, and Amyotrophic Lateral Sclerosis.

PubMed

Kori, Medi; Aydın, Busra; Unal, Semra; Arga, Kazim Yalcin; Kazan, Dilek

2016-11-01

Neurodegenerative diseases such as Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS) lack robust diagnostics and prognostic biomarkers. Metabolomics is a postgenomics field that offers fresh insights for biomarkers of common complex as well as rare diseases. Using data on metabolite-disease associations published in the previous decade (2006-2016) in PubMed, ScienceDirect, Scopus, and Web of Science, we identified 101 metabolites as putative biomarkers for these three neurodegenerative diseases. Notably, uric acid, choline, creatine, L-glutamine, alanine, creatinine, and N-acetyl-L-aspartate were the shared metabolite signatures among the three diseases. The disease-metabolite-pathway associations pointed out the importance of membrane transport (through ATP binding cassette transporters), particularly of arginine and proline amino acids in all three neurodegenerative diseases. When disease-specific and common metabolic pathways were queried by using the pathway enrichment analyses, we found that alanine, aspartate, glutamate, and purine metabolism might act as alternative pathways to overcome inadequate glucose supply and energy crisis in neurodegeneration. These observations underscore the importance of metabolite-based biomarker research in deciphering the elusive pathophysiology of neurodegenerative diseases. Future research investments in metabolomics of complex diseases might provide new insights on AD, PD, and ALS that continue to place a significant burden on global health.

Geomorphology controls the trophic base of stream food webs in a boreal watershed .

PubMed

Smits, Adrianne P; Schindler, Daniel E; Brett, Michael T

2015-07-01

Abstract. Physical attributes of rivers control the quantity and quality of energy sources available to consumers, but it remains untested whether geomorphic conditions of whole watersheds affect the assimilation of different resources by stream organisms. We compared the fatty acid (FA) compositions of two invertebrate taxa (caddisflies, mayflies) collected from 16 streams in southwest Alaska, USA, to assess how assimilation of terrestrial organic matter (OM) and algae varied across a landscape gradient in watershed features. We found relatively higher assimilation of algae in high-gradient streams compared with low-gradient streams, and the opposite pattern for assimilation of terrestrial OM and microbes. The strength of these patterns was more pronounced for caddisflies than mayflies. Invertebrates from low-gradient watersheds had FA markers unique to methane-oxidizing bacteria and sulfate-reducing microbes, indicating a contribution of anaerobic pathways to primary consumers. Diversity of FA composition was highest in watersheds of intermediate slopes that contain both significant terrestrial inputs as well as high algal biomass. By controlling the accumulation rate and processing of terrestrial OM, watershed features influence the energetic base of food webs in boreal streams.

The online Tabloid Proteome: an annotated database of protein associations

PubMed Central

Turan, Demet; Tavernier, Jan

2018-01-01

Abstract A complete knowledge of the proteome can only be attained by determining the associations between proteins, along with the nature of these associations (e.g. physical contact in protein–protein interactions, participation in complex formation or different roles in the same pathway). Despite extensive efforts in elucidating direct protein interactions, our knowledge on the complete spectrum of protein associations remains limited. We therefore developed a new approach that detects protein associations from identifications obtained after re-processing of large-scale, public mass spectrometry-based proteomics data. Our approach infers protein association based on the co-occurrence of proteins across many different proteomics experiments, and provides information that is almost completely complementary to traditional direct protein interaction studies. We here present a web interface to query and explore the associations derived from this method, called the online Tabloid Proteome. The online Tabloid Proteome also integrates biological knowledge from several existing resources to annotate our derived protein associations. The online Tabloid Proteome is freely available through a user-friendly web interface, which provides intuitive navigation and data exploration options for the user at http://iomics.ugent.be/tabloidproteome. PMID:29040688

The Biofuel Feedstock Genomics Resource: a web-based portal and database to enable functional genomics of plant biofuel feedstock species.

PubMed

Childs, Kevin L; Konganti, Kranti; Buell, C Robin

2012-01-01

Major feedstock sources for future biofuel production are likely to be high biomass producing plant species such as poplar, pine, switchgrass, sorghum and maize. One active area of research in these species is genome-enabled improvement of lignocellulosic biofuel feedstock quality and yield. To facilitate genomic-based investigations in these species, we developed the Biofuel Feedstock Genomic Resource (BFGR), a database and web-portal that provides high-quality, uniform and integrated functional annotation of gene and transcript assembly sequences from species of interest to lignocellulosic biofuel feedstock researchers. The BFGR includes sequence data from 54 species and permits researchers to view, analyze and obtain annotation at the gene, transcript, protein and genome level. Annotation of biochemical pathways permits the identification of key genes and transcripts central to the improvement of lignocellulosic properties in these species. The integrated nature of the BFGR in terms of annotation methods, orthologous/paralogous relationships and linkage to seven species with complete genome sequences allows comparative analyses for biofuel feedstock species with limited sequence resources. Database URL: http://bfgr.plantbiology.msu.edu.

Determination of selenium bioavailability to a benthic bivalve from particulate and solute pathways

USGS Publications Warehouse

Luoma, S.N.; Johns, C.; Fisher, N.S.; Steinberg, N.A.; Oremland, R.S.; Reinfelder, J.R.

1992-01-01

Particulate organo-Se was assimilated with 86% efficiency by the deposit feeding bivalve Macoma balthica, when the clam was fed 75Se-labeled diatoms. Absorption efficiencies of participate elemental Se were 22%, when the animals were fed 75Se-labeled sediments in which elemental Se was precipitated by microbial dissimilatory reduction. Precipitation of elemental Se did not eliminate biological availability of the element. Selenite was taken up from solution slowly by M. balthica (mean concentration factor was 712). Concentrations of selenite high enough to influence Se bioaccumulation by M. balthica did not occur in the oxidized water column of San Francisco Bay. However, 98-99% of the Se observed in M. balthica could be explained by ingestion of the concentrations of participate Se found in the bay. The potential for adverse biological effects occurred at much lower concentrations of environmental Se when food web transfer was considered than when predictions of effects were based upon bioassays with solute forms of the element. Selenium clearly requires a protective criterion based upon particulate concentrations or food web transfer. ?? 1992 American Chemical Society.

PathCase-SB architecture and database design

PubMed Central

2011-01-01

Background Integration of metabolic pathways resources and regulatory metabolic network models, and deploying new tools on the integrated platform can help perform more effective and more efficient systems biology research on understanding the regulation in metabolic networks. Therefore, the tasks of (a) integrating under a single database environment regulatory metabolic networks and existing models, and (b) building tools to help with modeling and analysis are desirable and intellectually challenging computational tasks. Description PathCase Systems Biology (PathCase-SB) is built and released. The PathCase-SB database provides data and API for multiple user interfaces and software tools. The current PathCase-SB system provides a database-enabled framework and web-based computational tools towards facilitating the development of kinetic models for biological systems. PathCase-SB aims to integrate data of selected biological data sources on the web (currently, BioModels database and KEGG), and to provide more powerful and/or new capabilities via the new web-based integrative framework. This paper describes architecture and database design issues encountered in PathCase-SB's design and implementation, and presents the current design of PathCase-SB's architecture and database. Conclusions PathCase-SB architecture and database provide a highly extensible and scalable environment with easy and fast (real-time) access to the data in the database. PathCase-SB itself is already being used by researchers across the world. PMID:22070889

Productivity and linkages of the food web of the southern region of the western Antarctic Peninsula continental shelf

USGS Publications Warehouse

Ballerini, Tosca; Hofmann, Eileen E.; Ainley, David G.; Daly, Kendra L.; Marrari, Marina; Ribic, Christine A.; Smith, Walker O.; Steele, John H.

2014-01-01

The productivity and linkages in the food web of the southern region of the west Antarctic Peninsula continental shelf were investigated using a multi-trophic level mass balance model. Data collected during the Southern Ocean Global Ocean Ecosystem Dynamics field program were combined with data from the literature on the abundance and diet composition of zooplankton, fish, seabirds and marine mammals to calculate energy flows in the food web and to infer the overall food web structure at the annual level. Sensitivity analyses investigated the effects of variability in growth and biomass of Antarctic krill (Euphausia superba) and in the biomass of Antarctic krill predators on the structure and energy fluxes in the food web. Scenario simulations provided insights into the potential responses of the food web to a reduced contribution of large phytoplankton (diatom) production to total primary production, and to reduced consumption of primary production by Antarctic krill and mesozooplankton coincident with increased consumption by microzooplankton and salps. Model-derived estimates of primary production were 187–207 g C m−2 y−1, which are consistent with observed values (47–351 g C m−2 y−1). Simulations showed that Antarctic krill provide the majority of energy needed to sustain seabird and marine mammal production, thereby exerting a bottom-up control on higher trophic level predators. Energy transfer to top predators via mesozooplanton was a less efficient pathway, and salps were a production loss pathway because little of the primary production they consumed was passed to higher trophic levels. Increased predominance of small phytoplankton (nanoflagellates and cryptophytes) reduced the production of Antarctic krill and of its predators, including seabirds and seals.

Productivity and linkages of the food web of the southern region of the western Antarctic Peninsula continental shelf

NASA Astrophysics Data System (ADS)

Ballerini, Tosca; Hofmann, Eileen E.; Ainley, David G.; Daly, Kendra; Marrari, Marina; Ribic, Christine A.; Smith, Walker O.; Steele, John H.

2014-03-01

The productivity and linkages in the food web of the southern region of the west Antarctic Peninsula continental shelf were investigated using a multi-trophic level mass balance model. Data collected during the Southern Ocean Global Ocean Ecosystem Dynamics field program were combined with data from the literature on the abundance and diet composition of zooplankton, fish, seabirds and marine mammals to calculate energy flows in the food web and to infer the overall food web structure at the annual level. Sensitivity analyses investigated the effects of variability in growth and biomass of Antarctic krill (Euphausia superba) and in the biomass of Antarctic krill predators on the structure and energy fluxes in the food web. Scenario simulations provided insights into the potential responses of the food web to a reduced contribution of large phytoplankton (diatom) production to total primary production, and to reduced consumption of primary production by Antarctic krill and mesozooplankton coincident with increased consumption by microzooplankton and salps. Model-derived estimates of primary production were 187-207 g C m-2 y-1, which are consistent with observed values (47-351 g C m-2 y-1). Simulations showed that Antarctic krill provide the majority of energy needed to sustain seabird and marine mammal production, thereby exerting a bottom-up control on higher trophic level predators. Energy transfer to top predators via mesozooplanton was a less efficient pathway, and salps were a production loss pathway because little of the primary production they consumed was passed to higher trophic levels. Increased predominance of small phytoplankton (nanoflagellates and cryptophytes) reduced the production of Antarctic krill and of its predators, including seabirds and seals.

ADaCGH: A Parallelized Web-Based Application and R Package for the Analysis of aCGH Data

PubMed Central

Díaz-Uriarte, Ramón; Rueda, Oscar M.

2007-01-01

Background Copy number alterations (CNAs) in genomic DNA have been associated with complex human diseases, including cancer. One of the most common techniques to detect CNAs is array-based comparative genomic hybridization (aCGH). The availability of aCGH platforms and the need for identification of CNAs has resulted in a wealth of methodological studies. Methodology/Principal Findings ADaCGH is an R package and a web-based application for the analysis of aCGH data. It implements eight methods for detection of CNAs, gains and losses of genomic DNA, including all of the best performing ones from two recent reviews (CBS, GLAD, CGHseg, HMM). For improved speed, we use parallel computing (via MPI). Additional information (GO terms, PubMed citations, KEGG and Reactome pathways) is available for individual genes, and for sets of genes with altered copy numbers. Conclusions/Significance ADaCGH represents a qualitative increase in the standards of these types of applications: a) all of the best performing algorithms are included, not just one or two; b) we do not limit ourselves to providing a thin layer of CGI on top of existing BioConductor packages, but instead carefully use parallelization, examining different schemes, and are able to achieve significant decreases in user waiting time (factors up to 45×); c) we have added functionality not currently available in some methods, to adapt to recent recommendations (e.g., merging of segmentation results in wavelet-based and CGHseg algorithms); d) we incorporate redundancy, fault-tolerance and checkpointing, which are unique among web-based, parallelized applications; e) all of the code is available under open source licenses, allowing to build upon, copy, and adapt our code for other software projects. PMID:17710137

ADaCGH: A parallelized web-based application and R package for the analysis of aCGH data.

PubMed

Díaz-Uriarte, Ramón; Rueda, Oscar M

2007-08-15

Copy number alterations (CNAs) in genomic DNA have been associated with complex human diseases, including cancer. One of the most common techniques to detect CNAs is array-based comparative genomic hybridization (aCGH). The availability of aCGH platforms and the need for identification of CNAs has resulted in a wealth of methodological studies. ADaCGH is an R package and a web-based application for the analysis of aCGH data. It implements eight methods for detection of CNAs, gains and losses of genomic DNA, including all of the best performing ones from two recent reviews (CBS, GLAD, CGHseg, HMM). For improved speed, we use parallel computing (via MPI). Additional information (GO terms, PubMed citations, KEGG and Reactome pathways) is available for individual genes, and for sets of genes with altered copy numbers. ADACGH represents a qualitative increase in the standards of these types of applications: a) all of the best performing algorithms are included, not just one or two; b) we do not limit ourselves to providing a thin layer of CGI on top of existing BioConductor packages, but instead carefully use parallelization, examining different schemes, and are able to achieve significant decreases in user waiting time (factors up to 45x); c) we have added functionality not currently available in some methods, to adapt to recent recommendations (e.g., merging of segmentation results in wavelet-based and CGHseg algorithms); d) we incorporate redundancy, fault-tolerance and checkpointing, which are unique among web-based, parallelized applications; e) all of the code is available under open source licenses, allowing to build upon, copy, and adapt our code for other software projects.

Reciprocal subsidies and food web pathways leading to chum salmon fry in a temperate marine-terrestrial ecotone.

PubMed

Romanuk, Tamara N; Levings, Colin D

2010-04-08

Stable isotope analysis was used to determine the relative proportions of terrestrial and marine subsidies of carbon to invertebrates along a tidal gradient (low-intertidal, mid-intertidal, high-intertidal, supralittoral) and to determine the relative importance of terrestrial carbon in food web pathways leading to chum salmon fry Oncorhynchus keta (Walbaum) in Howe Sound, British Columbia. We found a clear gradient in the proportion of terrestrially derived carbon along the tidal gradient ranging from 68% across all invertebrate taxa in the supralittoral to 25% in the high-intertidal, 20% in the mid-intertidal, and 12% in the low-intertidal. Stable isotope values of chum salmon fry indicated carbon contributions from both terrestrial and marine sources, with terrestrially derived carbon ranging from 12.8 to 61.5% in the muscle tissue of chum salmon fry (mean 30%). Our results provide evidence for reciprocal subsidies of marine and terrestrially derived carbon on beaches in the estuary and suggest that the vegetated supralittoral is an important trophic link in supplying terrestrial carbon to nearshore food webs.

DAPD: A Knowledgebase for Diabetes Associated Proteins.

PubMed

Gopinath, Krishnasamy; Jayakumararaj, Ramaraj; Karthikeyan, Muthusamy

2015-01-01

Recent advancements in genomics and proteomics provide a solid foundation for understanding the pathogenesis of diabetes. Proteomics of diabetes associated pathways help to identify the most potent target for the management of diabetes. The relevant datasets are scattered in various prominent sources which takes much time to select the therapeutic target for the clinical management of diabetes. However, additional information about target proteins is needed for validation. This lacuna may be resolved by linking diabetes associated genes, pathways and proteins and it will provide a strong base for the treatment and planning management strategies of diabetes. Thus, a web source "Diabetes Associated Proteins Database (DAPD)" has been developed to link the diabetes associated genes, pathways and proteins using PHP, MySQL. The current version of DAPD has been built with proteins associated with different types of diabetes. In addition, DAPD has been linked to external sources to gain the access to more participatory proteins and their pathway network. DAPD will reduce the time and it is expected to pave the way for the discovery of novel anti-diabetic leads using computational drug designing for diabetes management. DAPD is open accessed via following url www.mkarthikeyan.bioinfoau.org/dapd.

Effects of Seasonal and Spatial Differences in Food Webs on Mercury Concentrations in Fish in the Everglades

NASA Astrophysics Data System (ADS)

Kendall, C.; Bemis, B. E.; Wankel, S. D.; Rawlik, P. S.; Lange, T.; Krabbenhoft, D. P.

2002-05-01

A clear understanding of the aquatic food web is essential for determining the entry points and subsequent biomagnification pathways of contaminants such as methyl-mercury (MeHg) in the Everglades. Anthropogenic changes in nutrients can significantly affect the entry points of MeHg by changing food web structure from one dominated by algal productivity to one dominated by macrophytes and associated microbial activity. These changes in the base of the food web can also influence the distribution of animals within the ecosystem, and subsequently the bioaccumulation of MeHg up the food chain. As part of several collaborations with local and other federal agencies, more than 7000 Everglades samples were collected in 1995-99, and analysed for d13C and d15N. Many organisms were also analysed for d34S, gut contents, total Hg, and MeHg. Carbon isotopes effectively distinguish between two main types of food webs: ones where algae is the dominant base of the food web, which are characteristic of relatively pristine marsh sites with long hydroperiods, and ones where macrophyte debris appears to be a significant source of nutrients, which are apparently characteristic of shorter hydroperiod sites, and nutrient-impacted marshes and canals. Many organisms show significant (5-12%) spatial and temporal differences in d13C and d15N values across the Everglades. These differences may reflect site and season-specific differences in the relative importance of algae vs. macrophyte debris to the food web. However, there is a lack of evidence that these sites otherwise differ in food chain length (as determined by d15N values). This conclusion is generally supported by gut contents and mercury data. Furthermore, there are no statistically significant differences between the Delta d15N (predator-algae) values at pristine marsh, nutrient-impacted marsh, or canal sites. The main conclusions from this preliminary comparison of gut contents, stable isotope, and Hg data are: (1) there is little evidence for spatial variations in food chain length - hence, this does not appear to be the dominant explanation for spatial variations in Hg in predators, (2) the poor correlation of d15N and Hg for many organisms, reflective of the heterogeneous and dynamic nature of the ecosystem, makes it difficult to account for changes in Hg with trophic position, and (3) seasonal and spatial variations in hydrology and nutrient conditions, which are often reflected in changes in the base of the food web, appear to be the dominant controls on the isotopic compositions of organisms in the Everglades. Hence, biota isotopes provide a tool for monitoring how future ecosystem changes affect the distribution of algae vs. macrophyte-dominated food webs across the Everglades.

The Pathway Tools software.

PubMed

Karp, Peter D; Paley, Suzanne; Romero, Pedro

2002-01-01

Bioinformatics requires reusable software tools for creating model-organism databases (MODs). The Pathway Tools is a reusable, production-quality software environment for creating a type of MOD called a Pathway/Genome Database (PGDB). A PGDB such as EcoCyc (see http://ecocyc.org) integrates our evolving understanding of the genes, proteins, metabolic network, and genetic network of an organism. This paper provides an overview of the four main components of the Pathway Tools: The PathoLogic component supports creation of new PGDBs from the annotated genome of an organism. The Pathway/Genome Navigator provides query, visualization, and Web-publishing services for PGDBs. The Pathway/Genome Editors support interactive updating of PGDBs. The Pathway Tools ontology defines the schema of PGDBs. The Pathway Tools makes use of the Ocelot object database system for data management services for PGDBs. The Pathway Tools has been used to build PGDBs for 13 organisms within SRI and by external users.

Behind the energetics of the asiatic clam, Potamocorbula amurensis, in San Francisco Bay

USGS Publications Warehouse

Thompson, Janet K.; Parchaso, Francis

2001-01-01

The Asian clam (Potamocorbula amurensis) has played a key role in the food web of northern San Francisco Bay since its invasion in the fall of 1986. It has been associated with a dramatic decline in primary production, loss of a zooplankton species and a native mysid shrimp, the probable decline in striped bass, and has introduced alternative pathways for contaminant cycling in the bay food web.

Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network

PubMed Central

Hwang, Sohyun; Rhee, Seung Y; Marcotte, Edward M; Lee, Insuk

2012-01-01

AraNet is a functional gene network for the reference plant Arabidopsis and has been constructed in order to identify new genes associated with plant traits. It is highly predictive for diverse biological pathways and can be used to prioritize genes for functional screens. Moreover, AraNet provides a web-based tool with which plant biologists can efficiently discover novel functions of Arabidopsis genes (http://www.functionalnet.org/aranet/). This protocol explains how to conduct network-based prediction of gene functions using AraNet and how to interpret the prediction results. Functional discovery in plant biology is facilitated by combining candidate prioritization by AraNet with focused experimental tests. PMID:21886106

Gene- and pathway-based association tests for multiple traits with GWAS summary statistics.

PubMed

Kwak, Il-Youp; Pan, Wei

2017-01-01

To identify novel genetic variants associated with complex traits and to shed new insights on underlying biology, in addition to the most popular single SNP-single trait association analysis, it would be useful to explore multiple correlated (intermediate) traits at the gene- or pathway-level by mining existing single GWAS or meta-analyzed GWAS data. For this purpose, we present an adaptive gene-based test and a pathway-based test for association analysis of multiple traits with GWAS summary statistics. The proposed tests are adaptive at both the SNP- and trait-levels; that is, they account for possibly varying association patterns (e.g. signal sparsity levels) across SNPs and traits, thus maintaining high power across a wide range of situations. Furthermore, the proposed methods are general: they can be applied to mixed types of traits, and to Z-statistics or P-values as summary statistics obtained from either a single GWAS or a meta-analysis of multiple GWAS. Our numerical studies with simulated and real data demonstrated the promising performance of the proposed methods. The methods are implemented in R package aSPU, freely and publicly available at: https://cran.r-project.org/web/packages/aSPU/ CONTACT: weip@biostat.umn.eduSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Transcriptator: An Automated Computational Pipeline to Annotate Assembled Reads and Identify Non Coding RNA.

PubMed

Tripathi, Kumar Parijat; Evangelista, Daniela; Zuccaro, Antonio; Guarracino, Mario Rosario

2015-01-01

RNA-seq is a new tool to measure RNA transcript counts, using high-throughput sequencing at an extraordinary accuracy. It provides quantitative means to explore the transcriptome of an organism of interest. However, interpreting this extremely large data into biological knowledge is a problem, and biologist-friendly tools are lacking. In our lab, we developed Transcriptator, a web application based on a computational Python pipeline with a user-friendly Java interface. This pipeline uses the web services available for BLAST (Basis Local Search Alignment Tool), QuickGO and DAVID (Database for Annotation, Visualization and Integrated Discovery) tools. It offers a report on statistical analysis of functional and Gene Ontology (GO) annotation's enrichment. It helps users to identify enriched biological themes, particularly GO terms, pathways, domains, gene/proteins features and protein-protein interactions related informations. It clusters the transcripts based on functional annotations and generates a tabular report for functional and gene ontology annotations for each submitted transcript to the web server. The implementation of QuickGo web-services in our pipeline enable the users to carry out GO-Slim analysis, whereas the integration of PORTRAIT (Prediction of transcriptomic non coding RNA (ncRNA) by ab initio methods) helps to identify the non coding RNAs and their regulatory role in transcriptome. In summary, Transcriptator is a useful software for both NGS and array data. It helps the users to characterize the de-novo assembled reads, obtained from NGS experiments for non-referenced organisms, while it also performs the functional enrichment analysis of differentially expressed transcripts/genes for both RNA-seq and micro-array experiments. It generates easy to read tables and interactive charts for better understanding of the data. The pipeline is modular in nature, and provides an opportunity to add new plugins in the future. Web application is freely available at: http://www-labgtp.na.icar.cnr.it/Transcriptator.

Discovering causal signaling pathways through gene-expression patterns

PubMed Central

Parikh, Jignesh R.; Klinger, Bertram; Xia, Yu; Marto, Jarrod A.; Blüthgen, Nils

2010-01-01

High-throughput gene-expression studies result in lists of differentially expressed genes. Most current meta-analyses of these gene lists include searching for significant membership of the translated proteins in various signaling pathways. However, such membership enrichment algorithms do not provide insight into which pathways caused the genes to be differentially expressed in the first place. Here, we present an intuitive approach for discovering upstream signaling pathways responsible for regulating these differentially expressed genes. We identify consistently regulated signature genes specific for signal transduction pathways from a panel of single-pathway perturbation experiments. An algorithm that detects overrepresentation of these signature genes in a gene group of interest is used to infer the signaling pathway responsible for regulation. We expose our novel resource and algorithm through a web server called SPEED: Signaling Pathway Enrichment using Experimental Data sets. SPEED can be freely accessed at http://speed.sys-bio.net/. PMID:20494976

Effects of littoral habitat complexity and sunfish composition on fish production

USGS Publications Warehouse

Carey, Michael P.; Maloney, K.O.; Chipps, S.R.; Wahl, David H.

2010-01-01

Habitat complexity is a key driver of food web dynamics because physical structure dictates resource availability to a community. Changes in fish diversity can also alter trophic interactions and energy pathways in food webs. Few studies have examined the direct, indirect, and interactive effects of biodiversity and habitat complexity on fish production. We explored the effects of habitat complexity (simulated vegetation), sunfish diversity (intra‐ vs. inter‐specific sunfish), and their interaction using a mesocosm experiment. Total fish production was examined across two levels of habitat complexity (low: 161 strands m−2 and high: 714 strands m−2) and two sunfish diversity treatments: bluegill only (Lepomis macrochirus) and bluegill, redear sunfish (Lepomis microlophus), and green sunfish (Lepomis cyanellus) combination. We also measured changes in total phosphorus, phytoplankton, periphyton, and invertebrates to explain patterns in fish production. Bluegill and total fish production were unaffected by the sunfish treatments. Habitat complexity had a large influence on food web structure by shifting primary productivity from pelagic to a more littoral pathway in the high habitat treatments. Periphyton was higher with dense vegetation, leading to reductions in total phosphorus, phytoplankton, cladoceran abundance and fish biomass. In tanks with low vegetation, bluegill exhibited increased growth. Habitat complexity can alter energy flow through food webs ultimately influencing higher trophic levels. The lack of an effect of sunfish diversity on fish production does not imply that conserving biodiversity is unimportant; rather, we suggest that understanding the context in which biodiversity is important to food web dynamics is critical to conservation planning

Redesigning Instruction through Web-based Course Authoring Tools.

ERIC Educational Resources Information Center

Dabbagh, Nada H.; Schmitt, Jeff

1998-01-01

Examines the pedagogical implications of redesigning instruction for Web-based delivery through a case study of an undergraduate computer science course. Initially designed for a traditional learning environment, this course transformed to a Web-based course using WebCT, a Web-based course authoring tool. Discusses the specific features of WebCT.…

Impacts of food web structure and feeding behavior on mercury exposure in Greenland Sharks (Somniosus microcephalus).

PubMed

McMeans, Bailey C; Arts, Michael T; Fisk, Aaron T

2015-03-15

Benthic and pelagic food web components in Cumberland Sound, Canada were explored as sources of total mercury (THg) to Greenland Sharks (Somniosus microcephalus) via both bottom-up food web transfer and top-down shark feeding behavior. Log10THg increased significantly with δ(15)N and trophic position from invertebrates (0.01 ± 0.01 μg · g(-1) [113 ± 1 ng · g(-1)] dw in copepods) to Greenland Sharks (3.54 ± 1.02 μg · g(-1)). The slope of the log10THg vs. δ(15)N linear regression was higher for pelagic compared to benthic food web components (excluding Greenland Sharks, which could not be assigned to either food web), which resulted from THg concentrations being higher at the base of the benthic food web (i.e., in benthic than pelagic primary consumers). However, feeding habitat is unlikely to consistently influence shark THg exposure in Cumberland Sound because THg concentrations did not consistently differ between benthic and pelagic shark prey. Further, size, gender and feeding behavior (inferred from stable isotopes and fatty acids) were unable to significantly explain THg variability among individual Greenland Sharks. Possible reasons for this result include: 1) individual sharks feeding as generalists, 2) high overlap in THg among shark prey, and 3) differences in turnover time between ecological tracers and THg. This first assessment of Greenland Shark THg within an Arctic food web revealed high concentrations consistent with biomagnification, but low ability to explain intra-specific THg variability. Our findings of high THg levels and consumption of multiple prey types, however, suggest that Greenland Sharks acquire THg through a variety of trophic pathways and are a significant contributor to the total biotic THg pool in northern seas. Copyright © 2014 Elsevier B.V. All rights reserved.

Plankton food-web functioning in anthropogenically impacted coastal waters (SW Mediterranean Sea): An ecological network analysis

NASA Astrophysics Data System (ADS)

Meddeb, Marouan; Grami, Boutheïna; Chaalali, Aurélie; Haraldsson, Matilda; Niquil, Nathalie; Pringault, Olivier; Sakka Hlaili, Asma

2018-03-01

The study is the first attempt to (i) model spring food webs in three SW Mediterranean ecosystems which are under different anthropogenic pressures and (ii) to project the consequence of this stress on their function. Linear inverse models were built using the Monte Carlo method coupled with Markov Chains to characterize the food-web status of the Lagoon, the Channel (inshore waters under high eutrophication and chemical contamination) and the Bay of Bizerte (offshore waters under less anthropogenic pressure). Ecological network analysis was used for the description of structural and functional properties of each food web and for inter-ecosystem comparisons. Our results showed that more carbon was produced by phytoplankton in the inshore waters (966-1234 mg C m-2 d-1) compared to the Bay (727 mg C m-2 d-1). The total ecosystem carbon inputs into the three food webs was supported by high primary production, which was mainly due to >10 μm algae. However, the three carbon pathways were characterized by low detritivory and a high herbivory which was mainly assigned to protozooplankton. This latter was efficient in channelling biogenic carbon. In the Lagoon and the Channel, foods webs acted almost as a multivorous structure with a tendency towards herbivorous one, whereas in the Bay the herbivorous pathway was more dominant. Ecological indices revealed that the Lagoon and the Channel food webs/systems had high total system throughput and thus were more active than the Bay. The Bay food web, which had a high relative ascendency value, was more organized and specialized. This inter-ecosystem difference could be due to the varying levels of anthropogenic impact among sites. Indeed, the low value of Finn's cycling index indicated that the three systems are disturbed, but the Lagoon and the Channel, with low average path lengths, appeared to be more stressed, as both sites have undergone higher chemical pollution and nutrient loading. This study shows that ecosystem models combined with ecological indices provide a powerful approach to detect change in environmental status and anthropogenic impacts.

GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes.

PubMed

Arakawa, Kazuharu; Yamada, Yohei; Shinoda, Kosaku; Nakayama, Yoichi; Tomita, Masaru

2006-03-23

Successful realization of a "systems biology" approach to analyzing cells is a grand challenge for our understanding of life. However, current modeling approaches to cell simulation are labor-intensive, manual affairs, and therefore constitute a major bottleneck in the evolution of computational cell biology. We developed the Genome-based Modeling (GEM) System for the purpose of automatically prototyping simulation models of cell-wide metabolic pathways from genome sequences and other public biological information. Models generated by the GEM System include an entire Escherichia coli metabolism model comprising 968 reactions of 1195 metabolites, achieving 100% coverage when compared with the KEGG database, 92.38% with the EcoCyc database, and 95.06% with iJR904 genome-scale model. The GEM System prototypes qualitative models to reduce the labor-intensive tasks required for systems biology research. Models of over 90 bacterial genomes are available at our web site.

Perfluorinated compounds in the Antarctic region: ocean circulation provides prolonged protection from distant sources.

PubMed

Bengtson Nash, Susan; Rintoul, Stephen R; Kawaguchi, So; Staniland, Iain; van den Hoff, John; Tierney, Megan; Bossi, Rossana

2010-09-01

In order to investigate the extent to which Perfluorinated Contaminants (PFCs) have permeated the Southern Ocean food web to date, a range of Antarctic, sub-Antarctic and Antarctic-migratory biota were analysed for key ionic PFCs. Based upon the geographical distribution pattern and ecology of biota with detectable vs. non-detectable PFC burdens, an evaluation of the potential contributory roles of alternative system input pathways is made. Our analytical findings, together with previous reports, reveal only the occasional occurrence of PFCs in migratory biota and vertebrate predators with foraging ranges extending into or north of the Antarctic Circumpolar Current (ACC). Geographical contamination patterns observed correspond most strongly with those expected from delivery via hydrospheric transport as governed by the unique oceanographic features of the Southern Ocean. We suggest that hydrospheric transport will form a slow, but primary, input pathway of PFCs to the Antarctic region. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Social influence in childhood obesity interventions: a systematic review.

PubMed

Jalali, M S; Sharafi-Avarzaman, Z; Rahmandad, H; Ammerman, A S

2016-09-01

The objective of this study is to understand the pathways through which social influence at the family level moderates the impact of childhood obesity interventions. We conducted a systematic review of obesity interventions in which parents' behaviours are targeted to change children's obesity outcomes, because of the potential social and environmental influence of parents on the nutrition and physical activity behaviours of children. PubMed (1966-2013) and the Web of Science (1900-2013) were searched, and 32 studies satisfied our inclusion criteria. Results for existing mechanisms that moderate parents' influence on children's behaviour are discussed, and a causal pathway diagram is developed to map out social influence mechanisms that affect childhood obesity. We provide health professionals and researchers with recommendations for leveraging family-based social influence mechanisms to increase the efficacy of obesity intervention programmes. © 2016 World Obesity. © 2016 World Obesity.

Introduced predators transform subarctic islands from grassland to tundra

USGS Publications Warehouse

Croll, D.A.; Maron, J.L.; Estes, J.A.; Danner, E.M.; Byrd, G.V.

2005-01-01

Top predators often have powerful direct effects on prey populations, but whether these direct effects propagate to the base of terrestrial food webs is debated. There are few examples of trophic cascades strong enough to alter the abundance and composition of entire plant communities. We show that the introduction of arctic foxes (Alopex lagopus) to the Aleutian archipelago induced strong shifts in plant productivity and community structure via a previously unknown pathway. By preying on seabirds, foxes reduced nutrient transport from ocean to land, affecting soil fertility and transforming grasslands to dwarf shrub/forb-dominated ecosystems.

Unravelling Some of the Key Transformations in the Hydrothermal Liquefaction of Lignin.

PubMed

Lui, Matthew Y; Chan, Bun; Yuen, Alexander K L; Masters, Anthony F; Montoya, Alejandro; Maschmeyer, Thomas

2017-05-22

Using both experimental and computational methods, focusing on intermediates and model compounds, some of the main features of the reaction mechanisms that operate during the hydrothermal processing of lignin were elucidated. Key reaction pathways and their connection to different structural features of lignin were proposed. Under neutral conditions, subcritical water was demonstrated to act as a bifunctional acid/base catalyst for the dissection of lignin structures. In a complex web of mutually dependent interactions, guaiacyl units within lignin were shown to significantly affect overall lignin reactivity. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Design and evaluation of web-based image transmission and display with different protocols

NASA Astrophysics Data System (ADS)

Tan, Bin; Chen, Kuangyi; Zheng, Xichuan; Zhang, Jianguo

2011-03-01

There are many Web-based image accessing technologies used in medical imaging area, such as component-based (ActiveX Control) thick client Web display, Zerofootprint thin client Web viewer (or called server side processing Web viewer), Flash Rich Internet Application(RIA) ,or HTML5 based Web display. Different Web display methods have different peformance in different network environment. In this presenation, we give an evaluation on two developed Web based image display systems. The first one is used for thin client Web display. It works between a PACS Web server with WADO interface and thin client. The PACS Web server provides JPEG format images to HTML pages. The second one is for thick client Web display. It works between a PACS Web server with WADO interface and thick client running in browsers containing ActiveX control, Flash RIA program or HTML5 scripts. The PACS Web server provides native DICOM format images or JPIP stream for theses clients.

Pivotal role of the muscle-contraction pathway in cryptorchidism and evidence for genomic connections with cardiomyopathy pathways in RASopathies.

PubMed

Cannistraci, Carlo V; Ogorevc, Jernej; Zorc, Minja; Ravasi, Timothy; Dovc, Peter; Kunej, Tanja

2013-02-14

Cryptorchidism is the most frequent congenital disorder in male children; however the genetic causes of cryptorchidism remain poorly investigated. Comparative integratomics combined with systems biology approach was employed to elucidate genetic factors and molecular pathways underlying testis descent. Literature mining was performed to collect genomic loci associated with cryptorchidism in seven mammalian species. Information regarding the collected candidate genes was stored in MySQL relational database. Genomic view of the loci was presented using Flash GViewer web tool (http://gmod.org/wiki/Flashgviewer/). DAVID Bioinformatics Resources 6.7 was used for pathway enrichment analysis. Cytoscape plug-in PiNGO 1.11 was employed for protein-network-based prediction of novel candidate genes. Relevant protein-protein interactions were confirmed and visualized using the STRING database (version 9.0). The developed cryptorchidism gene atlas includes 217 candidate loci (genes, regions involved in chromosomal mutations, and copy number variations) identified at the genomic, transcriptomic, and proteomic level. Human orthologs of the collected candidate loci were presented using a genomic map viewer. The cryptorchidism gene atlas is freely available online: http://www.integratomics-time.com/cryptorchidism/. Pathway analysis suggested the presence of twelve enriched pathways associated with the list of 179 literature-derived candidate genes. Additionally, a list of 43 network-predicted novel candidate genes was significantly associated with four enriched pathways. Joint pathway analysis of the collected and predicted candidate genes revealed the pivotal importance of the muscle-contraction pathway in cryptorchidism and evidence for genomic associations with cardiomyopathy pathways in RASopathies. The developed gene atlas represents an important resource for the scientific community researching genetics of cryptorchidism. The collected data will further facilitate development of novel genetic markers and could be of interest for functional studies in animals and human. The proposed network-based systems biology approach elucidates molecular mechanisms underlying co-presence of cryptorchidism and cardiomyopathy in RASopathies. Such approach could also aid in molecular explanation of co-presence of diverse and apparently unrelated clinical manifestations in other syndromes.

Integrated analysis of microRNA and gene expression profiles reveals a functional regulatory module associated with liver fibrosis.

PubMed

Chen, Wei; Zhao, Wenshan; Yang, Aiting; Xu, Anjian; Wang, Huan; Cong, Min; Liu, Tianhui; Wang, Ping; You, Hong

2017-12-15

Liver fibrosis, characterized with the excessive accumulation of extracellular matrix (ECM) proteins, represents the final common pathway of chronic liver inflammation. Ever-increasing evidence indicates microRNAs (miRNAs) dysregulation has important implications in the different stages of liver fibrosis. However, our knowledge of miRNA-gene regulation details pertaining to such disease remains unclear. The publicly available Gene Expression Omnibus (GEO) datasets of patients suffered from cirrhosis were extracted for integrated analysis. Differentially expressed miRNAs (DEMs) and genes (DEGs) were identified using GEO2R web tool. Putative target gene prediction of DEMs was carried out using the intersection of five major algorithms: DIANA-microT, TargetScan, miRanda, PICTAR5 and miRWalk. Functional miRNA-gene regulatory network (FMGRN) was constructed based on the computational target predictions at the sequence level and the inverse expression relationships between DEMs and DEGs. DAVID web server was selected to perform KEGG pathway enrichment analysis. Functional miRNA-gene regulatory module was generated based on the biological interpretation. Internal connections among genes in liver fibrosis-related module were determined using String database. MiRNA-gene regulatory modules related to liver fibrosis were experimentally verified in recombinant human TGFβ1 stimulated and specific miRNA inhibitor treated LX-2 cells. We totally identified 85 and 923 dysregulated miRNAs and genes in liver cirrhosis biopsy samples compared to their normal controls. All evident miRNA-gene pairs were identified and assembled into FMGRN which consisted of 990 regulations between 51 miRNAs and 275 genes, forming two big sub-networks that were defined as down-network and up-network, respectively. KEGG pathway enrichment analysis revealed that up-network was prominently involved in several KEGG pathways, in which "Focal adhesion", "PI3K-Akt signaling pathway" and "ECM-receptor interaction" were remarked significant (adjusted p<0.001). Genes enriched in these pathways coupled with their regulatory miRNAs formed a functional miRNA-gene regulatory module that contains 7 miRNAs, 22 genes and 42 miRNA-gene connections. Gene interaction analysis based on String database revealed that 8 out of 22 genes were highly clustered. Finally, we experimentally confirmed a functional regulatory module containing 5 miRNAs (miR-130b-3p, miR-148a-3p, miR-345-5p, miR-378a-3p, and miR-422a) and 6 genes (COL6A1, COL6A2, COL6A3, PIK3R3, COL1A1, CCND2) associated with liver fibrosis. Our integrated analysis of miRNA and gene expression profiles highlighted a functional miRNA-gene regulatory module associated with liver fibrosis, which, to some extent, may provide important clues to better understand the underlying pathogenesis of liver fibrosis. Copyright © 2017. Published by Elsevier B.V.

The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications

PubMed Central

2011-01-01

Background The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability between such tools. To ensure interoperability initiatives are effectively deployed, end-user applications need to be aware of, and support, best practices and standards. Here, we report on an initiative in which software developers and genome biologists came together to explore and raise awareness of these issues: BioHackathon 2009. Results Developers in attendance came from diverse backgrounds, with experts in Web services, workflow tools, text mining and visualization. Genome biologists provided expertise and exemplar data from the domains of sequence and pathway analysis and glyco-informatics. One goal of the meeting was to evaluate the ability to address real world use cases in these domains using the tools that the developers represented. This resulted in i) a workflow to annotate 100,000 sequences from an invertebrate species; ii) an integrated system for analysis of the transcription factor binding sites (TFBSs) enriched based on differential gene expression data obtained from a microarray experiment; iii) a workflow to enumerate putative physical protein interactions among enzymes in a metabolic pathway using protein structure data; iv) a workflow to analyze glyco-gene-related diseases by searching for human homologs of glyco-genes in other species, such as fruit flies, and retrieving their phenotype-annotated SNPs. Conclusions Beyond deriving prototype solutions for each use-case, a second major purpose of the BioHackathon was to highlight areas of insufficiency. We discuss the issues raised by our exploration of the problem/solution space, concluding that there are still problems with the way Web services are modeled and annotated, including: i) the absence of several useful data or analysis functions in the Web service "space"; ii) the lack of documentation of methods; iii) lack of compliance with the SOAP/WSDL specification among and between various programming-language libraries; and iv) incompatibility between various bioinformatics data formats. Although it was still difficult to solve real world problems posed to the developers by the biological researchers in attendance because of these problems, we note the promise of addressing these issues within a semantic framework. PMID:21806842

The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications.

PubMed

Katayama, Toshiaki; Wilkinson, Mark D; Vos, Rutger; Kawashima, Takeshi; Kawashima, Shuichi; Nakao, Mitsuteru; Yamamoto, Yasunori; Chun, Hong-Woo; Yamaguchi, Atsuko; Kawano, Shin; Aerts, Jan; Aoki-Kinoshita, Kiyoko F; Arakawa, Kazuharu; Aranda, Bruno; Bonnal, Raoul Jp; Fernández, José M; Fujisawa, Takatomo; Gordon, Paul Mk; Goto, Naohisa; Haider, Syed; Harris, Todd; Hatakeyama, Takashi; Ho, Isaac; Itoh, Masumi; Kasprzyk, Arek; Kido, Nobuhiro; Kim, Young-Joo; Kinjo, Akira R; Konishi, Fumikazu; Kovarskaya, Yulia; von Kuster, Greg; Labarga, Alberto; Limviphuvadh, Vachiranee; McCarthy, Luke; Nakamura, Yasukazu; Nam, Yunsun; Nishida, Kozo; Nishimura, Kunihiro; Nishizawa, Tatsuya; Ogishima, Soichi; Oinn, Tom; Okamoto, Shinobu; Okuda, Shujiro; Ono, Keiichiro; Oshita, Kazuki; Park, Keun-Joon; Putnam, Nicholas; Senger, Martin; Severin, Jessica; Shigemoto, Yasumasa; Sugawara, Hideaki; Taylor, James; Trelles, Oswaldo; Yamasaki, Chisato; Yamashita, Riu; Satoh, Noriyuki; Takagi, Toshihisa

2011-08-02

The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability between such tools. To ensure interoperability initiatives are effectively deployed, end-user applications need to be aware of, and support, best practices and standards. Here, we report on an initiative in which software developers and genome biologists came together to explore and raise awareness of these issues: BioHackathon 2009. Developers in attendance came from diverse backgrounds, with experts in Web services, workflow tools, text mining and visualization. Genome biologists provided expertise and exemplar data from the domains of sequence and pathway analysis and glyco-informatics. One goal of the meeting was to evaluate the ability to address real world use cases in these domains using the tools that the developers represented. This resulted in i) a workflow to annotate 100,000 sequences from an invertebrate species; ii) an integrated system for analysis of the transcription factor binding sites (TFBSs) enriched based on differential gene expression data obtained from a microarray experiment; iii) a workflow to enumerate putative physical protein interactions among enzymes in a metabolic pathway using protein structure data; iv) a workflow to analyze glyco-gene-related diseases by searching for human homologs of glyco-genes in other species, such as fruit flies, and retrieving their phenotype-annotated SNPs. Beyond deriving prototype solutions for each use-case, a second major purpose of the BioHackathon was to highlight areas of insufficiency. We discuss the issues raised by our exploration of the problem/solution space, concluding that there are still problems with the way Web services are modeled and annotated, including: i) the absence of several useful data or analysis functions in the Web service "space"; ii) the lack of documentation of methods; iii) lack of compliance with the SOAP/WSDL specification among and between various programming-language libraries; and iv) incompatibility between various bioinformatics data formats. Although it was still difficult to solve real world problems posed to the developers by the biological researchers in attendance because of these problems, we note the promise of addressing these issues within a semantic framework.

Reorganization of a marine trophic network along an inshore-offshore gradient due to stronger pelagic-benthic coupling in coastal areas

NASA Astrophysics Data System (ADS)

Kopp, Dorothée; Lefebvre, Sébastien; Cachera, Marie; Villanueva, Maria Ching; Ernande, Bruno

2015-01-01

Recent theoretical considerations have highlighted the importance of the pelagic-benthic coupling in marine food webs. In continental shelf seas, it was hypothesized that the trophic network structure may change along an inshore-offshore gradient due to weakening of the pelagic-benthic coupling from coastal to offshore areas. We tested this assumption empirically using the eastern English Channel (EEC) as a case study. We sampled organisms from particulate organic matter to predatory fishes and used baseline-corrected carbon and nitrogen stable isotope ratios (δ13C and δ15N) to determine their trophic position. First, hierarchical clustering on δ13C and δ15N coupled to bootstrapping and estimates of the relative contribution of pelagic and benthic carbon sources to consumers' diet showed that, at mesoscale, the EEC food web forms a continuum of four trophic levels with trophic groups spread across a pelagic and a benthic trophic pathway. Second, based on the same methods, a discrete approach examined changes in the local food web structure across three depth strata in order to investigate the inshore-offshore gradient. It showed stronger pelagic-benthic coupling in shallow coastal areas mostly due to a reorganization of the upper consumers relative to the two trophic pathways, benthic carbon sources being available to pelagic consumers and, reciprocally, pelagic sources becoming accessible to benthic species. Third a continuous approach examined changes in the mean and variance of upper consumers' δ13C and δ15N with depth. It detected a significant decrease in δ13C variance and a significant increase in δ15N variance as depth increases. A theoretical two-source mixing model showed that an inshore-offshore decrease in the pelagic-benthic coupling was a sufficient condition to produce the δ13C variance pattern, thus supporting the conclusions of the discrete approach. These results suggest that environmental gradients such as the inshore-offshore one should be accounted for to better understand marine food webs dynamics.

PANDA: pathway and annotation explorer for visualizing and interpreting gene-centric data.

PubMed

Hart, Steven N; Moore, Raymond M; Zimmermann, Michael T; Oliver, Gavin R; Egan, Jan B; Bryce, Alan H; Kocher, Jean-Pierre A

2015-01-01

Objective. Bringing together genomics, transcriptomics, proteomics, and other -omics technologies is an important step towards developing highly personalized medicine. However, instrumentation has advances far beyond expectations and now we are able to generate data faster than it can be interpreted. Materials and Methods. We have developed PANDA (Pathway AND Annotation) Explorer, a visualization tool that integrates gene-level annotation in the context of biological pathways to help interpret complex data from disparate sources. PANDA is a web-based application that displays data in the context of well-studied pathways like KEGG, BioCarta, and PharmGKB. PANDA represents data/annotations as icons in the graph while maintaining the other data elements (i.e., other columns for the table of annotations). Custom pathways from underrepresented diseases can be imported when existing data sources are inadequate. PANDA also allows sharing annotations among collaborators. Results. In our first use case, we show how easy it is to view supplemental data from a manuscript in the context of a user's own data. Another use-case is provided describing how PANDA was leveraged to design a treatment strategy from the somatic variants found in the tumor of a patient with metastatic sarcomatoid renal cell carcinoma. Conclusion. PANDA facilitates the interpretation of gene-centric annotations by visually integrating this information with context of biological pathways. The application can be downloaded or used directly from our website: http://bioinformaticstools.mayo.edu/research/panda-viewer/.

How to implement a clinical pathway for intensive glucose regulation in acute coronary syndromes.

PubMed

de Mulder, Maarten; Zwaan, Esther; Wielinga, Yvonne; Stam, Frank; Umans, Victor A W M

2009-06-01

Hyperglycemia upon admission of myocardial infarction patients predicts inferior clinical outcomes. Current strategies investigating hyperglycemia correction mostly use glucose-driven protocols. Implementation of these often labor-intensive protocols might be facilitated with the approach of a clinical pathway. Therefore, we evaluated the implementation of our glucose-driven protocol.We adapted a protocol for use in our coronary care unit (CCU), which was implemented according to the steps of a clinical pathway. To compensate for carbohydrates in meals we additionally developed a regimen of subcutaneous insulin.Protocol adherence was facilitated with a Web-based insulin calculator. All hyperglycemic patients admitted to the CCU were eligible for treatment according to this protocol.In a 4-month period, 643 glucose measurements were obtained in hyperglycemic patients admitted to our CCU. Patients were treated intensively with IV insulin for 35 hours and had 23 glucose measurements in this time span on average. This regimen achieved a median glucose of 6.2 mmol/L. Severe hypoglycemia occurred in only 1.1% of measurements and was without severe clinical side effects.Introduction of new intensive insulin protocol according to the steps of a clinical pathway is safe and feasible. The presence of a clinical pathway coordinator and sound communication are important conditions for successful introduction, which can be further aided with a computerized calculator.

Installing a Local Copy of the Reactome Web Site and Knowledgebase

PubMed Central

McKay, Sheldon J; Weiser, Joel

2015-01-01

The Reactome project builds, maintains, and publishes a knowledgebase of biological pathways. The information in the knowledgebase is gathered from the experts in the field, peer reviewed, and edited by Reactome editorial staff and then published to the Reactome Web site, http://www.reactome.org (see UNIT 8.7; Croft et al., 2013). The Reactome software is open source and builds on top of other open-source or freely available software. Reactome data and code can be freely downloaded in its entirety and the Web site installed locally. This allows for more flexible interrogation of the data and also makes it possible to add one’s own information to the knowledgebase. PMID:26087747

Building a virtual archive using brain architecture and Web 3D to deliver neuropsychopharmacology content over the Internet.

PubMed

Mongeau, R; Casu, M A; Pani, L; Pillolla, G; Lianas, L; Giachetti, A

2008-05-01

The vast amount of heterogeneous data generated in various fields of neurosciences such as neuropsychopharmacology can hardly be classified using traditional databases. We present here the concept of a virtual archive, spatially referenced over a simplified 3D brain map and accessible over the Internet. A simple prototype (available at http://aquatics.crs4.it/neuropsydat3d) has been realized using current Web-based virtual reality standards and technologies. It illustrates how primary literature or summary information can easily be retrieved through hyperlinks mapped onto a 3D schema while navigating through neuroanatomy. Furthermore, 3D navigation and visualization techniques are used to enhance the representation of brain's neurotransmitters, pathways and the involvement of specific brain areas in any particular physiological or behavioral functions. The system proposed shows how the use of a schematic spatial organization of data, widely exploited in other fields (e.g. Geographical Information Systems) can be extremely useful to develop efficient tools for research and teaching in neurosciences.

Web-based learning in professional development: experiences of Finnish nurse managers.

PubMed

Korhonen, Teija; Lammintakanen, Johanna

2005-11-01

The aim of this article is to describe the nurse managers' expectations, attitudes and experiences on web-based learning before and after participation in a web-based course. Information technology has rapidly become more common in health care settings. However, little is known about nurse managers' experiences on web-based learning, although they have a crucial role in promoting the professional development of their staff. Diagnostic assignments (n = 18) written before and interviews (n = 8) taken after the web-based education. The data were analysed by inductive content analysis. Nurse managers found web-based education to be a suitable and modern method of learning. On the basis of their experience they found multiple ways to utilize web-based learning environments in health care. Information technology skills, equipment, support and time were considered essential in web-based learning. Additionally, they found that their own experience might lead to more widespread implementation of web-based learning in health care settings. Information technology skills of nurse managers and staff need to be developed in order to use information technology effectively. In order to learn in a web-based environment, everyone needs the opportunity and access to required resources. Additionally, nurse managers' own experiences are important to promote wider utilization of web-based learning.

g:Profiler-a web server for functional interpretation of gene lists (2016 update).

PubMed

Reimand, Jüri; Arak, Tambet; Adler, Priit; Kolberg, Liis; Reisberg, Sulev; Peterson, Hedi; Vilo, Jaak

2016-07-08

Functional enrichment analysis is a key step in interpreting gene lists discovered in diverse high-throughput experiments. g:Profiler studies flat and ranked gene lists and finds statistically significant Gene Ontology terms, pathways and other gene function related terms. Translation of hundreds of gene identifiers is another core feature of g:Profiler. Since its first publication in 2007, our web server has become a popular tool of choice among basic and translational researchers. Timeliness is a major advantage of g:Profiler as genome and pathway information is synchronized with the Ensembl database in quarterly updates. g:Profiler supports 213 species including mammals and other vertebrates, plants, insects and fungi. The 2016 update of g:Profiler introduces several novel features. We have added further functional datasets to interpret gene lists, including transcription factor binding site predictions, Mendelian disease annotations, information about protein expression and complexes and gene mappings of human genetic polymorphisms. Besides the interactive web interface, g:Profiler can be accessed in computational pipelines using our R package, Python interface and BioJS component. g:Profiler is freely available at http://biit.cs.ut.ee/gprofiler/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii.

PubMed

May, Patrick; Christian, Jan-Ole; Kempa, Stefan; Walther, Dirk

2009-05-04

The unicellular green alga Chlamydomonas reinhardtii is an important eukaryotic model organism for the study of photosynthesis and plant growth. In the era of modern high-throughput technologies there is an imperative need to integrate large-scale data sets from high-throughput experimental techniques using computational methods and database resources to provide comprehensive information about the molecular and cellular organization of a single organism. In the framework of the German Systems Biology initiative GoFORSYS, a pathway database and web-portal for Chlamydomonas (ChlamyCyc) was established, which currently features about 250 metabolic pathways with associated genes, enzymes, and compound information. ChlamyCyc was assembled using an integrative approach combining the recently published genome sequence, bioinformatics methods, and experimental data from metabolomics and proteomics experiments. We analyzed and integrated a combination of primary and secondary database resources, such as existing genome annotations from JGI, EST collections, orthology information, and MapMan classification. ChlamyCyc provides a curated and integrated systems biology repository that will enable and assist in systematic studies of fundamental cellular processes in Chlamydomonas. The ChlamyCyc database and web-portal is freely available under http://chlamycyc.mpimp-golm.mpg.de.

P-Finder: Reconstruction of Signaling Networks from Protein-Protein Interactions and GO Annotations.

PubMed

Young-Rae Cho; Yanan Xin; Speegle, Greg

2015-01-01

Because most complex genetic diseases are caused by defects of cell signaling, illuminating a signaling cascade is essential for understanding their mechanisms. We present three novel computational algorithms to reconstruct signaling networks between a starting protein and an ending protein using genome-wide protein-protein interaction (PPI) networks and gene ontology (GO) annotation data. A signaling network is represented as a directed acyclic graph in a merged form of multiple linear pathways. An advanced semantic similarity metric is applied for weighting PPIs as the preprocessing of all three methods. The first algorithm repeatedly extends the list of nodes based on path frequency towards an ending protein. The second algorithm repeatedly appends edges based on the occurrence of network motifs which indicate the link patterns more frequently appearing in a PPI network than in a random graph. The last algorithm uses the information propagation technique which iteratively updates edge orientations based on the path strength and merges the selected directed edges. Our experimental results demonstrate that the proposed algorithms achieve higher accuracy than previous methods when they are tested on well-studied pathways of S. cerevisiae. Furthermore, we introduce an interactive web application tool, called P-Finder, to visualize reconstructed signaling networks.

Where are the parasites in food webs?

PubMed Central

2012-01-01

This review explores some of the reasons why food webs seem to contain relatively few parasite species when compared to the full diversity of free living species in the system. At present, there are few coherent food web theories to guide scientific studies on parasites, and this review posits that the methods, directions and questions in the field of food web ecology are not always congruent with parasitological inquiry. For example, topological analysis (the primary tool in food web studies) focuses on only one of six important steps in trematode life cycles, each of which requires a stable community dynamic to evolve. In addition, these transmission strategies may also utilize pathways within the food web that are not considered in traditional food web investigations. It is asserted that more effort must be focused on parasite-centric models, and a central theme is that many different approaches will be required. One promising approach is the old energetic perspective, which considers energy as the critical resource for all organisms, and the currency of all food web interactions. From the parasitological point of view, energy can be used to characterize the roles of parasites at all levels in the food web, from individuals to populations to community. The literature on parasite energetics in food webs is very sparse, but the evidence suggests that parasite species richness is low in food webs because parasites are limited by the quantity of energy available to their unique lifestyles. PMID:23092160

Web-based Therapy Plus Support by a Coach in Depressed Patients Referred to Secondary Mental Health Care: Randomized Controlled Trial.

PubMed

Hatcher, Simon; Whittaker, Robyn; Patton, Murray; Miles, Wayne Sylvester; Ralph, Nicola; Kercher, Katharina; Sharon, Cynthia

2018-01-23

The evidence for the effectiveness of Web-based therapies comes mainly from nonclinical populations, with a few studies in primary care. There is little evidence from patients referred to secondary mental health care with depression. Adherence to Web-based therapies is often poor. One way to increase this is to create a new health service role of a coach to guide people through the therapy. This study aimed to test in people referred to secondary care with depression if a Web-based therapy (The Journal) supported by a coach plus usual care would be more effective in reducing depression compared with usual care plus an information leaflet about Web-based resources after 12 weeks. We conducted a randomized controlled trial with two parallel arms and a process evaluation that included structured qualitative interviews analyzed using thematic analysis. The coach had a background in occupational therapy. Participants were recruited face-to-face at community mental health centers. We recruited 63 people into the trial (intervention 35, control 28). There were no statistically significant differences in the change from baseline in Patient Health Questionnaire-9 (PHQ-9) scores at 12 weeks comparing The Journal with usual care (mean change in PHQ-9 score 9.4 in the intervention group and 7.1 in the control group, t 41 =1.05, P=.30; mean difference=2.3, 95% CI -2.1 to 6.7). People who were offered The Journal attended on average about one less outpatient appointment compared with usual care, although this difference was not statistically significant (intervention mean number of visits 2.8 (SD 5.5) compared with 4.1 (SD 6.7) in the control group, t 45 =-0.80, P=.43; mean difference=1.3, 95% CI -4.5 to 2.0). The process evaluation found that the mean number of lessons completed in the intervention group was 2.5 (SD=1.9; range=0-6) and the number of contacts with the coach was a mean of 8.1 (SD=4.4; range=0-17). The qualitative interviews highlighted the problem of engaging clinicians in research and their resistance to recruitment: technical difficulties with The Journal, which prevented people logging in easily; difficulty accessing The Journal as it was not available on mobile devices; participants finding some lessons difficult; and participants saying they were too busy to complete the sessions. The study demonstrated that it is feasible to use a coach in this setting, that people found it helpful, and that it did not conflict with other care that participants were receiving. Future trials need to engage clinicians at an early stage to articulate where Web-based therapies fit into existing clinical pathways; Web-based therapies should be available on mobile devices, and logging in should be easy. The role of the coach should be explored in larger trials. Australian New Zealand Clinical Trials Registry (ACTRN): 12613000015741; https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=363351&isReview=true (Archived by WebCite at http://www.webcitation.org/6wEyCc6Ss). ©Simon Hatcher, Robyn Whittaker, Murray Patton, Wayne Sylvester Miles, Nicola Ralph, Katharina Kercher, Cynthia Sharon. Originally published in JMIR Mental Health (http://mental.jmir.org), 23.01.2018.

SPIRE: Systematic protein investigative research environment.

PubMed

Kolker, Eugene; Higdon, Roger; Morgan, Phil; Sedensky, Margaret; Welch, Dean; Bauman, Andrew; Stewart, Elizabeth; Haynes, Winston; Broomall, William; Kolker, Natali

2011-12-10

The SPIRE (Systematic Protein Investigative Research Environment) provides web-based experiment-specific mass spectrometry (MS) proteomics analysis (https://www.proteinspire.org). Its emphasis is on usability and integration of the best analytic tools. SPIRE provides an easy to use web-interface and generates results in both interactive and simple data formats. In contrast to run-based approaches, SPIRE conducts the analysis based on the experimental design. It employs novel methods to generate false discovery rates and local false discovery rates (FDR, LFDR) and integrates the best and complementary open-source search and data analysis methods. The SPIRE approach of integrating X!Tandem, OMSSA and SpectraST can produce an increase in protein IDs (52-88%) over current combinations of scoring and single search engines while also providing accurate multi-faceted error estimation. One of SPIRE's primary assets is combining the results with data on protein function, pathways and protein expression from model organisms. We demonstrate some of SPIRE's capabilities by analyzing mitochondrial proteins from the wild type and 3 mutants of C. elegans. SPIRE also connects results to publically available proteomics data through its Model Organism Protein Expression Database (MOPED). SPIRE can also provide analysis and annotation for user supplied protein ID and expression data. Copyright © 2011. Published by Elsevier B.V.

SuperTarget goes quantitative: update on drug–target interactions

PubMed Central

Hecker, Nikolai; Ahmed, Jessica; von Eichborn, Joachim; Dunkel, Mathias; Macha, Karel; Eckert, Andreas; Gilson, Michael K.; Bourne, Philip E.; Preissner, Robert

2012-01-01

There are at least two good reasons for the on-going interest in drug–target interactions: first, drug-effects can only be fully understood by considering a complex network of interactions to multiple targets (so-called off-target effects) including metabolic and signaling pathways; second, it is crucial to consider drug-target-pathway relations for the identification of novel targets for drug development. To address this on-going need, we have developed a web-based data warehouse named SuperTarget, which integrates drug-related information associated with medical indications, adverse drug effects, drug metabolism, pathways and Gene Ontology (GO) terms for target proteins. At present, the updated database contains >6000 target proteins, which are annotated with >330 000 relations to 196 000 compounds (including approved drugs); the vast majority of interactions include binding affinities and pointers to the respective literature sources. The user interface provides tools for drug screening and target similarity inclusion. A query interface enables the user to pose complex queries, for example, to find drugs that target a certain pathway, interacting drugs that are metabolized by the same cytochrome P450 or drugs that target proteins within a certain affinity range. SuperTarget is available at http://bioinformatics.charite.de/supertarget. PMID:22067455

Reactome graph database: Efficient access to complex pathway data

PubMed Central

Korninger, Florian; Viteri, Guilherme; Marin-Garcia, Pablo; Ping, Peipei; Wu, Guanming; Stein, Lincoln; D’Eustachio, Peter

2018-01-01

Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. One of its main priorities is to provide easy and efficient access to its high quality curated data. At present, biological pathway databases typically store their contents in relational databases. This limits access efficiency because there are performance issues associated with queries traversing highly interconnected data. The same data in a graph database can be queried more efficiently. Here we present the rationale behind the adoption of a graph database (Neo4j) as well as the new ContentService (REST API) that provides access to these data. The Neo4j graph database and its query language, Cypher, provide efficient access to the complex Reactome data model, facilitating easy traversal and knowledge discovery. The adoption of this technology greatly improved query efficiency, reducing the average query time by 93%. The web service built on top of the graph database provides programmatic access to Reactome data by object oriented queries, but also supports more complex queries that take advantage of the new underlying graph-based data storage. By adopting graph database technology we are providing a high performance pathway data resource to the community. The Reactome graph database use case shows the power of NoSQL database engines for complex biological data types. PMID:29377902

BMDExpress Data Viewer: A Visualization Tool to Analyze ...

EPA Pesticide Factsheets

Regulatory agencies increasingly apply benchmark dose (BMD) modeling to determine points of departure in human risk assessments. BMDExpress applies BMD modeling to transcriptomics datasets and groups genes to biological processes and pathways for rapid assessment of doses at which biological perturbations occur. However, graphing and analytical capabilities within BMDExpress are limited, and the analysis of output files is challenging. We developed a web-based application, BMDExpress Data Viewer, for visualization and graphical analyses of BMDExpress output files. The software application consists of two main components: ‘Summary Visualization Tools’ and ‘Dataset Exploratory Tools’. We demonstrate through two case studies that the ‘Summary Visualization Tools’ can be used to examine and assess the distributions of probe and pathway BMD outputs, as well as derive a potential regulatory BMD through the modes or means of the distributions. The ‘Functional Enrichment Analysis’ tool presents biological processes in a two-dimensional bubble chart view. By applying filters of pathway enrichment p-value and minimum number of significant genes, we showed that the Functional Enrichment Analysis tool can be applied to select pathways that are potentially sensitive to chemical perturbations. The ‘Multiple Dataset Comparison’ tool enables comparison of BMDs across multiple experiments (e.g., across time points, tissues, or organisms, etc.). The ‘BMDL-BM

Reactome graph database: Efficient access to complex pathway data.

PubMed

Fabregat, Antonio; Korninger, Florian; Viteri, Guilherme; Sidiropoulos, Konstantinos; Marin-Garcia, Pablo; Ping, Peipei; Wu, Guanming; Stein, Lincoln; D'Eustachio, Peter; Hermjakob, Henning

2018-01-01

Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. One of its main priorities is to provide easy and efficient access to its high quality curated data. At present, biological pathway databases typically store their contents in relational databases. This limits access efficiency because there are performance issues associated with queries traversing highly interconnected data. The same data in a graph database can be queried more efficiently. Here we present the rationale behind the adoption of a graph database (Neo4j) as well as the new ContentService (REST API) that provides access to these data. The Neo4j graph database and its query language, Cypher, provide efficient access to the complex Reactome data model, facilitating easy traversal and knowledge discovery. The adoption of this technology greatly improved query efficiency, reducing the average query time by 93%. The web service built on top of the graph database provides programmatic access to Reactome data by object oriented queries, but also supports more complex queries that take advantage of the new underlying graph-based data storage. By adopting graph database technology we are providing a high performance pathway data resource to the community. The Reactome graph database use case shows the power of NoSQL database engines for complex biological data types.

Integrating Sustainability into the Curriculum: Crossing Disciplinary Boundaries

NASA Astrophysics Data System (ADS)

Pushnik, J.

2012-12-01

The next generation will confront an increased number of global issues that interface the complexities of socioeconomic perspectives, environmental stability, poverty and development. Recently California State University Chico undertook a general education reform, providing a unique opportunity to craft a general education pathway to prepare students for these challenges by focusing a curriculum on sustainability. The Sustainability Pathway emphasizes a system thinking approach to help students understand and be able to address a set of problems involving the biosphere processes, human institutions and the economic vitality. The curriculum intentionally integrates courses from across the disciplines of natural sciences, social sciences, agriculture, engineering, economics, arts and humanities into a central focused theme of sustainability. The diverse backgrounds and academic focus of the participating faculty has necessitate the development of a common language and a cohesion within the curriculum. To address these needs a faculty learning community (FLC) was established to build on a common set of case studies. Three regional environmental water related issues were selected that had demonstrable socioeconomic, equity/ethical dimensions and environmental consequences. These case studies are Klamath River basin in northern California, the Bay-Delta project in the central part of the state and the Sultan Sea in southern California. Members of the FLC has contributed a perspective from their academic discipline which includes proposed reading lists, web based resources and PowerPoint presentations which are housed in common web- based resource repository. The pedagogical rational is to create linkages and cohesion among the courses in the curriculum by iteratively examining these case studies as basis for development of a multidisciplinary perspective as students progress through their general education.

75 FR 6208 - Proposed Collection; Comment Request; Web Based Training for Pain Management Providers

Federal Register 2010, 2011, 2012, 2013, 2014

2010-02-08

... Request; Web Based Training for Pain Management Providers SUMMARY: Under the provisions of Section 3507(a... comment. Proposed Collection Title: Web Based Training for Pain Management Providers. Type of Information... effectiveness of the Web Based Training for Pain Management Providers, via the Web site PainAndAddiction...

Borderline personality disorder traits and their relationship with dimensions of normative personality: a web-based cohort and twin study

PubMed Central

Kendler, K. S.; Myers, J.; Reichborn-Kjennerud, T.

2011-01-01

Objective To describe the structure of genetic and environmental risk factors for four dimensions of borderline personality disorder (BPD) and to understand the source of resemblance of these dimensions and normal personality. Method A web-based sample (n = 44,112 including 542 twin pairs) completed items from 4 scales of the Dimensional Assessment of Personality Pathology Basic Questionnaire and the Big Five Inventory. Results A one-factor common pathway model best fits the 4 BPD scales producing a highly heritable latent liability (heritability = 60%) and strong loadings on all 4 dimensions. Affective instability had the lowest trait-specific genetic loading, suggesting that it was a core feature of BPD. A complex pattern of genetic and environmental associations was found between the big five personality traits and BPD dimensions. The strongest genetic correlations with the BPD traits were generally seen for neuroticism (positive), followed by conscientiousness and agreeableness, both negative. Conclusion In the general population, these four BPD dimensions reflect one underlying highly heritable factor. The association between normative personality and dimensions of BPD is complex with high degrees of genetic correlation. PMID:21198457

Borderline personality disorder traits and their relationship with dimensions of normative personality: a web-based cohort and twin study.

PubMed

Kendler, K S; Myers, J; Reichborn-Kjennerud, T

2011-05-01

To describe the structure of genetic and environmental risk factors for four dimensions of borderline personality disorder (BPD) and to understand the source of resemblance of these dimensions and normal personality. A web-based sample (n = 44,112 including 542 twin pairs) completed items from 4 scales of the Dimensional Assessment of Personality Pathology Basic Questionnaire and the Big Five Inventory. A one-factor common pathway model best fits the 4 BPD scales producing a highly heritable latent liability (heritability = 60%) and strong loadings on all 4 dimensions. Affective instability had the lowest trait-specific genetic loading, suggesting that it was a core feature of BPD. A complex pattern of genetic and environmental associations was found between the big five personality traits and BPD dimensions. The strongest genetic correlations with the BPD traits were generally seen for neuroticism (positive), followed by conscientiousness and agreeableness, both negative. In the general population, these four BPD dimensions reflect one underlying highly heritable factor. The association between normative personality and dimensions of BPD is complex with high degrees of genetic correlation. © 2010 John Wiley & Sons A/S.

A web platform for the network analysis of high-throughput data in melanoma and its use to investigate mechanisms of resistance to anti-PD1 immunotherapy.

PubMed

Dreyer, Florian S; Cantone, Martina; Eberhardt, Martin; Jaitly, Tanushree; Walter, Lisa; Wittmann, Jürgen; Gupta, Shailendra K; Khan, Faiz M; Wolkenhauer, Olaf; Pützer, Brigitte M; Jäck, Hans-Martin; Heinzerling, Lucie; Vera, Julio

2018-06-01

Cellular phenotypes are established and controlled by complex and precisely orchestrated molecular networks. In cancer, mutations and dysregulations of multiple molecular factors perturb the regulation of these networks and lead to malignant transformation. High-throughput technologies are a valuable source of information to establish the complex molecular relationships behind the emergence of malignancy, but full exploitation of this massive amount of data requires bioinformatics tools that rely on network-based analyses. In this report we present the Virtual Melanoma Cell, an online tool developed to facilitate the mining and interpretation of high-throughput data on melanoma by biomedical researches. The platform is based on a comprehensive, manually generated and expert-validated regulatory map composed of signaling pathways important in malignant melanoma. The Virtual Melanoma Cell is a tool designed to accept, visualize and analyze user-generated datasets. It is available at: https://www.vcells.net/melanoma. To illustrate the utilization of the web platform and the regulatory map, we have analyzed a large publicly available dataset accounting for anti-PD1 immunotherapy treatment of malignant melanoma patients. Copyright © 2018 Elsevier B.V. All rights reserved.

Web-based health resources at US colleges: early patterns and missed opportunities in preventive health.

PubMed

Jue, J Jane S; Metlay, Joshua P

2011-11-01

Web-based health resources on college websites have the potential to reach a substantial number of college students. The objective of this study was to characterize how colleges use their websites to educate about and promote health. This study was a cross-sectional analysis of websites from a nationally representative sample of 426 US colleges. Reviewers abstracted information about Web-based health resources from college websites, namely health information, Web links to outside health resources, and interactive Web-based health programs. Nearly 60% of US colleges provided health resources on their websites, 49% provided health information, 48% provided links to outside resources, and 28% provided interactive Web-based health programs. The most common topics of Web-based health resources were mental health and general health. We found widespread presence of Web-based health resources available from various delivery modes and covering a range of health topics. Although further research in this new modality is warranted, Web-based health resources hold promise for reaching more US college students.

Exploring the efficacy of replacing linear paper-based patient cases in problem-based learning with dynamic Web-based virtual patients: randomized controlled trial.

PubMed

Poulton, Terry; Ellaway, Rachel H; Round, Jonathan; Jivram, Trupti; Kavia, Sheetal; Hilton, Sean

2014-11-05

Problem-based learning (PBL) is well established in medical education and beyond, and continues to be developed and explored. Challenges include how to connect the somewhat abstract nature of classroom-based PBL with clinical practice and how to maintain learner engagement in the process of PBL over time. A study was conducted to investigate the efficacy of decision-PBL (D-PBL), a variant form of PBL that replaces linear PBL cases with virtual patients. These Web-based interactive cases provided learners with a series of patient management pathways. Learners were encouraged to consider and discuss courses of action, take their chosen management pathway, and experience the consequences of their decisions. A Web-based application was essential to allow scenarios to respond dynamically to learners' decisions, to deliver the scenarios to multiple PBL classrooms in the same timeframe, and to record centrally the paths taken by the PBL groups. A randomized controlled trial in crossover design was run involving all learners (N=81) in the second year of the graduate entry stream for the undergraduate medicine program at St George's University of London. Learners were randomized to study groups; half engaged in a D-PBL activity whereas the other half had a traditional linear PBL activity on the same subject material. Groups alternated D-PBL and linear PBL over the semester. The measure was mean cohort performance on specific face-to-face exam questions at the end of the semester. D-PBL groups performed better than linear PBL groups on questions related to D-PBL with the difference being statistically significant for all questions. Differences between the exam performances of the 2 groups were not statistically significant for the questions not related to D-PBL. The effect sizes for D-PBL-related questions were large and positive (>0.6) except for 1 question that showed a medium positive effect size. The effect sizes for questions not related to D-PBL were all small (≤0.3) with a mix of positive and negative values. The efficacy of D-PBL was indicated by improved exam performance for learners who had D-PBL compared to those who had linear PBL. This suggests that the use of D-PBL leads to better midterm learning outcomes than linear PBL, at least for learners with prior experience with linear PBL. On the basis of tutor and student feedback, St George's University of London and the University of Nicosia, Cyprus have replaced paper PBL cases for midstage undergraduate teaching with D-PBL virtual patients, and 6 more institutions in the ePBLnet partnership will be implementing D-PBL in Autumn 2015.

Nearshore energy subsidies support Lake Michigan fishes and invertebrates following major changes in food web structure

USGS Publications Warehouse

Turschak, Benjamin A; Bunnell, David B.; Czesny, Sergiusz J.; Höök, Tomas O.; Janssen, John; Warner, David M.; Bootsma, Harvey A

2014-01-01

Aquatic food webs that incorporate multiple energy channels (e.g. nearshore benthic or pelagic) with varying productivity and turnover rates convey stability to biological communities by providing multiple independent energy sources. Within the Lake Michigan food web, invasive dreissenid mussels have caused rapid changes to food web structure and potentially altered the channels through which consumers acquire energy. We used stable C and N isotopes to determine how Lake Michigan food web structure has changed in the past decade, coincident with the expansion of dreissenid mussels, decreased pelagic phytoplankton production and increased nearshore benthic algal production. Fish and invertebrate samples collected from sites around Lake Michigan were analyzed to determine taxa-specific 13C:12C (delta 13C) and 15N:14N (delta 15N) ratios. Sampling took place during two distinct periods, 2002-2003 and 2010-2012, that spanned the period of dreissenid expansion, and included nearshore, pelagic and profundal fish and invertebrate taxa. Magnitude and direction of the 13C shift indicated significantly greater reliance upon nearshore benthic energy sources among nearly all fish taxa as well as profundal invertebrates. Although the mechanisms underlying this 13C shift likely varied among species, possible causes include the transport of benthic algal production to offshore waters and an increased reliance on nearshore prey items. Delta 15N shifts were more variable and of smaller magnitude across taxa although declines in delta 15N among some pelagic fishes may indicate a shift to alternative prey resources. Lake Michigan fishes and invertebrates appear to have responded to dreissenid induced changes in nutrient and energy pathways by switching from pelagic to alternative nearshore energy subsidies. Although large shifts in energy allocation (i.e. pelagic to nearshore benthic) resulting from invasive species appear to have affected total production at upper trophic levels, changes in trophic structure and utilization of novel energy pathways may help to stabilize food webs following species invasions.

NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways.

PubMed

Brohée, Sylvain; Faust, Karoline; Lima-Mendez, Gipsi; Sand, Olivier; Janky, Rekin's; Vanderstocken, Gilles; Deville, Yves; van Helden, Jacques

2008-07-01

The network analysis tools (NeAT) (http://rsat.ulb.ac.be/neat/) provide a user-friendly web access to a collection of modular tools for the analysis of networks (graphs) and clusters (e.g. microarray clusters, functional classes, etc.). A first set of tools supports basic operations on graphs (comparison between two graphs, neighborhood of a set of input nodes, path finding and graph randomization). Another set of programs makes the connection between networks and clusters (graph-based clustering, cliques discovery and mapping of clusters onto a network). The toolbox also includes programs for detecting significant intersections between clusters/classes (e.g. clusters of co-expression versus functional classes of genes). NeAT are designed to cope with large datasets and provide a flexible toolbox for analyzing biological networks stored in various databases (protein interactions, regulation and metabolism) or obtained from high-throughput experiments (two-hybrid, mass-spectrometry and microarrays). The web interface interconnects the programs in predefined analysis flows, enabling to address a series of questions about networks of interest. Each tool can also be used separately by entering custom data for a specific analysis. NeAT can also be used as web services (SOAP/WSDL interface), in order to design programmatic workflows and integrate them with other available resources.

NAWeb 2000: Web-Based Learning - On Track! International Conference on Web-Based Learning. (6th, New Brunswick, Canada, October 14-17, 2000).

ERIC Educational Resources Information Center

Hall, Richard., Ed.

This proceedings of the Sixth International Conference on Web-Based Learning, NAWeb 2000, includes the following papers: "Is a Paradigm Shift Required To Effectively Teach Web-Based Instruction?"; "Issues in Courseware Reuse for a Web-Based Information System"; "The Digital Curriculum Database: Meeting the Needs of Industry and the Challenge of…

High spatial resolution with zoomable saw-tooth refractive lenses?

NASA Astrophysics Data System (ADS)

Jark, Werner

2011-09-01

Refractive x-ray lenses can be assembled from two opposing saw-tooth structures, when they are inclined with respect to each other and almost touch at one end. An incident plane wave will then traverse a varying number of triangular prisms, which direct the beam towards the optical axis and focus it. Optically speaking the plane wave traverses a parabolic lens profile, which is approximated by trapezoidal segments. The parabolic profile will focus ideally, when a lens can be discussed in the "thin lens" approximation. Now the saw-tooth refractive lens is found to be too "thick". The residual aberrations limit the focusing capability to just submicrometer focusing, significantly above the limit in diffraction limited focusing. It is shown that the aberrations can be removed by introducing a variation into the originally constant saw-tooth angle. After this modification the lens can be operated in the diffraction limited regime. Spot sizes even below 0.1 micrometer are then feasible. This performance in terms of spatial resolution is found to be limited to focusing to microspots and is not available, when the saw-tooth refractive lens is used in an imaging setup. In this case the spatial resolution deteriorates rapidly with increasing off axis distance of the object to be imaged.

Platelet-activating factor receptor (PAF-R)-dependent pathways control tumour growth and tumour response to chemotherapy

PubMed Central

2010-01-01

Background Phagocytosis of apoptotic cells by macrophages induces a suppressor phenotype. Previous data from our group suggested that this occurs via Platelet-activating factor receptor (PAF-R)-mediated pathways. In the present study, we investigated the impact of apoptotic cell inoculation or induction by a chemotherapeutic agent (dacarbazine, DTIC) on tumour growth, microenvironmental parameters and survival, and the effect of treatment with a PAF-R antagonist (WEB2170). These studies were performed in murine tumours: Ehrlich Ascitis Tumour (EAT) and B16F10 melanoma. Methods Tumour growth was assessed by direct counting of EAT cells in the ascitis or by measuring the volume of the solid tumour. Parameters of the tumour microenvironment, such as the frequency of cells expressing cyclo-oxygenase-2 (COX-2), caspase-3 and galectin-3, and microvascular density, were determined by immunohistochemistry. Levels of vascular endothelium growth factor (VEGF) and prostaglandin E2 (PGE2) were determined by ELISA, and levels of nitric oxide (NO) by Griess reaction. PAF-R expression was analysed by immunohistochemistry and flow cytometry. Results Inoculation of apoptotic cells before EAT implantation stimulated tumour growth. This effect was reversed by in vivo pre-treatment with WEB2170. This treatment also reduced tumour growth and modified the microenvironment by reducing PGE2, VEGF and NO production. In B16F10 melanoma, WEB2170 alone or in association with DTIC significantly reduced tumour volume. Survival of the tumour-bearing mice was not affected by WEB2170 treatment but was significantly improved by the combination of DTIC with WEB2170. Tumour microenvironment elements were among the targets of the combination therapy since the relative frequency of COX-2 and galectin-3 positive cells and the microvascular density within the tumour mass were significantly reduced by treatment with WEB2170 or DTIC alone or in combination. Antibodies to PAF-R stained the cells from inside the tumour, but not the tumour cells grown in vitro. At the tissue level, a few cells (probably macrophages) stained positively with antibodies to PAF-R. Conclusions We suggest that PAF-R-dependent pathways are activated during experimental tumour growth, modifying the microenvironment and the phenotype of the tumour macrophages in such a way as to favour tumour growth. Combination therapy with a PAF-R antagonist and a chemotherapeutic drug may represent a new and promising strategy for the treatment of some tumours. PMID:20465821

Practical guidelines for development of web-based interventions.

PubMed

Chee, Wonshik; Lee, Yaelim; Chee, Eunice; Im, Eun-Ok

2014-10-01

Despite a recent high funding priority on technological aspects of research and a high potential impact of Web-based interventions on health, few guidelines for the development of Web-based interventions are currently available. In this article, we propose practical guidelines for development of Web-based interventions based on an empirical study and an integrative literature review. The empirical study aimed at development of a Web-based physical activity promotion program that was specifically tailored to Korean American midlife women. The literature review included a total of 202 articles that were retrieved through multiple databases. On the basis of the findings of the study and the literature review, we propose directions for development of Web-based interventions in the following steps: (1) meaningfulness and effectiveness, (2) target population, (3) theoretical basis/program theory, (4) focus and objectives, (5) components, (6) technological aspects, and (7) logistics for users. The guidelines could help promote further development of Web-based interventions at this early stage of Web-based interventions in nursing.

Web-Based Testing: Exploring the Relationship between Hardware Usability and Test Performance

ERIC Educational Resources Information Center

Huff, Kyle; Cline, Melinda; Guynes, Carl S.

2012-01-01

Web-based testing has recently become common in both academic and professional settings. A web-based test is administered through a web browser. Individuals may complete a web-based test at nearly any time and at any place. In addition, almost any computer lab can become a testing center. It is important to understand the environmental issues that…

Enable Web-Based Tracking and Guiding by Integrating Location-Awareness with the World Wide Web

ERIC Educational Resources Information Center

Zhou, Rui

2008-01-01

Purpose: The aim of this research is to enable web-based tracking and guiding by integrating location-awareness with the Worldwide Web so that the users can use various location-based applications without installing extra software. Design/methodology/approach: The concept of web-based tracking and guiding is introduced and the relevant issues are…

MinePath: Mining for Phenotype Differential Sub-paths in Molecular Pathways

PubMed Central

Koumakis, Lefteris; Kartsaki, Evgenia; Chatzimina, Maria; Zervakis, Michalis; Vassou, Despoina; Marias, Kostas; Moustakis, Vassilis; Potamias, George

2016-01-01

Pathway analysis methodologies couple traditional gene expression analysis with knowledge encoded in established molecular pathway networks, offering a promising approach towards the biological interpretation of phenotype differentiating genes. Early pathway analysis methodologies, named as gene set analysis (GSA), view pathways just as plain lists of genes without taking into account either the underlying pathway network topology or the involved gene regulatory relations. These approaches, even if they achieve computational efficiency and simplicity, consider pathways that involve the same genes as equivalent in terms of their gene enrichment characteristics. Most recent pathway analysis approaches take into account the underlying gene regulatory relations by examining their consistency with gene expression profiles and computing a score for each profile. Even with this approach, assessing and scoring single-relations limits the ability to reveal key gene regulation mechanisms hidden in longer pathway sub-paths. We introduce MinePath, a pathway analysis methodology that addresses and overcomes the aforementioned problems. MinePath facilitates the decomposition of pathways into their constituent sub-paths. Decomposition leads to the transformation of single-relations to complex regulation sub-paths. Regulation sub-paths are then matched with gene expression sample profiles in order to evaluate their functional status and to assess phenotype differential power. Assessment of differential power supports the identification of the most discriminant profiles. In addition, MinePath assess the significance of the pathways as a whole, ranking them by their p-values. Comparison results with state-of-the-art pathway analysis systems are indicative for the soundness and reliability of the MinePath approach. In contrast with many pathway analysis tools, MinePath is a web-based system (www.minepath.org) offering dynamic and rich pathway visualization functionality, with the unique characteristic to color regulatory relations between genes and reveal their phenotype inclination. This unique characteristic makes MinePath a valuable tool for in silico molecular biology experimentation as it serves the biomedical researchers’ exploratory needs to reveal and interpret the regulatory mechanisms that underlie and putatively govern the expression of target phenotypes. PMID:27832067

MinePath: Mining for Phenotype Differential Sub-paths in Molecular Pathways.

PubMed

Koumakis, Lefteris; Kanterakis, Alexandros; Kartsaki, Evgenia; Chatzimina, Maria; Zervakis, Michalis; Tsiknakis, Manolis; Vassou, Despoina; Kafetzopoulos, Dimitris; Marias, Kostas; Moustakis, Vassilis; Potamias, George

2016-11-01

Pathway analysis methodologies couple traditional gene expression analysis with knowledge encoded in established molecular pathway networks, offering a promising approach towards the biological interpretation of phenotype differentiating genes. Early pathway analysis methodologies, named as gene set analysis (GSA), view pathways just as plain lists of genes without taking into account either the underlying pathway network topology or the involved gene regulatory relations. These approaches, even if they achieve computational efficiency and simplicity, consider pathways that involve the same genes as equivalent in terms of their gene enrichment characteristics. Most recent pathway analysis approaches take into account the underlying gene regulatory relations by examining their consistency with gene expression profiles and computing a score for each profile. Even with this approach, assessing and scoring single-relations limits the ability to reveal key gene regulation mechanisms hidden in longer pathway sub-paths. We introduce MinePath, a pathway analysis methodology that addresses and overcomes the aforementioned problems. MinePath facilitates the decomposition of pathways into their constituent sub-paths. Decomposition leads to the transformation of single-relations to complex regulation sub-paths. Regulation sub-paths are then matched with gene expression sample profiles in order to evaluate their functional status and to assess phenotype differential power. Assessment of differential power supports the identification of the most discriminant profiles. In addition, MinePath assess the significance of the pathways as a whole, ranking them by their p-values. Comparison results with state-of-the-art pathway analysis systems are indicative for the soundness and reliability of the MinePath approach. In contrast with many pathway analysis tools, MinePath is a web-based system (www.minepath.org) offering dynamic and rich pathway visualization functionality, with the unique characteristic to color regulatory relations between genes and reveal their phenotype inclination. This unique characteristic makes MinePath a valuable tool for in silico molecular biology experimentation as it serves the biomedical researchers' exploratory needs to reveal and interpret the regulatory mechanisms that underlie and putatively govern the expression of target phenotypes.

Blinded by the light? Nearshore energy pathway coupling and relative predator biomass increase with reduced water transparency across lakes.

PubMed

Tunney, Tyler D; McCann, Kevin S; Jarvis, Lauren; Lester, Nigel P; Shuter, Brian J

2018-04-01

Habitat coupling is a concept that refers to consumer integration of resources derived from different habitats. This coupling unites fundamental food web pathways (e.g., cross-habitat trophic linkages) that mediate key ecological processes such as biomass flows, nutrient cycling, and stability. We consider the influence of water transparency, an important environmental driver in aquatic ecosystems, on habitat coupling by a light-sensitive predator, walleye (Sander vitreus), and its prey in 33 Canadian lakes. Our large-scale, across-lake study shows that the contribution of nearshore carbon (δ 13 C) relative to offshore carbon (δ 13 C) to walleye is higher in less transparent lakes. To a lesser degree, the contribution of nearshore carbon increased with a greater proportion of prey in nearshore compared to offshore habitats. Interestingly, water transparency and habitat coupling predict among-lake variation in walleye relative biomass. These findings support the idea that predator responses to changing conditions (e.g., water transparency) can fundamentally alter carbon pathways, and predator biomass, in aquatic ecosystems. Identifying environmental factors that influence habitat coupling is an important step toward understanding spatial food web structure in a changing world.

Participant Recruitment and Engagement in Automated eHealth Trial Registration: Challenges and Opportunities for Recruiting Women Who Experience Violence

PubMed Central

McLean, Christine; Rohan, Maheswaran; Sisk, Rose; Dobbs, Terry; Nada-Raja, Shyamala; Wilson, Denise; Vandal, Alain C

2016-01-01

Background Automated eHealth Web-based research trials offer people an accessible, confidential opportunity to engage in research that matters to them. eHealth trials may be particularly useful for sensitive issues when seeking health care may be accompanied by shame and mistrust. Yet little is known about people’s early engagement with eHealth trials, from recruitment to preintervention autoregistration processes. A recent randomized controlled trial that tested the effectiveness of an eHealth safety decision aid for New Zealand women in the general population who experienced intimate partner violence (isafe) provided the opportunity to examine recruitment and preintervention participant engagement with a fully automated Web-based registration process. The trial aimed to recruit 340 women within 24 months. Objective The objective of our study was to examine participant preintervention engagement and recruitment efficiency for the isafe trial, and to analyze dropout through the registration pathway, from recruitment to eligibility screening and consent, to completion of baseline measures. Methods In this case study, data collection sources included the trial recruitment log, Google Analytics reports, registration and program metadata, and costs. Analysis included a qualitative narrative of the recruitment experience and descriptive statistics of preintervention participant engagement and dropout rates. A Koyck model investigated the relationship between Web-based online marketing website advertisements (ads) and participant accrual. Results The isafe trial was launched on September 17, 2012. Placement of ads in an online classified advertising platform increased the average number of recruited participants per month from 2 to 25. Over the 23-month recruitment period, the registration website recorded 4176 unique visitors. Among 1003 women meeting eligibility criteria, 51.55% (517) consented to participate; among the 501 women who enrolled (consented, validated, and randomized), 412 (82.2%) were accrued (completed baseline assessments). The majority (n=52, 58%) of the 89 women who dropped out between enrollment and accrual never logged in to the allocated isafe website. Of every 4 accrued women, 3 (314/412, 76.2%) identified the classified ad as their referral source, followed by friends and family (52/412, 12.6%). Women recruited through a friend or relative were more likely to self-identify as indigenous Māori and live in the highest-deprivation areas. Ads increased the accrual rate by a factor of 74 (95% CI 49–112). Conclusions Print advertisements, website links, and networking were costly and inefficient methods for recruiting participants to a Web-based eHealth trial. Researchers are advised to limit their recruitment efforts to Web-based online marketplace and classified advertising platforms, as in the isafe case, or to social media. Online classified advertising in “Jobs–Other–volunteers” successfully recruited a diverse sample of women experiencing intimate partner violence. Preintervention recruitment data provide critical information to inform future research and critical analysis of Web-based eHealth trials. ClinicalTrial Australian New Zealand Clinical Trials Registry (ANZCTR): ACTRN12612000708853; https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?ACTRN=12612000708853 (Archived by WebCite at http://www.webcitation/6lMGuVXdK) PMID:27780796

Participant Recruitment and Engagement in Automated eHealth Trial Registration: Challenges and Opportunities for Recruiting Women Who Experience Violence.

PubMed

Koziol-McLain, Jane; McLean, Christine; Rohan, Maheswaran; Sisk, Rose; Dobbs, Terry; Nada-Raja, Shyamala; Wilson, Denise; Vandal, Alain C

2016-10-25

Automated eHealth Web-based research trials offer people an accessible, confidential opportunity to engage in research that matters to them. eHealth trials may be particularly useful for sensitive issues when seeking health care may be accompanied by shame and mistrust. Yet little is known about people's early engagement with eHealth trials, from recruitment to preintervention autoregistration processes. A recent randomized controlled trial that tested the effectiveness of an eHealth safety decision aid for New Zealand women in the general population who experienced intimate partner violence (isafe) provided the opportunity to examine recruitment and preintervention participant engagement with a fully automated Web-based registration process. The trial aimed to recruit 340 women within 24 months. The objective of our study was to examine participant preintervention engagement and recruitment efficiency for the isafe trial, and to analyze dropout through the registration pathway, from recruitment to eligibility screening and consent, to completion of baseline measures. In this case study, data collection sources included the trial recruitment log, Google Analytics reports, registration and program metadata, and costs. Analysis included a qualitative narrative of the recruitment experience and descriptive statistics of preintervention participant engagement and dropout rates. A Koyck model investigated the relationship between Web-based online marketing website advertisements (ads) and participant accrual. The isafe trial was launched on September 17, 2012. Placement of ads in an online classified advertising platform increased the average number of recruited participants per month from 2 to 25. Over the 23-month recruitment period, the registration website recorded 4176 unique visitors. Among 1003 women meeting eligibility criteria, 51.55% (517) consented to participate; among the 501 women who enrolled (consented, validated, and randomized), 412 (82.2%) were accrued (completed baseline assessments). The majority (n=52, 58%) of the 89 women who dropped out between enrollment and accrual never logged in to the allocated isafe website. Of every 4 accrued women, 3 (314/412, 76.2%) identified the classified ad as their referral source, followed by friends and family (52/412, 12.6%). Women recruited through a friend or relative were more likely to self-identify as indigenous Māori and live in the highest-deprivation areas. Ads increased the accrual rate by a factor of 74 (95% CI 49-112). Print advertisements, website links, and networking were costly and inefficient methods for recruiting participants to a Web-based eHealth trial. Researchers are advised to limit their recruitment efforts to Web-based online marketplace and classified advertising platforms, as in the isafe case, or to social media. Online classified advertising in "Jobs-Other-volunteers" successfully recruited a diverse sample of women experiencing intimate partner violence. Preintervention recruitment data provide critical information to inform future research and critical analysis of Web-based eHealth trials. Australian New Zealand Clinical Trials Registry (ANZCTR): ACTRN12612000708853; https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?ACTRN=12612000708853 (Archived by WebCite at http://www.webcitation/6lMGuVXdK).

A service oriented approach for guidelines-based clinical decision support using BPMN.

PubMed

Rodriguez-Loya, Salvador; Aziz, Ayesha; Chatwin, Chris

2014-01-01

Evidence-based medical practice requires that clinical guidelines need to be documented in such a way that they represent a clinical workflow in its most accessible form. In order to optimize clinical processes to improve clinical outcomes, we propose a Service Oriented Architecture (SOA) based approach for implementing clinical guidelines that can be accessed from an Electronic Health Record (EHR) application with a Web Services enabled communication mechanism with the Enterprise Service Bus. We have used Business Process Modelling Notation (BPMN) for modelling and presenting the clinical pathway in the form of a workflow. The aim of this study is to produce spontaneous alerts in the healthcare workflow in the diagnosis of Chronic Obstructive Pulmonary Disease (COPD). The use of BPMN as a tool to automate clinical guidelines has not been previously employed for providing Clinical Decision Support (CDS).

Systems view of adipogenesis via novel omics-driven and tissue-specific activity scoring of network functional modules

NASA Astrophysics Data System (ADS)

Nassiri, Isar; Lombardo, Rosario; Lauria, Mario; Morine, Melissa J.; Moyseos, Petros; Varma, Vijayalakshmi; Nolen, Greg T.; Knox, Bridgett; Sloper, Daniel; Kaput, Jim; Priami, Corrado

2016-07-01

The investigation of the complex processes involved in cellular differentiation must be based on unbiased, high throughput data processing methods to identify relevant biological pathways. A number of bioinformatics tools are available that can generate lists of pathways ranked by statistical significance (i.e. by p-value), while ideally it would be desirable to functionally score the pathways relative to each other or to other interacting parts of the system or process. We describe a new computational method (Network Activity Score Finder - NASFinder) to identify tissue-specific, omics-determined sub-networks and the connections with their upstream regulator receptors to obtain a systems view of the differentiation of human adipocytes. Adipogenesis of human SBGS pre-adipocyte cells in vitro was monitored with a transcriptomic data set comprising six time points (0, 6, 48, 96, 192, 384 hours). To elucidate the mechanisms of adipogenesis, NASFinder was used to perform time-point analysis by comparing each time point against the control (0 h) and time-lapse analysis by comparing each time point with the previous one. NASFinder identified the coordinated activity of seemingly unrelated processes between each comparison, providing the first systems view of adipogenesis in culture. NASFinder has been implemented into a web-based, freely available resource associated with novel, easy to read visualization of omics data sets and network modules.

Online Learning: A Comparison of Web-Based and Land-Based Courses

ERIC Educational Resources Information Center

Brown, Joy L. M.

2012-01-01

Distance learning has become more popular in recent years. Due to concern about the quality of web-based courses, the purpose of this study was to explore the differences in web-based versus land-based courses. In this study, the researcher compares web-based and land-based education courses to explore the strengths and weaknesses of each type of…

Learning Tools for Knowledge Nomads: Using Personal Digital Assistants (PDAs) in Web-based Learning Environments.

ERIC Educational Resources Information Center

Loh, Christian Sebastian

2001-01-01

Examines how mobile computers, or personal digital assistants (PDAs), can be used in a Web-based learning environment. Topics include wireless networks on college campuses; online learning; Web-based learning technologies; synchronous and asynchronous communication via the Web; content resources; Web connections; and collaborative learning. (LRW)

Concept Mapping Your Web Searches: A Design Rationale and Web-Enabled Application

ERIC Educational Resources Information Center

Lee, Y.-J.

2004-01-01

Although it has become very common to use World Wide Web-based information in many educational settings, there has been little research on how to better search and organize Web-based information. This paper discusses the shortcomings of Web search engines and Web browsers as learning environments and describes an alternative Web search environment…

A Risk-Analysis Approach to Implementing Web-Based Assessment

ERIC Educational Resources Information Center

Ricketts, Chris; Zakrzewski, Stan

2005-01-01

Computer-Based Assessment is a risky business. This paper proposes the use of a model for web-based assessment systems that identifies pedagogic, operational, technical (non web-based), web-based and financial risks. The strategies and procedures for risk elimination or reduction arise from risk analysis and management and are the means by which…

Network analyses based on comprehensive molecular interaction maps reveal robust control structures in yeast stress response pathways

PubMed Central

Kawakami, Eiryo; Singh, Vivek K; Matsubara, Kazuko; Ishii, Takashi; Matsuoka, Yukiko; Hase, Takeshi; Kulkarni, Priya; Siddiqui, Kenaz; Kodilkar, Janhavi; Danve, Nitisha; Subramanian, Indhupriya; Katoh, Manami; Shimizu-Yoshida, Yuki; Ghosh, Samik; Jere, Abhay; Kitano, Hiroaki

2016-01-01

Cellular stress responses require exquisite coordination between intracellular signaling molecules to integrate multiple stimuli and actuate specific cellular behaviors. Deciphering the web of complex interactions underlying stress responses is a key challenge in understanding robust biological systems and has the potential to lead to the discovery of targeted therapeutics for diseases triggered by dysregulation of stress response pathways. We constructed large-scale molecular interaction maps of six major stress response pathways in Saccharomyces cerevisiae (baker’s or budding yeast). Biological findings from over 900 publications were converted into standardized graphical formats and integrated into a common framework. The maps are posted at http://www.yeast-maps.org/yeast-stress-response/ for browse and curation by the research community. On the basis of these maps, we undertook systematic analyses to unravel the underlying architecture of the networks. A series of network analyses revealed that yeast stress response pathways are organized in bow–tie structures, which have been proposed as universal sub-systems for robust biological regulation. Furthermore, we demonstrated a potential role for complexes in stabilizing the conserved core molecules of bow–tie structures. Specifically, complex-mediated reversible reactions, identified by network motif analyses, appeared to have an important role in buffering the concentration and activity of these core molecules. We propose complex-mediated reactions as a key mechanism mediating robust regulation of the yeast stress response. Thus, our comprehensive molecular interaction maps provide not only an integrated knowledge base, but also a platform for systematic network analyses to elucidate the underlying architecture in complex biological systems. PMID:28725465

GraphSAW: a web-based system for graphical analysis of drug interactions and side effects using pharmaceutical and molecular data.

PubMed

Shoshi, Alban; Hoppe, Tobias; Kormeier, Benjamin; Ogultarhan, Venus; Hofestädt, Ralf

2015-02-28

Adverse drug reactions are one of the most common causes of death in industrialized Western countries. Nowadays, empirical data from clinical studies for the approval and monitoring of drugs and molecular databases is available. The integration of database information is a promising method for providing well-based knowledge to avoid adverse drug reactions. This paper presents our web-based decision support system GraphSAW which analyzes and evaluates drug interactions and side effects based on data from two commercial and two freely available molecular databases. The system is able to analyze single and combined drug-drug interactions, drug-molecule interactions as well as single and cumulative side effects. In addition, it allows exploring associative networks of drugs, molecules, metabolic pathways, and diseases in an intuitive way. The molecular medication analysis includes the capabilities of the upper features. A statistical evaluation of the integrated data and top 20 drugs concerning drug interactions and side effects is performed. The results of the data analysis give an overview of all theoretically possible drug interactions and side effects. The evaluation shows a mismatch between pharmaceutical and molecular databases. The concordance of drug interactions was about 12% and 9% of drug side effects. An application case with prescribed data of 11 patients is presented in order to demonstrate the functionality of the system under real conditions. For each patient at least two interactions occured in every medication and about 8% of total diseases were possibly induced by drug therapy. GraphSAW (http://tunicata.techfak.uni-bielefeld.de/graphsaw/) is meant to be a web-based system for health professionals and researchers. GraphSAW provides comprehensive drug-related knowledge and an improved medication analysis which may support efforts to reduce the risk of medication errors and numerous drastic side effects.

The internet as psychological laboratory.

PubMed

Skitka, Linda J; Sargis, Edward G

2006-01-01

This chapter reviews studies published in American Psychological Association (APA) journals from 2003-2004 and additional studies (received in response to listserv requests) that used the Internet to collect data (N=121 total studies). Specific examples of three kinds of Web-based research are reviewed: (a) translational (established methods and research questions are adapted to the Web), (b) phenomenological (behavior on the Web is the focus of study), and (c) novel (methodologically innovations unique to Web-based research). Among other findings, our review indicated that 21% of APA journals published at least one article that reported on Web-based research, most Web-based psychological research uses experimental methods, a surprising number use college student samples, and deception in Web-based research is not uncommon. Strengths and weaknesses of Web-based psychological research in general, and our sample of studies in particular, are reviewed with special attention to possible concerns about sampling and the use of deception.

RaMP: A Comprehensive Relational Database of Metabolomics Pathways for Pathway Enrichment Analysis of Genes and Metabolites

PubMed Central

Zhang, Bofei; Hu, Senyang; Baskin, Elizabeth; Patt, Andrew; Siddiqui, Jalal K.

2018-01-01

The value of metabolomics in translational research is undeniable, and metabolomics data are increasingly generated in large cohorts. The functional interpretation of disease-associated metabolites though is difficult, and the biological mechanisms that underlie cell type or disease-specific metabolomics profiles are oftentimes unknown. To help fully exploit metabolomics data and to aid in its interpretation, analysis of metabolomics data with other complementary omics data, including transcriptomics, is helpful. To facilitate such analyses at a pathway level, we have developed RaMP (Relational database of Metabolomics Pathways), which combines biological pathways from the Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome, WikiPathways, and the Human Metabolome DataBase (HMDB). To the best of our knowledge, an off-the-shelf, public database that maps genes and metabolites to biochemical/disease pathways and can readily be integrated into other existing software is currently lacking. For consistent and comprehensive analysis, RaMP enables batch and complex queries (e.g., list all metabolites involved in glycolysis and lung cancer), can readily be integrated into pathway analysis tools, and supports pathway overrepresentation analysis given a list of genes and/or metabolites of interest. For usability, we have developed a RaMP R package (https://github.com/Mathelab/RaMP-DB), including a user-friendly RShiny web application, that supports basic simple and batch queries, pathway overrepresentation analysis given a list of genes or metabolites of interest, and network visualization of gene-metabolite relationships. The package also includes the raw database file (mysql dump), thereby providing a stand-alone downloadable framework for public use and integration with other tools. In addition, the Python code needed to recreate the database on another system is also publicly available (https://github.com/Mathelab/RaMP-BackEnd). Updates for databases in RaMP will be checked multiple times a year and RaMP will be updated accordingly. PMID:29470400

RaMP: A Comprehensive Relational Database of Metabolomics Pathways for Pathway Enrichment Analysis of Genes and Metabolites.

PubMed

Zhang, Bofei; Hu, Senyang; Baskin, Elizabeth; Patt, Andrew; Siddiqui, Jalal K; Mathé, Ewy A

2018-02-22

The value of metabolomics in translational research is undeniable, and metabolomics data are increasingly generated in large cohorts. The functional interpretation of disease-associated metabolites though is difficult, and the biological mechanisms that underlie cell type or disease-specific metabolomics profiles are oftentimes unknown. To help fully exploit metabolomics data and to aid in its interpretation, analysis of metabolomics data with other complementary omics data, including transcriptomics, is helpful. To facilitate such analyses at a pathway level, we have developed RaMP (Relational database of Metabolomics Pathways), which combines biological pathways from the Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome, WikiPathways, and the Human Metabolome DataBase (HMDB). To the best of our knowledge, an off-the-shelf, public database that maps genes and metabolites to biochemical/disease pathways and can readily be integrated into other existing software is currently lacking. For consistent and comprehensive analysis, RaMP enables batch and complex queries (e.g., list all metabolites involved in glycolysis and lung cancer), can readily be integrated into pathway analysis tools, and supports pathway overrepresentation analysis given a list of genes and/or metabolites of interest. For usability, we have developed a RaMP R package (https://github.com/Mathelab/RaMP-DB), including a user-friendly RShiny web application, that supports basic simple and batch queries, pathway overrepresentation analysis given a list of genes or metabolites of interest, and network visualization of gene-metabolite relationships. The package also includes the raw database file (mysql dump), thereby providing a stand-alone downloadable framework for public use and integration with other tools. In addition, the Python code needed to recreate the database on another system is also publicly available (https://github.com/Mathelab/RaMP-BackEnd). Updates for databases in RaMP will be checked multiple times a year and RaMP will be updated accordingly.

Web-Based Training Methods for Behavioral Health Providers: A Systematic Review.

PubMed

Jackson, Carrie B; Quetsch, Lauren B; Brabson, Laurel A; Herschell, Amy D

2018-07-01

There has been an increase in the use of web-based training methods to train behavioral health providers in evidence-based practices. This systematic review focuses solely on the efficacy of web-based training methods for training behavioral health providers. A literature search yielded 45 articles meeting inclusion criteria. Results indicated that the serial instruction training method was the most commonly studied web-based training method. While the current review has several notable limitations, findings indicate that participating in a web-based training may result in greater post-training knowledge and skill, in comparison to baseline scores. Implications and recommendations for future research on web-based training methods are discussed.

75 FR 15693 - Extension of Web-Based TRICARE Assistance Program Demonstration Project

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-30

... DEPARTMENT OF DEFENSE Office of the Secretary Extension of Web-Based TRICARE Assistance Program Demonstration Project AGENCY: Department of Defense (DoD). ACTION: Notice of a Web-Based TRICARE Assistance... States Code, Section 1092, entitled Web-Based TRICARE Assistance Program. This demonstration was...

High-performance spider webs: integrating biomechanics, ecology and behaviour

PubMed Central

Harmer, Aaron M. T.; Blackledge, Todd A.; Madin, Joshua S.; Herberstein, Marie E.

2011-01-01

Spider silks exhibit remarkable properties, surpassing most natural and synthetic materials in both strength and toughness. Orb-web spider dragline silk is the focus of intense research by material scientists attempting to mimic these naturally produced fibres. However, biomechanical research on spider silks is often removed from the context of web ecology and spider foraging behaviour. Similarly, evolutionary and ecological research on spiders rarely considers the significance of silk properties. Here, we highlight the critical need to integrate biomechanical and ecological perspectives on spider silks to generate a better understanding of (i) how silk biomechanics and web architectures interacted to influence spider web evolution along different structural pathways, and (ii) how silks function in an ecological context, which may identify novel silk applications. An integrative, mechanistic approach to understanding silk and web function, as well as the selective pressures driving their evolution, will help uncover the potential impacts of environmental change and species invasions (of both spiders and prey) on spider success. Integrating these fields will also allow us to take advantage of the remarkable properties of spider silks, expanding the range of possible silk applications from single threads to two- and three-dimensional thread networks. PMID:21036911

The Food Web of Potter Cove (Antarctica): complexity, structure and function

NASA Astrophysics Data System (ADS)

Marina, Tomás I.; Salinas, Vanesa; Cordone, Georgina; Campana, Gabriela; Moreira, Eugenia; Deregibus, Dolores; Torre, Luciana; Sahade, Ricardo; Tatián, Marcos; Barrera Oro, Esteban; De Troch, Marleen; Doyle, Santiago; Quartino, María Liliana; Saravia, Leonardo A.; Momo, Fernando R.

2018-01-01

Knowledge of the food web structure and complexity are central to better understand ecosystem functioning. A food-web approach includes both species and energy flows among them, providing a natural framework for characterizing species' ecological roles and the mechanisms through which biodiversity influences ecosystem dynamics. Here we present for the first time a high-resolution food web for a marine ecosystem at Potter Cove (northern Antarctic Peninsula). Eleven food web properties were analyzed in order to document network complexity, structure and topology. We found a low linkage density (3.4), connectance (0.04) and omnivory percentage (45), as well as a short path length (1.8) and a low clustering coefficient (0.08). Furthermore, relating the structure of the food web to its dynamics, an exponential degree distribution (in- and out-links) was found. This suggests that the Potter Cove food web may be vulnerable if the most connected species became locally extinct. For two of the three more connected functional groups, competition overlap graphs imply high trophic interaction between demersal fish and niche specialization according to feeding strategies in amphipods. On the other hand, the prey overlap graph shows also that multiple energy pathways of carbon flux exist across benthic and pelagic habitats in the Potter Cove ecosystem. Although alternative food sources might add robustness to the web, network properties (low linkage density, connectance and omnivory) suggest fragility and potential trophic cascade effects.

Quality evaluation on an e-learning system in continuing professional education of nurses.

PubMed

Lin, I-Chun; Chien, Yu-Mei; Chang, I-Chiu

2006-01-01

Maintaining high quality in Web-based learning is a powerful means of increasing the overall efficiency and effectiveness of distance learning. Many studies have evaluated Web-based learning but seldom evaluate from the information systems (IS) perspective. This study applied the famous IS Success model in measuring the quality of a Web-based learning system using a Web-based questionnaire for data collection. One hundred and fifty four nurses participated in the survey. Based on confirmatory factor analysis, the variables of the research model fit for measuring the quality of a Web-based learning system. As Web-based education continues to grow worldwide, the results of this study may assist the system adopter (hospital executives), the learner (nurses), and the system designers in making reasonable and informed judgments with regard to the quality of Web-based learning system in continuing professional education.

Randomized, Controlled Trial of CBT Training for PTSD Providers

DTIC Science & Technology

2016-10-29

trial and comparative effectiveness study is to design, implement and evaluate a cost effective, web based self paced training program to provide skills...without web -centered supervision, may provide an effective means to train increasing numbers of mental health providers in relevant, evidence-based...in equal numbers to three parallel intervention condition: a) Web -based training plus web -centered supervision; b) Web - based training alone; and c

Randomized, Controlled Trial of CBT Training for PTSD Providers

DTIC Science & Technology

2016-10-01

implement and evaluate a cost effective, web based self-paced training program to provide skills-oriented continuing education for mental health...professionals. The objective is to learn whether novel, internet-based training methods, with or without web -centered supervision, may provide an...condition: a) Web -based training plus web -centered supervision; b) Web - based training alone; and c) Training-as-usual control group. An equal number of

LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources.

PubMed

Karchin, Rachel; Diekhans, Mark; Kelly, Libusha; Thomas, Daryl J; Pieper, Ursula; Eswar, Narayanan; Haussler, David; Sali, Andrej

2005-06-15

The NCBI dbSNP database lists over 9 million single nucleotide polymorphisms (SNPs) in the human genome, but currently contains limited annotation information. SNPs that result in amino acid residue changes (nsSNPs) are of critical importance in variation between individuals, including disease and drug sensitivity. We have developed LS-SNP, a genomic scale software pipeline to annotate nsSNPs. LS-SNP comprehensively maps nsSNPs onto protein sequences, functional pathways and comparative protein structure models, and predicts positions where nsSNPs destabilize proteins, interfere with the formation of domain-domain interfaces, have an effect on protein-ligand binding or severely impact human health. It currently annotates 28,043 validated SNPs that produce amino acid residue substitutions in human proteins from the SwissProt/TrEMBL database. Annotations can be viewed via a web interface either in the context of a genomic region or by selecting sets of SNPs, genes, proteins or pathways. These results are useful for identifying candidate functional SNPs within a gene, haplotype or pathway and in probing molecular mechanisms responsible for functional impacts of nsSNPs. http://www.salilab.org/LS-SNP CONTACT: rachelk@salilab.org http://salilab.org/LS-SNP/supp-info.pdf.

Proteome reference map and regulation network of neonatal rat cardiomyocyte

PubMed Central

Li, Zi-jian; Liu, Ning; Han, Qi-de; Zhang, You-yi

2011-01-01

Aim: To study and establish a proteome reference map and regulation network of neonatal rat cardiomyocyte. Methods: Cultured cardiomyocytes of neonatal rats were used. All proteins expressed in the cardiomyocytes were separated and identified by two-dimensional polyacrylamide gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS). Biological networks and pathways of the neonatal rat cardiomyocytes were analyzed using the Ingenuity Pathway Analysis (IPA) program (www.ingenuity.com). A 2-DE database was made accessible on-line by Make2ddb package on a web server. Results: More than 1000 proteins were separated on 2D gels, and 148 proteins were identified. The identified proteins were used for the construction of an extensible markup language-based database. Biological networks and pathways were constructed to analyze the functions associate with cardiomyocyte proteins in the database. The 2-DE database of rat cardiomyocyte proteins can be accessed at http://2d.bjmu.edu.cn. Conclusion: A proteome reference map and regulation network of the neonatal rat cardiomyocytes have been established, which may serve as an international platform for storage, analysis and visualization of cardiomyocyte proteomic data. PMID:21841810

Bringing Control System User Interfaces to the Web

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Xihui; Kasemir, Kay

With the evolution of web based technologies, especially HTML5 [1], it becomes possible to create web-based control system user interfaces (UI) that are cross-browser and cross-device compatible. This article describes two technologies that facilitate this goal. The first one is the WebOPI [2], which can seamlessly display CSS BOY [3] Operator Interfaces (OPI) in web browsers without modification to the original OPI file. The WebOPI leverages the powerful graphical editing capabilities of BOY and provides the convenience of re-using existing OPI files. On the other hand, it uses generic JavaScript and a generic communication mechanism between the web browser andmore » web server. It is not optimized for a control system, which results in unnecessary network traffic and resource usage. Our second technology is the WebSocket-based Process Data Access (WebPDA) [4]. It is a protocol that provides efficient control system data communication using WebSocket [5], so that users can create web-based control system UIs using standard web page technologies such as HTML, CSS and JavaScript. WebPDA is control system independent, potentially supporting any type of control system.« less

Future View: Web Navigation based on Learning User's Browsing Strategy

NASA Astrophysics Data System (ADS)

Nagino, Norikatsu; Yamada, Seiji

In this paper, we propose a Future View system that assists user's usual Web browsing. The Future View will prefetch Web pages based on user's browsing strategies and present them to a user in order to assist Web browsing. To learn user's browsing strategy, the Future View uses two types of learning classifier systems: a content-based classifier system for contents change patterns and an action-based classifier system for user's action patterns. The results of learning is applied to crawling by Web robots, and the gathered Web pages are presented to a user through a Web browser interface. We experimentally show effectiveness of navigation using the Future View.

HBVPathDB: a database of HBV infection-related molecular interaction network.

PubMed

Zhang, Yi; Bo, Xiao-Chen; Yang, Jing; Wang, Sheng-Qi

2005-03-21

To describe molecules or genes interaction between hepatitis B viruses (HBV) and host, for understanding how virus' and host's genes and molecules are networked to form a biological system and for perceiving mechanism of HBV infection. The knowledge of HBV infection-related reactions was organized into various kinds of pathways with carefully drawn graphs in HBVPathDB. Pathway information is stored with relational database management system (DBMS), which is currently the most efficient way to manage large amounts of data and query is implemented with powerful Structured Query Language (SQL). The search engine is written using Personal Home Page (PHP) with SQL embedded and web retrieval interface is developed for searching with Hypertext Markup Language (HTML). We present the first version of HBVPathDB, which is a HBV infection-related molecular interaction network database composed of 306 pathways with 1 050 molecules involved. With carefully drawn graphs, pathway information stored in HBVPathDB can be browsed in an intuitive way. We develop an easy-to-use interface for flexible accesses to the details of database. Convenient software is implemented to query and browse the pathway information of HBVPathDB. Four search page layout options-category search, gene search, description search, unitized search-are supported by the search engine of the database. The database is freely available at http://www.bio-inf.net/HBVPathDB/HBV/. The conventional perspective HBVPathDB have already contained a considerable amount of pathway information with HBV infection related, which is suitable for in-depth analysis of molecular interaction network of virus and host. HBVPathDB integrates pathway data-sets with convenient software for query, browsing, visualization, that provides users more opportunity to identify regulatory key molecules as potential drug targets and to explore the possible mechanism of HBV infection based on gene expression datasets.

Delivering Electronic Resources with Web OPACs and Other Web-based Tools: Needs of Reference Librarians.

ERIC Educational Resources Information Center

Bordeianu, Sever; Carter, Christina E.; Dennis, Nancy K.

2000-01-01

Describes Web-based online public access catalogs (Web OPACs) and other Web-based tools as gateway methods for providing access to library collections. Addresses solutions for overcoming barriers to information, such as through the implementation of proxy servers and other authentication tools for remote users. (Contains 18 references.)…

78 FR 35312 - Trinity Adaptive Management Working Group; Public Meeting, Teleconference and Web-Based Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-12

...-FF08EACT00] Trinity Adaptive Management Working Group; Public Meeting, Teleconference and Web-Based Meeting... Service, announce a public meeting, teleconference and web-based meeting of the Trinity Adaptive Management Working Group (TAMWG). DATES: Public meeting, Teleconference, and web-based meeting: Tuesday June...

78 FR 49281 - Trinity Adaptive Management Working Group; Public Meeting, Teleconference and Web-Based Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-13

...-FF08EACT00] Trinity Adaptive Management Working Group; Public Meeting, Teleconference and Web-Based Meeting... Service, announce a public meeting, teleconference, and web-based meeting of the Trinity Adaptive Management Working Group (TAMWG). DATES: Public meeting, Teleconference, and web-based meeting: Tuesday...

78 FR 17226 - Trinity Adaptive Management Working Group; Public Meeting, Teleconference and Web-Based Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-20

...-FF08EACT00] Trinity Adaptive Management Working Group; Public Meeting, Teleconference and Web-Based Meeting... Service, announce a public meeting, teleconference and web-based meeting of the Trinity Adaptive Management Working Group (TAMWG). DATES: Public meeting, Teleconference, and web-based meeting: Monday April...

77 FR 8837 - Termination of the Department of Defense Web-Based TRICARE Assistance Program Demonstration

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-15

... DEPARTMENT OF DEFENSE Office of the Secretary Termination of the Department of Defense Web-Based..., entitled Web-Based TRICARE Assistance Program (TRIAP). The demonstration project uses existing health care support contracts (HCSC) to allow web-based behavioral health and related services including non-medical...

76 FR 12073 - Extension of Web-Based TRICARE Assistance Program Demonstration Program

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-04

... DEPARTMENT OF DEFENSE Office of the Secretary Extension of Web-Based TRICARE Assistance Program Demonstration Program AGENCY: Department of Defense. ACTION: Notice of a Two Year Extension of the Web-Based..., entitled Web-Based TRICARE Assistance Program. This demonstration was effective August 1, 2009, as...

Using Web-Based and Paper-Based Questionnaires for Collecting Data on Fertility Issues Among Female Childhood Cancer Survivors: Differences in Response Characteristics

PubMed Central

Overbeek, Annelies; van der Pal, Helena J; Versluys, A. Birgitta; Bresters, Dorine; van Leeuwen, Flora E; Lambalk, Cornelis B; Kaspers, Gertjan J.L; van Dulmen-den Broeder, Eline

2011-01-01

Background Web-based questionnaires have become increasingly popular in health research. However, reported response rates vary and response bias may be introduced. Objective The aim of this study was to evaluate whether sending a mixed invitation (paper-based together with Web-based questionnaire) rather than a Web-only invitation (Web-based questionnaire only) results in higher response and participation rates for female childhood cancer survivors filling out a questionnaire on fertility issues. In addition, differences in type of response and characteristics of the responders and nonresponders were investigated. Moreover, factors influencing preferences for either the Web- or paper-based version of the questionnaire were examined. Methods This study is part of a nationwide study on reproductive function, ovarian reserve, and risk of premature menopause in female childhood cancer survivors. The Web-based version of the questionnaire was available for participants through the Internet by means of a personalized user name and password. Participants were randomly selected to receive either a mixed invitation (paper-based questionnaire together with log-in details for Web-based questionnaire, n = 137) or a Web-only invitation (log-in details only, n = 140). Furthermore, the latter group could request a paper-based version of the questionnaire by filling out a form. Results Overall response rates were comparable in both randomization groups (83% mixed invitation group vs 89% in Web-only invitation group, P = .20). In addition, participation rates appeared not to differ (66% or 90/137, mixed invitation group vs 59% or 83/140, Web-only invitation group, P =.27). However, in the mixed invitation group, significantly more respondents filled out the paper-based questionnaire compared with the Web-only invitation group (83% or 75/90 and 65% or 54/83, respectively, P = .01). The 44 women who filled out the Web-based version of the questionnaire had a higher educational level than the 129 women who filled out the paper-based version (P = .01). Furthermore, the probability of filling out the Web-based questionnaire appeared to be greater for women who were allocated to the Web-only invitation group (OR = 2.85, 95% CI 1.31 - 6.21), were older (OR = 1.08, 95% CI 1.02 - 1.15), had a higher educational level (OR high vs low = 0.06, 95% CI 0.01 - 0.52), or were students (OR employed vs student = 3.25, 95% CI 1.00 - 10.56). Conclusions Although overall response as well as participation rates to both types of invitations were similar, adding a paper version of a questionnaire to a Web-only invitation resulted in more respondents filling out the paper-based version. In addition, women who were older, had a higher level of education, or were students, were more likely to have filled out the Web-based version of the questionnaire. Given the many advantages of Web-based over paper-based questionnaires, researchers should strongly consider using Web-based questionnaires, although possible response bias when using these types of questionnaires should be taken into account. Trial Registration Nederlands Trial Register NTR2922; http://www.trialregister.nl/trialreg/admin/rctview.asp?TC=2922 (Archived by WebCite at http://www.webcitation.org/5zRRdMrDv) PMID:21955527

Using web-based and paper-based questionnaires for collecting data on fertility issues among female childhood cancer survivors: differences in response characteristics.

PubMed

van den Berg, Marleen H; Overbeek, Annelies; van der Pal, Helena J; Versluys, A Birgitta; Bresters, Dorine; van Leeuwen, Flora E; Lambalk, Cornelis B; Kaspers, Gertjan J L; van Dulmen-den Broeder, Eline

2011-09-29

Web-based questionnaires have become increasingly popular in health research. However, reported response rates vary and response bias may be introduced. The aim of this study was to evaluate whether sending a mixed invitation (paper-based together with Web-based questionnaire) rather than a Web-only invitation (Web-based questionnaire only) results in higher response and participation rates for female childhood cancer survivors filling out a questionnaire on fertility issues. In addition, differences in type of response and characteristics of the responders and nonresponders were investigated. Moreover, factors influencing preferences for either the Web- or paper-based version of the questionnaire were examined. This study is part of a nationwide study on reproductive function, ovarian reserve, and risk of premature menopause in female childhood cancer survivors. The Web-based version of the questionnaire was available for participants through the Internet by means of a personalized user name and password. Participants were randomly selected to receive either a mixed invitation (paper-based questionnaire together with log-in details for Web-based questionnaire, n = 137) or a Web-only invitation (log-in details only, n = 140). Furthermore, the latter group could request a paper-based version of the questionnaire by filling out a form. Overall response rates were comparable in both randomization groups (83% mixed invitation group vs 89% in Web-only invitation group, P = .20). In addition, participation rates appeared not to differ (66% or 90/137, mixed invitation group vs 59% or 83/140, Web-only invitation group, P =.27). However, in the mixed invitation group, significantly more respondents filled out the paper-based questionnaire compared with the Web-only invitation group (83% or 75/90 and 65% or 54/83, respectively, P = .01). The 44 women who filled out the Web-based version of the questionnaire had a higher educational level than the 129 women who filled out the paper-based version (P = .01). Furthermore, the probability of filling out the Web-based questionnaire appeared to be greater for women who were allocated to the Web-only invitation group (OR = 2.85, 95% CI 1.31-6.21), were older (OR = 1.08, 95% CI 1.02-1.15), had a higher educational level (OR high vs low = 0.06, 95% CI 0.01-0.52), or were students (OR employed vs student = 3.25, 95% CI 1.00-10.56). Although overall response as well as participation rates to both types of invitations were similar, adding a paper version of a questionnaire to a Web-only invitation resulted in more respondents filling out the paper-based version. In addition, women who were older, had a higher level of education, or were students, were more likely to have filled out the Web-based version of the questionnaire. Given the many advantages of Web-based over paper-based questionnaires, researchers should strongly consider using Web-based questionnaires, although possible response bias when using these types of questionnaires should be taken into account. Nederlands Trial Register NTR2922; http://www.trialregister.nl/trialreg/admin/rctview.asp?TC=2922 (Archived by WebCite at http://www.webcitation.org/5zRRdMrDv).

Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology

PubMed Central

Latendresse, Mario; Paley, Suzanne M.; Krummenacker, Markus; Ong, Quang D.; Billington, Richard; Kothari, Anamika; Weaver, Daniel; Lee, Thomas; Subhraveti, Pallavi; Spaulding, Aaron; Fulcher, Carol; Keseler, Ingrid M.; Caspi, Ron

2016-01-01

Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer and comparative-genomics operations. It offers metabolic-informatics tools, such as metabolic reconstruction, quantitative metabolic modeling, prediction of reaction atom mappings and metabolic route search. Pathway Tools also provides regulatory-informatics tools, such as the ability to represent and visualize a wide range of regulatory interactions. This article outlines the advances in Pathway Tools in the past 5 years. Major additions include components for metabolic modeling, metabolic route search, computation of atom mappings and estimation of compound Gibbs free energies of formation; addition of editors for signaling pathways, for genome sequences and for cellular architecture; storage of gene essentiality data and phenotype data; display of multiple alignments, and of signaling and electron-transport pathways; and development of Python and web-services application programming interfaces. Scientists around the world have created more than 9800 Pathway/Genome Databases by using Pathway Tools, many of which are curated databases for important model organisms. PMID:26454094

KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats.

PubMed

Wrzodek, Clemens; Dräger, Andreas; Zell, Andreas

2011-08-15

The KEGG PATHWAY database provides a widely used service for metabolic and nonmetabolic pathways. It contains manually drawn pathway maps with information about the genes, reactions and relations contained therein. To store these pathways, KEGG uses KGML, a proprietary XML-format. Parsers and translators are needed to process the pathway maps for usage in other applications and algorithms. We have developed KEGGtranslator, an easy-to-use stand-alone application that can visualize and convert KGML formatted XML-files into multiple output formats. Unlike other translators, KEGGtranslator supports a plethora of output formats, is able to augment the information in translated documents (e.g. MIRIAM annotations) beyond the scope of the KGML document, and amends missing components to fragmentary reactions within the pathway to allow simulations on those. KEGGtranslator is freely available as a Java(™) Web Start application and for download at http://www.cogsys.cs.uni-tuebingen.de/software/KEGGtranslator/. KGML files can be downloaded from within the application. clemens.wrzodek@uni-tuebingen.de Supplementary data are available at Bioinformatics online.

A web-based platform to support an evidence-based mental health intervention: lessons from the CBITS web site.

PubMed

Vona, Pamela; Wilmoth, Pete; Jaycox, Lisa H; McMillen, Janey S; Kataoka, Sheryl H; Wong, Marleen; DeRosier, Melissa E; Langley, Audra K; Kaufman, Joshua; Tang, Lingqi; Stein, Bradley D

2014-11-01

To explore the role of Web-based platforms in behavioral health, the study examined usage of a Web site for supporting training and implementation of an evidence-based intervention. Using data from an online registration survey and Google Analytics, the investigators examined user characteristics and Web site utilization. Site engagement was substantial across user groups. Visit duration differed by registrants' characteristics. Less experienced clinicians spent more time on the Web site. The training section accounted for most page views across user groups. Individuals previously trained in the Cognitive-Behavioral Intervention for Trauma in Schools intervention viewed more implementation assistance and online community pages than did other user groups. Web-based platforms have the potential to support training and implementation of evidence-based interventions for clinicians of varying levels of experience and may facilitate more rapid dissemination. Web-based platforms may be promising for trauma-related interventions, because training and implementation support should be readily available after a traumatic event.

WebBio, a web-based management and analysis system for patient data of biological products in hospital.

PubMed

Lu, Ying-Hao; Kuo, Chen-Chun; Huang, Yaw-Bin

2011-08-01

We selected HTML, PHP and JavaScript as the programming languages to build "WebBio", a web-based system for patient data of biological products and used MySQL as database. WebBio is based on the PHP-MySQL suite and is run by Apache server on Linux machine. WebBio provides the functions of data management, searching function and data analysis for 20 kinds of biological products (plasma expanders, human immunoglobulin and hematological products). There are two particular features in WebBio: (1) pharmacists can rapidly find out whose patients used contaminated products for medication safety, and (2) the statistics charts for a specific product can be automatically generated to reduce pharmacist's work loading. WebBio has successfully turned traditional paper work into web-based data management.

Utility of a Web-based intervention for individuals with type 2 diabetes: the impact on physical activity levels and glycemic control.

PubMed

Kim, Chun-Ja; Kang, Duck-Hee

2006-01-01

Despite the numerous benefits of physical activity for patients with diabetes, most healthcare providers in busy clinical settings rarely find time to counsel their patients about it. A Web-based program for healthcare providers can be used as an effective counseling tool, when strategies are outlined for specific stages of readiness for physical activity. Seventy-three adults with type 2 diabetes were randomly assigned to Web-based intervention, printed-material intervention, or usual care. After 12 weeks, the effects of the interventions on physical activity, fasting blood sugar, and glycosylated hemoglobin were evaluated. Both Web-based and printed material intervention, compared with usual care, were effective in increasing physical activity (P < .001) and decreasing fasting blood sugar (P<.01) and glycosylated hemoglobin (P < .01). Post hoc analysis for change scores indicated significant differences between Web-based intervention and usual care and between printed material intervention and usual care, but not between web-based and printed material intervention. The findings of this study support the value of Web-based and printed material interventions in healthcare counseling. With increasing Web access, the effectiveness of Web-based programs offered directly to patients needs to be tested.

The use of advanced web-based survey design in Delphi research.

PubMed

Helms, Christopher; Gardner, Anne; McInnes, Elizabeth

2017-12-01

A discussion of the application of metadata, paradata and embedded data in web-based survey research, using two completed Delphi surveys as examples. Metadata, paradata and embedded data use in web-based Delphi surveys has not been described in the literature. The rapid evolution and widespread use of online survey methods imply that paper-based Delphi methods will likely become obsolete. Commercially available web-based survey tools offer a convenient and affordable means of conducting Delphi research. Researchers and ethics committees may be unaware of the benefits and risks of using metadata in web-based surveys. Discussion paper. Two web-based, three-round Delphi surveys were conducted sequentially between August 2014 - January 2015 and April - May 2016. Their aims were to validate the Australian nurse practitioner metaspecialties and their respective clinical practice standards. Our discussion paper is supported by researcher experience and data obtained from conducting both web-based Delphi surveys. Researchers and ethics committees should consider the benefits and risks of metadata use in web-based survey methods. Web-based Delphi research using paradata and embedded data may introduce efficiencies that improve individual participant survey experiences and reduce attrition across iterations. Use of embedded data allows the efficient conduct of multiple simultaneous Delphi surveys across a shorter timeframe than traditional survey methods. The use of metadata, paradata and embedded data appears to improve response rates, identify bias and give possible explanation for apparent outlier responses, providing an efficient method of conducting web-based Delphi surveys. © 2017 John Wiley & Sons Ltd.

Quality of reporting web-based and non-web-based survey studies: What authors, reviewers and consumers should consider.

PubMed

Turk, Tarek; Elhady, Mohamed Tamer; Rashed, Sherwet; Abdelkhalek, Mariam; Nasef, Somia Ahmed; Khallaf, Ashraf Mohamed; Mohammed, Abdelrahman Tarek; Attia, Andrew Wassef; Adhikari, Purushottam; Amin, Mohamed Alsabbahi; Hirayama, Kenji; Huy, Nguyen Tien

2018-01-01

Several influential aspects of survey research have been under-investigated and there is a lack of guidance on reporting survey studies, especially web-based projects. In this review, we aim to investigate the reporting practices and quality of both web- and non-web-based survey studies to enhance the quality of reporting medical evidence that is derived from survey studies and to maximize the efficiency of its consumption. Reporting practices and quality of 100 random web- and 100 random non-web-based articles published from 2004 to 2016 were assessed using the SUrvey Reporting GuidelinE (SURGE). The CHERRIES guideline was also used to assess the reporting quality of Web-based studies. Our results revealed a potential gap in the reporting of many necessary checklist items in both web-based and non-web-based survey studies including development, description and testing of the questionnaire, the advertisement and administration of the questionnaire, sample representativeness and response rates, incentives, informed consent, and methods of statistical analysis. Our findings confirm the presence of major discrepancies in reporting results of survey-based studies. This can be attributed to the lack of availability of updated universal checklists for quality of reporting standards. We have summarized our findings in a table that may serve as a roadmap for future guidelines and checklists, which will hopefully include all types and all aspects of survey research.

Model Data Interoperability for the United States Integrated Ocean Observing System (IOOS)

NASA Astrophysics Data System (ADS)

Signell, Richard P.

2010-05-01

Model data interoperability for the United States Integrated Ocean Observing System (IOOS) was initiated with a focused one year project. The problem was that there were many regional and national providers of oceanographic model data; each had unique file conventions, distribution techniques and analysis tools that made it difficult to compare model results and observational data. To solve this problem, a distributed system was built utilizing a customized middleware layer and a common data model. This allowed each model data provider to keep their existing model and data files unchanged, yet deliver model data via web services in a common form. With standards-based applications that used these web services, end users then had a common way to access data from any of the models. These applications included: (1) a 2D mapping and animation using a web browser application, (2) an advanced 3D visualization and animation using a desktop application, and (3) a toolkit for a common scientific analysis environment. Due to the flexibility and low impact of the approach on providers, rapid progress was made. The system was implemented in all eleven US IOOS regions and at the NOAA National Coastal Data Development Center, allowing common delivery of regional and national oceanographic model forecast and archived results that cover all US waters. The system, based heavily on software technology from the NSF-sponsored Unidata Program Center, is applicable to any structured gridded data, not just oceanographic model data. There is a clear pathway to expand the system to include unstructured grid (e.g. triangular grid) data.

Solar System Treks: Interactive Web Portals or STEM, Exploration and Beyond

NASA Astrophysics Data System (ADS)

Law, E.; Day, B. H.; Viotti, M.

2017-12-01

NASA's Solar System Treks project produces a suite of online visualization and analysis tools for lunar and planetary mapping and modeling. These portals offer great benefits for education and public outreach, providing access to data from a wide range of instruments aboard a variety of past and current missions. As a component of NASA's STEM Activation Infrastructure, they are available as resources for NASA STEM programs, and to the greater STEM community. As new missions are planned to a variety of planetary bodies, these tools facilitate public understanding of the missions and engage the public in the process of identifying and selecting where these missions will land. There are currently three web portals in the program: Moon Trek (https://moontrek.jpl.nasa.gov), Mars Trek (https://marstrek.jpl.nasa.gov), and Vesta Trek (https://vestatrek.jpl.nasa.gov). A new release of Mars Trek includes new tools and data products focusing on human landing site selection. Backed by evidence-based cognitive and computer science findings, an additional version is available for educational and public audiences in support of earning along novice-to-expert pathways, enabling authentic, real-world interaction with planetary data. Portals for additional planetary bodies are planned. As web-based toolsets, the portals do not require users to purchase or install any software beyond current web browsers. The portals provide analysis tools for measurement and study of planetary terrain. They allow data to be layered and adjusted to optimize visualization. Visualizations are easily stored and shared. The portals provide 3D visualization and give users the ability to mark terrain for generation of STL/OBJ files that can be directed to 3D printers. Such 3D prints are valuable tools in museums, public exhibits, and classrooms - especially for the visually impaired. The program supports additional clients, web services, and APIs facilitating dissemination of planetary data to external applications and venues. NASA challenges and hackathons also provide members of the software development community opportunities to participate in tool development and leverage data from the portals.

A Web-Based and Print-Based Computer-Tailored Physical Activity Intervention for Prostate and Colorectal Cancer Survivors: A Comparison of User Characteristics and Intervention Use

PubMed Central

Bolman, Catherine; Peels, Denise Astrid; Volders, Esmee; de Vries, Hein; Lechner, Lilian

2017-01-01

Background Physical activity (PA) is beneficial in improving negative physical and psychological effects of cancer. The rapidly increasing number of cancer survivors, resulting from aging and improved cancer care, emphasizes the importance to develop and provide low cost, easy accessible PA programs. Such programs could be provided through the Internet, but that could result in the exclusion of cancer survivors not familiar with the Internet. Therefore, we developed a computer-tailored PA intervention for prostate and colorectal cancer survivors in which both Web-based and print materials are provided, and participants can choose their own preferred delivery mode. Objective The aim of this study was to assess participants’ characteristics related to delivery mode and use of intervention materials. Methods We studied characteristics of participants using Web-based and printed intervention materials in a randomized controlled trial (RCT). Prostate and colorectal cancer survivors recruited from hospitals were randomized to OncoActive (computer-tailored PA intervention) or a usual-care control group. OncoActive participants received both Web-based and printed materials. Participants were classified into initial print- or Web-based participants based on their preferred mode of completion of the first questionnaire, which was needed for the computer-tailored PA advice. Intervention material use during the remainder of the intervention was compared for initial print- or Web-based participants. Additionally, participants were classified into those using only print materials and those using Web-based materials. Differences in participant characteristics and intervention material use were studied through analysis of variance (ANOVAs), chi-square tests, and logistic regressions. Results The majority of the participants in the intervention group were classified as initial Web-based participants (170/249, 68.3%), and 84.9% (191/249) used Web-based intervention materials. Dropout was low (15/249, 6.0%) and differed between initial Web-based (4/170, 2.4%) and print-based (11/79, 14%) participants. Participants were less likely to start Web-based with higher age (odds ratio [OR]=0.93), longer time since last treatment (OR=0.87), and higher fatigue (OR=0.96), and more likely with higher education (OR=4.08) and having completed treatments (OR=5.58). Those who were older (OR=0.93) and post treatment for a longer time (OR=0.86) were less likely to use Web-based intervention materials. Initial print-based participants predominantly used print-based materials, whereas initial Web-based participants used both print- and Web-based materials. Conclusions To our knowledge, this is one of the first studies that assessed participant characteristics related to delivery mode in an intervention in which participants had a free choice of delivery modes. Use of print-based materials among the initial Web-based participants was substantial, indicating the importance of print-based materials. According to our findings, it may be important to offer Web- and print-based materials alongside each other. Providing Web-based materials only may exclude older, less educated, more fatigued, or currently treated participants; these groups are especially more vulnerable and could benefit most from PA interventions. PMID:28835353

Pelagic food web patterns: do they modulate virus and nanoflagellate effects on picoplankton during the phytoplankton spring bloom?

PubMed

Ory, Pascaline; Hartmann, Hans J; Jude, Florence; Dupuy, Christine; Del Amo, Yolanda; Catala, Philippe; Mornet, Françoise; Huet, Valérie; Jan, Benoit; Vincent, Dorothée; Sautour, Benoit; Montanié, Hélène

2010-10-01

As agents of mortality, viruses and nanoflagellates impact on picoplankton populations. We examined the differences in interactions between these compartments in two French Atlantic bays. Microbes, considered here as central actors of the planktonic food web, were first monitored seasonally in Arcachon (2005) and Marennes-Oléron (2006) bays. Their dynamics were evaluated to categorize trophic periods using the models of Legendre and Rassoulzadegan as a reference framework. Microbial interactions were then compared through 48 h batch culture experiments performed during the phytoplankton spring bloom, identified as herbivorous in Marennes and multivorous in Arcachon. Marennes was spatially homogeneous compared with Arcachon. The former was potentially more productive, featuring a large number of heterotrophic pathways, while autotrophic mechanisms dominated in Arcachon. A link was found between viruses and phytoplankton in Marennes, suggesting a role of virus in the regulation of autotroph biomass. Moreover, the virus-bacteria relation was weaker in Marennes, with a bacterial lysis potential of 2.6% compared with 39% in Arcachon. The batch experiments (based on size-fractionation and viral enrichment) revealed different microbial interactions that corresponded to the spring-bloom trophic interactions in each bay. In Arcachon, where there is a multivorous web, flagellate predation and viral lysis acted in an opposite way on picophytoplankton. When together they both reduced viral production. Conversely, in Marennes (herbivorous web), flagellates and viruses together increased viral production. Differences in the composition of the bacterial community composition explained the combined flagellate-virus effects on viral production in the two bays. © 2010 Society for Applied Microbiology and Blackwell Publishing Ltd.

78 FR 46361 - Trinity Adaptive Management Working Group; Public Meeting, Teleconference and Web-Based Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-31

...-FF08EACT00] Trinity Adaptive Management Working Group; Public Meeting, Teleconference and Web-Based Meeting... Trinity Management Council (TMC). DATES: Public meeting, Teleconference, and web-based meeting: TAMWG and..., Douglas City, CA 96024. You may participate in person or by teleconference or web-based meeting from your...

75 FR 42376 - Proposed Information Collection; Comment Request; NTIA/FCC Web-based Frequency Coordination System

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-21

... Information Collection; Comment Request; NTIA/FCC Web- based Frequency Coordination System AGENCY: National.... Abstract The National Telecommunications and Information Administration (NTIA) hosts a Web-based system...) bands that are shared on a co-primary basis by federal and non-federal users. The Web-based system...

Examining the Relationship between Teachers' Attitudes and Motivation toward Web-Based Professional Development: A Structural Equation Modeling Approach

ERIC Educational Resources Information Center

Chien, Hui-Min; Kao, Chia-Pin; Yeh, I-Jan; Lin, Kuen-Yi

2012-01-01

This study was conducted to investigate elementary school teachers' attitudes and motivation toward web-based professional development. The relationship between teachers' attitudes and motivation was explored using the AWPD (Attitudes toward Web-based Professional Development) and MWPD (Motivation toward Web-based Professional Development)…

An Experiment to Test the Feasibility and Quality of a Web-Based Questionnaire of Teachers

ERIC Educational Resources Information Center

Jacob, Robin Tepper

2011-01-01

The use of web-based surveys to gather information from teachers has become increasingly common primarily based on the premise that they can reduce costs. Yet, relatively, little is known about the quality or cost effectiveness of web-based versus mail surveys for teachers. To study the efficacy of web-based teacher surveys, the author randomly…

Personalization of Rule-based Web Services.

PubMed

Choi, Okkyung; Han, Sang Yong

2008-04-04

Nowadays Web users have clearly expressed their wishes to receive personalized services directly. Personalization is the way to tailor services directly to the immediate requirements of the user. However, the current Web Services System does not provide any features supporting this such as consideration of personalization of services and intelligent matchmaking. In this research a flexible, personalized Rule-based Web Services System to address these problems and to enable efficient search, discovery and construction across general Web documents and Semantic Web documents in a Web Services System is proposed. This system utilizes matchmaking among service requesters', service providers' and users' preferences using a Rule-based Search Method, and subsequently ranks search results. A prototype of efficient Web Services search and construction for the suggested system is developed based on the current work.

Validation of the Female Sexual Function Index (FSFI) for web-based administration.

PubMed

Crisp, Catrina C; Fellner, Angela N; Pauls, Rachel N

2015-02-01

Web-based questionnaires are becoming increasingly valuable for clinical research. The Female Sexual Function Index (FSFI) is the gold standard for evaluating female sexual function; yet, it has not been validated in this format. We sought to validate the Female Sexual Function Index (FSFI) for web-based administration. Subjects enrolled in a web-based research survey of sexual function from the general population were invited to participate in this validation study. The first 151 respondents were included. Validation participants completed the web-based version of the FSFI followed by a mailed paper-based version. Demographic data were collected for all subjects. Scores were compared using the paired t test and the intraclass correlation coefficient. One hundred fifty-one subjects completed both web- and paper-based versions of the FSFI. Those subjects participating in the validation study did not differ in demographics or FSFI scores from the remaining subjects in the general population study. Total web-based and paper-based FSFI scores were not significantly different (mean 20.31 and 20.29 respectively, p = 0.931). The six domains or subscales of the FSFI were similar when comparing web and paper scores. Finally, intraclass correlation analysis revealed a high degree of correlation between total and subscale scores, r = 0.848-0.943, p < 0.001. Web-based administration of the FSFI is a valid alternative to the paper-based version.

An Approach of Web-based Point Cloud Visualization without Plug-in

NASA Astrophysics Data System (ADS)

Ye, Mengxuan; Wei, Shuangfeng; Zhang, Dongmei

2016-11-01

With the advances in three-dimensional laser scanning technology, the demand for visualization of massive point cloud is increasingly urgent, but a few years ago point cloud visualization was limited to desktop-based solutions until the introduction of WebGL, several web renderers are available. This paper addressed the current issues in web-based point cloud visualization, and proposed a method of web-based point cloud visualization without plug-in. The method combines ASP.NET and WebGL technologies, using the spatial database PostgreSQL to store data and the open web technologies HTML5 and CSS3 to implement the user interface, a visualization system online for 3D point cloud is developed by Javascript with the web interactions. Finally, the method is applied to the real case. Experiment proves that the new model is of great practical value which avoids the shortcoming of the existing WebGIS solutions.

Strong pathways for incorporation of terrestrially derived organic matter into benthic communities

NASA Astrophysics Data System (ADS)

McLeod, Rebecca J.; Wing, Stephen R.

2009-05-01

In Fiordland, New Zealand, large volumes of organic matter are deposited into the marine environment from pristine forested catchments. Analyses of δ15N, δ13C and δ34S were employed to determine whether these inputs were contributing to marine food webs via assimilation by common macroinvertebrates inhabiting the inner reaches of the fjords. Terrestrially derived organic matter (TOM) had values of δ15N, δ13C and δ34S that were distinct from other carbon source pools, providing sufficient power to quantify the contribution of TOM to the benthic food web. Isotopic values among macroinvertebrates varied significantly, with consistently low values of δ15N, δ13C and δ34S for the abundant deposit feeders Echinocardium cordatum (Echinodermata) and Pectinaria australis (Annelida), indicating assimilation of TOM. High concentrations of bacterial fatty acid biomarkers in E. cordatum, and values of δ13C of these biomarkers similar to TOM (-27 to -30‰) confirmed that TOM is indirectly assimilated by these sea urchins via heterotrophic bacteria. TOM was also found to enter the infaunal food web via chemoautotrophic bacteria that live symbiotically within Solemya parkinsonii (Bivalvia). Echinocardium cordatum, Pectinaria australis and S. parkinsonii comprised up to 33.5% of the biomass of the macroinfaunal community, and thus represent strong pathways for movement of organic matter from the forested catchments into the benthic food web. This demonstration of connectivity among adjacent marine and terrestrial habitats has important implications for coastal land management, and highlights the importance of intact coastal forests to marine ecosystem function.

Applying Web Usage Mining for Personalizing Hyperlinks in Web-Based Adaptive Educational Systems

ERIC Educational Resources Information Center

Romero, Cristobal; Ventura, Sebastian; Zafra, Amelia; de Bra, Paul

2009-01-01

Nowadays, the application of Web mining techniques in e-learning and Web-based adaptive educational systems is increasing exponentially. In this paper, we propose an advanced architecture for a personalization system to facilitate Web mining. A specific Web mining tool is developed and a recommender engine is integrated into the AHA! system in…

Attitudes to, and experience of, pooled sampling for sexually transmitted infection testing: a web-based survey of English sexual health services.

PubMed

Shaw, Jonathan; Saunders, John Michael; Hughes, Gwenda

2018-05-01

Chlamydia trachomatis and Neisseria gonorrhoeae testing guidance recommends extragenital screening with locally validated nucleic acid amplification tests, with anatomical sites tested separately. Evidence supports multi-patient combined aliquot pooled sampling (PS) for population screening; evidence for within-patient PS is sparse. Within-patient PS could be more cost-effective for triple-site testing, but requires distinct clinical pathways and consideration over loss of information to guide risk assessments and treatment. We explored PS attitudes and practices amongst clinicians in England. A cross-sectional web-based survey was distributed to clinical leads of sexual health services throughout England in February 2016. Fifty-two (52/216, 23%) services responded. One service reported current within-patient PS and two were awaiting implementation. Of the 49 services not pooling, five were considering implementation. Concerns raised included the inability to distinguish infection site(s) (36/52, 69%), absence of national guidance (34/52, 65%) and reduced assay performance (18/52, 34%). Only 8/52 (15%) considered the current level of evidence sufficient to support PS, with 40/52 (77%) requesting further validation studies and 39/52 (77%) national guidance. PS was rarely used by respondents to this survey, although the response rate was low. The clinical challenges presented by PS need to be addressed through further development of the evidence base.

Development of a data mining and imaging informatics display tool for a multiple sclerosis e-folder system

NASA Astrophysics Data System (ADS)

Liu, Margaret; Loo, Jerry; Ma, Kevin; Liu, Brent

2011-03-01

Multiple sclerosis (MS) is a debilitating autoimmune disease of the central nervous system that damages axonal pathways through inflammation and demyelination. In order to address the need for a centralized application to manage and study MS patients, the MS e-Folder - a web-based, disease-specific electronic medical record system - was developed. The e-Folder has a PHP and MySQL based graphical user interface (GUI) that can serve as both a tool for clinician decision support and a data mining tool for researchers. This web-based GUI gives the e-Folder a user friendly interface that can be securely accessed through the internet and requires minimal software installation on the client side. The e-Folder GUI displays and queries patient medical records--including demographic data, social history, past medical history, and past MS history. In addition, DICOM format imaging data, and computer aided detection (CAD) results from a lesion load algorithm are also displayed. The GUI interface is dynamic and allows manipulation of the DICOM images, such as zoom, pan, and scrolling, and the ability to rotate 3D images. Given the complexity of clinical management and the need to bolster research in MS, the MS e-Folder system will improve patient care and provide MS researchers with a function-rich patient data hub.

Metacognitive Skills Development: A Web-Based Approach in Higher Education

ERIC Educational Resources Information Center

Shen, Chun-Yi; Liu, Hsiu-Chuan

2011-01-01

Although there were studies that presented the applications of metacognitive skill training, the research on web-based metacognitive skills training are few. The purpose of this study is to design a web-based learning environment and further examine the effect of the web-based training. A pretest-posttest quasi-experimental design was used in this…

78 FR 25416 - Information Collection Request: Web-Based Supply Chain Management Commodity Offer Forms

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-01

... Request: Web-Based Supply Chain Management Commodity Offer Forms AGENCY: Farm Service Agency and Commodity..., and yearly bases. Special invitations, however, are issued throughout the month. Web-Based Supply... will be posted to the FSA Web site and also to the WBSCM portal and FedBizOpps ( https://www.fbo.gov...

Learning Strategies for Success in a Web-Based Course: A Descriptive Exploration

ERIC Educational Resources Information Center

Hu, Haihong; Gramling, Jennifer

2009-01-01

Web-based distance instruction has become a popular delivery method for education. How are learning strategies helping make the connection between Web-based technologies and educational goals? The purpose of this study was to examine learners' use of self-regulated learning strategies in a Web-based course. Twelve students from an information…

Large-Scale Multiobjective Static Test Generation for Web-Based Testing with Integer Programming

ERIC Educational Resources Information Center

Nguyen, M. L.; Hui, Siu Cheung; Fong, A. C. M.

2013-01-01

Web-based testing has become a ubiquitous self-assessment method for online learning. One useful feature that is missing from today's web-based testing systems is the reliable capability to fulfill different assessment requirements of students based on a large-scale question data set. A promising approach for supporting large-scale web-based…

Effects of a self-guided, web-based activity programme for patients with persistent musculoskeletal pain in primary healthcare: A randomized controlled trial.

PubMed

Calner, T; Nordin, C; Eriksson, M K; Nyberg, L; Gard, G; Michaelson, P

2017-07-01

Web-based interventions for pain management are increasingly used with possible benefits, but never used in addition to multimodal rehabilitation (MMR). MMR is recommended treatment for persistent pain in Sweden. The aim was to evaluate the effects of a self-guided, web-based programme added to MMR for work ability, pain, disability and health-related quality of life. We included 99 participants with persistent musculoskeletal pain in a randomized study with two intervention arms: (1) MMR and web-based intervention, and (2) MMR. Data was collected at baseline, 4 and 12 months. Outcome measures were work ability, working percentage, average pain intensity, pain-related disability, and health-related quality of life. There were no significant effects of adding the web-based intervention to MMR regarding any of the outcome variables. This trial provides no support for adding a self-guided, web-based activity programme to MMR for patients with persistent musculoskeletal pain. The comprehensive self-guided, web-based programme for activity, Web-BCPA, added to multimodal treatment in primary health care had no effect on work ability, pain, disability or health-related quality of life. Future web-based interventions should be tailored to patients' individual needs and expectations. © 2017 European Pain Federation - EFIC®.

Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology

PubMed Central

Paley, Suzanne M.; Krummenacker, Markus; Latendresse, Mario; Dale, Joseph M.; Lee, Thomas J.; Kaipa, Pallavi; Gilham, Fred; Spaulding, Aaron; Popescu, Liviu; Altman, Tomer; Paulsen, Ian; Keseler, Ingrid M.; Caspi, Ron

2010-01-01

Pathway Tools is a production-quality software environment for creating a type of model-organism database called a Pathway/Genome Database (PGDB). A PGDB such as EcoCyc integrates the evolving understanding of the genes, proteins, metabolic network and regulatory network of an organism. This article provides an overview of Pathway Tools capabilities. The software performs multiple computational inferences including prediction of metabolic pathways, prediction of metabolic pathway hole fillers and prediction of operons. It enables interactive editing of PGDBs by DB curators. It supports web publishing of PGDBs, and provides a large number of query and visualization tools. The software also supports comparative analyses of PGDBs, and provides several systems biology analyses of PGDBs including reachability analysis of metabolic networks, and interactive tracing of metabolites through a metabolic network. More than 800 PGDBs have been created using Pathway Tools by scientists around the world, many of which are curated DBs for important model organisms. Those PGDBs can be exchanged using a peer-to-peer DB sharing system called the PGDB Registry. PMID:19955237

A Web-Based and Print-Based Computer-Tailored Physical Activity Intervention for Prostate and Colorectal Cancer Survivors: A Comparison of User Characteristics and Intervention Use.

PubMed

Golsteijn, Rianne Henrica Johanna; Bolman, Catherine; Peels, Denise Astrid; Volders, Esmee; de Vries, Hein; Lechner, Lilian

2017-08-23

Physical activity (PA) is beneficial in improving negative physical and psychological effects of cancer. The rapidly increasing number of cancer survivors, resulting from aging and improved cancer care, emphasizes the importance to develop and provide low cost, easy accessible PA programs. Such programs could be provided through the Internet, but that could result in the exclusion of cancer survivors not familiar with the Internet. Therefore, we developed a computer-tailored PA intervention for prostate and colorectal cancer survivors in which both Web-based and print materials are provided, and participants can choose their own preferred delivery mode. The aim of this study was to assess participants' characteristics related to delivery mode and use of intervention materials. We studied characteristics of participants using Web-based and printed intervention materials in a randomized controlled trial (RCT). Prostate and colorectal cancer survivors recruited from hospitals were randomized to OncoActive (computer-tailored PA intervention) or a usual-care control group. OncoActive participants received both Web-based and printed materials. Participants were classified into initial print- or Web-based participants based on their preferred mode of completion of the first questionnaire, which was needed for the computer-tailored PA advice. Intervention material use during the remainder of the intervention was compared for initial print- or Web-based participants. Additionally, participants were classified into those using only print materials and those using Web-based materials. Differences in participant characteristics and intervention material use were studied through analysis of variance (ANOVAs), chi-square tests, and logistic regressions. The majority of the participants in the intervention group were classified as initial Web-based participants (170/249, 68.3%), and 84.9% (191/249) used Web-based intervention materials. Dropout was low (15/249, 6.0%) and differed between initial Web-based (4/170, 2.4%) and print-based (11/79, 14%) participants. Participants were less likely to start Web-based with higher age (odds ratio [OR]=0.93), longer time since last treatment (OR=0.87), and higher fatigue (OR=0.96), and more likely with higher education (OR=4.08) and having completed treatments (OR=5.58). Those who were older (OR=0.93) and post treatment for a longer time (OR=0.86) were less likely to use Web-based intervention materials. Initial print-based participants predominantly used print-based materials, whereas initial Web-based participants used both print- and Web-based materials. To our knowledge, this is one of the first studies that assessed participant characteristics related to delivery mode in an intervention in which participants had a free choice of delivery modes. Use of print-based materials among the initial Web-based participants was substantial, indicating the importance of print-based materials. According to our findings, it may be important to offer Web- and print-based materials alongside each other. Providing Web-based materials only may exclude older, less educated, more fatigued, or currently treated participants; these groups are especially more vulnerable and could benefit most from PA interventions. ©Rianne Henrica Johanna Golsteijn, Catherine Bolman, Denise Astrid Peels, Esmee Volders, Hein de Vries, Lilian Lechner. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 23.08.2017.

Learning cellular sorting pathways using protein interactions and sequence motifs.

PubMed

Lin, Tien-Ho; Bar-Joseph, Ziv; Murphy, Robert F

2011-11-01

Proper subcellular localization is critical for proteins to perform their roles in cellular functions. Proteins are transported by different cellular sorting pathways, some of which take a protein through several intermediate locations until reaching its final destination. The pathway a protein is transported through is determined by carrier proteins that bind to specific sequence motifs. In this article, we present a new method that integrates protein interaction and sequence motif data to model how proteins are sorted through these sorting pathways. We use a hidden Markov model (HMM) to represent protein sorting pathways. The model is able to determine intermediate sorting states and to assign carrier proteins and motifs to the sorting pathways. In simulation studies, we show that the method can accurately recover an underlying sorting model. Using data for yeast, we show that our model leads to accurate prediction of subcellular localization. We also show that the pathways learned by our model recover many known sorting pathways and correctly assign proteins to the path they utilize. The learned model identified new pathways and their putative carriers and motifs and these may represent novel protein sorting mechanisms. Supplementary results and software implementation are available from http://murphylab.web.cmu.edu/software/2010_RECOMB_pathways/.

VisANT 3.0: new modules for pathway visualization, editing, prediction and construction.

PubMed

Hu, Zhenjun; Ng, David M; Yamada, Takuji; Chen, Chunnuan; Kawashima, Shuichi; Mellor, Joe; Linghu, Bolan; Kanehisa, Minoru; Stuart, Joshua M; DeLisi, Charles

2007-07-01

With the integration of the KEGG and Predictome databases as well as two search engines for coexpressed genes/proteins using data sets obtained from the Stanford Microarray Database (SMD) and Gene Expression Omnibus (GEO) database, VisANT 3.0 supports exploratory pathway analysis, which includes multi-scale visualization of multiple pathways, editing and annotating pathways using a KEGG compatible visual notation and visualization of expression data in the context of pathways. Expression levels are represented either by color intensity or by nodes with an embedded expression profile. Multiple experiments can be navigated or animated. Known KEGG pathways can be enriched by querying either coexpressed components of known pathway members or proteins with known physical interactions. Predicted pathways for genes/proteins with unknown functions can be inferred from coexpression or physical interaction data. Pathways produced in VisANT can be saved as computer-readable XML format (VisML), graphic images or high-resolution Scalable Vector Graphics (SVG). Pathways in the format of VisML can be securely shared within an interested group or published online using a simple Web link. VisANT is freely available at http://visant.bu.edu.

Lake Michigan offshore ecosystem structure and food web changes from 1987 to 2008

USGS Publications Warehouse

Rogers, Mark W.; Bunnell, David B.; Madenjian, Charles P.; Warner, David M.

2014-01-01

Ecosystems undergo dynamic changes owing to species invasions, fisheries management decisions, landscape modifications, and nutrient inputs. At Lake Michigan, new invaders (e.g., dreissenid mussels (Dreissena spp.), spiny water flea (Bythotrephes longimanus), round goby (Neogobius melanostomus)) have proliferated and altered energy transfer pathways, while nutrient concentrations and stocking rates to support fisheries have changed. We developed an ecosystem model to describe food web structure in 1987 and ran simulations through 2008 to evaluate changes in biomass of functional groups, predator consumption, and effects of recently invading species. Keystone functional groups from 1987 were identified as Mysis, burbot (Lota lota), phytoplankton, alewife (Alosa pseudoharengus), nonpredatory cladocerans, and Chinook salmon (Oncorhynchus tshawytscha). Simulations predicted biomass reductions across all trophic levels and predicted biomasses fit observed trends for most functional groups. The effects of invasive species (e.g., dreissenid grazing) increased across simulation years, but were difficult to disentangle from other changes (e.g., declining offshore nutrient concentrations). In total, our model effectively represented recent changes to the Lake Michigan ecosystem and provides an ecosystem-based tool for exploring future resource management scenarios.

75 FR 27182 - Energy Conservation Program: Web-Based Compliance and Certification Management System

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-14

... Conservation Program: Web-Based Compliance and Certification Management System AGENCY: Office of Energy... certification reports to the Department of Energy (DOE) through an electronic Web-based tool, the Compliance and... following means: 1. Compliance and Certification Management System (CCMS)--via the Web portal: http...

Paradigms, Citations, and Maps of Science: A Personal History.

ERIC Educational Resources Information Center

Small, Henry

2003-01-01

Discusses mapping science and Kuhn's theories of paradigms and scientific development. Highlights include cocitation clustering; bibliometric definition of a paradigm; specialty dynamics; pathways through science; a new Web tool called Essential Science Indicators (ESI) for studying the structure of science; and microrevolutions. (Author/LRW)

A methodology for ecosystem-scale modeling of selenium

USGS Publications Warehouse

Presser, T.S.; Luoma, S.N.

2010-01-01

The main route of exposure for selenium (Se) is dietary, yet regulations lack biologically based protocols for evaluations of risk. We propose here an ecosystem-scale model that conceptualizes and quantifies the variables that determinehow Se is processed from water through diet to predators. This approach uses biogeochemical and physiological factors from laboratory and field studies and considers loading, speciation, transformation to particulate material, bioavailability, bioaccumulation in invertebrates, and trophic transfer to predators. Validation of the model is through data sets from 29 historic and recent field case studies of Se-exposed sites. The model links Se concentrations across media (water, particulate, tissue of different food web species). It can be used to forecast toxicity under different management or regulatory proposals or as a methodology for translating a fish-tissue (or other predator tissue) Se concentration guideline to a dissolved Se concentration. The model illustrates some critical aspects of implementing a tissue criterion: 1) the choice of fish species determines the food web through which Se should be modeled, 2) the choice of food web is critical because the particulate material to prey kinetics of bioaccumulation differs widely among invertebrates, 3) the characterization of the type and phase of particulate material is important to quantifying Se exposure to prey through the base of the food web, and 4) the metric describing partitioning between particulate material and dissolved Se concentrations allows determination of a site-specific dissolved Se concentration that would be responsible for that fish body burden in the specific environment. The linked approach illustrates that environmentally safe dissolved Se concentrations will differ among ecosystems depending on the ecological pathways and biogeochemical conditions in that system. Uncertainties and model sensitivities can be directly illustrated by varying exposure scenarios based on site-specific knowledge. The model can also be used to facilitate site-specific regulation and to present generic comparisons to illustrate limitations imposed by ecosystem setting and inhabitants. Used optimally, the model provides a tool for framing a site-specific ecological problem or occurrence of Se exposure, quantify exposure within that ecosystem, and narrow uncertainties abouthowto protect it by understanding the specifics of the underlying system ecology, biogeochemistry, and hydrology.?? 2010 SETAC.

A methodology for ecosystem-scale modeling of selenium.

PubMed

Presser, Theresa S; Luoma, Samuel N

2010-10-01

The main route of exposure for selenium (Se) is dietary, yet regulations lack biologically based protocols for evaluations of risk. We propose here an ecosystem-scale model that conceptualizes and quantifies the variables that determine how Se is processed from water through diet to predators. This approach uses biogeochemical and physiological factors from laboratory and field studies and considers loading, speciation, transformation to particulate material, bioavailability, bioaccumulation in invertebrates, and trophic transfer to predators. Validation of the model is through data sets from 29 historic and recent field case studies of Se-exposed sites. The model links Se concentrations across media (water, particulate, tissue of different food web species). It can be used to forecast toxicity under different management or regulatory proposals or as a methodology for translating a fish-tissue (or other predator tissue) Se concentration guideline to a dissolved Se concentration. The model illustrates some critical aspects of implementing a tissue criterion: 1) the choice of fish species determines the food web through which Se should be modeled, 2) the choice of food web is critical because the particulate material to prey kinetics of bioaccumulation differs widely among invertebrates, 3) the characterization of the type and phase of particulate material is important to quantifying Se exposure to prey through the base of the food web, and 4) the metric describing partitioning between particulate material and dissolved Se concentrations allows determination of a site-specific dissolved Se concentration that would be responsible for that fish body burden in the specific environment. The linked approach illustrates that environmentally safe dissolved Se concentrations will differ among ecosystems depending on the ecological pathways and biogeochemical conditions in that system. Uncertainties and model sensitivities can be directly illustrated by varying exposure scenarios based on site-specific knowledge. The model can also be used to facilitate site-specific regulation and to present generic comparisons to illustrate limitations imposed by ecosystem setting and inhabitants. Used optimally, the model provides a tool for framing a site-specific ecological problem or occurrence of Se exposure, quantify exposure within that ecosystem, and narrow uncertainties about how to protect it by understanding the specifics of the underlying system ecology, biogeochemistry, and hydrology. © 2010 SETAC.

Pathways between primary production and fisheries yields of large marine ecosystems.

PubMed

Friedland, Kevin D; Stock, Charles; Drinkwater, Kenneth F; Link, Jason S; Leaf, Robert T; Shank, Burton V; Rose, Julie M; Pilskaln, Cynthia H; Fogarty, Michael J

2012-01-01

The shift in marine resource management from a compartmentalized approach of dealing with resources on a species basis to an approach based on management of spatially defined ecosystems requires an accurate accounting of energy flow. The flow of energy from primary production through the food web will ultimately limit upper trophic-level fishery yields. In this work, we examine the relationship between yield and several metrics including net primary production, chlorophyll concentration, particle-export ratio, and the ratio of secondary to primary production. We also evaluate the relationship between yield and two additional rate measures that describe the export of energy from the pelagic food web, particle export flux and mesozooplankton productivity. We found primary production is a poor predictor of global fishery yields for a sample of 52 large marine ecosystems. However, chlorophyll concentration, particle-export ratio, and the ratio of secondary to primary production were positively associated with yields. The latter two measures provide greater mechanistic insight into factors controlling fishery production than chlorophyll concentration alone. Particle export flux and mesozooplankton productivity were also significantly related to yield on a global basis. Collectively, our analyses suggest that factors related to the export of energy from pelagic food webs are critical to defining patterns of fishery yields. Such trophic patterns are associated with temperature and latitude and hence greater yields are associated with colder, high latitude ecosystems.

Pathways between Primary Production and Fisheries Yields of Large Marine Ecosystems

PubMed Central

Friedland, Kevin D.; Stock, Charles; Drinkwater, Kenneth F.; Link, Jason S.; Leaf, Robert T.; Shank, Burton V.; Rose, Julie M.; Pilskaln, Cynthia H.; Fogarty, Michael J.

2012-01-01

The shift in marine resource management from a compartmentalized approach of dealing with resources on a species basis to an approach based on management of spatially defined ecosystems requires an accurate accounting of energy flow. The flow of energy from primary production through the food web will ultimately limit upper trophic-level fishery yields. In this work, we examine the relationship between yield and several metrics including net primary production, chlorophyll concentration, particle-export ratio, and the ratio of secondary to primary production. We also evaluate the relationship between yield and two additional rate measures that describe the export of energy from the pelagic food web, particle export flux and mesozooplankton productivity. We found primary production is a poor predictor of global fishery yields for a sample of 52 large marine ecosystems. However, chlorophyll concentration, particle-export ratio, and the ratio of secondary to primary production were positively associated with yields. The latter two measures provide greater mechanistic insight into factors controlling fishery production than chlorophyll concentration alone. Particle export flux and mesozooplankton productivity were also significantly related to yield on a global basis. Collectively, our analyses suggest that factors related to the export of energy from pelagic food webs are critical to defining patterns of fishery yields. Such trophic patterns are associated with temperature and latitude and hence greater yields are associated with colder, high latitude ecosystems. PMID:22276100

Land use alters the resistance and resilience of soil food webs to drought

USGS Publications Warehouse

de Vries, Franciska T.; Liiri, Mira E.; Bjørnlund, Lisa; Bowker, Matthew A.; Christensen, Søren; Setälä, Heikki; Bardgett, Richard D.

2012-01-01

Soils deliver several ecosystem services including carbon sequestration and nutrient cycling, which are of central importance to climate mitigation and sustainable food production. Soil biota play an important role in carbon and nitrogen cycling, and, although the effects of land use on soil food webs are well documented the consequences for their resistance and resilience to climate change are not known. We compared the resistance and resilience to drought--which is predicted to increase under climate change of soil food webs of two common land-use systems: intensively managed wheat with a bacterial-based soil food web and extensively managed grassland with a fungal-based soil food web. We found that the fungal-based food web, and the processes of C and N loss it governs, of grassland soil was more resistant, although not resilient, and better able to adapt to drought than the bacterial-based food web of wheat soil. Structural equation modelling revealed that fungal-based soil food webs and greater microbial evenness mitigated C and N loss. Our findings show that land use strongly affects the resistance and resilience of soil food webs to climate change, and that extensively managed grassland promotes more resistant, and adaptable, fungal-based soil food webs.

An Automatic Web Service Composition Framework Using QoS-Based Web Service Ranking Algorithm.

PubMed

Mallayya, Deivamani; Ramachandran, Baskaran; Viswanathan, Suganya

2015-01-01

Web service has become the technology of choice for service oriented computing to meet the interoperability demands in web applications. In the Internet era, the exponential addition of web services nominates the "quality of service" as essential parameter in discriminating the web services. In this paper, a user preference based web service ranking (UPWSR) algorithm is proposed to rank web services based on user preferences and QoS aspect of the web service. When the user's request cannot be fulfilled by a single atomic service, several existing services should be composed and delivered as a composition. The proposed framework allows the user to specify the local and global constraints for composite web services which improves flexibility. UPWSR algorithm identifies best fit services for each task in the user request and, by choosing the number of candidate services for each task, reduces the time to generate the composition plans. To tackle the problem of web service composition, QoS aware automatic web service composition (QAWSC) algorithm proposed in this paper is based on the QoS aspects of the web services and user preferences. The proposed framework allows user to provide feedback about the composite service which improves the reputation of the services.

An Automatic Web Service Composition Framework Using QoS-Based Web Service Ranking Algorithm

PubMed Central

Mallayya, Deivamani; Ramachandran, Baskaran; Viswanathan, Suganya

2015-01-01

Web service has become the technology of choice for service oriented computing to meet the interoperability demands in web applications. In the Internet era, the exponential addition of web services nominates the “quality of service” as essential parameter in discriminating the web services. In this paper, a user preference based web service ranking (UPWSR) algorithm is proposed to rank web services based on user preferences and QoS aspect of the web service. When the user's request cannot be fulfilled by a single atomic service, several existing services should be composed and delivered as a composition. The proposed framework allows the user to specify the local and global constraints for composite web services which improves flexibility. UPWSR algorithm identifies best fit services for each task in the user request and, by choosing the number of candidate services for each task, reduces the time to generate the composition plans. To tackle the problem of web service composition, QoS aware automatic web service composition (QAWSC) algorithm proposed in this paper is based on the QoS aspects of the web services and user preferences. The proposed framework allows user to provide feedback about the composite service which improves the reputation of the services. PMID:26504894

Ontology-Based Administration of Web Directories

NASA Astrophysics Data System (ADS)

Horvat, Marko; Gledec, Gordan; Bogunović, Nikola

Administration of a Web directory and maintenance of its content and the associated structure is a delicate and labor intensive task performed exclusively by human domain experts. Subsequently there is an imminent risk of a directory structures becoming unbalanced, uneven and difficult to use to all except for a few users proficient with the particular Web directory and its domain. These problems emphasize the need to establish two important issues: i) generic and objective measures of Web directories structure quality, and ii) mechanism for fully automated development of a Web directory's structure. In this paper we demonstrate how to formally and fully integrate Web directories with the Semantic Web vision. We propose a set of criteria for evaluation of a Web directory's structure quality. Some criterion functions are based on heuristics while others require the application of ontologies. We also suggest an ontology-based algorithm for construction of Web directories. By using ontologies to describe the semantics of Web resources and Web directories' categories it is possible to define algorithms that can build or rearrange the structure of a Web directory. Assessment procedures can provide feedback and help steer the ontology-based construction process. The issues raised in the article can be equally applied to new and existing Web directories.

Be-safe travel, a web-based geographic application to explore safe-route in an area

NASA Astrophysics Data System (ADS)

Utamima, Amalia; Djunaidy, Arif

2017-08-01

In large cities in developing countries, the various forms of criminality are often found. For instance, the most prominent crimes in Surabaya, Indonesia is 3C, that is theft with violence (curas), theft by weighting (curat), and motor vehicle theft (curanmor). 3C case most often occurs on the highway and residential areas. Therefore, new entrants in an area should be aware of these kind of crimes. Route Planners System or route planning system such as Google Maps only consider the shortest distance in the calculation of the optimal route. The selection of the optimal path in this study not only consider the shortest distance, but also involves other factors, namely the security level. This research considers at the need for an application to recommend the safest road to be passed by the vehicle passengers while drive an area. This research propose Be-Safe Travel, a web-based application using Google API that can be accessed by people who like to drive in an area, but still lack of knowledge of the pathways which are safe from crime. Be-Safe Travel is not only useful for the new entrants, but also useful for delivery courier of valuables goods to go through the safest streets.

Isotopic evidence for methane-based chemosynthesis in the Upper Floridan aquifer food web.

PubMed

Opsahl, Stephen P; Chanton, Jeffrey P

2006-11-01

Anecdotal observations of the Dougherty plain cave crayfish (Cambarus cryptodytes), the Georgia blind cave salamander (Haideotriton wallacei), and albinistic isopods (Caecidotea sp.) at great depths below the land surface and distant from river corridors suggest that obligate aquifer-dwelling (troglobitic) organisms are widely distributed throughout the limestone Upper Floridan aquifer (UFA). One mechanism by which subterranean life can proliferate in an environment void of plant productivity is through a microbial food web that includes chemosynthesis. We examined this possibility in the UFA by measuring the isotopic composition ((13)C, (14)C, and (15)N) of tissues from troglobitic macrofauna. Organisms that were captured by cave divers entering into spring conduits had delta(13)C values that suggested plant matter as a primary food resource (cave crayfish, -24.6 +/- 2.7 per thousand, n = 9). In contrast, delta(13)C values were significantly depleted in organisms retrieved from wells drilled into areas of the UFA remote from spring and sinkhole conduits (cave crayfish -34.7 +/- 9.8 per thousand, n = 10). Depleted (13)C values in crayfish were correlated with radiocarbon (Delta(14)C) depletion relative to modern values. The results suggest that methane-based microbial chemosynthetic pathways support organisms living in the remote interior of the aquifer, at least in part.

Differences in reach and attrition between Web-based and print-delivered tailored interventions among adults over 50 years of age: clustered randomized trial.

PubMed

Peels, Denise Astrid; Bolman, Catherine; Golsteijn, Rianne Henrica Johanna; De Vries, Hein; Mudde, Aart Nicolaas; van Stralen, Maartje Marieke; Lechner, Lilian

2012-12-17

The Internet has the potential to provide large populations with individual health promotion advice at a relatively low cost. Despite the high rates of Internet access, actual reach by Web-based interventions is often disappointingly low, and differences in use between demographic subgroups are present. Furthermore, Web-based interventions often have to deal with high rates of attrition. This study aims to assess user characteristics related to participation and attrition when comparing Web-based and print-delivered tailored interventions containing similar content and thereby to provide recommendations in choosing the appropriate delivery mode for a particular target audience. We studied the distribution of a Web-based and a print-delivered version of the Active Plus intervention in a clustered randomized controlled trial (RCT). Participants were recruited via direct mailing within the participating Municipal Health Council regions and randomized to the printed or Web-based intervention by their region. Based on the answers given in a prior assessment, participants received tailored advice on 3 occasions: (1) within 2 weeks after the baseline, (2) 2 months after the baseline, and (3) within 4 months after the baseline (based on a second assessment at 3 months). The baseline (printed or Web-based) results were analyzed using ANOVA and chi-square tests to establish the differences in user characteristics between both intervention groups. We used logistic regression analyses to study the interaction between the user characteristics and the delivery mode in the prediction of dropout rate within the intervention period. The printed intervention resulted in a higher participation rate (19%) than the Web-based intervention (12%). Participants of the Web-based intervention were significantly younger (P<.001), more often men (P=.01), had a higher body mass index (BMI) (P=.001) and a lower intention to be physically active (P=.03) than participants of the printed intervention. The dropout rate was significantly higher in the Web-based intervention group (53%) compared to the print-delivered intervention (39%, P<.001). A low intention to be physically active was a strong predictor for dropout within both delivery modes (P<.001). The difference in dropout rate between the Web-based and the printed intervention was not explained by user characteristics. The reach of the same tailored physical activity (PA) intervention in a printed or Web-based delivery mode differed between sociodemographic subgroups of participants over 50 years of age. Although the reach of the Web-based intervention is lower, Web-based interventions can be a good channel to reach high-risk populations (lower PA intention and higher BMI). While the dropout rate was significantly higher in the Web-based intervention group, no specific user characteristics explained the difference in dropout rates between the delivery modes. More research is needed to determine what caused the high rate of dropout in the Web-based intervention. Dutch Trial Register (NTR): 2297: http://www.trialregister.nl/trialreg/admin/rctview.asp?TC=2297 (Archived by WebCite at http://www.webcitation.org/65TkwoESp).

Differences in Reach and Attrition Between Web-Based and Print-Delivered Tailored Interventions Among Adults over 50 Years of Age: Clustered Randomized Trial

PubMed Central

Bolman, Catherine; Golsteijn, Rianne Henrica Johanna; De Vries, Hein; Mudde, Aart Nicolaas; van Stralen, Maartje Marieke; Lechner, Lilian

2012-01-01

Background The Internet has the potential to provide large populations with individual health promotion advice at a relatively low cost. Despite the high rates of Internet access, actual reach by Web-based interventions is often disappointingly low, and differences in use between demographic subgroups are present. Furthermore, Web-based interventions often have to deal with high rates of attrition. Objective This study aims to assess user characteristics related to participation and attrition when comparing Web-based and print-delivered tailored interventions containing similar content and thereby to provide recommendations in choosing the appropriate delivery mode for a particular target audience. Methods We studied the distribution of a Web-based and a print-delivered version of the Active Plus intervention in a clustered randomized controlled trial (RCT). Participants were recruited via direct mailing within the participating Municipal Health Council regions and randomized to the printed or Web-based intervention by their region. Based on the answers given in a prior assessment, participants received tailored advice on 3 occasions: (1) within 2 weeks after the baseline, (2) 2 months after the baseline, and (3) within 4 months after the baseline (based on a second assessment at 3 months). The baseline (printed or Web-based) results were analyzed using ANOVA and chi-square tests to establish the differences in user characteristics between both intervention groups. We used logistic regression analyses to study the interaction between the user characteristics and the delivery mode in the prediction of dropout rate within the intervention period. Results The printed intervention resulted in a higher participation rate (19%) than the Web-based intervention (12%). Participants of the Web-based intervention were significantly younger (P<.001), more often men (P=.01), had a higher body mass index (BMI) (P=.001) and a lower intention to be physically active (P=.03) than participants of the printed intervention. The dropout rate was significantly higher in the Web-based intervention group (53%) compared to the print-delivered intervention (39%, P<.001). A low intention to be physically active was a strong predictor for dropout within both delivery modes (P<.001). The difference in dropout rate between the Web-based and the printed intervention was not explained by user characteristics. Conclusions The reach of the same tailored physical activity (PA) intervention in a printed or Web-based delivery mode differed between sociodemographic subgroups of participants over 50 years of age. Although the reach of the Web-based intervention is lower, Web-based interventions can be a good channel to reach high-risk populations (lower PA intention and higher BMI). While the dropout rate was significantly higher in the Web-based intervention group, no specific user characteristics explained the difference in dropout rates between the delivery modes. More research is needed to determine what caused the high rate of dropout in the Web-based intervention. Trial Registration Dutch Trial Register (NTR): 2297: http://www.trialregister.nl/trialreg/admin/rctview.asp?TC=2297 (Archived by WebCite at http://www.webcitation.org/65TkwoESp). PMID:23246790

GoWeb: a semantic search engine for the life science web.

PubMed

Dietze, Heiko; Schroeder, Michael

2009-10-01

Current search engines are keyword-based. Semantic technologies promise a next generation of semantic search engines, which will be able to answer questions. Current approaches either apply natural language processing to unstructured text or they assume the existence of structured statements over which they can reason. Here, we introduce a third approach, GoWeb, which combines classical keyword-based Web search with text-mining and ontologies to navigate large results sets and facilitate question answering. We evaluate GoWeb on three benchmarks of questions on genes and functions, on symptoms and diseases, and on proteins and diseases. The first benchmark is based on the BioCreAtivE 1 Task 2 and links 457 gene names with 1352 functions. GoWeb finds 58% of the functional GeneOntology annotations. The second benchmark is based on 26 case reports and links symptoms with diseases. GoWeb achieves 77% success rate improving an existing approach by nearly 20%. The third benchmark is based on 28 questions in the TREC genomics challenge and links proteins to diseases. GoWeb achieves a success rate of 79%. GoWeb's combination of classical Web search with text-mining and ontologies is a first step towards answering questions in the biomedical domain. GoWeb is online at: http://www.gopubmed.org/goweb.

Optimizing real-time Web-based user interfaces for observatories

NASA Astrophysics Data System (ADS)

Gibson, J. Duane; Pickering, Timothy E.; Porter, Dallan; Schaller, Skip

2008-08-01

In using common HTML/Ajax approaches for web-based data presentation and telescope control user interfaces at the MMT Observatory (MMTO), we rapidly were confronted with web browser performance issues. Much of the operational data at the MMTO is highly dynamic and is constantly changing during normal operations. Status of telescope subsystems must be displayed with minimal latency to telescope operators and other users. A major motivation of migrating toward web-based applications at the MMTO is to provide easy access to current and past observatory subsystem data for a wide variety of users on their favorite operating system through a familiar interface, their web browser. Performance issues, especially for user interfaces that control telescope subsystems, led to investigations of more efficient use of HTML/Ajax and web server technologies as well as other web-based technologies, such as Java and Flash/Flex. The results presented here focus on techniques for optimizing HTML/Ajax web applications with near real-time data display. This study indicates that direct modification of the contents or "nodeValue" attribute of text nodes is the most efficient method of updating data values displayed on a web page. Other optimization techniques are discussed for web-based applications that display highly dynamic data.

Web-Based Geographic Information Systems: Experience and Perspectives of Planners and the Implications for Extension

ERIC Educational Resources Information Center

Göçmen, Z. Asligül

2016-01-01

Web-based geographic information system (GIS) technology, or web-based GIS, offers many opportunities for public planners and Extension educators who have limited GIS backgrounds or resources. However, investigation of its use in planning has been limited. The study described here examined the use of web-based GIS by public planning agencies. A…

Development of Web-Based Learning Environment Model to Enhance Cognitive Skills for Undergraduate Students in the Field of Electrical Engineering

ERIC Educational Resources Information Center

Lakonpol, Thongmee; Ruangsuwan, Chaiyot; Terdtoon, Pradit

2015-01-01

This research aimed to develop a web-based learning environment model for enhancing cognitive skills of undergraduate students in the field of electrical engineering. The research is divided into 4 phases: 1) investigating the current status and requirements of web-based learning environment models. 2) developing a web-based learning environment…

Elementary School Teachers' Motivation toward Web-Based Professional Development, and the Relationship with Internet Self-Efficacy and Belief about Web-Based Learning

ERIC Educational Resources Information Center

Kao, Chia-Pin; Wu, Ying-Tien; Tsai, Chin-Chung

2011-01-01

This study was conducted to explore the relationships between teachers' motivation toward web-based professional development, Internet self-efficacy, and beliefs about web-based learning. By gathering questionnaire data from 484 elementary school teachers, this study indicated that the teachers' Internet self-efficacy and behavioral beliefs about…

Teachers' Attitudes toward Web-Based Professional Development, with Relation to Internet Self-Efficacy and Beliefs about Web-Based Learning

ERIC Educational Resources Information Center

Kao, Chia-Pin; Tsai, Chin-Chung

2009-01-01

This study was conducted to explore the relationships between teachers' Internet self-efficacy, beliefs about web-based learning and attitudes toward web-based professional development. The sample of this study included 421 teachers, coming from 20 elementary schools in Taiwan. The three instruments used to assess teachers' Internet self-efficacy…

77 FR 15753 - Request for Nominations of Experts for a Science Advisory Board Panel To Review EPA's Web-Based...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-16

... Advisory Board Panel To Review EPA's Web-Based Report on the Environment AGENCY: Environmental Protection... nominations of technical experts to form an SAB panel to review the Agency's Web-based Report on the... procedural policies. EPA's Web-based Report on the Environment (ROE) has been developed to provide a...

Examining High-School Students' Preferences toward Learning Environments, Personal Beliefs and Concept Learning in Web-Based Contexts

ERIC Educational Resources Information Center

Yang, Fang-Ying; Chang, Cheng-Chieh

2009-01-01

The purpose of the study is to explore three kinds of personal affective traits among high-school students and their effects on web-based concept learning. The affective traits include personal preferences about web-based learning environments, personal epistemological beliefs, and beliefs about web-based learning. One hundred 11th graders…

The Impact of Web Based Resource Material on Learning Outcome in Open Distance Higher Education

ERIC Educational Resources Information Center

Masrur, Rehana

2010-01-01

One of the most powerful educational option in open and distance education is web-based learning. A blended (hybrid) course combines traditional face to face and web-based learning approaches in an educational environment that is nonspecific as to time and place. The study reported here investigated the impact of web based resource material…

A Brief Introduction to Web-Based Note Capture

ERIC Educational Resources Information Center

Ovadia, Steven

2012-01-01

While physical notebooks and locally saved electronic files are certainly helpful, there are a number of web-based solutions that might be useful to someone conducting research online, or looking to hold their notes in a web-based environment. The main advantage of a web-based note capture tool is that one is able to access it from just about…

Live and Web-based orientations are comparable for a required rotation.

PubMed

Prunuske, Jacob

2010-03-01

Studies show equivalency in knowledge when measured following Web-based learning and live lecture. However, the effectiveness of a Web-based orientation for a required clinical rotation is unknown. Medical students viewed a Web-based orientation and completed a 13-item evaluation before beginning a required 6-week community medicine rotation. Evaluation data from 2007-2008 live orientation sessions were compared to responses from 2008-2009 Web-based orientation sessions. Data were analyzed by two-sample tests of proportion. A total of 169 students completed surveys during the study period--78 following the live and 91 following the Web-based orientation. Response rates were equal in the two groups. The survey tool had a high level of reliability (Cronbach's alpha=0.96). There was no statistical difference in student evaluations for 12 of 13 orientation evaluation items. Live and Web-based formats are comparable for presenting orientation materials to a required clinical rotation. Students felt the purpose of the rotation, educational goals, course structure, and requirements were clearly presented regardless of format. Transition from a live to Web-based format reduced faculty time required to present at rotation orientations.

GSCALite: A Web Server for Gene Set Cancer Analysis.

PubMed

Liu, Chun-Jie; Hu, Fei-Fei; Xia, Mengxuan; Han, Leng; Zhang, Qiong; Guo, An-Yuan

2018-05-22

The availability of cancer genomic data makes it possible to analyze genes related to cancer. Cancer is usually the result of a set of genes and the signal of a single gene could be covered by background noise. Here, we present a web server named Gene Set Cancer Analysis (GSCALite) to analyze a set of genes in cancers with the following functional modules. (i) Differential expression in tumor vs normal, and the survival analysis; (ii) Genomic variations and their survival analysis; (iii) Gene expression associated cancer pathway activity; (iv) miRNA regulatory network for genes; (v) Drug sensitivity for genes; (vi) Normal tissue expression and eQTL for genes. GSCALite is a user-friendly web server for dynamic analysis and visualization of gene set in cancer and drug sensitivity correlation, which will be of broad utilities to cancer researchers. GSCALite is available on http://bioinfo.life.hust.edu.cn/web/GSCALite/. guoay@hust.edu.cn or zhangqiong@hust.edu.cn. Supplementary data are available at Bioinformatics online.

Bioaccumulation of per- and polyfluorinated alkyl substances (PFAS) in selected species from the Barents Sea food web.

PubMed

Haukås, Marianne; Berger, Urs; Hop, Haakon; Gulliksen, Bjørn; Gabrielsen, Geir W

2007-07-01

The present study reports concentrations and biomagnification potential of per- and polyfluorinated alkyl substances (PFAS) in species from the Barents Sea food web. The examined species included sea ice amphipod (Gammarus wilkitzkii), polar cod (Boreogadus saida), black guillemot (Cepphus grylle) and glaucous gull (Larus hyperboreus). These were analyzed for PFAS, polychlorinated biphenyls (PCBs), dichlorodiphenyltrichloroethanes (DDTs) and polybrominated diphenyl ethers (PBDEs). Perfluorooctane sulfonate (PFOS) was the predominant of the detected PFAS. Trophic levels and food web transfer of PFAS were determined using stable nitrogen isotopes (delta(15)N). No correlation was found between PFOS concentrations and trophic level within species. However, a non-linear relationship was established when the entire food web was analyzed. Biomagnification factors displayed values >1 for perfluorohexane sulfonate (PFHxS), perfluorononanoic acid (PFNA), PFOS and SigmaPFAS(7). Multivariate analyses showed that the degree of trophic transfer of PFAS is similar to that of PCB, DDT and PBDE, despite their accumulation through different pathways.

Improving Adherence to Smoking Cessation Treatment: Intervention Effects in a Web-Based Randomized Trial.

PubMed

Graham, Amanda L; Papandonatos, George D; Cha, Sarah; Erar, Bahar; Amato, Michael S; Cobb, Nathan K; Niaura, Raymond S; Abrams, David B

2017-03-01

Web-based smoking cessation interventions can deliver evidence-based treatments to a wide swath of the population, but effectiveness is often limited by insufficient adherence to proven treatment components. This study evaluated the impact of a social network (SN) intervention and free nicotine replacement therapy (NRT) on adherence to evidence-based components of smoking cessation treatment in the context of a Web-based intervention. A sample of adult U.S. smokers (N = 5290) was recruited via BecomeAnEX.org, a free smoking cessation Web site. Smokers were randomized to one of four arms: (1) an interactive, evidence-based smoking cessation Web site (WEB) alone; (2) WEB in conjunction with an SN intervention designed to integrate participants into the online community (WEB+SN); (3) WEB plus free NRT (WEB+NRT); and (4) the combination of all treatments (WEB+SN+NRT). Adherence outcomes assessed at 3-month follow-up were as follows: Web site utilization metrics, use of skills training components, intratreatment social support, and pharmacotherapy use. WEB+SN+NRT outperformed all others on Web site utilization metrics, use of practical counseling tools, intratreatment social support, and NRT use. It was the only intervention to promote the sending of private messages and the viewing of community pages over WEB alone. Both social network arms outperformed WEB on most metrics of online community engagement. Both NRT arms showed higher medication use compared to WEB alone. This study demonstrated the effectiveness of two approaches for improving adherence to evidence-based components of smoking cessation treatment. Integrated approaches to medication provision and social network engagement can enhance adherence to components known to improve cessation. This study demonstrated that an integrated approach to medication provision and social network integration, when delivered through an online program, can enhance adherence across all three recommended components of an evidence-based smoking cessation program (skills training, social support, and pharmacotherapy use). Nicotine replacement therapy-when provided as part of an integrated program-increases adherence to other program elements, which in turn augment its own therapeutic effects. An explicit focus on approaches to improve treatment adherence is an important first step to identifying leverage points for optimizing intervention effectiveness. © The Author 2016. Published by Oxford University Press on behalf of the Society for Research on Nicotine and Tobacco. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Viability of a Web-Based Module for Teaching Electrocardiogram Reading Skills to Psychiatry Residents: Learning Outcomes and Trainee Interest.

PubMed

DeBonis, Katrina; Blair, Thomas R; Payne, Samuel T; Wigan, Katherine; Kim, Sara

2015-12-01

Web-based instruction in post-graduate psychiatry training has shown comparable effectiveness to in-person instruction, but few topics have been addressed in this format. This study sought to evaluate the viability of a web-based curriculum in teaching electrocardiogram (EKG) reading skills to psychiatry residents. Interest in receiving educational materials in this format was also assessed. A web-based curriculum of 41 slides, including eight pre-test and eight post-test questions with emphasis on cardiac complications of psychotropic medications, was made available to all psychiatry residents via email. Out of 57 residents, 30 initiated and 22 completed the module. Mean improvement from pre-test to post-test was 25 %, and all 22 completing participants indicated interest in future web-based instruction. This pilot study suggests that web-based instruction is feasible and under-utilized as a means of teaching psychiatry residents. Potential uses of web-based instruction, such as tracking learning outcomes or patient care longitudinally, are also discussed.

Food Web Topology in High Mountain Lakes

PubMed Central

Sánchez-Hernández, Javier; Cobo, Fernando; Amundsen, Per-Arne

2015-01-01

Although diversity and limnology of alpine lake systems are well studied, their food web structure and properties have rarely been addressed. Here, the topological food webs of three high mountain lakes in Central Spain were examined. We first addressed the pelagic networks of the lakes, and then we explored how food web topology changed when benthic biota was included to establish complete trophic networks. We conducted a literature search to compare our alpine lacustrine food webs and their structural metrics with those of 18 published lentic webs using a meta-analytic approach. The comparison revealed that the food webs in alpine lakes are relatively simple, in terms of structural network properties (linkage density and connectance), in comparison with lowland lakes, but no great differences were found among pelagic networks. The studied high mountain food webs were dominated by a high proportion of omnivores and species at intermediate trophic levels. Omnivores can exploit resources at multiple trophic levels, and this characteristic might reduce competition among interacting species. Accordingly, the trophic overlap, measured as trophic similarity, was very low in all three systems. Thus, these alpine networks are characterized by many omnivorous consumers with numerous prey species and few consumers with a single or few prey and with low competitive interactions among species. The present study emphasizes the ecological significance of omnivores in high mountain lakes as promoters of network stability and as central players in energy flow pathways via food partitioning and enabling energy mobility among trophic levels. PMID:26571235

Food Web Topology in High Mountain Lakes.

PubMed

Sánchez-Hernández, Javier; Cobo, Fernando; Amundsen, Per-Arne

2015-01-01

Although diversity and limnology of alpine lake systems are well studied, their food web structure and properties have rarely been addressed. Here, the topological food webs of three high mountain lakes in Central Spain were examined. We first addressed the pelagic networks of the lakes, and then we explored how food web topology changed when benthic biota was included to establish complete trophic networks. We conducted a literature search to compare our alpine lacustrine food webs and their structural metrics with those of 18 published lentic webs using a meta-analytic approach. The comparison revealed that the food webs in alpine lakes are relatively simple, in terms of structural network properties (linkage density and connectance), in comparison with lowland lakes, but no great differences were found among pelagic networks. The studied high mountain food webs were dominated by a high proportion of omnivores and species at intermediate trophic levels. Omnivores can exploit resources at multiple trophic levels, and this characteristic might reduce competition among interacting species. Accordingly, the trophic overlap, measured as trophic similarity, was very low in all three systems. Thus, these alpine networks are characterized by many omnivorous consumers with numerous prey species and few consumers with a single or few prey and with low competitive interactions among species. The present study emphasizes the ecological significance of omnivores in high mountain lakes as promoters of network stability and as central players in energy flow pathways via food partitioning and enabling energy mobility among trophic levels.

Representing metabolic pathway information: an object-oriented approach.

PubMed

Ellis, L B; Speedie, S M; McLeish, R

1998-01-01

The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) is a website providing information and dynamic links for microbial metabolic pathways, enzyme reactions, and their substrates and products. The Compound, Organism, Reaction and Enzyme (CORE) object-oriented database management system was developed to contain and serve this information. CORE was developed using Java, an object-oriented programming language, and PSE persistent object classes from Object Design, Inc. CORE dynamically generates descriptive web pages for reactions, compounds and enzymes, and reconstructs ad hoc pathway maps starting from any UM-BBD reaction. CORE code is available from the authors upon request. CORE is accessible through the UM-BBD at: http://www. labmed.umn.edu/umbbd/index.html.

Googling DNA sequences on the World Wide Web.

PubMed

Hajibabaei, Mehrdad; Singer, Gregory A C

2009-11-10

New web-based technologies provide an excellent opportunity for sharing and accessing information and using web as a platform for interaction and collaboration. Although several specialized tools are available for analyzing DNA sequence information, conventional web-based tools have not been utilized for bioinformatics applications. We have developed a novel algorithm and implemented it for searching species-specific genomic sequences, DNA barcodes, by using popular web-based methods such as Google. We developed an alignment independent character based algorithm based on dividing a sequence library (DNA barcodes) and query sequence to words. The actual search is conducted by conventional search tools such as freely available Google Desktop Search. We implemented our algorithm in two exemplar packages. We developed pre and post-processing software to provide customized input and output services, respectively. Our analysis of all publicly available DNA barcode sequences shows a high accuracy as well as rapid results. Our method makes use of conventional web-based technologies for specialized genetic data. It provides a robust and efficient solution for sequence search on the web. The integration of our search method for large-scale sequence libraries such as DNA barcodes provides an excellent web-based tool for accessing this information and linking it to other available categories of information on the web.

Autophagic compound database: A resource connecting autophagy-modulating compounds, their potential targets and relevant diseases.

PubMed

Deng, Yiqi; Zhu, Lingjuan; Cai, Haoyang; Wang, Guan; Liu, Bo

2018-06-01

Autophagy, a highly conserved lysosomal degradation process in eukaryotic cells, can digest long-lived proteins and damaged organelles through vesicular trafficking pathways. Nowadays, mechanisms of autophagy have been gradually elucidated and thus the discovery of small-molecule drugs targeting autophagy has always been drawing much attention. So far, some autophagy-related web servers have been available online to facilitate scientists to obtain the information relevant to autophagy conveniently, such as HADb, CTLPScanner, iLIR server and ncRDeathDB. However, to the best of our knowledge, there is not any web server available about the autophagy-modulating compounds. According to published articles, all the compounds and their relations with autophagy were anatomized. Subsequently, an online Autophagic Compound Database (ACDB) (http://www.acdbliulab.com/) was constructed, which contained information of 357 compounds with 164 corresponding signalling pathways and potential targets in different diseases. We achieved a great deal of information of autophagy-modulating compounds, including compounds, targets/pathways and diseases. ACDB is a valuable resource for users to access to more than 300 curated small-molecule compounds correlated with autophagy. Autophagic compound database will facilitate to the discovery of more novel therapeutic drugs in the near future. © 2017 John Wiley & Sons Ltd.

IntPath--an integrated pathway gene relationship database for model organisms and important pathogens.

PubMed

Zhou, Hufeng; Jin, Jingjing; Zhang, Haojun; Yi, Bo; Wozniak, Michal; Wong, Limsoon

2012-01-01

Pathway data are important for understanding the relationship between genes, proteins and many other molecules in living organisms. Pathway gene relationships are crucial information for guidance, prediction, reference and assessment in biochemistry, computational biology, and medicine. Many well-established databases--e.g., KEGG, WikiPathways, and BioCyc--are dedicated to collecting pathway data for public access. However, the effectiveness of these databases is hindered by issues such as incompatible data formats, inconsistent molecular representations, inconsistent molecular relationship representations, inconsistent referrals to pathway names, and incomprehensive data from different databases. In this paper, we overcome these issues through extraction, normalization and integration of pathway data from several major public databases (KEGG, WikiPathways, BioCyc, etc). We build a database that not only hosts our integrated pathway gene relationship data for public access but also maintains the necessary updates in the long run. This public repository is named IntPath (Integrated Pathway gene relationship database for model organisms and important pathogens). Four organisms--S. cerevisiae, M. tuberculosis H37Rv, H. Sapiens and M. musculus--are included in this version (V2.0) of IntPath. IntPath uses the "full unification" approach to ensure no deletion and no introduced noise in this process. Therefore, IntPath contains much richer pathway-gene and pathway-gene pair relationships and much larger number of non-redundant genes and gene pairs than any of the single-source databases. The gene relationships of each gene (measured by average node degree) per pathway are significantly richer. The gene relationships in each pathway (measured by average number of gene pairs per pathway) are also considerably richer in the integrated pathways. Moderate manual curation are involved to get rid of errors and noises from source data (e.g., the gene ID errors in WikiPathways and relationship errors in KEGG). We turn complicated and incompatible xml data formats and inconsistent gene and gene relationship representations from different source databases into normalized and unified pathway-gene and pathway-gene pair relationships neatly recorded in simple tab-delimited text format and MySQL tables, which facilitates convenient automatic computation and large-scale referencing in many related studies. IntPath data can be downloaded in text format or MySQL dump. IntPath data can also be retrieved and analyzed conveniently through web service by local programs or through web interface by mouse clicks. Several useful analysis tools are also provided in IntPath. We have overcome in IntPath the issues of compatibility, consistency, and comprehensiveness that often hamper effective use of pathway databases. We have included four organisms in the current release of IntPath. Our methodology and programs described in this work can be easily applied to other organisms; and we will include more model organisms and important pathogens in future releases of IntPath. IntPath maintains regular updates and is freely available at http://compbio.ddns.comp.nus.edu.sg:8080/IntPath.

Ondex Web: web-based visualization and exploration of heterogeneous biological networks.

PubMed

Taubert, Jan; Hassani-Pak, Keywan; Castells-Brooke, Nathalie; Rawlings, Christopher J

2014-04-01

Ondex Web is a new web-based implementation of the network visualization and exploration tools from the Ondex data integration platform. New features such as context-sensitive menus and annotation tools provide users with intuitive ways to explore and manipulate the appearance of heterogeneous biological networks. Ondex Web is open source, written in Java and can be easily embedded into Web sites as an applet. Ondex Web supports loading data from a variety of network formats, such as XGMML, NWB, Pajek and OXL. http://ondex.rothamsted.ac.uk/OndexWeb.

78 FR 49480 - Proposed Information Collection; Comment Request; NTIA/FCC Web-based Frequency Coordination System

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-14

... Information Collection; Comment Request; NTIA/FCC Web- based Frequency Coordination System AGENCY: National... INFORMATION: I. Abstract The National Telecommunications and Information Administration (NTIA) hosts a web... (RF) bands that are shared on a co-primary basis by federal and non-federal users. The web-based...

77 FR 31027 - Submission for OMB Review; Comment Request; Web-Based Assessment of the Clinical Studies Support...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-24

...; Comment Request; Web-Based Assessment of the Clinical Studies Support Center (CSSC) Summary: Under the... current valid OMB control number. Proposed Collection: Title: Web-Based Assessment of the Clinical Studies... Operations and Procedures (MOP); coordinating meeting space and logistics for in-person meetings, Web...

75 FR 29307 - Web Based Supply Chain Management Commodity Offer Form, Paperwork Collection Notice

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-25

... DEPARTMENT OF AGRICULTURE Agricultural Marketing Service [Doc. No FV10-CP-01, AMS-FV-10-0041] Web... collection request is required for the implementation of a new system named Web Based Supply Chain Management...-2782. Mail: David Tuckwiller, Project Manager, Web Based Supply Chain Management System, Agricultural...

76 FR 28439 - Submission for OMB Review; Comment Request; NCI Cancer Genetics Services Directory Web-Based...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-17

...; Comment Request; NCI Cancer Genetics Services Directory Web-Based Application Form and Update Mailer... currently valid OMB control number. Proposed Collection: Title: NCI Cancer Genetics Services Directory Web... application form and the Web-based update mailer is to collect information about genetics professionals to be...

Adding Interactivity to Web Based Distance Learning.

ERIC Educational Resources Information Center

Cafolla, Ralph; Knee, Richard

Web Based Distance Learning (WBDL) is a form of distance learning based on providing instruction mainly on the World Wide Web. This paradigm has limitations, especially the lack of interactivity inherent in the Web. The purpose of this paper is to discuss some of the technologies the authors have used in their courses at Florida Atlantic…

Is Teacher Assessment Reliable or Valid for High School Students under a Web-Based Portfolio Environment?

ERIC Educational Resources Information Center

Chang, Chi-Cheng; Wu, Bing-Hong

2012-01-01

This study explored the reliability and validity of teacher assessment under a Web-based portfolio assessment environment (or Web-based teacher portfolio assessment). Participants were 72 eleventh graders taking the "Computer Application" course. The students perform portfolio creation, inspection, self- and peer-assessment using the Web-based…

Validation of Web-Based Physical Activity Measurement Systems Using Doubly Labeled Water

PubMed Central

Yamaguchi, Yukio; Yamada, Yosuke; Tokushima, Satoru; Hatamoto, Yoichi; Sagayama, Hiroyuki; Kimura, Misaka; Higaki, Yasuki; Tanaka, Hiroaki

2012-01-01

Background Online or Web-based measurement systems have been proposed as convenient methods for collecting physical activity data. We developed two Web-based physical activity systems—the 24-hour Physical Activity Record Web (24hPAR WEB) and 7 days Recall Web (7daysRecall WEB). Objective To examine the validity of two Web-based physical activity measurement systems using the doubly labeled water (DLW) method. Methods We assessed the validity of the 24hPAR WEB and 7daysRecall WEB in 20 individuals, aged 25 to 61 years. The order of email distribution and subsequent completion of the two Web-based measurements systems was randomized. Each measurement tool was used for a week. The participants’ activity energy expenditure (AEE) and total energy expenditure (TEE) were assessed over each week using the DLW method and compared with the respective energy expenditures estimated using the Web-based systems. Results The mean AEE was 3.90 (SD 1.43) MJ estimated using the 24hPAR WEB and 3.67 (SD 1.48) MJ measured by the DLW method. The Pearson correlation for AEE between the two methods was r = .679 (P < .001). The Bland-Altman 95% limits of agreement ranged from –2.10 to 2.57 MJ between the two methods. The Pearson correlation for TEE between the two methods was r = .874 (P < .001). The mean AEE was 4.29 (SD 1.94) MJ using the 7daysRecall WEB and 3.80 (SD 1.36) MJ by the DLW method. The Pearson correlation for AEE between the two methods was r = .144 (P = .54). The Bland-Altman 95% limits of agreement ranged from –3.83 to 4.81 MJ between the two methods. The Pearson correlation for TEE between the two methods was r = .590 (P = .006). The average input times using terminal devices were 8 minutes and 10 seconds for the 24hPAR WEB and 6 minutes and 38 seconds for the 7daysRecall WEB. Conclusions Both Web-based systems were found to be effective methods for collecting physical activity data and are appropriate for use in epidemiological studies. Because the measurement accuracy of the 24hPAR WEB was moderate to high, it could be suitable for evaluating the effect of interventions on individuals as well as for examining physical activity behavior. PMID:23010345

BioSWR – Semantic Web Services Registry for Bioinformatics

PubMed Central

Repchevsky, Dmitry; Gelpi, Josep Ll.

2014-01-01

Despite of the variety of available Web services registries specially aimed at Life Sciences, their scope is usually restricted to a limited set of well-defined types of services. While dedicated registries are generally tied to a particular format, general-purpose ones are more adherent to standards and usually rely on Web Service Definition Language (WSDL). Although WSDL is quite flexible to support common Web services types, its lack of semantic expressiveness led to various initiatives to describe Web services via ontology languages. Nevertheless, WSDL 2.0 descriptions gained a standard representation based on Web Ontology Language (OWL). BioSWR is a novel Web services registry that provides standard Resource Description Framework (RDF) based Web services descriptions along with the traditional WSDL based ones. The registry provides Web-based interface for Web services registration, querying and annotation, and is also accessible programmatically via Representational State Transfer (REST) API or using a SPARQL Protocol and RDF Query Language. BioSWR server is located at http://inb.bsc.es/BioSWR/and its code is available at https://sourceforge.net/projects/bioswr/under the LGPL license. PMID:25233118

BioSWR--semantic web services registry for bioinformatics.

PubMed

Repchevsky, Dmitry; Gelpi, Josep Ll

2014-01-01

Despite of the variety of available Web services registries specially aimed at Life Sciences, their scope is usually restricted to a limited set of well-defined types of services. While dedicated registries are generally tied to a particular format, general-purpose ones are more adherent to standards and usually rely on Web Service Definition Language (WSDL). Although WSDL is quite flexible to support common Web services types, its lack of semantic expressiveness led to various initiatives to describe Web services via ontology languages. Nevertheless, WSDL 2.0 descriptions gained a standard representation based on Web Ontology Language (OWL). BioSWR is a novel Web services registry that provides standard Resource Description Framework (RDF) based Web services descriptions along with the traditional WSDL based ones. The registry provides Web-based interface for Web services registration, querying and annotation, and is also accessible programmatically via Representational State Transfer (REST) API or using a SPARQL Protocol and RDF Query Language. BioSWR server is located at http://inb.bsc.es/BioSWR/and its code is available at https://sourceforge.net/projects/bioswr/under the LGPL license.

Blended learning: emerging best practices in allied health workforce development.

PubMed

Brandt, Barbara F; Quake-Rapp, Cindee; Shanedling, Janet; Spannaus-Martin, Donna; Martin, Peggy

2010-01-01

To remain dynamic and viable, academic institutions preparing the future workforce need to convert to a more accessible and convenient pathway for students. The need for responsiveness is especially true when considering strategies to prepare an allied health workforce in areas of shortages and to meet the needs of the underserved. A blended or hybrid learning model that strategically uses web-based and face-to-face teaching/learning methods is an innovative and strategic way that promotes learner-centered higher education and facilitates a higher learning experience. A model and emerging best practices for implementation are presented from our experience at the Center for Allied Health Programs at the University of Minnesota.

Are web-based questionnaires accepted in patients attending rehabilitation?

PubMed

Engan, Harald K; Hilmarsen, Christina; Sittlinger, Sverre; Sandmæl, Jon Arne; Skanke, Frode; Oldervoll, Line M

2016-12-01

The aim of the present paper was to study preferences for web based self-administered questionnaires (web SAQs) vs. paper-based self-administered questionnaires (paper SAQs) and to evaluate the feasibility of using web SAQs in patients referred to cardiac, lung, occupational and cancer rehabilitation programs. The patients were approached by mail and given the choice to answer the compulsory SAQs either on paper or on a web-based platform. Hundred and twenty seven out of 183 eligible patients (69.3%) were willing to participate and 126 completed the study. Web SAQs were preferred by 77.7%, and these patients were significantly younger, more often cohabiting and tended to have higher level of education than paper SAQ users. Mean number of data missing per patient was less among the web SAQ users than the paper SAQ users (0.55 vs. 2.15, p < 0.001). Costs related to human resources were estimated to be 60% lower with web SAQs compared to paper SAQs. Web SAQs were well accepted among the patients scheduled for rehabilitation, led to less missing data and considerable cost savings related to human resources. Patients referred to rehabilitation should be offered the choice to complete self-administered questionnaires on internet platforms when internet access is common and available. Implications for Rehabilitation The high acceptability of web-based self-administered questionnaires among rehabilitation patients suggests that internet platforms are suitable tools to collect patient information for rehabilitation units. Web-based modes of patient data collection demonstrate low number of missing data and can therefore improve the quality of data collection from rehabilitation patients. Use of web-based questionnaires considerably reduces administrative costs of data collection in rehabilitation settings compared to traditional pen and paper methods.

Location-based Web Search

NASA Astrophysics Data System (ADS)

Ahlers, Dirk; Boll, Susanne

In recent years, the relation of Web information to a physical location has gained much attention. However, Web content today often carries only an implicit relation to a location. In this chapter, we present a novel location-based search engine that automatically derives spatial context from unstructured Web resources and allows for location-based search: our focused crawler applies heuristics to crawl and analyze Web pages that have a high probability of carrying a spatial relation to a certain region or place; the location extractor identifies the actual location information from the pages; our indexer assigns a geo-context to the pages and makes them available for a later spatial Web search. We illustrate the usage of our spatial Web search for location-based applications that provide information not only right-in-time but also right-on-the-spot.

Web-Based Mindfulness Interventions for People With Physical Health Conditions: Systematic Review

PubMed Central

Toivonen, Kirsti I; Zernicke, Kristin

2017-01-01

Background Mindfulness-based interventions (MBIs) are becoming increasingly popular for helping people with physical health conditions. Expanding from traditional face-to-face program delivery, there is growing interest in Web-based application of MBIs, though Web-based MBIs for people with physical health conditions specifically have not been thoroughly reviewed to date. Objective The objective of this paper was to review Web-based MBIs for people with physical health conditions and to examine all outcomes reported (eg, efficacy or effectiveness for physical changes or psychological changes; feasibility). Methods Databases PubMed, PsycINFO, Science Direct, CINAHL Plus, and Web of Science were searched. Full-text English papers that described any Web-based MBI, examining any outcome, for people with chronic physical health conditions were included. Randomized, nonrandomized, controlled, and uncontrolled trials were all included. Extracted data included intervention characteristics, population characteristics, outcomes, and quality indicators. Intervention characteristics (eg, synchronicity and guidance) were examined as potential factors related to study outcomes. Results Of 435 publications screened, 19 published papers describing 16 studies were included. They examined Web-based MBIs for people with cancer, chronic pain or fibromyalgia, irritable bowel syndrome (IBS), epilepsy, heart disease, tinnitus, and acquired brain injury. Overall, most studies reported positive effects of Web-based MBIs compared with usual care on a variety of outcomes including pain acceptance, coping measures, and depressive symptoms. There were mixed results regarding the effectiveness of Web-based MBIs compared with active control treatment conditions such as cognitive behavioral therapy. Condition-specific symptoms (eg, cancer-related fatigue and IBS symptoms) targeted by treatment had the largest effect size improvements following MBIs. Results are inconclusive regarding physical variables. Conclusions Preliminary evidence suggests that Web-based MBIs may be helpful in alleviating symptom burden that those with physical health conditions can experience, particularly when interventions are tailored for specific symptoms. There was no evidence of differences between synchronous versus asynchronous or facilitated versus self-directed Web-based MBIs. Future investigations of Web-based MBIs should evaluate the effects of program adherence, effects on mindfulness levels, and whether synchronous or asynchronous, or facilitated or self-directed interventions elicit greater improvements. PMID:28860106

The Development and Implementation of a Competency-Based Curriculum for Training in Global Health Research

PubMed Central

Ton, Thanh G. N.; Gladding, Sophia P.; Zunt, Joseph R.; John, Chandy; Nerurkar, Vivek R.; Moyer, Cheryl A.; Hobbs, Nicole; McCoy, Molly; Kolars, Joseph C.

2015-01-01

The Fogarty International Center (FIC) Global Health Fellows Program provides trainees with the opportunity to develop research skills through a mentored research experience, increase their content expertise, and better understand trends in global health research, funding organizations, and pathways to generate support. The Northern Pacific Global Health Fellows Research and Training Consortium, which hosts one of the FIC Global Health Programs, sought to enhance research training by developing, implementing, and evaluating a competency-based curriculum that uses a modular, asynchronous, web-based format. The curriculum has 8 core competencies, 36 learning objectives, and 58 assignments. Nineteen trainees completed their 11-month fellowship, engaged in the curriculum, and provided pre- and post-fellowship self-assessments. Self-assessed scores significantly improved for all competencies. Trainees identified the curriculum as one of the strengths of the program. This competency-based curriculum represents a first step toward creating a framework of global health research competencies on which further efforts could be based. PMID:25371189

More than who eats who: Discerning ecological processes from stable isotopes data

EPA Science Inventory

Stable isotope analyses of biota are now commonly used to discern trophic pathways between consumers and their foods. However, those same isotope data also hold information about processes that influence the physicochemical setting of food webs as well as biological processes ope...

CoP Sensing Framework on Web-Based Environment

NASA Astrophysics Data System (ADS)

Mustapha, S. M. F. D. Syed

The Web technologies and Web applications have shown similar high growth rate in terms of daily usages and user acceptance. The Web applications have not only penetrated in the traditional domains such as education and business but have also encroached into areas such as politics, social, lifestyle, and culture. The emergence of Web technologies has enabled Web access even to the person on the move through PDAs or mobile phones that are connected using Wi-Fi, HSDPA, or other communication protocols. These two phenomena are the inducement factors toward the need of building Web-based systems as the supporting tools in fulfilling many mundane activities. In doing this, one of the many focuses in research has been to look at the implementation challenges in building Web-based support systems in different types of environment. This chapter describes the implementation issues in building the community learning framework that can be supported on the Web-based platform. The Community of Practice (CoP) has been chosen as the community learning theory to be the case study and analysis as it challenges the creativity of the architectural design of the Web system in order to capture the presence of learning activities. The details of this chapter describe the characteristics of the CoP to understand the inherent intricacies in modeling in the Web-based environment, the evidences of CoP that need to be traced automatically in a slick manner such that the evidence-capturing process is unobtrusive, and the technologies needed to embrace a full adoption of Web-based support system for the community learning framework.

Online Adjuncts.

ERIC Educational Resources Information Center

Reeves, Kimberly

2002-01-01

Describes how some universities are hiring adjuncts to teach Web-based educational administration courses. Includes descriptions of administrators' experiences with Web-based teaching and four major universities that offer Web-based graduate and undergraduate education courses. (PKP)

Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology.

PubMed

Karp, Peter D; Latendresse, Mario; Paley, Suzanne M; Krummenacker, Markus; Ong, Quang D; Billington, Richard; Kothari, Anamika; Weaver, Daniel; Lee, Thomas; Subhraveti, Pallavi; Spaulding, Aaron; Fulcher, Carol; Keseler, Ingrid M; Caspi, Ron

2016-09-01

Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer and comparative-genomics operations. It offers metabolic-informatics tools, such as metabolic reconstruction, quantitative metabolic modeling, prediction of reaction atom mappings and metabolic route search. Pathway Tools also provides regulatory-informatics tools, such as the ability to represent and visualize a wide range of regulatory interactions. This article outlines the advances in Pathway Tools in the past 5 years. Major additions include components for metabolic modeling, metabolic route search, computation of atom mappings and estimation of compound Gibbs free energies of formation; addition of editors for signaling pathways, for genome sequences and for cellular architecture; storage of gene essentiality data and phenotype data; display of multiple alignments, and of signaling and electron-transport pathways; and development of Python and web-services application programming interfaces. Scientists around the world have created more than 9800 Pathway/Genome Databases by using Pathway Tools, many of which are curated databases for important model organisms. © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

How and for whom does web-based acceptance and commitment therapy work? Mediation and moderation analyses of web-based ACT for depressive symptoms.

PubMed

Pots, Wendy T M; Trompetter, Hester R; Schreurs, Karlein M G; Bohlmeijer, Ernst T

2016-05-23

Acceptance and Commitment Therapy (ACT) has been demonstrated to be effective in reducing depressive symptoms. However, little is known how and for whom therapeutic change occurs, specifically in web-based interventions. This study focuses on the mediators, moderators and predictors of change during a web-based ACT intervention. Data from 236 adults from the general population with mild to moderate depressive symptoms, randomized to either web-based ACT (n = 82) or one of two control conditions (web-based Expressive Writing (EW; n = 67) and a waiting list (n = 87)), were analysed. Single and multiple mediation analyses, and exploratory linear regression analyses were performed using PROCESS and linear regression analyses, to examine mediators, moderators and predictors on pre- to post- and follow-up treatment change of depressive symptoms. The treatment effect of ACT versus the waiting list was mediated by psychological flexibility and two mindfulness facets. The treatment effect of ACT versus EW was not significantly mediated. The moderator analyses demonstrated that the effects of web-based ACT did not vary according to baseline patient characteristics when compared to both control groups. However, higher baseline depressive symptoms and positive mental health and lower baseline anxiety were identified as predictors of outcome across all conditions. Similar results are found for follow-up. The findings of this study corroborate the evidence that psychological flexibility and mindfulness are distinct process mechanisms that mediate the effects of web-based ACT intervention. The results indicate that there are no restrictions to the allocation of web-based ACT intervention and that web-based ACT can work for different subpopulations. Netherlands Trial Register NTR2736 . Registered 6 February 2011.

Satisfaction with web-based training in an integrated healthcare delivery network: do age, education, computer skills and attitudes matter?

PubMed Central

Atreja, Ashish; Mehta, Neil B; Jain, Anil K; Harris, CM; Ishwaran, Hemant; Avital, Michel; Fishleder, Andrew J

2008-01-01

Background Healthcare institutions spend enormous time and effort to train their workforce. Web-based training can potentially streamline this process. However the deployment of web-based training in a large-scale setting with a diverse healthcare workforce has not been evaluated. The aim of this study was to evaluate the satisfaction of healthcare professionals with web-based training and to determine the predictors of such satisfaction including age, education status and computer proficiency. Methods Observational, cross-sectional survey of healthcare professionals from six hospital systems in an integrated delivery network. We measured overall satisfaction to web-based training and response to survey items measuring Website Usability, Course Usefulness, Instructional Design Effectiveness, Computer Proficiency and Self-learning Attitude. Results A total of 17,891 healthcare professionals completed the web-based training on HIPAA Privacy Rule; and of these, 13,537 completed the survey (response rate 75.6%). Overall course satisfaction was good (median, 4; scale, 1 to 5) with more than 75% of the respondents satisfied with the training (rating 4 or 5) and 65% preferring web-based training over traditional instructor-led training (rating 4 or 5). Multivariable ordinal regression revealed 3 key predictors of satisfaction with web-based training: Instructional Design Effectiveness, Website Usability and Course Usefulness. Demographic predictors such as gender, age and education did not have an effect on satisfaction. Conclusion The study shows that web-based training when tailored to learners' background, is perceived as a satisfactory mode of learning by an interdisciplinary group of healthcare professionals, irrespective of age, education level or prior computer experience. Future studies should aim to measure the long-term outcomes of web-based training. PMID:18922178

Attitudes and awareness of web-based self-care resources in the military: a preliminary survey study.

PubMed

Luxton, David D; Armstrong, Christina M; Fantelli, Emily E; Thomas, Elissa K

2011-09-01

Web-based self-care resources have a number of potential benefits for military service members (SMs) and their families such as convenience, anonymity, and immediate 24/7 access to useful information. There is limited data available, however, regarding SM and military healthcare provider use of online self-care resources. Our goal with this study was to conduct a preliminary survey assessment of self-care Web site awareness, general attitudes about use, and usage behaviors of Web-based self-care resources among SMs and military healthcare providers. Results show that the majority of SMs and providers use the Internet often, use Internet self-care resources, and are willing to use additional Web-based resources and capabilities. SMs and providers also indicated a preference for Web-based self-care resources as adjunct tools to face-to-face/in-person care. Data from this preliminary study are useful for informing additional research and best practices for integrating Web-based self-care for the military community.

Web-based tailored intervention for preparation of parents and children for outpatient surgery (WebTIPS): development.

PubMed

Kain, Zeev N; Fortier, Michelle A; Chorney, Jill MacLaren; Mayes, Linda

2015-04-01

As a result of cost-containment efforts, preparation programs for outpatient surgery are currently not available to the majority of children and parents. The recent dramatic growth in the Internet presents a unique opportunity to transform how children and their parents are prepared for surgery. In this article, we describe the development of a Web-based Tailored Intervention for Preparation of parents and children undergoing Surgery (WebTIPS). A multidisciplinary taskforce agreed that a Web-based tailored intervention consisting of intake, matrix, and output modules was the preferred approach. Next, the content of the various intake variables, the matrix logic, and the output content was developed. The output product has a parent component and a child component and is described in http://surgerywebtips.com/about.php. The child component makes use of preparation strategies such as information provision, modeling, play, and coping skills training. The parent component of WebTIPS includes strategies such as information provision, coping skills training, and relaxation and distraction techniques. A reputable animation and Web design company developed a secured Web-based product based on the above description. In this article, we describe the development of a Web-based tailored preoperative preparation program that can be accessed by children and parents multiple times before and after surgery. A follow-up article in this issue of Anesthesia & Analgesia describes formative evaluation and preliminary efficacy testing of this Web-based tailored preoperative preparation program.

Web-based Tailored Intervention for Preparation of Parents and Children for Outpatient Surgery (WebTIPS): Development

PubMed Central

Kain, Zeev N.; Fortier, Michelle A.; Chorney, Jill MacLaren; Mayes, Linda

2014-01-01

Background Due to cost-containment efforts, preparation programs for outpatient surgery are currently not available to the majority of children and parents. The recent dramatic growth in the Internet presents a unique opportunity to transform how children and their parents are prepared for surgery. In this article we describe the development of a Web-based tailored preparation program for children and parents undergoing surgery (WebTIPS). Development of Program A multidisciplinary taskforce agreed that a Web-based tailored intervention comprised of intake, matrix and output modules was the preferred approach. Next, the content of the various intake variables, the matrix logic and the output content was developed. The output product has a parent component and a child component and is described in http://surgerywebtips.com/about.php. The child component makes use of preparation strategies such as information provision, modeling, play and coping skills training. The parent component of WebTIPS includes strategies such as information provision, coping skills training, relaxation and distraction techniques. A reputable animation and Web-design company developed a secured Web-based product based on the above description. Conclusions In this article we describe the development of a Web-based tailored preoperative preparation program that can be accessed by children and parents multiple times before and after surgery. A follow-up article in this issue of Anesthesia & Analgesia describes formative evaluation and preliminary efficacy testing of this Web-based tailored preoperative preparation program. PMID:25790212

GenePublisher: Automated analysis of DNA microarray data.

PubMed

Knudsen, Steen; Workman, Christopher; Sicheritz-Ponten, Thomas; Friis, Carsten

2003-07-01

GenePublisher, a system for automatic analysis of data from DNA microarray experiments, has been implemented with a web interface at http://www.cbs.dtu.dk/services/GenePublisher. Raw data are uploaded to the server together with a specification of the data. The server performs normalization, statistical analysis and visualization of the data. The results are run against databases of signal transduction pathways, metabolic pathways and promoter sequences in order to extract more information. The results of the entire analysis are summarized in report form and returned to the user.

Understanding Instructional Support Needs of Emerging Internet Users for Web-Based Information Seeking

ERIC Educational Resources Information Center

Gupta, Naman K.; Penstein Rosé, Carolyn

2010-01-01

As the wealth of information available on the Web increases, Web-based information seeking becomes a more and more important skill for supporting both formal education and lifelong learning. However, Web-based information access poses hurdles that must be overcome by certain student populations, such as low English competency users, low literacy…

Student Perceptions of Learning in a Web-Based Tutorial.

ERIC Educational Resources Information Center

Brescia, William; McAuley, Sean

This case study used both quantitative and qualitative methods to investigate students' perceptions of learning using a Web-based tutorial. Students participated in a Web-based tutorial to learn basic HTML as part of a graduate-level Web design course. Four of five students agreed to participate in the survey and interviews. After completing the…

Collaboration of Students and Faculty Creating a Web-Site Based for Homework.

ERIC Educational Resources Information Center

Packard, Abbot L.; Holmes, Glen A.

This paper chronicles the building of a student based Web site method of quickly getting homework graded and back to the students with feedback. A Web site-supported statistics class offers an opportunity for students to check answers, get immediate feedback, and submit homework. A web-based support system should provide assistant for students of…

ChemVoyage: A Web-Based, Simulated Learning Environment with Scaffolding and Linking Visualization to Conceptualization

ERIC Educational Resources Information Center

McRae, Christopher; Karuso, Peter; Liu, Fei

2012-01-01

The Web is now a standard tool for information access and dissemination in higher education. The prospect of Web-based, simulated learning platforms and technologies, however, remains underexplored. We have developed a Web-based tutorial program (ChemVoyage) for a third-year organic chemistry class on the topic of pericyclic reactions to…

75 FR 44020 - Biweekly Notice; Applications and Amendments to Facility Operating Licenses Involving No...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-27

... representative, already holds an NRC- issued digital ID certificate). Based upon this information, the Secretary... online, Web-based submission form. In order to serve documents through EIE, users will be required to install a Web browser plug-in from the NRC Web site. Further information on the Web- based submission form...

Web-Based Undergraduate Chemistry Problem-Solving: The Interplay of Task Performance, Domain Knowledge and Web-Searching Strategies

ERIC Educational Resources Information Center

She, Hsiao-Ching; Cheng, Meng-Tzu; Li, Ta-Wei; Wang, Chia-Yu; Chiu, Hsin-Tien; Lee, Pei-Zon; Chou, Wen-Chi; Chuang, Ming-Hua

2012-01-01

This study investigates the effect of Web-based Chemistry Problem-Solving, with the attributes of Web-searching and problem-solving scaffolds, on undergraduate students' problem-solving task performance. In addition, the nature and extent of Web-searching strategies students used and its correlation with task performance and domain knowledge also…

Community diversity, structure and carbon footprint of nematode food web following reforestation on degraded Karst soil.

PubMed

Hu, Ning; Li, Hui; Tang, Zheng; Li, Zhongfang; Tian, Jing; Lou, Yilai; Li, Jianwei; Li, Guichun; Hu, Xiaomin

2016-06-17

We examined community diversity, structure and carbon footprint of nematode food web along a chronosequence of T. Sinensis reforestation on degraded Karst. In general, after the reforestation: a serious of diversity parameters and community indices (Shannon-Weinier index (H'), structure index (SI), etc.) were elevated; biomass ratio of fungivores to bacterivores (FFC/BFC), and fungi to bacteria (F/B) were increased, and nematode channel ratio (NCR) were decreased; carbon footprints of all nematode trophic groups, and biomass of bacteria and fungi were increased. Our results indicate that the Karst aboveground vegetation restoration was accompanied with belowground nematode food web development: increasing community complexity, function and fungal dominance in decomposition pathway, and the driving forces included the bottom-up effect (resource control), connectedness of functional groups, as well as soil environments.

Community diversity, structure and carbon footprint of nematode food web following reforestation on degraded Karst soil

PubMed Central

Hu, Ning; Li, Hui; Tang, Zheng; Li, Zhongfang; Tian, Jing; Lou, Yilai; Li, Jianwei; Li, Guichun; Hu, Xiaomin

2016-01-01

We examined community diversity, structure and carbon footprint of nematode food web along a chronosequence of T. Sinensis reforestation on degraded Karst. In general, after the reforestation: a serious of diversity parameters and community indices (Shannon-Weinier index (H′), structure index (SI), etc.) were elevated; biomass ratio of fungivores to bacterivores (FFC/BFC), and fungi to bacteria (F/B) were increased, and nematode channel ratio (NCR) were decreased; carbon footprints of all nematode trophic groups, and biomass of bacteria and fungi were increased. Our results indicate that the Karst aboveground vegetation restoration was accompanied with belowground nematode food web development: increasing community complexity, function and fungal dominance in decomposition pathway, and the driving forces included the bottom-up effect (resource control), connectedness of functional groups, as well as soil environments. PMID:27311984

Development of a Web-Based Periscope Simulator for Submarine Officer Training

DTIC Science & Technology

2014-09-01

31 2. The Evolution of Web-Based technology .........................................32...DEVELOPMENT ............................................................................65 A. TECHNOLOGY ...the possibility to deliver 3D simulations using the web browsers and web technology . The objective is to create an effective and efficient WBLE that

Life Cycle Project Plan Outline: Web Sites and Web-based Applications

EPA Pesticide Factsheets

This tool is a guideline for planning and checking for 508 compliance on web sites and web based applications. Determine which EIT components are covered or excepted, which 508 standards and requirements apply, and how to implement them.

Do Students Use Contextual Protective Behaviors to Reduce Alcohol-Related Sexual Risk? Examination of a Dual-Process Decision-Making Model

PubMed Central

Scaglione, Nichole M.; Hultgren, Brittney A.; Reavy, Racheal; Mallett, Kimberly A.; Turrisi, Rob; Cleveland, Michael J.; Sell, Nichole M.

2015-01-01

Objective Recent studies suggest drinking protective behaviors (DPBs) and contextual protective behaviors (CPBs) can uniquely reduce alcohol-related sexual risk in college students. Few studies have examined CPBs independently, and even fewer have utilized theory to examine modifiable psychosocial predictors of students’ decisions to use CPBs. The current study used a prospective design to examine 1) rational and reactive pathways and psychosocial constructs predictive of CPB use, and 2) how gender might moderate these influences in a sample of college students. Method Students (n = 508) completed web-based baseline (mid-spring semester) and 1- and 6-month follow-up assessments of CPB use; psychosocial constructs (expectancies, normative beliefs, attitudes, and self-concept); and rational and reactive pathways (intentions and willingness). Regression was used to examine rational and reactive influences as proximal predictors of CPB use at the 6-month follow-up. Subsequent path analyses examined the effects of psychosocial constructs, as distal predictors of CPB use, mediated through the rational and reactive pathways. Results Both rational (intentions to use CPB) and reactive (willingness to use CPB) influences were significantly associated with increased CPB use. The examined distal predictors were found to effect CPB use differentially through the rational and reactive pathways. Gender did not significantly moderate any relationships within in the model. Discussion Findings suggest potential entry points for increasing CPB use that include both rational and reactive pathways. Overall, this study demonstrates the mechanisms underlying how to increase the use of CPBs in programs designed to reduce alcohol-related sexual consequences and victimization. PMID:26415062

Do students use contextual protective behaviors to reduce alcohol-related sexual risk? Examination of a dual-process decision-making model.

PubMed

Scaglione, Nichole M; Hultgren, Brittney A; Reavy, Racheal; Mallett, Kimberly A; Turrisi, Rob; Cleveland, Michael J; Sell, Nichole M

2015-09-01

Recent studies suggest drinking protective behaviors (DPBs) and contextual protective behaviors (CPBs) can uniquely reduce alcohol-related sexual risk in college students. Few studies have examined CPBs independently, and even fewer have utilized theory to examine modifiable psychosocial predictors of students' decisions to use CPBs. The current study used a prospective design to examine (a) rational and reactive pathways and psychosocial constructs predictive of CPB use and (b) how gender might moderate these influences in a sample of college students. Students (n = 508) completed Web-based baseline (mid-Spring semester) and 1- and 6-month follow-up assessments of CPB use; psychosocial constructs (expectancies, normative beliefs, attitudes, and self-concept); and rational and reactive pathways (intentions and willingness). Regression was used to examine rational and reactive influences as proximal predictors of CPB use at the 6-month follow-up. Subsequent path analyses examined the effects of psychosocial constructs, as distal predictors of CPB use, mediated through the rational and reactive pathways. Both rational (intentions to use CPB) and reactive (willingness to use CPB) influences were significantly associated with increased CPB use. The examined distal predictors were found to effect CPB use differentially through the rational and reactive pathways. Gender did not significantly moderate any relationships within in the model. Findings suggest potential entry points for increasing CPB use that include both rational and reactive pathways. Overall, this study demonstrates the mechanisms underlying how to increase the use of CPBs in programs designed to reduce alcohol-related sexual consequences and victimization. (c) 2015 APA, all rights reserved).

Developing creativity and problem-solving skills of engineering students: a comparison of web- and pen-and-paper-based approaches

NASA Astrophysics Data System (ADS)

Valentine, Andrew; Belski, Iouri; Hamilton, Margaret

2017-11-01

Problem-solving is a key engineering skill, yet is an area in which engineering graduates underperform. This paper investigates the potential of using web-based tools to teach students problem-solving techniques without the need to make use of class time. An idea generation experiment involving 90 students was designed. Students were surveyed about their study habits and reported they use electronic-based materials more than paper-based materials while studying, suggesting students may engage with web-based tools. Students then generated solutions to a problem task using either a paper-based template or an equivalent web interface. Students who used the web-based approach performed as well as students who used the paper-based approach, suggesting the technique can be successfully adopted and taught online. Web-based tools may therefore be adopted as supplementary material in a range of engineering courses as a way to increase students' options for enhancing problem-solving skills.

Agent-Based Modeling in Molecular Systems Biology.

PubMed

Soheilypour, Mohammad; Mofrad, Mohammad R K

2018-07-01

Molecular systems orchestrating the biology of the cell typically involve a complex web of interactions among various components and span a vast range of spatial and temporal scales. Computational methods have advanced our understanding of the behavior of molecular systems by enabling us to test assumptions and hypotheses, explore the effect of different parameters on the outcome, and eventually guide experiments. While several different mathematical and computational methods are developed to study molecular systems at different spatiotemporal scales, there is still a need for methods that bridge the gap between spatially-detailed and computationally-efficient approaches. In this review, we summarize the capabilities of agent-based modeling (ABM) as an emerging molecular systems biology technique that provides researchers with a new tool in exploring the dynamics of molecular systems/pathways in health and disease. © 2018 WILEY Periodicals, Inc.

Mercury in Arctic Marine Ecosystems: Sources, Pathways, and Exposure

PubMed Central

Kirk, Jane L.; Lehnherr, Igor; Andersson, Maria; Braune, Birgit M.; Chan, Laurie; Dastoor, Ashu P.; Durnford, Dorothy; Gleason, Amber L.; Loseto, Lisa L.; Steffen, Alexandra; St. Louis, Vincent L.

2014-01-01

Mercury in the Arctic is an important environmental and human health issue. The reliance of Northern Peoples on traditional foods, such as marine mammals, for subsistence means that they are particularly at risk from mercury exposure. The cycling of mercury in Arctic marine systems is reviewed here, with emphasis placed on the key sources, pathways and processes which regulate mercury levels in marine food webs and ultimately the exposure of human populations to this contaminant. While many knowledge gaps exist limiting our ability to make strong conclusions, it appears that the long range transport of mercury from Asian emissions is an important source of atmospheric Hg to the Arctic and that mercury methylation resulting in monomethylmercury production (an organic form of mercury which is both toxic and bioaccumulated) in Arctic marine waters is the principal source of mercury incorporated into food webs. Mercury concentrations in biological organisms have increased since the onset of the industrial age and are controlled by a combination of abiotic factors (e.g., monomethylmercury supply), food web dynamics and structure, and animal behavior (e.g., habitat selection and feeding behavior). Finally, although some Northern Peoples have high mercury concentrations of mercury in their blood and hair, harvesting and consuming traditional foods has many nutritional, social, cultural and physical health benefits which must be considered in risk management and communication. PMID:23102902

A continuous scale-space method for the automated placement of spot heights on maps

NASA Astrophysics Data System (ADS)

Rocca, Luigi; Jenny, Bernhard; Puppo, Enrico

2017-12-01

Spot heights and soundings explicitly indicate terrain elevation on cartographic maps. Cartographers have developed design principles for the manual selection, placement, labeling, and generalization of spot height locations, but these processes are work-intensive and expensive. Finding an algorithmic criterion that matches the cartographers' judgment in ranking the significance of features on a terrain is a difficult endeavor. This article proposes a method for the automated selection of spot heights locations representing natural features such as peaks, saddles and depressions. A lifespan of critical points in a continuous scale-space model is employed as the main measure of the importance of features, and an algorithm and a data structure for its computation are described. We also introduce a method for the comparison of algorithmically computed spot height locations with manually produced reference compilations. The new method is compared with two known techniques from the literature. Results show spot height locations that are closer to reference spot heights produced manually by swisstopo cartographers, compared to previous techniques. The introduced method can be applied to elevation models for the creation of topographic and bathymetric maps. It also ranks the importance of extracted spot height locations, which allows for a variation in the size of symbols and labels according to the significance of represented features. The importance ranking could also be useful for adjusting spot height density of zoomable maps in real time.

76 FR 14034 - Proposed Collection; Comment Request; NCI Cancer Genetics Services Directory Web-Based...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-15

... Request; NCI Cancer Genetics Services Directory Web-Based Application Form and Update Mailer Summary: In... Cancer Genetics Services Directory Web-based Application Form and Update Mailer. [[Page 14035

Isotopic study of mercury sources and transfer between a freshwater lake and adjacent forest food web.

PubMed

Kwon, Sae Yun; Blum, Joel D; Nadelhoffer, Knute J; Timothy Dvonch, J; Tsui, Martin Tsz-Ki

2015-11-01

Studies of monomethylmercury (MMHg) sources and biogeochemical pathways have been extensive in aquatic ecosystems, but limited in forest ecosystems. Increasing evidence suggests that there is significant mercury (Hg) exchange between aquatic and forest ecosystems. We use Hg stable isotope ratios (δ(202)Hg and Δ(199)Hg) to investigate the relative importance of MMHg sources and assess Hg transfer pathways between Douglas Lake and adjacent forests located at the University of Michigan Biological Station, USA. We characterize Hg isotopic compositions of basal resources and use linear regression of % MMHg versus δ(202)Hg and Δ(199)Hg to estimate Hg isotope values for inorganic mercury (IHg) and MMHg in the aquatic and adjacent forest food webs. In the aquatic ecosystem, we found that lake sediment represents a mixture of IHg pools deposited via watershed runoff and precipitation. The δ(202)Hg and Δ(199)Hg values estimated for IHg are consistent with other studies that measured forest floor in temperate forests. The Δ(199)Hg value estimated for MMHg in the aquatic food web indicates that MMHg is subjected to ~20% photochemical degradation prior to bioaccumulation. In the forest ecosystem, we found a significant negative relationship between total Hg and δ(202)Hg and Δ(199)Hg of soil collected at multiple distances from the lakeshore and lake sediment. This suggests that IHg input from watershed runoff provides an important Hg transfer pathway between the forest and aquatic ecosystems. We measured Δ(199)Hg values for high trophic level insects and compared these insects at multiple distances perpendicular to the lake shoreline. The Δ(199)Hg values correspond to the % canopy cover suggesting that forest MMHg is subjected to varying extents of photochemical degradation and the extent may be controlled by sunlight. Our study demonstrates that the use of Hg isotopes adds important new insight into the relative importance of MMHg sources and complex Hg transfer pathways across ecosystem boundaries. Copyright © 2015 Elsevier B.V. All rights reserved.

A semantic web ontology for small molecules and their biological targets.

PubMed

Choi, Jooyoung; Davis, Melissa J; Newman, Andrew F; Ragan, Mark A

2010-05-24

A wide range of data on sequences, structures, pathways, and networks of genes and gene products is available for hypothesis testing and discovery in biological and biomedical research. However, data describing the physical, chemical, and biological properties of small molecules have not been well-integrated with these resources. Semantically rich representations of chemical data, combined with Semantic Web technologies, have the potential to enable the integration of small molecule and biomolecular data resources, expanding the scope and power of biomedical and pharmacological research. We employed the Semantic Web technologies Resource Description Framework (RDF) and Web Ontology Language (OWL) to generate a Small Molecule Ontology (SMO) that represents concepts and provides unique identifiers for biologically relevant properties of small molecules and their interactions with biomolecules, such as proteins. We instanced SMO using data from three public data sources, i.e., DrugBank, PubChem and UniProt, and converted to RDF triples. Evaluation of SMO by use of predetermined competency questions implemented as SPARQL queries demonstrated that data from chemical and biomolecular data sources were effectively represented and that useful knowledge can be extracted. These results illustrate the potential of Semantic Web technologies in chemical, biological, and pharmacological research and in drug discovery.

A comparison of web-based versus print-based decision AIDS for prostate cancer screening: participants' evaluation and utilization.

PubMed

Tomko, Catherine; Davis, Kimberly M; Luta, George; Krist, Alexander H; Woolf, Steven H; Taylor, Kathryn L

2015-01-01

Patient decision aids facilitate informed decision making for medical tests and procedures that have uncertain benefits. To describe participants' evaluation and utilization of print-based and web-based prostate cancer screening decision aids that were found to improve decisional outcomes in a prior randomized controlled trial. Men completed brief telephone interviews at baseline, one month, and 13 months post-randomization. Participants were primary care patients, 45-70 years old, who received the print-based (N = 628) or web-based decision aid (N = 625) and completed the follow-up assessments. We assessed men's baseline preference for web-based or print-based materials, time spent using the decision aids, comprehension of the overall message, and ratings of the content. Decision aid use was self-reported by 64.3 % (web) and 81.8 % (print) of participants. Significant predictors of decision aid use were race (white vs. non-white, OR = 2.43, 95 % CI: 1.77, 3.35), higher education (OR = 1.68, 95 % CI: 1.06, 2.70) and trial arm (print vs. web, OR = 2.78, 95 % CI: 2.03, 3.83). Multivariable analyses indicated that web-arm participants were more likely to use the website when they preferred web-based materials (OR: 1.91, CI: 1.17, 3.12), whereas use of the print materials was not significantly impacted by a preference for print-based materials (OR: 0.69, CI: 0.38, 1.25). Comprehension of the decision aid message (i.e., screening is an individual decision) did not significantly differ between arms in adjusted analyses (print: 61.9 % and web: 68.2 %, p = 0.42). Decision aid use was independently influenced by race, education, and the decision aid medium, findings consistent with the 'digital divide.' These results suggest that when it is not possible to provide this age cohort with their preferred decision aid medium, print materials will be more highly used than web-based materials. Although there are many advantages to web-based decision aids, providing an option for print-based decision aids should be considered.

Web-Based Versus Conventional Training for Medical Students on Infant Gross Motor Screening.

PubMed

Pusponegoro, Hardiono D; Soebadi, Amanda; Surya, Raymond

2015-12-01

Early detection of developmental abnormalities is important for early intervention. A simple screening method is needed for use by general practitioners, as is an effective and efficient training method. This study aims to evaluate the effectiveness, acceptability, and usability of Web-based training for medical students on a simple gross motor screening method in infants. Fifth-year medical students at University of Indonesia in Jakarta were randomized into two groups. A Web-based training group received online video modules, discussions, and assessments (at www.schoology.com ). A conventional training group received a 1-day live training using the same module. Both groups completed identical pre- and posttests and the User Satisfaction Questionnaire (USQ). The Web-based group also completed the System Usability Scale (SUS). The module was based on a gross motor screening method used in the World Health Organization Multicentre Growth Reference Study. There were 39 and 32 subjects in the Web-based and conventional groups, respectively. Mean pretest versus posttest scores (correct answers out of 20) were 9.05 versus 16.95 (p=0.0001) in the Web-based group and 9.31 versus 16.88 (p=0.0001) in the conventional group. Mean difference between pre- and posttest scores did not differ significantly between the Web-based and conventional groups (mean [standard deviation], 7.56 [3.252] versus 7.90 [5.170]; p=0.741]. Both training methods were acceptable based on USQ scores. Based on SUS scores, the Web-based training had good usability. Web-based training is an effective, efficient, and acceptable training method for medical students on simple infant gross motor screening and is as effective as conventional training.

Trophic shift, not collapse

USGS Publications Warehouse

Madenjian, Charles P.; Rutherford, Edward S.; Stow, Craig A.; Roseman, Edward F.; He, Ji X.

2013-01-01

scientists who are closely monitoring Lake Huron’s food web, we believe that the ongoing changes are more accurately characterized as a trophic shift in which benthic pathways have become more prominent. While decreases in abundance have occurred for some species, others are experiencing improved reproduction resulting in the restoration of several important native species.

An online model composition tool for system biology models

PubMed Central

2013-01-01

Background There are multiple representation formats for Systems Biology computational models, and the Systems Biology Markup Language (SBML) is one of the most widely used. SBML is used to capture, store, and distribute computational models by Systems Biology data sources (e.g., the BioModels Database) and researchers. Therefore, there is a need for all-in-one web-based solutions that support advance SBML functionalities such as uploading, editing, composing, visualizing, simulating, querying, and browsing computational models. Results We present the design and implementation of the Model Composition Tool (Interface) within the PathCase-SB (PathCase Systems Biology) web portal. The tool helps users compose systems biology models to facilitate the complex process of merging systems biology models. We also present three tools that support the model composition tool, namely, (1) Model Simulation Interface that generates a visual plot of the simulation according to user’s input, (2) iModel Tool as a platform for users to upload their own models to compose, and (3) SimCom Tool that provides a side by side comparison of models being composed in the same pathway. Finally, we provide a web site that hosts BioModels Database models and a separate web site that hosts SBML Test Suite models. Conclusions Model composition tool (and the other three tools) can be used with little or no knowledge of the SBML document structure. For this reason, students or anyone who wants to learn about systems biology will benefit from the described functionalities. SBML Test Suite models will be a nice starting point for beginners. And, for more advanced purposes, users will able to access and employ models of the BioModels Database as well. PMID:24006914

Modeling selenium bioaccumulation through arthropod food webs in San Francisco Bay, California, USA.

PubMed

Schlekat, Christian E; Purkerson, David G; Luoma, Samuel N

2004-12-01

Trophic transfer is the main process by which upper trophic level wildlife are exposed to selenium. Transfers through lower levels of a predator's food web thus can be instrumental in determining the threat of selenium in an ecosystem. Little is known about Se transfer through pelagic, zooplankton-based food webs in San Francisco Bay ([SFB], CA, USA), which serve as an energy source for important predators such as striped bass: A dynamic multipathway bioaccumulation model was used to model Se transfer from phytoplankton to pelagic copepods to carnivorous mysids (Neomysis mercedis). Uptake rates of dissolved Se, depuration rates, and assimilation efficiencies (AE) for the model were determined for copepods and mysids in the laboratory. Small (73-250 microm) and large (250-500 microm) herbivorous zooplankton collected from SFB (Oithona/Limnoithona and Acartia sp.) assimilated Se with similar efficiencies (41-52%) from phytoplankton. Mysids assimilated 73% of Se from small herbivorous zooplankton; Se AE was significantly lower (61%) than larger herbivorous zooplankton. Selenium depuration rates were high for both zooplankton and mysids (12-25% d(-1)), especially compared to bivalves (2-3% d(-1)). The model predicted steady state Se concentrations in mysids similar to those observed in the field. The predicted concentration range (1.5-5.4 microg g(-1)) was lower than concentrations of 4.5 to 24 microg g(-1) observed in bivalves from the bay. Differences in efflux between mysids and bivalves were the best explanation for the differences in uptake. The results suggest that the risk of selenium toxicity to predators feeding on N. mercedis would be less than the risk to predators feeding on bivalves. Management of selenium contamination should include food webs analyses to focus on the most important exposure pathways identified for a given watershed.

Modeling selenium bioaccumulation through arthropod food webs in San Francisco Bay, California, USA

USGS Publications Warehouse

Schlekat, C.E.; Purkerson, D.G.; Luoma, S.N.

2004-01-01

Trophic transfer is the main process by which upper trophic level wildlife are exposed to selenium. Transfers through lower levels of a predator's food web thus can be instrumental in determining the threat of selenium in an ecosystem. Little is known about Se transfer through pelagic, zooplankton-based food webs in San Francisco Bay ([SFB], CA, USA), which serve as an energy source for important predators such as striped bass. A dynamic multipathway bioaccumulation model was used to model Se transfer from phytoplankton to pelagic copepods to carnivorous mysids (Neomysis mercedis). Uptake rates of dissolved Se, depuration rates, and assimilation efficiencies (AE) for the model were determined for copepods and mysids in the laboratory. Small (73-250 ??m) and large (250-500 ??m) herbivorous zooplankton collected from SFB (Oithona/Limnoithona and Acartia sp.) assimilated Se with similar efficiencies (41-52%) from phytoplankton. Mysids assimilated 73% of Se from small herbivorous zooplankton; Se AE was significantly lower (61%) than larger herbivorous zooplankton. Selenium depuration rates were high for both zooplankton and mysids (12-25% d-1), especially compared to bivalves (2-3% d-1). The model predicted steady state Se concentrations in mysids similar to those observed in the field. The predicted concentration range (1.5-5.4 ??g g -1) was lower than concentrations of 4.5 to 24 ??g g-1 observed in bivalves from the bay. Differences in efflux between mysids and bivalves were the best explanation for the differences in uptake. The results suggest that the risk of selenium toxicity to predators feeding on N. mercedis would be less than the risk to predators feeding on bivalves. Management of selenium contamination should include food webs analyses to focus on the most important exposure pathways identified for a given watershed.

The Effects of Different Interaction Types in Web-Based Teaching on the Attitudes of Learners towards Web-Based Teaching and Internet

ERIC Educational Resources Information Center

Turkish Online Journal of Distance Education, 2013

2013-01-01

It might be said that attitudes impact success directly in web-based teaching and timely and appropriate fulfillment of learners' expectations bear utmost significance for their success. From this perspective a properly designed web supported teaching application can provide positive contribution as well to learners' attitudes towards web…

The Development of Web-Based Collaborative Training Model for Enhancing Human Performances on ICT for Students in Banditpattanasilpa Institute

ERIC Educational Resources Information Center

Pumipuntu, Natawut; Kidrakarn, Pachoen; Chetakarn, Somchock

2015-01-01

This research aimed to develop the model of Web-based Collaborative (WBC) Training model for enhancing human performances on ICT for students in Banditpattanasilpa Institute. The research is divided into three phases: 1) investigating students and teachers' training needs on ICT web-based contents and performance, 2) developing a web-based…

Communication and Gamification in the Web-Based Foreign Language Educational System: Web- Based Foreign Language Educational System

ERIC Educational Resources Information Center

Osipov, Ilya V.; Volinsky, Alex A.; Nikulchev, Evgeny; Prasikova, Anna Y.

2016-01-01

The paper describes development of the educational online web communication platform for teaching and learning foreign languages. The main objective was to develop a web application for teaching foreigners to understand casual fluent speech. The system is based on the time bank principle, allowing users to teach others their native language along…

The Turkish Version of Web-Based Learning Platform Evaluation Scale: Reliability and Validity Study

ERIC Educational Resources Information Center

Dag, Funda

2016-01-01

The purpose of this study is to determine the language equivalence and the validity and reliability of the Turkish version of the "Web-Based Learning Platform Evaluation Scale" ("Web Tabanli Ögrenme Ortami Degerlendirme Ölçegi" [WTÖODÖ]) used in the selection and evaluation of web-based learning environments. Within this scope,…

The Knowledge of Web 2.0 by Library and Information Science Academics

ERIC Educational Resources Information Center

Al-Daihani, Sultan

2009-01-01

This research paper reports the results of a Web-based survey designed to explore the attitude of Library and Information Science (LIS) academics to Web 2.0. It investigates their familiarity with Web 2.0 concepts, tools and services and applications as these relate to LIS education, and the barriers to their use. A Web-based questionnaire was…

Inquiry-Based Learning and Technology: Designing and Exploring WebQuests

ERIC Educational Resources Information Center

Lacina, Jan

2007-01-01

A WebQuest is an inquiry-based technology activity designed by Bernie Dodge and Tom March at San Diego State University in 1995. Dodge and March describe WebQuests as activities in which most, or all, of the information used by learners is drawn from the Web. WebQuests are a powerful instructional activity for teachers and students. Students will…

Conceptual Web Users' Actions Prediction for Ontology-Based Browsing Recommendations

NASA Astrophysics Data System (ADS)

Robal, Tarmo; Kalja, Ahto

The Internet consists of thousands of web sites with different kinds of structures. However, users are browsing the web according to their informational expectations towards the web site searched, having an implicit conceptual model of the domain in their minds. Nevertheless, people tend to repeat themselves and have partially shared conceptual views while surfing the web, finding some areas of web sites more interesting than others. Herein, we take advantage of the latter and provide a model and a study on predicting users' actions based on the web ontology concepts and their relations.

Dynamic selection mechanism for quality of service aware web services

NASA Astrophysics Data System (ADS)

D'Mello, Demian Antony; Ananthanarayana, V. S.

2010-02-01

A web service is an interface of the software component that can be accessed by standard Internet protocols. The web service technology enables an application to application communication and interoperability. The increasing number of web service providers throughout the globe have produced numerous web services providing the same or similar functionality. This necessitates the use of tools and techniques to search the suitable services available over the Web. UDDI (universal description, discovery and integration) is the first initiative to find the suitable web services based on the requester's functional demands. However, the requester's requirements may also include non-functional aspects like quality of service (QoS). In this paper, the authors define a QoS model for QoS aware and business driven web service publishing and selection. The authors propose a QoS requirement format for the requesters, to specify their complex demands on QoS for the web service selection. The authors define a tree structure called quality constraint tree (QCT) to represent the requester's variety of requirements on QoS properties having varied preferences. The paper proposes a QoS broker based architecture for web service selection, which facilitates the requesters to specify their QoS requirements to select qualitatively optimal web service. A web service selection algorithm is presented, which ranks the functionally similar web services based on the degree of satisfaction of the requester's QoS requirements and preferences. The paper defines web service provider qualities to distinguish qualitatively competitive web services. The paper also presents the modelling and selection mechanism for the requester's alternative constraints defined on the QoS. The authors implement the QoS broker based system to prove the correctness of the proposed web service selection mechanism.

WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research.

PubMed

Slenter, Denise N; Kutmon, Martina; Hanspers, Kristina; Riutta, Anders; Windsor, Jacob; Nunes, Nuno; Mélius, Jonathan; Cirillo, Elisa; Coort, Susan L; Digles, Daniela; Ehrhart, Friederike; Giesbertz, Pieter; Kalafati, Marianthi; Martens, Marvin; Miller, Ryan; Nishida, Kozo; Rieswijk, Linda; Waagmeester, Andra; Eijssen, Lars M T; Evelo, Chris T; Pico, Alexander R; Willighagen, Egon L

2018-01-04

WikiPathways (wikipathways.org) captures the collective knowledge represented in biological pathways. By providing a database in a curated, machine readable way, omics data analysis and visualization is enabled. WikiPathways and other pathway databases are used to analyze experimental data by research groups in many fields. Due to the open and collaborative nature of the WikiPathways platform, our content keeps growing and is getting more accurate, making WikiPathways a reliable and rich pathway database. Previously, however, the focus was primarily on genes and proteins, leaving many metabolites with only limited annotation. Recent curation efforts focused on improving the annotation of metabolism and metabolic pathways by associating unmapped metabolites with database identifiers and providing more detailed interaction knowledge. Here, we report the outcomes of the continued growth and curation efforts, such as a doubling of the number of annotated metabolite nodes in WikiPathways. Furthermore, we introduce an OpenAPI documentation of our web services and the FAIR (Findable, Accessible, Interoperable and Reusable) annotation of resources to increase the interoperability of the knowledge encoded in these pathways and experimental omics data. New search options, monthly downloads, more links to metabolite databases, and new portals make pathway knowledge more effortlessly accessible to individual researchers and research communities. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

PubMed Central

Caspi, Ron; Altman, Tomer; Dale, Joseph M.; Dreher, Kate; Fulcher, Carol A.; Gilham, Fred; Kaipa, Pallavi; Karthikeyan, Athikkattuvalasu S.; Kothari, Anamika; Krummenacker, Markus; Latendresse, Mario; Mueller, Lukas A.; Paley, Suzanne; Popescu, Liviu; Pujar, Anuradha; Shearer, Alexander G.; Zhang, Peifen; Karp, Peter D.

2010-01-01

The MetaCyc database (MetaCyc.org) is a comprehensive and freely accessible resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecule metabolic pathways and are curated from the primary scientific literature. With more than 1400 pathways, MetaCyc is the largest collection of metabolic pathways currently available. Pathways reactions are linked to one or more well-characterized enzymes, and both pathways and enzymes are annotated with reviews, evidence codes, and literature citations. BioCyc (BioCyc.org) is a collection of more than 500 organism-specific Pathway/Genome Databases (PGDBs). Each BioCyc PGDB contains the full genome and predicted metabolic network of one organism. The network, which is predicted by the Pathway Tools software using MetaCyc as a reference, consists of metabolites, enzymes, reactions and metabolic pathways. BioCyc PGDBs also contain additional features, such as predicted operons, transport systems, and pathway hole-fillers. The BioCyc Web site offers several tools for the analysis of the PGDBs, including Omics Viewers that enable visualization of omics datasets on two different genome-scale diagrams and tools for comparative analysis. The BioCyc PGDBs generated by SRI are offered for adoption by any party interested in curation of metabolic, regulatory, and genome-related information about an organism. PMID:19850718

Surveillance Among Men Who have Sex with Men in the United States: A Comparison of Web-Based and Venue-Based Samples.

PubMed

Chen, Yen-Tyng; Bowles, Kristina; An, Qian; DiNenno, Elizabeth; Finlayson, Teresa; Hoots, Brooke; Paz-Bailey, Gabriela; Wejnert, Cyprian

2018-07-01

Although men who have sex with men (MSM) recruited through web-based and venue-based sampling methods have been compared, no large web-based and venue-based samples using similar survey instruments have been examined in the U.S. This study describes the differences in sociodemographic characteristics and risk behaviors between the 2012 Web-based HIV Behavioral Survey (n = 3221) and 2011 National HIV Behavioral Surveillance (n = 9256). Compared with participants in the venue-based sample, participants in the web-based sample were older, less likely to be black or Hispanic, more likely to have higher socioeconomic status, and more likely to have anal sex without a condom with their last male sex partner. Web-based participants were less likely to have multiple male sex partners, ever injected drugs, been tested for HIV in the past 12 months, and received free condoms than venue-based participants. The method for sampling MSM into a behavioral survey should consider the sub-population of MSM to be reached.

Surveying ourselves: examining the use of a web-based approach for a physician survey.

PubMed

Matteson, Kristen A; Anderson, Britta L; Pinto, Stephanie B; Lopes, Vrishali; Schulkin, Jay; Clark, Melissa A

2011-12-01

A survey was distributed, using a sequential mixed-mode approach, to a national sample of obstetrician-gynecologists. Differences between responses to the web-based mode and the on-paper mode were compared to determine if there were systematic differences between respondents. Only two differences in respondents between the two modes were identified. University-based physicians were more likely to complete the web-based mode than private practice physicians. Mail respondents reported a greater volume of endometrial ablations compared to online respondents. The web-based mode had better data quality than the paper-based mailed mode in terms of less missing and inappropriate responses. Together, these findings suggest that, although a few differences were identified, the web-based survey mode attained adequate representativeness and improved data quality. Given the metrics examined for this study, exclusive use of web-based data collection may be appropriate for physician surveys with a minimal reduction in sample coverage and without a reduction in data quality.

Web-based tailored lifestyle programs: exploration of the target group's interests and implications for practice.

PubMed

Verheijden, Marieke W; Jans, Marielle P; Hildebrandt, Vincent H

2008-01-01

An important challenge in Web-based health promotion is to increase the reach of the target audience by taking the target groups' desires into consideration. Data from 505 members of a Dutch Internet panel (representative for Dutch Internet users) were used to asses the target group's interests and needs. 28% participated in Web-based tailored lifestyle programs, 57% expressed an interest in such programs, and 15% expressed no interest. Interest in Web-based programs was predominantly caused by a general interest in lifestyle and online tests. Participation in Web-based tailored lifestyle programs should not take more than 17 minutes per occasion. 84% were interested in follow-up testing after the initial participation. Responders were particularly interested in physical activity and nutrition. Hardly anyone was willing to pay for participation. The results from this study support the use of Web-based tailored lifestyle programs in behavior change efforts.

Web-based learning resources - new opportunities for competency development.

PubMed

Moen, Anne; Nygård, Kathrine A; Gauperaa, Torunn

2009-01-01

Creating web-based learning environments holds great promise for on the job training and competence development in nursing. The web-based learning environment was designed and customized by four professional development nurses. We interviewed five RNs that pilot tested the web-based resource. Our findings give some insight into how the web-based design tool are perceived and utilized, and how content is represented in the learning environment. From a competency development perspective, practicing authentic tasks in a web-based learning environment can be useful to train skills and keep up important routines. The approach found in this study also needs careful consideration. Emphasizing routines and skills can be important to reduce variation and ensure more streamlined practice from an institution-wide quality improvement efforts. How the emphasis on routines and skills plays out towards the individual's overall professional development needs further careful studies.

Creation of a web-based lecture series for psychiatry clerkship students: initial findings.

PubMed

Martin, Vicki L; Bennett, David S

2004-01-01

In recent years, the trend in medical education has been to utilize clerkship settings outside the medical school. Subsequently, students rotate at distant sites from the main campus and have lectures of varying quantity and quality. The objective of the present study was to standardize the core didactic experience for students in the Psychiatry clerkship by using web-based lectures and to assess student satisfaction with such lectures. Students completed a brief satisfaction questionnaire after viewing both web-based and live lectures. Students rated both web-based and live lectures positively, although overall satisfaction ratings were higher for live lectures. Shelf-exam scores improved for the current year, suggesting that learning was not negatively affected by the use of web-based lectures. Web-based lectures appear to be a feasible and satisfactory way to ensure didactic comparability across clinical sites.

Are patients satisfied with a web-based followup after total joint arthroplasty?

PubMed

Marsh, Jacquelyn; Bryant, Dianne; MacDonald, Steven J; Naudie, Douglas; Remtulla, Alliya; McCalden, Richard; Howard, James; Bourne, Robert; McAuley, James

2014-06-01

A web-based followup assessment may be a feasible, cost-saving alternative of tracking patient outcomes after total joint arthroplasty. However, before implementing a web-based program, it is important to determine patient satisfaction levels with the new followup method. Satisfaction with the care received is becoming an increasingly important metric, and we do not know to what degree patients are satisfied with an approach to followup that does not involve an in-person visit with their surgeons. We determined (1) patient satisfaction and (2) patients' preferences for followup method (web-based or in-person) after total joint arthroplasty. We randomized patients who were at least 12 months after primary THA or TKA to complete a web-based followup or to have their appointment at the clinic. There were 410 eligible patients contacted for the study during the recruitment period. Of these, 256 agreed to participate, and a total of 229 patients completed the study (89% of those enrolled, 56% of those potentially eligible; 111 in the usual-care group, 118 in the web-based group). Their mean age was 69 years (range, 38-86 years). There was no crossover between groups. All 229 patients completed a satisfaction questionnaire at the time of their followup appointments. Patients in the web-based group also completed a satisfaction and preference questionnaire 1 year later. Only patients from the web-based group were asked to indicate preference as they had experienced the web-based and in-person followup methods. We used descriptive statistics to summarize the satisfaction questionnaires and compared results using Pearson's chi-square test. Ninety-one patients (82.0%) in the usual-care group indicated that they were either extremely or very satisfied with the followup process compared with 90 patients (75.6%) who were in the web-based group (p < 0.01; odds ratio [OR] = 3.95; 95% CI, 1.79-8.76). Similarly, patients in the usual care group were more satisfied with the care they received from their surgeon, compared with patients in the web-based group (92.8% versus 73.9%; p < 0.01, OR = 1.37; 95% CI, 0.73-2.57). Forty-four percent of patients preferred the web-based method, 36% preferred the usual method, and 16% had no preference (p = 0.01). Our results show moderate to high satisfaction levels with a web-based followup assessment. Patients who completed the usual method of in-person followup assessment reported greater satisfaction; however, the difference was small and may not outweigh the additional cost and time-saving benefits of the web-based followup method. Level I, therapeutic study. See the Instructions for Authors for a complete description of levels of evidence.

FOCIH: Form-Based Ontology Creation and Information Harvesting

NASA Astrophysics Data System (ADS)

Tao, Cui; Embley, David W.; Liddle, Stephen W.

Creating an ontology and populating it with data are both labor-intensive tasks requiring a high degree of expertise. Thus, scaling ontology creation and population to the size of the web in an effort to create a web of data—which some see as Web 3.0—is prohibitive. Can we find ways to streamline these tasks and lower the barrier enough to enable Web 3.0? Toward this end we offer a form-based approach to ontology creation that provides a way to create Web 3.0 ontologies without the need for specialized training. And we offer a way to semi-automatically harvest data from the current web of pages for a Web 3.0 ontology. In addition to harvesting information with respect to an ontology, the approach also annotates web pages and links facts in web pages to ontological concepts, resulting in a web of data superimposed over the web of pages. Experience with our prototype system shows that mappings between conceptual-model-based ontologies and forms are sufficient for creating the kind of ontologies needed for Web 3.0, and experiments with our prototype system show that automatic harvesting, automatic annotation, and automatic superimposition of a web of data over a web of pages work well.

Matching and selection of a specific subjective experience: conjugate matching and experience.

PubMed

Vimal, Ram Lakhan Pandey

2010-06-01

We incorporate the dual-mode concept in our dual-aspect PE-SE (proto-experience-subjective experience) framework. The two modes are: (1) the non-tilde mode that is the physical (material) and mental aspect of cognition (memory and attention) related feedback signals in a neural-network, which refers to the cognitive nearest past approaching towards present; and (2) the tilde mode that is the material and mental aspect of the feed-forward signals due to external environmental input and internal endogenous input, which pertains to the nearest future approaching towards present and is a entropy-reversed representation of non-tilde mode. Furthermore, one could argue that there are at least five sub-pathways in the stimulus-dependent feed-forward pathway and cognitive feedback pathway for information transfer in the brain dynamics: (i) classical axonal-dendritic neural sub-pathway including electromagnetic information field sub-pathway; (ii) quantum dendritic-dendritic microtubule (MT) (dendritic webs) sub-pathway; (iii) Ca(++)-related astroglial-neural sub-pathway; (iv) (a) the sub-pathway related to extrasynaptic signal transmission between fine distal dendrites of cortical neurons for the local subtle modulation due to voltages created by intradendritic dual-aspect charged surface effects within the Debye layer around endogenous structures such as microtubules (MT) and endoplasmic reticulum (ER) in dendrites, and (b) the sub-pathway related to extracellular volume transmission as fields of neural activity for the global modulation in axonal-dendritic neural sub-pathway; and (v) the sub-pathway related to information transmission via soliton propagation. We propose that: (i) the quantum conjugate matching between experiences in the mental aspect of the tilde mode and that of the non-tilde mode is related more to the mental aspect of the quantum microtubule-dendritic-web and less to that of the non-quantum sub-pathways; and (ii) the classical matching between experiences in the mental aspect of the tilde mode and that of the non-tilde mode is related to the mental aspect of the non-quantum sub-pathways (such as classical axonal-dendritic neural sub-pathway). In both cases, a specific SE is selected when the tilde mode interacts with the non-tilde mode to match for a specific SE, and when the necessary ingredients of SEs (such as the formation of neural networks, wakefulness, re-entry, attention, working memory, and so on) are satisfied. When the conjugate match is made between the two modes, the world-presence (Now) is disclosed. The material aspects in the tilde mode and that in the non-tilde mode are matched to link structure with function, whereas the mental aspects in the tilde mode and that in the non-tilde mode are matched to link experience with structure and function.

Visionmaker NYC: A bottom-up approach to finding shared socioeconomic pathways in New York City

NASA Astrophysics Data System (ADS)

Sanderson, E. W.; Fisher, K.; Giampieri, M.; Barr, J.; Meixler, M.; Allred, S. B.; Bunting-Howarth, K. E.; DuBois, B.; Parris, A. S.

2015-12-01

Visionmaker NYC is a free, public participatory, bottom-up web application to develop and share climate mitigation and adaptation strategies for New York City neighborhoods. The goal is to develop shared socioeconomic pathways by allowing a broad swath of community members - from schoolchildren to architects and developers to the general public - to input their concepts for a desired future. Visions are comprised of climate scenarios, lifestyle choices, and ecosystem arrangements, where ecosystems are broadly defined to include built ecosystems (e.g. apartment buildings, single family homes, etc.), transportation infrastructure (e.g. highways, connector roads, sidewalks), and natural land cover types (e.g. wetlands, forests, estuary.) Metrics of water flows, carbon cycling, biodiversity patterns, and population are estimated for the user's vision, for the same neighborhood today, and for that neighborhood as it existed in the pre-development state, based on the Welikia Project (welikia.org.) Users can keep visions private, share them with self-defined groups of other users, or distribute them publicly. Users can also propose "challenges" - specific desired states of metrics for specific parts of the city - and others can post visions in response. Visionmaker contributes by combining scenario planning, scientific modelling, and social media to create new, wide-open possibilities for discussion, collaboration, and imagination regarding future, shared socioeconomic pathways.

Stigma-related stressors, coping self-efficacy, and physical health in lesbian, gay, and bisexual individuals.

PubMed

Denton, F Nicholas; Rostosky, Sharon Scales; Danner, Fred

2014-07-01

Understanding and intervening to address health disparities is part of the expanding role of psychologists (Johnson, 2013). We drew on Hatzenbuehler's (2009) psychological mediation framework and Lick, Durso, and Johnson's (2013) conceptual pathways to lesbian, gay, and bisexual (LGB) physical health disparities to test a serial mediation model in which 2 types of cognitive appraisals (proximal minority stressors and coping self-efficacy) partially account for the association between perceived discrimination and prejudice (distal minority stressor) and self-reported physical health symptoms in a nationally recruited sample of 564 LGB individuals (270 women, 294 men) who participated in a web-based survey. Results indicated that perceived experiences of discrimination and prejudice were associated with expectations of rejection and internalized homonegativity. These 2 proximal stressors were associated with lower coping self-efficacy, and the combined cognitive appraisal pathways were associated with higher levels of self-reported physical symptom severity. The pathway through emotion-focused coping self-efficacy was particularly salient in accounting for the overall mediation. Interventions to address distal and proximal minority stressors and improve emotion-focused coping self-efficacy may be particularly helpful in reducing the negative effects of stigma on physical health. PsycINFO Database Record (c) 2014 APA, all rights reserved.

Major regulatory mechanisms involved in sperm motility

PubMed Central

Pereira, Rute; Sá, Rosália; Barros, Alberto; Sousa, Mário

2017-01-01

The genetic bases and molecular mechanisms involved in the assembly and function of the flagellum components as well as in the regulation of the flagellar movement are not fully understood, especially in humans. There are several causes for sperm immotility, of which some can be avoided and corrected, whereas other are related to genetic defects and deserve full investigation to give a diagnosis to patients. This review was performed after an extensive literature search on the online databases PubMed, ScienceDirect, and Web of Science. Here, we review the involvement of regulatory pathways responsible for sperm motility, indicating possible causes for sperm immotility. These included the calcium pathway, the cAMP-dependent protein kinase pathway, the importance of kinases and phosphatases, the function of reactive oxygen species, and how the regulation of cell volume and osmolarity are also fundamental components. We then discuss main gene defects associated with specific morphological abnormalities. Finally, we slightly discuss some preventive and treatments approaches to avoid development of conditions that are associated with unspecified sperm immotility. We believe that in the near future, with the development of more powerful techniques, the genetic causes of sperm immotility and the regulatory mechanisms of sperm motility will be better understand, thus enabling to perform a full diagnosis and uncover new therapies. PMID:26680031

Demonstration of the Web-based Interspecies Correlation Estimation (Web-ICE) modeling application

EPA Science Inventory

The Web-based Interspecies Correlation Estimation (Web-ICE) modeling application is available to the risk assessment community through a user-friendly internet platform (http://epa.gov/ceampubl/fchain/webice/). ICE models are log-linear least square regressions that predict acute...

Web-based Academic Roadmaps for Careers in the Geosciences

NASA Astrophysics Data System (ADS)

Murray, D. P.; Veeger, A. I.; Grossman-Garber, D.

2007-12-01

To a greater extent than most science programs, geology is underrepresented in K-12 curricula and the media. Thus potential majors have scant knowledge of academic requirements and career trajectories, and their idea of what geologists do--if they have one at all--is outdated. We have addressed these concerns by developing a dynamic, web-based academic roadmap for current and prospective students, their families, and others who are contemplating careers in the geosciences. The goals of this visually attractive "educational pathway" are to not only improve student recruitment and retention, but to empower student learning by creating better communication and advising tools that can render our undergraduate program transparent for learners and their families. Although we have developed academic roadmaps for four environmental and life science programs at the University of Rhode Island, we focus here on the roadmap for the geosciences, which illustrates educational pathways along the academic and early-career continuum for current and potential (i.e., high school) students who are considering the earth sciences. In essence, the Geosciences Academic Roadmap is a "one-stop'" portal to the discipline. It includes user- friendly information about our curriculum, outcomes (which at URI are tightly linked to performance in courses and the major), extracurricular activities (e.g., field camp, internships), careers, graduate programs, and training. In the presentation of this material extensive use is made of streaming video, interviews with students and earth scientists, and links to other relevant sites. Moreover, through the use of "Hot Topics", particular attention is made to insure that examples of geoscience activities are not only of relevance to today's students, but show geologists using the modern methods of the discipline in exciting ways. Although this is a "work-in-progress", evaluation of the sites, by high school through graduate students, has been strongly positive. Our presentation will include a demonstration of the Academic Roadmap, and a template that can be used by other geoscience departments to easily design websites.

NCI-60 Whole Exome Sequencing and Pharmacological CellMiner Analyses

PubMed Central

Reinhold, William C.; Varma, Sudhir; Sousa, Fabricio; Sunshine, Margot; Abaan, Ogan D.; Davis, Sean R.; Reinhold, Spencer W.; Kohn, Kurt W.; Morris, Joel; Meltzer, Paul S.; Doroshow, James H.; Pommier, Yves

2014-01-01

Exome sequencing provides unprecedented insights into cancer biology and pharmacological response. Here we assess these two parameters for the NCI-60, which is among the richest genomic and pharmacological publicly available cancer cell line databases. Homozygous genetic variants that putatively affect protein function were identified in 1,199 genes (approximately 6% of all genes). Variants that are either enriched or depleted compared to non-cancerous genomes, and thus may be influential in cancer progression and differential drug response were identified for 2,546 genes. Potential gene knockouts are made available. Assessment of cell line response to 19,940 compounds, including 110 FDA-approved drugs, reveals ≈80-fold range in resistance versus sensitivity response across cell lines. 103,422 gene variants were significantly correlated with at least one compound (at p<0.0002). These include genes of known pharmacological importance such as IGF1R, BRAF, RAD52, MTOR, STAT2 and TSC2 as well as a large number of candidate genes such as NOM1, TLL2, and XDH. We introduce two new web-based CellMiner applications that enable exploration of variant-to-compound relationships for a broad range of researchers, especially those without bioinformatics support. The first tool, “Genetic variant versus drug visualization”, provides a visualization of significant correlations between drug activity-gene variant combinations. Examples are given for the known vemurafenib-BRAF, and novel ifosfamide-RAD52 pairings. The second, “Genetic variant summation” allows an assessment of cumulative genetic variations for up to 150 combined genes together; and is designed to identify the variant burden for molecular pathways or functional grouping of genes. An example of its use is provided for the EGFR-ERBB2 pathway gene variant data and the identification of correlated EGFR, ERBB2, MTOR, BRAF, MEK and ERK inhibitors. The new tools are implemented as an updated web-based CellMiner version, for which the present publication serves as a compendium. PMID:25032700

Pedagogy for teaching and learning cooperatively on the Web: a Web-based pharmacology course.

PubMed

Tse, Mimi M Y; Pun, Sandra P Y; Chan, Moon Fai

2007-02-01

The Internet is becoming a preferred place to find information. Millions of people go online in the search of health and medical information. Likewise, the demand for Web-based courses grows. This article presents the development, utilization and evaluation of a web-based pharmacology course for nursing students. The course was developed based on 150 commonly used drugs. There were 110 year 1 nursing students took part in the course. After attending six hours face to face lecture of pharmacology over three weeks, students were invited to complete a questionnaire (pre-test) about learning pharmacology. The course materials were then uploaded to a WebCT for student's self-directed learning and attempts to pass two scheduled online quizzes. At the end of the semester, students were given the same questionnaire (post-test). There were a significant increase in the understanding compared with memorizing the subject content, the development of problem solving ability in learning pharmacology and becoming an independent learner (p ,0.05). Online quizzes yielded satisfactory results. In the focused group interview, students appreciated the time flexibility and convenience associated with web-based learning, also, they had made good suggestions in enhancing web-based learning. Web-based approach is promising for teaching and learning pharmacology for nurses and other health-care professionals.

Efficacy of an Experiential, Dissonance-Based Smoking Intervention for College Students Delivered via the Internet

PubMed Central

Simmons, Vani Nath; Heckman, Bryan W.; Fink, Angelina C.; Small, Brent J.; Brandon, Thomas H.

2015-01-01

Objective College represents a window of opportunity to reach the sizeable number of cigarette smokers who are vulnerable to lifelong smoking. The underutilization of typical cessation programs suggests the need for novel and more engaging approaches for reaching college smokers. The aim of the present study was to test the efficacy of a dissonance-enhancing, Web-based experiential intervention for increasing smoking cessation motivation and behavior. Method We used a 4-arm, randomized design to examine the efficacy of a Web-based, experiential smoking intervention (Web-Smoke). The control conditions included a didactic smoking intervention (Didactic), a group-based experiential intervention (Group), and a Web-based nutrition experiential intervention (Web-Nutrition). We recruited 341 college smokers. Primary outcomes were motivation to quit, assessed immediately postintervention, and smoking abstinence at 1 and 6 months following the intervention. Results As hypothesized, the Web-Smoke intervention was more effective than control groups in increasing motivation to quit. At 6-month follow-up, the Web-Smoke intervention produced higher rates of smoking cessation than the Web-Nutrition control intervention. Daily smoking moderated intervention outcomes. Among daily smokers, the Web-Smoke intervention produced greater abstinence rates than both the Web-Nutrition and Didactic control conditions. Conclusion Findings demonstrate the efficacy of a theory-based intervention delivered over the Internet for increasing motivation to quit and smoking abstinence among college smokers. The intervention has potential for translation and implementation as a secondary prevention strategy for college-aged smokers. PMID:23668667

Efficacy of an experiential, dissonance-based smoking intervention for college students delivered via the internet.

PubMed

Simmons, Vani Nath; Heckman, Bryan W; Fink, Angelina C; Small, Brent J; Brandon, Thomas H

2013-10-01

College represents a window of opportunity to reach the sizeable number of cigarette smokers who are vulnerable to lifelong smoking. The underutilization of typical cessation programs suggests the need for novel and more engaging approaches for reaching college smokers. The aim of the present study was to test the efficacy of a dissonance-enhancing, Web-based experiential intervention for increasing smoking cessation motivation and behavior. We used a 4-arm, randomized design to examine the efficacy of a Web-based, experiential smoking intervention (Web-Smoke). The control conditions included a didactic smoking intervention (Didactic), a group-based experiential intervention (Group), and a Web-based nutrition experiential intervention (Web-Nutrition). We recruited 341 college smokers. Primary outcomes were motivation to quit, assessed immediately postintervention, and smoking abstinence at 1 and 6 months following the intervention. As hypothesized, the Web-Smoke intervention was more effective than control groups in increasing motivation to quit. At 6-month follow-up, the Web-Smoke intervention produced higher rates of smoking cessation than the Web-Nutrition control intervention. Daily smoking moderated intervention outcomes. Among daily smokers, the Web-Smoke intervention produced greater abstinence rates than both the Web-Nutrition and Didactic control conditions. Findings demonstrate the efficacy of a theory-based intervention delivered over the Internet for increasing motivation to quit and smoking abstinence among college smokers. The intervention has potential for translation and implementation as a secondary prevention strategy for college-aged smokers. (PsycINFO Database Record (c) 2013 APA, all rights reserved).

Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs

PubMed Central

Lin, Tien-Ho; Bar-Joseph, Ziv

2011-01-01

Abstract Proper subcellular localization is critical for proteins to perform their roles in cellular functions. Proteins are transported by different cellular sorting pathways, some of which take a protein through several intermediate locations until reaching its final destination. The pathway a protein is transported through is determined by carrier proteins that bind to specific sequence motifs. In this article, we present a new method that integrates protein interaction and sequence motif data to model how proteins are sorted through these sorting pathways. We use a hidden Markov model (HMM) to represent protein sorting pathways. The model is able to determine intermediate sorting states and to assign carrier proteins and motifs to the sorting pathways. In simulation studies, we show that the method can accurately recover an underlying sorting model. Using data for yeast, we show that our model leads to accurate prediction of subcellular localization. We also show that the pathways learned by our model recover many known sorting pathways and correctly assign proteins to the path they utilize. The learned model identified new pathways and their putative carriers and motifs and these may represent novel protein sorting mechanisms. Supplementary results and software implementation are available from http://murphylab.web.cmu.edu/software/2010_RECOMB_pathways/. PMID:21999284

A Web-Based Learning Support System for Inquiry-Based Learning

NASA Astrophysics Data System (ADS)

Kim, Dong Won; Yao, Jingtao

The emergence of the Internet and Web technology makes it possible to implement the ideals of inquiry-based learning, in which students seek truth, information, or knowledge by questioning. Web-based learning support systems can provide a good framework for inquiry-based learning. This article presents a study on a Web-based learning support system called Online Treasure Hunt. The Web-based learning support system mainly consists of a teaching support subsystem, a learning support subsystem, and a treasure hunt game. The teaching support subsystem allows instructors to design their own inquiry-based learning environments. The learning support subsystem supports students' inquiry activities. The treasure hunt game enables students to investigate new knowledge, develop ideas, and review their findings. Online Treasure Hunt complies with a treasure hunt model. The treasure hunt model formalizes a general treasure hunt game to contain the learning strategies of inquiry-based learning. This Web-based learning support system empowered with the online-learning game and founded on the sound learning strategies furnishes students with the interactive and collaborative student-centered learning environment.

Web-Based Mindfulness Interventions for People With Physical Health Conditions: Systematic Review.

PubMed

Toivonen, Kirsti I; Zernicke, Kristin; Carlson, Linda E

2017-08-31

Mindfulness-based interventions (MBIs) are becoming increasingly popular for helping people with physical health conditions. Expanding from traditional face-to-face program delivery, there is growing interest in Web-based application of MBIs, though Web-based MBIs for people with physical health conditions specifically have not been thoroughly reviewed to date. The objective of this paper was to review Web-based MBIs for people with physical health conditions and to examine all outcomes reported (eg, efficacy or effectiveness for physical changes or psychological changes; feasibility). Databases PubMed, PsycINFO, Science Direct, CINAHL Plus, and Web of Science were searched. Full-text English papers that described any Web-based MBI, examining any outcome, for people with chronic physical health conditions were included. Randomized, nonrandomized, controlled, and uncontrolled trials were all included. Extracted data included intervention characteristics, population characteristics, outcomes, and quality indicators. Intervention characteristics (eg, synchronicity and guidance) were examined as potential factors related to study outcomes. Of 435 publications screened, 19 published papers describing 16 studies were included. They examined Web-based MBIs for people with cancer, chronic pain or fibromyalgia, irritable bowel syndrome (IBS), epilepsy, heart disease, tinnitus, and acquired brain injury. Overall, most studies reported positive effects of Web-based MBIs compared with usual care on a variety of outcomes including pain acceptance, coping measures, and depressive symptoms. There were mixed results regarding the effectiveness of Web-based MBIs compared with active control treatment conditions such as cognitive behavioral therapy. Condition-specific symptoms (eg, cancer-related fatigue and IBS symptoms) targeted by treatment had the largest effect size improvements following MBIs. Results are inconclusive regarding physical variables. Preliminary evidence suggests that Web-based MBIs may be helpful in alleviating symptom burden that those with physical health conditions can experience, particularly when interventions are tailored for specific symptoms. There was no evidence of differences between synchronous versus asynchronous or facilitated versus self-directed Web-based MBIs. Future investigations of Web-based MBIs should evaluate the effects of program adherence, effects on mindfulness levels, and whether synchronous or asynchronous, or facilitated or self-directed interventions elicit greater improvements. ©Kirsti I Toivonen, Kristin Zernicke, Linda E Carlson. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 31.08.2017.

The Web Resource Collaboration Center

ERIC Educational Resources Information Center

Dunlap, Joanna C.

2004-01-01

The Web Resource Collaboration Center (WRCC) is a web-based tool developed to help software engineers build their own web-based learning and performance support systems. Designed using various online communication and collaboration technologies, the WRCC enables people to: (1) build a learning and professional development resource that provides…

Leveraging Student Feedback To Improve Teaching in Web-Based Courses.

ERIC Educational Resources Information Center

Schnorr, Donna; Hazari, Sunil

1999-01-01

Explores cognitive aspects of learning and demonstrates how student feedback can be applied to improve Web-based teaching drawing on experiences with undergraduate courses at California State University, San Bernardino. Highlights include Web interactivity; HTML forms; and Web resources with forms for informal assessment. (LRW)

Utilization of services in a randomized trial testing phone- and web-based interventions for smoking cessation.

PubMed

Zbikowski, Susan M; Jack, Lisa M; McClure, Jennifer B; Deprey, Mona; Javitz, Harold S; McAfee, Timothy A; Catz, Sheryl L; Richards, Julie; Bush, Terry; Swan, Gary E

2011-05-01

Phone counseling has become standard for behavioral smoking cessation treatment. Newer options include Web and integrated phone-Web treatment. No prior research, to our knowledge, has systematically compared the effectiveness of these three treatment modalities in a randomized trial. Understanding how utilization varies by mode, the impact of utilization on outcomes, and predictors of utilization across each mode could lead to improved treatments. One thousand two hundred and two participants were randomized to phone, Web, or combined phone-Web cessation treatment. Services varied by modality and were tracked using automated systems. All participants received 12 weeks of varenicline, printed guides, an orientation call, and access to a phone supportline. Self-report data were collected at baseline and 6-month follow-up. Overall, participants utilized phone services more often than the Web-based services. Among treatment groups with Web access, a significant proportion logged in only once (37% phone-Web, 41% Web), and those in the phone-Web group logged in less often than those in the Web group (mean = 2.4 vs. 3.7, p = .0001). Use of the phone also was correlated with increased use of the Web. In multivariate analyses, greater use of the phone- or Web-based services was associated with higher cessation rates. Finally, older age and the belief that certain treatments could improve success were consistent predictors of greater utilization across groups. Other predictors varied by treatment group. Opportunities for enhancing treatment utilization exist, particularly for Web-based programs. Increasing utilization more broadly could result in better overall treatment effectiveness for all intervention modalities.

A food web modeling analysis of a Midwestern, USA eutrophic lake dominated by non-native Common Carp and Zebra Mussels

USGS Publications Warehouse

Colvin, Michael E.; Pierce, Clay; Stewart, Timothy W.

2015-01-01

Food web modeling is recognized as fundamental to understanding the complexities of aquatic systems. Ecopath is the most common mass-balance model used to represent food webs and quantify trophic interactions among groups. We constructed annual Ecopath models for four consecutive years during the first half-decade of a zebra mussel invasion in shallow, eutrophic Clear Lake, Iowa, USA, to evaluate changes in relative biomass and total system consumption among food web groups, evaluate food web impacts of non-native common carp and zebra mussels on food web groups, and to interpret food web impacts in light of on-going lake restoration. Total living biomass increased each year of the study; the majority of the increase due to a doubling in planktonic blue green algae, but several other taxa also increased including a more than two-order of magnitude increase in zebra mussels. Common carp accounted for the largest percentage of total fish biomass throughout the study even with on-going harvest. Chironomids, common carp, and zebra mussels were the top-three ranking consumer groups. Non-native common carp and zebra mussels accounted for an average of 42% of the total system consumption. Despite the relatively high biomass densities of common carp and zebra mussel, food web impacts was minimal due to excessive benthic and primary production in this eutrophic system. Consumption occurring via benthic pathways dominated system consumption in Clear Lake throughout our study, supporting the argument that benthic food webs are significant in shallow, eutrophic lake ecosystems and must be considered if ecosystem-level understanding is to be obtained.

iHOPerator: user-scripting a personalized bioinformatics Web, starting with the iHOP website

PubMed Central

Good, Benjamin M; Kawas, Edward A; Kuo, Byron Yu-Lin; Wilkinson, Mark D

2006-01-01

Background User-scripts are programs stored in Web browsers that can manipulate the content of websites prior to display in the browser. They provide a novel mechanism by which users can conveniently gain increased control over the content and the display of the information presented to them on the Web. As the Web is the primary medium by which scientists retrieve biological information, any improvements in the mechanisms that govern the utility or accessibility of this information may have profound effects. GreaseMonkey is a Mozilla Firefox extension that facilitates the development and deployment of user-scripts for the Firefox web-browser. We utilize this to enhance the content and the presentation of the iHOP (information Hyperlinked Over Proteins) website. Results The iHOPerator is a GreaseMonkey user-script that augments the gene-centred pages on iHOP by providing a compact, configurable visualization of the defining information for each gene and by enabling additional data, such as biochemical pathway diagrams, to be collected automatically from third party resources and displayed in the same browsing context. Conclusion This open-source script provides an extension to the iHOP website, demonstrating how user-scripts can personalize and enhance the Web browsing experience in a relevant biological setting. The novel, user-driven controls over the content and the display of Web resources made possible by user-scripts, such as the iHOPerator, herald the beginning of a transition from a resource-centric to a user-centric Web experience. We believe that this transition is a necessary step in the development of Web technology that will eventually result in profound improvements in the way life scientists interact with information. PMID:17173692

Using a Learning Styles Inventory to Examine Student Satisfaction with Web-Based Instruction: A 15-Year Study of One Professor's Web-Based Course Instruction

ERIC Educational Resources Information Center

Olliges, Ralph

2017-01-01

This article examines Active Engagement, Active Communication, and Peer Engagement learning practices among various student groups. It examines which tools are most important for increasing student satisfaction with web-based and web-enhanced instruction. Second, it looks at how different tools lead to greater satisfaction among different types of…

Teaching with technology: free Web resources for teaching and learning.

PubMed

Wink, Diane M; Smith-Stoner, Marilyn

2011-01-01

In this bimonthly series, the department editor examines how nurse educators can use Internet and Web-based computer technologies such as search, communication, collaborative writing tools; social networking, and social bookmarking sites; virtual worlds; and Web-based teaching and learning programs. In this article, the department editor and her coauthor describe free Web-based resources that can be used to support teaching and learning.

Exploring Individual, Social and Organisational Effects on Web 2.0-Based Workplace Learning: A Research Agenda for a Systematic Approach

ERIC Educational Resources Information Center

Zhao, Fang; Kemp, Linzi

2013-01-01

Web 2.0-based workplace learning is defined in this article as informal learning that takes place in the workplace through connections and collaborations mediated by Web 2.0 technology. Web 2.0-based workplace learning has the potential to enhance organisational learning and development. However, little systematic research has been published that…

Achieving Better Buying Power through Acquisition of Open Architecture Software Systems for Web-Based and Mobile Devices

DTIC Science & Technology

2015-05-01

Achieving Better Buying Power through Acquisition of Open Architecture Software Systems for Web-Based and Mobile Devices Walt Scacchi and Thomas...2015 to 00-00-2015 4. TITLE AND SUBTITLE Achieving Better Buying Power through Acquisition of Open Architecture Software Systems for Web-Based and...architecture (OA) software systems  Emerging challenges in achieving Better Buying Power (BBP) via OA software systems for Web- based and Mobile devices

A web-based application for initial screening of living kidney donors: development, implementation and evaluation.

PubMed

Moore, D R; Feurer, I D; Zavala, E Y; Shaffer, D; Karp, S; Hoy, H; Moore, D E

2013-02-01

Most centers utilize phone or written surveys to screen candidates who self-refer to be living kidney donors. To increase efficiency and reduce resource utilization, we developed a web-based application to screen kidney donor candidates. The aim of this study was to evaluate the use of this web-based application. Method and time of referral were tabulated and descriptive statistics summarized demographic characteristics. Time series analyses evaluated use over time. Between January 1, 2011 and March 31, 2012, 1200 candidates self-referred to be living kidney donors at our center. Eight hundred one candidates (67%) completed the web-based survey and 399 (33%) completed a phone survey. Thirty-nine percent of donors accessed the application on nights and weekends. Postimplementation of the web-based application, there was a statistically significant increase (p < 0.001) in the number of self-referrals via the web-based application as opposed to telephone contact. Also, there was a significant increase (p = 0.025) in the total number of self-referrals post-implementation from 61 to 116 per month. An interactive web-based application is an effective strategy for the initial screening of donor candidates. The web-based application increased the ability to interface with donors, process them efficiently and ultimately increased donor self-referral at our center. © Copyright 2012 The American Society of Transplantation and the American Society of Transplant Surgeons.

A Web-based e-learning course: integration of pathophysiology into pharmacology.

PubMed

Tse, Mimi M Y; Lo, Lisa W L

2008-11-01

The Internet is becoming the preferred place to find information. Millions of people go online in search of health and medical information. Likewise, the demand for Web-based courses is growing. This paper presents the development, utilization, and evaluation of a Web-based e-learning course for nursing students, entitled Integration of Pathophysiology into Pharmacology. The pathophysiology component included cardiovascular, respiratory, central nervous and immune system diseases, while the pharmacology component was developed based on 150 commonly used drugs. One hundred and nineteen Year 1 nursing students took part in the course. The Web-based e-learning course materials were uploaded to a WebCT for students' self-directed learning and attempts to pass two scheduled online quizzes. At the end of the semester, students were given a questionnaire to measure the e-learning experience. Their experience in the e-learning course was a positive one. Students stated that they were able to understand rather than memorize the subject content, and develop their problem solving and critical thinking abilities. Online quizzes yielded satisfactory results. In the focus group interview, students indicated that they appreciated the time flexibility and convenience associated with Web-based learning, and also made good suggestions for enhancing Web-based learning. The Web-based approach is promising for teaching and learning pathophysiology and pharmacology for nurses and other healthcare professionals.

Factors that influence acceptance of web-based e-learning systems for the in-service education of junior high school teachers in Taiwan.

PubMed

Chen, Hong-Ren; Tseng, Hsiao-Fen

2012-08-01

Web-based e-learning is not restricted by time or place and can provide teachers with a learning environment that is flexible and convenient, enabling them to efficiently learn, quickly develop their professional expertise, and advance professionally. Many research reports on web-based e-learning have neglected the role of the teacher's perspective in the acceptance of using web-based e-learning systems for in-service education. We distributed questionnaires to 402 junior high school teachers in central Taiwan. This study used the Technology Acceptance Model (TAM) as our theoretical foundation and employed the Structure Equation Model (SEM) to examine factors that influenced intentions to use in-service training conducted through web-based e-learning. The results showed that motivation to use and Internet self-efficacy were significantly positively associated with behavioral intentions regarding the use of web-based e-learning for in-service training through the factors of perceived usefulness and perceived ease of use. The factor of computer anxiety had a significantly negative effect on behavioral intentions toward web-based e-learning in-service training through the factor of perceived ease of use. Perceived usefulness and motivation to use were the primary reasons for the acceptance by junior high school teachers of web-based e-learning systems for in-service training. Copyright © 2011 Elsevier Ltd. All rights reserved.

Testing the efficacy of web-based cognitive behavioural therapy for adult patients with chronic fatigue syndrome (CBIT): study protocol for a randomized controlled trial.

PubMed

Janse, Anthonie; Worm-Smeitink, Margreet; Bussel-Lagarde, José; Bleijenberg, Gijs; Nikolaus, Stephanie; Knoop, Hans

2015-08-12

Cognitive behavioural therapy (CBT) is an effective treatment for fatigue and disabilities in patients with chronic fatigue syndrome (CFS). However, treatment capacity is limited. Providing web-based CBT and tailoring the amount of contact with the therapist to the individual needs of the patient may increase the efficiency of the intervention. Web-based CBT for adolescents with CFS has proven to be effective in reducing fatigue and increasing school attendance. In the proposed study the efficacy of a web-based CBT intervention for adult patients with CFS will be explored. Two different formats of web-based CBT will be tested. In the first format named protocol driven feedback, patients report on their progress and receive feedback from a therapist according to a preset schedule. In the second format named support on demand, feedback and support of the therapist is only given when patients ask for it. The primary objective of the study is to determine the efficacy of a web-based CBT intervention on fatigue severity. A randomized clinical trial will be conducted. Two-hundred-forty adults who have been diagnosed with CFS according to the US Centers for Disease Control and Prevention (CDC) consensus criteria will be recruited and randomized to one of three conditions: web-based CBT with protocol driven feedback, web-based CBT with support on demand, or wait list. Feedback will be delivered by therapists specialized in CBT for CFS. Each of the web-based CBT interventions will be compared to a wait list condition with respect to its effect on the primary outcome measure; fatigue severity. Secondary outcome measures are level of disability, physical functioning, psychological distress, and the proportion of patients with clinical significant improvement in fatigue severity. Outcomes will be assessed at baseline and six months post randomization. The web-based CBT formats will be compared with respect to the time therapists need to deliver the intervention. As far as we know this is the first randomized controlled trial (RCT) that evaluates the efficacy of a web-based CBT intervention for adult patients with CFS. NTR4013.

Overcoming Recruitment Challenges of Web-based Interventions for Tobacco Use: The Case of Web-based Acceptance and Commitment Therapy for Smoking Cessation

PubMed Central

Heffner, Jaimee L; Wyszynski, Christopher M; Comstock, Bryan; Mercer, Laina D.; Bricker, Jonathan

2013-01-01

Web-based behavioral interventions for substance use are being developed at a rapid pace, yet there is a dearth of information regarding the most effective methods for recruiting participants into web-based intervention trials. In this paper, we describe our successful recruitment of participants into a pilot trial of web-based Acceptance and Commitment Therapy (ACT) for smoking cessation and compare traditional and web-based methods of recruitment in terms of their effects on baseline participant characteristics, association with study retention and treatment outcome, yield, and cost-effectiveness. Over a 10-week period starting June 15, 2010, we recruited 222 smokers for a web-based smoking cessation study using a variety of recruitment methods. The largest portion of randomized participants were recruited through Google AdWords (36%), followed by medical Internet media (23%), standard media (14%), word of mouth (12%), broadcast emails (11%), and social media (6%). Recruitment source was not related to baseline participant characteristics, 3-month data retention, or 30-day point prevalence smoking abstinence at the 3-month outcome assessment. Cost per randomized participant ranged from $5.27/participant for word of mouth to $172.76/participant for social media, with a mean cost of $42.48/participant. Our diversified approach to recruitment, including both traditional and web-based methods, enabled timely enrollment of participants into the study. Because there was no evidence of a substantive difference in baseline characteristics, retention, or outcomes based on recruitment channel, the yield and cost-effectiveness of recruitment methods may be the more critical considerations in developing a feasible recruitment plan for a web-based smoking cessation intervention study. PMID:23770645

Overcoming recruitment challenges of web-based interventions for tobacco use: the case of web-based acceptance and commitment therapy for smoking cessation.

PubMed

Heffner, Jaimee L; Wyszynski, Christopher M; Comstock, Bryan; Mercer, Laina D; Bricker, Jonathan

2013-10-01

Web-based behavioral interventions for substance use are being developed at a rapid pace, yet there is a dearth of information regarding the most effective methods for recruiting participants into web-based intervention trials. In this paper, we describe our successful recruitment of participants into a pilot trial of web-based Acceptance and Commitment Therapy (ACT) for smoking cessation and compare traditional and web-based methods of recruitment in terms of their effects on baseline participant characteristics, association with study retention and treatment outcome, yield, and cost-effectiveness. Over a 10-week period starting June 15, 2010, we recruited 222 smokers for a web-based smoking cessation study using a variety of recruitment methods. The largest portion of randomized participants were recruited through Google AdWords (36%), followed by medical Internet media (23%), standard media (14%), word of mouth (12%), broadcast emails (11%), and social media (6%). Recruitment source was not related to baseline participant characteristics, 3-month data retention, or 30-day point prevalence smoking abstinence at the 3-month outcome assessment. Cost per randomized participant ranged from $5.27/participant for word of mouth to $172.76/participant for social media, with a mean cost of $42.48/participant. Our diversified approach to recruitment, including both traditional and web-based methods, enabled timely enrollment of participants into the study. Because there was no evidence of a substantive difference in baseline characteristics, retention, or outcomes based on recruitment channel, the yield and cost-effectiveness of recruitment methods may be the more critical considerations in developing a feasible recruitment plan for a web-based smoking cessation intervention study. Copyright © 2013 Elsevier Ltd. All rights reserved.

Web-Based Instruction, Learning Effectiveness and Learning Behavior: The Impact of Relatedness

ERIC Educational Resources Information Center

Shieh, Chich-Jen; Liao, Ying; Hu, Ridong

2013-01-01

This study aims to discuss the effects of Web-based Instruction and Learning Behavior on Learning Effectiveness. Web-based Instruction contains the dimensions of Active Learning, Simulation-based Learning, Interactive Learning, and Accumulative Learning; and, Learning Behavior covers Learning Approach, Learning Habit, and Learning Attitude. The…

Research and Development of Web-Based Virtual Online Classroom

ERIC Educational Resources Information Center

Yang, Zongkai; Liu, Qingtang

2007-01-01

To build a web-based virtual learning environment depends on information technologies, concerns technology supporting learning methods and theories. A web-based virtual online classroom is designed and developed based on learning theories and streaming media technologies. And it is composed of two parts: instructional communicating environment…

Trophic Interactions in Louisiana Salt Marshes: Combining Stomach Content, Stable Isotope, and Fatty Acid Approaches

NASA Astrophysics Data System (ADS)

Lopez-Duarte, P. C.; Able, K.; Fodrie, J.; McCann, M. J.; Melara, S.; Noji, C.; Olin, J.; Pincin, J.; Plank, K.; Polito, M. J.; Jensen, O.

2016-02-01

Multiple studies conducted over five years since the 2010 Macondo oil spill in the Gulf of Mexico indicate that oil impacts vary widely among taxonomic groups. For instance, fishes inhabiting the marsh surface show no clear differences in either community composition or population characteristics between oiled and unoiled sites, despite clear evidence of physiological impacts on individual fish. In contrast, marsh insects and spiders are sensitive to the effects of hydrocarbons. Both insects and spiders are components of the marsh food web and represent an important trophic link between marsh plants and higher trophic levels. Because differences in oil impacts throughout the marsh food web have the potential to significantly alter food webs and energy flow pathways and reduce food web resilience, our goal is to quantify differences in marsh food webs between oiled and unoiled sites to test the hypothesis that oiling has resulted in simpler and less resilient food webs. Diets and food web connections were quantified through a combination of stomach content, stable isotope, and fatty acid analysis. The combination of these three techniques provides a more robust approach to quantifying trophic relationships than any of these methods alone. Stomach content analysis provides a detailed snapshot of diets, while fatty acid and stable isotopes reflect diets averaged over weeks to months. Initial results focus on samples collected in May 2015 from a range of terrestrial and aquatic consumer species, including insects, mollusks, crustaceans, and piscivorous fishes.

Prerequisites required for the provision and use of web-based communication for psychosocial support in haematologic care.

PubMed

Högberg, K; Sandman, L; Nyström, M; Stockelberg, D; Broström, A

2013-10-01

The purpose of this study was to describe the prerequisites required for the provision and use of web-based communication for psychosocial support within a haematology clinic, from a patient and family perspective. A qualitative design using content analysis was used. A strategically selected sample of patients (n = 11) and family members (n = 6) were offered access to a web-based communication capability with a nurse. After four months, individual interviews were conducted with all participants, in order to identify necessary prerequisites. Preferences and characteristics of the individual patient or family member are crucial as to whether web-based communication for support is perceived as useful. To feel comfortable with writing and to self-identify the need for support are fundamental in getting motivated to use web-based communication. An effective organization around psychosocial support in general is another prerequisite. Goals and responsibilities must be clearly defined for patients and family members to understand their rights and enable the transformation of opportunities into practice. The use of web-based communication must also be a convenient and naturally incorporated part of both individual and organizational use of the web in general. Prerequisites of taking into account caretakers' different preferences and needs, providing highly structured psychosocial support activities and providing a congruent range of web services, are necessary for successful provision and use of web-based communication for psychosocial support. Copyright © 2013 Elsevier Ltd. All rights reserved.

SPIKE – a database, visualization and analysis tool of cellular signaling pathways

PubMed Central

Elkon, Ran; Vesterman, Rita; Amit, Nira; Ulitsky, Igor; Zohar, Idan; Weisz, Mali; Mass, Gilad; Orlev, Nir; Sternberg, Giora; Blekhman, Ran; Assa, Jackie; Shiloh, Yosef; Shamir, Ron

2008-01-01

Background Biological signaling pathways that govern cellular physiology form an intricate web of tightly regulated interlocking processes. Data on these regulatory networks are accumulating at an unprecedented pace. The assimilation, visualization and interpretation of these data have become a major challenge in biological research, and once met, will greatly boost our ability to understand cell functioning on a systems level. Results To cope with this challenge, we are developing the SPIKE knowledge-base of signaling pathways. SPIKE contains three main software components: 1) A database (DB) of biological signaling pathways. Carefully curated information from the literature and data from large public sources constitute distinct tiers of the DB. 2) A visualization package that allows interactive graphic representations of regulatory interactions stored in the DB and superposition of functional genomic and proteomic data on the maps. 3) An algorithmic inference engine that analyzes the networks for novel functional interplays between network components. SPIKE is designed and implemented as a community tool and therefore provides a user-friendly interface that allows registered users to upload data to SPIKE DB. Our vision is that the DB will be populated by a distributed and highly collaborative effort undertaken by multiple groups in the research community, where each group contributes data in its field of expertise. Conclusion The integrated capabilities of SPIKE make it a powerful platform for the analysis of signaling networks and the integration of knowledge on such networks with omics data. PMID:18289391

75 FR 19978 - Proposed Collection; Comment Request; Web Based Training for Pain Management Providers

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-16

..., information will be collected from health care providers before exposure to the Web based materials (pre-test), after exposure to the web based materials (post-test), and 4-6 weeks after the program has been...

[A web-based biomedical image mosaicing system].

PubMed

Zhang, Meng; Yan, Zhuang-zhi; Pan, Zhi-jun; Shao, Shi-jie

2006-11-01

This paper describes a web service for biomedical image mosaicing. A web site based on CGI (Common Gateway Interface) is implemented. The system is based on Browser/Server model and is tested in www. Finally implementation examples and experiment results are provided.

Web-Based Course Management and Web Services

ERIC Educational Resources Information Center

Mandal, Chittaranjan; Sinha, Vijay Luxmi; Reade, Christopher M. P.

2004-01-01

The architecture of a web-based course management tool that has been developed at IIT [Indian Institute of Technology], Kharagpur and which manages the submission of assignments is discussed. Both the distributed architecture used for data storage and the client-server architecture supporting the web interface are described. Further developments…

Visual Based Retrieval Systems and Web Mining--Introduction.

ERIC Educational Resources Information Center

Iyengar, S. S.

2001-01-01

Briefly discusses Web mining and image retrieval techniques, and then presents a summary of articles in this special issue. Articles focus on Web content mining, artificial neural networks as tools for image retrieval, content-based image retrieval systems, and personalizing the Web browsing experience using media agents. (AEF)

From Web 2.0 to Teacher 2.0

ERIC Educational Resources Information Center

Thomas, David A.; Li, Qing

2008-01-01

The World Wide Web is evolving in response to users who demand faster and more efficient access to information, portability, and reusability of digital objects between Web-based and computer-based applications and powerful communication, publication, collaboration, and teaching and learning tools. This article reviews current uses of Web-based…

On Building a Web-Based University

ERIC Educational Resources Information Center

Constantinescu, Dana; Stefansson, Gunnar

2010-01-01

This paper describes some of the principles for building a freely available web-based university with open content. The "tutor-web" is an international project for web-assisted education, including such free and open access. This project was initiated by the University of Iceland in partnership with many universities around the world,…

SoyBase Simple Semantic Web Architecture and Protocol (SSWAP) Services

USDA-ARS?s Scientific Manuscript database

Semantic web technologies offer the potential to link internet resources and data by shared concepts without having to rely on absolute lexical matches. Thus two web sites or web resources which are concerned with similar data types could be identified based on similar semantics. In the biological...

Web-based Interspecies Correlation Estimation (Web-ICE) for Acute Toxicity: User Manual Version 3.1

EPA Science Inventory

Predictive toxicological models are integral to ecological risk assessment because data for most species are limited. Web-based Interspecies Correlation Estimation (Web-ICE) models are least square regressions that predict acute toxicity (LC50/LD50) of a chemical to a species, ge...

WEB-BASED INTERSPECIES CORRELATION ESTIMATION (WEB-ICE) FOR ACUTE TOXICITY: USER MANUAL V2

EPA Science Inventory

Predictive toxicological models are integral to environmental risk Assessment where data for most species are limited. Web-based Interspecies Correlation Estimation (Web-ICE) models are least square regressions that predict acute toxicity (LC50/LD50) of a chemical to a species, ...

Carbon flows in the benthic food web at the deep-sea observatory HAUSGARTEN (Fram Strait)

NASA Astrophysics Data System (ADS)

van Oevelen, Dick; Bergmann, Melanie; Soetaert, Karline; Bauerfeind, Eduard; Hasemann, Christiane; Klages, Michael; Schewe, Ingo; Soltwedel, Thomas; Budaeva, Nataliya E.

2011-11-01

The HAUSGARTEN observatory is located in the eastern Fram Strait (Arctic Ocean) and used as long-term monitoring site to follow changes in the Arctic benthic ecosystem. Linear inverse modelling was applied to decipher carbon flows among the compartments of the benthic food web at the central HAUSGARTEN station (2500 m) based on an empirical data set consisting of data on biomass, prokaryote production, total carbon deposition and community respiration. The model resolved 99 carbon flows among 4 abiotic and 10 biotic compartments, ranging from prokaryotes up to megafauna. Total carbon input was 3.78±0.31 mmol C m -2 d -1, which is a comparatively small fraction of total primary production in the area. The community respiration of 3.26±0.20 mmol C m -2 d -1 is dominated by prokaryotes (93%) and has lower contributions from surface-deposit feeding macro- (1.7%) and suspension feeding megafauna (1.9%), whereas contributions from nematode and other macro- and megabenthic compartments were limited to <1%. The high prokaryotic contribution to carbon processing suggests that functioning of the benthic food web at the central HAUSGARTEN station is comparable to abyssal plain sediments that are characterised by strong energy limitation. Faunal diet compositions suggest that labile detritus is important for deposit-feeding nematodes (24% of their diet) and surface-deposit feeding macrofauna (˜44%), but that semi-labile detritus is more important in the diets of deposit-feeding macro- and megafauna. Dependency indices on these food sources were also calculated as these integrate direct (i.e. direct grazing and predator-prey interactions) and indirect (i.e. longer loops in the food web) pathways in the food web. Projected sea-ice retreats for the Arctic Ocean typically anticipate a decrease in the labile detritus flux to the already food-limited benthic food web. The dependency indices indicate that faunal compartments depend similarly on labile and semi-labile detritus, which suggests that the benthic biota may be more sensitive to changes in labile detritus inputs than when assessed from diet composition alone. Species-specific responses to different types of labile detritus inputs, e.g. pelagic algae versus sympagic algae, however, are presently unknown and are needed to assess the vulnerability of individual components of the benthic food web.

A Software Engineering Approach based on WebML and BPMN to the Mediation Scenario of the SWS Challenge

NASA Astrophysics Data System (ADS)

Brambilla, Marco; Ceri, Stefano; Valle, Emanuele Della; Facca, Federico M.; Tziviskou, Christina

Although Semantic Web Services are expected to produce a revolution in the development of Web-based systems, very few enterprise-wide design experiences are available; one of the main reasons is the lack of sound Software Engineering methods and tools for the deployment of Semantic Web applications. In this chapter, we present an approach to software development for the Semantic Web based on classical Software Engineering methods (i.e., formal business process development, computer-aided and component-based software design, and automatic code generation) and on semantic methods and tools (i.e., ontology engineering, semantic service annotation and discovery).

Web-based versus traditional paper questionnaires: a mixed-mode survey with a Nordic perspective.

PubMed

Hohwü, Lena; Lyshol, Heidi; Gissler, Mika; Jonsson, Stefan Hrafn; Petzold, Max; Obel, Carsten

2013-08-26

Survey response rates have been declining over the past decade. The more widespread use of the Internet and Web-based technologies among potential health survey participants suggests that Web-based questionnaires may be an alternative to paper questionnaires in future epidemiological studies. To compare response rates in a population of parents by using 4 different modes of data collection for a questionnaire survey of which 1 involved a nonmonetary incentive. A random sample of 3148 parents of Danish children aged 2-17 years were invited to participate in the Danish part of the NordChild 2011 survey on their children's health and welfare. NordChild was conducted in 1984 and 1996 in collaboration with Finland, Iceland, Norway, and Sweden using mailed paper questionnaires only. In 2011, all countries used conventional paper versions only except Denmark where the parents were randomized into 4 groups: (1) 789 received a paper questionnaire only (paper), (2) 786 received the paper questionnaire and a log-in code to the Web-based questionnaire (paper/Web), (3) 787 received a log-in code to the Web-based questionnaire (Web), and (4) 786 received log-in details to the Web-based questionnaire and were given an incentive consisting of a chance to win a tablet computer (Web/tablet). In connection with the first reminder, the nonresponders in the paper, paper/Web, and Web groups were also present with the opportunity to win a tablet computer as a means of motivation. Descriptive analysis was performed using chi-square tests. Odds ratios were used to estimate differences in response rates between the 4 modes. In 2011, 1704 of 3148 (54.13%) respondents answered the Danish questionnaire. The highest response rate was with the paper mode (n=443, 56.2%). The other groups had similar response rates: paper/Web (n=422, 53.7%), Web (n=420, 53.4%), and Web/tablet (n=419, 53.3%) modes. Compared to the paper mode, the odds for response rate in the paper/Web decreased by 9% (OR 0.91, 95% CI 0.74-1.10) and by 11% (OR 0.89, 95% CI 0.73-1.09) in the Web and Web/tablet modes. The total number of responders for NordChild declined from 10,291 of 15,339 (67.09%) in 1984 and 10,667 of 15,254 (69.93%) in 1996 to 7805 of 15,945 (48.95%) in 2011 with similar declines in all 5 Nordic countries. Web-based questionnaires could replace traditional paper questionnaires with minor effects on response rates and lower costs. The increasing effect on the response rate on participants replying for a nonmonetary incentive could only be estimated within the 2 Web-based questionnaire modes before the first reminder. Alternative platforms to reach higher participation rates in population surveys should reflect the development of electronic devices and the ways in which the population primarily accesses the Internet.

Web-Based Versus Traditional Paper Questionnaires: A Mixed-Mode Survey With a Nordic Perspective

PubMed Central

Lyshol, Heidi; Gissler, Mika; Jonsson, Stefan Hrafn; Petzold, Max; Obel, Carsten

2013-01-01

Background Survey response rates have been declining over the past decade. The more widespread use of the Internet and Web-based technologies among potential health survey participants suggests that Web-based questionnaires may be an alternative to paper questionnaires in future epidemiological studies. Objective To compare response rates in a population of parents by using 4 different modes of data collection for a questionnaire survey of which 1 involved a nonmonetary incentive. Methods A random sample of 3148 parents of Danish children aged 2-17 years were invited to participate in the Danish part of the NordChild 2011 survey on their children’s health and welfare. NordChild was conducted in 1984 and 1996 in collaboration with Finland, Iceland, Norway, and Sweden using mailed paper questionnaires only. In 2011, all countries used conventional paper versions only except Denmark where the parents were randomized into 4 groups: (1) 789 received a paper questionnaire only (paper), (2) 786 received the paper questionnaire and a log-in code to the Web-based questionnaire (paper/Web), (3) 787 received a log-in code to the Web-based questionnaire (Web), and (4) 786 received log-in details to the Web-based questionnaire and were given an incentive consisting of a chance to win a tablet computer (Web/tablet). In connection with the first reminder, the nonresponders in the paper, paper/Web, and Web groups were also present with the opportunity to win a tablet computer as a means of motivation. Descriptive analysis was performed using chi-square tests. Odds ratios were used to estimate differences in response rates between the 4 modes. Results In 2011, 1704 of 3148 (54.13%) respondents answered the Danish questionnaire. The highest response rate was with the paper mode (n=443, 56.2%). The other groups had similar response rates: paper/Web (n=422, 53.7%), Web (n=420, 53.4%), and Web/tablet (n=419, 53.3%) modes. Compared to the paper mode, the odds for response rate in the paper/Web decreased by 9% (OR 0.91, 95% CI 0.74-1.10) and by 11% (OR 0.89, 95% CI 0.73-1.09) in the Web and Web/tablet modes. The total number of responders for NordChild declined from 10,291 of 15,339 (67.09%) in 1984 and 10,667 of 15,254 (69.93%) in 1996 to 7805 of 15,945 (48.95%) in 2011 with similar declines in all 5 Nordic countries. Conclusions Web-based questionnaires could replace traditional paper questionnaires with minor effects on response rates and lower costs. The increasing effect on the response rate on participants replying for a nonmonetary incentive could only be estimated within the 2 Web-based questionnaire modes before the first reminder. Alternative platforms to reach higher participation rates in population surveys should reflect the development of electronic devices and the ways in which the population primarily accesses the Internet. PMID:23978658

IntPath--an integrated pathway gene relationship database for model organisms and important pathogens

PubMed Central

2012-01-01

Background Pathway data are important for understanding the relationship between genes, proteins and many other molecules in living organisms. Pathway gene relationships are crucial information for guidance, prediction, reference and assessment in biochemistry, computational biology, and medicine. Many well-established databases--e.g., KEGG, WikiPathways, and BioCyc--are dedicated to collecting pathway data for public access. However, the effectiveness of these databases is hindered by issues such as incompatible data formats, inconsistent molecular representations, inconsistent molecular relationship representations, inconsistent referrals to pathway names, and incomprehensive data from different databases. Results In this paper, we overcome these issues through extraction, normalization and integration of pathway data from several major public databases (KEGG, WikiPathways, BioCyc, etc). We build a database that not only hosts our integrated pathway gene relationship data for public access but also maintains the necessary updates in the long run. This public repository is named IntPath (Integrated Pathway gene relationship database for model organisms and important pathogens). Four organisms--S. cerevisiae, M. tuberculosis H37Rv, H. Sapiens and M. musculus--are included in this version (V2.0) of IntPath. IntPath uses the "full unification" approach to ensure no deletion and no introduced noise in this process. Therefore, IntPath contains much richer pathway-gene and pathway-gene pair relationships and much larger number of non-redundant genes and gene pairs than any of the single-source databases. The gene relationships of each gene (measured by average node degree) per pathway are significantly richer. The gene relationships in each pathway (measured by average number of gene pairs per pathway) are also considerably richer in the integrated pathways. Moderate manual curation are involved to get rid of errors and noises from source data (e.g., the gene ID errors in WikiPathways and relationship errors in KEGG). We turn complicated and incompatible xml data formats and inconsistent gene and gene relationship representations from different source databases into normalized and unified pathway-gene and pathway-gene pair relationships neatly recorded in simple tab-delimited text format and MySQL tables, which facilitates convenient automatic computation and large-scale referencing in many related studies. IntPath data can be downloaded in text format or MySQL dump. IntPath data can also be retrieved and analyzed conveniently through web service by local programs or through web interface by mouse clicks. Several useful analysis tools are also provided in IntPath. Conclusions We have overcome in IntPath the issues of compatibility, consistency, and comprehensiveness that often hamper effective use of pathway databases. We have included four organisms in the current release of IntPath. Our methodology and programs described in this work can be easily applied to other organisms; and we will include more model organisms and important pathogens in future releases of IntPath. IntPath maintains regular updates and is freely available at http://compbio.ddns.comp.nus.edu.sg:8080/IntPath. PMID:23282057

Designing and Evaluating an Interactive Multimedia Web-Based Simulation for Developing Nurses’ Competencies in Acute Nursing Care: Randomized Controlled Trial

PubMed Central

Wong, Lai Fun; Chan, Sally Wai-Chi; Ho, Jasmine Tze Yin; Mordiffi, Siti Zubaidah; Ang, Sophia Bee Leng; Goh, Poh Sun; Ang, Emily Neo Kim

2015-01-01

Background Web-based learning is becoming an increasingly important instructional tool in nursing education. Multimedia advancements offer the potential for creating authentic nursing activities for developing nursing competency in clinical practice. Objective This study aims to describe the design, development, and evaluation of an interactive multimedia Web-based simulation for developing nurses’ competencies in acute nursing care. Methods Authentic nursing activities were developed in a Web-based simulation using a variety of instructional strategies including animation video, multimedia instructional material, virtual patients, and online quizzes. A randomized controlled study was conducted on 67 registered nurses who were recruited from the general ward units of an acute care tertiary hospital. Following a baseline evaluation of all participants’ clinical performance in a simulated clinical setting, the experimental group received 3 hours of Web-based simulation and completed a survey to evaluate their perceptions of the program. All participants were re-tested for their clinical performances using a validated tool. Results The clinical performance posttest scores of the experimental group improved significantly (P<.001) from the pretest scores after the Web-based simulation. In addition, compared to the control group, the experimental group had significantly higher clinical performance posttest scores (P<.001) after controlling the pretest scores. The participants from the experimental group were satisfied with their learning experience and gave positive ratings for the quality of the Web-based simulation. Themes emerging from the comments about the most valuable aspects of the Web-based simulation include relevance to practice, instructional strategies, and fostering problem solving. Conclusions Engaging in authentic nursing activities using interactive multimedia Web-based simulation can enhance nurses’ competencies in acute care. Web-based simulations provide a promising educational tool in institutions where large groups of nurses need to be trained in acute nursing care and accessibility to repetitive training is essential for achieving long-term retention of clinical competency. PMID:25583029

General Practitioners' Attitudes Toward a Web-Based Mental Health Service for Adolescents: Implications for Service Design and Delivery.

PubMed

Subotic-Kerry, Mirjana; King, Catherine; O'Moore, Kathleen; Achilles, Melinda; O'Dea, Bridianne

2018-03-23

Anxiety disorders and depression are prevalent among youth. General practitioners (GPs) are often the first point of professional contact for treating health problems in young people. A Web-based mental health service delivered in partnership with schools may facilitate increased access to psychological care among adolescents. However, for such a model to be implemented successfully, GPs' views need to be measured. This study aimed to examine the needs and attitudes of GPs toward a Web-based mental health service for adolescents, and to identify the factors that may affect the provision of this type of service and likelihood of integration. Findings will inform the content and overall service design. GPs were interviewed individually about the proposed Web-based service. Qualitative analysis of transcripts was performed using thematic coding. A short follow-up questionnaire was delivered to assess background characteristics, level of acceptability, and likelihood of integration of the Web-based mental health service. A total of 13 GPs participated in the interview and 11 completed a follow-up online questionnaire. Findings suggest strong support for the proposed Web-based mental health service. A wide range of factors were found to influence the likelihood of GPs integrating a Web-based service into their clinical practice. Coordinated collaboration with parents, students, school counselors, and other mental health care professionals were considered important by nearly all GPs. Confidence in Web-based care, noncompliance of adolescents and GPs, accessibility, privacy, and confidentiality were identified as potential barriers to adopting the proposed Web-based service. GPs were open to a proposed Web-based service for the monitoring and management of anxiety and depression in adolescents, provided that a collaborative approach to care is used, the feedback regarding the client is clear, and privacy and security provisions are assured. ©Mirjana Subotic-Kerry, Catherine King, Kathleen O'Moore, Melinda Achilles, Bridianne O'Dea. Originally published in JMIR Human Factors (http://humanfactors.jmir.org), 23.03.2018.

Designing and evaluating an interactive multimedia Web-based simulation for developing nurses' competencies in acute nursing care: randomized controlled trial.

PubMed

Liaw, Sok Ying; Wong, Lai Fun; Chan, Sally Wai-Chi; Ho, Jasmine Tze Yin; Mordiffi, Siti Zubaidah; Ang, Sophia Bee Leng; Goh, Poh Sun; Ang, Emily Neo Kim

2015-01-12

Web-based learning is becoming an increasingly important instructional tool in nursing education. Multimedia advancements offer the potential for creating authentic nursing activities for developing nursing competency in clinical practice. This study aims to describe the design, development, and evaluation of an interactive multimedia Web-based simulation for developing nurses' competencies in acute nursing care. Authentic nursing activities were developed in a Web-based simulation using a variety of instructional strategies including animation video, multimedia instructional material, virtual patients, and online quizzes. A randomized controlled study was conducted on 67 registered nurses who were recruited from the general ward units of an acute care tertiary hospital. Following a baseline evaluation of all participants' clinical performance in a simulated clinical setting, the experimental group received 3 hours of Web-based simulation and completed a survey to evaluate their perceptions of the program. All participants were re-tested for their clinical performances using a validated tool. The clinical performance posttest scores of the experimental group improved significantly (P<.001) from the pretest scores after the Web-based simulation. In addition, compared to the control group, the experimental group had significantly higher clinical performance posttest scores (P<.001) after controlling the pretest scores. The participants from the experimental group were satisfied with their learning experience and gave positive ratings for the quality of the Web-based simulation. Themes emerging from the comments about the most valuable aspects of the Web-based simulation include relevance to practice, instructional strategies, and fostering problem solving. Engaging in authentic nursing activities using interactive multimedia Web-based simulation can enhance nurses' competencies in acute care. Web-based simulations provide a promising educational tool in institutions where large groups of nurses need to be trained in acute nursing care and accessibility to repetitive training is essential for achieving long-term retention of clinical competency.