Water-resources data for the United States: water year 2008

USGS Publications Warehouse

,

2008-01-01

Water resources data are published annually for use by engineers, scientists, managers, educators, and the general public. These archival products supplement direct access to current and historical water data provided by NWISWeb. Beginning with Water Year 2006, annual water data reports are available as individual electronic Site Data Sheets for the entire Nation for retrieval, download, and localized printing on demand. National distribution includes tabular and map interfaces for search, query, display and download of data. From 1962 until 2005, reports were published by State as paper documents, although most reports since the mid-1990s are also available in electronic form through this web page. Reports prior to 1962 were published in occasional USGS Water-Supply Papers and other reports.

Siberian Earth System Science Cluster - A web-based Geoportal to provide user-friendly Earth Observation Products for supporting NEESPI scientists

NASA Astrophysics Data System (ADS)

Eberle, J.; Gerlach, R.; Hese, S.; Schmullius, C.

2012-04-01

To provide earth observation products in the area of Siberia, the Siberian Earth System Science Cluster (SIB-ESS-C) was established as a spatial data infrastructure at the University of Jena (Germany), Department for Earth Observation. This spatial data infrastructure implements standards published by the Open Geospatial Consortium (OGC) and the International Organizsation for Standardization (ISO) for data discovery, data access, data processing and data analysis. The objective of SIB-ESS-C is to faciliate environmental research and Earth system science in Siberia. The region for this project covers the entire Asian part of the Russian Federation approximately between 58°E - 170°W and 48°N - 80°N. To provide discovery, access and analysis services a webportal was published for searching and visualisation of available data. This webportal is based on current web technologies like AJAX, Drupal Content Management System as backend software and a user-friendly surface with Drag-n-Drop and further mouse events. To have a wide range of regular updated earth observation products, some products from sensor MODIS at the satellites Aqua and Terra were processed. A direct connection to NASA archive servers makes it possible to download MODIS Level 3 and 4 products and integrate it in the SIB-ESS-C infrastructure. These data can be downloaded in a file format called Hierarchical Data Format (HDF). For visualisation and further analysis, this data is reprojected, converted to GeoTIFF and global products clipped to the project area. All these steps are implemented as an automatic process chain. If new MODIS data is available within the infrastructure this process chain is executed. With the link to a MODIS catalogue system, the system gets new data daily. With the implemented analysis processes, timeseries data can be analysed, for example to plot a trend or different time series against one another. Scientists working in this area and working with MODIS data can make use of this service over the webportal. Both searching manually the NASA archive for MODIS data, processing these data automatically and then download it for further processing and using the regular updated products.

Recent trends in biomedical informatics: a study based on JAMIA articles

PubMed Central

Jiang, Xiaoqian; Tse, Krystal; Wang, Shuang; Doan, Son; Kim, Hyeoneui; Ohno-Machado, Lucila

2013-01-01

In a growing interdisciplinary field like biomedical informatics, information dissemination and citation trends are changing rapidly due to many factors. To understand these factors better, we analyzed the evolution of the number of articles per major biomedical informatics topic, download/online view frequencies, and citation patterns (using Web of Science) for articles published from 2009 to 2012 in JAMIA. The number of articles published in JAMIA increased significantly from 2009 to 2012, and there were some topic differences in the last 4 years. Medical Record Systems, Algorithms, and Methods are topic categories that are growing fast in several publications. We observed a significant correlation between download frequencies and the number of citations per month since publication for a given article. Earlier free availability of articles to non-subscribers was associated with a higher number of downloads and showed a trend towards a higher number of citations. This trend will need to be verified as more data accumulate in coming years. PMID:24214018

If I tweet will you cite? The effect of social media exposure of articles on downloads and citations.

PubMed

Tonia, Thomy; Van Oyen, Herman; Berger, Anke; Schindler, Christian; Künzli, Nino

2016-05-01

We sought to investigate whether exposing scientific papers to social media (SM) has an effect on article downloads and citations. We randomized all International Journal of Public Health (IJPH) original articles published between December 2012 and December 2014 to SM exposure (blog post, Twitter and Facebook) or no exposure at three different time points after first online publication. 130 papers (SM exposure = 65, control = 65) were randomized. The number of downloads did not differ significantly between groups (p = 0.60) nor did the number of citations (p = 0.88). Adjusting for length of observation and paper's geographical origin did not change these results. There was no difference in the number of downloads and citations between the SM exposure and control group when we stratified for open access status. The number of downloads and number of citations were significantly correlated in both groups. SM exposure did not have a significant effect on traditional impact metrics, such as downloads and citations. However, other metrics may measure the added value that social media might offer to a scientific journal, such as wider dissemination.

Practical Downloading to Desktop Publishing: Enhancing the Delivery of Information.

ERIC Educational Resources Information Center

Danziger, Pamela N.

This paper is addressed to librarians and information managers who, as one of the many activities they routinely perform, frequently publish information in such formats as newsletters, manuals, brochures, forms, presentations, or reports. It is argued that desktop publishing--a personal computer-based software package used to generate documents of…

Indicators for the Data Usage Index (DUI): an incentive for publishing primary biodiversity data through global information infrastructure

PubMed Central

2011-01-01

Background A professional recognition mechanism is required to encourage expedited publishing of an adequate volume of 'fit-for-use' biodiversity data. As a component of such a recognition mechanism, we propose the development of the Data Usage Index (DUI) to demonstrate to data publishers that their efforts of creating biodiversity datasets have impact by being accessed and used by a wide spectrum of user communities. Discussion We propose and give examples of a range of 14 absolute and normalized biodiversity dataset usage indicators for the development of a DUI based on search events and dataset download instances. The DUI is proposed to include relative as well as species profile weighted comparative indicators. Conclusions We believe that in addition to the recognition to the data publisher and all players involved in the data life cycle, a DUI will also provide much needed yet novel insight into how users use primary biodiversity data. A DUI consisting of a range of usage indicators obtained from the GBIF network and other relevant access points is within reach. The usage of biodiversity datasets leads to the development of a family of indicators in line with well known citation-based measurements of recognition. PMID:22373200

Quantum information processing with trapped electrons and superconducting electronics (Open Access, Publisher’s Version)

DTIC Science & Technology

2013-07-05

This content has been downloaded from IOPscience. Please scroll down to see the full text. Download details: IP Address: 198.81.129.186 This content...structures with a quadratic nonlinearity, i.e. electrodes with a quadrupolar potential. The pump for this parametric coupling process is a classical...approximation. The system operates as a parametric frequency converter, with the classical drive providing pump photons which allow coherent coupling between

40 CFR 1042.130 - Installation instructions for vessel manufacturers.

Code of Federal Regulations, 2010 CFR

2010-07-01

... engine in a way that makes the engine's emission control information label hard to read during normal... equivalent format. For example, you may post instructions on a publicly available Web site for downloading or...

Milestones and impact factors.

PubMed

Ozonoff, David M; Grandjean, Philippe

2010-07-08

Environmental Health has just received its first Impact Factor by Thomson ISI. At a level of 2.48, this achievement is quite satisfactory and places Environmental Health in the top 25% of environmental science journals. When the journal was launched in 2002, it was still unclear whether the Open Access publishing model could be made into a viable commercial enterprise within the biomedical field. During the past eight years, Open Access journals have become widely available, although still covering only about 15% of journal titles. Major funding agencies and institutions, including prominent US universities, now require that researchers publish in Open Access journals. Because of the profound role of scientific journals for the sharing of results and communication between researchers, the advent of Open Access may be of as much significance as the transition from handwriting to printing via moveable type. As Environmental Health is an electronic Open Access journal, the numbers of downloads at the journal website can be retrieved. The top-20 list of articles most frequently accessed shows that all of them have been downloaded over 10,000 times. Back in 2002, the first article published was accessed only 49 times during the following month. A year later, the server had over 1,000 downloads per month, and now the total number of monthly downloads approaches 50,000. These statistics complement the Impact Factor and confirm the viability of Open Access in our field of research. The advent of digital media and its decentralized mode of distribution - the internet - have dramatically changed the control and financing of scientific information dissemination, while facilitating peer review, accelerating editorial handling, and supporting much needed transparency. Both the meaning and means of "having an impact" are therefore changing, as will the degree and way in which scientific journals remain "factors" in that impact.

Milestones and Impact Factors

PubMed Central

2010-01-01

Environmental Health has just received its first Impact Factor by Thomson ISI. At a level of 2.48, this achievement is quite satisfactory and places Environmental Health in the top 25% of environmental science journals. When the journal was launched in 2002, it was still unclear whether the Open Access publishing model could be made into a viable commercial enterprise within the biomedical field. During the past eight years, Open Access journals have become widely available, although still covering only about 15% of journal titles. Major funding agencies and institutions, including prominent US universities, now require that researchers publish in Open Access journals. Because of the profound role of scientific journals for the sharing of results and communication between researchers, the advent of Open Access may be of as much significance as the transition from handwriting to printing via moveable type. As Environmental Health is an electronic Open Access journal, the numbers of downloads at the journal website can be retrieved. The top-20 list of articles most frequently accessed shows that all of them have been downloaded over 10,000 times. Back in 2002, the first article published was accessed only 49 times during the following month. A year later, the server had over 1,000 downloads per month, and now the total number of monthly downloads approaches 50,000. These statistics complement the Impact Factor and confirm the viability of Open Access in our field of research. The advent of digital media and its decentralized mode of distribution - the internet - have dramatically changed the control and financing of scientific information dissemination, while facilitating peer review, accelerating editorial handling, and supporting much needed transparency. Both the meaning and means of "having an impact" are therefore changing, as will the degree and way in which scientific journals remain "factors" in that impact. PMID:20615249

AquaPathogen X--A template database for tracking field isolates of aquatic pathogens

USGS Publications Warehouse

Emmenegger, Evi; Kurath, Gael

2012-01-01

AquaPathogen X is a template database for recording information on individual isolates of aquatic pathogens and is available for download from the U.S. Geological Survey (USGS) Western Fisheries Research Center (WFRC) website (http://wfrc.usgs.gov). This template database can accommodate the nucleotide sequence data generated in molecular epidemiological studies along with the myriad of abiotic and biotic traits associated with isolates of various pathogens (for example, viruses, parasites, or bacteria) from multiple aquatic animal host species (for example, fish, shellfish, or shrimp). The simultaneous cataloging of isolates from different aquatic pathogens is a unique feature to the AquaPathogen X database, which can be used in surveillance of emerging aquatic animal diseases and clarification of main risk factors associated with pathogen incursions into new water systems. As a template database, the data fields are empty upon download and can be modified to user specifications. For example, an application of the template database that stores the epidemiological profiles of fish virus isolates, called Fish ViroTrak (fig. 1), was also developed (Emmenegger and others, 2011).

40 CFR 1045.130 - What installation instructions must I give to vessel manufacturers?

Code of Federal Regulations, 2010 CFR

2010-07-01

... engine's emission control information label hard to read during normal engine maintenance, you must place... equivalent format. For example, you may post instructions on a publicly available Web site for downloading or...

Spatial Digital Database for the Geologic Map of Oregon

USGS Publications Warehouse

Walker, George W.; MacLeod, Norman S.; Miller, Robert J.; Raines, Gary L.; Connors, Katherine A.

2003-01-01

Introduction This report describes and makes available a geologic digital spatial database (orgeo) representing the geologic map of Oregon (Walker and MacLeod, 1991). The original paper publication was printed as a single map sheet at a scale of 1:500,000, accompanied by a second sheet containing map unit descriptions and ancillary data. A digital version of the Walker and MacLeod (1991) map was included in Raines and others (1996). The dataset provided by this open-file report supersedes the earlier published digital version (Raines and others, 1996). This digital spatial database is one of many being created by the U.S. Geological Survey as an ongoing effort to provide geologic information for use in spatial analysis in a geographic information system (GIS). This database can be queried in many ways to produce a variety of geologic maps. This database is not meant to be used or displayed at any scale larger than 1:500,000 (for example, 1:100,000). This report describes the methods used to convert the geologic map data into a digital format, describes the ArcInfo GIS file structures and relationships, and explains how to download the digital files from the U.S. Geological Survey public access World Wide Web site on the Internet. Scanned images of the printed map (Walker and MacLeod, 1991), their correlation of map units, and their explanation of map symbols are also available for download.

DeepBlue epigenomic data server: programmatic data retrieval and analysis of epigenome region sets.

PubMed

Albrecht, Felipe; List, Markus; Bock, Christoph; Lengauer, Thomas

2016-07-08

Large amounts of epigenomic data are generated under the umbrella of the International Human Epigenome Consortium, which aims to establish 1000 reference epigenomes within the next few years. These data have the potential to unravel the complexity of epigenomic regulation. However, their effective use is hindered by the lack of flexible and easy-to-use methods for data retrieval. Extracting region sets of interest is a cumbersome task that involves several manual steps: identifying the relevant experiments, downloading the corresponding data files and filtering the region sets of interest. Here we present the DeepBlue Epigenomic Data Server, which streamlines epigenomic data analysis as well as software development. DeepBlue provides a comprehensive programmatic interface for finding, selecting, filtering, summarizing and downloading region sets. It contains data from four major epigenome projects, namely ENCODE, ROADMAP, BLUEPRINT and DEEP. DeepBlue comes with a user manual, examples and a well-documented application programming interface (API). The latter is accessed via the XML-RPC protocol supported by many programming languages. To demonstrate usage of the API and to enable convenient data retrieval for non-programmers, we offer an optional web interface. DeepBlue can be openly accessed at http://deepblue.mpi-inf.mpg.de. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Electronic Books: A Major Publishing Revolution. Part 1: General Considerations and Issues.

ERIC Educational Resources Information Center

Hawkins, Donald T.

2000-01-01

Discusses electronic books and their impact on the publishing industry. Topics include a history of the book industry; downloadable ebooks; dedicated ebook readers; Web-accessible ebooks; print-on-demand books; advantages and disadvantages; copyright; ebook concerns in libraries, including licensing, lack of standards, bibliographic control, and…

Alternative Fuels Data Center: About the Laws and Incentives Data

Science.gov Websites

... Search Federal State Local Examples Summary Tables About the Laws and Incentives Data Download Data You final rules. Existing information is reviewed at the same time new information is added to ensure it is

Distributed Structure-Searchable Toxicity (DSSTox) Database

EPA Pesticide Factsheets

The Distributed Structure-Searchable Toxicity network provides a public forum for publishing downloadable, structure-searchable, standardized chemical structure files associated with chemical inventories or toxicity data sets of environmental relevance.

Using Biblio-Link...For Those Other Databases.

ERIC Educational Resources Information Center

Joy, Albert

1989-01-01

Sidebar describes the use of the Biblio-Link software packages to download citations from online databases and convert them into a form that can be automatically uploaded into a Pro-Cite database. An example of this procedure using DIALOG2 is given. (CLB)

Selecting Full-Text Undergraduate Periodicals Databases.

ERIC Educational Resources Information Center

Still, Julie M.; Kassabian, Vibiana

1999-01-01

Examines how libraries and librarians can compare full-text general periodical indices, using ProQuest Direct, Periodical Abstracts (via Ovid), and EBSCOhost as examples. Explores breadth and depth of coverage; manipulation of results (email/download/print); ease of use (searching); and indexing quirks. (AEF)

Heroin

MedlinePlus

... View Online Download PDF Monitoring the Future 2015 Survey Results Published: December 16, 2015 NIH’s 2015 Monitoring ... the National Drug and Alcohol Facts Week logo design are registered marks of the U.S. Department of ...

Inhalants

MedlinePlus

... View Online Download PDF Monitoring the Future 2015 Survey Results Published: December 16, 2015 NIH’s 2015 Monitoring ... the National Drug and Alcohol Facts Week logo design are registered marks of the U.S. Department of ...

AAS Publishing News: Preparing Your Manuscript Just Got Easier

NASA Astrophysics Data System (ADS)

Kohler, Susanna

2016-03-01

Watermarking using the command watermark{DRAFT, v2}.Are you an astronomer considering submitting a paper to an AAS journal (i.e., AJ, ApJ, ApJ Letters, or ApJ Supplements)? If so, this post is for you! Read on to find out about the exciting new things you can do with the AASs newest LaTeX class file, available for download now.Why the Update?AAS publishing has maintained a consistent class file for LaTeX manuscript preparation for the past decade. But academic publishing is changing rapidly in todays era of electronic journals! Since its journals went fully electronic, the AAS has been continuously adding new publishing capabilities based on the recommendations of the Journals Task Force and the needs and requests of AAS authors. The AASs manuscript preparation tools are now being updated accordingly.Whats New in AASTex 6.0?There are many exciting new features and capabilities in AASTex 6.0. Here are just a few:Tracking options for author revisions include added{text}, deleted{text}, replaced{old}{new}, and explain{text}.Based on emulateapjDo you use the popular class file emulateapj to prepare your manuscripts? AASTex 6.0 is based on emulateapj, rather than on the older AASTex 5.2 (though 5.2 is still supported). This means that it is easy to produce a double-columned, single-spaced, and astro-ph-ready manuscript. Since two thirds of the AAS journals authors use emulateapj, this transition was designed to make manuscript preparation and sharing an easier and more seamless process.Tools for collaborationsDo you work in a large collaboration? AASTex now includes new tools to make preparing a manuscript within a collaboration easier. Drafts can now be watermarked to differentiate between versions. New markup for large author lists streamlines the display so that readers can access article information immediately, yet they can still access the full author list and affiliations at the end of the paper. And author revision markup allows members of a collaboration to track their edits within a manuscript, for clearer organization of versions and edits.An example figure set, which the reader can download as a .tar.gz high-resolution set or as PowerPoint slides.Additional figure supportDo you have a lot of similar figures that youd like associated with the electronic journal article but dont all need to be included in the article pdf? New support is now available for figure sets, which allow readers efficient access to the full set of images without slowing down their ability to read your article. In addition, AASTex 6.0 now offers new markup for displaying figures in a grid, providing authors with more control over figure placement.New features for tablesDo you frequently work with large data tables? You might be especially happy with the changes in table-handling in AASTex 6.0. Now you can automatically number columns, hide columns with a single command, specify math mode automatically for a designated column, control decimal alignment, and even split wide tables into multiple parts.Example use of the new software command.Software citation supportDo you want to cite software and third-party repositories within your articles? With AASTex 6.0, theres now a software command that can be used to highlight and link to software that you used in your work. In addition, the ApJ BibTeX style file has been updated to support software citation.Where Can You Get More Information?Learn more about AASTex 6.0Watch a video presentation about AASTex 6.0 by AAS Data Scientist Greg SchwarzDownload AASTex 6.0Wishing for still more improvements?The AAS publishing team would love your input! You can contact them at aastex-help@aas.org with additional suggestions or ideas for the next iteration of AASTex.

TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data

PubMed Central

Colaprico, Antonio; Silva, Tiago C.; Olsen, Catharina; Garofano, Luciano; Cava, Claudia; Garolini, Davide; Sabedot, Thais S.; Malta, Tathiane M.; Pagnotta, Stefano M.; Castiglioni, Isabella; Ceccarelli, Michele; Bontempi, Gianluca; Noushmehr, Houtan

2016-01-01

The Cancer Genome Atlas (TCGA) research network has made public a large collection of clinical and molecular phenotypes of more than 10 000 tumor patients across 33 different tumor types. Using this cohort, TCGA has published over 20 marker papers detailing the genomic and epigenomic alterations associated with these tumor types. Although many important discoveries have been made by TCGA's research network, opportunities still exist to implement novel methods, thereby elucidating new biological pathways and diagnostic markers. However, mining the TCGA data presents several bioinformatics challenges, such as data retrieval and integration with clinical data and other molecular data types (e.g. RNA and DNA methylation). We developed an R/Bioconductor package called TCGAbiolinks to address these challenges and offer bioinformatics solutions by using a guided workflow to allow users to query, download and perform integrative analyses of TCGA data. We combined methods from computer science and statistics into the pipeline and incorporated methodologies developed in previous TCGA marker studies and in our own group. Using four different TCGA tumor types (Kidney, Brain, Breast and Colon) as examples, we provide case studies to illustrate examples of reproducibility, integrative analysis and utilization of different Bioconductor packages to advance and accelerate novel discoveries. PMID:26704973

PLACNETw: a web-based tool for plasmid reconstruction from bacterial genomes.

PubMed

Vielva, Luis; de Toro, María; Lanza, Val F; de la Cruz, Fernando

2017-12-01

PLACNET is a graph-based tool for reconstruction of plasmids from next generation sequence pair-end datasets. PLACNET graphs contain two types of nodes (assembled contigs and reference genomes) and two types of edges (scaffold links and homology to references). Manual pruning of the graphs is a necessary requirement in PLACNET, but this is difficult for users without solid bioinformatic background. PLACNETw, a webtool based on PLACNET, provides an interactive graphic interface, automates BLAST searches, and extracts the relevant information for decision making. It allows a user with domain expertise to visualize the scaffold graphs and related information of contigs as well as reference sequences, so that the pruning operations can be done interactively from a personal computer without the need for additional tools. After successful pruning, each plasmid becomes a separate connected component subgraph. The resulting data are automatically downloaded by the user. PLACNETw is freely available at https://castillo.dicom.unican.es/upload/. delacruz@unican.es. A tutorial video and several solved examples are available at https://castillo.dicom.unican.es/placnetw_video/ and https://castillo.dicom.unican.es/examples/. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Methamphetamine (Meth)

MedlinePlus

... View Online Download PDF Monitoring the Future 2015 Survey Results Published: December 16, 2015 NIH’s 2015 Monitoring ... the National Drug and Alcohol Facts Week logo design are registered marks of the U.S. Department of ...

The Virtual Geophysics Laboratory (VGL): Scientific Workflows Operating Across Organizations and Across Infrastructures

NASA Astrophysics Data System (ADS)

Cox, S. J.; Wyborn, L. A.; Fraser, R.; Rankine, T.; Woodcock, R.; Vote, J.; Evans, B.

2012-12-01

The Virtual Geophysics Laboratory (VGL) is web portal that provides geoscientists with an integrated online environment that: seamlessly accesses geophysical and geoscience data services from the AuScope national geoscience information infrastructure; loosely couples these data to a variety of gesocience software tools; and provides large scale processing facilities via cloud computing. VGL is a collaboration between CSIRO, Geoscience Australia, National Computational Infrastructure, Monash University, Australian National University and the University of Queensland. The VGL provides a distributed system whereby a user can enter an online virtual laboratory to seamlessly connect to OGC web services for geoscience data. The data is supplied in open standards formats using international standards like GeoSciML. A VGL user uses a web mapping interface to discover and filter the data sources using spatial and attribute filters to define a subset. Once the data is selected the user is not required to download the data. VGL collates the service query information for later in the processing workflow where it will be staged directly to the computing facilities. The combination of deferring data download and access to Cloud computing enables VGL users to access their data at higher resolutions and to undertake larger scale inversions, more complex models and simulations than their own local computing facilities might allow. Inside the Virtual Geophysics Laboratory, the user has access to a library of existing models, complete with exemplar workflows for specific scientific problems based on those models. For example, the user can load a geological model published by Geoscience Australia, apply a basic deformation workflow provided by a CSIRO scientist, and have it run in a scientific code from Monash. Finally the user can publish these results to share with a colleague or cite in a paper. This opens new opportunities for access and collaboration as all the resources (models, code, data, processing) are shared in the one virtual laboratory. VGL provides end users with access to an intuitive, user-centered interface that leverages cloud storage and cloud and cluster processing from both the research communities and commercial suppliers (e.g. Amazon). As the underlying data and information services are agnostic of the scientific domain, they can support many other data types. This fundamental characteristic results in a highly reusable virtual laboratory infrastructure that could also be used for example natural hazards, satellite processing, soil geochemistry, climate modeling, agriculture crop modeling.

What Is Spice?

MedlinePlus

... View Online Download PDF Monitoring the Future 2015 Survey Results Published: December 16, 2015 NIH’s 2015 Monitoring ... the National Drug and Alcohol Facts Week logo design are registered marks of the U.S. Department of ...

What Is Salvia?

MedlinePlus

... View Online Download PDF Monitoring the Future 2015 Survey Results Published: December 16, 2015 NIH’s 2015 Monitoring ... the National Drug and Alcohol Facts Week logo design are registered marks of the U.S. Department of ...

MDMA (Ecstasy or Molly)

MedlinePlus

... View Online Download PDF Monitoring the Future 2015 Survey Results Published: December 16, 2015 NIH’s 2015 Monitoring ... the National Drug and Alcohol Facts Week logo design are registered marks of the U.S. Department of ...

Prescription Pain Medications (Opioids)

MedlinePlus

... View Online Download PDF Monitoring the Future 2015 Survey Results Published: December 16, 2015 NIH’s 2015 Monitoring ... the National Drug and Alcohol Facts Week logo design are registered marks of the U.S. Department of ...

Podcasting the Sciences: A Practical Overview

ERIC Educational Resources Information Center

Barsky, Eugene; Lindstrom, Kevin

2008-01-01

University science education has been undergoing great amount of change since the commercialization of the Internet a decade ago. Mobile technologies in science education can encompass more than the proximal teaching and learning environment. Podcasting, for example, allows audio content from user-selected feeds to be automatically downloaded to…

Embedding and Publishing Interactive, 3-Dimensional, Scientific Figures in Portable Document Format (PDF) Files

PubMed Central

Barnes, David G.; Vidiassov, Michail; Ruthensteiner, Bernhard; Fluke, Christopher J.; Quayle, Michelle R.; McHenry, Colin R.

2013-01-01

With the latest release of the S2PLOT graphics library, embedding interactive, 3-dimensional (3-d) scientific figures in Adobe Portable Document Format (PDF) files is simple, and can be accomplished without commercial software. In this paper, we motivate the need for embedding 3-d figures in scholarly articles. We explain how 3-d figures can be created using the S2PLOT graphics library, exported to Product Representation Compact (PRC) format, and included as fully interactive, 3-d figures in PDF files using the movie15 LaTeX package. We present new examples of 3-d PDF figures, explain how they have been made, validate them, and comment on their advantages over traditional, static 2-dimensional (2-d) figures. With the judicious use of 3-d rather than 2-d figures, scientists can now publish, share and archive more useful, flexible and faithful representations of their study outcomes. The article you are reading does not have embedded 3-d figures. The full paper, with embedded 3-d figures, is recommended and is available as a supplementary download from PLoS ONE (File S2). PMID:24086243

Embedding and publishing interactive, 3-dimensional, scientific figures in Portable Document Format (PDF) files.

PubMed

Barnes, David G; Vidiassov, Michail; Ruthensteiner, Bernhard; Fluke, Christopher J; Quayle, Michelle R; McHenry, Colin R

2013-01-01

With the latest release of the S2PLOT graphics library, embedding interactive, 3-dimensional (3-d) scientific figures in Adobe Portable Document Format (PDF) files is simple, and can be accomplished without commercial software. In this paper, we motivate the need for embedding 3-d figures in scholarly articles. We explain how 3-d figures can be created using the S2PLOT graphics library, exported to Product Representation Compact (PRC) format, and included as fully interactive, 3-d figures in PDF files using the movie15 LaTeX package. We present new examples of 3-d PDF figures, explain how they have been made, validate them, and comment on their advantages over traditional, static 2-dimensional (2-d) figures. With the judicious use of 3-d rather than 2-d figures, scientists can now publish, share and archive more useful, flexible and faithful representations of their study outcomes. The article you are reading does not have embedded 3-d figures. The full paper, with embedded 3-d figures, is recommended and is available as a supplementary download from PLoS ONE (File S2).

Identifying kinase dependency in cancer cells by integrating high-throughput drug screening and kinase inhibition data.

PubMed

Ryall, Karen A; Shin, Jimin; Yoo, Minjae; Hinz, Trista K; Kim, Jihye; Kang, Jaewoo; Heasley, Lynn E; Tan, Aik Choon

2015-12-01

Targeted kinase inhibitors have dramatically improved cancer treatment, but kinase dependency for an individual patient or cancer cell can be challenging to predict. Kinase dependency does not always correspond with gene expression and mutation status. High-throughput drug screens are powerful tools for determining kinase dependency, but drug polypharmacology can make results difficult to interpret. We developed Kinase Addiction Ranker (KAR), an algorithm that integrates high-throughput drug screening data, comprehensive kinase inhibition data and gene expression profiles to identify kinase dependency in cancer cells. We applied KAR to predict kinase dependency of 21 lung cancer cell lines and 151 leukemia patient samples using published datasets. We experimentally validated KAR predictions of FGFR and MTOR dependence in lung cancer cell line H1581, showing synergistic reduction in proliferation after combining ponatinib and AZD8055. KAR can be downloaded as a Python function or a MATLAB script along with example inputs and outputs at: http://tanlab.ucdenver.edu/KAR/. aikchoon.tan@ucdenver.edu. Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Integration of EGA secure data access into Galaxy.

PubMed

Hoogstrate, Youri; Zhang, Chao; Senf, Alexander; Bijlard, Jochem; Hiltemann, Saskia; van Enckevort, David; Repo, Susanna; Heringa, Jaap; Jenster, Guido; J A Fijneman, Remond; Boiten, Jan-Willem; A Meijer, Gerrit; Stubbs, Andrew; Rambla, Jordi; Spalding, Dylan; Abeln, Sanne

2016-01-01

High-throughput molecular profiling techniques are routinely generating vast amounts of data for translational medicine studies. Secure access controlled systems are needed to manage, store, transfer and distribute these data due to its personally identifiable nature. The European Genome-phenome Archive (EGA) was created to facilitate access and management to long-term archival of bio-molecular data. Each data provider is responsible for ensuring a Data Access Committee is in place to grant access to data stored in the EGA. Moreover, the transfer of data during upload and download is encrypted. ELIXIR, a European research infrastructure for life-science data, initiated a project (2016 Human Data Implementation Study) to understand and document the ELIXIR requirements for secure management of controlled-access data. As part of this project, a full ecosystem was designed to connect archived raw experimental molecular profiling data with interpreted data and the computational workflows, using the CTMM Translational Research IT (CTMM-TraIT) infrastructure http://www.ctmm-trait.nl as an example. Here we present the first outcomes of this project, a framework to enable the download of EGA data to a Galaxy server in a secure way. Galaxy provides an intuitive user interface for molecular biologists and bioinformaticians to run and design data analysis workflows. More specifically, we developed a tool -- ega_download_streamer - that can download data securely from EGA into a Galaxy server, which can subsequently be further processed. This tool will allow a user within the browser to run an entire analysis containing sensitive data from EGA, and to make this analysis available for other researchers in a reproducible manner, as shown with a proof of concept study.  The tool ega_download_streamer is available in the Galaxy tool shed: https://toolshed.g2.bx.psu.edu/view/yhoogstrate/ega_download_streamer.

Integration of EGA secure data access into Galaxy

PubMed Central

Hoogstrate, Youri; Zhang, Chao; Senf, Alexander; Bijlard, Jochem; Hiltemann, Saskia; van Enckevort, David; Repo, Susanna; Heringa, Jaap; Jenster, Guido; Fijneman, Remond J.A.; Boiten, Jan-Willem; A. Meijer, Gerrit; Stubbs, Andrew; Rambla, Jordi; Spalding, Dylan; Abeln, Sanne

2016-01-01

High-throughput molecular profiling techniques are routinely generating vast amounts of data for translational medicine studies. Secure access controlled systems are needed to manage, store, transfer and distribute these data due to its personally identifiable nature. The European Genome-phenome Archive (EGA) was created to facilitate access and management to long-term archival of bio-molecular data. Each data provider is responsible for ensuring a Data Access Committee is in place to grant access to data stored in the EGA. Moreover, the transfer of data during upload and download is encrypted. ELIXIR, a European research infrastructure for life-science data, initiated a project (2016 Human Data Implementation Study) to understand and document the ELIXIR requirements for secure management of controlled-access data. As part of this project, a full ecosystem was designed to connect archived raw experimental molecular profiling data with interpreted data and the computational workflows, using the CTMM Translational Research IT (CTMM-TraIT) infrastructure http://www.ctmm-trait.nl as an example. Here we present the first outcomes of this project, a framework to enable the download of EGA data to a Galaxy server in a secure way. Galaxy provides an intuitive user interface for molecular biologists and bioinformaticians to run and design data analysis workflows. More specifically, we developed a tool -- ega_download_streamer - that can download data securely from EGA into a Galaxy server, which can subsequently be further processed. This tool will allow a user within the browser to run an entire analysis containing sensitive data from EGA, and to make this analysis available for other researchers in a reproducible manner, as shown with a proof of concept study.  The tool ega_download_streamer is available in the Galaxy tool shed: https://toolshed.g2.bx.psu.edu/view/yhoogstrate/ega_download_streamer. PMID:28232859

Rural Transportation: An Annotated Bibliography

DOT National Transportation Integrated Search

1999-03-01

This bibliography is downloadable in MS Word format. The annotated bibliography : is intended to provide an overview of different aspects of transportation in : rural America. Emphasis is on those studies published within the last 10 years, : but som...

An Introduction to Services Accessible on the Internet.

ERIC Educational Resources Information Center

Giguere, Marlene

1992-01-01

Provides an overview of the INTERNET and INTERNET services of interest to libraries, including electronic mail, bulletin boards, electronic publishing, online public access catalogs and databases, and downloaded texts and software. (16 references) (MES)

APOD Data Release of Social Network Footprint for 2015

NASA Astrophysics Data System (ADS)

Nemiroff, Robert J.; Russell, David; Allen, Alice; Connelly, Paul; Lowe, Stuart R.; Petz, Sydney; Haring, Ralf; Bonnell, Jerry T.; APOD Team

2017-01-01

APOD data for 2015 are being made freely available for download and analysis. The data includes page view statistics for the main NASA APOD website at https://apod.nasa.gov, as well as for APOD's social media sites on Facebook, Instagram, Google Plus, and Twitter. General APOD-specific demographic information for each site is included. Popularity statistics that have been archived including Page Views, Likes, Shares, Hearts, and Retweets. The downloadable Excel-type spreadsheet also includes the APOD title and (unlinked) explanation. This data is released not to highlight APOD's popularity but to encourage analyses, with potential examples involving which astronomy topics trend the best and whether popularity is social group dependent.

Digital Citizenship: Addressing Appropriate Technology Behavior

ERIC Educational Resources Information Center

Ribble, Mike S.; Bailey, Gerald D.; Ross, Tweed W.

2004-01-01

Recently, the popular press has pointed to increasing evidence of misuse and abuse of emerging technologies in U.S. schools. Some examples include using Web sites to intimidate or threaten students, downloading music illegally from the Internet, plagiarizing information using the Internet, using cellular phones during class time, and playing games…

MGDS: Free, on-line, cutting-edge tools to enable the democratisation of geoscience data

NASA Astrophysics Data System (ADS)

Goodwillie, A. M.; Ryan, W. B.; O'Hara, S.; Ferrini, V.; Arko, R. A.; Coplan, J.; Chan, S.; Carbotte, S. M.; Nitsche, F. O.; Bonczkowski, J.; Morton, J. J.; Weissel, R.; Leung, A.

2010-12-01

The availability of user-friendly, effective cyber-information resources for accessing and manipulating geoscience data has grown rapidly in recent years. Based at Lamont-Doherty Earth Observatory the MGDS group has developed a number of free tools that have wide application across the geosciences for both educators and researchers. A simple web page (http://www.marine-geo.org/) allows users to search for and download many types of data by key word, geographical region, or published citation. The popular Create Maps and Grids function and the downloadable Google Earth-compatible KML files appeal to a wide user base. MGDS MediaBank galleries (http://media.marine-geo.org/) enable users to view and download compelling images that are purposefully selected for their educational value from NSF-funded field programs. GeoMapApp (http://www.geomapapp.org), a free map-based interactive tool that works on any machine, is increasingly being adopted across a broad suite of users from middle school students to university researchers. GeoMapApp allows users to plot, manipulate and present data in an intuitive geographical reference frame. GeoMapApp offers a convenient way to explore the wide range of built-in data sets, to quickly generate maps and images that aid visualisation and, when importing their own gridded and tabular data sets, to access the same rich built-in functionality. A user guide, short multi-media tutorials, and webinar are available on-line. The regularly-updated Global Multi-Resolution Topography (GMRT) Synthesis is used as the default GeoMapApp base map and is an increasingly popular means to rapidly create location maps. Additionally, the layer manager offers a fast way to overlay and compare multiple data sets and is augmented by the ability to alter layer transparency so that underlying layers become visible. Examples of GeoMapApp built-in data sets include high-resolution land topography and ocean floor bathymetry derived from satellite and multi-beam swath mapping systems - these can be profiled, shaded, and contoured; geo-registered geochemical sample analyses from the EarthChem database; plate boundary, earthquake and volcano catalogues; physical oceanography global and water column data; seafloor photos and Alvin dive video images; geological maps at various scales; and, high-quality coastline, lakes and rivers data. Customised data portals offer enhanced functionality for multi-channel seismic profiles, drill core logs, and earthquake animations. GeoMapApp is used in many MARGINS undergraduate-level off-the-shelf interactive learning activities called mini-lessons (http://serc.carleton.edu/margins/collection.html). Examples of educational applicability will be shown.

Articles Published and Downloaded by Public Health Scientists: Analysis of Data From the CDC Public Health Library, 2011-2013.

PubMed

Iskander, John; Bang, Gail; Stupp, Emma; Connick, Kathy; Gomez, Onnalee; Gidudu, Jane

2016-01-01

To describe scientific information usage and publication patterns of the Centers for Disease Control and Prevention (CDC) Public Health Library and Information Center patrons. Administratively collected patron usage data and aggregate data on CDC-authored publications from the CDC Library for 3 consecutive years were analyzed. The CDC Public Health Library and Information Center, which serves CDC employees nationally and internationally. Internal patrons and external users of the CDC Library. Three-year trends in full-text article publication and downloads including most common journals used for each purpose, systematic literature searches requested and completed, and subscriptions to a weekly public health current literature awareness service. From 2011 to 2013, CDC scientists published a total of 7718 articles in the peer-reviewed literature. During the same period, article downloads from the CDC Library increased 25% to more than 1.1 million, completed requests for reviews of the scientific literature increased by 34%, and electronic subscriptions to literature compilation services increased by 23%. CDC's scientific output and information use via the CDC Library are both increasing. Researchers and field staff are making greater use of literature review services and other customized information content delivery. Virtual public health library access is an increasingly important resource for the scientific practice of public health.

40 CFR 1037.810 - Incorporation by reference.

Code of Federal Regulations, 2012 CFR

2012-07-01

... must publish a notice of the change in the Federal Register and the material must be available to the... software is also available for download at http://www.epa.gov/otaq/climate/gem.htm. (2) [Reserved] (d...

Online Imagery: Finding Pictures for Business Documents.

ERIC Educational Resources Information Center

Cosden, Chris

1995-01-01

Discusses the use of America Online and CompuServe to find clip art, photos, and other images for use in desktop publishing projects. Highlights include copyright issues, different graphic formats, graphic conversion programs, compression programs, and downloading. (LRW)

Houston, We Still Have a Problem.

PubMed

Buchheit, Martin

2017-09-01

Apollo 13 was initially looking like it would be the smoothest flight ever. After the explosion of an oxygen tank, however, the astronauts were close to spending the rest of their lives in rotation around the planet. This well-known incident is used to further discuss the link, or lack thereof, between sport-science research and current field practices. There is a feeling that the academic culture and its publishing requirements have created a bit of an Apollo 13-like orbiting world (eg, journals and conferences) that is mostly disconnected from the reality of elite performance. The author discusses how poor research discredits our profession and provides some examples from the field where the research does not apply. In fact, the reality is that sport scientists often do not have the right answers. Some perspectives to improve translation are finally discussed, including a rethink of the overall publishing process: promotion of relevant submission types (eg, short-paper format, short reports, as provided by IJSPP), improvement of the review process (faster turnaround, reviewers identified to increase accountability, and, in turn, review quality), and media types (eg, free downloads, simplified versions published in coaching journals, book chapters, infographics, dissemination via social media). When it comes to guiding practitioners and athletes, instead of using an evidence-based approach, we should rather promote an "evidence-led" or "informed-practice" approach-one that appreciates context over simple scientific conclusions.

Developing GIOVANNI-based Online Prototypes to Intercompare TRMM-Related Global Gridded-Precipitation Products

NASA Technical Reports Server (NTRS)

Liu, Zhong; Ostrenga, Dana; Teng, William; Kempler, Steven; Milich, Lenard

2014-01-01

New online prototypes have been developed to extend and enhance the previous effort by facilitating investigation of product characteristics and intercomparison of precipitation products in different algorithms as well as in different versions at different spatial scales ranging from local to global without downloading data and software. Several popular Tropical Rainfall Measuring Mission (TRMM) products and the TRMM Composite Climatology are included. In addition, users can download customized data in several popular formats for further analysis. Examples show product quality problems and differences in several monthly precipitation products. It is seen that differences in daily and monthly precipitation products are distributed unevenly in space and it is necessary to have tools such as those presented here for customized and detailed investigations. A simple time series and two area maps allow the discovery of abnormal values of 3A25 in one of the months. An example shows a V-shaped valley issue in the Version 6 3B43 time series and another example shows a sudden drop in 3A25 monthly rain rate, all of which provide important information when the products are used for long-term trend studies. Future plans include adding more products and statistical functionality in the prototypes.

Stem Cell Treatments: What to Ask

MedlinePlus

... many haven’t? Have your findings been published? Patient rights What are my rights as a participant—for ... any new information that might come up, my right to withdraw from the treatment ... Patient Handbook (PDF) Download a guide to help you ...

40 CFR 1060.130 - What installation instructions must I give to equipment manufacturers?

Code of Federal Regulations, 2010 CFR

2010-07-01

... specify the requirements for the fuel cap, such as the allowable materials, thread pattern, how it must... liquid fuel. (4) Describe instructions for installing components so they will operate according to design... equivalent format. For example, you may post instructions on a publicly available Web site for downloading or...

Reflections on Jokes and Cartoons about Suicide

ERIC Educational Resources Information Center

Lester, David

2012-01-01

This article is intended to engage others in a dialogue about the role and meaning of jokes about suicide. Types of jokes involving suicide are examined to distinguish the different types of humor involved. A sample of 118 recent political cartoons in an online website was downloaded, of which 73 concerned suicide bombers. Examples of suicide…

Walkabout the Galaxy: Podcasting for Informal and Accessible Astronomy Outreach and Education

NASA Astrophysics Data System (ADS)

Colwell, J. E.; Dove, A.; Kehoe, A.; Becker, T. M.

2014-12-01

"Walkabout the Galaxy" is a weekly podcast we have been publishing since May 2014 discussing astronomical news that is in the popular media at the time of recording. Episodes are 25-30 minutes in length and are informal in style: we emphasize one or two basic points while engaging in a free-form discussion of the topic with frequent tangential asides. The target audience is the interested layperson rather than a student, professional, or amateur of astronomy. The informal style is deliberately chosen to keep the podcast from sounding like a classroom lesson and to improve the reach of the podcast to a broader public. Guests have included both experts and laypeople. The number of episode downloads varies by nearly a factor of two from episode to episode (~450 to 750). We will present statistics on downloads and subscriptions, and correlations with episode length, subject matter, and style of episode title. The style of the content cannot influence download statistics, however, and it is not possible to track actual listenership data once the episodes are downloaded. We will discuss lessons learned in creating and producing an educational podcast as well as listener feedback.

The DynaMine webserver: predicting protein dynamics from sequence.

PubMed

Cilia, Elisa; Pancsa, Rita; Tompa, Peter; Lenaerts, Tom; Vranken, Wim F

2014-07-01

Protein dynamics are important for understanding protein function. Unfortunately, accurate protein dynamics information is difficult to obtain: here we present the DynaMine webserver, which provides predictions for the fast backbone movements of proteins directly from their amino-acid sequence. DynaMine rapidly produces a profile describing the statistical potential for such movements at residue-level resolution. The predicted values have meaning on an absolute scale and go beyond the traditional binary classification of residues as ordered or disordered, thus allowing for direct dynamics comparisons between protein regions. Through this webserver, we provide molecular biologists with an efficient and easy to use tool for predicting the dynamical characteristics of any protein of interest, even in the absence of experimental observations. The prediction results are visualized and can be directly downloaded. The DynaMine webserver, including instructive examples describing the meaning of the profiles, is available at http://dynamine.ibsquare.be. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Physics Trends flyers & high school flyers

NASA Astrophysics Data System (ADS)

White, Susan C.

2016-03-01

Since 2000, we have published a series of flyers highlighting various data of interest to physics faculty members and students. For example, our Fall 2015 Physics Trends flyers display the employment sectors where physics bachelor's degree recipients work, the knowledge used frequently by mid-career PhD physicists working primarily in private sector jobs, and the proportion of women among physics faculty members. We have recently added a new resource for high school physics teachers: flyers focusing on high school physics. PDFs of both the Physics Trends and high school flyers are available for download at: www.aip.org/statistics/physics-trends and www.aip.org/statistics/highschool. We also have a limited number of printed copies of the Physics Trends flyers which we are happy to send to you upon request. We appreciate the responses from each of you who has helped us collect these data. Next month we will look at Hispanic representation among bachelor's degree recipients in physical sciences and engineering.

FAA statistical handbook of aviation, calendar year 1988

DOT National Transportation Integrated Search

1988-08-15

The FAA Statistical Handbook of Aviation is published annually by the Federal Aviation Administration (FAA). The handbook is provided here in MS Excel. format as downloadable files and as text tables that can be viewed in PDF format. The prime purpos...

Information Delivery Options over Three Decades.

ERIC Educational Resources Information Center

Kennedy, H. E.

1986-01-01

Reviews the development of technological innovations in information delivery, including microforms, electronic processing, online distribution, full-text abstracts online, floppy disks, downloading, vertical integration, electronic publishing, and optical disks. The impact of technology on the information industry and the need to use technology…

Ligand.Info small-molecule Meta-Database.

PubMed

von Grotthuss, Marcin; Koczyk, Grzegorz; Pas, Jakub; Wyrwicz, Lucjan S; Rychlewski, Leszek

2004-12-01

Ligand.Info is a compilation of various publicly available databases of small molecules. The total size of the Meta-Database is over 1 million entries. The compound records contain calculated three-dimensional coordinates and sometimes information about biological activity. Some molecules have information about FDA drug approving status or about anti-HIV activity. Meta-Database can be downloaded from the http://Ligand.Info web page. The database can also be screened using a Java-based tool. The tool can interactively cluster sets of molecules on the user side and automatically download similar molecules from the server. The application requires the Java Runtime Environment 1.4 or higher, which can be automatically downloaded from Sun Microsystems or Apple Computer and installed during the first use of Ligand.Info on desktop systems, which support Java (Ms Windows, Mac OS, Solaris, and Linux). The Ligand.Info Meta-Database can be used for virtual high-throughput screening of new potential drugs. Presented examples showed that using a known antiviral drug as query the system was able to find others antiviral drugs and inhibitors.

77 FR 10593 - Self-Regulatory Organizations; EDGA Exchange, Inc.; Notice of Filing and Immediate Effectiveness...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-22

... 1TB of data. For the first two levels ($750 and $1500/month for FlexDownload), the Exchange is... (reviewed over a three month period), and relates to a multiplier that increases Hit quantity. For example... Hits than subscribed to for two consecutive months, the Purchaser's subscription will be automatically...

Remote Sensing Data Visualization, Fusion and Analysis via Giovanni

NASA Technical Reports Server (NTRS)

Leptoukh, G.; Zubko, V.; Gopalan, A.; Khayat, M.

2007-01-01

We describe Giovanni, the NASA Goddard developed online visualization and analysis tool that allows users explore various phenomena without learning remote sensing data formats and downloading voluminous data. Using MODIS aerosol data as an example, we formulate an approach to the data fusion for Giovanni to further enrich online multi-sensor remote sensing data comparison and analysis.

Quantitative Microbial Risk Assessment Tutorial - SDMProjectBuilder: Import Local Data Files to Identify and Modify Contamination Sources and Input ParametersUpdated 2017

EPA Science Inventory

Twelve example local data support files are automatically downloaded when the SDMProjectBuilder is installed on a computer. They allow the user to modify values to parameters that impact the release, migration, fate, and transport of microbes within a watershed, and control delin...

Quantitative Microbial Risk Assessment Tutorial – SDMProjectBuilder: Import Local Data Files to Identify and Modify Contamination Sources and Input Parameters

EPA Science Inventory

Twelve example local data support files are automatically downloaded when the SDMProjectBuilder is installed on a computer. They allow the user to modify values to parameters that impact the release, migration, fate, and transport of microbes within a watershed, and control delin...

Take Action against Hepatitis C (for People in Recovery from Mental Illness or Addiction)

MedlinePlus

... combined. Either way, you get a series of shots, not just one. You need to have all the shots to get the protection. Complete the full series ... Keep a positive attitude. It all helps. * for example, large ... Knowledge Application Program (KAP): 1. Download or order from the SAMHSA Store at ...

Demonstrating the value of publishing open data by linking DOI-based citations of source datasets to uses in research and policy

NASA Astrophysics Data System (ADS)

Copas, K.; Legind, J. K.; Hahn, A.; Braak, K.; Høftt, M.; Noesgaard, D.; Robertson, T.; Méndez Hernández, F.; Schigel, D.; Ko, C.

2017-12-01

GBIF—the Global Biodiversity Information Facility—has recently demonstrated a system that tracks publications back to individual datasets, giving data providers demonstrable evidence of the benefit and utility of sharing data to support an array of scholarly topics and practical applications. GBIF is an open-data network and research infrastructure funded by the world's governments. Its community consists of more than 90 formal participants and almost 1,000 data-publishing institutions, which currently make tens of thousands of datasets containing nearly 800 million species occurrence records freely and publicly available for discovery, use and reuse across a wide range of biodiversity-related research and policy investigations. Starting in 2015 with the help of DataONE, GBIF introduced DOIs as persistent identifiers for the datasets shared through its network. This enhancement soon extended to the assignment of DOIs to user downloads from GBIF.org, which typically filter the available records with a variety of taxonomic, geographic, temporal and other search terms. Despite the lack of widely accepted standards for citing data among researchers and publications, this technical infrastructure is beginning to take hold and support open, transparent, persistent and repeatable use and reuse of species occurrence data. These `download DOIs' provide canonical references for the search results researchers process and use in peer-reviewed articles—a practice GBIF encourages by confirming new DOIs with each download and offering guidelines on citation. GBIF has recently started linking these citation results back to dataset and publisher pages, offering more consistent, traceable evidence of the value of sharing data to support others' research. GBIF's experience may be a useful model for other repositories to follow.

MetPetDB: A database for metamorphic geochemistry

NASA Astrophysics Data System (ADS)

Spear, Frank S.; Hallett, Benjamin; Pyle, Joseph M.; Adalı, Sibel; Szymanski, Boleslaw K.; Waters, Anthony; Linder, Zak; Pearce, Shawn O.; Fyffe, Matthew; Goldfarb, Dennis; Glickenhouse, Nickolas; Buletti, Heather

2009-12-01

We present a data model for the initial implementation of MetPetDB, a geochemical database specific to metamorphic rock samples. The database is designed around the concept of preservation of spatial relationships, at all scales, of chemical analyses and their textural setting. Objects in the database (samples) represent physical rock samples; each sample may contain one or more subsamples with associated geochemical and image data. Samples, subsamples, geochemical data, and images are described with attributes (some required, some optional); these attributes also serve as search delimiters. All data in the database are classified as published (i.e., archived or published data), public or private. Public and published data may be freely searched and downloaded. All private data is owned; permission to view, edit, download and otherwise manipulate private data may be granted only by the data owner; all such editing operations are recorded by the database to create a data version log. The sharing of data permissions among a group of collaborators researching a common sample is done by the sample owner through the project manager. User interaction with MetPetDB is hosted by a web-based platform based upon the Java servlet application programming interface, with the PostgreSQL relational database. The database web portal includes modules that allow the user to interact with the database: registered users may save and download public and published data, upload private data, create projects, and assign permission levels to project collaborators. An Image Viewer module provides for spatial integration of image and geochemical data. A toolkit consisting of plotting and geochemical calculation software for data analysis and a mobile application for viewing the public and published data is being developed. Future issues to address include population of the database, integration with other geochemical databases, development of the analysis toolkit, creation of data models for derivative data, and building a community-wide user base. It is believed that this and other geochemical databases will enable more productive collaborations, generate more efficient research efforts, and foster new developments in basic research in the field of solid earth geochemistry.

Earth Science Datacasting v2.0

NASA Technical Reports Server (NTRS)

Bingham, Andrew W.; Deen, Robert G.; Hussey, Kevin J.; Stough, Timothy M.; McCleese, Sean W.; Toole, Nicholas T.

2012-01-01

The Datacasting software, which consists of a server and a client, has been developed as part of the Earth Science (ES) Datacasting project. The goal of ES Datacasting is to provide scientists the ability to automatically and continuously download Earth science data that meets a precise, predefined need, and then to instantaneously visualize it on a local computer. This is achieved by applying the concept of podcasting to deliver science data over the Internet using RSS (Really Simple Syndication) XML feeds. By extending the RSS specification, scientists can filter a feed and only download the files that are required for a particular application (for example, only files that contain information about a particular event, such as a hurricane or flood). The extension also provides the ability for the client to understand the format of the data and visualize the information locally. The server part enables a data provider to create and serve basic Datacasting (RSS-based) feeds. The user can subscribe to any number of feeds, view the information related to each item contained within a feed (including browse pre-made images), manually download files associated with items, and place these files in a local store. The client-server architecture enables users to: a) Subscribe and interpret multiple Datacasting feeds (same look and feel as a typical mail client), b) Maintain a list of all items within each feed, c) Enable filtering on the lists based on different metadata attributes contained within the feed (list will reference only data files of interest), d) Visualize the reference data and associated metadata, e) Download files referenced within the list, and f) Automatically download files as new items become available.

Geospatial resources for the geologic community: The USGS National Map

USGS Publications Warehouse

Witt, Emitt C.

2015-01-01

Geospatial data are a key component of investigating, interpreting, and communicating the geological sciences. Locating geospatial data can be time-consuming, which detracts from time spent on a study because these data are not obviously placed in central locations or are served from many disparate databases. The National Map of the US Geological Survey is a publicly available resource for accessing the geospatial base map data needs of the geological community from a central location. The National Map data are available through a viewer and download platform providing access to eight primary data themes, plus the US Topo and scanned historical topographic maps. The eight themes are elevation, orthoimagery, hydrography, geographic names, boundaries, transportation, structures, and land cover, and they are being offered for download as predefined tiles in formats supported by leading geographic information system software. Data tiles are periodically refreshed to capture the most current content and are an efficient method for disseminating and receiving geospatial information. Elevation data, for example, are offered as a download from the National Map as 1° × 1° tiles for the 10- and 30- m products and as 15′ × 15′ tiles for the higher-resolution 3-m product. Vector data sets with smaller file sizes are offered at several tile sizes and formats. Partial tiles are not a download option—any prestaged data that intersect the requesting bounding box will be, in their entirety, part of the download order. While there are many options for accessing geospatial data via the Web, the National Map represents authoritative sources of data that are documented and can be referenced for citation and inclusion in scientific publications. Therefore, National Map products and services should be part of a geologist’s first stop for geospatial information and data.

Public accessibility of biomedical articles from PubMed Central reduces journal readership--retrospective cohort analysis.

PubMed

Davis, Philip M

2013-07-01

Does PubMed Central--a government-run digital archive of biomedical articles--compete with scientific society journals? A longitudinal, retrospective cohort analysis of 13,223 articles (5999 treatment, 7224 control) published in 14 society-run biomedical research journals in nutrition, experimental biology, physiology, and radiology between February 2008 and January 2011 reveals a 21.4% reduction in full-text hypertext markup language (HTML) article downloads and a 13.8% reduction in portable document format (PDF) article downloads from the journals' websites when U.S. National Institutes of Health-sponsored articles (treatment) become freely available from the PubMed Central repository. In addition, the effect of PubMed Central on reducing PDF article downloads is increasing over time, growing at a rate of 1.6% per year. There was no longitudinal effect for full-text HTML downloads. While PubMed Central may be providing complementary access to readers traditionally underserved by scientific journals, the loss of article readership from the journal website may weaken the ability of the journal to build communities of interest around research papers, impede the communication of news and events to scientific society members and journal readers, and reduce the perceived value of the journal to institutional subscribers.

Best Audiobooks of 2007

ERIC Educational Resources Information Center

Burns, Ann

2008-01-01

Heard any good books lately? Apparently, lots of people are listening. According to a survey conducted by the Audio Publishers Association, annual audiobook sales are now estimated at $923 million. Customers find books at libraries, retail stores, and through downloading, which is becoming the fastest-growing audiobook format. This article…

SnapShot: The Bacterial Cytoskeleton.

PubMed

Fink, Gero; Szewczak-Harris, Andrzej; Löwe, Jan

2016-07-14

Most bacteria and archaea contain filamentous proteins and filament systems that are collectively known as the bacterial cytoskeleton, though not all of them are cytoskeletal, affect cell shape, or maintain intracellular organization. To view this SnapShot, open or download the PDF. Copyright © 2016. Published by Elsevier Inc.

Brief Pictorial Description of New Mobile Technologies Used in Cultural Institutions in Japan

ERIC Educational Resources Information Center

Awano, Yumi

2007-01-01

Many Japanese museums and other cultural institutions have been exploring ways to enrich visitors' experiences using new digital devices. This paper briefly describes some examples in Japan, ranging from a PDA, a mobile phone, podcasting, and an audio guide speaker-equipped vest to a Quick Response (QR) code on a brochure for downloading a short…

The CEBAF Element Database and Related Operational Software

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

Larrieu, Theodore; Slominski, Christopher; Keesee, Marie

The newly commissioned 12GeV CEBAF accelerator relies on a flexible, scalable and comprehensive database to define the accelerator. This database delivers the configuration for CEBAF operational tools, including hardware checkout, the downloadable optics model, control screens, and much more. The presentation will describe the flexible design of the CEBAF Element Database (CED), its features and assorted use case examples.

Students' Use of Mobile Technologies: Motivational Factors

ERIC Educational Resources Information Center

Baytiyeh, Hoda

2018-01-01

Mobile technologies are all-pervasive in the current digital generation, and college students rely on their mobile phones to communicate on a daily basis. In the midst of the myriad of applications available to download on the mobile, some tools have become more well-known and more often adopted than others. An example of such a tool is WhatsApp,…

AnnotCompute: annotation-based exploration and meta-analysis of genomics experiments

PubMed Central

Zheng, Jie; Stoyanovich, Julia; Manduchi, Elisabetta; Liu, Junmin; Stoeckert, Christian J.

2011-01-01

The ever-increasing scale of biological data sets, particularly those arising in the context of high-throughput technologies, requires the development of rich data exploration tools. In this article, we present AnnotCompute, an information discovery platform for repositories of functional genomics experiments such as ArrayExpress. Our system leverages semantic annotations of functional genomics experiments with controlled vocabulary and ontology terms, such as those from the MGED Ontology, to compute conceptual dissimilarities between pairs of experiments. These dissimilarities are then used to support two types of exploratory analysis—clustering and query-by-example. We show that our proposed dissimilarity measures correspond to a user's intuition about conceptual dissimilarity, and can be used to support effective query-by-example. We also evaluate the quality of clustering based on these measures. While AnnotCompute can support a richer data exploration experience, its effectiveness is limited in some cases, due to the quality of available annotations. Nonetheless, tools such as AnnotCompute may provide an incentive for richer annotations of experiments. Code is available for download at http://www.cbil.upenn.edu/downloads/AnnotCompute. Database URL: http://www.cbil.upenn.edu/annotCompute/ PMID:22190598

Creating the High-Resolution Settlement Layer - lessons learned

NASA Astrophysics Data System (ADS)

Gros, A.

2017-12-01

Facebook publishes the High-resolution Settlement Layer (HRSL: https://ciesin.columbia.edu/data/hrsl/) in collaboration with Columbia University's CIESIN institute and the World Bank. So far, data for 13 countries have been published over the past nine months. HRSL data for Burkina Faso, Ghana, Haiti, Ivory Coast, Madagascar, Malawi, Mexico, The Philippines, Rwanda, South Africa, Sri Lanka, Thailand, and Uganda are available for download. We will present a status update and report on lessons learned.

Archive of Digital Chirp Subbottom Profile Data Collected During USGS Cruise 14BIM05 Offshore of Breton Island, Louisiana, August 2014

USGS Publications Warehouse

Forde, Arnell S.; Flocks, James G.; Wiese, Dana S.; Fredericks, Jake J.

2016-03-29

The archived trace data are in standard SEG Y rev. 0 format (Barry and others, 1975); the first 3,200 bytes of the card image header are in American Standard Code for Information Interchange (ASCII) format instead of Extended Binary Coded Decimal Interchange Code (EBCDIC) format. The SEG Y files are available on the DVD version of this report or online, downloadable via the USGS Coastal and Marine Geoscience Data System (http://cmgds.marine.usgs.gov). The data are also available for viewing using GeoMapApp (http://www.geomapapp.org) and Virtual Ocean (http://www.virtualocean.org) multi-platform open source software. The Web version of this archive does not contain the SEG Y trace files. To obtain the complete DVD archive, contact USGS Information Services at 1-888-ASK-USGS or infoservices@usgs.gov. The SEG Y files may be downloaded and processed with commercial or public domain software such as Seismic Unix (SU) (Cohen and Stockwell, 2010). See the How To Download SEG Y Data page for download instructions. The printable profiles are provided as Graphics Interchange Format (GIF) images processed and gained using SU software and can be viewed from theProfiles page or by using the links located on the trackline maps; refer to the Software page for links to example SU processing scripts.

Book It!

ERIC Educational Resources Information Center

Baird, Diane; Vesper, Virginia

On the Internet, one can not only buy books but also obtain information about publishers and vendors, book reviews, authors, and other book-related information. Even electronic texts are available for downloading or browsing online. The paper discusses World Wide Web sites for many book-related information needs, whether a person is searching for…

76 FR 38585 - Proposed Establishment of Class E Airspace; Wilkes-Barre, PA

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-01

... may also submit and review received comments through the Internet at http:[sol][sol]www.regulations... submit comments through the Internet at http:[sol][sol]www.regulations.gov. Annotators wishing the FAA to... downloaded from and comments submitted through http:[sol][sol]www.regulations.gov. Recently published...

37 CFR 385.22 - Calculation of royalty payments in general.

Code of Federal Regulations, 2014 CFR

2014-07-01

..., LIBRARY OF CONGRESS RATES AND TERMS FOR STATUTORY LICENSES RATES AND TERMS FOR USE OF MUSICAL WORKS UNDER COMPULSORY LICENSE FOR MAKING AND DISTRIBUTING OF PHYSICAL AND DIGITAL PHONORECORDS Limited Offerings, Mixed..., permanent digital download, ringtone) in accordance with the ratios that the standalone published prices of...

Replacing the IRAF/PyRAF Code-base at STScI: The Advanced Camera for Surveys (ACS)

NASA Astrophysics Data System (ADS)

Lucas, Ray A.; Desjardins, Tyler D.; STScI ACS (Advanced Camera for Surveys) Team

2018-06-01

IRAF/PyRAF are no longer viable on the latest hardware often used by HST observers, therefore STScI no longer actively supports IRAF or PyRAF for most purposes. STScI instrument teams are in the process of converting all of our data processing and analysis code from IRAF/PyRAF to Python, including our calibration reference file pipelines and data reduction software. This is exemplified by our latest ACS Data Handbook, version 9.0, which was recently published in February 2018. Examples of IRAF and PyRAF commands have now been replaced by code blocks in Python, with references linked to documentation on how to download and install the latest Python software via Conda and AstroConda. With the temporary exception of the ACS slitless spectroscopy tool aXe, all ACS-related software is now independent of IRAF/PyRAF. A concerted effort has been made across STScI divisions to help the astronomical community transition from IRAF/PyRAF to Python, with tools such as Python Jupyter notebooks being made to give users workable examples. In addition to our code changes, the new ACS data handbook discusses the latest developments in charge transfer efficiency (CTE) correction, bias de-striping, and updates to the creation and format of calibration reference files among other topics.

Observer's Interface for Solar System Target Specification

NASA Astrophysics Data System (ADS)

Roman, Anthony; Link, Miranda; Moriarty, Christopher; Stansberry, John A.

2016-10-01

When observing an asteroid or comet with HST, it has been necessary for the observer to manually enter the target's orbital elements into the Astronomer's Proposal Tool (APT). This allowed possible copy/paste transcription errors from the observer's source of orbital elements data. In order to address this issue, APT has now been improved with the capability to identify targets in and then download orbital elements from JPL Horizons. The observer will first use a target name resolver to choose the intended target from the Horizons database, and then download the orbital elements from Horizons directly into APT. A manual entry option is also still retained if the observer does not wish to use elements from Horizons. This new capability is available for HST observing, and it will also be supported for JWST observing. The poster shows examples of this new interface.

Observer's Interface for Solar System Target Specification

NASA Astrophysics Data System (ADS)

Roman, Anthony; Link, Miranda; Moriarty, Christopher; Stansberry, John A.

2016-01-01

When observing an asteroid or comet with HST, it has been necessary for the observer to manually enter the target's orbital elements into the Astronomer's Proposal Tool (APT). This allowed possible copy/paste transcription errors from the observer's source of orbital elements data. In order to address this issue, APT has now been improved with the capability to identify targets in and then download orbital elements from JPL Horizons. The observer will first use a target name resolver to choose the intended target from the Horizons database, and then download the orbital elements from Horizons directly into APT. A manual entry option is also still retained if the observer does not wish to use elements from Horizons. This new capability is available for HST observing, and it will also be supported for JWST observing. The poster shows examples of this new interface.

Virtual and Printed 3D Models for Teaching Crystal Symmetry and Point Groups

ERIC Educational Resources Information Center

Casas, Lluís; Estop, Euge`nia

2015-01-01

Both, virtual and printed 3D crystal models can help students and teachers deal with chemical education topics such as symmetry and point groups. In the present paper, two freely downloadable tools (interactive PDF files and a mobile app) are presented as examples of the application of 3D design to study point-symmetry. The use of 3D printing to…

Exploring NASA and ESA Atmospheric Data Using GIOVANNI, the Online Visualization and Analysis Tool

NASA Technical Reports Server (NTRS)

Leptoukh, Gregory

2007-01-01

Giovanni, the NASA Goddard online visualization and analysis tool (http://giovanni.gsfc.nasa.gov) allows users explore various atmospheric phenomena without learning remote sensing data formats and downloading voluminous data. Using NASA MODIS (Terra and Aqua) and ESA MERIS (ENVISAT) aerosol data as an example, we demonstrate Giovanni usage for online multi-sensor remote sensing data comparison and analysis.

CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API.

PubMed

Ono, Keiichiro; Muetze, Tanja; Kolishovski, Georgi; Shannon, Paul; Demchak, Barry

2015-01-01

As bioinformatic workflows become increasingly complex and involve multiple specialized tools, so does the difficulty of reliably reproducing those workflows. Cytoscape is a critical workflow component for executing network visualization, analysis, and publishing tasks, but it can be operated only manually via a point-and-click user interface. Consequently, Cytoscape-oriented tasks are laborious and often error prone, especially with multistep protocols involving many networks. In this paper, we present the new cyREST Cytoscape app and accompanying harmonization libraries. Together, they improve workflow reproducibility and researcher productivity by enabling popular languages (e.g., Python and R, JavaScript, and C#) and tools (e.g., IPython/Jupyter Notebook and RStudio) to directly define and query networks, and perform network analysis, layouts and renderings. We describe cyREST's API and overall construction, and present Python- and R-based examples that illustrate how Cytoscape can be integrated into large scale data analysis pipelines. cyREST is available in the Cytoscape app store (http://apps.cytoscape.org) where it has been downloaded over 1900 times since its release in late 2014.

seismo-live: Training in Seismology using Jupyter Notebooks

NASA Astrophysics Data System (ADS)

Igel, Heiner; Krischer, Lion; van Driel, Martin; Tape, Carl

2017-04-01

Practical training in computational methodologies is still underrepresented in Earth science curriculae despite the increasing use of sometimes highly sophisticated simulation and data processing technologies in research projects. At the same time well-engineered community codes make it easy to return results yet with the danger that the inherent traps of black-box solutions are not well understood. For this purpose we have initiated a community platform (www.seismo-live.org) where Python-based Jupyter notebooks can be accessed and run without necessary downloads or local software installations. The increasingly popular Jupyter notebooks allow combining markup language, graphics, equations, with interactive, executable python codes. The platform already includes general Python training, introduction to the ObsPy library for seismology as well as seismic data processing, noise analysis, and a variety of forward solvers for seismic wave propagation. In addition, an example is shown how Jupyter notebooks can be used to increase reproducibility of published results. Submission of Jupyter notebooks for general seismology are encouraged. The platform can be used for complementary teaching in Earth Science courses on compute-intensive research areas. We present recent developments and new features.

CCTOP: a Consensus Constrained TOPology prediction web server.

PubMed

Dobson, László; Reményi, István; Tusnády, Gábor E

2015-07-01

The Consensus Constrained TOPology prediction (CCTOP; http://cctop.enzim.ttk.mta.hu) server is a web-based application providing transmembrane topology prediction. In addition to utilizing 10 different state-of-the-art topology prediction methods, the CCTOP server incorporates topology information from existing experimental and computational sources available in the PDBTM, TOPDB and TOPDOM databases using the probabilistic framework of hidden Markov model. The server provides the option to precede the topology prediction with signal peptide prediction and transmembrane-globular protein discrimination. The initial result can be recalculated by (de)selecting any of the prediction methods or mapped experiments or by adding user specified constraints. CCTOP showed superior performance to existing approaches. The reliability of each prediction is also calculated, which correlates with the accuracy of the per protein topology prediction. The prediction results and the collected experimental information are visualized on the CCTOP home page and can be downloaded in XML format. Programmable access of the CCTOP server is also available, and an example of client-side script is provided. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API

PubMed Central

Ono, Keiichiro; Muetze, Tanja; Kolishovski, Georgi; Shannon, Paul; Demchak, Barry

2015-01-01

As bioinformatic workflows become increasingly complex and involve multiple specialized tools, so does the difficulty of reliably reproducing those workflows. Cytoscape is a critical workflow component for executing network visualization, analysis, and publishing tasks, but it can be operated only manually via a point-and-click user interface. Consequently, Cytoscape-oriented tasks are laborious and often error prone, especially with multistep protocols involving many networks. In this paper, we present the new cyREST Cytoscape app and accompanying harmonization libraries. Together, they improve workflow reproducibility and researcher productivity by enabling popular languages (e.g., Python and R, JavaScript, and C#) and tools (e.g., IPython/Jupyter Notebook and RStudio) to directly define and query networks, and perform network analysis, layouts and renderings. We describe cyREST’s API and overall construction, and present Python- and R-based examples that illustrate how Cytoscape can be integrated into large scale data analysis pipelines. cyREST is available in the Cytoscape app store (http://apps.cytoscape.org) where it has been downloaded over 1900 times since its release in late 2014. PMID:26672762

Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article

PubMed Central

Shotton, David; Portwin, Katie; Klyne, Graham; Miles, Alistair

2009-01-01

Scientific innovation depends on finding, integrating, and re-using the products of previous research. Here we explore how recent developments in Web technology, particularly those related to the publication of data and metadata, might assist that process by providing semantic enhancements to journal articles within the mainstream process of scholarly journal publishing. We exemplify this by describing semantic enhancements we have made to a recent biomedical research article taken from PLoS Neglected Tropical Diseases, providing enrichment to its content and increased access to datasets within it. These semantic enhancements include provision of live DOIs and hyperlinks; semantic markup of textual terms, with links to relevant third-party information resources; interactive figures; a re-orderable reference list; a document summary containing a study summary, a tag cloud, and a citation analysis; and two novel types of semantic enrichment: the first, a Supporting Claims Tooltip to permit “Citations in Context”, and the second, Tag Trees that bring together semantically related terms. In addition, we have published downloadable spreadsheets containing data from within tables and figures, have enriched these with provenance information, and have demonstrated various types of data fusion (mashups) with results from other research articles and with Google Maps. We have also published machine-readable RDF metadata both about the article and about the references it cites, for which we developed a Citation Typing Ontology, CiTO (http://purl.org/net/cito/). The enhanced article, which is available at http://dx.doi.org/10.1371/journal.pntd.0000228.x001, presents a compelling existence proof of the possibilities of semantic publication. We hope the showcase of examples and ideas it contains, described in this paper, will excite the imaginations of researchers and publishers, stimulating them to explore the possibilities of semantic publishing for their own research articles, and thereby break down present barriers to the discovery and re-use of information within traditional modes of scholarly communication. PMID:19381256

Piracy among Undergraduate and Graduate Students: Influences on Unauthorized Book Copies

ERIC Educational Resources Information Center

Dionisio, Pedro; Leal, Carmo; Pereira, Helia; Salgueiro, Maria Fatima

2013-01-01

The unauthorized duplication of books through photocopies and Internet downloads, especially in the case of academic books, is currently one of the most challenging problems facing the publishing industry. Photocopying has become widespread with these texts, apparently without major ethical concerns on the part of students. The purpose of this…

Millennium Ecosystem Assessment

Science.gov Websites

Well-Being. Learn more Download the Statement About the MA Board of Directors A Framework for Assessment In late 2003, the MA and Island Press published Ecosystems and Human Well-being: A Framework for Board Panel Secretariat Authors By Country By Chapter Reviewers Round 1 Reviewers Round 2 Reviewers

Ligandbook: an online repository for small and drug-like molecule force field parameters.

PubMed

Domanski, Jan; Beckstein, Oliver; Iorga, Bogdan I

2017-06-01

Ligandbook is a public database and archive for force field parameters of small and drug-like molecules. It is a repository for parameter sets that are part of published work but are not easily available to the community otherwise. Parameter sets can be downloaded and immediately used in molecular dynamics simulations. The sets of parameters are versioned with full histories and carry unique identifiers to facilitate reproducible research. Text-based search on rich metadata and chemical substructure search allow precise identification of desired compounds or functional groups. Ligandbook enables the rapid set up of reproducible molecular dynamics simulations of ligands and protein-ligand complexes. Ligandbook is available online at https://ligandbook.org and supports all modern browsers. Parameters can be searched and downloaded without registration, including access through a programmatic RESTful API. Deposition of files requires free user registration. Ligandbook is implemented in the PHP Symfony2 framework with TCL scripts using the CACTVS toolkit. oliver.beckstein@asu.edu or bogdan.iorga@cnrs.fr ; contact@ligandbook.org . Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

GIS Data Downloads | USDA Plant Hardiness Zone Map

Science.gov Websites

Acknowledgments & Citation Copyright Map & Data Downloads Map Downloads Geography (GIS) Downloads Multi & Data Downloads / GIS Data Downloads Topics Map Downloads Geography (GIS) Downloads Multi-Zip Code

What will the future of cloud-based astronomical data processing look like?

NASA Astrophysics Data System (ADS)

Green, Andrew W.; Mannering, Elizabeth; Harischandra, Lloyd; Vuong, Minh; O'Toole, Simon; Sealey, Katrina; Hopkins, Andrew M.

2017-06-01

Astronomy is rapidly approaching an impasse: very large datasets require remote or cloud-based parallel processing, yet many astronomers still try to download the data and develop serial code locally. Astronomers understand the need for change, but the hurdles remain high. We are developing a data archive designed from the ground up to simplify and encourage cloud-based parallel processing. While the volume of data we host remains modest by some standards, it is still large enough that download and processing times are measured in days and even weeks. We plan to implement a python based, notebook-like interface that automatically parallelises execution. Our goal is to provide an interface sufficiently familiar and user-friendly that it encourages the astronomer to run their analysis on our system in the cloud-astroinformatics as a service. We describe how our system addresses the approaching impasse in astronomy using the SAMI Galaxy Survey as an example.

The braingraph.org database of high resolution structural connectomes and the brain graph tools.

PubMed

Kerepesi, Csaba; Szalkai, Balázs; Varga, Bálint; Grolmusz, Vince

2017-10-01

Based on the data of the NIH-funded Human Connectome Project, we have computed structural connectomes of 426 human subjects in five different resolutions of 83, 129, 234, 463 and 1015 nodes and several edge weights. The graphs are given in anatomically annotated GraphML format that facilitates better further processing and visualization. For 96 subjects, the anatomically classified sub-graphs can also be accessed, formed from the vertices corresponding to distinct lobes or even smaller regions of interests of the brain. For example, one can easily download and study the connectomes, restricted to the frontal lobes or just to the left precuneus of 96 subjects using the data. Partially directed connectomes of 423 subjects are also available for download. We also present a GitHub-deposited set of tools, called the Brain Graph Tools, for several processing tasks of the connectomes on the site http://braingraph.org.

Report on Distance Learning Technologies.

DTIC Science & Technology

1995-09-01

26 cities. The CSX system includes full-motion video, animations , audio, and interactive examples and testing to teach the use of a new computer...video. The change to all-digital media now permits the use of full-motion video, animation , and audio on networks. It is possible to have independent...is possible to download entire multimedia presentations from the network. To date there is not a great deal known about teaching courses using the

Publications - NL 2002-1 | Alaska Division of Geological & Geophysical

Science.gov Websites

Visiting Alaska State Employees DGGS State of Alaska search Alaska Division of Geological & Geophysical 2002 Publisher: Alaska Division of Geological & Geophysical Surveys Ordering Info: Download below Reference DGGS Staff, and Werdon, M.B., 2002, Alaska GeoSurvey News - Geologic Investigations in the Salcha

Teachers' Use of Digital Technology in Secondary Music Education: Illustrations of Changing Classrooms

ERIC Educational Resources Information Center

Wise, Stuart; Greenwood, Janinka; Davis, Niki

2011-01-01

The music industry in the 21st century uses digital technology in a wide range of applications including performance, composition and in recording and publishing. Much of this digital technology is freely available via downloads from the internet, as part of software included with computers when they are purchased and via applications that are…

How Institutionalized Are Model License Use Terms? An Analysis of E-Journal License Use Rights Clauses from 2000 to 2009

ERIC Educational Resources Information Center

Eschenfelder, Kristin R.; Tsai, Tien-I; Zhu, Xiaohua; Stewart, Brenton

2013-01-01

This paper explored the degree to which use terms proposed by model licenses have become institutionalized across different publishers' licenses. It examined model license use terms in four areas: downloading, scholarly sharing, interlibrary loan, and electronic reserves. Data collection and analysis involved content analysis of 224 electronic…

Energy map of southwestern Wyoming - Energy data archived, organized, integrated, and accessible

USGS Publications Warehouse

Biewick, Laura; Jones, Nicholas R.; Wilson, Anna B.

2013-01-01

The Wyoming Landscape Conservation Initiative (WLCI) focuses on conserving world-class wildlife resources while facilitating responsible energy development in southwestern Wyoming. To further advance the objectives of the WLCI long-term, science-based effort, a comprehensive inventory of energy resource and production data is being published in two parts. Energy maps, data, documentation and spatial data processing capabilities are available in geodatabase, published map file (pmf), ArcMap document (mxd), Adobe Acrobat PDF map, and other digital formats that can be downloaded at the USGS website.

Digital Forensics Research: The Next 10 Years

DTIC Science & Technology

2010-01-01

techniques were developed primarily for data recovery. For example, Wood et al. relate a story about two local data recovery experts working for 70 h to...recover the only copy of a highly fragmented database file inadvertently erased by a careless researcher (pp.123e124 Wood et al., 1987). By the late 1980s... Apple , Blackberry, Windows Mobile, Symbian), more than a dozen “proprietary” systems, and more than 100,000 downloadable applications. There are

GeneSigDB: a manually curated database and resource for analysis of gene expression signatures

PubMed Central

Culhane, Aedín C.; Schröder, Markus S.; Sultana, Razvan; Picard, Shaita C.; Martinelli, Enzo N.; Kelly, Caroline; Haibe-Kains, Benjamin; Kapushesky, Misha; St Pierre, Anne-Alyssa; Flahive, William; Picard, Kermshlise C.; Gusenleitner, Daniel; Papenhausen, Gerald; O'Connor, Niall; Correll, Mick; Quackenbush, John

2012-01-01

GeneSigDB (http://www.genesigdb.org or http://compbio.dfci.harvard.edu/genesigdb/) is a database of gene signatures that have been extracted and manually curated from the published literature. It provides a standardized resource of published prognostic, diagnostic and other gene signatures of cancer and related disease to the community so they can compare the predictive power of gene signatures or use these in gene set enrichment analysis. Since GeneSigDB release 1.0, we have expanded from 575 to 3515 gene signatures, which were collected and transcribed from 1604 published articles largely focused on gene expression in cancer, stem cells, immune cells, development and lung disease. We have made substantial upgrades to the GeneSigDB website to improve accessibility and usability, including adding a tag cloud browse function, facetted navigation and a ‘basket’ feature to store genes or gene signatures of interest. Users can analyze GeneSigDB gene signatures, or upload their own gene list, to identify gene signatures with significant gene overlap and results can be viewed on a dynamic editable heatmap that can be downloaded as a publication quality image. All data in GeneSigDB can be downloaded in numerous formats including .gmt file format for gene set enrichment analysis or as a R/Bioconductor data file. GeneSigDB is available from http://www.genesigdb.org. PMID:22110038

The Caviar software package for the astrometric reduction of Cassini ISS images: description and examples

NASA Astrophysics Data System (ADS)

Cooper, N. J.; Lainey, V.; Meunier, L.-E.; Murray, C. D.; Zhang, Q.-F.; Baillie, K.; Evans, M. W.; Thuillot, W.; Vienne, A.

2018-02-01

Aims: Caviar is a software package designed for the astrometric measurement of natural satellite positions in images taken using the Imaging Science Subsystem (ISS) of the Cassini spacecraft. Aspects of the structure, functionality, and use of the software are described, and examples are provided. The integrity of the software is demonstrated by generating new measurements of the positions of selected major satellites of Saturn, 2013-2016, along with their observed minus computed (O-C) residuals relative to published ephemerides. Methods: Satellite positions were estimated by fitting a model to the imaged limbs of the target satellites. Corrections to the nominal spacecraft pointing were computed using background star positions based on the UCAC5 and Tycho2 star catalogues. UCAC5 is currently used in preference to Gaia-DR1 because of the availability of proper motion information in UCAC5. Results: The Caviar package is available for free download. A total of 256 new astrometric observations of the Saturnian moons Mimas (44), Tethys (58), Dione (55), Rhea (33), Iapetus (63), and Hyperion (3) have been made, in addition to opportunistic detections of Pandora (20), Enceladus (4), Janus (2), and Helene (5), giving an overall total of 287 new detections. Mean observed-minus-computed residuals for the main moons relative to the JPL SAT375 ephemeris were - 0.66 ± 1.30 pixels in the line direction and 0.05 ± 1.47 pixels in the sample direction. Mean residuals relative to the IMCCE NOE-6-2015-MAIN-coorb2 ephemeris were -0.34 ± 0.91 pixels in the line direction and 0.15 ± 1.65 pixels in the sample direction. The reduced astrometric data are provided in the form of satellite positions for each image. The reference star positions are included in order to allow reprocessing at some later date using improved star catalogues, such as later releases of Gaia, without the need to re-estimate the imaged star positions. The Caviar software is available for free download from: ftp://ftp://ftp.imcce.fr/pub/softwares/caviar.Full Tables 1 and 5 are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/610/A2

USGS compilation of geographic information system (GIS) data representing coal mines and coal-bearing areas in China

USGS Publications Warehouse

Trippi, Michael H.; Belkin, Harvey E.; Dai, Shifeng; Tewalt, Susan J.; Chou, Chiu-Jung; Trippi, Michael H.; Belkin, Harvey E.; Dai, Shifeng; Tewalt, Susan J.; Chou, Chiu-Jung

2015-01-01

Geographic information system (GIS) information may facilitate energy studies, which in turn provide input for energy policy decisions. The U.S. Geological Survey (USGS) has compiled geographic information system (GIS) data representing the known coal mine locations and coal-mining areas of China as of 2001. These data are now available for download, and may be used in a GIS for a variety of energy resource and environmental studies of China. Province-scale maps were also created to display the point locations of coal mines and the coal-mining areas. In addition, coal-field outlines from a previously published map by Dai and others (2012) were also digitized and are available for download as a separate GIS data file, and shown in a nation-scale map of China. Chemical data for 332 coal samples from a previous USGS study of China and Taiwan (Tewalt and others, 2010) are included in a downloadable GIS point shapefile, and shown on a nation-scale map of China. A brief report summarizes the methodology used for creation of the shapefiles and the chemical analyses run on the samples.

Site Map | USDA Plant Hardiness Zone Map

Science.gov Websites

Acknowledgments & Citation Copyright Map & Data Downloads Map Downloads Geography (GIS) Downloads Multi ; Citation Copyright Map & Data Downloads Map Downloads Geography (GIS) Downloads Multi-ZIP Code Finder

Pro-smoking apps: where, how and who are most at risk.

PubMed

BinDhim, Nasser F; Freeman, Becky; Trevena, Lyndal

2015-03-01

Pro-smoking applications (app) provide information about brands of tobacco products, where to buy them, and encourage their use. It is unclear in which countries these apps are being downloaded, or whether app stores play a role in promoting or regulating these apps, particularly those that appear to target children. The lifetime popularity of 107 pro-smoking apps was investigated, using a third-party app metrics service that aggregates data from app stores about app download popularity by country. Apps were deemed popular if at any time in their lifespan they achieved a top 25 ranking overall across all apps, or a top 25 ranking in any particular category of apps, such as 'educational games'. Fifty-eight pro-smoking apps reached 'popularity' status in Apple and Android stores in one or more of 49 countries, particularly Italy, Egypt, Germany, Belgium and the USA. The daily downloads in each country ranged from approximately 2000 to 80 000. The Apple store featured five of the pro-smoking apps in various categories, and two apps were featured by the Android market. Two pro-smoking apps in the Apple store were extremely popular in the 'Educational Games' and 'Kids' Games' categories. Pro-smoking apps were popular in many countries. Most apps were assigned to entertainment and games categories, with some apps specifically targeting children through placement in categories directed at children. App stores that feature pro-smoking apps may be in violation of tobacco control laws. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Commentary on the Integration of Model Sharing and Reproducibility Analysis to Scholarly Publishing Workflow in Computational Biomechanics

PubMed Central

Erdemir, Ahmet; Guess, Trent M.; Halloran, Jason P.; Modenese, Luca; Reinbolt, Jeffrey A.; Thelen, Darryl G.; Umberger, Brian R.

2016-01-01

Objective The overall goal of this document is to demonstrate that dissemination of models and analyses for assessing the reproducibility of simulation results can be incorporated in the scientific review process in biomechanics. Methods As part of a special issue on model sharing and reproducibility in IEEE Transactions on Biomedical Engineering, two manuscripts on computational biomechanics were submitted: A. Rajagopal et al., IEEE Trans. Biomed. Eng., 2016 and A. Schmitz and D. Piovesan, IEEE Trans. Biomed. Eng., 2016. Models used in these studies were shared with the scientific reviewers and the public. In addition to the standard review of the manuscripts, the reviewers downloaded the models and performed simulations that reproduced results reported in the studies. Results There was general agreement between simulation results of the authors and those of the reviewers. Discrepancies were resolved during the necessary revisions. The manuscripts and instructions for download and simulation were updated in response to the reviewers’ feedback; changes that may otherwise have been missed if explicit model sharing and simulation reproducibility analysis were not conducted in the review process. Increased burden on the authors and the reviewers, to facilitate model sharing and to repeat simulations, were noted. Conclusion When the authors of computational biomechanics studies provide access to models and data, the scientific reviewers can download and thoroughly explore the model, perform simulations, and evaluate simulation reproducibility beyond the traditional manuscript-only review process. Significance Model sharing and reproducibility analysis in scholarly publishing will result in a more rigorous review process, which will enhance the quality of modeling and simulation studies and inform future users of computational models. PMID:28072567

A slide down a slippery slope: ethical guidelines in the dissemination of computer-based presentations

Treesearch

Patrick C. Tobin; James L. Frazier

2009-01-01

The continual development of technology opens many new and exciting doors in all walks of life, including science. Undoubtedly, we all have benefited from the ability to rapidly disseminate and acquire scientific information. Published articles can be downloaded from the Internet even prior to their "actual" publication date, requests for pdf reprints of...

First Approved Kinase Inhibitor for AML.

PubMed

Rasko, John E J; Hughes, Timothy P

2017-11-16

Activating mutations of FLT3 occur in about 30% of acute myeloid leukemia (AML) cases and are associated with relapse and poor prognosis. Midostaurin is the first drug approved for AML since 2000, and the first multi-kinase inhibitor approved for the FLT3-mutant subtype. To view this Bench to Bedside, open or download the PDF. Copyright © 2017. Published by Elsevier Inc.

Building Global Capacity for Conducting Operational Research Using the SORT IT Model: Where and Who?

PubMed

Zachariah, Rony; Rust, Stefanie; Berger, Selma Dar; Guillerm, Nathalie; Bissell, Karen; Delaunois, Paul; Reid, Anthony J; Kumar, Ajay M V; Olliaro, Piero L; Reeder, John C; Harries, Anthony D; Ramsay, Andrew

2016-01-01

Research capacity is weakest in low and middle-income countries (LMICs) where operational research is highly relevant and needed. Structured Operational Research and Training Initiative (SORT IT) courses have been developed to train participants to conduct and publish operational research and influence policy and practice. Twenty courses were completed in Asia, Africa, Europe and the South Pacific between 2009 and 2014. In the 20 completed SORT IT courses, to assess where the research was conducted, who was trained, who became facilitators in subsequent courses and course outcomes. A cohort study of completed SORT IT courses. There were 236 participants (41% female) including 64 nationalities who conducted research in 59 countries, mostly from Asia and Africa (mean course duration = 9.7 months). Most participants (68%) were from government health programs and non-governmental agencies. A total of 213(90%) participants completed all milestones successfully with 41(19%) becoming subsequent course facilitators, 88% of whom were from LMICs. Of 228 manuscripts submitted to scientific journals, 197(86%) were either published or in press; in 86%, the principal investigator (first author) was a LMIC national. Papers were published in 23 scientific journals (impact factor 0.5-4.4) and covered 21 disease categories (median publication time = 5.7 months). Published papers (186) had 94,794 cumulative article views/downloads. Article views/downloads for immediate open access articles were double those from closed access journals. The SORT IT model has been effective in training personnel to produce relevant operational research in LMICs. It merits continued commitment and support for further scale-up and development.

MELOC - Memory and Location Optimized Caching for Mobile Ad Hoc Networks

DTIC Science & Technology

2011-01-01

required for such environments. Moreover, nodes located at centre have to be chosen as cache location, since it reduces the chance of being attacked...Figure 1.1. MANET Formed by Armed Forces 47 Example 3: Sharing of music and videos are famous among mobile users. Instead of downloading...The two tier caching scheme discussed in this paper is acoustic . The characteristics of two-tier caching are as follows, the content of data to be

SERDP and ESTCP Expert Panel Workshop on Research and Development Needs for the Environmental Remediation Application of Molecular Biological Tools

DTIC Science & Technology

2005-10-01

used to infer metabolic rates in marine systems. For example, there is evidence from both pure cultures and environmental samples that rbcL...It includes many useful bioinformatics features such as constructing a neighbor-joining tree for a subset of sequences, downloading a subset of...further provide software that allow users to extract useful information from sequences. The most commonly used feature is probe/primer design

Algorithm design for automated transportation photo enforcement camera image and video quality diagnostic check modules

NASA Astrophysics Data System (ADS)

Raghavan, Ajay; Saha, Bhaskar

2013-03-01

Photo enforcement devices for traffic rules such as red lights, toll, stops, and speed limits are increasingly being deployed in cities and counties around the world to ensure smooth traffic flow and public safety. These are typically unattended fielded systems, and so it is important to periodically check them for potential image/video quality problems that might interfere with their intended functionality. There is interest in automating such checks to reduce the operational overhead and human error involved in manually checking large camera device fleets. Examples of problems affecting such camera devices include exposure issues, focus drifts, obstructions, misalignment, download errors, and motion blur. Furthermore, in some cases, in addition to the sub-algorithms for individual problems, one also has to carefully design the overall algorithm and logic to check for and accurately classifying these individual problems. Some of these issues can occur in tandem or have the potential to be confused for each other by automated algorithms. Examples include camera misalignment that can cause some scene elements to go out of focus for wide-area scenes or download errors that can be misinterpreted as an obstruction. Therefore, the sequence in which the sub-algorithms are utilized is also important. This paper presents an overview of these problems along with no-reference and reduced reference image and video quality solutions to detect and classify such faults.

RiboMaker: computational design of conformation-based riboregulation.

PubMed

Rodrigo, Guillermo; Jaramillo, Alfonso

2014-09-01

The ability to engineer control systems of gene expression is instrumental for synthetic biology. Thus, bioinformatic methods that assist such engineering are appealing because they can guide the sequence design and prevent costly experimental screening. In particular, RNA is an ideal substrate to de novo design regulators of protein expression by following sequence-to-function models. We have implemented a novel algorithm, RiboMaker, aimed at the computational, automated design of bacterial riboregulation. RiboMaker reads the sequence and structure specifications, which codify for a gene regulatory behaviour, and optimizes the sequences of a small regulatory RNA and a 5'-untranslated region for an efficient intermolecular interaction. To this end, it implements an evolutionary design strategy, where random mutations are selected according to a physicochemical model based on free energies. The resulting sequences can then be tested experimentally, providing a new tool for synthetic biology, and also for investigating the riboregulation principles in natural systems. Web server is available at http://ribomaker.jaramillolab.org/. Source code, instructions and examples are freely available for download at http://sourceforge.net/projects/ribomaker/. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Mental health first aid guidelines: an evaluation of impact following download from the World Wide Web.

PubMed

Hart, Laura M; Jorm, Anthony F; Paxton, Susan J; Cvetkovski, Stefan

2012-11-01

Mental health first aid guidelines provide the public with consensus-based information about how to assist someone who is developing a mental illness or experiencing a mental health crisis. The aim of the current study was to evaluate the usefulness and impact of the guidelines on web users who download them. Web users who downloaded the documents were invited to respond to an initial demographic questionnaire, then a follow up about how the documents had been used, their perceived usefulness, whether first-aid situations had been encountered and if these were influenced by the documents. Over 9.8 months, 706 web users responded to the initial questionnaire and 154 responded to the second. A majority reported downloading the document because their job involved contact with people with mental illness. Sixty-three web users reported providing first aid, 44 of whom reported that the person they were assisting had sought professional care as a result of their suggestion. Twenty-three web users reported seeking care themselves. A majority of those who provided first aid reported feeling that they had been successful in helping the person, that they had been able to assist in a way that was more knowledgeable, skilful and supportive, and that the guidelines had contributed to these outcomes. Information made freely available on the Internet, about how to provide mental health first aid to someone who is developing a mental health problem or experiencing a mental health crisis, is associated with more positive, empathic and successful helping behaviours. © 2012 Wiley Publishing Asia Pty Ltd.

SEGY to ASCII: Conversion and Plotting Program

USGS Publications Warehouse

Goldman, Mark R.

1999-01-01

This report documents a computer program to convert standard 4 byte, IBM floating point SEGY files to ASCII xyz format. The program then optionally plots the seismic data using the GMT plotting package. The material for this publication is contained in a standard tar file (of99-126.tar) that is uncompressed and 726 K in size. It can be downloaded by any Unix machine. Move the tar file to the directory you wish to use it in, then type 'tar xvf of99-126.tar' The archive files (and diskette) contain a NOTE file, a README file, a version-history file, source code, a makefile for easy compilation, and an ASCII version of the documentation. The archive files (and diskette) also contain example test files, including a typical SEGY file along with the resulting ASCII xyz and postscript files. Requirements for compiling the source code into an executable are a C++ compiler. The program has been successfully compiled using Gnu's g++ version 2.8.1, and use of other compilers may require modifications to the existing source code. The g++ compiler is a free, high quality C++ compiler and may be downloaded from the ftp site: ftp://ftp.gnu.org/gnu Requirements for plotting the seismic data is the existence of the GMT plotting package. The GMT plotting package may be downloaded from the web site: http://www.soest.hawaii.edu/gmt/

How to maximize science communication efficacy by combining old and new media

NASA Astrophysics Data System (ADS)

Nuccitelli, D. A.; Cook, J.

2014-12-01

Traditional science communication approaches (such as relying on university press releases about new scientific publications), and new communication approaches (such as utilizing infographics and social media), can each reach a wide audience when successful. However, probability of successful the science communication can be amplified by taking advantage of both traditional and new media, especially when 'sticky' messaging techniques are applied. The example of Cook et al., 2013 (C13), which found a 97% consensus in the peer-reviewed climate literature on human-caused global warming, is considered. C13 implemented this optimal combined communications approach strategy and became the most-downloaded study in all Institute of Physics journals, with over 200,000 downloads to date. Due to the effective 'sticky' messaging approaches implemented by the study authors, its results received broad coverage from international media and reached millions of people via social media. Strategies to avoid misrepresentations of one's work while maximizing the communications efficacy of its key points will also be discussed.

Sedimentologic characteristics of recent washover deposits from Assateague Island, Maryland

USGS Publications Warehouse

Bernier, Julie C.; Zaremba, Nicholas J.; Wheaton, Cathryn J.; Ellis, Alisha M.; Marot, Marci E.; Smith, Christopher G.

2016-06-08

This report describes sediment data collected using sand augers in active overwash zones on Assateague Island in Maryland. Samples were collected by the U.S. Geological Survey (USGS) during two surveys in March/April and October 2014 (USGS Field Activity Numbers [FAN] 2014-301-FA and 2014-322-FA, respectively). The physical characteristics (for example, sediment texture or bedding structure) of and spatial differences among these deposits will provide information about overwash processes and sediment transport from the sandy barrier-island reaches to the back-barrier environments. Metrics derived from these data, such as mean grain size or deposit thicknesses, can be used to ground-truth remote sensing and geophysical data and can also be incorporated into sediment transport models. Data products, including sample location tables, descriptive core logs, core photographs and x-radiographs, the results of sediment grain-size analyses, and Geographic Information System (GIS) data files with accompanying formal Federal Geographic Data Committee (FGDC) metadata can be downloaded from the Data Downloads page.

Persuading Teachers to Adopt Academic Theories (or Deontological Perspectives in Professional Motivation to Translate Academic Theories into Praxis): Developing a Communications Epistemology by Action Research

ERIC Educational Resources Information Center

Thody, Angela

2008-01-01

This article is to encourage debate about the challenges for academics wanting to see our theories translated into practice in schools. Conventional academic articles do not provide information ready for immediate download into daily school practice. Should academics therefore publish in alternative formats and styles as exemplified in the…

UQTk Version 3.0.3 User Manual

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

Sargsyan, Khachik; Safta, Cosmin; Chowdhary, Kamaljit Singh

2017-05-01

The UQ Toolkit (UQTk) is a collection of libraries and tools for the quantification of uncertainty in numerical model predictions. Version 3.0.3 offers intrusive and non-intrusive methods for propagating input uncertainties through computational models, tools for sen- sitivity analysis, methods for sparse surrogate construction, and Bayesian inference tools for inferring parameters from experimental data. This manual discusses the download and installation process for UQTk, provides pointers to the UQ methods used in the toolkit, and describes some of the examples provided with the toolkit.

TCIApathfinder: an R client for The Cancer Imaging Archive REST API.

PubMed

Russell, Pamela; Fountain, Kelly; Wolverton, Dulcy; Ghosh, Debashis

2018-06-05

The Cancer Imaging Archive (TCIA) hosts publicly available de-identified medical images of cancer from over 25 body sites and over 30,000 patients. Over 400 published studies have utilized freely available TCIA images. Images and metadata are available for download through a web interface or a REST API. Here we present TCIApathfinder, an R client for the TCIA REST API. TCIApathfinder wraps API access in user-friendly R functions that can be called interactively within an R session or easily incorporated into scripts. Functions are provided to explore the contents of the large database and to download image files. TCIApathfinder provides easy access to TCIA resources in the highly popular R programming environment. TCIApathfinder is freely available under the MIT license as a package on CRAN (https://cran.r-project.org/web/packages/TCIApathfinder/index.html) and at https://github.com/pamelarussell/TCIApathfinder. Copyright ©2018, American Association for Cancer Research.

25 CFR 547.12 - What are the minimum technical standards for downloading on a Class II gaming system?

Code of Federal Regulations, 2013 CFR

2013-04-01

... limited to software, files, data, and prize schedules. (2) Downloads must use secure methodologies that... date of the completion of the download; (iii) The Class II gaming system components to which software was downloaded; (iv) The version(s) of download package and any software downloaded. Logging of the...

25 CFR 547.12 - What are the minimum technical standards for downloading on a Class II gaming system?

Code of Federal Regulations, 2014 CFR

2014-04-01

... limited to software, files, data, and prize schedules. (2) Downloads must use secure methodologies that... date of the completion of the download; (iii) The Class II gaming system components to which software was downloaded; (iv) The version(s) of download package and any software downloaded. Logging of the...

Building Global Capacity for Conducting Operational Research Using the SORT IT Model: Where and Who?

PubMed Central

Zachariah, Rony; Rust, Stefanie; Berger, Selma Dar; Guillerm, Nathalie; Bissell, Karen; Delaunois, Paul; Reid, Anthony J.; Kumar, Ajay M. V.; Olliaro, Piero L.; Reeder, John C.; Harries, Anthony D.; Ramsay, Andrew

2016-01-01

Setting Research capacity is weakest in low and middle-income countries (LMICs) where operational research is highly relevant and needed. Structured Operational Research and Training Initiative (SORT IT) courses have been developed to train participants to conduct and publish operational research and influence policy and practice. Twenty courses were completed in Asia, Africa, Europe and the South Pacific between 2009 and 2014. Objectives In the 20 completed SORT IT courses, to assess where the research was conducted, who was trained, who became facilitators in subsequent courses and course outcomes. Design A cohort study of completed SORT IT courses Results There were 236 participants (41% female) including 64 nationalities who conducted research in 59 countries, mostly from Asia and Africa (mean course duration = 9.7 months). Most participants (68%) were from government health programs and non-governmental agencies. A total of 213(90%) participants completed all milestones successfully with 41(19%) becoming subsequent course facilitators, 88% of whom were from LMICs. Of 228 manuscripts submitted to scientific journals, 197(86%) were either published or in press; in 86%, the principal investigator (first author) was a LMIC national. Papers were published in 23 scientific journals (impact factor 0.5–4.4) and covered 21 disease categories (median publication time = 5.7 months). Published papers (186) had 94,794 cumulative article views/downloads. Article views/downloads for immediate open access articles were double those from closed access journals. Conclusion The SORT IT model has been effective in training personnel to produce relevant operational research in LMICs. It merits continued commitment and support for further scale-up and development. PMID:27505253

Alternative Fuels Data Center: Data Downloads

Science.gov Websites

Data Downloads to someone by E-mail Share Alternative Fuels Data Center: Data Downloads on Facebook Tweet about Alternative Fuels Data Center: Data Downloads on Twitter Bookmark Alternative Fuels Data Center: Data Downloads on Google Bookmark Alternative Fuels Data Center: Data Downloads on Delicious Rank

Analysing researchers’ outreach efforts and the association with publication metrics: A case study of Kudos

PubMed Central

Aung, Htet Htet; Aw, Ashley Sara; Rapple, Charlie; Theng, Yin-Leng

2017-01-01

With the growth of scholarly collaboration networks and social communication platforms, members of the scholarly community are experimenting with their approach to disseminating research outputs, in an effort to increase their audience and outreach. However, from a researcher’s point of view, it is difficult to determine whether efforts to make work more visible are worthwhile (in terms of the association with publication metrics) and within that, difficult to assess which platform or network is most effective for sharing work and connecting to a wider audience. We undertook a case study of Kudos (https://www.growkudos.com), a web-based service that claims to help researchers increase the outreach of their publications, to examine the most effective tools for sharing publications online, and to investigate which actions are associated with improved metrics. We extracted a dataset from Kudos of 830,565 unique publications claimed by authors, for which 20,775 had actions taken to explain or share via Kudos, and for 4,867 of these full text download data from publishers was available. Findings show that researchers are most likely to share their work on Facebook, but links shared on Twitter are more likely to be clicked on. A Mann-Whitney U test revealed that a treatment group (publications having actions in Kudos) had a significantly higher median average of 149 full text downloads (23.1% more) per publication as compared to a control group (having no actions in Kudos) with a median average of 121 full text downloads per publication. These findings suggest that performing actions on publications, such as sharing, explaining, or enriching, could help to increase the number of full text downloads of a publication. PMID:28817627

Downloading from the OPAC: The Innovative Interfaces Environment.

ERIC Educational Resources Information Center

Spore, Stuart

1991-01-01

Discussion of downloading from online public access catalogs focuses on downloading to MS-DOS microcomputers from the INNOPAC online catalog system. Tools for capturing and postprocessing downloaded files are described, technical and institutional constraints on downloading are addressed, and an innovative program for overcoming such constraints…

Biotool2Web: creating simple Web interfaces for bioinformatics applications.

PubMed

Shahid, Mohammad; Alam, Intikhab; Fuellen, Georg

2006-01-01

Currently there are many bioinformatics applications being developed, but there is no easy way to publish them on the World Wide Web. We have developed a Perl script, called Biotool2Web, which makes the task of creating web interfaces for simple ('home-made') bioinformatics applications quick and easy. Biotool2Web uses an XML document containing the parameters to run the tool on the Web, and generates the corresponding HTML and common gateway interface (CGI) files ready to be published on a web server. This tool is available for download at URL http://www.uni-muenster.de/Bioinformatics/services/biotool2web/ Georg Fuellen (fuellen@alum.mit.edu).

Achieving open access to conservation science.

PubMed

Fuller, Richard A; Lee, Jasmine R; Watson, James E M

2014-12-01

Conservation science is a crisis discipline in which the results of scientific enquiry must be made available quickly to those implementing management. We assessed the extent to which scientific research published since the year 2000 in 20 conservation science journals is publicly available. Of the 19,207 papers published, 1,667 (8.68%) are freely downloadable from an official repository. Moreover, only 938 papers (4.88%) meet the standard definition of open access in which material can be freely reused providing attribution to the authors is given. This compares poorly with a comparable set of 20 evolutionary biology journals, where 31.93% of papers are freely downloadable and 7.49% are open access. Seventeen of the 20 conservation journals offer an open access option, but fewer than 5% of the papers are available through open access. The cost of accessing the full body of conservation science runs into tens of thousands of dollars per year for institutional subscribers, and many conservation practitioners cannot access pay-per-view science through their workplace. However, important initiatives such as Research4Life are making science available to organizations in developing countries. We urge authors of conservation science to pay for open access on a per-article basis or to choose publication in open access journals, taking care to ensure the license allows reuse for any purpose providing attribution is given. Currently, it would cost $51 million to make all conservation science published since 2000 freely available by paying the open access fees currently levied to authors. Publishers of conservation journals might consider more cost effective models for open access and conservation-oriented organizations running journals could consider a broader range of options for open access to nonmembers such as sponsorship of open access via membership fees. © 2014 The Authors. Conservation Biology published by Wiley Periodicals, Inc., on behalf of the Society for Conservation Biology.

College Students' Moral Evaluations of Illegal Music Downloading

ERIC Educational Resources Information Center

Jambon, Marc M.; Smetana, Judith G.

2012-01-01

Although unauthorized music downloading is illegal, a majority of college students have downloaded music for free online. Evaluations of illegal music downloading and their association with downloading behavior were examined using social domain theory in a sample of 188 ethnically diverse college students (M[subscript age] = 19.80 years, SD =…

The GeoClaw software for depth-averaged flows with adaptive refinement

USGS Publications Warehouse

Berger, M.J.; George, D.L.; LeVeque, R.J.; Mandli, Kyle T.

2011-01-01

Many geophysical flow or wave propagation problems can be modeled with two-dimensional depth-averaged equations, of which the shallow water equations are the simplest example. We describe the GeoClaw software that has been designed to solve problems of this nature, consisting of open source Fortran programs together with Python tools for the user interface and flow visualization. This software uses high-resolution shock-capturing finite volume methods on logically rectangular grids, including latitude-longitude grids on the sphere. Dry states are handled automatically to model inundation. The code incorporates adaptive mesh refinement to allow the efficient solution of large-scale geophysical problems. Examples are given illustrating its use for modeling tsunamis and dam-break flooding problems. Documentation and download information is available at www.clawpack.org/geoclaw. ?? 2011.

Archive of digital chirp subbottom profile data collected during USGS cruise 12BIM03 offshore of the Chandeleur Islands, Louisiana, July 2012

USGS Publications Warehouse

Forde, Arnell S.; Miselis, Jennifer L.; Wiese, Dana S.

2014-01-01

From July 23 - 31, 2012, the U.S. Geological Survey conducted geophysical surveys to investigate the geologic controls on barrier island framework and long-term sediment transport along the oil spill mitigation sand berm constructed at the north end and just offshore of the Chandeleur Islands, La. (figure 1). This effort is part of a broader USGS study, which seeks to better understand barrier island evolution over medium time scales (months to years). This report serves as an archive of unprocessed digital chirp subbottom data, trackline maps, navigation files, Geographic Information System (GIS) files, Field Activity Collection System (FACS) logs, and formal Federal Geographic Data Committee (FGDC) metadata. Gained (showing a relative increase in signal amplitude) digital images of the seismic profiles are also provided. Refer to the Abbreviations page for expansions of acronyms and abbreviations used in this report. The USGS St. Petersburg Coastal and Marine Science Center (SPCMSC) assigns a unique identifier to each cruise or field activity. For example, 12BIM03 tells us the data were collected in 2012 during the third field activity for that project in that calendar year and BIM is a generic code, which represents efforts related to Barrier Island Mapping. Refer to http://walrus.wr.usgs.gov/infobank/programs/html/definition/activity.html for a detailed description of the method used to assign the field activity ID. All chirp systems use a signal of continuously varying frequency; the EdgeTech SB-424 system used during this survey produces high-resolution, shallow-penetration (typically less than 50 milliseconds (ms)) profile images of sub-seafloor stratigraphy. The towfish contains a transducer that transmits and receives acoustic energy and is typically towed 1 - 2 m below the sea surface. As transmitted acoustic energy intersects density boundaries, such as the seafloor or sub-surface sediment layers, energy is reflected back toward the transducer, received, and recorded by a PC-based seismic acquisition system. This process is repeated at regular time intervals (for example, 0.125 seconds (s)) and returned energy is recorded for a specific duration (for example, 50 ms). In this way, a two-dimensional (2-D) vertical image of the shallow geologic structure beneath the ship track is produced. Figure 2 displays the acquisition geometry. Refer to table 1 for a summary of acquisition parameters and table 2 for trackline statistics. The archived trace data are in standard Society of Exploration Geophysicists (SEG) SEG Y rev. 0 format (Barry and others, 1975); the first 3,200 bytes of the card image header are in ASCII format instead of EBCDIC format. The SEG Y files may be downloaded and processed with commercial or public domain software such as Seismic Unix (SU) (Cohen and Stockwell, 2010). See the How To Download SEG Y Data page for download instructions. The web version of this archive does not contain the SEG Y trace files. These files are very large and would require extremely long download times. To obtain the complete DVD archive, contact USGS Information Services at 1-888-ASK-USGS or infoservices@usgs.gov. The printable profiles provided here are GIF images that were processed and gained using SU software and can be viewed from the Profiles page or from links located on the trackline maps; refer to the Software page for links to example SU processing scripts. The SEG Y files are available on the DVD version of this report or on the Web, downloadable via the USGS Coastal and Marine Geoscience Data System (http://cmgds.marine.usgs.gov). The data are also available for viewing using GeoMapApp (http://www.geomapapp.org) and Virtual Ocean (http://www.virtualocean.org) multi-platform open source software. Detailed information about the navigation system used can be found in table 1 and the Field Activity Collection System (FACS) logs. To view the trackline maps and navigation files, and for more information about these items, see the Navigation page.

The Librarians' Dilemma: Should We Purchase the E-Book? The P-Book? Both? Neither?

NASA Astrophysics Data System (ADS)

Holmquist, J.

2012-08-01

Publishers of books in astronomy and astrophysics vary greatly in how they market the electronic versions of the print. In most cases, the electronic version for a single user costs the same as the print, and it costs even more for multiple simultaneous users. Some publishers encourage libraries to subscribe to an entire year's output by subject; others make single titles available via the publisher's website, or a vendor's platform such as ebrary. In the latter instance, readers are often surprised to discover that although they can read the entire text online, they can print or download only limited portions. Can we afford to purchase both print and online, if they are only using one? What is the library's obligation to future users and other questions will be addressed.

Visualization of spiral and scroll waves in simulated and experimental cardiac tissue

NASA Astrophysics Data System (ADS)

Cherry, E. M.; Fenton, F. H.

2008-12-01

The heart is a nonlinear biological system that can exhibit complex electrical dynamics, complete with period-doubling bifurcations and spiral and scroll waves that can lead to fibrillatory states that compromise the heart's ability to contract and pump blood efficiently. Despite the importance of understanding the range of cardiac dynamics, studying how spiral and scroll waves can initiate, evolve, and be terminated is challenging because of the complicated electrophysiology and anatomy of the heart. Nevertheless, over the last two decades advances in experimental techniques have improved access to experimental data and have made it possible to visualize the electrical state of the heart in more detail than ever before. During the same time, progress in mathematical modeling and computational techniques has facilitated using simulations as a tool for investigating cardiac dynamics. In this paper, we present data from experimental and simulated cardiac tissue and discuss visualization techniques that facilitate understanding of the behavior of electrical spiral and scroll waves in the context of the heart. The paper contains many interactive media, including movies and interactive two- and three-dimensional Java appletsDisclaimer: IOP Publishing was not involved in the programming of this software and does not accept any responsibility for it. You download and run the software at your own risk. If you experience any problems with the software, please contact the author directly. To the fullest extent permitted by law, IOP Publishing Ltd accepts no responsibility for any loss, damage and/or other adverse effect on your computer system caused by your downloading and running this software. IOP Publishing Ltd accepts no responsibility for consequential loss..

Comparing alternative and traditional dissemination metrics in medical education.

PubMed

Amath, Aysah; Ambacher, Kristin; Leddy, John J; Wood, Timothy J; Ramnanan, Christopher J

2017-09-01

The impact of academic scholarship has traditionally been measured using citation-based metrics. However, citations may not be the only measure of impact. In recent years, other platforms (e.g. Twitter) have provided new tools for promoting scholarship to both academic and non-academic audiences. Alternative metrics (altmetrics) can capture non-traditional dissemination data such as attention generated on social media platforms. The aims of this exploratory study were to characterise the relationships among altmetrics, access counts and citations in an international and pre-eminent medical education journal, and to clarify the roles of these metrics in assessing the impact of medical education academic scholarship. A database study was performed (September 2015) for all papers published in Medical Education in 2012 (n = 236) and 2013 (n = 246). Citation, altmetric and access (HTML views and PDF downloads) data were obtained from Scopus, the Altmetric Bookmarklet tool and the journal Medical Education, respectively. Pearson coefficients (r-values) between metrics of interest were then determined. Twitter and Mendeley (an academic bibliography tool) were the only altmetric-tracked platforms frequently (> 50%) utilised in the dissemination of articles. Altmetric scores (composite measures of all online attention) were driven by Twitter mentions. For short and full-length articles in 2012 and 2013, both access counts and citation counts were most strongly correlated with one another, as well as with Mendeley downloads. By comparison, Twitter metrics and altmetric scores demonstrated weak to moderate correlations with both access and citation counts. Whereas most altmetrics showed limited correlations with readership (access counts) and impact (citations), Mendeley downloads correlated strongly with both readership and impact indices for articles published in the journal Medical Education and may therefore have potential use that is complementary to that of citations in assessment of the impact of medical education scholarship. © 2017 John Wiley & Sons Ltd and The Association for the Study of Medical Education.

Images

Science.gov Websites

: Upload Date Photo Date 1 2 3 4 5 Next Arctic Edge 2018 Download Full Image Photo Details Arctic Edge 2018 Download Full Image Photo Details Arctic Edge 2018 Download Full Image Photo Details Arctic Edge 2018 Download Full Image Photo Details Arctic Edge 2018 Download Full Image Photo Details Arctic Edge 2018

How do I obtain CERES data?

Atmospheric Science Data Center

2017-10-12

Order online ASDC Web Ordering Tool data available for ftp download. Order online CERES Subsetter Ordering Page data available for ftp download. Order online Earthdata Search Tool data available for download. Download the ...

IDL Object Oriented Software for Hinode/XRT Image Analysis

NASA Astrophysics Data System (ADS)

Higgins, P. A.; Gallagher, P. T.

2008-09-01

We have developed a set of object oriented IDL routines that enable users to search, download and analyse images from the X-Ray Telescope (XRT) on-board Hinode. In this paper, we give specific examples of how the object can be used and how multi-instrument data analysis can be performed. The XRT object is a highly versatile and powerful IDL object, which will prove to be a useful tool for solar researchers. This software utilizes the generic Framework object available within the GEN branch of SolarSoft.

Development of a Spacecraft Materials Selector Expert System

NASA Technical Reports Server (NTRS)

Pippin, G.; Kauffman, W. (Technical Monitor)

2002-01-01

This report contains a description of the knowledge base tool and examples of its use. A downloadable version of the Spacecraft Materials Selector (SMS) knowledge base is available through the NASA Space Environments and Effects Program. The "Spacecraft Materials Selector" knowledge base is part of an electronic expert system. The expert system consists of an inference engine that contains the "decision-making" code and the knowledge base that contains the selected body of information. The inference engine is a software package previously developed at Boeing, called the Boeing Expert System Tool (BEST) kit.

Beam Propagator for Weather Radars, Modules 1 and 2

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

Ortega, Edwin Campos

2013-10-08

This program simulates the beam propagation of weather radar pulses under particular and realistic atmospheric conditions (without using the assumption of standard refraction conditions). It consists of two modules: radiosondings_refract_index_many.pro (MAIN MODULE) beam_propagation_function.pro(EXTERNAL FUNCTION) FOR THE MAIN MODULE, THE CODE DOES OUTPUT--INTO A FILE--THE BEAM HEIGHT AS A FUNCTION OF RANGE. THE RADIOSONDE INPUT FILES SHOULD BE ALREADY AVAILABLE BY THE USER. FOR EXAMPLE, RADIOSONDE OBSERVATION FILES CAN BE OBTAINED AT: RADIOSONDE OBSERVATIONS DOWNLOADED AT "http://weather.uwyo.edu/upperair/soounding.html" OR "http://jervis.pyr.ec.gc.ca" THE EXTERNAL FUNCTION DOES THE ACTUAL COMPUTATION OF BEAM PROPAGATION. IT INCLUDES CONDITIONS OF ANOMALOUS PROPAGATION AND NEGATIVE ELEVATION ANGLES. THE EQUATIONSmore » USED HERE WERE DERIVED BY EDWIN CAMPOS, BASED ON THE SNELL-DESCARTES LAW OF REFRACTION, CONSIDERING THE EARTH CURVATURE. THE PROGRAM REQUIRES A COMPILER FOR THE INTERACTIVE DATA LANGUAGE (IDL). DESCRIPTION AND VALIDATION DETAILS HAVE BEEN PUBLISHED IN THE PEER-REVIEWED SCIENTIFIC LITERATURE, AS FOLLOWS: Campos E. 2012. Estimating weather radar coverage over complex terrain, pp.26-32, peer reviewed, in Weather Radar and Hydrology, edited by Moore RJ, Cole SJ and Illingworth AJ. International Association of Hydrological Sciences (IAHS) Press, IAHS Publ. 351. ISBN 978-1-907161-26-1.« less

Alignment-Annotator web server: rendering and annotating sequence alignments.

PubMed

Gille, Christoph; Fähling, Michael; Weyand, Birgit; Wieland, Thomas; Gille, Andreas

2014-07-01

Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

A tool for optimization of the production and user analysis on the Grid, C. Grigoras for the ALICE Collaboration

NASA Astrophysics Data System (ADS)

Grigoras, Costin; Carminati, Federico; Vladimirovna Datskova, Olga; Schreiner, Steffen; Lee, Sehoon; Zhu, Jianlin; Gheata, Mihaela; Gheata, Andrei; Saiz, Pablo; Betev, Latchezar; Furano, Fabrizio; Mendez Lorenzo, Patricia; Grigoras, Alina Gabriela; Bagnasco, Stefano; Peters, Andreas Joachim; Saiz Santos, Maria Dolores

2011-12-01

With the LHC and ALICE entering a full operation and production modes, the amount of Simulation and RAW data processing and end user analysis computational tasks are increasing. The efficient management of all these tasks, all of which have large differences in lifecycle, amounts of processed data and methods to analyze the end result, required the development and deployment of new tools in addition to the already existing Grid infrastructure. To facilitate the management of the large scale simulation and raw data reconstruction tasks, ALICE has developed a production framework called a Lightweight Production Manager (LPM). The LPM is automatically submitting jobs to the Grid based on triggers and conditions, for example after a physics run completion. It follows the evolution of the job and publishes the results on the web for worldwide access by the ALICE physicists. This framework is tightly integrated with the ALICE Grid framework AliEn. In addition to the publication of the job status, LPM is also allowing a fully authenticated interface to the AliEn Grid catalogue, to browse and download files, and in the near future will provide simple types of data analysis through ROOT plugins. The framework is also being extended to allow management of end user jobs.

Navigating protected genomics data with UCSC Genome Browser in a Box.

PubMed

Haeussler, Maximilian; Raney, Brian J; Hinrichs, Angie S; Clawson, Hiram; Zweig, Ann S; Karolchik, Donna; Casper, Jonathan; Speir, Matthew L; Haussler, David; Kent, W James

2015-03-01

Genome Browser in a Box (GBiB) is a small virtual machine version of the popular University of California Santa Cruz (UCSC) Genome Browser that can be run on a researcher's own computer. Once GBiB is installed, a standard web browser is used to access the virtual server and add personal data files from the local hard disk. Annotation data are loaded on demand through the Internet from UCSC or can be downloaded to the local computer for faster access. Software downloads and installation instructions are freely available for non-commercial use at https://genome-store.ucsc.edu/. GBiB requires the installation of open-source software VirtualBox, available for all major operating systems, and the UCSC Genome Browser, which is open source and free for non-commercial use. Commercial use of GBiB and the Genome Browser requires a license (http://genome.ucsc.edu/license/). © The Author 2014. Published by Oxford University Press.

Share, steal, or buy? A social cognitive perspective of music downloading.

PubMed

LaRose, Robert; Kim, Junghyun

2007-04-01

The music downloading phenomenon presents a unique opportunity to examine normative influences on media consumption behavior. Downloaders face moral, legal, and ethical quandaries that can be conceptualized as normative influences within the self-regulatory mechanism of social cognitive theory. The music industry hopes to eliminate illegal file sharing and to divert illegal downloaders to pay services by asserting normative influence through selective prosecutions and public information campaigns. However the deficient self-regulation of downloaders counters these efforts maintaining file sharing as a persistent habit that defies attempts to establish normative control. The present research tests and extends the social cognitive theory of downloading on a sample of college students. The expected outcomes of downloading behavior and deficient self-regulation of that behavior were found to be important determinants of intentions to continue downloading. Consistent with social cognitive theory but in contrast to the theory of planned behavior, it was found that descriptive and prescriptive norms influenced deficient self-regulation but had no direct impact on behavioral intentions. Downloading intentions also had no direct relationship to either compact disc purchases or to subscription to online pay music services.

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

Nondestructive Evaluation (NDE) Technology Initiatives (NTIP). Delivery Order 0039: Statistical Comparison of Competing Material Models

DTIC Science & Technology

2003-01-01

adapted from Kass and Rafferty (1995) and Congdon (2001). Page 10 of 57 density adjusted for resin content, z, since resin contributes to the density...c.f.: Congdon , 2001). How to Download the WinBUGS Software Package BUGS was originally a statistical research project at the Medical Research...Likelihood Estimation,” July 2002, working paper to be published. 18) Congdon , Peter, Bayesian Statistical Modeling, Wiley, 2001 19) Cox, D. R. and

Coding Complete Genome for the Mogiana Tick Virus, a Jingmenvirus Isolated from Ticks in Brazil

DTIC Science & Technology

2017-05-04

sequences for all four genome segments. We downloaded the raw Illumina sequence reads from the NCBI Short Read Archive (GenBank...MGTV genome segments through sequence similarity (BLASTN) to the published genome of Jingmen tick virus (JMTV) isolate SY84 (GenBank: KJ001579-KJ001582...2014. Standards for sequencing viral genomes in the era of high-throughput sequencing . MBio 5:e01360–14. 8. Bankevich A, Nurk S, Antipov

The most downloaded and most cited articles in radiology journals: a comparative bibliometric analysis.

PubMed

Baek, Sora; Yoon, Dae Young; Lim, Kyoung Ja; Cho, Young Kwon; Seo, Young Lan; Yun, Eun Joo

2018-05-07

To evaluate and compare the characteristics of the most downloaded and most cited articles in radiology journals. We selected 41 radiology journals that provided lists of both the most downloaded and most cited articles on their websites, and identified the 596 most downloaded articles and 596 most cited articles. We compared the following characteristics of the most downloaded and most cited articles: year of publication, journal title, department of the first author, country of origin, publication type, radiologic subspecialty, radiologic technique and accessibility. Compared to the most cited articles, the most downloaded articles were more frequently review articles (36.1% vs 17.1%, p < 0.05), case reports (5.9% vs 3.2%, p < 0.05), guidelines/consensus statements (5.4% vs 2.7%, p < 0.05), editorials/commentaries (3.7% vs 0.7%, p < 0.05) and pictorial essays (2.0% vs 0.2%, p < 0.05). Compared to the most cited articles, the most downloaded articles more frequently originated from the UK (8.7% vs 5.0%, p < 0.05) and were more frequently free-access articles (46.0% vs 39.4%, p < 0.05). Educational and free-access articles are more frequent among the most downloaded articles. • There was only small overlap between the most downloaded and most cited articles. • Educational articles were more frequent among the most downloaded articles. • Free-access articles are more frequent among the most downloaded articles.

The cyber-aspects of virtual communities: free downloader ethics, cognition, and perceived service quality.

PubMed

Lin, Chin-Feng

2008-02-01

This study examined the downloader cognitive structures toward Web service quality and the downloader ethical attitudes across various levels of participation in a virtual community. Using four types of free downloads as the research subjects, the researcher found that the users in different participation degrees have different perception preferences. Owners of the free downloading Web sites can use the findings of this study to develop effective Web marketing strategies.

Archive of digital chirp subbottom profile data collected during USGS cruise 10BIM04 offshore Cat Island, Mississippi, September 2010

USGS Publications Warehouse

Forde, Arnell S.; Dadisman, Shawn V.; Kindinger, Jack G.; Miselis, Jennifer L.; Wiese, Dana S.; Buster, Noreen A.

2012-01-01

In September of 2010, the U.S. Geological Survey (USGS), in cooperation with the U.S. Army Corps of Engineers (USACE), conducted a geophysical survey to investigate the geologic controls on barrier island framework of Cat Island, Miss., as part of a broader USGS study on Barrier Island Mapping (BIM). These surveys were funded through the Mississippi Coastal Improvements Program (MsCIP) and the Northern Gulf of Mexico (NGOM) Ecosystem Change and Hazard Susceptibility Project as part of the Holocene Coastal Evolution of the Mississippi-Alabama Region Subtask. This report serves as an archive of unprocessed digital chirp subbottom data, trackline maps, navigation files, GIS files, Field Activity Collection System (FACS) logs, and formal FGDC metadata. Gained (showing a relative increase in signal amplitude) digital images of the seismic profiles are also provided. Refer to the Acronyms page for expansions of acronyms and abbreviations used in this report. The USGS Saint Petersburg Coastal and Marine Science Center (SPCMSC) assigns a unique identifier to each cruise or field activity. For example, 10BIM04 tells us the data were collected in 2010 during the fourth field activity for that project in that calendar year. Refer to http://walrus.wr.usgs.gov/infobank/programs/html/definition/activity.html for a detailed description of the method used to assign the field activity identification (ID). All chirp systems use a signal of continuously varying frequency; the EdgeTech SB-512i system used during this survey produces high-resolution, shallow-penetration (typically less than 50 milliseconds (ms)) profile images of sub-seafloor stratigraphy. The towfish contains a transducer that transmits and receives acoustic energy; it was housed within a float system (built at the SPCMSC), which allows the towfish to be towed at a constant depth of 1.07 meters (m) below the sea surface. As transmitted acoustic energy intersects density boundaries, such as the seafloor or sub-surface sediment layers, some energy is reflected back toward the transducer, received, and recorded by a Personal Computer (PC)-based seismic acquisition system. This process is repeated at regular time intervals (for example, 0.125 seconds (s)), and returned energy is recorded for a specific duration (for example, 50 ms). In this way, a two-dimensional (2-D) vertical image of the shallow geologic structure beneath the ship track is produced. Figure 1 displays the acquisition geometry. Refer to table 1 for a summary of acquisition parameters and table 2 for trackline statistics. The archived trace data are in standard Society of Exploration Geophysicists (SEG) SEG Y rev. 0 format (Barry and others, 1975); the first 3,200 bytes of the card image header are in American Standard Code for Information Interchange (ASCII) format instead of Extended Binary Coded Decimal Interchange Code (EBCDIC) format. The SEG Y files may be downloaded and processed with commercial or public domain software such as Seismic Unix (SU) (Cohen and Stockwell, 2010). See the How To Download SEG Y Data page for download instructions. The printable profiles provided here are GIF images that were processed and gained using SU software, and they can be viewed from the Profiles page or from links located on the trackline maps; refer to the Software page for links to example SU processing scripts. The SEG Y files are available on the DVD version of this report or on the Web, downloadable via the USGS Coastal and Marine Geoscience Data System (http://cmgds.marine.usgs.gov). The data are also available for viewing using GeoMapApp (http://www.geomapapp.org) and Virtual Ocean (http://www.virtualocean.org) multi-platform open source software.

Chain of Custody Item Monitor Message Viewer v.1.0 Beta

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

Schwartz, Steven Robert; Fielder, Laura; Hymel, Ross W.

The CoCIM Message Viewer software allows users to connect to and download messages from a Chain of Custody Item Monitor (CoCIM) connected to a serial port on the user’s computer. The downloaded messages are authenticated and displayed in a Graphical User Interface that allows the user a limited degree of sorting and filtering of the downloaded messages as well as the ability to save downloaded files or to open previously downloaded message history files.

Use of Crystalline Boron as a Burn Rate Retardant Toward the Development of Green-Colored Handheld Signal Formulations

DTIC Science & Technology

2011-01-01

This article was downloaded by: [US Ardec Technical Research Centre] On: 08 July 2011 , At: 11:46 Publisher: Taylor & Francis Informa Ltd Registered...Picatinny Arsenal, New Jersey Available online: 08 Jul 2011 To cite this article: Jesse J. Sabatini, Jay C. Poret & Russell N. Broad ( 2011 ): Use of...penalty for failing to comply with a collection of information if it does not display a currently valid OMB control number. 1. REPORT DATE 13 SEP 2011

PyCorrFit-generic data evaluation for fluorescence correlation spectroscopy.

PubMed

Müller, Paul; Schwille, Petra; Weidemann, Thomas

2014-09-01

We present a graphical user interface (PyCorrFit) for the fitting of theoretical model functions to experimental data obtained by fluorescence correlation spectroscopy (FCS). The program supports many data file formats and features a set of tools specialized in FCS data evaluation. The Python source code is freely available for download from the PyCorrFit web page at http://pycorrfit.craban.de. We offer binaries for Ubuntu Linux, Mac OS X and Microsoft Windows. © The Author 2014. Published by Oxford University Press.

The cataclysmic variable AE Aquarii: orbital variability in V band

NASA Astrophysics Data System (ADS)

Zamanov, R.; Latev, G.

2017-07-01

We present 62.7 hours observations of the cataclysmic variable AE Aqr in Johnson V band. These are non-published archive electro-photometric data obtained during the time period 1993 to 1999. We construct the orbital variability in V band and obtain a Fourier fit to the double-wave quiescent light curve. The strongest flares in our data set are in phase interval 0.6 - 0.8. The data can be downloaded from http://www.astro.bas.bg/~rz/DATA/AEAqr.elphot.dat.

Archive of Digital Boomer Seismic Reflection Data Collected During USGS Field Activity 02LCA02 in Lakes Ada, Crystal, Jennie, Mary, Rice, and Sylvan, Central Florida, July 2002

USGS Publications Warehouse

Harrison, Arnell S.; Dadisman, Shawn V.; Davis, Jeffrey B.; Wiese, Dana S.

2008-01-01

In July of 2002, the U.S. Geological Survey and St. Johns River Water Management District (SJRWMD) conducted geophysical surveys in Lakes Ada, Crystal, Jennie, Mary, Rice, and Sylvan, central Florida, as part of the USGS Lakes and Coastal Aquifers (LCA) study. This report serves as an archive of unprocessed digital boomer seismic reflection data, trackline maps, navigation files, Geographic Information System (GIS) files, and formal Federal Geographic Data Committee (FGDC) metadata. Filtered and gained (a relative increase in signal amplitude) digital images of the seismic profiles are also provided. Refer to the Acronyms page for expansions of acronyms and abbreviations used in this report. The archived trace data are in standard Society of Exploration Geophysicists (SEG) SEG-Y format (Barry and others, 1975) and may be downloaded and processed with commercial or public domain software such as Seismic Unix (SU). Example SU processing scripts and USGS software for viewing the SEG-Y files (Zihlman, 1992) are also provided. The USGS Florida Integrated Science Center (FISC) - St. Petersburg assigns a unique identifier to each cruise or field activity. For example, 02LCA02 tells us the data were collected in 2002 for the Lakes and Coastal Aquifers (LCA) study and the data were collected during the second field activity for that study in that calendar year. Refer to http://walrus.wr.usgs.gov/infobank/programs/html/definition/activity.html for a detailed description of the method used to assign the field activity ID. The boomer plate is an acoustic energy source that consists of capacitors charged to a high voltage and discharged through a transducer in the water. The transducer is towed on a sled floating on the water surface and when discharged emits a short acoustic pulse, or shot, which propagates through the water, sediment column, or rock beneath. The acoustic energy is reflected at density boundaries (such as the seafloor, sediment, or rock layers beneath the seafloor), detected by the receiver, and recorded by a PC-based seismic acquisition system. This process is repeated at timed intervals (for example, 0.5 s) and recorded for specific intervals of time (for example, 100 ms). In this way, a two-dimensional (2-D) vertical profile of the shallow geologic structure beneath the ship track is produced. Figure 1 displays the acquisition geometry. Refer to table 1 for a summary of acquisition parameters. Table 2 lists trackline statistics. The unprocessed seismic data are stored in SEG-Y format (Barry and others, 1975). For a detailed description of the data format, refer to the SEG-Y Format page. See the How To Download SEG-Y Data page for download instructions. The printable profiles provided here are GIF images that were filtered and gained using Seismic Unix software. Refer to the Software page for details about the processing and examples of the processing scripts. The processed SEG-Y data were exported to Chesapeake Technology, Inc. (CTI) SonarWeb software to produce an interactive Web page of the profile, which allows the user to obtain a geographic location and depth from the profile for a curser position. This information is displayed in the status bar of the browser.

Evaluation of Implementation, Adaptation and Use of the Recently Proposed Urea Cycle Disorders Guidelines.

PubMed

Häberle, Johannes; Huemer, Martina

2015-01-01

Implementation of guidelines and assessment of their adaptation is not an extensively investigated process in the field of rare diseases. However, whether targeted recipients are reached and willing and able to follow the recommendations has significant impact on the efficacy of guidelines. In 2012, a guideline for the management of urea cycle disorders (UCDs) has been published. We evaluate the efficacy of implementation, adaptation, and use of the UCD guidelines by applying different strategies. (i) Download statistics from online sources were recorded. (ii) Facilities relevant for the implementation of the guidelines were assessed in pediatric units in Germany and Austria. (iii) The guidelines were evaluated by targeted recipients using the AGREE instrument. (iv) A regional networking-based implementation process was evaluated. (i) Download statistics revealed high access with an increase in downloads over time. (ii) In 18% of hospitals ammonia testing was not available 24/7, and emergency drugs were often not available. (iii) Recipient criticism expressed in the AGREE instrument focused on incomplete inclusion of patients' perspectives. (iv) The implementation process improved the availability of ammonia measurements and access to emergency medication, patient care processes, and cooperation between nonspecialists and specialists. Interest in the UCD guidelines is high and sustained, but more precise targeting of the guidelines is advisable. Surprisingly, many hospitals do not possess all facilities necessary to apply the guidelines. Regional network and awareness campaigns result in the improvement of both facilities and knowledge.

Excel VBA for Physicists; A Primer

NASA Astrophysics Data System (ADS)

Liengme, Bernard V.

2016-11-01

This book is both an introduction and a demonstration of how Visual Basic for Applications (VBA) can greatly enhance Microsoft Excel® by giving users the ability to create their own functions within a worksheet and to create subroutines to perform repetitive actions. The book is written so readers are encouraged to experiment with VBA programming with examples using fairly simple physics or non-complicated mathematics such as root finding and numerical integration. Tested Excel® workbooks are available for each chapter and there is nothing to buy or install. A tested Excel workbook for each chapter can be downloaded from Book information

Practical Session: Simple Linear Regression

NASA Astrophysics Data System (ADS)

Clausel, M.; Grégoire, G.

2014-12-01

Two exercises are proposed to illustrate the simple linear regression. The first one is based on the famous Galton's data set on heredity. We use the lm R command and get coefficients estimates, standard error of the error, R2, residuals …In the second example, devoted to data related to the vapor tension of mercury, we fit a simple linear regression, predict values, and anticipate on multiple linear regression. This pratical session is an excerpt from practical exercises proposed by A. Dalalyan at EPNC (see Exercises 1 and 2 of http://certis.enpc.fr/~dalalyan/Download/TP_ENPC_4.pdf).

Standardized Tobacco Assessment for Retail Settings (STARS): dissemination and implementation research.

PubMed

Henriksen, Lisa; Ribisl, Kurt M; Rogers, Todd; Moreland-Russell, Sarah; Barker, Dianne M; Sarris Esquivel, Nikie; Loomis, Brett; Crew, Erin; Combs, Todd

2016-10-01

The Standardized Tobacco Assessment for Retail Settings (STARS) was designed to characterise the availability, placement, promotion and price of tobacco products, with items chosen for relevance to regulating the retail tobacco environment. This study describes the process to develop the STARS instrument and protocol employed by a collaboration of US government agencies, US state tobacco control programmes (TCPs), advocacy organisations, public health attorneys and researchers from the National Cancer Institute's State and Community Tobacco Control (SCTC) Research Initiative. To evaluate dissemination and early implementation experiences, we conducted telephone surveys with state TCP leaders (n=50, response rate=100%), and with individuals recruited via a STARS download registry on the SCTC website. Website registrants were surveyed within 6 months of the STARS release (n=105, response rate=66%) and again after ∼5 months (retention rate=62%). Among the state TCPs, 42 reported conducting any retail marketing surveillance, with actual or planned STARS use in 34 of these states and in 12 of the 17 states where marketing surveillance was not previously reported. Within 6 months of the STARS release, 21% of surveyed registrants reported using STARS and 35% were likely/very likely to use it in the next 6 months. To investigate implementation fidelity, we compared data collected by self-trained volunteers and by trained professionals, the latter method being more typically in retail marketing surveillance studies. Results suggest high or moderate reliability for most STARS measures. The study concludes with examples of states that used STARS to inform policy change. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Bionimbus: a cloud for managing, analyzing and sharing large genomics datasets.

PubMed

Heath, Allison P; Greenway, Matthew; Powell, Raymond; Spring, Jonathan; Suarez, Rafael; Hanley, David; Bandlamudi, Chai; McNerney, Megan E; White, Kevin P; Grossman, Robert L

2014-01-01

As large genomics and phenotypic datasets are becoming more common, it is increasingly difficult for most researchers to access, manage, and analyze them. One possible approach is to provide the research community with several petabyte-scale cloud-based computing platforms containing these data, along with tools and resources to analyze it. Bionimbus is an open source cloud-computing platform that is based primarily upon OpenStack, which manages on-demand virtual machines that provide the required computational resources, and GlusterFS, which is a high-performance clustered file system. Bionimbus also includes Tukey, which is a portal, and associated middleware that provides a single entry point and a single sign on for the various Bionimbus resources; and Yates, which automates the installation, configuration, and maintenance of the software infrastructure required. Bionimbus is used by a variety of projects to process genomics and phenotypic data. For example, it is used by an acute myeloid leukemia resequencing project at the University of Chicago. The project requires several computational pipelines, including pipelines for quality control, alignment, variant calling, and annotation. For each sample, the alignment step requires eight CPUs for about 12 h. BAM file sizes ranged from 5 GB to 10 GB for each sample. Most members of the research community have difficulty downloading large genomics datasets and obtaining sufficient storage and computer resources to manage and analyze the data. Cloud computing platforms, such as Bionimbus, with data commons that contain large genomics datasets, are one choice for broadening access to research data in genomics. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Pharmaco-miR: linking microRNAs and drug effects

PubMed Central

Rukov, Jakob Lewin; Wilentzik, Roni; Jaffe, Ishai; Vinther, Jeppe; Shomron, Noam

2014-01-01

MicroRNAs (miRNAs) are short regulatory RNAs that down-regulate gene expression. They are essential for cell homeostasis and active in many disease states. A major discovery is the ability of miRNAs to determine the efficacy of drugs, which has given rise to the field of ‘miRNA pharmacogenomics’ through ‘Pharmaco-miRs’. miRNAs play a significant role in pharmacogenomics by down-regulating genes that are important for drug function. These interactions can be described as triplet sets consisting of a miRNA, a target gene and a drug associated with the gene. We have developed a web server which links miRNA expression and drug function by combining data on miRNA targeting and protein–drug interactions. miRNA targeting information derive from both experimental data and computational predictions, and protein–drug interactions are annotated by the Pharmacogenomics Knowledge base (PharmGKB). Pharmaco-miR’s input consists of miRNAs, genes and/or drug names and the output consists of miRNA pharmacogenomic sets or a list of unique associated miRNAs, genes and drugs. We have furthermore built a database, named Pharmaco-miR Verified Sets (VerSe), which contains miRNA pharmacogenomic data manually curated from the literature, can be searched and downloaded via Pharmaco-miR and informs on trends and generalities published in the field. Overall, we present examples of how Pharmaco-miR provides possible explanations for previously published observations, including how the cisplatin and 5-fluorouracil resistance induced by miR-148a may be caused by miR-148a targeting of the gene KIT. The information is available at www.Pharmaco-miR.org. PMID:23376192

Tools for knowledge acquisition within the NeuroScholar system and their application to anatomical tract-tracing data

PubMed Central

Burns, Gully APC; Cheng, Wei-Cheng

2006-01-01

Background Knowledge bases that summarize the published literature provide useful online references for specific areas of systems-level biology that are not otherwise supported by large-scale databases. In the field of neuroanatomy, groups of small focused teams have constructed medium size knowledge bases to summarize the literature describing tract-tracing experiments in several species. Despite years of collation and curation, these databases only provide partial coverage of the available published literature. Given that the scientists reading these papers must all generate the interpretations that would normally be entered into such a system, we attempt here to provide general-purpose annotation tools to make it easy for members of the community to contribute to the task of data collation. Results In this paper, we describe an open-source, freely available knowledge management system called 'NeuroScholar' that allows straightforward structured markup of the PDF files according to a well-designed schema to capture the essential details of this class of experiment. Although, the example worked through in this paper is quite specific to neuroanatomical connectivity, the design is freely extensible and could conceivably be used to construct local knowledge bases for other experiment types. Knowledge representations of the experiment are also directly linked to the contributing textual fragments from the original research article. Through the use of this system, not only could members of the community contribute to the collation task, but input data can be gathered for automated approaches to permit knowledge acquisition through the use of Natural Language Processing (NLP). Conclusion We present a functional, working tool to permit users to populate knowledge bases for neuroanatomical connectivity data from the literature through the use of structured questionnaires. This system is open-source, fully functional and available for download from [1]. PMID:16895608

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

PubMed Central

2010-01-01

Background Quantitative models of biochemical and cellular systems are used to answer a variety of questions in the biological sciences. The number of published quantitative models is growing steadily thanks to increasing interest in the use of models as well as the development of improved software systems and the availability of better, cheaper computer hardware. To maximise the benefits of this growing body of models, the field needs centralised model repositories that will encourage, facilitate and promote model dissemination and reuse. Ideally, the models stored in these repositories should be extensively tested and encoded in community-supported and standardised formats. In addition, the models and their components should be cross-referenced with other resources in order to allow their unambiguous identification. Description BioModels Database http://www.ebi.ac.uk/biomodels/ is aimed at addressing exactly these needs. It is a freely-accessible online resource for storing, viewing, retrieving, and analysing published, peer-reviewed quantitative models of biochemical and cellular systems. The structure and behaviour of each simulation model distributed by BioModels Database are thoroughly checked; in addition, model elements are annotated with terms from controlled vocabularies as well as linked to relevant data resources. Models can be examined online or downloaded in various formats. Reaction network diagrams generated from the models are also available in several formats. BioModels Database also provides features such as online simulation and the extraction of components from large scale models into smaller submodels. Finally, the system provides a range of web services that external software systems can use to access up-to-date data from the database. Conclusions BioModels Database has become a recognised reference resource for systems biology. It is being used by the community in a variety of ways; for example, it is used to benchmark different simulation systems, and to study the clustering of models based upon their annotations. Model deposition to the database today is advised by several publishers of scientific journals. The models in BioModels Database are freely distributed and reusable; the underlying software infrastructure is also available from SourceForge https://sourceforge.net/projects/biomodels/ under the GNU General Public License. PMID:20587024

Reaching the Public in 2016

NASA Astrophysics Data System (ADS)

Grauer, Albert D.; Catalina Sky Survey

2016-10-01

Travelers in the Night is a series of 2 minute audio programs whose topics include Catalina Sky Survey discoveries as well as other current research in astronomy and the space sciences. Each episode is first published on Public Radio Exchange [PRX] which makes it available to NPR and Community Radio Stations free of charge. After about 3 weeks it is published as an audio podcast on the internet via spreaker.com, iHeart Radio, Stitcher, iTunes and a few other outlets. The most interesting aspect of the Travelers In The Night experiment is the insight it provides into the rapidly changing means by which people obtain information in 2016. The demographics, and devices used to obtain more than 175,000 plays and downloads are presented in this poster.

Does a Graphical Abstract Bring More Visibility to Your Paper?

PubMed Central

Pferschy-Wenzig, Eva-Maria; Pferschy, Ulrich; Wang, Dongdong; Mocan, Andrei; Atanasov, Atanas G.

2017-01-01

A graphical abstract (GA) represents a piece of artwork that is intended to summarize the main findings of an article for readers at a single glance. Many publishers currently encourage authors to supplement their articles with GAs, in the hope that such a convenient visual summary will facilitate readers with a clearer outline of papers that are of interest and will result in improved overall visibility of the respective publication. To test this assumption, we statistically compared publications with or without GA published in Molecules between March 2014 and March 2015 with regard to several output parameters reflecting visibility. Contrary to our expectations, manuscripts published without GA performed significantly better in terms of PDF downloads, abstract views, and total citations than manuscripts with GA. To the best of our knowledge, this is the first empirical study on the effectiveness of GA for attracting attention to scientific publications. PMID:27649137

Does a Graphical Abstract Bring More Visibility to Your Paper?

PubMed

Pferschy-Wenzig, Eva-Maria; Pferschy, Ulrich; Wang, Dongdong; Mocan, Andrei; Atanasov, Atanas G

2016-09-18

A graphical abstract (GA) represents a piece of artwork that is intended to summarize the main findings of an article for readers at a single glance. Many publishers currently encourage authors to supplement their articles with GAs, in the hope that such a convenient visual summary will facilitate readers with a clearer outline of papers that are of interest and will result in improved overall visibility of the respective publication. To test this assumption, we statistically compared publications with or without GA published in Molecules between March 2014 and March 2015 with regard to several output parameters reflecting visibility. Contrary to our expectations, manuscripts published without GA performed significantly better in terms of PDF downloads, abstract views, and total citations than manuscripts with GA. To the best of our knowledge, this is the first empirical study on the effectiveness of GA for attracting attention to scientific publications.

DLRS: gene tree evolution in light of a species tree.

PubMed

Sjöstrand, Joel; Sennblad, Bengt; Arvestad, Lars; Lagergren, Jens

2012-11-15

PrIME-DLRS (or colloquially: 'Delirious') is a phylogenetic software tool to simultaneously infer and reconcile a gene tree given a species tree. It accounts for duplication and loss events, a relaxed molecular clock and is intended for the study of homologous gene families, for example in a comparative genomics setting involving multiple species. PrIME-DLRS uses a Bayesian MCMC framework, where the input is a known species tree with divergence times and a multiple sequence alignment, and the output is a posterior distribution over gene trees and model parameters. PrIME-DLRS is available for Java SE 6+ under the New BSD License, and JAR files and source code can be downloaded from http://code.google.com/p/jprime/. There is also a slightly older C++ version available as a binary package for Ubuntu, with download instructions at http://prime.sbc.su.se. The C++ source code is available upon request. joel.sjostrand@scilifelab.se or jens.lagergren@scilifelab.se. PrIME-DLRS is based on a sound probabilistic model (Åkerborg et al., 2009) and has been thoroughly validated on synthetic and biological datasets (Supplementary Material online).

MCPB.py: A Python Based Metal Center Parameter Builder.

PubMed

Li, Pengfei; Merz, Kenneth M

2016-04-25

MCPB.py, a python based metal center parameter builder, has been developed to build force fields for the simulation of metal complexes employing the bonded model approach. It has an optimized code structure, with far fewer required steps than the previous developed MCPB program. It supports various AMBER force fields and more than 80 metal ions. A series of parametrization schemes to derive force constants and charge parameters are available within the program. We give two examples (one metalloprotein example and one organometallic compound example), indicating the program's ability to build reliable force fields for different metal ion containing complexes. The original version was released with AmberTools15. It is provided via the GNU General Public License v3.0 (GNU_GPL_v3) agreement and is free to download and distribute. MCPB.py provides a bridge between quantum mechanical calculations and molecular dynamics simulation software packages thereby enabling the modeling of metal ion centers. It offers an entry into simulating metal ions in a number of situations by providing an efficient way for researchers to handle the vagaries and difficulties associated with metal ion modeling.

25 CFR 547.12 - What are the minimum technical standards for downloading on a Class II gaming system?

Code of Federal Regulations, 2010 CFR

2010-04-01

... OF CLASS II GAMES § 547.12 What are the minimum technical standards for downloading on a Class II... software, files, data, and prize schedules. (2) Downloads of software, games, prize schedules, or other... performed in a manner that will not affect game play. (5) Downloads shall not affect the integrity of...

25 CFR 547.12 - What are the minimum technical standards for downloading on a Class II gaming system?

Code of Federal Regulations, 2011 CFR

2011-04-01

... OF CLASS II GAMES § 547.12 What are the minimum technical standards for downloading on a Class II... software, files, data, and prize schedules. (2) Downloads of software, games, prize schedules, or other... performed in a manner that will not affect game play. (5) Downloads shall not affect the integrity of...

25 CFR 547.12 - What are the minimum technical standards for downloading on a Class II gaming system?

Code of Federal Regulations, 2012 CFR

2012-04-01

... OF CLASS II GAMES § 547.12 What are the minimum technical standards for downloading on a Class II... software, files, data, and prize schedules. (2) Downloads of software, games, prize schedules, or other... performed in a manner that will not affect game play. (5) Downloads shall not affect the integrity of...

Technical Support | Division of Cancer Prevention

Cancer.gov

To view the live webinar, you will need to have the software, Microsoft Live Meeting, downloaded onto your computer before the event. In most cases, the software will automatically download when you open the program on your system. However, in the event that you need to download it manually, you can access the software at the link below: Download the Microsoft Office Live

Using Open and Interoperable Ways to Publish and Access LANCE AIRS Near-Real Time Data

NASA Astrophysics Data System (ADS)

Zhao, P.; Lynnes, C.; Vollmer, B.; Savtchenko, A. K.; Yang, W.

2011-12-01

Atmospheric Infrared Sounder (AIRS) Near-Real Time (NRT) data from the Land Atmosphere Near real time Capability for EOS (LANCE) provide the information on the global and regional atmospheric state with very low latency. An open and interoperable platform is useful to facilitate access to and integration of LANCE AIRS NRT data. This paper discusses the use of open-source software components to build Web services for publishing and accessing AIRS NRT data in the context of Service Oriented Architecture (SOA). The AIRS NRT data have also been made available through an OPeNDAP server. OPeNDAP allows several open-source netCDF-based tools such as Integrated Data Viewer, Ferret and Panoply to directly display the Level 2 data over the network. To enable users to locate swath data files in the OPeNDAP server that lie within a certain geographical area, graphical "granule maps" are being added to show the outline of each file on a map of the Earth. The metadata of AIRS NRT data and services is then explored to implement information advertisement and discovery in catalogue systems. Datacasting, an RSS-based technology for accessing Earth Science data and information to facilitate the subscriptions to AIRS NRT data availability, filtering, downloading and viewing data, is also discussed. To provide an easy entry point to AIRS NRT data and services, a Web portal designed for customized data downloading and visualization is introduced.

Advantages to Geoscience and Disaster Response from QuakeSim Implementation of Interferometric Radar Maps in a GIS Database System

NASA Astrophysics Data System (ADS)

Parker, Jay; Donnellan, Andrea; Glasscoe, Margaret; Fox, Geoffrey; Wang, Jun; Pierce, Marlon; Ma, Yu

2015-08-01

High-resolution maps of earth surface deformation are available in public archives for scientific interpretation, but are primarily available as bulky downloads on the internet. The NASA uninhabited aerial vehicle synthetic aperture radar (UAVSAR) archive of airborne radar interferograms delivers very high resolution images (approximately seven meter pixels) making remote handling of the files that much more pressing. Data exploration requiring data selection and exploratory analysis has been tedious. QuakeSim has implemented an archive of UAVSAR data in a web service and browser system based on GeoServer (http://geoserver.org). This supports a variety of services that supply consistent maps, raster image data and geographic information systems (GIS) objects including standard earthquake faults. Browsing the database is supported by initially displaying GIS-referenced thumbnail images of the radar displacement maps. Access is also provided to image metadata and links for full file downloads. One of the most widely used features is the QuakeSim line-of-sight profile tool, which calculates the radar-observed displacement (from an unwrapped interferogram product) along a line specified through a web browser. Displacement values along a profile are updated to a plot on the screen as the user interactively redefines the endpoints of the line and the sampling density. The profile and also a plot of the ground height are available as CSV (text) files for further examination, without any need to download the full radar file. Additional tools allow the user to select a polygon overlapping the radar displacement image, specify a downsampling rate and extract a modest sized grid of observations for display or for inversion, for example, the QuakeSim simplex inversion tool which estimates a consistent fault geometry and slip model.

Hip Replacement Surgery

MedlinePlus

... Download Download EPUB Download PDF What is it? Points To Remember About Hip Replacement Surgery Hip replacement ... This leaves your hands and arms free for balance or to use crutches. Use a long-handled " ...

Growth Plate Injuries

MedlinePlus

... Download Download EPUB Download PDF What are they? Points To Remember About Growth Plate Injuries Injuries to ... Neurological disorders that cause people to lose their balance and fall. Some inherited disorders. Bone infections. Metabolic ...

Investigating Access Performance of Long Time Series with Restructured Big Model Data

NASA Astrophysics Data System (ADS)

Shen, S.; Ostrenga, D.; Vollmer, B.; Meyer, D. J.

2017-12-01

Data sets generated by models are substantially increasing in volume, due to increases in spatial and temporal resolution, and the number of output variables. Many users wish to download subsetted data in preferred data formats and structures, as it is getting increasingly difficult to handle the original full-size data files. For example, application research users, such as those involved with wind or solar energy, or extreme weather events, are likely only interested in daily or hourly model data at a single point or for a small area for a long time period, and prefer to have the data downloaded in a single file. With native model file structures, such as hourly data from NASA Modern-Era Retrospective analysis for Research and Applications Version-2 (MERRA-2), it may take over 10 hours for the extraction of interested parameters at a single point for 30 years. The NASA Goddard Earth Sciences Data and Information Services Center (GES DISC) is exploring methods to address this particular user need. One approach is to create value-added data by reconstructing the data files. Taking MERRA-2 data as an example, we have tested converting hourly data from one-day-per-file into different data cubes, such as one-month, one-year, or whole-mission. Performance are compared for reading local data files and accessing data through interoperable service, such as OPeNDAP. Results show that, compared to the original file structure, the new data cubes offer much better performance for accessing long time series. We have noticed that performance is associated with the cube size and structure, the compression method, and how the data are accessed. An optimized data cube structure will not only improve data access, but also may enable better online analytic services.

Investigating Access Performance of Long Time Series with Restructured Big Model Data

NASA Technical Reports Server (NTRS)

Shen, Suhung; Ostrenga, Dana M.; Vollmer, Bruce E.; Meyer, Dave

2017-01-01

Data sets generated by models are substantially increasing in volume, due to increases in spatial and temporal resolution, and the number of output variables. Many users wish to download subsetted data in preferred data formats and structures, as it is getting increasingly difficult to handle the original full-size data files. For example, application research users such as those involved with wind or solar energy, or extreme weather events are likely only interested in daily or hourly model data at a single point (or for a small area) for a long time period, and prefer to have the data downloaded in a single file. With native model file structures, such as hourly data from NASA Modern-Era Retrospective analysis for Research and Applications Version-2 (MERRA-2), it may take over 10 hours for the extraction of parameters-of-interest at a single point for 30 years. The NASA Goddard Earth Sciences Data and Information Services Center (GES DISC) is exploring methods to address this particular user need. One approach is to create value-added data by reconstructing the data files. Taking MERRA-2 data as an example, we have tested converting hourly data from one-day-per-file into different data cubes, such as one-month, or one-year. Performance is compared for reading local data files and accessing data through interoperable services, such as OPeNDAP. Results show that, compared to the original file structure, the new data cubes offer much better performance for accessing long time series. We have noticed that performance is associated with the cube size and structure, the compression method, and how the data are accessed. An optimized data cube structure will not only improve data access, but also may enable better online analysis services

Unifying Water Data Sources: How the CUAHSI Water Data Center is Enabling and Improving Access to a Growing Catalog of over 100 Data Providers

NASA Astrophysics Data System (ADS)

Pollak, J.; Berry, K.; Couch, A.; Arrigo, J.; Hooper, R. P.

2013-12-01

Scientific data about water are collected and distributed by numerous sources which can differ tremendously in scale. As competition for water resources increases, increasing access to and understanding of information about water will be critical. The mission of the new CUAHSI Water Data Center (WDC) is to provide those researchers who collect data a medium to publish their datasets and give those wanting to discover data the proper tools to efficiently find the data that they seek. These tools include standards-based data publication, data discovery tools based upon faceted and telescoping search, and a data analysis tool HydroDesktop that downloads and unifies data in standardized formats. The CUAHSI Hydrologic Information System (HIS) is a community developed and open source system for sharing water data. As a federated, web service oriented system it enables data publication for a diverse user population including scientific investigators (Research Coordination Networks, Critical Zone Observatories), government agencies (USGS, NASA, EPA), and citizen scientists (watershed associations). HydroDesktop is an end user application for data consumption in this system that the WDC supports. This application can be used for finding, downloading, and analyzing data from the HIS. It provides a GIS interface that allows users to incorporate spatial data that are not accessible via HIS, simple analysis tools to facilitate graphing and visualization, tools to export data to common file types, and provides an extensible architecture that developers can build upon. HydroDesktop, however, is just one example of a data access client for HIS. The web service oriented architecture enables data access by an unlimited number of clients provided they can consume the web services used in HIS. One such example developed at the WDC is the 'Faceted Search Client', which capitalizes upon exploratory search concepts to improve accuracy and precision during search. We highlight such features of the CUAHSI-HIS which make it particularly appropriate for providing unified access to several sources of water data. A growing community of researchers and educators are employing these tools for education; including sharing best practices around creating modules, supporting researchers and educators in accessing the services, and cataloging and sharing modules. The CUAHSI WDC is a community governed organization. Our agenda is driven by the community's voice through a Board of Directors and committees that decide strategic direction (new products), tactical decisions (product improvement), and evaluation of usability. By providing the aforementioned services within a community driven framework, we believe the WDC is providing critical services that include improving water data discoverability, accessibility and usability within a sustainable governance structure.

Learning and Behavior

MedlinePlus

... Aggression Sensory Processing Disorder Social Interactions Book: The Psychology of Duchenne (download) Guide: Learning & Behavior (download) Home ❯ ... a teen and adult. Additional Resources Book: The Psychology of Duchenne (download) Education Matters Guide: Learning & Behavior ( ...

Postpartum Depression Facts

MedlinePlus

... Where can I find more information? Share Postpartum Depression Facts Download PDF Download ePub Download Mobi Order ... for herself or her family. What is postpartum depression? Postpartum depression is a mood disorder that can ...

Schroedinger’s Code: A Preliminary Study on Research Source Code Availability and Link Persistence in Astrophysics

NASA Astrophysics Data System (ADS)

Allen, Alice; Teuben, Peter J.; Ryan, P. Wesley

2018-05-01

We examined software usage in a sample set of astrophysics research articles published in 2015 and searched for the source codes for the software mentioned in these research papers. We categorized the software to indicate whether the source code is available for download and whether there are restrictions to accessing it, and if the source code is not available, whether some other form of the software, such as a binary, is. We also extracted hyperlinks from one journal’s 2015 research articles, as links in articles can serve as an acknowledgment of software use and lead to the data used in the research, and tested them to determine which of these URLs are still accessible. For our sample of 715 software instances in the 166 articles we examined, we were able to categorize 418 records as according to whether source code was available and found that 285 unique codes were used, 58% of which offered the source code for download. Of the 2558 hyperlinks extracted from 1669 research articles, at best, 90% of them were available over our testing period.

Evaluation of hierarchical models for integrative genomic analyses.

PubMed

Denis, Marie; Tadesse, Mahlet G

2016-03-01

Advances in high-throughput technologies have led to the acquisition of various types of -omic data on the same biological samples. Each data type gives independent and complementary information that can explain the biological mechanisms of interest. While several studies performing independent analyses of each dataset have led to significant results, a better understanding of complex biological mechanisms requires an integrative analysis of different sources of data. Flexible modeling approaches, based on penalized likelihood methods and expectation-maximization (EM) algorithms, are studied and tested under various biological relationship scenarios between the different molecular features and their effects on a clinical outcome. The models are applied to genomic datasets from two cancer types in the Cancer Genome Atlas project: glioblastoma multiforme and ovarian serous cystadenocarcinoma. The integrative models lead to improved model fit and predictive performance. They also provide a better understanding of the biological mechanisms underlying patients' survival. Source code implementing the integrative models is freely available at https://github.com/mgt000/IntegrativeAnalysis along with example datasets and sample R script applying the models to these data. The TCGA datasets used for analysis are publicly available at https://tcga-data.nci.nih.gov/tcga/tcgaDownload.jsp marie.denis@cirad.fr or mgt26@georgetown.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Features of a Mobile Support App for Patients With Chronic Obstructive Pulmonary Disease: Literature Review and Current Applications.

PubMed

Sobnath, Drishty D; Philip, Nada; Kayyali, Reem; Nabhani-Gebara, Shereen; Pierscionek, Barbara; Vaes, Anouk W; Spruit, Martijn A; Kaimakamis, Evangelos

2017-02-20

Chronic obstructive pulmonary disease (COPD) is a serious long-term lung disease in which the airflow from the lungs is progressively reduced. By 2030, COPD will become the third cause of mortality and seventh cause of morbidity worldwide. With advances in technology and mobile communications, significant progress in the mobile health (mHealth) sector has been recently observed. Mobile phones with app capabilities (smartphones) are now considered as potential media for the self-management of certain types of diseases such as asthma, cancer, COPD, or cardiovascular diseases. While many mobile apps for patients with COPD are currently found on the market, there is little published material on the effectiveness of most of them, their features, and their adoption in health care settings. The aim of this study was to search the literature for current systems related to COPD and identify any missing links and studies that were carried out to evaluate the effectiveness of COPD mobile apps. In addition, we reviewed existing mHealth apps from different stores in order to identify features that can be considered in the initial design of a COPD support tool to improve health care services and patient outcomes. In total, 206 articles related to COPD management systems were identified from different databases. Irrelevant materials and duplicates were excluded. Of those, 38 articles were reviewed to extract important features. We identified 214 apps from online stores. Following exclusion of irrelevant apps, 48 were selected and 20 of them were downloaded to review some of their common features. Our review found that out of the 20 apps downloaded, 13 (65%, 13/20) had an education section, 5 (25%, 5/20) consisted of medication and guidelines, 6 (30%, 6/20) included a calendar or diary and other features such as reminders or symptom tracking. There was little published material on the effectiveness of the identified COPD apps. Features such as (1) a social networking tool; (2) personalized education; (3) feedback; (4) e-coaching; and (5) psychological motivation to enhance behavioral change were found to be missing in many of the downloaded apps. This paper summarizes the features of a COPD patient-support mobile app that can be taken into consideration for the initial design of an integrated care system to encourage the self-management of their condition at home. ©Drishty D Sobnath, Nada Philip, Reem Kayyali, Shereen Nabhani-Gebara, Barbara Pierscionek, Anouk W Vaes, Martijn A Spruit, Evangelos Kaimakamis. Originally published in JMIR Mhealth and Uhealth (http://mhealth.jmir.org), 20.02.2017.

What Is Reactive Arthritis?

MedlinePlus

... Breadcrumb Home Health Topics Reactive Arthritis English Español Reactive Arthritis Basics In-Depth Download Download EPUB Download PDF What is it? Points To Remember About Reactive Arthritis Reactive arthritis is pain or swelling in ...

Normal Pancreas Anatomy

MedlinePlus

... hyphen, e.g. -historical Searches are case-insensitive Pancreas Anatomy Add to My Pictures View /Download : Small: ... 1586x1534 View Download Large: 3172x3068 View Download Title: Pancreas Anatomy Description: Anatomy of the pancreas; drawing shows ...

BenMAP Downloads

EPA Pesticide Factsheets

Download the current and legacy versions of the BenMAP program. Download configuration and aggregation/pooling/valuation files to estimate benefits. BenMAP-CE is free and open source software, and the source code is available upon request.

Developing Sustainable and Impactful Mobile Phone HIV Testing Interventions for Spanish-Speaking Men Who Have Sex With Men in the United States: Lessons Learned From Informative Interviews.

PubMed

Mitchell, Jason; Torres, Maria Beatriz; Asmar, Lucy; Danh, Thu; Horvath, Keith J

2018-04-24

Although many men who have sex with men (MSM) test for HIV at least once in their lifetime, opportunities to improve regular HIV testing, particularly among Hispanic or Latino MSM, is needed. Many mHealth interventions in development, including the ones on HIV testing, have primarily focused on English-speaking white, black, and MSM of other races. To date, no studies have assessed app use, attitudes, and motivations for downloading and sustaining use of mobile apps and preferences with respect to HIV prevention among Spanish-speaking, Hispanic MSM in the United States. The primary aims of this study were to determine what features and functions of smartphone apps do Hispanic, Spanish-speaking MSM believe are associated with downloading apps to their smartphones, (2) what features and functions of smartphone apps are most likely to influence men's sustained use of apps over time, and (3) what features and functions do men prefer in a smartphone app aimed to promote regular testing for HIV. Interviews (N=15) were conducted with a racially diverse group of sexually active, HIV-negative, Spanish-speaking, Hispanic MSM in Miami, Florida. Interviews were digitally recorded, transcribed verbatim, translated back to English, and de-identified for analysis. A constant-comparison method (ie, grounded theory coding) was employed to examine themes that emerged from the interviews. Personal interest was the primary reason associated with whether men downloaded an app. Keeping personal information secure, cost, influence by peers and posted reviews, ease of use, and functionality affected whether they downloaded and used the app over time. Men also reported that entertainment value and frequency of updates influenced whether they kept and continued to use an app over time. There were 4 reasons why participants chose to delete an app-dislike, lack of use, cost, and lack of memory or space. Participants also shared their preferences for an app to encourage regular HIV testing by providing feedback on test reminders, tailored testing interval recommendations, HIV test locator, and monitoring of personal sexual behaviors. The features and functions of mobile apps that Spanish-speaking MSM in this study believed were associated with downloading and/or sustained engagement of an app generally reflected the priorities mentioned in an earlier study with English-speaking MSM. Unlike the earlier study, Spanish-speaking MSM prioritized personal interest in a mobile app and de-emphasized the efficiency of an app to make their lives easier in their decision to download an app to their mobile device. Tailoring mobile apps to the language and needs of Spanish-speaking MSM is critical to help increase their willingness to download a mobile app. Despite the growing number of HIV-prevention apps in development, few are tailored to Spanish-speaking MSM, representing an important gap that should be addressed in future research. ©Jason Mitchell, Maria Beatriz Torres, Lucy Asmar, Thu Danh, Keith J Horvath. Originally published in JMIR Public Health and Surveillance (http://publichealth.jmir.org), 24.04.2018.

Osteoarthritis

MedlinePlus

... Topics Osteoarthritis English Español 繁體中文 한국어 tiếng Việt Osteoarthritis Basics In-Depth Download Download EPUB Download PDF What is it? Points To Remember About Osteoarthritis Osteoarthritis is a disease that damages the slippery ...

Alternative Fuels Data Center: Hydrogen Drive

Science.gov Websites

, contact Greater Washington Region Clean Cities Coalition. Download QuickTime Video QuickTime (.mov ) Download Windows Media Video Windows Media (.wmv) Video Download Help Text version See more videos provided

Who Uses Smoking Cessation Apps? A Feasibility Study Across Three Countries via Smartphones

PubMed Central

McGeechan, Kevin; Trevena, Lyndal

2014-01-01

Background Smartphone use is growing worldwide. While hundreds of smoking cessation apps are currently available in the app stores, there is no information about who uses them. Smartphones also offer potential as a research tool, but this has not previously been explored. Objective This study aims to measure and compare the uptake of a smoking cessation app over one year in Australia, the United Kingdom, and the United States. It also assesses the feasibility of conducting research via an app, describing respondents’ characteristics (demographics, smoking status, and other health related app use), and examining differences across countries. Methods This is a cross-sectional exploratory study of adults 18 years and older, passively recruited over one year in 2012, who downloaded this study app (Quit Advisor) via the two largest app stores (Apple and Android). Results The total number of app downloads after one year was 1751, 72.98% (1278/1751) of them were Apple operation system users. Of these 1751 participants, 47.68% (835/1751) were from the United States, 29.18% (511/1751) were from the United Kingdom, and 16.68% (292/1751) were from Australia. There were 602 participants, 36.75% (602/1638) that completed a questionnaire within the app. Of these 602 participants, 58.8% (354/602) were female and the mean age was 32 years. There were no significant differences between countries in terms of age, operation system used, number of quitting attempts, and language spoken at home. However, there were significant differences between countries in terms of gender and stage of change. There were 77.2% (465/602) of the respondents that were ready to quit in the next 30 days and the majority of these had never sought professional help (eg, “Quitline”). More than half had downloaded smoking cessation apps in the past and of these, three-quarters had made quitting attempts (lasted at least 24 hours) using an app before. Respondents who had attempted to quit three times or more in the previous year were more likely to have tried smoking cessation apps (OR 3.3, 95% CI 2.1-5.2). There were 50.2% (302/602) of the respondents that had used other health related apps before. Of these, 89.4% (270/302) were using health related apps at least once a week, but 77.5% (234/302) never checked the credibility of the health app publishers before downloading. Conclusions A smartphone app was able to reach smokers across three countries that were not seeking professional help, but were ready to quit within the next 30 days. Respondents were relatively young and almost demographically similar across all three countries. They also frequently used other health related apps, mostly without checking the credibility of their publishers. PMID:25098439

Who Uses Smoking Cessation Apps? A Feasibility Study Across Three Countries via Smartphones.

PubMed

BinDhim, Nasser F; McGeechan, Kevin; Trevena, Lyndal

2014-02-06

Smartphone use is growing worldwide. While hundreds of smoking cessation apps are currently available in the app stores, there is no information about who uses them. Smartphones also offer potential as a research tool, but this has not previously been explored. This study aims to measure and compare the uptake of a smoking cessation app over one year in Australia, the United Kingdom, and the United States. It also assesses the feasibility of conducting research via an app, describing respondents' characteristics (demographics, smoking status, and other health related app use), and examining differences across countries. This is a cross-sectional exploratory study of adults 18 years and older, passively recruited over one year in 2012, who downloaded this study app (Quit Advisor) via the two largest app stores (Apple and Android). The total number of app downloads after one year was 1751, 72.98% (1278/1751) of them were Apple operation system users. Of these 1751 participants, 47.68% (835/1751) were from the United States, 29.18% (511/1751) were from the United Kingdom, and 16.68% (292/1751) were from Australia. There were 602 participants, 36.75% (602/1638) that completed a questionnaire within the app. Of these 602 participants, 58.8% (354/602) were female and the mean age was 32 years. There were no significant differences between countries in terms of age, operation system used, number of quitting attempts, and language spoken at home. However, there were significant differences between countries in terms of gender and stage of change. There were 77.2% (465/602) of the respondents that were ready to quit in the next 30 days and the majority of these had never sought professional help (eg, "Quitline"). More than half had downloaded smoking cessation apps in the past and of these, three-quarters had made quitting attempts (lasted at least 24 hours) using an app before. Respondents who had attempted to quit three times or more in the previous year were more likely to have tried smoking cessation apps (OR 3.3, 95% CI 2.1-5.2). There were 50.2% (302/602) of the respondents that had used other health related apps before. Of these, 89.4% (270/302) were using health related apps at least once a week, but 77.5% (234/302) never checked the credibility of the health app publishers before downloading. A smartphone app was able to reach smokers across three countries that were not seeking professional help, but were ready to quit within the next 30 days. Respondents were relatively young and almost demographically similar across all three countries. They also frequently used other health related apps, mostly without checking the credibility of their publishers.

Simulated single molecule microscopy with SMeagol.

PubMed

Lindén, Martin; Ćurić, Vladimir; Boucharin, Alexis; Fange, David; Elf, Johan

2016-08-01

SMeagol is a software tool to simulate highly realistic microscopy data based on spatial systems biology models, in order to facilitate development, validation and optimization of advanced analysis methods for live cell single molecule microscopy data. SMeagol runs on Matlab R2014 and later, and uses compiled binaries in C for reaction-diffusion simulations. Documentation, source code and binaries for Mac OS, Windows and Ubuntu Linux can be downloaded from http://smeagol.sourceforge.net johan.elf@icm.uu.se Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

XtalOpt  version r9: An open-source evolutionary algorithm for crystal structure prediction

DOE PAGES

Falls, Zackary; Lonie, David C.; Avery, Patrick; ...

2015-10-23

This is a new version of XtalOpt, an evolutionary algorithm for crystal structure prediction available for download from the CPC library or the XtalOpt website, http://xtalopt.github.io. XtalOpt is published under the Gnu Public License (GPL), which is an open source license that is recognized by the Open Source Initiative. We have detailed the new version incorporates many bug-fixes and new features here and predict the crystal structure of a system from its stoichiometry alone, using evolutionary algorithms.

Cytoscape.js: a graph theory library for visualisation and analysis.

PubMed

Franz, Max; Lopes, Christian T; Huck, Gerardo; Dong, Yue; Sumer, Onur; Bader, Gary D

2016-01-15

Cytoscape.js is an open-source JavaScript-based graph library. Its most common use case is as a visualization software component, so it can be used to render interactive graphs in a web browser. It also can be used in a headless manner, useful for graph operations on a server, such as Node.js. Cytoscape.js is implemented in JavaScript. Documentation, downloads and source code are available at http://js.cytoscape.org. gary.bader@utoronto.ca. © The Author 2015. Published by Oxford University Press.

Normal Female Reproductive Anatomy

MedlinePlus

... hyphen, e.g. -historical Searches are case-insensitive Reproductive System, Female, Anatomy Add to My Pictures View /Download : ... 1500x1575 View Download Large: 3000x3150 View Download Title: Reproductive System, Female, Anatomy Description: Anatomy of the female reproductive ...

CADDIS Volume 4. Data Analysis: Download Software

EPA Pesticide Factsheets

Overview of the data analysis tools available for download on CADDIS. Provides instructions for downloading and installing CADStat, access to Microsoft Excel macro for computing SSDs, a brief overview of command line use of R, a statistical software.

pyNBS: A Python implementation for network-based stratification of tumor mutations.

PubMed

Huang, Justin K; Jia, Tongqiu; Carlin, Daniel E; Ideker, Trey

2018-03-28

We present pyNBS: a modularized Python 2.7 implementation of the network-based stratification (NBS) algorithm for stratifying tumor somatic mutation profiles into molecularly and clinically relevant subtypes. In addition to release of the software, we benchmark its key parameters and provide a compact cancer reference network that increases the significance of tumor stratification using the NBS algorithm. The structure of the code exposes key steps of the algorithm to foster further collaborative development. The package, along with examples and data, can be downloaded and installed from the URL http://www.github.com/huangger/pyNBS/. jkh013@ucsd.edu.

jSquid: a Java applet for graphical on-line network exploration.

PubMed

Klammer, Martin; Roopra, Sanjit; Sonnhammer, Erik L L

2008-06-15

jSquid is a graph visualization tool for exploring graphs from protein-protein interaction or functional coupling networks. The tool was designed for the FunCoup web site, but can be used for any similar network exploring purpose. The program offers various visualization and graph manipulation techniques to increase the utility for the user. jSquid is available for direct usage and download at http://jSquid.sbc.su.se including source code under the GPLv3 license, and input examples. It requires Java version 5 or higher to run properly. erik.sonnhammer@sbc.su.se Supplementary data are available at Bioinformatics online.

Factor Analytic Approach to Transitive Text Mining using Medline Descriptors

NASA Astrophysics Data System (ADS)

Stegmann, J.; Grohmann, G.

Matrix decomposition methods were applied to examples of noninteractive literature sets sharing implicit relations. Document-by-term matrices were created from downloaded PubMed literature sets, the terms being the Medical Subject Headings (MeSH descriptors) assigned to the documents. The loadings of the factors derived from singular value or eigenvalue matrix decomposition were sorted according to absolute values and subsequently inspected for positions of terms relevant to the discovery of hidden connections. It was found that only a small number of factors had to be screened to find key terms in close neighbourhood, being separated by a small number of terms only.

Weighted comparison of two cumulative incidence functions with R-CIFsmry package.

PubMed

Li, Jianing; Le-Rademacher, Jennifer; Zhang, Mei-Jie

2014-10-01

In this paper we propose a class of flexible weight functions for use in comparison of two cumulative incidence functions. The proposed weights allow the users to focus their comparison on an early or a late time period post treatment or to treat all time points with equal emphasis. These weight functions can be used to compare two cumulative incidence functions via their risk difference, their relative risk, or their odds ratio. The proposed method has been implemented in the R-CIFsmry package which is readily available for download and is easy to use as illustrated in the example. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Practical Session: Multiple Linear Regression

NASA Astrophysics Data System (ADS)

Clausel, M.; Grégoire, G.

2014-12-01

Three exercises are proposed to illustrate the simple linear regression. In the first one investigates the influence of several factors on atmospheric pollution. It has been proposed by D. Chessel and A.B. Dufour in Lyon 1 (see Sect. 6 of http://pbil.univ-lyon1.fr/R/pdf/tdr33.pdf) and is based on data coming from 20 cities of U.S. Exercise 2 is an introduction to model selection whereas Exercise 3 provides a first example of analysis of variance. Exercises 2 and 3 have been proposed by A. Dalalyan at ENPC (see Exercises 2 and 3 of http://certis.enpc.fr/~dalalyan/Download/TP_ENPC_5.pdf).

ODES (Online Data Extraction Service) for hydrology

NASA Astrophysics Data System (ADS)

Rosmorduc, Vinca; Birol, Florence; Briol, Frederic; Bronner, Emilie; Dibarboure, Gerald; Guinle, Thierry; Nicolas, Clara; Nino, Fernando; Valladeau, Guillaume

2015-04-01

AVISO+ proposes a new dissemination service, the Online Data Extraction Service (ODES), in order to provide users and applications with a wider range of altimetry-derived data (including high-resolution and experimental data). The platform is designed to distribute both operational products from CNES and partner Agencies (Eumetsat, ESA, NOAA, NASA) but also research-grade data from LEGOS/CTOH and CLS and other contributions from the OSTST research community. An example of use of ODES to extract hydrology experimental expert product (from Pistach processor) for hydrology will be shown. ODES is available at http://odes.altimetry.cnes.fr, download with your Aviso FTP login / password.

ODES (Online Data Extraction Service) for cryosphere studies

NASA Astrophysics Data System (ADS)

Rosmorduc, Vinca; Birol, Florence; Briol, Frederic; Bronner, Emilie; Dibarboure, Gerald; Guinle, Thierry; Nicolas, Clara; Nino, Fernando; Valladeau, Guillaume

2015-04-01

AVISO+ proposes a new dissemination service, the Online Data Extraction Service (ODES), in order to provide users and applications with a wider range of altimetry-derived data (including high-resolution and experimental data). The platform is designed to distribute both operational products from CNES and partner Agencies (Eumetsat, ESA, NOAA, NASA) but also research-grade data from LEGOS/CTOH and CLS and other contributions from the OSTST research community. An example of the use of ODES to extract AltiKa experimental expert products (from PEACHI prototype) over iced areas will be shown. ODES is available at http://odes.altimetry.cnes.fr, download with your Aviso FTP login / password.

Comparative Protein Structure Modeling Using MODELLER

PubMed Central

Webb, Benjamin; Sali, Andrej

2016-01-01

Comparative protein structure modeling predicts the three-dimensional structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target-template alignment, model building, and model evaluation. This unit describes how to calculate comparative models using the program MODELLER and how to use the ModBase database of such models, and discusses all four steps of comparative modeling, frequently observed errors, and some applications. Modeling lactate dehydrogenase from Trichomonas vaginalis (TvLDH) is described as an example. The download and installation of the MODELLER software is also described. PMID:27322406

Rheumatoid Arthritis

MedlinePlus

... Rheumatoid Arthritis English Español 繁體中文 한국어 tiếng Việt Rheumatoid Arthritis Basics In-Depth Download Download EPUB Download PDF What is it? Points To Remember About Rheumatoid Arthritis Rheumatoid arthritis is a disease that causes pain, ...

37 CFR 385.11 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 385.11 Patents, Trademarks, and Copyrights COPYRIGHT ROYALTY BOARD, LIBRARY OF CONGRESS RATES AND... MAKING AND DISTRIBUTING OF PHYSICAL AND DIGITAL PHONORECORDS Interactive Streaming and Limited Downloads... interactive streams or limited downloads of musical works, as applicable. Limited download means a digital...

The Internet: How Fast Can You Download?

ERIC Educational Resources Information Center

Shearer, Ron

1997-01-01

Discusses faster modems for downloading information from the Internet that may become available through cable or telephone industries. Topics include ADSL (Asymmetric Digital Subscriber Line) modems; Direct PC--downloading satellite transmissions; Land Multichannel Distribution System (LMDS)--a wireless communication device; and Internet…

How the Scientific Community Reacts to Newly Submitted Preprints: Article Downloads, Twitter Mentions, and Citations

PubMed Central

Shuai, Xin; Pepe, Alberto; Bollen, Johan

2012-01-01

We analyze the online response to the preprint publication of a cohort of 4,606 scientific articles submitted to the preprint database arXiv.org between October 2010 and May 2011. We study three forms of responses to these preprints: downloads on the arXiv.org site, mentions on the social media site Twitter, and early citations in the scholarly record. We perform two analyses. First, we analyze the delay and time span of article downloads and Twitter mentions following submission, to understand the temporal configuration of these reactions and whether one precedes or follows the other. Second, we run regression and correlation tests to investigate the relationship between Twitter mentions, arXiv downloads, and article citations. We find that Twitter mentions and arXiv downloads of scholarly articles follow two distinct temporal patterns of activity, with Twitter mentions having shorter delays and narrower time spans than arXiv downloads. We also find that the volume of Twitter mentions is statistically correlated with arXiv downloads and early citations just months after the publication of a preprint, with a possible bias that favors highly mentioned articles. PMID:23133597

Stream valleys and the coast, a reconnaissance soil-landscape analysis

NASA Astrophysics Data System (ADS)

van den Ancker, J. A. M.; Jungerius, P. D.

2012-04-01

The Council of Earth Sciences of the KNAW, the Royal Dutch Academy of Art and Sciences, started in 2008 a working group to discuss the low awareness of Dutch geoheritage and the operationalization of the geodiversity concept for modern sustainable spatial planning. More than forty earth scientists participated in the workgroup. Both authors of this poster were part of the organizing committee. The development of a new planning tool, based on the seven soil functions of the EU Soil Directive (2006) was proposed for a modern multi-functional and sustainable approach towards spatial planning. For reconnaissance purposes, two simplified examples were developed to illustrate the possibilities of the approach. The coastal example became part of the report, the stream valley example was never published. Both examples are presented in a short cross-table format on this poster. The Dutch stream valleys first were divided into five valley types according to present land-use and management. Next, it was recorded how each valley type performed on each of the seven EU soil functions. The results show that the majority of the stream valleys, probably more than 90 %, are mono-functional and directed at high agricultural production, which has an adverse effect on all the other soil functions in the area (and areas and waters outside the valley area studied). Along the coast the importance of the beach as a sea defence buffer and an economic tourism asset clearly showed. This is of course nothing new, but in spatial planning the economic role of tourism and especially the important role of the beach in sea defence are normally overlooked. The cross-tables of the EU soil functions show to be a good and simple tool to promote insight and discussion towards a more sustainable and multi-functional landuse. The KNAW report was presented to the Minister of the Environment in 2009, with the recommendation that the approach needed further development. Due to political shifts and government reorganisation the functional soil-landscape approach of the EU Soil Directive still awaits further development. In the meantime investments in technical mono-functional sustainable land management solutions prevail. Also present-day scientists prefer to work on mono-functional soil-landscape issues, urged by the need to publish in peer reviewed articles and by the fact that research programmes sponsored by the government address mono-issued problems. Literature Bouma J., et al., 2008. Geïntegreerd aardwetenschappelijk onderzoek ten behoeve van de ruimtelijke ordening. KNAW report, Amsterdam. (with an English summary) Pdf can be downloaded http://www.knaw.nl/smartsite.dws?lang=NL&id=26102&pub=20071087 Directive of the European parliament and of the council establishing a framework for the protection of soil: a Framework for a EU Soil Directive, COM (2006) 232 final http://ec.europa.eu/environment/soil/three_en.htm

Teaching Resources

Science.gov Websites

& Legislation Links Discussion Lists Quick Links AAPT eMentoring ComPADRE Review of High School Take Physics" Poster Why Physics Poster Thumbnail Download normal resolution JPEG Download high resolution JPEG Download Spanish Version Recruiting Physics Students in High School (FED newsletter article

Expert Involvement Predicts mHealth App Downloads: Multivariate Regression Analysis of Urology Apps

PubMed Central

Osório, Luís; Cavadas, Vitor; Fraga, Avelino; Carrasquinho, Eduardo; Cardoso de Oliveira, Eduardo; Castelo-Branco, Miguel; Roobol, Monique J

2016-01-01

Background Urological mobile medical (mHealth) apps are gaining popularity with both clinicians and patients. mHealth is a rapidly evolving and heterogeneous field, with some urology apps being downloaded over 10,000 times and others not at all. The factors that contribute to medical app downloads have yet to be identified, including the hypothetical influence of expert involvement in app development. Objective The objective of our study was to identify predictors of the number of urology app downloads. Methods We reviewed urology apps available in the Google Play Store and collected publicly available data. Multivariate ordinal logistic regression evaluated the effect of publicly available app variables on the number of apps being downloaded. Results Of 129 urology apps eligible for study, only 2 (1.6%) had >10,000 downloads, with half having ≤100 downloads and 4 (3.1%) having none at all. Apps developed with expert urologist involvement (P=.003), optional in-app purchases (P=.01), higher user rating (P<.001), and more user reviews (P<.001) were more likely to be installed. App cost was inversely related to the number of downloads (P<.001). Only data from the Google Play Store and the developers’ websites, but not other platforms, were publicly available for analysis, and the level and nature of expert involvement was not documented. Conclusions The explicit participation of urologists in app development is likely to enhance its chances to have a higher number of downloads. This finding should help in the design of better apps and further promote urologist involvement in mHealth. Official certification processes are required to ensure app quality and user safety. PMID:27421338

Seabed photographs, sediment texture analyses, and sun-illuminated sea floor topography in the Stellwagen Bank National Marine Sanctuary region off Boston, Massachusetts

USGS Publications Warehouse

Valentine, Page C.; Gallea, Leslie B.; Blackwood, Dann S.; Twomey, Erin R.

2010-01-01

The U.S. Geological Survey, in collaboration with National Oceanic and Atmospheric Administration's National Marine Sanctuary Program, conducted seabed mapping and related research in the Stellwagen Bank National Marine Sanctuary region from 1993 to 2004. The mapped area is approximately 3,700 km (1,100 nmi) in size and was subdivided into 18 quadrangles. An extensive series of sea-floor maps of the region based on multibeam sonar surveys has been published as paper maps and online in digital format (PDF, EPS, PS). In addition, 2,628 seabed-sediment samples were collected and analyzed and are in the usSEABED: Atlantic Coast Offshore Surficial Sediment Data Release. This report presents for viewing and downloading the more than 10,600 still seabed photographs that were acquired during the project. The digital images are provided in thumbnail, medium (1536 x 1024 pixels), and high (3071 x 2048) resolution. The images can be viewed by quadrangle on the U.S. Geological Survey Woods Hole Coastal and Marine Science Center's photograph database. Photograph metadata are embedded in each image in Exchangeable Image File Format and also provided in spreadsheet format. Published digital topographic maps and descriptive text for seabed features are included here for downloading and serve as context for the photographs. An interactive topographic map for each quadrangle shows locations of photograph stations, and each location is linked to the photograph database. This map also shows stations where seabed sediment was collected for texture analysis; the results of grain-size analysis and associated metadata are presented in spreadsheet format.

Performance Evaluation of Peer-to-Peer Progressive Download in Broadband Access Networks

NASA Astrophysics Data System (ADS)

Shibuya, Megumi; Ogishi, Tomohiko; Yamamoto, Shu

P2P (Peer-to-Peer) file sharing architectures have scalable and cost-effective features. Hence, the application of P2P architectures to media streaming is attractive and expected to be an alternative to the current video streaming using IP multicast or content delivery systems because the current systems require expensive network infrastructures and large scale centralized cache storage systems. In this paper, we investigate the P2P progressive download enabling Internet video streaming services. We demonstrated the capability of the P2P progressive download in both laboratory test network as well as in the Internet. Through the experiments, we clarified the contribution of the FTTH links to the P2P progressive download in the heterogeneous access networks consisting of FTTH and ADSL links. We analyzed the cause of some download performance degradation occurred in the experiment and discussed about the effective methods to provide the video streaming service using P2P progressive download in the current heterogeneous networks.

PubChemSR: A search and retrieval tool for PubChem

PubMed Central

Hur, Junguk; Wild, David J

2008-01-01

Background Recent years have seen an explosion in the amount of publicly available chemical and related biological information. A significant step has been the emergence of PubChem, which contains property information for millions of chemical structures, and acts as a repository of compounds and bioassay screening data for the NIH Roadmap. There is a strong need for tools designed for scientists that permit easy download and use of these data. We present one such tool, PubChemSR. Implementation PubChemSR (Search and Retrieve) is a freely available desktop application written for Windows using Microsoft .NET that is designed to assist scientists in search, retrieval and organization of chemical and biological data from the PubChem database. It employs SOAP web services made available by NCBI for extraction of information from PubChem. Results and Discussion The program supports a wide range of searching techniques, including queries based on assay or compound keywords and chemical substructures. Results can be examined individually or downloaded and exported in batch for use in other programs such as Microsoft Excel. We believe that PubChemSR makes it straightforward for researchers to utilize the chemical, biological and screening data available in PubChem. We present several examples of how it can be used. PMID:18482452

FDRAnalysis: a tool for the integrated analysis of tandem mass spectrometry identification results from multiple search engines.

PubMed

Wedge, David C; Krishna, Ritesh; Blackhurst, Paul; Siepen, Jennifer A; Jones, Andrew R; Hubbard, Simon J

2011-04-01

Confident identification of peptides via tandem mass spectrometry underpins modern high-throughput proteomics. This has motivated considerable recent interest in the postprocessing of search engine results to increase confidence and calculate robust statistical measures, for example through the use of decoy databases to calculate false discovery rates (FDR). FDR-based analyses allow for multiple testing and can assign a single confidence value for both sets and individual peptide spectrum matches (PSMs). We recently developed an algorithm for combining the results from multiple search engines, integrating FDRs for sets of PSMs made by different search engine combinations. Here we describe a web-server and a downloadable application that makes this routinely available to the proteomics community. The web server offers a range of outputs including informative graphics to assess the confidence of the PSMs and any potential biases. The underlying pipeline also provides a basic protein inference step, integrating PSMs into protein ambiguity groups where peptides can be matched to more than one protein. Importantly, we have also implemented full support for the mzIdentML data standard, recently released by the Proteomics Standards Initiative, providing users with the ability to convert native formats to mzIdentML files, which are available to download.

FDRAnalysis: A tool for the integrated analysis of tandem mass spectrometry identification results from multiple search engines

PubMed Central

Wedge, David C; Krishna, Ritesh; Blackhurst, Paul; Siepen, Jennifer A; Jones, Andrew R.; Hubbard, Simon J.

2013-01-01

Confident identification of peptides via tandem mass spectrometry underpins modern high-throughput proteomics. This has motivated considerable recent interest in the post-processing of search engine results to increase confidence and calculate robust statistical measures, for example through the use of decoy databases to calculate false discovery rates (FDR). FDR-based analyses allow for multiple testing and can assign a single confidence value for both sets and individual peptide spectrum matches (PSMs). We recently developed an algorithm for combining the results from multiple search engines, integrating FDRs for sets of PSMs made by different search engine combinations. Here we describe a web-server, and a downloadable application, which makes this routinely available to the proteomics community. The web server offers a range of outputs including informative graphics to assess the confidence of the PSMs and any potential biases. The underlying pipeline provides a basic protein inference step, integrating PSMs into protein ambiguity groups where peptides can be matched to more than one protein. Importantly, we have also implemented full support for the mzIdentML data standard, recently released by the Proteomics Standards Initiative, providing users with the ability to convert native formats to mzIdentML files, which are available to download. PMID:21222473

DeepBlue epigenomic data server: programmatic data retrieval and analysis of epigenome region sets

PubMed Central

Albrecht, Felipe; List, Markus; Bock, Christoph; Lengauer, Thomas

2016-01-01

Large amounts of epigenomic data are generated under the umbrella of the International Human Epigenome Consortium, which aims to establish 1000 reference epigenomes within the next few years. These data have the potential to unravel the complexity of epigenomic regulation. However, their effective use is hindered by the lack of flexible and easy-to-use methods for data retrieval. Extracting region sets of interest is a cumbersome task that involves several manual steps: identifying the relevant experiments, downloading the corresponding data files and filtering the region sets of interest. Here we present the DeepBlue Epigenomic Data Server, which streamlines epigenomic data analysis as well as software development. DeepBlue provides a comprehensive programmatic interface for finding, selecting, filtering, summarizing and downloading region sets. It contains data from four major epigenome projects, namely ENCODE, ROADMAP, BLUEPRINT and DEEP. DeepBlue comes with a user manual, examples and a well-documented application programming interface (API). The latter is accessed via the XML-RPC protocol supported by many programming languages. To demonstrate usage of the API and to enable convenient data retrieval for non-programmers, we offer an optional web interface. DeepBlue can be openly accessed at http://deepblue.mpi-inf.mpg.de. PMID:27084938

Interactive, Automated Management of Icing Data

NASA Technical Reports Server (NTRS)

Levinson, Laurie H.

2009-01-01

IceVal DatAssistant is software (see figure) that provides an automated, interactive solution for the management of data from research on aircraft icing. This software consists primarily of (1) a relational database component used to store ice shape and airfoil coordinates and associated data on operational and environmental test conditions and (2) a graphically oriented database access utility, used to upload, download, process, and/or display data selected by the user. The relational database component consists of a Microsoft Access 2003 database file with nine tables containing data of different types. Included in the database are the data for all publicly releasable ice tracings with complete and verifiable test conditions from experiments conducted to date in the Glenn Research Center Icing Research Tunnel. Ice shapes from computational simulations with the correspond ing conditions performed utilizing the latest version of the LEWICE ice shape prediction code are likewise included, and are linked to the equivalent experimental runs. The database access component includes ten Microsoft Visual Basic 6.0 (VB) form modules and three VB support modules. Together, these modules enable uploading, downloading, processing, and display of all data contained in the database. This component also affords the capability to perform various database maintenance functions for example, compacting the database or creating a new, fully initialized but empty database file.

SlugIn 1.0: A Free Tool for Automated Slug Test Analysis.

PubMed

Martos-Rosillo, Sergio; Guardiola-Albert, Carolina; Padilla Benítez, Alberto; Delgado Pastor, Joaquín; Azcón González, Antonio; Durán Valsero, Juan José

2018-05-01

The correct characterization of aquifer parameters is essential for water-supply and water-quality investigations. Slug tests are widely used for these purposes. While free software is available to interpret slug tests, some codes are not user-friendly, or do not include a wide range of methods to interpret the results, or do not include automatic, inverse solutions to the test data. The private sector has also generated several good programs to interpret slug test data, but they are not free of charge. The computer program SlugIn 1.0 is available online for free download, and is demonstrated to aid in the analysis of slug tests to estimate hydraulic parameters. The program provides an easy-to-use Graphical User Interface. SlugIn 1.0 incorporates automated parameter estimation and facilitates the visualization of several interpretations of the same test. It incorporates solutions for confined and unconfined aquifers, partially penetrating wells, skin effects, shape factor, anisotropy, high hydraulic conductivity formations and the Mace test for large-diameter wells. It is available in English and Spanish and can be downloaded from the web site of the Geological Survey of Spain. Two field examples are presented to illustrate how the software operates. © 2018, National Ground Water Association.

Application of the Golden Software Surfer mapping software for automation of visualisation of meteorological and oceanographic data in IMGW Maritime Branch.

NASA Astrophysics Data System (ADS)

Piliczewski, B.

2003-04-01

The Golden Software Surfer has been used in IMGW Maritime Branch for more than ten years. This tool provides ActiveX Automation objects, which allow scripts to control practically every feature of Surfer. These objects can be accessed from any Automation-enabled environment, such as Visual Basic or Excel. Several applications based on Surfer has been developed in IMGW. The first example is an on-line oceanographic service, which presents forecasts of the water temperature, sea level and currents originating from the HIROMB model and is automatically updated every day. Surfer was also utilised in MERMAID, an international project supported by EC under the 5th Framework Programme. The main aim of this project was to create a prototype of the Internet-based data brokerage system, which would enable to search, extract, buy and download datasets containing meteorological or oceanographic data. During the project IMGW developed an online application, called Mermaid Viewer, which enables communication with the data broker and automatic visualisation of the downloaded data using Surfer. Both the above mentioned applications were developed in Visual Basic. Currently it is considered to adopt Surfer for the monitoring service, which provides access to the data collected in the monitoring of the Baltic Sea environment.

Providing Access to a Diverse Set of Global Reanalysis Dataset Collections

NASA Astrophysics Data System (ADS)

Schuster, D.; Worley, S. J.

2015-12-01

The National Center for Atmospheric Research (NCAR) Research Data Archive (RDA, http://rda.ucar.edu) provides open access to a variety of global reanalysis dataset collections to support atmospheric and related sciences research worldwide. These include products from the European Centre for Medium-Range Weather Forecasts (ECMWF), Japan Meteorological Agency (JMA), National Centers for Environmental Prediction (NCEP), National Oceanic and Atmospheric Administration (NOAA), and NCAR.All RDA hosted reanalysis collections are freely accessible to registered users through a variety of methods. Standard access methods include traditional browser and scripted HTTP file download. Enhanced downloads are available through the Globus GridFTP "fire and forget" data transfer service, which provides an efficient, reliable, and preferred alternative to traditional HTTP-based methods. For those that favor interoperable access using compatible tools, the Unidata THREDDS Data server provides remote access to complete reanalysis collections by virtual dataset aggregation "files". Finally, users can request data subsets and format conversions to be prepared for them through web interface form requests or web service API batch requests. This approach uses NCAR HPC and central file systems to effectively prepare products from the high-resolution and very large reanalyses archives. The presentation will include a detailed inventory of all RDA reanalysis dataset collection holdings, and highlight access capabilities to these collections through use case examples.

It takes a community to define a discipline: the 5th anniversary of Environmental Research Letters It takes a community to define a discipline: the 5th anniversary of Environmental Research Letters

NASA Astrophysics Data System (ADS)

Kammen, Dan

2012-03-01

When does a scientific journal become a community? This is not the question that we explicitly set out to address five years ago when IOP Publishing agreed to launch a new format interdisciplinary journal, Environmental Research Letters (ERL). However, on reflection, that is what ERL has become, and what it needs to continue to explore during its next years of growth and evolution. The motivation for founding ERL was initially more focused: to alter the mode of publication and review in the diverse, yet linked fields of environmental and resource studies and to ensure new levels of interaction, inclusion and equity, providing the platform for the world-changing research findings published in ERL. The key driver in this conversation was the issue of access. Specifically the situation that too many research findings were produced by, and for, very specific academic 'clubs', and that the opportunity to engage in discussion and debate over important emerging findings about our world was being severely limited by the process of publication in frequently slow-to-publish and tremendously expensive traditional academic journals. The need for change was, and still is, obvious. Environmental and resource studies have been the fastest growing and most diverse nexus of academic research, private sector concern and public sector action. Universities worldwide are adding academic and extension professorships and staff as well as experiencing increasing student interest in this area at a record pace. Corporate social and environmental sustainability has been changing dramatically and, in lurching fits and starts, a mosaic of environmental regulations—both carrots and sticks—are emerging worldwide. The 'Rio + 20' Earth Summit in June 2012 will be a testament to both the dramatic broadening of this interest, and the frustration about the lack of progress at building strong global institutions to permit international cooperation. This is a clear call for an on-going and evolving process of community building. ERL sought and continues to seek ways to lead this conversation. 1. Open access and equity First, all ERL articles and data sets are entirely open access. Once published, the materials are free to all users, affluent and poor, anywhere in the world. This is vital for a number of reasons. Environmental stress, degradation, and the creation of innovative solutions involves a global dialog, where traditional expensive subscription and single article costs, as some journals charge, are a complete barrier to researchers, fledgling entrepreneurs, and the public sector in developing nations and in poor communities. Instead, ERL charges authors a fee, generally covered by research grants. Further, we have been able to waive the open access article charge for authors based in areas of the world where this fee may prove prohibitive, as it can be in many developing countries. In this open access format, ERL publishes cutting-edge original research letters, commentary-style 'Perspective' pieces and editorial articles. ERL is committed to staying at the forefront of the 'gold standard' for open access publishing of articles and data—something that journals are increasingly taking up—and as new ideas come in as to how to improve this process, we will look to put them into practice. 2. Build a network researching sustainability Second, a journal that reaches across so many disciplines needs to be a place where results are not only reviewed and published quickly, but are then accessible to a broad audience, and are available for debate and conversation. ERL strives to maintain a 90 day timeline from submission to fully peer-reviewed publication online. This process in particular has only been possible with the incredible support of two groups: (1) the dedication of IOP Publishing and the amazingly talented staff they have been able to identify and recruit to work on ERL, and (2) the journal's Editorial Board. We have a team of Editors made up of the most remarkable researchers in their fields, each of whom have committed to this rapid review process. I have often remarked that my academic dream would be to be on a faculty with this group, and ERL has facilitated that vision both virtually and through our meetings. This group is responsible for both the quality of published articles and the speed of our review process. Rapid publication of rigorously reviewed short-format articles that in their language and style are widely accessible across disciplines has a huge impact. Young researchers doing innovative cutting-edge work often need to get papers out rapidly, and researchers, both junior and senior, gravitate to a journal where important findings can appear rapidly. The results here have been striking and can be showcased by a selection of highlights, such as: Achieved an ISI Impact Factor of 3.049 in 2010. An average of over 40 000 downloads per month in 2011. Hit 50 000 downloads in January 2012. Individual articles published in 2011 were downloaded over 650 times each on average during the same year. Submissions are up over 50% in 2011 compared to 2010. Citations to ERL content up 80% from 2009 to 2010. 3. Build a network conversation about sustainability The second part of the community building around sustainability, which ERL is now working to develop, is how to facilitate conversation about ideas that the research articles raise. Several exciting developments have shown that we can, in fact, do this particularly effectively, even in these early stages. As an example, ERL's sister community website, environmentalresearchweb, launched in 2007, publishing news, opinion, commentary, jobs, events and promotion of ERL authors' work. To date there are over 9000 registered users and over 6000 weekly newswire subscribers, popularity that reflects the incredibly high standards and wide accessibility of the expert journalistic content published on the site. environmentalresearchweb provides a discussion and commentary environment, a unique service in itself, and also a specific forum for research published in ERL. Individual topics often come up that warrant not only single articles, but collections of assessments, and ERL has published focus issues in key areas of environmental science including: tropical deforestation, wind energy, the Deepwater Horizon oil spill and climate engineering. ERL is currently publishing seven high-quality focus issues in cutting-edge areas such as arctic vegetation dynamics and cryospheric changes. Research letters appearing in ERL have received regular and significant coverage in the wider media, with several major news outlets and agencies choosing to cover ERL research, such as Nature, BBC News, New Scientist, The Guardian, Scientific American, Le Monde and many others. 4.The future community of ERL The process of community support will take many forms at ERL. The journal is growing—we have published the highest number of articles ever in a single volume in 2011 and are looking to continue this growth through into 2012. ERL had an over 50% increase in submissions from 2010 to 2011. One initiative to mark the journal's 5th anniversary was the 'Best articles' collection [1] a nominated compilation of articles showcasing the quality of published work in ERL as well as the subject area breadth. Co-authors of the five winning articles have been awarded free publication in ERL until the end of 2012. We can also see the open access model working, in that our articles are highly downloaded outside of the traditionally strong geographical areas of academia (North America and Western Europe), showing that the journal's readership is geographically diverse with high interest from Asia, South America and Africa. The journal is committed to progress and innovation; coming soon will be a set of new communication tools and online innovations, including: Video abstracts from the start of 2012 (for example, the video commentary published alongside this editorial). Enhanced HTML format of the full-text article from 2012 onwards—'Article Evolution', an on-going community feedback-driven project to improve the online delivery of research articles. New focus issues covering the latest cutting-edge areas of environmental science, with seven planned focus issues for 2012, including: second-generation biofuels, biodiversity, human health and well-being and environmental risks and migration. These innovations are improving all the time as a result of community response and feedback, both in terms of rating and critiquing the services that ERL provides, and also in looking for ways that the science-practitioner-implementer-regulator nexus can be strengthened. On all of these I offer my thanks to the ERL community; readers, authors, Editorial Board Members and many others, and extend a request for further suggested innovations for us to try in the next five-year window. References [1] Kammen D and Wright G 2011 'Best article' prize for the 5th anniversary of Environmental Research Letters Environ. Res. Lett. 6 040201

Examples and Case Studies for the 2012 Chemical Data Reporting

EPA Pesticide Factsheets

This document presents examples and case studies to help you in reporting for 2012 Chemical Data Reporting (CDR), formerly known as Inventory Update Reporting (IUR).EPA designed these examples to illustrate the new reporting requirements, which were published as part of the CDR Rule (published August 16, 2011), and to address general reporting issues from the 2006 IUR.

Archive of digital boomer subbottom data collected during USGS cruise 05FGS01 offshore east-central Florida, July 17-29, 2005

USGS Publications Warehouse

Forde, Arnell S.; Dadisman, Shawn V.; Wiese, Dana S.; Phelps, Daniel C.

2012-01-01

In July of 2005, the U.S. Geological Survey (USGS), in cooperation with the Florida Geological Survey (FGS), conducted a geophysical survey of the Atlantic Ocean offshore of Florida's east coast from Flagler Beach to Daytona Beach. This report serves as an archive of unprocessed digital boomer subbottom data, trackline maps, navigation files, Geographic Information System (GIS) files, Field Activity Collection System (FACS) logs and formal Federal Geographic Data Committee (FGDC) metadata. Filtered and gained (showing a relative increase in signal amplitude) digital images of the seismic profiles are also provided. Refer to the Acronyms page for expansions of acronyms and abbreviations used in this report. The USGS Saint Petersburg Coastal and Marine Science Center (SPCMSC) assigns a unique identifier to each cruise or field activity. For example, 05FGS01 tells us the data were collected in 2005 for cooperative work with the FGS and the data were collected during the first field activity for that project in that calendar year. Refer to http://walrus.wr.usgs.gov/infobank/programs/html/definition/activity.html for a detailed description of the method used to assign the field activity ID. The boomer subbottom processing system consists of an acoustic energy source that is made up of capacitors charged to a high voltage and discharged through a transducer in the water. The transducer is towed on a sled floating on the water surface and when discharged emits a short acoustic pulse, or shot, which propagates through the water column and shallow stratrigraphy below. The acoustic energy is reflected at density boundaries (such as the seafloor or sediment layers beneath the seafloor), detected by the receiver (a hydrophone streamer), and recorded by a PC-based seismic acquisition system. This process is repeated at timed intervals (for example, 0.5 s) and recorded for specific intervals of time (for example, 100 ms). In this way, a two-dimensional (2-D) vertical image of the shallow geologic structure beneath the ship track is produced. Figure 1 displays the acquisition geometry. Refer to table 1 for a summary of acquisition parameters and table 2 for trackline statistics. The archived trace data are in standard Society of Exploration Geophysicists (SEG) SEG Y format (Barry and others, 1975), except an ASCII format is used for the first 3,200 bytes of the card image header instead of the standard EBCDIC format. For a detailed description about the recorded trace headers, refer to the SEG Y Format page. The SEG Y files may be downloaded and processed with commercial or public domain software such as Seismic Unix (Cohen and Stockwell, 2005). See the How To Download SEG Y Data page for download instructions. The printable profiles provided here are GIF images that were processed and gained using SU software; refer to the Software page for links to example SU processing scripts. The processed SEG Y data were also exported to Chesapeake Technology, Inc. (CTI) SonarWeb software to produce a geospatially interactive version of the profile that allows the user to obtain a geographic location and depth from the profile for a given cursor position; this information is displayed in the status bar of the browser. Please note that clicking on the profile image switches it to "Expanded View" (a compressed image of the entire line) and cursor tracking is not available in this mode.

COMPILATION OF CONVERSION COEFFICIENTS FOR THE DOSE TO THE LENS OF THE EYE.

PubMed

Behrens, R

2017-04-28

A compilation of fluence-to-absorbed dose conversion coefficients for the dose to the lens of the eye is presented. The compilation consists of both previously published data and newly calculated values: photon data (5 keV-50 MeV for both kerma approximation and full electron transport), electron data (10 keV-50 MeV), and positron data (1 keV-50 MeV) - neutron data will be published separately. Values are given for angles of incidence from 0° up to 90° in steps of 15° and for rotational irradiation. The data presented can be downloaded from this article's website and they are ready for use by Report Committee (RC) 26. This committee has been set up by the International Commission on Radiation Units and Measurements (ICRU) and is working on a 'proposal for a redefinition of the operational quantities for external radiation exposure'. © The Author 2016. Published by Oxford University Press.

Letter from the Editor

NASA Astrophysics Data System (ADS)

Strassmeier, Klaus G.

2009-01-01

As of 2007, Astronomische Nachrichten -- Astronomical Notes has reached its all-time high regarding the ISI journal impact factor, with an impressive increase of 60% compared to 2005. We now rank at 1,461, as shown in the statistics below. This is solely due to the increased quality of the published articles: In 2006, Astronomische Nachrichten -- Astronomical Notes published 208 research papers and received 1,033 citations -- five citations per paper on average. In 2007, we have published 177 research papers with roughly the same number of citations. In co-operation with Wiley InterScience we have achieved an average online publication time of just 4.5 months. We hope that the year 2008 will be comparably prosperous. As in the past, publication in Astronomische Nachrichten -- Astronomical Notes continues to be free of charge. Also, all articles of the first issue of each volume can be downloaded free of charge, as can all articles labelled ``Editor's Choice'', which are additionally featured with a color image on the front cover.

Letter from the Editor

NASA Astrophysics Data System (ADS)

Strassmeier, Klaus G.

2008-01-01

As of 2006, Astronomische Nachrichten -- Astronomical Notes has reached its all-time high regarding the ISI journal impact factor, with an impressive increase of 60% compared to 2005. We now rank at position 1,399, as shown in the statistics below. This is solely due to the increased number and quality of published articles: In 2006, Astronomische Nachrichten -- Astronomical Notes published 208 research papers and received 1,033 citations -- five citations per paper on average. In 2007, we have published 177 research papers, and one may be curious to see how their factor will develop. In co-operation with Wiley InterScience we have achieved an average o nline publication time of just 4.5 months. As in the past, publication in Astronomische Nachrichten -- Astronomical Notes} continues to be free of charge. Also, all articles of the first issue of each volume can be downloaded free of charge, as can all articles labelled ``Editor's Choice'', which are additionally featured with a color image on the front cover.

EDITORIAL: The present and future

NASA Astrophysics Data System (ADS)

Durand, Dominique M.

2006-09-01

Neural engineering has grown substantially in the last few years and it is time to review the progress of the first journal in this field. Journal of Neural Engineering (JNE) is a quarterly publication that started in 2004. The journal is now in its third volume and eleven issues, consisting of 114 articles in total, have been published since its launch. The editorial processing times have been kept to a minimum, the receipt to first decision time is 41 days, on average, and the time from receipt to publication has been maintained below three months. It is also worth noting that it is free to publish in Journal of Neural Engineering—there are no author fees—and once published the articles are free online for the first month. The journal has been listed in Pubmed® since 2005 and has been accepted by ISI® in 2006. Who is reading Journal of Neural Engineering? The number of readers of JNE has increased significantly from 8050 full-text downloads in 2004 to 14 900 in 2005 and the first seven months of 2006 have already seen 12 800 downloads. The top users in 2005 were the Microsoft Corporation, Stanford University and the University of Michigan. The list of top ten users also includes non-US institutions: University of Toronto, University of Tokyo, Hong Kong Polytechnic, National Library of China and University College London, reflecting the international flavor of the journal. What are the hot topics in neural engineering? Based on the number of downloads and citations for 2004-2005, the top three topics are: (1) Brain-computer interfaces (2) Visual prostheses (3) Neural modelling Several other topics such as microelectrode arrays, neural signal processing, neural dynamics and neural circuit engineering are also in the top ten. Where are Journal of Neural Engineering articles cited? JNE articles have reached a wide audience and have been cited in of some of the best journals in physiology and neuroscience such as Nature Neuroscience, Journal of Neuroscience, Trends in Neuroscience, Journal of Physiology, Proceedings of the National Academy of Science as well as in engineering and physics journals such as Annals of Biomedical Engineering, Physical Review Letters and IEEE Transactions on Biomedical Engineering. However, the number of citations in clinical journals is limited. What is special about Journal of Neural Engineering? JNE has published two special issues: (1) The Eye and the Chip (visual prostheses) (vol. 2, (1), 2005) and (2) Sensory Integration: Role of Internal Models (vol. 2, (3), 2005). These special issues have attracted a lot of attention based on the number of article downloads. JNE also publishes tutorials intended to provide background information on specific topics such as classification, sensory substitution and cortical neural prosthetics. A series of tutorials from the 3rd Neuro-IT and Neuroengineering Summer School has been published with the first appearing in vol. 2 (4), 2005. What is in the future for Journal of Neural Engineering? The goal of any journal should be to provide a particular field with the best venue for scientists and engineers to make their work available and noticeable to the rest of the community. In particular, attracting a strong readership base and high quality manuscripts should be the first priority. Providing accurate, reliable and speedy reviews should be the next. With an international board of experts in the field of neural engineering, a solid base of reviewers, readers and contributors, JNE is in a strong position to continue to serve the neural engineering community. However, this is still a small community and growth is essential for continued success in this area. There are two areas of expansion of great interest for the field of neural engineering currently poised between basic science on one hand and clinical implementation on the other: translational neuroscience and therapeutic neural engineering. We should strive to bridge the gap between basic neuroscience, clinical science and engineering by attracting contributions from neuroscientists and clinicians with an interest in neural engineering. I urge members of the neural engineering community to encourage their colleagues in these areas to consider JNE for publication of those manuscripts at the interface with neuroscience and engineering. I would like to take this opportunity to acknowledge the work of the board members, the reviewers of the articles and the staff at the Institute of Physics Publishing for their contribution to the Journal of Neural Engineering.

Academic Software Downloads from Google Code: Useful Usage Indicators?

ERIC Educational Resources Information Center

Thelwall, Mike; Kousha, Kayvan

2016-01-01

Introduction: Computer scientists and other researchers often make their programs freely available online. If this software makes a valuable contribution inside or outside of academia then its creators may want to demonstrate this with a suitable indicator, such as download counts. Methods: Download counts, citation counts, labels and licenses…

Wing download reduction using vortex trapping plates

NASA Technical Reports Server (NTRS)

Light, Jeffrey S.; Stremel, Paul M.; Bilanin, Alan J.

1994-01-01

A download reduction technique using spanwise plates on the upper and lower wing surfaces has been examined. Experimental and analytical techniques were used to determine the download reduction obtained using this technique. Simple two-dimensional wind tunnel testing confirmed the validity of the technique for reducing two-dimensional airfoil drag. Computations using a two-dimensional Navier-Stokes analysis provided insight into the mechanism causing the drag reduction. Finally, the download reduction technique was tested using a rotor and wing to determine the benefits for a semispan configuration representative of a tilt rotor aircraft.

AstroBlend: An astrophysical visualization package for Blender

NASA Astrophysics Data System (ADS)

Naiman, J. P.

2016-04-01

The rapid growth in scale and complexity of both computational and observational astrophysics over the past decade necessitates efficient and intuitive methods for examining and visualizing large datasets. Here, I present AstroBlend, an open-source Python library for use within the three dimensional modeling software, Blender. While Blender has been a popular open-source software among animators and visual effects artists, in recent years it has also become a tool for visualizing astrophysical datasets. AstroBlend combines the three dimensional capabilities of Blender with the analysis tools of the widely used astrophysical toolset, yt, to afford both computational and observational astrophysicists the ability to simultaneously analyze their data and create informative and appealing visualizations. The introduction of this package includes a description of features, work flow, and various example visualizations. A website - www.astroblend.com - has been developed which includes tutorials, and a gallery of example images and movies, along with links to downloadable data, three dimensional artistic models, and various other resources.

JANIS: NEA JAva-based Nuclear Data Information System

NASA Astrophysics Data System (ADS)

Soppera, Nicolas; Bossant, Manuel; Cabellos, Oscar; Dupont, Emmeric; Díez, Carlos J.

2017-09-01

JANIS (JAva-based Nuclear Data Information System) software is developed by the OECD Nuclear Energy Agency (NEA) Data Bank to facilitate the visualization and manipulation of nuclear data, giving access to evaluated nuclear data libraries, such as ENDF, JEFF, JENDL, TENDL etc., and also to experimental nuclear data (EXFOR) and bibliographical references (CINDA). It is available as a standalone Java program, downloadable and distributed on DVD and also a web application available on the NEA website. One of the main new features in JANIS is the scripting capability via command line, which notably automatizes plots generation and permits automatically extracting data from the JANIS database. Recent NEA software developments rely on these JANIS features to access nuclear data, for example the Nuclear Data Sensitivity Tool (NDaST) makes use of covariance data in BOXER and COVERX formats, which are retrieved from the JANIS database. New features added in this version of the JANIS software are described along this paper with some examples.

Metadata tables to enable dynamic data modeling and web interface design: the SEER example.

PubMed

Weiner, Mark; Sherr, Micah; Cohen, Abigail

2002-04-01

A wealth of information addressing health status, outcomes and resource utilization is compiled and made available by various government agencies. While exploration of the data is possible using existing tools, in general, would-be users of the resources must acquire CD-ROMs or download data from the web, and upload the data into their own database. Where web interfaces exist, they are highly structured, limiting the kinds of queries that can be executed. This work develops a web-based database interface engine whose content and structure is generated through interaction with a metadata table. The result is a dynamically generated web interface that can easily accommodate changes in the underlying data model by altering the metadata table, rather than requiring changes to the interface code. This paper discusses the background and implementation of the metadata table and web-based front end and provides examples of its use with the NCI's Surveillance, Epidemiology and End-Results (SEER) database.

Mean of the typical decoding rates: a new translation efficiency index based on the analysis of ribosome profiling data.

PubMed

Dana, Alexandra; Tuller, Tamir

2014-12-01

Gene translation modeling and prediction is a fundamental problem that has numerous biomedical implementations. In this work we present a novel, user-friendly tool/index for calculating the mean of the typical decoding rates that enables predicting translation elongation efficiency of protein coding genes for different tissue types, developmental stages, and experimental conditions. The suggested translation efficiency index is based on the analysis of the organism's ribosome profiling data. This index could be used for example to predict changes in translation elongation efficiency of lowly expressed genes that usually have relatively low and/or biased ribosomal densities and protein levels measurements, or can be used for example for predicting translation efficiency of new genetically engineered genes. We demonstrate the usability of this index via the analysis of six organisms in different tissues and developmental stages. Distributable cross platform application and guideline are available for download at: http://www.cs.tau.ac.il/~tamirtul/MTDR/MTDR_Install.html. Copyright © 2015 Dana and Tuller.

Archive of digital Chirp sub-bottom profile data collected during USGS Cruise 07SCC01 offshore of the Chandeleur Islands, Louisiana, June 2007

USGS Publications Warehouse

Forde, Arnell S.; Dadisman, Shawn V.; Flocks, James G.; Wiese, Dana S.

2010-01-01

In June of 2007, the U.S. Geological Survey (USGS) conducted a geophysical survey offshore of the Chandeleur Islands, Louisiana, in cooperation with the Louisiana Department of Natural Resources (LDNR) as part of the USGS Barrier Island Comprehensive Monitoring (BICM) project. This project is part of a broader study focused on Subsidence and Coastal Change (SCC). The purpose of the study was to investigate the shallow geologic framework and monitor the enviromental impacts of Hurricane Katrina (Louisiana landfall was on August 29, 2005) on the Gulf Coast's barrier island chains. This report serves as an archive of unprocessed digital 512i and 424 Chirp sub-bottom profile data, trackline maps, navigation files, Geographic Information System (GIS) files, Field Activity Collection System (FACS) logs, observer's logbook, and formal Federal Geographic Data Committee (FGDC) metadata. Gained (a relative increase in signal amplitude) digital images of the seismic profiles are also provided. Refer to the Acronyms page for expansion of acronyms and abbreviations used in this report. The USGS St. Petersburg Coastal and Marine Science Center (SPCMSC) assigns a unique identifier to each cruise or field activity. For example, 07SCC01 tells us the data were collected in 2007 for the Subsidence and Coastal Change (SCC) study and the data were collected during the first field activity for that study in that calendar year. Refer to http://walrus.wr.usgs.gov/infobank/programs/html/definition/activity.html for a detailed description of the method used to assign the field activity identification (ID). All Chirp systems use a signal of continuously varying frequency; the Chirp systems used during this survey produce high resolution, shallow penetration profile images beneath the seafloor. The towfish is a sound source and receiver, which is typically towed 1 - 2 m below the sea surface. The acoustic energy is reflected at density boundaries (such as the seafloor or sediment layers beneath the seafloor), detected by a receiver, and recorded by a PC-based seismic acquisition system. This process is repeated at timed intervals (for example, 0.125 s) and recorded for specific intervals of time (for example, 50 ms). In this way, a two-dimensional vertical image of the shallow geologic structure beneath the ship track is produced. Figure 1 displays the acquisition geometry. Refer to table 1 for a summary of acquisition parameters. See the digital FACS equipment log (11-KB PDF) for details about the acquisition equipment used. Table 2 lists trackline statistics. Scanned images of the handwritten FACS logs and handwritten science logbook (449-KB PDF) are also provided. The archived trace data are in standard Society of Exploration Geophysicists (SEG) SEG-Y rev 1 format (Norris and Faichney, 2002); ASCII character encoding is used for the first 3,200 bytes of the card image header instead of the SEG-Y rev 0 (Barry and others, 1975) EBCDIC format. The SEG-Y files may be downloaded and processed with commercial or public domain software such as Seismic Unix (SU) (Cohen and Stockwell, 2010). See the How To Download SEG-Y Data page for download instructions. The web version of this archive does not contain the SEG-Y trace files. These files are very large and would require extremely long download times. To obtain the complete DVD archive, contact USGS Information at 1-888-ASK-USGS or infoservices@usgs.gov. The printable profiles provided here are GIF images that were processed and gained using SU software; refer to the Software page for links to example SU processing scripts and USGS software for viewing the SEG-Y files (Zihlman, 1992). The processed SEG-Y data were also exported to Chesapeake Technology, Inc. (CTI) SonarWeb software to produce an interactive version of the profile that allows the user to obtain a geographic location and depth from the profile for a given cursor position. This information is displayed in the status bar of the browser.

Systematic downloading and analysis of data from automated external defibrillators used in out-of-hospital cardiac arrest.

PubMed

Hansen, Marco Bo; Lippert, Freddy Knudsen; Rasmussen, Lars Simon; Nielsen, Anne Møller

2014-12-01

Valuable information can be retrieved from automated external defibrillators (AEDs) used in victims of out-of-hospital cardiac arrest (OHCA). We describe our experience with systematic downloading of data from deployed AEDs. The primary aim was to compare the proportion of shockable rhythm from AEDs used by laypersons with the corresponding proportion recorded by the Emergency Medical Services (EMS) on arrival. In a 20-month study, we collected data on OHCAs in the Capital Region of Denmark where an AED was deployed prior to arrival of EMS. The AEDs were brought to the emergency medical dispatch centre for data downloading and rhythm analysis. Patient data were retrieved from the medical records from the admitting hospital, whereas data on EMS rhythm analyses were obtained from the Danish Cardiac Arrest Register between 2001 and 2010. A total of 121 AEDs were deployed, of which 91 cases were OHCAs with presumed cardiac origin. The prevalence of initial shockable rhythm was 55.0% (95% CI [44.7-64.8%]). This was significantly greater than the proportion recorded by the EMS (27.6%, 95% CI [27.0-28.3%], p<0.0001). Shockable arrests were significantly more likely to be witnessed (92% vs. 34%, p<0.0001) and the bystander CPR rate was higher (98% vs. 85%, p=0.04). More patients with initial shockable rhythm achieved return of spontaneous circulation upon hospital arrival (88% vs. 7%, p<0.0001) and had higher 30-day survival rate (72% vs. 5%, p<0.0001). AEDs used by laypersons revealed a higher proportion of shockable rhythms compared to the EMS rhythm analyses. Copyright © 2014 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Initial Experience of the American Society of Regional Anesthesia and Pain Medicine Coags Regional Smartphone Application: A Novel Report of Global Distribution and Clinical Usage of an Electronic Decision Support Tool to Enhance Guideline Use.

PubMed

Gupta, Rajnish K; McEvoy, Matthew D

2016-01-01

Decision support tools have been demonstrated to improve adherence to medical guidelines; however, smartphone applications (apps) have not been studied in this regard. In a collaboration between Vanderbilt University and the American Society of Regional Anesthesia and Pain Medicine (ASRA), the ASRA Coags Regional app was created to be a decision support tool for the 2010 published guideline on regional anesthesia for patients receiving anticoagulation. This is a review of the distribution and usage of this app. The app was created to be a user-friendly version of the guideline. Download statistics were collected from April 2014 to October 2015, and app usage data were collected from October 2014 to October 2015. Usage data were analyzed for number of devices, number of search sessions, medications searched, and types of procedures. There were 8381 downloads, with 83% from North America. Of users who allowed data tracking, 4504 unique devices were identified with 30,003 separate search events. The most searched-for medications were rivaroxaban (n = 4427; 11%), clopidogrel (n = 4042; 10%), and enoxaparin, prophylactic twice daily dosing (n = 3249; 8%). Neuraxial procedures (n = 22,477; 78%) were the most commonly searched-for procedures and over half (n = 22,773; 52%) the users were interested in how long to hold a medication before performing a procedure. This is the first publication of download and usage data concerning medical smartphone apps. It provides a template for future app uptake and use in clinical practice. The app platform provides a new mechanism of rapidly disseminating guidelines and facilitating distribution of frequent updates.

PhysiomeSpace: digital library service for biomedical data

PubMed Central

Testi, Debora; Quadrani, Paolo; Viceconti, Marco

2010-01-01

Every research laboratory has a wealth of biomedical data locked up, which, if shared with other experts, could dramatically improve biomedical and healthcare research. With the PhysiomeSpace service, it is now possible with a few clicks to share with selected users biomedical data in an easy, controlled and safe way. The digital library service is managed using a client–server approach. The client application is used to import, fuse and enrich the data information according to the PhysiomeSpace resource ontology and upload/download the data to the library. The server services are hosted on the Biomed Town community portal, where through a web interface, the user can complete the metadata curation and share and/or publish the data resources. A search service capitalizes on the domain ontology and on the enrichment of metadata for each resource, providing a powerful discovery environment. Once the users have found the data resources they are interested in, they can add them to their basket, following a metaphor popular in e-commerce web sites. When all the necessary resources have been selected, the user can download the basket contents into the client application. The digital library service is now in beta and open to the biomedical research community. PMID:20478910

Antimicrobial resistance dashboard application for mapping environmental occurrence and resistant pathogens

PubMed Central

Stedtfeld, Robert D.; Williams, Maggie R.; Fakher, Umama; Johnson, Timothy A.; Stedtfeld, Tiffany M.; Wang, Fang; Khalife, Walid T.; Hughes, Mary; Etchebarne, Brett E.; Tiedje, James M.; Hashsham, Syed A.

2016-01-01

An antibiotic resistance (AR) Dashboard application is being developed regarding the occurrence of antibiotic resistance genes (ARG) and bacteria (ARB) in environmental and clinical settings. The application gathers and geospatially maps AR studies, reported occurrence and antibiograms, which can be downloaded for offline analysis. With the integration of multiple data sets, the database can be used on a regional or global scale to identify hot spots for ARGs and ARB; track and link spread and transmission, quantify environmental or human factors influencing presence and persistence of ARG harboring organisms; differentiate natural ARGs from those distributed via human or animal activity; cluster and compare ARGs connections in different environments and hosts; and identify genes that can be used as proxies to routinely monitor anthropogenic pollution. To initially populate and develop the AR Dashboard, a qPCR ARG array was tested with 30 surface waters, primary influent from three waste water treatment facilities, ten clinical isolates from a regional hospital and data from previously published studies including river, park soil and swine farm samples. Interested users are invited to download a beta version (available on iOS or Android), submit AR information using the application, and provide feedback on current and prospective functionalities. PMID:26850162

PhysiomeSpace: digital library service for biomedical data.

PubMed

Testi, Debora; Quadrani, Paolo; Viceconti, Marco

2010-06-28

Every research laboratory has a wealth of biomedical data locked up, which, if shared with other experts, could dramatically improve biomedical and healthcare research. With the PhysiomeSpace service, it is now possible with a few clicks to share with selected users biomedical data in an easy, controlled and safe way. The digital library service is managed using a client-server approach. The client application is used to import, fuse and enrich the data information according to the PhysiomeSpace resource ontology and upload/download the data to the library. The server services are hosted on the Biomed Town community portal, where through a web interface, the user can complete the metadata curation and share and/or publish the data resources. A search service capitalizes on the domain ontology and on the enrichment of metadata for each resource, providing a powerful discovery environment. Once the users have found the data resources they are interested in, they can add them to their basket, following a metaphor popular in e-commerce web sites. When all the necessary resources have been selected, the user can download the basket contents into the client application. The digital library service is now in beta and open to the biomedical research community.

Neuronvisio: A Graphical User Interface with 3D Capabilities for NEURON.

PubMed

Mattioni, Michele; Cohen, Uri; Le Novère, Nicolas

2012-01-01

The NEURON simulation environment is a commonly used tool to perform electrical simulation of neurons and neuronal networks. The NEURON User Interface, based on the now discontinued InterViews library, provides some limited facilities to explore models and to plot their simulation results. Other limitations include the inability to generate a three-dimensional visualization, no standard mean to save the results of simulations, or to store the model geometry within the results. Neuronvisio (http://neuronvisio.org) aims to address these deficiencies through a set of well designed python APIs and provides an improved UI, allowing users to explore and interact with the model. Neuronvisio also facilitates access to previously published models, allowing users to browse, download, and locally run NEURON models stored in ModelDB. Neuronvisio uses the matplotlib library to plot simulation results and uses the HDF standard format to store simulation results. Neuronvisio can be viewed as an extension of NEURON, facilitating typical user workflows such as model browsing, selection, download, compilation, and simulation. The 3D viewer simplifies the exploration of complex model structure, while matplotlib permits the plotting of high-quality graphs. The newly introduced ability of saving numerical results allows users to perform additional analysis on their previous simulations.

DelPhiPKa web server: predicting pKa of proteins, RNAs and DNAs.

PubMed

Wang, Lin; Zhang, Min; Alexov, Emil

2016-02-15

A new pKa prediction web server is released, which implements DelPhi Gaussian dielectric function to calculate electrostatic potentials generated by charges of biomolecules. Topology parameters are extended to include atomic information of nucleotides of RNA and DNA, which extends the capability of pKa calculations beyond proteins. The web server allows the end-user to protonate the biomolecule at particular pH based on calculated pKa values and provides the downloadable file in PQR format. Several tests are performed to benchmark the accuracy and speed of the protocol. The web server follows a client-server architecture built on PHP and HTML and utilizes DelPhiPKa program. The computation is performed on the Palmetto supercomputer cluster and results/download links are given back to the end-user via http protocol. The web server takes advantage of MPI parallel implementation in DelPhiPKa and can run a single job on up to 24 CPUs. The DelPhiPKa web server is available at http://compbio.clemson.edu/pka_webserver. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Genome-scale strain designs based on regulatory minimal cut sets.

PubMed

Mahadevan, Radhakrishnan; von Kamp, Axel; Klamt, Steffen

2015-09-01

Stoichiometric and constraint-based methods of computational strain design have become an important tool for rational metabolic engineering. One of those relies on the concept of constrained minimal cut sets (cMCSs). However, as most other techniques, cMCSs may consider only reaction (or gene) knockouts to achieve a desired phenotype. We generalize the cMCSs approach to constrained regulatory MCSs (cRegMCSs), where up/downregulation of reaction rates can be combined along with reaction deletions. We show that flux up/downregulations can virtually be treated as cuts allowing their direct integration into the algorithmic framework of cMCSs. Because of vastly enlarged search spaces in genome-scale networks, we developed strategies to (optionally) preselect suitable candidates for flux regulation and novel algorithmic techniques to further enhance efficiency and speed of cMCSs calculation. We illustrate the cRegMCSs approach by a simple example network and apply it then by identifying strain designs for ethanol production in a genome-scale metabolic model of Escherichia coli. The results clearly show that cRegMCSs combining reaction deletions and flux regulations provide a much larger number of suitable strain designs, many of which are significantly smaller relative to cMCSs involving only knockouts. Furthermore, with cRegMCSs, one may also enable the fine tuning of desired behaviours in a narrower range. The new cRegMCSs approach may thus accelerate the implementation of model-based strain designs for the bio-based production of fuels and chemicals. MATLAB code and the examples can be downloaded at http://www.mpi-magdeburg.mpg.de/projects/cna/etcdownloads.html. krishna.mahadevan@utoronto.ca or klamt@mpi-magdeburg.mpg.de Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Inductive matrix completion for predicting gene-disease associations.

PubMed

Natarajan, Nagarajan; Dhillon, Inderjit S

2014-06-15

Most existing methods for predicting causal disease genes rely on specific type of evidence, and are therefore limited in terms of applicability. More often than not, the type of evidence available for diseases varies-for example, we may know linked genes, keywords associated with the disease obtained by mining text, or co-occurrence of disease symptoms in patients. Similarly, the type of evidence available for genes varies-for example, specific microarray probes convey information only for certain sets of genes. In this article, we apply a novel matrix-completion method called Inductive Matrix Completion to the problem of predicting gene-disease associations; it combines multiple types of evidence (features) for diseases and genes to learn latent factors that explain the observed gene-disease associations. We construct features from different biological sources such as microarray expression data and disease-related textual data. A crucial advantage of the method is that it is inductive; it can be applied to diseases not seen at training time, unlike traditional matrix-completion approaches and network-based inference methods that are transductive. Comparison with state-of-the-art methods on diseases from the Online Mendelian Inheritance in Man (OMIM) database shows that the proposed approach is substantially better-it has close to one-in-four chance of recovering a true association in the top 100 predictions, compared to the recently proposed Catapult method (second best) that has <15% chance. We demonstrate that the inductive method is particularly effective for a query disease with no previously known gene associations, and for predicting novel genes, i.e. genes that are previously not linked to diseases. Thus the method is capable of predicting novel genes even for well-characterized diseases. We also validate the novelty of predictions by evaluating the method on recently reported OMIM associations and on associations recently reported in the literature. Source code and datasets can be downloaded from http://bigdata.ices.utexas.edu/project/gene-disease. © The Author 2014. Published by Oxford University Press.

Scanning and georeferencing historical USGS quadrangles

USGS Publications Warehouse

Davis, Larry R.; Allord, G.J.

2011-01-01

The USGS Historical Quadrangle Scanning Project (HQSP) is scanning all scales and all editions of approximately 250,000 topographic maps published by the U.S. Geological Survey (USGS) since the inception of the topographic mapping program in 1884. This scanning will provide a comprehensive digital repository of USGS topographic maps, available to the public at no cost. This project serves the dual purpose of creating a master catalog and digital archive copies of the irreplaceable collection of topographic maps in the USGS Reston Map Library as well as making the maps available for viewing and downloading from the USGS Store and The National Map Viewer.

Light-Duty Automotive Technology, Carbon Dioxide Emissions, and Fuel Economy Trends Data

EPA Pesticide Factsheets

The Light-Duty Automotive Technology, Carbon Dioxide Emissions, and Fuel Economy Trends report is the authoritative reference for carbon dioxide (CO2) emissions, fuel economy, and powertrain technology trends for new personal vehicles in the United States. The ??Trends?? report has been published annually since 1975 and covers all passenger cars, sport utility vehicles, minivans, and all but the largest pickup trucks and vans. This report does not provide formal compliance values for EPA CO2 emissions standards and NHTSA CAFE standards. The downloadable data are available in PDF or spreadsheet (XLS) formats.

Drive Cycle Data | Transportation Secure Data Center | NREL

Science.gov Websites

one file. Download Individual Survey and Study Drive Cycle Data Below you'll find drive cycle data download files for individual surveys and studies. Greater Fairbanks, Alaska, Transportation Survey Drive Cycle Data by Vehicle (24-hour period of operation) Download Learn more about the survey. California

Alternative Fuels Data Center: Schwan's Home Service Delivers With

Science.gov Websites

distribute products across the United States. For information about this project, contact Twin Cities Clean Cities Coalition. Download QuickTime Video QuickTime (.mov) Download Windows Media Video Windows Media (.wmv) Video Download Help Text version See more videos provided by Clean Cities TV and FuelEconomy.gov

Gene Model Annotations for Drosophila melanogaster: The Rule-Benders

PubMed Central

Crosby, Madeline A.; Gramates, L. Sian; dos Santos, Gilberto; Matthews, Beverley B.; St. Pierre, Susan E.; Zhou, Pinglei; Schroeder, Andrew J.; Falls, Kathleen; Emmert, David B.; Russo, Susan M.; Gelbart, William M.

2015-01-01

In the context of the FlyBase annotated gene models in Drosophila melanogaster, we describe the many exceptional cases we have curated from the literature or identified in the course of FlyBase analysis. These range from atypical but common examples such as dicistronic and polycistronic transcripts, noncanonical splices, trans-spliced transcripts, noncanonical translation starts, and stop-codon readthroughs, to single exceptional cases such as ribosomal frameshifting and HAC1-type intron processing. In FlyBase, exceptional genes and transcripts are flagged with Sequence Ontology terms and/or standardized comments. Because some of the rule-benders create problems for handlers of high-throughput data, we discuss plans for flagging these cases in bulk data downloads. PMID:26109356

Features of a Mobile Support App for Patients With Chronic Obstructive Pulmonary Disease: Literature Review and Current Applications

PubMed Central

Philip, Nada; Kayyali, Reem; Nabhani-Gebara, Shereen; Pierscionek, Barbara; Vaes, Anouk W; Spruit, Martijn A; Kaimakamis, Evangelos

2017-01-01

Background Chronic obstructive pulmonary disease (COPD) is a serious long-term lung disease in which the airflow from the lungs is progressively reduced. By 2030, COPD will become the third cause of mortality and seventh cause of morbidity worldwide. With advances in technology and mobile communications, significant progress in the mobile health (mHealth) sector has been recently observed. Mobile phones with app capabilities (smartphones) are now considered as potential media for the self-management of certain types of diseases such as asthma, cancer, COPD, or cardiovascular diseases. While many mobile apps for patients with COPD are currently found on the market, there is little published material on the effectiveness of most of them, their features, and their adoption in health care settings. Objectives The aim of this study was to search the literature for current systems related to COPD and identify any missing links and studies that were carried out to evaluate the effectiveness of COPD mobile apps. In addition, we reviewed existing mHealth apps from different stores in order to identify features that can be considered in the initial design of a COPD support tool to improve health care services and patient outcomes. Methods In total, 206 articles related to COPD management systems were identified from different databases. Irrelevant materials and duplicates were excluded. Of those, 38 articles were reviewed to extract important features. We identified 214 apps from online stores. Following exclusion of irrelevant apps, 48 were selected and 20 of them were downloaded to review some of their common features. Results Our review found that out of the 20 apps downloaded, 13 (65%, 13/20) had an education section, 5 (25%, 5/20) consisted of medication and guidelines, 6 (30%, 6/20) included a calendar or diary and other features such as reminders or symptom tracking. There was little published material on the effectiveness of the identified COPD apps. Features such as (1) a social networking tool; (2) personalized education; (3) feedback; (4) e-coaching; and (5) psychological motivation to enhance behavioral change were found to be missing in many of the downloaded apps. Conclusions This paper summarizes the features of a COPD patient-support mobile app that can be taken into consideration for the initial design of an integrated care system to encourage the self-management of their condition at home. PMID:28219878

Archive of Digital Boomer Seismic Reflection Data Collected During USGS Field Activity 96LCA04 in Lakes Mabel and Starr, Central Florida, August 1996

USGS Publications Warehouse

Harrison, Arnell S.; Dadisman, Shawn V.; Swancar, Amy; Tihansky, Ann B.; Flocks, James G.; Wiese, Dana S.

2008-01-01

In August of 1996, the U.S. Geological Survey conducted geophysical surveys of Lakes Mabel and Starr, central Florida, as part of the Central Highlands Lakes project, which is part of a larger USGS Lakes and Coastal Aquifers (LCA) study. This report serves as an archive of unprocessed digital boomer seismic reflection data, trackline maps, navigation files, Geographic Information System (GIS) files, observer's logbook; and formal Federal Geographic Data Committee (FGDC) metadata. Filtered and gained (a relative increase in signal amplitude) digital images of the seismic profiles are also provided. Refer to the Acronyms page for expansions of acronyms and abbreviations used in this report. For detailed information about the hydrologic setting of Lake Starr and the interpretation of some of these seismic reflection data, see Swancar and others (2000) at http://fl.water.usgs.gov/publications/Abstracts/wri00_4030_swancar.html. The archived trace data are in standard Society of Exploration Geophysicists (SEG) SEG-Y format (Barry and others, 1975) and may be downloaded and processed with commercial or public domain software such as Seismic Unix (SU). Example SU processing scripts and USGS software for viewing the SEG-Y files (Zihlman, 1992) are also provided. The USGS Florida Integrated Science Center (FISC) - St. Petersburg assigns a unique identifier to each cruise or field activity. For example, 96LCA04 tells us the data were collected in 1996 for the Lakes and Coastal Aquifers (LCA) study and the data were collected during the fourth field activity for that project in that calendar year. Refer to http://walrus.wr.usgs.gov/infobank/programs/html/definition/activity.html for a detailed description of the method used to assign the field activity ID. The boomer plate is an acoustic energy source that consists of capacitors charged to a high voltage and discharged through a transducer in the water. The transducer is towed on a sled floating on the water surface and when discharged emits a short acoustic pulse, or shot, which propagates through the water and sediment column. The acoustic energy is reflected at density boundaries (such as the seafloor or sediment layers beneath the lake bottom), detected by the receiver (a hydrophone streamer), and recorded by a PC-based seismic acquisition system. This process is repeated at timed intervals (for example, 0.5 s) and recorded for specific intervals of time (for example, 100 ms). In this way, a two-dimensional (2-D) vertical image of the shallow geologic structure beneath the ship track is produced. Figure 1 displays the acquisition geometry. Refer to table 1 for a summary of acquisition parameters. Table 2 lists trackline statistics. Scanned images of the handwritten cruise logbook (1,020-KB PDF) is also provided as a PDF file. The unprocessed seismic data are stored in SEG-Y format (Barry and others, 1975). For a detailed description of the data format, refer to the SEG-Y Format page. See the How To Download SEG-Y Data page for download instructions. The printable profiles provided here are GIF images that were filtered and gained using Seismic Unix software. Refer to the Software page for details about the processing and examples of the processing scripts. The processed SEG-Y data were exported to Chesapeake Technology, Inc. (CTI) SonarWeb software to produce an interactive version of the seismic profile that allows the user to obtain a geographic location and depth from the profile for a curser position. This information is displayed in the status bar of the browser.

Archive of digital boomer seismic reflection data collected offshore east-central Florida during USGS cruise 00FGS01, July 14-22, 2000

USGS Publications Warehouse

Subino, Janice A.; Dadisman, Shawn V.; Wiese, Dana S.; Calderon, Karynna; Phelps, Daniel C.

2009-01-01

In July of 2000, the U.S. Geological Survey (USGS), in cooperation with the Florida Geological Survey (FGS), conducted a geophysical survey of the Atlantic Ocean offshore Florida's east coast from Brevard County to northern Martin County. This report serves as an archive of unprocessed digital boomer seismic reflection data, trackline maps, navigation files, Geographic Information System (GIS) information, digital and handwritten Field Activity Collection System (FACS) logs, and Federal Geographic Data Committee (FGDC) metadata. A filtered and gained (a relative increase in signal amplitude) digital image of each seismic profile is also provided. Refer to the Acronyms page for expansions of all acronyms and abbreviations used in this report. The archived trace data are in standard Society of Exploration Geophysicists (SEG) SEG-Y format (Barry and others, 1975) and may be downloaded and processed with commercial or public domain software such as Seismic Unix (SU) (Cohen and Stockwell, 2005). Example SU processing scripts and USGS Software for viewing the SEG-Y files (Zihlman, 1992) are also provided. The USGS St. Petersburg Coastal and Marine Science Center assigns a unique identifier to each cruise or field activity. For example, 00FGS01 tells us the data were collected in 2000 for cooperative work with the Florida Geological Survey (FGS) and the data were collected during the first field activity for that study in that calendar year. Refer to http://walrus.wr.usgs.gov/infobank/programs/html/definition/activity.html for a detailed description of the method used to assign the field activity ID. The boomer plate is an acoustic energy source that consists of capacitors charged to a high voltage and discharged through a transducer in the water. The transducer is towed on a sled floating on the water surface and when discharged, emits a short acoustic pulse, or shot, which propagates through the water, sediment column, or rock beneath. The acoustic energy is reflected at density boundaries (such as the seafloor, sediment, or rock layers beneath the seafloor), detected by the receiver, and recorded by a PC-based seismic acquisition system. This process is repeated at timed intervals (for example, 0.5 s) and recorded for specific intervals of time (for example, 100 ms). In this way, a two-dimensional (2D) vertical profile of the shallow geologic structure beneath the ship track is produced. Figure 1 displays the acquisition geometry. Refer to table 1 for a summary of acquisition parameters. The unprocessed seismic data are stored in SEG-Y format (Barry and others, 1975). For a detailed description of the data format, refer to the SEG-Y Format page. See the How To Download SEG-Y Data page for download instructions. The printable profiles provided are GIF images that were filtered and gained using Seismic Unix software. Refer to the Software page for details about the processing and examples of the processing scripts. The printable profiles can be viewed from the Profiles page or from links located on the trackline maps. To view the trackline maps and navigation files, and for more information about these items, see the Navigation page. Detailed information about the navigation system used can be found in table 1. Of a total record length of 200 ms, only the upper 100 ms of each profile are displayed because no useful information was observed deeper in the sections. A 10 ms deep water delay appears on lines b57-b63 and sl2-sl28. No digital data were collected for line sl6. However, line sl6r is a second attempt to collect digital data for this line. Digital data and 500-shot-interval location navigation are not available for the last 1,161 shots of line sl26 due to an equipment malfunction.

Archive of digital boomer subbottom profile data collected in the Atlantic Ocean offshore northeast Florida during USGS cruises 03FGS01 and 03FGS02 in September and October of 2003

USGS Publications Warehouse

Calderon, Karynna; Forde, Arnell S.; Dadisman, Shawn V.; Wiese, Dana S.; Phelps, Daniel C.

2012-01-01

In September and October of 2003, the U.S. Geological Survey (USGS), in cooperation with the Florida Geological Survey, conducted geophysical surveys of the Atlantic Ocean offshore northeast Florida from St. Augustine, Florida, to the Florida-Georgia border. This report serves as an archive of unprocessed digital boomer subbottom profile data, trackline maps, navigation files, Geographic Information System (GIS) files, Field Activity Collection System (FACS) logs, and formal Federal Geographic Data Committee (FGDC) metadata. Filtered and gained (a relative increase in signal amplitude) digital images of the seismic profiles are also provided. Refer to the Acronyms page for expansions of all acronyms and abbreviations used in this report. The USGS St. Petersburg Coastal and Marine Science Center (SPCMSC) assigns a unique identifier to each cruise or field activity. For example, 03FGS01 tells us the data were collected in 2003 as part of cooperative work with the Florida Geological Survey (FGS) and that the data were collected during the first field activity for that project in that calendar year. Refer to http://walrus.wr.usgs.gov/infobank/programs/html/definition/activity.html for a detailed description of the method used to assign the field activity identification (ID). The naming convention used for each seismic line is as follows: yye##a, where 'yy' are the last two digits of the year in which the data were collected, 'e' is a 1-letter abbreviation for the equipment type (for example, b for boomer), '##' is a 2-digit number representing a specific track, and 'a' is a letter representing the section of a line if recording was prematurely terminated or rerun for quality or acquisition problems. The boomer plate is an acoustic energy source that consists of capacitors charged to a high voltage and discharged through a transducer in the water. The transducer is towed on a sled floating on the water surface and when discharged emits a short acoustic pulse, or shot, which propagates through the water, sediment column, or rock beneath. The acoustic energy is reflected at density boundaries (such as the seafloor, sediment, or rock layers beneath the seafloor), detected by hydrophone receivers, and recorded by a PC-based seismic acquisition system. This process is repeated at timed intervals (for example, 0.5 seconds) and recorded for specific intervals of time (for example, 100 milliseconds). In this way, a two-dimensional (2-D) vertical profile of the shallow geologic structure beneath the ship track is produced. Refer to the handwritten FACS operation log (PDF, 442 KB) for diagrams and descriptions of acquisition geometry, which varied throughout the cruises. Table 1 displays a summary of acquisition parameters. See the digital FACS equipment logs (PDF, 9-13 KB each) for details about the acquisition equipment used. The archived trace data are in standard Society of Exploration Geophysicists (SEG) SEG Y (Barry and others, 1975) format (rev. 0), except for the first 3,200 bytes of the card image header, which are stored in ASCII format instead of the standard EBCDIC format. The SEG Y files may be downloaded and processed with commercial or public domain software such as Seismic Unix (SU) (Cohen and Stockwell, 2005). See the How To Download SEG Y Data page for download instructions. The printable profiles provided here are Graphics Interchange Format (GIF) images that were filtered and gained using SU software. Refer to the Software page for details about the processing and links to example SU processing scripts and USGS software for viewing the SEG Y files (Zihlman, 1992).

PD5: a general purpose library for primer design software.

PubMed

Riley, Michael C; Aubrey, Wayne; Young, Michael; Clare, Amanda

2013-01-01

Complex PCR applications for large genome-scale projects require fast, reliable and often highly sophisticated primer design software applications. Presently, such applications use pipelining methods to utilise many third party applications and this involves file parsing, interfacing and data conversion, which is slow and prone to error. A fully integrated suite of software tools for primer design would considerably improve the development time, the processing speed, and the reliability of bespoke primer design software applications. The PD5 software library is an open-source collection of classes and utilities, providing a complete collection of software building blocks for primer design and analysis. It is written in object-oriented C(++) with an emphasis on classes suitable for efficient and rapid development of bespoke primer design programs. The modular design of the software library simplifies the development of specific applications and also integration with existing third party software where necessary. We demonstrate several applications created using this software library that have already proved to be effective, but we view the project as a dynamic environment for building primer design software and it is open for future development by the bioinformatics community. Therefore, the PD5 software library is published under the terms of the GNU General Public License, which guarantee access to source-code and allow redistribution and modification. The PD5 software library is downloadable from Google Code and the accompanying Wiki includes instructions and examples: http://code.google.com/p/primer-design.

Use of mobile devices for medical imaging.

PubMed

Hirschorn, David S; Choudhri, Asim F; Shih, George; Kim, Woojin

2014-12-01

Mobile devices have fundamentally changed personal computing, with many people forgoing the desktop and even laptop computer altogether in favor of a smaller, lighter, and cheaper device with a touch screen. Doctors and patients are beginning to expect medical images to be available on these devices for consultative viewing, if not actual diagnosis. However, this raises serious concerns with regard to the ability of existing mobile devices and networks to quickly and securely move these images. Medical images often come in large sets, which can bog down a network if not conveyed in an intelligent manner, and downloaded data on a mobile device are highly vulnerable to a breach of patient confidentiality should that device become lost or stolen. Some degree of regulation is needed to ensure that the software used to view these images allows all relevant medical information to be visible and manipulated in a clinically acceptable manner. There also needs to be a quality control mechanism to ensure that a device's display accurately conveys the image content without loss of contrast detail. Furthermore, not all mobile displays are appropriate for all types of images. The smaller displays of smart phones, for example, are not well suited for viewing entire chest radiographs, no matter how small and numerous the pixels of the display may be. All of these factors should be taken into account when deciding where, when, and how to use mobile devices for the display of medical images. Copyright © 2014 American College of Radiology. Published by Elsevier Inc. All rights reserved.

Discovery and Annotation of Plant Endogenous Target Mimicry Sequences from Public Transcriptome Libraries: A Case Study of Prunus persica.

PubMed

Karakülah, Gökhan

2017-06-28

Novel transcript discovery through RNA sequencing has substantially improved our understanding of the transcriptome dynamics of biological systems. Endogenous target mimicry (eTM) transcripts, a novel class of regulatory molecules, bind to their target microRNAs (miRNAs) by base pairing and block their biological activity. The objective of this study was to provide a computational analysis framework for the prediction of putative eTM sequences in plants, and as an example, to discover previously un-annotated eTMs in Prunus persica (peach) transcriptome. Therefore, two public peach transcriptome libraries downloaded from Sequence Read Archive (SRA) and a previously published set of long non-coding RNAs (lncRNAs) were investigated with multi-step analysis pipeline, and 44 putative eTMs were found. Additionally, an eTM-miRNA-mRNA regulatory network module associated with peach fruit organ development was built via integration of the miRNA target information and predicted eTM-miRNA interactions. My findings suggest that one of the most widely expressed miRNA families among diverse plant species, miR156, might be potentially sponged by seven putative eTMs. Besides, the study indicates eTMs potentially play roles in the regulation of development processes in peach fruit via targeting specific miRNAs. In conclusion, by following the step-by step instructions provided in this study, novel eTMs can be identified and annotated effectively in public plant transcriptome libraries.

Modes of Access: The Influence of Dissemination Channels on the Use of Open Access Monographs

ERIC Educational Resources Information Center

Snijder, Ronald

2014-01-01

Introduction: This paper studies the effects of several dissemination channels in an open access environment by analysing the download data of the OAPEN Library. Method: Download data were obtained containing the number of downloads and the name of the Internet provider. Based on public information, each Internet provider was categorised. The…

Alternative Fuels Data Center: Maine's Only Biodiesel Manufacturer Powers

Science.gov Websites

this project, contact Maine Clean Communities. Download QuickTime Video QuickTime (.mov) Download Windows Media Video Windows Media (.wmv) Video Download Help Text version See more videos provided by truck Krug Energy Opens Natural Gas Fueling Station in Arkansas June 18, 2016 photo of natural gas

Alternative Fuels Data Center: Texas Taxis Go Hybrid

Science.gov Websites

information about this project, contact Alamo Area Clean Cities (San Antonio). Download QuickTime Video QuickTime (.mov) Download Windows Media Video Windows Media (.wmv) Video Download Help Text version See more car Hydrogen Powers Fuel Cell Vehicles in California Nov. 18, 2017 Photo of a car Smart Car Shopping

enviroCar - citizen science for sustainable traffic

NASA Astrophysics Data System (ADS)

Stasch, Christoph; Remke, Albert; Jirka, Simon; Nuest, Daniel

2015-04-01

Optimizing traffic flow is a challenging task, affecting both the mobility of people and the environment. Up to now, traffic monitoring is based on small samples using GPS devices or remote sensors such as cameras. Citizens are usually not actively involved in the process of collecting or analyzing traffic data. The enviroCar project (www.envirocar.org) aims at addressing this situation by providing an open platform that can be used by everyone to collect and analyze traffic-related data and thus to achieve sustainable traffic management by answering questions such as: How is the average speed on a certain route? Where are exceptionally long waiting times in front of traffic lights? At which crossings do more cars stop than drive through? Where are hotspots of fuel consumption and air pollutant emission during a certain time interval? In this presentation, an overview on the enviroCar project is given and current research challenges addressed in the context of the project are presented. Citizens are able to participate by registering at the enviroCar portal and downloading the enviroCar Android app. Once installed, the Android app allows citizens to collect car sensor data, e.g. speed, mass air flow, or intake temperature via an On-Board Diagnosis 2 (OBD-II) Adapter. After finishing a car ride, the data can be uploaded to the central enviroCar server where the data is anonymized and published as open data. Each enviroCar member has a profile page giving control on his own data and providing statistics on personal driving behavior. The portal also allows comparing personal statistics with the statistics of other members. It thus facilitates analysis whether, for example, a member is driving in a more fuel saving manner than other users. Besides only acting as a data collector, citizens can also explore the enviroCar data in online maps or download the data in standard formats for certain spatial areas and/or time intervals allowing them to conduct spatio-temporal analyses by themselves. Thus, the platform also provides a means to analyze issues, such as repeated stops at a particular traffic light, and to communicate the results to other stakeholders, e.g. traffic planners or politicians. For traffic planners, the enviroCar project can also serve as a valuable additional data source for evaluating certain decisions, e.g. changing traffic light sequences. As not only the pure GPS data but also the car sensor data is collected, enviroCar enables to directly relate the traffic data to environmental parameters such as air pollutant emissions and thus to identify, for example, hotspots of CO2 emissions in a street network. Current research activities comprise technical issues, such as implementing scalable solutions for visualizing and analyzing big data sets, on improving estimation methods for fuel consumption and air pollutant emissions, but also include the development of novel spatio-temporal analysis and visualization methods and novel incentives for participation in crowd-sourcing and analyzing geospatial information.

UV LED-based lightweight fixed-wavelength detector: for the development of a miniaturized high-performance liquid chromatography (HPLC) system (Erratum)

NASA Astrophysics Data System (ADS)

Guan, Wen Yin; Lee, Wei Yan; Liew, Mervyn Wing On; Tan, Soo Choon; Lim, Jit Kang

2018-02-01

Publisher's Note: This paper, originally published on 14 February, 2018, was replaced with a corrected/revised version on 30 March, 2018. If you downloaded the original PDF but are unable to access the revision, please contact SPIE Digital Library Customer Service for assistance. General discussion on the development of portable and miniaturized instrumentation for High Performance Liquid Chromatography (HPLC) is given, specifically the design of UV absorbance detector for field applications. UV/Vis absorption detectors are the most commonly used detector in HPLC for the identification of organic compounds, detection of peptides, proteins and nucleic acids. Opportunities for miniaturization arise from trends which focus on ease of use, portability, and application-specific instruments for example in environmental applications - detection of phenols (water pollutant) and contaminants. Further usage is such as detection of polycyclic aromatic hydrocarbons (PAHs) and carcinogens in edible oils and growth promoter residues in meat. Significant improvement in size and complexity were realized using a simplified optical configuration, efficient low-power LED driver circuit and detector electronics. Firstly, the detector's optical configuration is discussed as an essential part of the miniature fixed-wavelength design. UV-LED with different wavelengths can be installed interchangeably without the need for complicated assembly and precise alignment process. In the second part, each functional block of the detector hardware design are also discussed. The electronics consist of mainly sample photodiode and reference photodiode, Log-ratio amplifier and signal conditioning electronics built with precision analog design techniques and low-noise electronic components. Finally, baseline noise and drift measurements and chromatography performance are presented and the results are compared with conventional detector under identical conditions as benchmark. The advantages of miniaturized HPLC system are portability for onsite analysis, increased efficiency, lower solvent requirements and fully integrated separation and detection system.

Alternative Fuels Data Center: America's Largest Home Runs on Biodiesel in

Science.gov Websites

Coalition (Western North Carolina). Download QuickTime Video QuickTime (.mov) Download Windows Media Video Windows Media (.wmv) Video Download Help Text version See more videos provided by Clean Cities TV and Photo of a car Hydrogen Powers Fuel Cell Vehicles in California Nov. 18, 2017 Photo of a car Smart Car

Alternative Fuels Data Center: Rhode Island EV Initiative Adds Chargers

Science.gov Websites

Ocean State Clean Cities. Download QuickTime Video QuickTime (.mov) Download Windows Media Video Windows Media (.wmv) Video Download Help Text version See more videos provided by Clean Cities TV and Photo of a car Hydrogen Powers Fuel Cell Vehicles in California Nov. 18, 2017 Photo of a car Smart Car

Alternative Fuels Data Center: Worcester Regional Transit Authority Drives

Science.gov Websites

Clean Cities. Download QuickTime Video QuickTime (.mov) Download Windows Media Video Windows Media (.wmv ) Video Download Help Text version See more videos provided by Clean Cities TV and FuelEconomy.gov Fuel Cell Vehicles in California Nov. 18, 2017 Photo of a car Smart Car Shopping Nov. 4, 2017 Image of

Alternative Fuels Data Center: Propane Powers Airport Shuttles in New

Science.gov Websites

Clean Fuel Partnership. Download QuickTime Video QuickTime (.mov) Download Windows Media Video Windows Media (.wmv) Video Download Help Text version See more videos provided by Clean Cities TV and Vehicles in California Nov. 18, 2017 Photo of a car Smart Car Shopping Nov. 4, 2017 Photo of a truck

High Performance Data Distribution for Scientific Community

NASA Astrophysics Data System (ADS)

Tirado, Juan M.; Higuero, Daniel; Carretero, Jesus

2010-05-01

Institutions such as NASA, ESA or JAXA find solutions to distribute data from their missions to the scientific community, and their long term archives. This is a complex problem, as it includes a vast amount of data, several geographically distributed archives, heterogeneous architectures with heterogeneous networks, and users spread around the world. We propose a novel architecture (HIDDRA) that solves this problem aiming to reduce user intervention in data acquisition and processing. HIDDRA is a modular system that provides a highly efficient parallel multiprotocol download engine, using a publish/subscribe policy which helps the final user to obtain data of interest transparently. Our system can deal simultaneously with multiple protocols (HTTP,HTTPS, FTP, GridFTP among others) to obtain the maximum bandwidth, reducing the workload in data server and increasing flexibility. It can also provide high reliability and fault tolerance, as several sources of data can be used to perform one file download. HIDDRA architecture can be arranged into a data distribution network deployed on several sites that can cooperate to provide former features. HIDDRA has been addressed by the 2009 e-IRG Report on Data Management as a promising initiative for data interoperability. Our first prototype has been evaluated in collaboration with the ESAC centre in Villafranca del Castillo (Spain) that shows a high scalability and performance, opening a wide spectrum of opportunities. Some preliminary results have been published in the Journal of Astrophysics and Space Science [1]. [1] D. Higuero, J.M. Tirado, J. Carretero, F. Félix, and A. de La Fuente. HIDDRA: a highly independent data distribution and retrieval architecture for space observation missions. Astrophysics and Space Science, 321(3):169-175, 2009

Making geospatial data in ASF archive readily accessible

NASA Astrophysics Data System (ADS)

Gens, R.; Hogenson, K.; Wolf, V. G.; Drew, L.; Stern, T.; Stoner, M.; Shapran, M.

2015-12-01

The way geospatial data is searched, managed, processed and used has changed significantly in recent years. A data archive such as the one at the Alaska Satellite Facility (ASF), one of NASA's twelve interlinked Distributed Active Archive Centers (DAACs), used to be searched solely via user interfaces that were specifically developed for its particular archive and data sets. ASF then moved to using an application programming interface (API) that defined a set of routines, protocols, and tools for distributing the geospatial information stored in the database in real time. This provided a more flexible access to the geospatial data. Yet, it was up to user to develop the tools to get a more tailored access to the data they needed. We present two new approaches for serving data to users. In response to the recent Nepal earthquake we developed a data feed for distributing ESA's Sentinel data. Users can subscribe to the data feed and are provided with the relevant metadata the moment a new data set is available for download. The second approach was an Open Geospatial Consortium (OGC) web feature service (WFS). The WFS hosts the metadata along with a direct link from which the data can be downloaded. It uses the open-source GeoServer software (Youngblood and Iacovella, 2013) and provides an interface to include the geospatial information in the archive directly into the user's geographic information system (GIS) as an additional data layer. Both services are run on top of a geospatial PostGIS database, an open-source geographic extension for the PostgreSQL object-relational database (Marquez, 2015). Marquez, A., 2015. PostGIS essentials. Packt Publishing, 198 p. Youngblood, B. and Iacovella, S., 2013. GeoServer Beginner's Guide, Packt Publishing, 350 p.

COMPILATION OF CONVERSION COEFFICIENTS FOR THE DOSE TO THE LENS OF THE EYE

PubMed Central

2017-01-01

Abstract A compilation of fluence-to-absorbed dose conversion coefficients for the dose to the lens of the eye is presented. The compilation consists of both previously published data and newly calculated values: photon data (5 keV–50 MeV for both kerma approximation and full electron transport), electron data (10 keV–50 MeV), and positron data (1 keV–50 MeV) – neutron data will be published separately. Values are given for angles of incidence from 0° up to 90° in steps of 15° and for rotational irradiation. The data presented can be downloaded from this article's website and they are ready for use by Report Committee (RC) 26. This committee has been set up by the International Commission on Radiation Units and Measurements (ICRU) and is working on a ‘proposal for a redefinition of the operational quantities for external radiation exposure’. PMID:27542816

Publisher Correction: Unravelling the immune signature of Plasmodium falciparum transmission-reducing immunity.

PubMed

Stone, Will J R; Campo, Joseph J; Ouédraogo, André Lin; Meerstein-Kessel, Lisette; Morlais, Isabelle; Da, Dari; Cohuet, Anna; Nsango, Sandrine; Sutherland, Colin J; van de Vegte-Bolmer, Marga; Siebelink-Stoter, Rianne; van Gemert, Geert-Jan; Graumans, Wouter; Lanke, Kjerstin; Shandling, Adam D; Pablo, Jozelyn V; Teng, Andy A; Jones, Sophie; de Jong, Roos M; Fabra-García, Amanda; Bradley, John; Roeffen, Will; Lasonder, Edwin; Gremo, Giuliana; Schwarzer, Evelin; Janse, Chris J; Singh, Susheel K; Theisen, Michael; Felgner, Phil; Marti, Matthias; Drakeley, Chris; Sauerwein, Robert; Bousema, Teun; Jore, Matthijs M

2018-04-11

The original version of this Article contained errors in Fig. 3. In panel a, bars from a chart depicting the percentage of antibody-positive individuals in non-infectious and infectious groups were inadvertently included in place of bars depicting the percentage of infectious individuals, as described in the Article and figure legend. However, the p values reported in the Figure and the resulting conclusions were based on the correct dataset. The corrected Fig. 3a now shows the percentage of infectious individuals in antibody-negative and -positive groups, in both the PDF and HTML versions of the Article. The incorrect and correct versions of Figure 3a are also presented for comparison in the accompanying Publisher Correction as Figure 1.The HTML version of the Article also omitted a link to Supplementary Data 6. The error has now been fixed and Supplementary Data 6 is available to download.

Specification for the U.S. Geological Survey Historical Topographic Map Collection

USGS Publications Warehouse

Allord, Gregory J.; Walter, Jennifer L.; Fishburn, Kristin A.; Shea, Gale A.

2014-01-01

This document provides the detailed requirements for producing, archiving, and disseminating a comprehensive digital collection of topographic maps for the U.S. Geological Survey (USGS) Historical Topographic Map Collection (HTMC). The HTMC is a digital archive of about 190,000 printed topographic maps published by the USGS from the inception of the topographic mapping program in 1884 until the last paper topographic map using lithographic printing technology was published in 2006. The HTMC provides a comprehensive digital repository of all scales and all editions of USGS printed topographic maps that is easily discovered, browsed, and downloaded by the public at no cost. The HTMC provides ready access to maps that are no longer available for distribution in print. A digital file representing the original paper historical topographic map is produced for each historical map in the HTMC in georeferenced PDF (GeoPDF) format (a portable document format [PDF] with a geospatial extension).

XenoSite server: a web-available site of metabolism prediction tool.

PubMed

Matlock, Matthew K; Hughes, Tyler B; Swamidass, S Joshua

2015-04-01

Cytochrome P450 enzymes (P450s) are metabolic enzymes that process the majority of FDA-approved, small-molecule drugs. Understanding how these enzymes modify molecule structure is key to the development of safe, effective drugs. XenoSite server is an online implementation of the XenoSite, a recently published computational model for P450 metabolism. XenoSite predicts which atomic sites of a molecule--sites of metabolism (SOMs)--are modified by P450s. XenoSite server accepts input in common chemical file formats including SDF and SMILES and provides tools for visualizing the likelihood that each atomic site is a site of metabolism for a variety of important P450s, as well as a flat file download of SOM predictions. XenoSite server is available at http://swami.wustl.edu/xenosite. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Explanation of fields used in the Alaska Resource Data File of mines, prospects, and mineral occurrences in Alaska

USGS Publications Warehouse

,

1996-01-01

Descriptions of mines, prospects, and mineral occurrences in the Alaska Resource Data File (ARDF) are published for individual U.S. Geological Survey 1:250,000 scale quadrangles in Alaska (see accompanying map) and are available for downloading from USGS World Wide Web site: http://www-rnrs-ak.wr.usgs.gov/ardf.These descriptions are divided into a number of fields which describe features of each mine, prospect, or mineral occurrence. These descriptions were complied from published literature and from unpublished reports and data from industry, the U.S. Bureau of Mines, and the U.S. Geological Survey and other sources. Compilation of this database is an ongoing process and each report is essentially a progress report. The authors of the individual quadrangle reports would appreciate any corrections or additional information that users may be able to contribute.

The G3 Experience with Electronic Publishing: An Editor's Perspective

NASA Astrophysics Data System (ADS)

White, W. M.

2003-12-01

G3 (Geochemistry, Geophysics, Geosystems) is an all-electronic journal published jointly by the AGU, the Geochemical Society, and the European Association of Geochemistry. G3 publishes original scientific contributions pertaining to understanding the Earth as a system, including relevant observational, experimental, and theoretical investigations of the solid Earth, hydrosphere, atmosphere, and biosphere. The journal was initiated as a result of a grass roots effort with the following goals in mind: a copyright policy designed to enhance, rather than inhibit, the dissemination of scientific information (for example, allowing authors to post electronic reprints on their web sites), provide a means of publishing, in immediately useable formats, large data sets, provide a means for ready dissemination of computer modeling and analysis tools, and provide a forum where authors could use novel ways of illustrating both data and models (e.g., formats such as movies, virtual reality images, sound, mathematical models, etc.), and finally to reduce costs and speed publication. In most respects, G3 has been enormously successful and has met most of its goals. G3 began publishing in December of 1999; in the subsequent 3 1/2 years 625 papers have been submitted to it and 325 have been published. It currently has over 600 institutional and personal subscribers. Papers are submitted through the web (a variety of formats are accepted, however, Microsoft Word is most common) and are converted to Adobe pdf format for peer review. Except that it is fully electronic using the web and e-mail, the peer review process is traditional, which insures the quality of the papers published. Accepted papers are copyedited and converted to SGML for archival purposes. HTML and Acrobat pdf versions are then generated from the SGML and published as they are ready on the G3 web site (www.g-cubed.org). Large data sets are routinely published in digital formats that can be readily downloaded by readers and immediately imported into programs such as Excel. Numerous animations and movies have been published in animated GIF, Apple Quicktime, Macromedia Flash, and Wolfram Research Mathreader formats. Computer models and tools have been published as Excel Macros and MATLAB Scripts. Full color, high resolution images allow superior publication of detailed maps and photographs. While G3 is a success by most measures, the process of pioneering electronic publication has at times been painful and frustrating. Early on, there were problems and delays in converting files, particularly graphics, to pdf format for both review and final publication. Costs have been higher than anticipated - primarily due to the cost of file conversion and formatting. The time from acceptance to publication (currently 10 weeks), although improving, it still longer than the goal, again because of the time required for copy-editing and formatting. Automation of this process in the future is the primary opportunity to both reduce cost and further speed publication. Authors have been slow to take advantage of the new illustration formats, with most relying on tradition figures instead. This will likely change slowly in the future, as these new formats, and the software tools to create them, become more familiar.

Publishing and sharing of hydrologic models through WaterHUB

NASA Astrophysics Data System (ADS)

Merwade, V.; Ruddell, B. L.; Song, C.; Zhao, L.; Kim, J.; Assi, A.

2011-12-01

Most hydrologists use hydrologic models to simulate the hydrologic processes to understand hydrologic pathways and fluxes for research, decision making and engineering design. Once these tasks are complete including publication of results, the models generally are not published or made available to the public for further use and improvement. Although publication or sharing of models is not required for journal publications, sharing of models may open doors for new collaborations, and avoids duplication of efforts if other researchers are interested in simulating a particular watershed for which a model already exists. For researchers, who are interested in sharing models, there are limited avenues to publishing their models to the wider community. Towards filling this gap, a prototype cyberinfrastructure (CI), called WaterHUB, is developed for sharing hydrologic data and modeling tools in an interactive environment. To test the utility of WaterHUB for sharing hydrologic models, a system to publish and share SWAT (Soil Water Assessment Tool) is developed. Users can utilize WaterHUB to search and download existing SWAT models, and also upload new SWAT models. Metadata such as the name of the watershed, name of the person or agency who developed the model, simulation period, time step, and list of calibrated parameters also published with individual model.

Educational Publishing: Experiences from Asia and the Pacific.

ERIC Educational Resources Information Center

United Nations Educational, Scientific and Cultural Organization, Bangkok (Thailand). Asian Centre for Educational Innovation for Development.

This resource book on educational publishing presents examples of evaluation and planning; try-out procedures; the production process; and warehousing and distribution, all reinforced by examples of systems and structures and case studies which were presented at the 1985 Manila and Tonga Seminars. Part one, Planning, Try-out and Evaluation of…

Online Visualization and Value Added Services of MERRA-2 Data at GES DISC

NASA Technical Reports Server (NTRS)

Shen, Suhung; Ostrenga, Dana M.; Vollmer, Bruce E.; Hegde, Mahabaleshwa S.; Wei, Jennifer C.; Bosilovich, Michael G.

2017-01-01

NASA climate reanalysis datasets from MERRA-2, distributed at the Goddard Earth Sciences Data and Information Services Center (GES DISC), have been used in broad research areas, such as climate variations, extreme weather, agriculture, renewable energy, and air quality, etc. The datasets contain numerous variables for atmosphere, land, and ocean, grouped into 95 products. The total archived volume is approximately 337 TB ( approximately 562K files) at the end of October 2017. Due to the large number of products and files, and large data volumes, it may be a challenge for a user to find and download the data of interest. The support team at GES DISC, working closely with the MERRA-2 science team, has created and is continuing to work on value added data services to best meet the needs of a broad user community. This presentation, using aerosol over Asia Monsoon as an example, provides an overview of the MERRA-2 data services at GES DISC, including: How to find the data? How many data access methods are provided? What are the best data access methods for me? How do download the subsetted (parameter, spatial, temporal) data and save in preferred spatial resolution and data format? How to visualize and explore the data online? In addition, we introduce a future online analytic tool designed for supporting application research, focusing on long-term hourly time-series data access and analysis.

EPEPT: A web service for enhanced P-value estimation in permutation tests

PubMed Central

2011-01-01

Background In computational biology, permutation tests have become a widely used tool to assess the statistical significance of an event under investigation. However, the common way of computing the P-value, which expresses the statistical significance, requires a very large number of permutations when small (and thus interesting) P-values are to be accurately estimated. This is computationally expensive and often infeasible. Recently, we proposed an alternative estimator, which requires far fewer permutations compared to the standard empirical approach while still reliably estimating small P-values [1]. Results The proposed P-value estimator has been enriched with additional functionalities and is made available to the general community through a public website and web service, called EPEPT. This means that the EPEPT routines can be accessed not only via a website, but also programmatically using any programming language that can interact with the web. Examples of web service clients in multiple programming languages can be downloaded. Additionally, EPEPT accepts data of various common experiment types used in computational biology. For these experiment types EPEPT first computes the permutation values and then performs the P-value estimation. Finally, the source code of EPEPT can be downloaded. Conclusions Different types of users, such as biologists, bioinformaticians and software engineers, can use the method in an appropriate and simple way. Availability http://informatics.systemsbiology.net/EPEPT/ PMID:22024252

An Application Programming Interface for Synthetic Snowflake Particle Structure and Scattering Data

NASA Technical Reports Server (NTRS)

Lammers, Matthew; Kuo, Kwo-Sen

2017-01-01

The work by Kuo and colleagues on growing synthetic snowflakes and calculating their single-scattering properties has demonstrated great potential to improve the retrievals of snowfall. To grant colleagues flexible and targeted access to their large collection of sizes and shapes at fifteen (15) microwave frequencies, we have developed a web-based Application Programming Interface (API) integrated with NASA Goddard's Precipitation Processing System (PPS) Group. It is our hope that the API will enable convenient programmatic utilization of the database. To help users better understand the API's capabilities, we have developed an interactive web interface called the OpenSSP API Query Builder, which implements an intuitive system of mechanisms for selecting shapes, sizes, and frequencies to generate queries, with which the API can then extract and return data from the database. The Query Builder also allows for the specification of normalized particle size distributions by setting pertinent parameters, with which the API can also return mean geometric and scattering properties for each size bin. Additionally, the Query Builder interface enables downloading of raw scattering and particle structure data packages. This presentation will describe some of the challenges and successes associated with developing such an API. Examples of its usage will be shown both through downloading output and pulling it into a spreadsheet, as well as querying the API programmatically and working with the output in code.

LEO Download Capacity Analysis for a Network of Adaptive Array Ground Stations

NASA Technical Reports Server (NTRS)

Ingram, Mary Ann; Barott, William C.; Popovic, Zoya; Rondineau, Sebastien; Langley, John; Romanofsky, Robert; Lee, Richard Q.; Miranda, Felix; Steffes, Paul; Mandl, Dan

2005-01-01

To lower costs and reduce latency, a network of adaptive array ground stations, distributed across the United States, is considered for the downlink of a polar-orbiting low earth orbiting (LEO) satellite. Assuming the X-band 105 Mbps transmitter of NASA s Earth Observing 1 (EO-1) satellite with a simple line-of-sight propagation model, the average daily download capacity in bits for a network of adaptive array ground stations is compared to that of a single 11 m dish in Poker Flats, Alaska. Each adaptive array ground station is assumed to have multiple steerable antennas, either mechanically steered dishes or phased arrays that are mechanically steered in azimuth and electronically steered in elevation. Phased array technologies that are being developed for this application are the space-fed lens (SFL) and the reflectarray. Optimization of the different boresight directions of the phased arrays within a ground station is shown to significantly increase capacity; for example, this optimization quadruples the capacity for a ground station with eight SFLs. Several networks comprising only two to three ground stations are shown to meet or exceed the capacity of the big dish, Cutting the data rate by half, which saves modem costs and increases the coverage area of each ground station, is shown to increase the average daily capacity of the network for some configurations.

Archive of Digital Boomer Seismic Reflection Data Collected During USGS Field Activity 08LCA01 in 10 Central Florida Lakes, March 2008

USGS Publications Warehouse

Harrison, Arnell S.; Dadisman, Shawn V.; Davis, Jeffrey B.; Flocks, James G.; Wiese, Dana S.

2009-01-01

In March of 2008, the U.S. Geological Survey and St. Johns River Water Management District (SJRWMD) conducted geophysical surveys in Lakes Avalon, Big, Colby, Helen, Johns, Prevatt, Searcy, Saunders, Three Island, and Trout, located in central Florida, as part of the USGS Lakes and Coastal Aquifers (LCA) study. This report serves as an archive of unprocessed digital boomer seismic reflection data, trackline maps, navigation files, Field Activity Collection System (FACS) logs, Geographic Information System (GIS) files, and formal Federal Geographic Data Committee (FGDC) metadata. Filtered and gained (a relative increase in signal amplitude) digital images of the seismic profiles are also provided. Refer to the Acronyms page for expansions of acronyms and abbreviations used in this report. The archived trace data are in standard Society of Exploration Geophysicists (SEG) SEG-Y format (Barry and others, 1975) and may be downloaded and processed with commercial or public domain software such as Seismic Unix (SU) (Cohen and Stockwell, 2005). Example SU processing scripts and USGS software for viewing the SEG-Y files (Zihlman, 1992) are also provided. The USGS Florida Integrated Science Center (FISC) - St. Petersburg assigns a unique identifier to each cruise or field activity. For example, 08LCA01 tells us the data were collected in 2008 for the Lakes and Coastal Aquifers (LCA) study and the data were collected during the first field activity for that study in that calendar year. Refer to http://walrus.wr.usgs.gov/infobank/programs/html/definition/activity.html for a detailed description of the method used to assign the field activity ID. The naming convention used for each seismic line is as follows: yye##a, where yy is the last two digits of the year in which the data were collected, e is a 1-letter abbreviation for the equipment type (for example, b for boomer), ## is a 2-digit number representing a specific track, and a is a letter representing the section of a line if recording was prematurely terminated or rerun for quality or acquisition problems. The boomer plate is an acoustic energy source that consists of capacitors charged to a high voltage and discharged through a transducer in the water. The transducer is towed on a sled floating on the water surface and when discharged emits a short acoustic pulse, or shot, which propagates through the water, sediment column, or rock beneath. The acoustic energy is reflected at density boundaries (such as the lake bottom, sediment, or rock layers beneath the lake bottom), detected by the receiver, and recorded by a PC-based seismic acquisition system. This process is repeated at timed intervals (for example, 0.5 s) and recorded for specific intervals of time (for example, 100 ms). In this way, a two-dimensional (2-D) vertical profile of the shallow geologic structure beneath the ship track is produced. Figure 1 displays the three boomer acquisition geometries used during this survey. The second method was used because windy weather conditions hindered steerage, and driving the boat in reverse actually helped maintain course and prevented the possibility of the streamer cables becoming entangled in the boat propellers. The third method was used to help attenuate propeller and generator noise. Refer to table 1 for a summary of acquisition parameters. Table 2 lists trackline statistics. The unprocessed seismic data are stored in SEG-Y format (Barry and others, 1975). For a detailed description of the data format, refer to the SEG-Y Format page. See the How To Download SEG-Y Data page for download instructions. The printable profiles provided here are GIF images that were filtered and gained using Seismic Unix software. Refer to the Software page for details about the processing and examples of the processing scripts. The processed SEG-Y data were exported to Chesapeake Technology, Inc. (CTI) SonarWeb software to produce a geospatially interactive Web page of the profile,

Assessment of Department of Defense Basic Research

DTIC Science & Technology

2005-01-01

Sciences, the National Academy of Engineering, the Institute of Medicine, and the National Research Council: • Download hundreds of free books in PDF...with our innovative research tools Thank you for downloading this free PDF. If you have comments, questions or just want more information... downloaded from: http://www.nap.edu/catalog/11177.html Assessment of Department of Defense Basic Research Committee on Department of Defense Basic

Privacy as Part of the App Decision-Making Process

DTIC Science & Technology

2013-02-06

concerns they may not actively consider privacy while downloading apps from smartphone application marketplaces. Currently Android users have only the... Android permissions display which appears after they have selected an app to download to help them understand how applications access their information...marketplaces. Currently, Android users have only the Android permissions display, which appears after they have selected an app to download, to help

EPA Enforcement and Compliance History Online

EPA Pesticide Factsheets

The Environmental Protection Agency's Enforcement and Compliance History Online (ECHO) website provides customizable and downloadable information about environmental inspections, violations, and enforcement actions for EPA-regulated facilities related to the Clean Air Act, Clean Water Act, Resource Conservation and Recovery Act, and Safe Drinking Water Act. These data are updated weekly as part of the ECHO data refresh, and ECHO offers many user-friendly options to explore data, including:? Facility Search: ECHO information is searchable by varied criteria, including location, facility type, and compliance status. Search results are customizable and downloadable.? Comparative Maps and State Dashboards: These tools offer aggregated information about facility compliance status, regulatory agency compliance monitoring, and enforcement activity at the national and state level.? Bulk Data Downloads: One of ECHO??s most popular features is the ability to work offline by downloading large data sets. Users can take advantage of the ECHO Exporter, which provides summary information about each facility in comma-separated values (csv) file format, or download data sets by program as zip files.

A two dimensional study of rotor/airfoil interaction in hover

NASA Technical Reports Server (NTRS)

Lee, Chyang S.

1988-01-01

A two dimensional model for the chordwise flow near the wing tip of the tilt rotor in hover is presented. The airfoil is represented by vortex panels and the rotor is modeled by doublet panels. The rotor slipstream and the airfoil wake are simulated by free point vortices. Calculations on a 20 percent thick elliptical airfoil under a uniform rotor inflow are performed. Variations on rotor size, spacing between the rotor and the airfoil, ground effect, and the influence upper surface blowing in download reduction are analyzed. Rotor size has only a minor influence on download when it is small. Increase of the rotor/airfoil spacing causes a gradual decrease on download. Proximity to the ground effectively reduces the download and makes the wake unsteady. The surface blowing changes the whole flow structure and significantly reduces the download within the assumption of a potential solution. Improvement on the present model is recommended to estimate the wall jets induced suction on the airfoil lower surface.

The Research and Implementation of Vehicle Bluetooth Hands-free Devices Key Parameters Downloading Algorithm

NASA Astrophysics Data System (ADS)

Zhang, Xiao-bo; Wang, Zhi-xue; Li, Jian-xin; Ma, Jian-hui; Li, Yang; Li, Yan-qiang

In order to facilitate Bluetooth function realization and information can be effectively tracked in the process of production, the vehicle Bluetooth hands-free devices need to download such key parameters as Bluetooth address, CVC license and base plate numbers, etc. Therefore, it is the aim to search simple and effective methods to download parameters for each vehicle Bluetooth hands-free device, and to control and record the use of parameters. In this paper, by means of Bluetooth Serial Peripheral Interface programmer device, the parallel port is switched to SPI. The first step is to download parameters is simulating SPI with the parallel port. To perform SPI function, operating the parallel port in accordance with the SPI timing. The next step is to achieve SPI data transceiver functions according to the programming parameters of options. Utilizing the new method, downloading parameters is fast and accurate. It fully meets vehicle Bluetooth hands-free devices production requirements. In the production line, it has played a large role.

Archive of digital CHIRP seismic reflection data collected during USGS cruise 06FSH01 offshore of Siesta Key, Florida, May 2006

USGS Publications Warehouse

Harrison, Arnell S.; Dadisman, Shawn V.; Flocks, James G.; Wiese, Dana S.; Robbins, Lisa L.

2007-01-01

In May of 2006, the U.S. Geological Survey conducted geophysical surveys offshore of Siesta Key, Florida. This report serves as an archive of unprocessed digital chirp seismic reflection data, trackline maps, navigation files, GIS information, Field Activity Collection System (FACS) logs, observer's logbook, and formal FGDC metadata. Gained digital images of the seismic profiles are also provided. The archived trace data are in standard Society of Exploration Geophysicists (SEG) SEG-Y format (Barry and others, 1975) and may be downloaded and processed with commercial or public domain software such as Seismic Unix (SU). Example SU processing scripts and USGS software for viewing the SEG-Y files (Zihlman, 1992) are also provided.

Archive of digital CHIRP seismic reflection data collected during USGS cruise 06SCC01 offshore of Isles Dernieres, Louisiana, June 2006

USGS Publications Warehouse

Harrison, Arnell S.; Dadisman, Shawn V.; Ferina, Nick F.; Wiese, Dana S.; Flocks, James G.

2007-01-01

In June of 2006, the U.S. Geological Survey conducted a geophysical survey offshore of Isles Dernieres, Louisiana. This report serves as an archive of unprocessed digital CHIRP seismic reflection data, trackline maps, navigation files, GIS information, Field Activity Collection System (FACS) logs, observer's logbook, and formal FGDC metadata. Gained digital images of the seismic profiles are also provided. The archived trace data are in standard Society of Exploration Geophysicists (SEG) SEG-Y format (Barry and others, 1975) and may be downloaded and processed with commercial or public domain software such as Seismic UNIX (SU). Example SU processing scripts and USGS software for viewing the SEG-Y files (Zihlman, 1992) are also provided.

CTTITEM: SAS macro and SPSS syntax for classical item analysis.

PubMed

Lei, Pui-Wa; Wu, Qiong

2007-08-01

This article describes the functions of a SAS macro and an SPSS syntax that produce common statistics for conventional item analysis including Cronbach's alpha, item difficulty index (p-value or item mean), and item discrimination indices (D-index, point biserial and biserial correlations for dichotomous items and item-total correlation for polytomous items). These programs represent an improvement over the existing SAS and SPSS item analysis routines in terms of completeness and user-friendliness. To promote routine evaluations of item qualities in instrument development of any scale, the programs are available at no charge for interested users. The program codes along with a brief user's manual that contains instructions and examples are downloadable from suen.ed.psu.edu/-pwlei/plei.htm.

A scalable, self-analyzing digital locking system for use on quantum optics experiments.

PubMed

Sparkes, B M; Chrzanowski, H M; Parrain, D P; Buchler, B C; Lam, P K; Symul, T

2011-07-01

Digital control of optics experiments has many advantages over analog control systems, specifically in terms of the scalability, cost, flexibility, and the integration of system information into one location. We present a digital control system, freely available for download online, specifically designed for quantum optics experiments that allows for automatic and sequential re-locking of optical components. We show how the inbuilt locking analysis tools, including a white-noise network analyzer, can be used to help optimize individual locks, and verify the long term stability of the digital system. Finally, we present an example of the benefits of digital locking for quantum optics by applying the code to a specific experiment used to characterize optical Schrödinger cat states.

Caititu: a tool to graphically represent peptide sequence coverage and domain distribution.

PubMed

Carvalho, Paulo C; Junqueira, Magno; Valente, Richard H; Domont, Gilberto B

2008-10-07

Here we present Caititu, an easy-to-use proteomics software to graphically represent peptide sequence coverage and domain distribution for different correlated samples (e.g. originated from 2D gel spots) relatively to the full-sequence of the known protein they are related to. Although Caititu has a broad applicability, we exemplify its usefulness in Toxinology using snake venom as a model. For example, proteolytic processing may lead to inactivation or loss of domains. Therefore, our proposed graphic representation for peptides identified by two dimensional electrophoresis followed by mass spectrometric identification of excised spots can aid in inferring what kind of processing happened to the toxins, if any. Caititu is freely available to download at: http://pcarvalho.com/things/caititu.

Giovanni - The Bridge Between Data and Science

NASA Technical Reports Server (NTRS)

Liu, Zhong; Acker, James

2017-01-01

This article describes new features in the Geospatial Interactive Online Visualization ANd aNalysis Infrastructure (Giovanni), a user-friendly online tool that enables visualization, analysis, and assessment of NASA Earth science data sets without downloading data and software. Since the satellite era began, data collected from Earth-observing satellites have been widely used in research and applications; however, using satellite-based data sets can still be a challenge to many. To facilitate data access and evaluation, as well as scientific exploration and discovery, the NASA Goddard Earth Sciences (GES) Data and Information Services Center (DISC) has developed Giovanni for a wide range of users around the world. This article describes the latest capabilities of Giovanni with examples, and discusses future plans for this innovative system.

Research and realization of key technology in HILS interactive system

NASA Astrophysics Data System (ADS)

Liu, Che; Lu, Huiming; Wang, Fankai

2018-03-01

This paper designed HILS (Hardware In the Loop Simulation) interactive system based on xPC platform . Through the interface between C++ and MATLAB engine, establish the seamless data connection between Simulink and interactive system, complete data interaction between system and Simulink, realize the function development of model configuration, parameter modification and off line simulation. We establish the data communication between host and target machine through TCP/IP protocol to realize the model download and real-time simulation. Use database to store simulation data, implement real-time simulation monitoring and simulation data management. Realize system function integration by Qt graphic interface library and dynamic link library. At last, take the typical control system as an example to verify the feasibility of HILS interactive system.

PyFDAP: automated analysis of fluorescence decay after photoconversion (FDAP) experiments.

PubMed

Bläßle, Alexander; Müller, Patrick

2015-03-15

We developed the graphical user interface PyFDAP for the fitting of linear and non-linear decay functions to data from fluorescence decay after photoconversion (FDAP) experiments. PyFDAP structures and analyses large FDAP datasets and features multiple fitting and plotting options. PyFDAP was written in Python and runs on Ubuntu Linux, Mac OS X and Microsoft Windows operating systems. The software, a user guide and a test FDAP dataset are freely available for download from http://people.tuebingen.mpg.de/mueller-lab. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Satellite Communications Technology Database. Part 2

NASA Technical Reports Server (NTRS)

2001-01-01

The Satellite Communications Technology Database is a compilation of data on state-of-the-art Ka-band technologies current as of January 2000. Most U.S. organizations have not published much of their Ka-band technology data, and so the great majority of this data is drawn largely from Japanese, European, and Canadian publications and Web sites. The data covers antennas, high power amplifiers, low noise amplifiers, MMIC devices, microwave/IF switch matrices, SAW devices, ASIC devices, power and data storage. The data herein is raw, and is often presented simply as the download of a table or figure from a site, showing specified technical characteristics, with no further explanation.

Mysterious Roving Rocks of Racetrack Playa

NASA Image and Video Library

2017-12-08

Data from the sensors were downloaded, and then the sensors were reburied. The LPSA team plans to publish a research paper that will present their data and offer their explanation for how the rocks move. Photo credit: NASA/GSFC/Maggie McAdam To read a feature story on the Racetrack Playa go to: www.nasa.gov/topics/earth/features/roving-rocks.html NASA Goddard Space Flight Center is home to the nation's largest organization of combined scientists, engineers and technologists that build spacecraft, instruments and new technology to study the Earth, the sun, our solar system, and the universe. Follow us on Twitter Join us on Facebook

D-VASim: an interactive virtual laboratory environment for the simulation and analysis of genetic circuits.

PubMed

Baig, Hasan; Madsen, Jan

2017-01-15

Simulation and behavioral analysis of genetic circuits is a standard approach of functional verification prior to their physical implementation. Many software tools have been developed to perform in silico analysis for this purpose, but none of them allow users to interact with the model during runtime. The runtime interaction gives the user a feeling of being in the lab performing a real world experiment. In this work, we present a user-friendly software tool named D-VASim (Dynamic Virtual Analyzer and Simulator), which provides a virtual laboratory environment to simulate and analyze the behavior of genetic logic circuit models represented in an SBML (Systems Biology Markup Language). Hence, SBML models developed in other software environments can be analyzed and simulated in D-VASim. D-VASim offers deterministic as well as stochastic simulation; and differs from other software tools by being able to extract and validate the Boolean logic from the SBML model. D-VASim is also capable of analyzing the threshold value and propagation delay of a genetic circuit model. D-VASim is available for Windows and Mac OS and can be downloaded from bda.compute.dtu.dk/downloads/. haba@dtu.dk, jama@dtu.dk. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Antimicrobial resistance dashboard application for mapping environmental occurrence and resistant pathogens.

PubMed

Stedtfeld, Robert D; Williams, Maggie R; Fakher, Umama; Johnson, Timothy A; Stedtfeld, Tiffany M; Wang, Fang; Khalife, Walid T; Hughes, Mary; Etchebarne, Brett E; Tiedje, James M; Hashsham, Syed A

2016-03-01

An antibiotic resistance (AR) Dashboard application is being developed regarding the occurrence of antibiotic resistance genes (ARG) and bacteria (ARB) in environmental and clinical settings. The application gathers and geospatially maps AR studies, reported occurrence and antibiograms, which can be downloaded for offline analysis. With the integration of multiple data sets, the database can be used on a regional or global scale to identify hot spots for ARGs and ARB; track and link spread and transmission, quantify environmental or human factors influencing presence and persistence of ARG harboring organisms; differentiate natural ARGs from those distributed via human or animal activity; cluster and compare ARGs connections in different environments and hosts; and identify genes that can be used as proxies to routinely monitor anthropogenic pollution. To initially populate and develop the AR Dashboard, a qPCR ARG array was tested with 30 surface waters, primary influent from three waste water treatment facilities, ten clinical isolates from a regional hospital and data from previously published studies including river, park soil and swine farm samples. Interested users are invited to download a beta version (available on iOS or Android), submit AR information using the application, and provide feedback on current and prospective functionalities. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Assessing the Extent and Impact of Online Data Sharing in Eddy Covariance Flux Research

NASA Astrophysics Data System (ADS)

Dai, Sheng-Qi; Li, Hong; Xiong, Jun; Ma, Jun; Guo, Hai-Qiang; Xiao, Xiangming; Zhao, Bin

2018-01-01

Research data sharing is appealing for its potential benefits on sharers' scientific impact and is also advocated by various policies. How do scientific benefits and policies correlate with practical ecological data sharing? In this study, we investigated data-sharing practices in eddy covariance flux research as a typical case. First, we collected researchers' data-sharing information from major observation networks. Then, we downloaded bibliometric data from the Web of Science and evaluated scientific impact using LeaderRank, a synthetic algorithm that takes both citation and cooperation impacts into consideration. Our results demonstrated the following: (1) specific to eddy covariance flux research, 8% of researchers published information in public data portals, whereas 64% of researchers provided their available data online in a downloadable form; (2) regional differences in data sharing, publications, and observation networks existed; and (3) the data sharers in impact-ranked ecologists followed a long-tail distribution, which suggested that, although sharing data is not necessary for researchers to be influential, data sharers are more likely to be high-impact researchers. Differentiated policies should be proposed to encourage ecologists in the long tail of data sharers, and from regions with little tradition of data sharing, to embrace a more open model of science.

Web Delivery of Interactive Laboratories: Comparison of Three Authoring Tools

NASA Astrophysics Data System (ADS)

Silbar, Richard R.

2002-04-01

It is well-known that the more a student interacts with a subject, the better he or she will learn it. This is particularly true in technical subjects. One way to do this is to have computer-based "laboratories" in which the student manipulates objects on the screen with keyboard or mouse and then sees the outcome of those actions. One example of such a laboratory we have built, using Macromedia's Authorware, deals with addition of two vectors in the geometric approach. The problem with Authorware, however, is that, if one wants to deliver the training over the Web, that requires the download and installation of a big plug-in. Therefore, as an experiment, I built clones of the Vector Addition Laboratory using Macromedia's Director or Flash, each of which have smaller plug-ins which are often already installed in the user's browser. The Director and Flash versions are similar to (but definitely not the same as) the Authorware version. This talk goes into these differences and demonstrates the techniques used. You can view the three examples on-line at http://www.whistlesoft.com/ silbar.

Data Downloads | ECHO | US EPA

EPA Pesticide Factsheets

The ECHO website with its facility search features is designed to provide easy access to EPA's compliance and enforcement data with customizable onscreen display and download. For those with larger data needs, ECHO has several types of data sets available. These large data sets may be of particular use to developers, programmers, academics, and analysts. The data available here can be downloaded and used for many different functions and are certain to meet all data retrieval needs.

Ultrasound-Based Guidance for Partial Breast Irradiation Therapy

DTIC Science & Technology

2012-01-01

displace- 0278-0062/$20.00 © IEEE Authorized licensed use limited to: IEEE Xplore . Downloaded on January 5, 2009 at 17:37 from IEEE Xplore . Restrictions...Authorized licensed use limited to: IEEE Xplore . Downloaded on January 5, 2009 at 17:37 from IEEE Xplore . Restrictions apply. RIVAZ et al...better CNR values: the Authorized licensed use limited to: IEEE Xplore . Downloaded on January 5, 2009 at 17:37 from IEEE Xplore . Restrictions apply

Desktop Publishing.

ERIC Educational Resources Information Center

Stanley, Milt

1986-01-01

Defines desktop publishing, describes microcomputer developments and software tools that make it possible, and discusses its use as an instructional tool to improve writing skills. Reasons why students' work should be published, examples of what to publish, and types of software and hardware to facilitate publishing are reviewed. (MBR)

EPA Regional KML Download

EPA Pesticide Factsheets

The EPA collects information about facilities or sites subject to environmental regulation. The EPA Geospatial Data Access Project provides downloadable files of these facilities or sites in KML format.

Sharing is Winning: Cooperative Learning about Atmospheric Composition Change

NASA Astrophysics Data System (ADS)

Schuepbach, E.

2010-09-01

This contribution presents evolving good practice in disseminating the body of know-how, skills and competencies within the networked community of atmospheric scientists as established in ACCENT. The promotion of early-career scientists, and encouraging the next generation to move into the field were among the key issues addressed by the "Training and Education" programme in the European Network of Excellence in Atmospheric Composition Change (ACCENT). Dissemination avenues include a virtual knowledge train carrying the wealth of high-quality scientific learning material developed with experts involved in the ACCENT network. Learning opportunities on current research in atmospheric composition change in Europe were also created during face-to-face training workshops. Real-life examples of pressing air quality issues were addressed in meetings with stakeholder groups that offered opportunities for mutual learning in inspiring partnerships. In order to increase the expertise in atmospheric composition change across Europe, activities were organized with the general public (e.g., Café Scientifique), where the participating early-career scientists were confronted with questions from lay people. For interested teachers, didactic translations of compact overviews on air quality science topics developed in ACCENT offer links with the typical European science curriculum and go beyond school book content. Some of the educational events, methods and tools are described in a booklet published in 2009 ("We Care for Clean Air!", ISBN 978-88-95665-01-6). The electronic version and all training material can be downloaded from www.accent-network.org/portal/education - a valuable resource for teachers and learners around the globe.

Meta-analysis of published transcriptional and translational fold changes reveals a preference for low-fold inductions.

PubMed

Wren, Jonathan D; Conway, Tyrrell

2006-01-01

The goals of this study were to gain a better quantitative understanding of the dynamic range of transcriptional and translational response observed in biological systems and to examine the reporting of regulatory events for trends and biases. A straightforward pattern-matching routine extracted 3,408 independent observations regarding transcriptional fold-changes and 1,125 regarding translational fold-changes from over 15 million MEDLINE abstracts. Approximately 95% of reported changes were > or =2-fold. Further, the historical trend of reporting individual fold-changes is declining in favor of high-throughput methods for transcription but not translation. Where it was possible to compare the average fold-changes in transcription and translation for the same gene/product (203 examples), approximately 53% were a < or =2-fold difference, suggesting a loose tendency for the two to be coupled in magnitude. We found also that approximately three-fourths of reported regulatory events have been at the transcriptional level. The frequency distribution appears to be normally distributed and peaks near 2-fold, suggesting that nature selects for a low-energy solution to regulatory responses. Because high-throughput technologies ordinarily sacrifice measurement quality for quantity, this also suggests that many regulatory events may not be reliably detectable by such technologies. Text mining of regulatory events and responses provides additional information incorporable into microarray analysis, such as prior fold-change observations and flagging genes that are regulated post-transcription. All extracted regulation and response patterns can be downloaded at the following website: www.ou.edu/microarray/ oumcf/Meta_analysis.xls.

System analysis of wavelength beam combining of high-power diode lasers for photoacoustic endoscopy

NASA Astrophysics Data System (ADS)

Leggio, Luca; Gallego, Daniel C.; Gawali, Sandeep B.; Sánchez, Miguel; Rodriguez, Sergio; Osiński, Marek; Sacher, Joachim; Carpintero, Guillermo; Lamela, Horacio

2016-04-01

This paper, originally published on 27 April 2016, was replaced with a corrected/revised version on 8 June 2016. If you downloaded the original PDF but are unable to access the revision, please contact SPIE Digital Library Customer Service for assistance. The purpose of wavelength-beam combining (WBC) is to improve the output power of a multi-wavelength laser system while maintaining the quality of the combined beam. This technique has been primarily proposed for industrial applications, such as metal cutting and soldering, which require optical peak power between kilowatts and megawatts. In order to replace the bulkier solid-state lasers, we propose to use the WBC technique for photoacoustic (PA) applications, where a multi-wavelength focused beam with optical peak power between hundreds of watts up to several kilowatts is necessary to penetrate deeply into biological tissues. In this work we present an analytical study about the coupling of light beams emitted by diode laser bars at 808 nm, 880 nm, 910 nm, 940 nm, and 980 nm into a < 600-μm core-diameter optical fiber for PA endoscopy. In order to achieve an efficient coupling it is necessary to collimate the beams in both fast and slow axes by means of cylindrical lenses and to use partial reflection mirrors at 45° tilt. We show an example of beam collimation using cylindrical lenses in both fast and slow axes. In a real PA scenario, the resulting beam should have a sufficient peak power to generate significant PA signals from a turbid tissue>.

An interactive modelling tool for understanding hydrological processes in lowland catchments

NASA Astrophysics Data System (ADS)

Brauer, Claudia; Torfs, Paul; Uijlenhoet, Remko

2016-04-01

Recently, we developed the Wageningen Lowland Runoff Simulator (WALRUS), a rainfall-runoff model for catchments with shallow groundwater (Brauer et al., 2014ab). WALRUS explicitly simulates processes which are important in lowland catchments, such as feedbacks between saturated and unsaturated zone and between groundwater and surface water. WALRUS has a simple model structure and few parameters with physical connotations. Some default functions (which can be changed easily for research purposes) are implemented to facilitate application by practitioners and students. The effect of water management on hydrological variables can be simulated explicitly. The model description and applications are published in open access journals (Brauer et al, 2014). The open source code (provided as R package) and manual can be downloaded freely (www.github.com/ClaudiaBrauer/WALRUS). We organised a short course for Dutch water managers and consultants to become acquainted with WALRUS. We are now adapting this course as a stand-alone tutorial suitable for a varied, international audience. In addition, simple models can aid teachers to explain hydrological principles effectively. We used WALRUS to generate examples for simple interactive tools, which we will present at the EGU General Assembly. C.C. Brauer, A.J. Teuling, P.J.J.F. Torfs, R. Uijlenhoet (2014a): The Wageningen Lowland Runoff Simulator (WALRUS): a lumped rainfall-runoff model for catchments with shallow groundwater, Geosci. Model Dev., 7, 2313-2332. C.C. Brauer, P.J.J.F. Torfs, A.J. Teuling, R. Uijlenhoet (2014b): The Wageningen Lowland Runoff Simulator (WALRUS): application to the Hupsel Brook catchment and Cabauw polder, Hydrol. Earth Syst. Sci., 18, 4007-4028.

Acoustic Doppler Current Profiler Data Processing System manual [ADCP

USGS Publications Warehouse

Cote, Jessica M.; Hotchkiss, Frances S.; Martini, Marinna A.; Denham, Charles R.; revisions by Ramsey, Andree L.; Ruane, Stephen

2000-01-01

This open-file report describes the data processing software currently in use by the U.S. Geological Survey (USGS), Woods Hole Coastal and Marine Science Center (WHCMSC), to process time series of acoustic Doppler current data obtained by Teledyne RD Instruments Workhorse model ADCPs. The Sediment Transport Instrumentation Group (STG) at the WHCMSC has a long-standing commitment to providing scientists high quality oceanographic data published in a timely manner. To meet this commitment, STG has created this software to aid personnel in processing and reviewing data as well as evaluating hardware for signs of instrument malfunction. The output data format for the data is network Common Data Form (netCDF), which meets USGS publication standards. Typically, ADCP data are recorded in beam coordinates. This conforms to the USGS philosophy to post-process rather than internally process data. By preserving the original data quality indicators as well as the initial data set, data can be evaluated and reprocessed for different types of analyses. Beam coordinate data are desirable for internal and surface wave experiments, for example. All the code in this software package is intended to run using the MATLAB program available from The Mathworks, Inc. As such, it is platform independent and can be adapted by the USGS and others for specialized experiments with non-standard requirements. The software is continuously being updated and revised as improvements are required. The most recent revision may be downloaded from: http://woodshole.er.usgs.gov/operations/stg/Pubs/ADCPtools/adcp_index.htm The USGS makes this software available at the user?s discretion and responsibility.

Map of assessed shale gas in the United States, 2012

USGS Publications Warehouse

,; Biewick, Laura R. H.

2013-01-01

The U.S. Geological Survey has compiled a map of shale-gas assessments in the United States that were completed by 2012 as part of the National Assessment of Oil and Gas Project. Using a geology-based assessment methodology, the U.S. Geological Survey quantitatively estimated potential volumes of undiscovered gas within shale-gas assessment units. These shale-gas assessment units are mapped, and square-mile cells are shown to represent proprietary shale-gas wells. The square-mile cells include gas-producing wells from shale intervals. In some cases, shale-gas formations contain gas in deeper parts of a basin and oil at shallower depths (for example, the Woodford Shale and the Eagle Ford Shale). Because a discussion of shale oil is beyond the scope of this report, only shale-gas assessment units and cells are shown. The map can be printed as a hardcopy map or downloaded for interactive analysis in a Geographic Information System data package using the ArcGIS map document (file extension MXD) and published map file (file extension PMF). Also available is a publications access table with hyperlinks to current U.S. Geological Survey shale gas assessment publications and web pages. Assessment results and geologic reports are available as completed at the U.S. Geological Survey Energy Resources Program Web Site, http://energy.usgs.gov/OilGas/AssessmentsData/NationalOilGasAssessment.aspx. A historical perspective of shale gas activity in the United States is documented and presented in a video clip included as a PowerPoint slideshow.

Staying Well

MedlinePlus

... Brochure Vitamins, Minerals, and Herbs in MS: An Introduction (.pdf) Practical guide to diet supplements for people ... you Vitamins, Minerals, and Herbs in MS: An Introduction (.pdf) Download Brochure Taming Stress (.pdf) Download Brochure ...

Experience with Delay-Tolerant Networking from Orbit

NASA Technical Reports Server (NTRS)

Ivancic, W.; Eddy, W. M.; Stewart, D.; Wood, L.; Northam, J.; Jackson, C.

2010-01-01

We describe the first use from space of the Bundle Protocol for Delay-Tolerant Networking (DTN) and lessons learned from experiments made and experience gained with this protocol. The Disaster Monitoring Constellation (DMC), constructed by Surrey Satellite Technology Ltd (SSTL), is a multiple-satellite Earth-imaging low-Earth-orbit sensor network in which recorded image swaths are stored onboard each satellite and later downloaded from the satellite payloads to a ground station. Store-and-forward of images with capture and later download gives each satellite the characteristics of a node in a disruption-tolerant network. Originally developed for the Interplanetary Internet, DTNs are now under investigation in an Internet Research Task Force (IRTF) DTN research group (RG), which has developed a bundle architecture and protocol. The DMC is technically advanced in its adoption of the Internet Protocol (IP) for its imaging payloads and for satellite command and control, based around reuse of commercial networking and link protocols. These satellites use of IP has enabled earlier experiments with the Cisco router in Low Earth Orbit (CLEO) onboard the constellation s UK-DMC satellite. Earth images are downloaded from the satellites using a custom IP-based high-speed transfer protocol developed by SSTL, Saratoga, which tolerates unusual link environments. Saratoga has been documented in the Internet Engineering Task Force (IETF) for wider adoption. We experiment with the use of DTNRG bundle concepts onboard the UK-DMC satellite, by examining how Saratoga can be used as a DTN convergence layer to carry the DTNRG Bundle Protocol, so that sensor images can be delivered to ground stations and beyond as bundles. Our practical experience with the first successful use of the DTNRG Bundle Protocol in a space environment gives us insights into the design of the Bundle Protocol and enables us to identify issues that must be addressed before wider deployment of the Bundle Protocol. Published in 2010 by John Wiley & Sons, Ltd. KEY WORDS: Internet; UK-DMC; satellite; Delay-Tolerant Networking (DTN); Bundle Protocol

Effective? Engaging? Secure? Applying the ORCHA-24 framework to evaluate apps for chronic insomnia disorder.

PubMed

Leigh, Simon; Ouyang, Jing; Mimnagh, Chris

2017-11-01

Mobile health offers many opportunities; however, the 'side-effects' of health apps are often unclear. With no guarantee health apps first do no harm, their role as a viable, safe and effective therapeutic option is limited. To assess the quality of apps for chronic insomnia disorder, available on the Android Google Play Store, and determine whether a novel approach to app assessment could identify high-quality and low-risk health apps in the absence of indicators such as National Health Service (NHS) approval. The Organisation for the Review of Care and Health Applications- 24 Question Assessment (ORCHA-24), 24 app assessment criteria concerning data privacy, clinical efficacy and user experience, answered on a 'yes' or 'no' and evidence-driven basis, was applied to assess 18 insomnia apps identified via the Android Google Play Store, in addition to the NHS-approved iOS app Sleepio. 63.2% of apps (12/19) provided a privacy policy, with seven (36.8%) stating no user data would be shared without explicit consent. 10.5% (2/19) stated they had been shown to be of benefit to those with insomnia, with cognitive behavioural therapy apps outperforming hypnosis and meditation apps (p=0.046). Both the number of app downloads (p=0.29) and user-review scores (p=0.23) were unrelated to ORCHA-24 scores. The NHS-approved app Sleepio, consistently outperformed non-accredited apps across all domains of the ORCHA-24. Apps for chronic insomnia disorder exhibit substantial variation in adherence to published data privacy, user experience and clinical efficacy standards, which are not clearly correlated with app downloads or user-review scores. In absence of formal app accreditation, the ORCHA-24 could feasibly be used to highlight the risk-benefit profiles of health apps prior to downloading. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Obstructive Sleep Apnea

MedlinePlus Videos and Cool Tools

... Apnea (OSA) Download Download the ebook for further information Obstructive sleep apnea (OSA) is a serious and ... that can create the necessary air passageway. The information provided here is not intended as a substitute ...

Administration of Anesthesia

MedlinePlus Videos and Cool Tools

... more. Anesthesia Download Download the ebook for further information Anesthesia: Safety and Comfort in the OMS Office ... comfortable as possible when you get home. The information provided here is not intended as a substitute ...

Health and Wellness

MedlinePlus

... Disease T Cells d What Causes MS? Disproved Theories Viruses Clusters d Who Gets MS? Pediatric MS ... Brochure Vitamins, Minerals, and Herbs in MS: An Introduction (.pdf) Download Brochure Taming Stress (.pdf) Download Brochure ...

Fine-Root Ecology Database (FRED): A Global Collection of Root Trait Data with Coincident Site, Vegetation, Edaphic, and Climatic Data, Version 2.

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

Iversen, C.M.; Powell, A.S.; McCormack, M.L.

The second version of the Fine-Root Ecology Database is available for download! Download the full FRED 2.0 data set, user guidance document, map, and list of data sources here. Prior to downloading the data, please read and follow the Data Use Guidelines, and it's worth checking out some tips for using FRED before you begin your analyses. Also, see here for an updating list of corrections to FRED 2.0.

Extension of a Computer Assisted Decision Support (CADS) Study to Improve Outcomes in Patients with Type 2 DM Treated by Primary Care Providers (short title, CADS-X). Addendum

DTIC Science & Technology

2014-12-01

Hypertension is one of the most common co-morbidities associated with DM and substantially contributes to the macrovascular disease that occurs in...After Numera terminated the contract to provide glucometer download support Estenda activated the patient portal , Diabetes Mellitus Everywhere...several patients. Problem areas include having to download JAVA with first upload and accessing the DME portal . d. PO has downloaded glucose

Agricultural Census 2012: Publishing Mashable GIS Big Data Services

NASA Astrophysics Data System (ADS)

Mueller, R.

2014-12-01

The 2012 Agricultural Census was released by the US Department of Agriculture (USDA) on May 2nd 2014; published on a quinquennial basis covering all facets of American production agriculture. The Agricultural Census is a comprehensive source of uniform published agricultural data for every state and county in the US. This is the first Agricultural Census that is disseminated with web mapping services using REST APIs. USDA developed an open GIS mashable web portal that depicts over 250 maps on Crops and Plants, Economics, Farms, Livestock and Animals, and Operators. These mapping services written in JavaScript replace the traditional static maps published as the Ag Atlas. Web users can now visualize, interact, query, and download the Agricultural Census data in a means not previously discoverable. Stakeholders will now be able to leverage this data for activities such as community planning, agribusiness location suitability analytics, availability of loans/funds, service center locations and staffing, and farm programs and policies. Additional sites serving compatible mashable USDA Big Data web services are as follows: The Food Environment Atlas, The Atlas of Rural and Small-Town America, The Farm Program Atlas, SNAP Data System, CropScape, and VegScape. All portals use a similar data organization scheme of "Categories" and "Maps" providing interactive mashable web services for agricultural stakeholders to exploit.

PPIS Download Product Information Data

EPA Pesticide Factsheets

Downloadable Pesticide Product Information System data for Federal Insecticide Fungicide and Rodenticide Act section 3 and section 24(c) (Special Local Need), vocabulary, and U.S. companies and organizations with EPA Company Numbers.

Corrective Jaw Surgery

MedlinePlus Videos and Cool Tools

... Jaw Surgery Download Download the ebook for further information Corrective jaw, or orthognathic surgery is performed by ... your treatment. Correction of Common Dentofacial Deformities ​ ​ The information provided here is not intended as a substitute ...

Head, Neck, and Oral Cancer

MedlinePlus Videos and Cool Tools

... Neck Pathology Download Download the ebook for further information Your oral and maxillofacial surgeon (OMS) is the ... well be the key to complete recovery. The information provided here is not intended as a substitute ...

Facts and Stats - Hydrocephalus Association

MedlinePlus

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Downloading and Installing Estuary Data Mapper (EDM)

EPA Pesticide Factsheets

Estuary Data Mapper is a tool for geospatial data discovery, visualization, and data download for any of the approximately 2,000 estuaries and associated watersheds in along the five US coastal regions

Depression and College Students

MedlinePlus

... depression and other mental health issues? Reference Share Depression and College Students Download PDF Download ePub Order ... Answers to college students’ frequently asked questions about depression Feeling moody, sad, or grouchy? Who doesn’t ...

Gross and net land cover changes in the main plant functional types derived from the annual ESA CCI land cover maps (1992-2015)

NASA Astrophysics Data System (ADS)

Li, Wei; MacBean, Natasha; Ciais, Philippe; Defourny, Pierre; Lamarche, Céline; Bontemps, Sophie; Houghton, Richard A.; Peng, Shushi

2018-01-01

Land-use and land-cover change (LULCC) impacts local energy and water balance and contributes on global scale to a net carbon emission to the atmosphere. The newly released annual ESA CCI (climate change initiative) land cover maps provide continuous land cover changes at 300 m resolution from 1992 to 2015, and can be used in land surface models (LSMs) to simulate LULCC effects on carbon stocks and on surface energy budgets. Here we investigate the absolute areas and gross and net changes in different plant functional types (PFTs) derived from ESA CCI products. The results are compared with other datasets. Global areas of forest, cropland and grassland PFTs from ESA are 30.4, 19.3 and 35.7 million km2 in the year 2000. The global forest area is lower than that from LUH2v2h (Hurtt et al., 2011), Hansen et al. (2013) or Houghton and Nassikas (2017) while cropland area is higher than LUH2v2h (Hurtt et al., 2011), in which cropland area is from HYDE 3.2 (Klein Goldewijk et al., 2016). Gross forest loss and gain during 1992-2015 are 1.5 and 0.9 million km2 respectively, resulting in a net forest loss of 0.6 million km2, mainly occurring in South and Central America. The magnitudes of gross changes in forest, cropland and grassland PFTs in the ESA CCI are smaller than those in other datasets. The magnitude of global net cropland gain for the whole period is consistent with HYDE 3.2 (Klein Goldewijk et al., 2016), but most of the increases happened before 2004 in ESA and after 2007 in HYDE 3.2. Brazil, Bolivia and Indonesia are the countries with the largest net forest loss from 1992 to 2015, and the decreased areas are generally consistent with those from Hansen et al. (2013) based on Landsat 30 m resolution images. Despite discrepancies compared to other datasets, and uncertainties in converting into PFTs, the new ESA CCI products provide the first detailed long-term time series of land-cover change and can be implemented in LSMs to characterize recent carbon dynamics, and in climate models to simulate land-cover change feedbacks on climate. The annual ESA CCI land cover products can be downloaded from http://maps.elie.ucl.ac.be/CCI/viewer/download.php (Land Cover Maps - v2.0.7; see details in Sect. 5). The PFT map translation protocol and an example in 2000 can be downloaded from https://doi.org/10.5281/zenodo.834229. The annual ESA CCI PFT maps from 1992 to 2015 at 0.5° × 0.5° resolution can also be downloaded from https://doi.org/10.5281/zenodo.1048163.

Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies.

PubMed

Spielman, Stephanie J; Wilke, Claus O

2015-01-01

We introduce Pyvolve, a flexible Python module for simulating genetic data along a phylogeny using continuous-time Markov models of sequence evolution. Easily incorporated into Python bioinformatics pipelines, Pyvolve can simulate sequences according to most standard models of nucleotide, amino-acid, and codon sequence evolution. All model parameters are fully customizable. Users can additionally specify custom evolutionary models, with custom rate matrices and/or states to evolve. This flexibility makes Pyvolve a convenient framework not only for simulating sequences under a wide variety of conditions, but also for developing and testing new evolutionary models. Pyvolve is an open-source project under a FreeBSD license, and it is available for download, along with a detailed user-manual and example scripts, from http://github.com/sjspielman/pyvolve.

Archive of digital boomer and CHIRP seismic reflection data collected during USGS cruise 06FSH03 offshore of Fort Lauderdale, Florida, September 2006

USGS Publications Warehouse

Harrison, Arnell S.; Dadisman, Shawn V.; Reich, Christopher D.; Wiese, Dana S.; Greenwood, Jason W.; Swarzenski, Peter W.

2007-01-01

In September of 2006, the U.S. Geological Survey conducted geophysical surveys offshore of Fort Lauderdale, FL. This report serves as an archive of unprocessed digital boomer and CHIRP seismic reflection data, trackline maps, navigation files, GIS information, Field Activity Collection System (FACS) logs, observer's logbook, and formal FGDC metadata. Filtered and gained digital images of the seismic profiles are also provided. The archived trace data are in standard Society of Exploration Geophysicists (SEG) SEG-Y format (Barry and others, 1975) and may be downloaded and processed with commercial or public domain software such as Seismic Unix (SU). Example SU processing scripts and USGS software for viewing the SEG-Y files (Zihlman, 1992) are also provided.

Hydrogeologic applications for historical records and images from rock samples collected at the Nevada National Security Site and vicinity, Nye County, Nevada - A supplement to Data Series 297

USGS Publications Warehouse

Wood, David B.

2018-03-14

Rock samples have been collected, analyzed, and interpreted from drilling and mining operations at the Nevada National Security Site for over one-half of a century. Records containing geologic and hydrologic analyses and interpretations have been compiled into a series of databases. Rock samples have been photographed and thin sections scanned. Records and images are preserved and available for public viewing and downloading at the U.S. Geological Survey ScienceBase, Mercury Core Library and Data Center Web site at https://www.sciencebase.gov/mercury/ and documented in U.S. Geological Survey Data Series 297. Example applications of these data and images are provided in this report.

Reactome Pengine: A web-logic API to the homo sapiens reactome.

PubMed

Neaves, Samuel R; Tsoka, Sophia; Millard, Louise A C

2018-03-30

Existing ways of accessing data from the Reactome database are limited. Either a researcher is restricted to particular queries defined by a web application programming interface (API), or they have to download the whole database. Reactome Pengine is a web service providing a logic programming based API to the human reactome. This gives researchers greater flexibility in data access than existing APIs, as users can send their own small programs (alongside queries) to Reactome Pengine. The server and an example notebook can be found at https://apps.nms.kcl.ac.uk/reactome-pengine. Source code is available at https://github.com/samwalrus/reactome-pengine and a Docker image is available at https://hub.docker.com/r/samneaves/rp4/ . samuel.neaves@kcl.ac.uk. Supplementary data are available at Bioinformatics online.

AplusB: A Web Application for Investigating A + B Designs for Phase I Cancer Clinical Trials.

PubMed

Wheeler, Graham M; Sweeting, Michael J; Mander, Adrian P

2016-01-01

In phase I cancer clinical trials, the maximum tolerated dose of a new drug is often found by a dose-escalation method known as the A + B design. We have developed an interactive web application, AplusB, which computes and returns exact operating characteristics of A + B trial designs. The application has a graphical user interface (GUI), requires no programming knowledge and is free to access and use on any device that can open an internet browser. A customised report is available for download for each design that contains tabulated operating characteristics and informative plots, which can then be compared with other dose-escalation methods. We present a step-by-step guide on how to use this application and provide several illustrative examples of its capabilities.

The National Land Cover Database

USGS Publications Warehouse

Homer, Collin G.; Fry, Joyce A.; Barnes, Christopher A.

2012-01-01

The National Land Cover Database (NLCD) serves as the definitive Landsat-based, 30-meter resolution, land cover database for the Nation. NLCD provides spatial reference and descriptive data for characteristics of the land surface such as thematic class (for example, urban, agriculture, and forest), percent impervious surface, and percent tree canopy cover. NLCD supports a wide variety of Federal, State, local, and nongovernmental applications that seek to assess ecosystem status and health, understand the spatial patterns of biodiversity, predict effects of climate change, and develop land management policy. NLCD products are created by the Multi-Resolution Land Characteristics (MRLC) Consortium, a partnership of Federal agencies led by the U.S. Geological Survey. All NLCD data products are available for download at no charge to the public from the MRLC Web site: http://www.mrlc.gov.

PONDEROSA-C/S: client-server based software package for automated protein 3D structure determination.

PubMed

Lee, Woonghee; Stark, Jaime L; Markley, John L

2014-11-01

Peak-picking Of Noe Data Enabled by Restriction Of Shift Assignments-Client Server (PONDEROSA-C/S) builds on the original PONDEROSA software (Lee et al. in Bioinformatics 27:1727-1728. doi: 10.1093/bioinformatics/btr200, 2011) and includes improved features for structure calculation and refinement. PONDEROSA-C/S consists of three programs: Ponderosa Server, Ponderosa Client, and Ponderosa Analyzer. PONDEROSA-C/S takes as input the protein sequence, a list of assigned chemical shifts, and nuclear Overhauser data sets ((13)C- and/or (15)N-NOESY). The output is a set of assigned NOEs and 3D structural models for the protein. Ponderosa Analyzer supports the visualization, validation, and refinement of the results from Ponderosa Server. These tools enable semi-automated NMR-based structure determination of proteins in a rapid and robust fashion. We present examples showing the use of PONDEROSA-C/S in solving structures of four proteins: two that enable comparison with the original PONDEROSA package, and two from the Critical Assessment of automated Structure Determination by NMR (Rosato et al. in Nat Methods 6:625-626. doi: 10.1038/nmeth0909-625 , 2009) competition. The software package can be downloaded freely in binary format from http://pine.nmrfam.wisc.edu/download_packages.html. Registered users of the National Magnetic Resonance Facility at Madison can submit jobs to the PONDEROSA-C/S server at http://ponderosa.nmrfam.wisc.edu, where instructions, tutorials, and instructions can be found. Structures are normally returned within 1-2 days.

Journal searching in non-MEDLINE resources on Internet Web sites.

PubMed

Lingle, V A

1997-01-01

Internet access to the medical journal literature is absorbing the attention of all relevant parties, i.e., publishers, journal vendors, librarians, commercial providers, government agencies, and end users. Journal content on the Web sites spans the range from advertising and ordering information for the print version, to table of contents and abstracts, to downloadable full text and graphics of articles. The searching parameters for systems other than MEDLINE also differ extensively with a wide variety of features and resulting retrieval. This discussion reviews a selection of providers of medical information (particularly the journal literature) on the Internet, making a comparison of what is available on Web sites and how it can be searched.

ImageJ-MATLAB: a bidirectional framework for scientific image analysis interoperability.

PubMed

Hiner, Mark C; Rueden, Curtis T; Eliceiri, Kevin W

2017-02-15

ImageJ-MATLAB is a lightweight Java library facilitating bi-directional interoperability between MATLAB and ImageJ. By defining a standard for translation between matrix and image data structures, researchers are empowered to select the best tool for their image-analysis tasks. Freely available extension to ImageJ2 ( http://imagej.net/Downloads ). Installation and use instructions available at http://imagej.net/MATLAB_Scripting. Tested with ImageJ 2.0.0-rc-54 , Java 1.8.0_66 and MATLAB R2015b. eliceiri@wisc.edu. 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

XTALOPT version r11: An open-source evolutionary algorithm for crystal structure prediction

NASA Astrophysics Data System (ADS)

Avery, Patrick; Falls, Zackary; Zurek, Eva

2018-01-01

Version 11 of XTALOPT, an evolutionary algorithm for crystal structure prediction, has now been made available for download from the CPC library or the XTALOPT website, http://xtalopt.github.io. Whereas the previous versions of XTALOPT were published under the Gnu Public License (GPL), the current version is made available under the 3-Clause BSD License, which is an open source license that is recognized by the Open Source Initiative. Importantly, the new version can be executed via a command line interface (i.e., it does not require the use of a Graphical User Interface). Moreover, the new version is written as a stand-alone program, rather than an extension to AVOGADRO.

Electricity Data Browser

EIA Publications

The Electricity Data Browser shows generation, consumption, fossil fuel receipts, stockpiles, retail sales, and electricity prices. The data appear on an interactive web page and are updated each month. The Electricity Data Browser includes all the datasets collected and published in EIA's Electric Power Monthly and allows users to perform dynamic charting of data sets as well as map the data by state. The data browser includes a series of reports that appear in the Electric Power Monthly and allows readers to drill down to plant level statistics, where available. All images and datasets are available for download. Users can also link to the data series in EIA's Application Programming Interface (API). An API makes our data machine-readable and more accessible to users.

Biblio-Link and Pro-Cite: The Searcher's Workstation.

ERIC Educational Resources Information Center

Hoyle, Norman; McNamara, Kathleen

1987-01-01

Describes the Biblio-Link and Pro-Cite software packages, which can be used together to create local databases with downloaded records, or to reorganize and repackage downloaded records for client reports. (CLB)

Bringing Hometown Relevance to Introductory Geology Courses

NASA Astrophysics Data System (ADS)

Goodell, L. P.

2008-12-01

An abundance of on-line data and content is increasingly available, especially for the U.S., and can easily bring a "hometown touch" to geoscience courses. This is particularly valuable at the introductory level where student engagement can be a challenge. Students are naturally drawn to material with which they have a personal connection, and this connection can be exploited to instantly engage students in course content. For example, most students have never really thought about the topography of their hometowns and are fascinated to examine topographic maps that cover the areas in which they grew up. The theory of plate tectonics becomes real as students use high-precision GPS data to show near real-time plate motions of where they live (and GPS is something more and more students are familiar with). At Princeton and other institutions drawing students from a wide geographic area, students get the added benefit of being able to compare and contrast characteristics of each other's hometowns. Applications of hometown perspective include: 1) Hometown map exercises: obtain USGS 1:24000 topographic quadrangle maps of students' hometown areas. These can be inexpensively ordered from a variety of sources or printed from downloaded digital scans. 2) Hometown stream projects: students choose streams of personal interest, download NWIS discharge data and discover typical discharge patterns, examine unusual events such as floods or droughts, perform flood frequency analyses, and see changes over time (e.g. due to development or stream exploitation). 3) Hometown plate motions: students can use several independent methods to track both short-term and long-term average plate motions. They can download high-precision GPS data from stations near their hometowns to get near real-time plate motions. These can be compared to independent long-term averages from various "plate motion calculators" that are based on geologic data. 4) Hometown earthquakes: use USGS or IRIS seismic monitors to look at earthquake patterns in hometown regions. 5) Hometown seismic data: analyze remote earthquakes using seismograph data from stations near students' hometowns. 6) Hometown climate change: examine historic temperature and precipitation records from stations or regions near students' hometowns and analyze changes over time.

CProb: a computational tool for conducting conditional probability analysis.

PubMed

Hollister, Jeffrey W; Walker, Henry A; Paul, John F

2008-01-01

Conditional probability is the probability of observing one event given that another event has occurred. In an environmental context, conditional probability helps to assess the association between an environmental contaminant (i.e., the stressor) and the ecological condition of a resource (i.e., the response). These analyses, when combined with controlled experiments and other methodologies, show great promise in evaluating ecological conditions from observational data and in defining water quality and other environmental criteria. Current applications of conditional probability analysis (CPA) are largely done via scripts or cumbersome spreadsheet routines, which may prove daunting to end-users and do not provide access to the underlying scripts. Combining spreadsheets with scripts eases computation through a familiar interface (i.e., Microsoft Excel) and creates a transparent process through full accessibility to the scripts. With this in mind, we developed a software application, CProb, as an Add-in for Microsoft Excel with R, R(D)com Server, and Visual Basic for Applications. CProb calculates and plots scatterplots, empirical cumulative distribution functions, and conditional probability. In this short communication, we describe CPA, our motivation for developing a CPA tool, and our implementation of CPA as a Microsoft Excel Add-in. Further, we illustrate the use of our software with two examples: a water quality example and a landscape example. CProb is freely available for download at http://www.epa.gov/emap/nca/html/regions/cprob.

Civil Penalty Policies

EPA Pesticide Factsheets

The Environmental Protection Agency's Enforcement and Compliance History Online (ECHO) website provides customizable and downloadable information about environmental inspections, violations, and enforcement actions for EPA-regulated facilities, like power plants and factories. ECHO advances public information by sharing data related to facility compliance with and regulatory agency activity related to air, hazardous waste, clean water, and drinking water regulations. ECHO offers many user-friendly options to explore data, including:1. Facility Search (http://echo.epa.gov/facilities/facility-search?mediaSelected=all): ECHO information is searchable by varied criteria, including location, facility type, and compliance status related to the Clean Air Act, Clean Water Act, Resource Conservation and Recovery Act, and Safe Drinking Water Act. Search results are customizable and downloadable.2. Comparative Maps (http://echo.epa.gov/maps/state-comparative-maps) and State Dashboards (http://echo.epa.gov/trends/comparative-maps-dashboards/state-air-dashboard): These tools offer aggregated information about facility compliance status and regulatory agency compliance monitoring and enforcement activity at the national and state level.3. Bulk Data Downloads (http://echo.epa.gov/resources/echo-data/data-downloads): One of ECHO's most popular features is the ability to work offline by downloading large data sets. Users can take advantage of the ECHO Exporter, which provides su

The Brainomics/Localizer database.

PubMed

Papadopoulos Orfanos, Dimitri; Michel, Vincent; Schwartz, Yannick; Pinel, Philippe; Moreno, Antonio; Le Bihan, Denis; Frouin, Vincent

2017-01-01

The Brainomics/Localizer database exposes part of the data collected by the in-house Localizer project, which planned to acquire four types of data from volunteer research subjects: anatomical MRI scans, functional MRI data, behavioral and demographic data, and DNA sampling. Over the years, this local project has been collecting such data from hundreds of subjects. We had selected 94 of these subjects for their complete datasets, including all four types of data, as the basis for a prior publication; the Brainomics/Localizer database publishes the data associated with these 94 subjects. Since regulatory rules prevent us from making genetic data available for download, the database serves only anatomical MRI scans, functional MRI data, behavioral and demographic data. To publish this set of heterogeneous data, we use dedicated software based on the open-source CubicWeb semantic web framework. Through genericity in the data model and flexibility in the display of data (web pages, CSV, JSON, XML), CubicWeb helps us expose these complex datasets in original and efficient ways. Copyright © 2015 Elsevier Inc. All rights reserved.

PCDDB: new developments at the Protein Circular Dichroism Data Bank.

PubMed

Whitmore, Lee; Miles, Andrew John; Mavridis, Lazaros; Janes, Robert W; Wallace, B A

2017-01-04

The Protein Circular Dichroism Data Bank (PCDDB) has been in operation for more than 5 years as a public repository for archiving circular dichroism spectroscopic data and associated bioinformatics and experimental metadata. Since its inception, many improvements and new developments have been made in data display, searching algorithms, data formats, data content, auxillary information, and validation techniques, as well as, of course, an increase in the number of holdings. It provides a site (http://pcddb.cryst.bbk.ac.uk) for authors to deposit experimental data as well as detailed information on methods and calculations associated with published work. It also includes links for each entry to bioinformatics databases. The data are freely available to accessors either as single files or as complete data bank downloads. The PCDDB has found broad usage by the structural biology, bioinformatics, analytical and pharmaceutical communities, and has formed the basis for new software and methods developments. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Missing data reconstruction using Gaussian mixture models for fingerprint images

NASA Astrophysics Data System (ADS)

Agaian, Sos S.; Yeole, Rushikesh D.; Rao, Shishir P.; Mulawka, Marzena; Troy, Mike; Reinecke, Gary

2016-05-01

Publisher's Note: This paper, originally published on 25 May 2016, was replaced with a revised version on 16 June 2016. If you downloaded the original PDF, but are unable to access the revision, please contact SPIE Digital Library Customer Service for assistance. One of the most important areas in biometrics is matching partial fingerprints in fingerprint databases. Recently, significant progress has been made in designing fingerprint identification systems for missing fingerprint information. However, a dependable reconstruction of fingerprint images still remains challenging due to the complexity and the ill-posed nature of the problem. In this article, both binary and gray-level images are reconstructed. This paper also presents a new similarity score to evaluate the performance of the reconstructed binary image. The offered fingerprint image identification system can be automated and extended to numerous other security applications such as postmortem fingerprints, forensic science, investigations, artificial intelligence, robotics, all-access control, and financial security, as well as for the verification of firearm purchasers, driver license applicants, etc.

Saccharomyces genome database informs human biology.

PubMed

Skrzypek, Marek S; Nash, Robert S; Wong, Edith D; MacPherson, Kevin A; Hellerstedt, Sage T; Engel, Stacia R; Karra, Kalpana; Weng, Shuai; Sheppard, Travis K; Binkley, Gail; Simison, Matt; Miyasato, Stuart R; Cherry, J Michael

2018-01-04

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is an expertly curated database of literature-derived functional information for the model organism budding yeast, Saccharomyces cerevisiae. SGD constantly strives to synergize new types of experimental data and bioinformatics predictions with existing data, and to organize them into a comprehensive and up-to-date information resource. The primary mission of SGD is to facilitate research into the biology of yeast and to provide this wealth of information to advance, in many ways, research on other organisms, even those as evolutionarily distant as humans. To build such a bridge between biological kingdoms, SGD is curating data regarding yeast-human complementation, in which a human gene can successfully replace the function of a yeast gene, and/or vice versa. These data are manually curated from published literature, made available for download, and incorporated into a variety of analysis tools provided by SGD. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

MS2PIP prediction server: compute and visualize MS2 peak intensity predictions for CID and HCD fragmentation.

PubMed

Degroeve, Sven; Maddelein, Davy; Martens, Lennart

2015-07-01

We present an MS(2) peak intensity prediction server that computes MS(2) charge 2+ and 3+ spectra from peptide sequences for the most common fragment ions. The server integrates the Unimod public domain post-translational modification database for modified peptides. The prediction model is an improvement of the previously published MS(2)PIP model for Orbitrap-LTQ CID spectra. Predicted MS(2) spectra can be downloaded as a spectrum file and can be visualized in the browser for comparisons with observations. In addition, we added prediction models for HCD fragmentation (Q-Exactive Orbitrap) and show that these models compute accurate intensity predictions on par with CID performance. We also show that training prediction models for CID and HCD separately improves the accuracy for each fragmentation method. The MS(2)PIP prediction server is accessible from http://iomics.ugent.be/ms2pip. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

SEER*Explorer

Cancer.gov

This interactive website provides access to cancer statistics (rates and trends) for a cancer site by gender, race, calendar year, stage, and histology. Users can create custom graphs and tables, download data and images, download SEER*Stat sessions, and share results.

5 Things You Should Know about Stress

MedlinePlus

... Information Share 5 Things You Should Know About Stress Download PDF Download ePub Order a free hardcopy ... five things you should know about stress: 1. Stress affects everyone. Everyone feels stressed from time to ...

DefenseLink Special: Doolittle Raid, April 18, 1942

Science.gov Websites

enhanced viewing {Flash 8} Macromedia Flash Player 8 required Download free Macromedia Flash Player Download free Internet Explorer DOOLITTLE RAIDERS – Retired Lt. Col. Chase Nelson, a Doolittle Raider

7 CFR 318.13-14 - Movement of processed fruits, vegetables, and other products.

Code of Federal Regulations, 2010 CFR

2010-01-01

.../import_export/plants/manuals/ports/downloads/hawaii.pdf and http://www.aphis.usda.gov/import_export/plants/manuals/ports/downloads/puerto_rico.pdf. (b) Consignments of processed fruits, vegetables, or...

The Teen Brain: 6 Things to Know

MedlinePlus

... adults For More Information Reprints Share The Teen Brain: 6 Things to Know Download PDF Download ePub ... big and important changes are happening to the brain during adolescence? Here are 6 things to know ...

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.

Novel Low Cost High Efficiency Tunable RF Devices and Antenna Arrays Design based on the Ferroelectric Materials and the CTS Technologies

DTIC Science & Technology

2011-02-14

licensed use limited to: UNIV OF HAWAII LIBRARY. Downloaded on June 18,2010 at 22:24:49 UTC from IEEE Xplore . Restrictions apply. KIM et al.: MODIFIED...limited to: UNIV OF HAWAII LIBRARY. Downloaded on June 18,2010 at 22:24:49 UTC from IEEE Xplore . Restrictions apply. 404 IEEE TRANSACTIONS ON...licensed use limited to: UNIV OF HAWAII LIBRARY. Downloaded on June 18,2010 at 22:24:49 UTC from IEEE Xplore . Restrictions apply. KIM et al

Data::Downloader

NASA Technical Reports Server (NTRS)

Duggan, Brian

2012-01-01

Downloading and organizing large amounts of files is challenging, and often done using ad hoc methods. This software is capable of downloading and organizing files as an OpenSearch client. It can subscribe to RSS (Really Simple Syndication) feeds and Atom feeds containing arbitrary metadata, and maintains a local content addressable data store. It uses existing standards for obtaining the files, and uses efficient techniques for storing the files. Novel features include symbolic links to maintain a sane directory structure, checksums for validating file integrity during transfer and storage, and flexible use of server-provided metadata.

Panorama: A Targeted Proteomics Knowledge Base

PubMed Central

2015-01-01

Panorama is a web application for storing, sharing, analyzing, and reusing targeted assays created and refined with Skyline,1 an increasingly popular Windows client software tool for targeted proteomics experiments. Panorama allows laboratories to store and organize curated results contained in Skyline documents with fine-grained permissions, which facilitates distributed collaboration and secure sharing of published and unpublished data via a web-browser interface. It is fully integrated with the Skyline workflow and supports publishing a document directly to a Panorama server from the Skyline user interface. Panorama captures the complete Skyline document information content in a relational database schema. Curated results published to Panorama can be aggregated and exported as chromatogram libraries. These libraries can be used in Skyline to pick optimal targets in new experiments and to validate peak identification of target peptides. Panorama is open-source and freely available. It is distributed as part of LabKey Server,2 an open source biomedical research data management system. Laboratories and organizations can set up Panorama locally by downloading and installing the software on their own servers. They can also request freely hosted projects on https://panoramaweb.org, a Panorama server maintained by the Department of Genome Sciences at the University of Washington. PMID:25102069

Where, When, and How mmWave is Used in 5G and Beyond

NASA Astrophysics Data System (ADS)

Sakaguchi, Kei; Haustein, Thomas; Barbarossa, Sergio; Strinati, Emilio Calvanese; Clemente, Antonio; Destino, Giuseppe; Pärssinen, Aarno; Kim, Ilgyu; Chung, Heesang; Kim, Junhyeong; Keusgen, Wilhelm; Weiler, Richard J.; Takinami, Koji; Ceci, Elena; Sadri, Ali; Xian, Liang; Maltsev, Alexander; Tran, Gia Khanh; Ogawa, Hiroaki; Mahler, Kim; Heath, Robert W., Jr.

Wireless engineers and business planners commonly raise the question on where, when, and how millimeter-wave (mmWave) will be used in 5G and beyond. Since the next generation network is not just a new radio access standard, but instead an integration of networks for vertical markets with diverse applications, answers to the question depend on scenarios and use cases to be deployed. This paper gives four 5G mmWave deployment examples and describes in chronological order the scenarios and use cases of their probable deployment, including expected system architectures and hardware prototypes. The paper starts with 28 GHz outdoor backhauling for fixed wireless access and moving hotspots, which will be demonstrated at the PyeongChang winter Olympic games in 2018. The second deployment example is a 60 GHz unlicensed indoor access system at the Tokyo-Narita airport, which is combined with Mobile Edge Computing (MEC) to enable ultra-high speed content download with low latency. The third example is mmWave mesh network to be used as a micro Radio Access Network ({\\mu}-RAN), for cost-effective backhauling of small-cell Base Stations (BSs) in dense urban scenarios. The last example is mmWave based Vehicular-to-Vehicular (V2V) and Vehicular-to-Everything (V2X) communications system, which enables automated driving by exchanging High Definition (HD) dynamic map information between cars and Roadside Units (RSUs). For 5G and beyond, mmWave and MEC will play important roles for a diverse set of applications that require both ultra-high data rate and low latency communications.

GREAT: a web portal for Genome Regulatory Architecture Tools.

PubMed

Bouyioukos, Costas; Bucchini, François; Elati, Mohamed; Képès, François

2016-07-08

GREAT (Genome REgulatory Architecture Tools) is a novel web portal for tools designed to generate user-friendly and biologically useful analysis of genome architecture and regulation. The online tools of GREAT are freely accessible and compatible with essentially any operating system which runs a modern browser. GREAT is based on the analysis of genome layout -defined as the respective positioning of co-functional genes- and its relation with chromosome architecture and gene expression. GREAT tools allow users to systematically detect regular patterns along co-functional genomic features in an automatic way consisting of three individual steps and respective interactive visualizations. In addition to the complete analysis of regularities, GREAT tools enable the use of periodicity and position information for improving the prediction of transcription factor binding sites using a multi-view machine learning approach. The outcome of this integrative approach features a multivariate analysis of the interplay between the location of a gene and its regulatory sequence. GREAT results are plotted in web interactive graphs and are available for download either as individual plots, self-contained interactive pages or as machine readable tables for downstream analysis. The GREAT portal can be reached at the following URL https://absynth.issb.genopole.fr/GREAT and each individual GREAT tool is available for downloading. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs.

PubMed

Ito, Jun-ichi; Ikeda, Kazuyoshi; Yamada, Kazunori; Mizuguchi, Kenji; Tomii, Kentaro

2015-01-01

PoSSuM (http://possum.cbrc.jp/PoSSuM/) is a database for detecting similar small-molecule binding sites on proteins. Since its initial release in 2011, PoSSuM has grown to provide information related to 49 million pairs of similar binding sites discovered among 5.5 million known and putative binding sites. This enlargement of the database is expected to enhance opportunities for biological and pharmaceutical applications, such as predictions of new functions and drug discovery. In this release, we have provided a new service named PoSSuM drug search (PoSSuMds) at http://possum.cbrc.jp/PoSSuM/drug_search/, in which we selected 194 approved drug compounds retrieved from ChEMBL, and detected their known binding pockets and pockets that are similar to them. Users can access and download all of the search results via a new web interface, which is useful for finding ligand analogs as well as potential target proteins. Furthermore, PoSSuMds enables users to explore the binding pocket universe within PoSSuM. Additionally, we have improved the web interface with new functions, including sortable tables and a viewer for visualizing and downloading superimposed pockets. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

tranSMART-XNAT Connector tranSMART-XNAT connector-image selection based on clinical phenotypes and genetic profiles.

PubMed

He, Sijin; Yong, May; Matthews, Paul M; Guo, Yike

2017-03-01

TranSMART has a wide range of functionalities for translational research and a large user community, but it does not support imaging data. In this context, imaging data typically includes 2D or 3D sets of magnitude data and metadata information. Imaging data may summarise complex feature descriptions in a less biased fashion than user defined plain texts and numeric numbers. Imaging data also is contextualised by other data sets and may be analysed jointly with other data that can explain features or their variation. Here we describe the tranSMART-XNAT Connector we have developed. This connector consists of components for data capture, organisation and analysis. Data capture is responsible for imaging capture either from PACS system or directly from an MRI scanner, or from raw data files. Data are organised in a similar fashion as tranSMART and are stored in a format that allows direct analysis within tranSMART. The connector enables selection and download of DICOM images and associated resources using subjects' clinical phenotypic and genotypic criteria. tranSMART-XNAT connector is written in Java/Groovy/Grails. It is maintained and available for download at https://github.com/sh107/transmart-xnat-connector.git. sijin@ebi.ac.uk. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

MendelianRandomization: an R package for performing Mendelian randomization analyses using summarized data.

PubMed

Yavorska, Olena O; Burgess, Stephen

2017-12-01

MendelianRandomization is a software package for the R open-source software environment that performs Mendelian randomization analyses using summarized data. The core functionality is to implement the inverse-variance weighted, MR-Egger and weighted median methods for multiple genetic variants. Several options are available to the user, such as the use of robust regression, fixed- or random-effects models and the penalization of weights for genetic variants with heterogeneous causal estimates. Extensions to these methods, such as allowing for variants to be correlated, can be chosen if appropriate. Graphical commands allow summarized data to be displayed in an interactive graph, or the plotting of causal estimates from multiple methods, for comparison. Although the main method of data entry is directly by the user, there is also an option for allowing summarized data to be incorporated from the PhenoScanner database of genotype-phenotype associations. We hope to develop this feature in future versions of the package. The R software environment is available for download from [https://www.r-project.org/]. The MendelianRandomization package can be downloaded from the Comprehensive R Archive Network (CRAN) within R, or directly from [https://cran.r-project.org/web/packages/MendelianRandomization/]. Both R and the MendelianRandomization package are released under GNU General Public Licenses (GPL-2|GPL-3). © The Author 2017. Published by Oxford University Press on behalf of the International Epidemiological Association.

Modeling the degradation kinetics of ascorbic acid.

PubMed

Peleg, Micha; Normand, Mark D; Dixon, William R; Goulette, Timothy R

2018-06-13

Most published reports on ascorbic acid (AA) degradation during food storage and heat preservation suggest that it follows first-order kinetics. Deviations from this pattern include Weibullian decay, and exponential drop approaching finite nonzero retention. Almost invariably, the degradation rate constant's temperature-dependence followed the Arrhenius equation, and hence the simpler exponential model too. A formula and freely downloadable interactive Wolfram Demonstration to convert the Arrhenius model's energy of activation, E a , to the exponential model's c parameter, or vice versa, are provided. The AA's isothermal and non-isothermal degradation can be simulated with freely downloadable interactive Wolfram Demonstrations in which the model's parameters can be entered and modified by moving sliders on the screen. Where the degradation is known a priori to follow first or other fixed order kinetics, one can use the endpoints method, and in principle the successive points method too, to estimate the reaction's kinetic parameters from considerably fewer AA concentration determinations than in the traditional manner. Freeware to do the calculations by either method has been recently made available on the Internet. Once obtained in this way, the kinetic parameters can be used to reconstruct the entire degradation curves and predict those at different temperature profiles, isothermal or dynamic. Comparison of the predicted concentration ratios with experimental ones offers a way to validate or refute the kinetic model and the assumptions on which it is based.

Carnegie Science Academy Web Site

NASA Astrophysics Data System (ADS)

Kotwicki, John; Atzinger, Joe; Turso, Denise

1997-11-01

The Carnegie Science Academy is a professional society "For Teens...By Teens" at the Carnegie Science Center in Pittsburgh. The CSA Web Site [ http://csa.clpgh.org ] is designed for teens who have an interest in science and technology. This online or virtual science academy provides resources for teens in high school science classes. The Web site also allows students around the world to participate and communicate with other students, discuss current events in science, share opinions, find answers to questions, or make online friends. Visitors can enjoy the main components of the site or sign up for a free membership which allows access to our chat room for monthly meeting, online newsletter, members forum, and much more. Main components to the site include a spot for cool links and downloads, available for any visitor to download or view. Online exhibits are created by students to examine and publish an area of study and also allow teachers to easily post classroom activities as exhibits by submitting pictures and text. Random Access, the interactive part of the academy, allows users to share ideas and opinions. Planet CSA focuses on current events in science and the academy. In the future the CSA Web site will become a major resource for teens and science teachers providing materials that will allow students to further enhance their interest and experiences in science.

Digital Tidbits

ERIC Educational Resources Information Center

Kumaran, Maha; Geary, Joe

2011-01-01

Technology has transformed libraries. There are digital libraries, electronic collections, online databases and catalogs, ebooks, downloadable books, and much more. With free technology such as social websites, newspaper collections, downloadable online calendars, clocks and sticky notes, online scheduling, online document sharing, and online…

37 CFR 385.10 - General.

Code of Federal Regulations, 2014 CFR

2014-07-01

....10 Patents, Trademarks, and Copyrights COPYRIGHT ROYALTY BOARD, LIBRARY OF CONGRESS RATES AND TERMS... AND DISTRIBUTING OF PHYSICAL AND DIGITAL PHONORECORDS Interactive Streaming and Limited Downloads... interactive streams and limited downloads of musical works by subscription and nonsubscription digital music...

Publications - PR 121 | Alaska Division of Geological & Geophysical Surveys

Science.gov Websites

: Download below or please see our publication sales page for more information. Quadrangle(s): Philip Smith Philip Smith Mountains: Surficial Geology Data File Format File Size Info Download psm-surficial-geo

MultiMiTar: a novel multi objective optimization based miRNA-target prediction method.

PubMed

Mitra, Ramkrishna; Bandyopadhyay, Sanghamitra

2011-01-01

Machine learning based miRNA-target prediction algorithms often fail to obtain a balanced prediction accuracy in terms of both sensitivity and specificity due to lack of the gold standard of negative examples, miRNA-targeting site context specific relevant features and efficient feature selection process. Moreover, all the sequence, structure and machine learning based algorithms are unable to distribute the true positive predictions preferentially at the top of the ranked list; hence the algorithms become unreliable to the biologists. In addition, these algorithms fail to obtain considerable combination of precision and recall for the target transcripts that are translationally repressed at protein level. In the proposed article, we introduce an efficient miRNA-target prediction system MultiMiTar, a Support Vector Machine (SVM) based classifier integrated with a multiobjective metaheuristic based feature selection technique. The robust performance of the proposed method is mainly the result of using high quality negative examples and selection of biologically relevant miRNA-targeting site context specific features. The features are selected by using a novel feature selection technique AMOSA-SVM, that integrates the multi objective optimization technique Archived Multi-Objective Simulated Annealing (AMOSA) and SVM. MultiMiTar is found to achieve much higher Matthew's correlation coefficient (MCC) of 0.583 and average class-wise accuracy (ACA) of 0.8 compared to the others target prediction methods for a completely independent test data set. The obtained MCC and ACA values of these algorithms range from -0.269 to 0.155 and 0.321 to 0.582, respectively. Moreover, it shows a more balanced result in terms of precision and sensitivity (recall) for the translationally repressed data set as compared to all the other existing methods. An important aspect is that the true positive predictions are distributed preferentially at the top of the ranked list that makes MultiMiTar reliable for the biologists. MultiMiTar is now available as an online tool at www.isical.ac.in/~bioinfo_miu/multimitar.htm. MultiMiTar software can be downloaded from www.isical.ac.in/~bioinfo_miu/multimitar-download.htm.

Use of Pharmacogenomics and Biomarkers in the Development of New Drugs for Alzheimer Disease in Japan.

PubMed

Otsubo, Yasuto

2015-08-01

Pharmacogenomics (PGx) and biomarkers have been utilized for improving the benefit/risk ratios of drugs and the efficiency of drug development. In the development of drugs for Alzheimer disease (AD), a number of clinical trials have failed to demonstrate clinical efficacy. To overcome this circumstance, the importance of using PGx/biomarkers for enhancing recruitment into clinical trials and for evaluating the efficacy of treatments has been increasingly recognized. In this article, the current status and examples of the use of PGx/biomarkers in Japan for drug development are explained. Guidelines, notifications, and administrative notices related to PGx/biomarkers were downloaded from the Web sites of the Pharmaceuticals and Medical Devices Agency (PMDA), the US Food and Drug Administration, and the European Medicines Agency. Data from clinical studies of AD drugs were obtained from the review reports of the PMDA. To analyze the current status of the use of PGx/biomarkers in Japan, "Issues to Consider in the Clinical Evaluation and Development of Drugs for Alzheimer's Disease (Interim Summary)" was also downloaded from PMDA Web site. There are 2 major measures of utilizing PGx/biomarkers for drug development: (1) biomarker qualification and (2) companion diagnostics. Recently, the PMDA issued a number of guidelines and notifications for their practical use. Although examples of qualified PGx/biomarkers and approved companion diagnostics are limited at present, it is expected that the use of PGx/biomarkers for the development of drugs against AD would increase. For promoting the use of PGx/biomarkers in the development of drugs against AD, PGx/biomarkers should be qualified as early as possible. To that end, accumulating data on PGx/biomarkers from nonclinical or clinical trials and the concurrent development of reliable diagnostics in the early stage of the development process are indispensable. It is important to strengthen collaboration among the academia, industries, and regulatory agencies, followed by the establishment of an effective guideline in the area of AD. Copyright © 2015 Elsevier HS Journals, Inc. All rights reserved.

Current Directions in Adding Value to Earth Observation Products for Decision Support

NASA Astrophysics Data System (ADS)

Ryker, S. J.

2015-12-01

Natural resource managers and infrastructure planners face increasingly complex challenges, given competing demands for resources and changing conditions due to climate and land use change. These pressures create demand for high-quality, timely data; for both one-time decision support and long-term monitoring; and for techniques to articulate the value of resources in monetary and nonmonetary terms. To meet the need for data, the U.S. government invests several billion dollars per year in Earth observations collected from satellite, airborne, terrestrial, and ocean-based systems. Earth observation-based decision support is coming of age; user surveys show that these data are used in an increasing variety of analyses. For example, since the U.S. Department of the Interior/U.S. Geological Survey's (USGS) 2008 free and open data policy for the Landsat satellites, downloads from the USGS archive have increased from 20,000 Landsat scenes per year to 10 million per year and climbing, with strong growth in both research and decision support fields. However, Earth observation-based decision support still poses users a number of challenges. Many of those Landsat downloads support a specialized community of remote sensing scientists, though new technologies promise to increase the usability of remotely sensed data for the larger GIS community supporting planning and resource management. Serving this larger community also requires supporting the development of increasingly interpretive products, and of new approaches to host and update products. For example, automating updates will add value to new essential climate variable products such as surface water extent and wildfire burned area extent. Projections of future urbanization in the southeastern U.S. are most useful when long-term land cover trends are integrated with street-level community data and planning tools. The USGS assessment of biological carbon sequestration in vegetation and shallow soils required a significant research investment in satellite and in situ measurements and biogeochemical and climate modeling, and is already providing decision support at a variety of scales; once operationalized, it will be a tool for adaptive management from field-scale soil and wetland conservation projects to national-scale policy.

A method for vreating a three dimensional model from published geologic maps and cross sections

USGS Publications Warehouse

Walsh, Gregory J.

2009-01-01

This brief report presents a relatively inexpensive and rapid method for creating a 3D model of geology from published quadrangle-scale maps and cross sections using Google Earth and Google SketchUp software. An example from the Green Mountains of Vermont, USA, is used to illustrate the step by step methods used to create such a model. A second example is provided from the Jebel Saghro region of the Anti-Atlas Mountains of Morocco. The report was published to help enhance the public?s ability to use and visualize geologic map data.

Dissemination of evidence in paediatric emergency medicine: a quantitative descriptive evaluation of a 16-week social media promotion

PubMed Central

Featherstone, Robin; Shave, Kassi; Scott, Shannon D; Hartling, Lisa

2018-01-01

Objectives TRanslating Emergency Knowledge for Kids (TREKK) and Cochrane Child Health collaborate to develop knowledge products on paediatric emergency medicine topics. Via a targeted social media promotion, we aimed to increase user interaction with the TREKK and Cochrane Child Health Twitter accounts and the uptake of TREKK Bottom Line Recommendations (BLRs) and Cochrane systematic reviews (SRs). Design Quantitative descriptive evaluation. Setting We undertook this study and collected data via the internet. Participants Our target users included online healthcare providers and health consumers. Intervention For 16 weeks, we used Twitter accounts (@TREKKca and @Cochrane_Child) and the Cochrane Child Health blog to promote 6 TREKK BLRs and 16 related Cochrane SRs. We published 1 blog post and 98 image-based tweets per week. Primary and secondary outcome measures The primary outcome was user interaction with @TREKKca and @Cochrane_Child. Secondary outcomes were visits to TREKK’s website and the Cochrane Child Health blog, clicks to and views of the TREKK BLRs, and Altmetric scores and downloads of Cochrane SRs. Results Followers to @TREKKca and @Cochrane_Child increased by 24% and 15%, respectively. Monthly users of TREKK’s website increased by 29%. Clicks to the TREKK BLRs increased by 22%. The BLRs accrued 59% more views compared with the baseline period. The 16 blog posts accrued 28% more views compared with the 8 previous months when no new posts were published. The Altmetric scores for the Cochrane SRs increased by ≥10 points each. The mean number of full text downloads for the promotion period was higher for nine and lower for seven SRs compared with the 16-week average for the previous year (mean difference (SD), +4.0 (22.0%)). Conclusions There was increased traffic to TREKK knowledge products and Cochrane SRs during the social media promotion. Quantitative evidence supports blogging and tweeting as dissemination strategies for evidence-based knowledge products. PMID:29880576

A communication efficient and scalable distributed data mining for the astronomical data

NASA Astrophysics Data System (ADS)

Govada, A.; Sahay, S. K.

2016-07-01

In 2020, ∼60PB of archived data will be accessible to the astronomers. But to analyze such a paramount data will be a challenging task. This is basically due to the computational model used to download the data from complex geographically distributed archives to a central site and then analyzing it in the local systems. Because the data has to be downloaded to the central site, the network BW limitation will be a hindrance for the scientific discoveries. Also analyzing this PB-scale on local machines in a centralized manner is challenging. In this, virtual observatory is a step towards this problem, however, it does not provide the data mining model (Zhang et al., 2004). Adding the distributed data mining layer to the VO can be the solution in which the knowledge can be downloaded by the astronomers instead the raw data and thereafter astronomers can either reconstruct the data back from the downloaded knowledge or use the knowledge directly for further analysis. Therefore, in this paper, we present Distributed Load Balancing Principal Component Analysis for optimally distributing the computation among the available nodes to minimize the transmission cost and downloading cost for the end user. The experimental analysis is done with Fundamental Plane (FP) data, Gadotti data and complex Mfeat data. In terms of transmission cost, our approach performs better than Qi et al. and Yue et al. The analysis shows that with the complex Mfeat data ∼90% downloading cost can be reduced for the end user with the negligible loss in accuracy.

30-36 Months: Your Child's Development

MedlinePlus

... Resources & Services Parenting Resource 30–36 Months: Your Child’s Development Download Files Feb 10, 2016 Older toddlers are ... go?” Then you two can switch. Downloads Your Child's Development: 30–36 Months PDF 373 KB Read more ...

12-15 Months: Your Child's Development

MedlinePlus

... Resources & Services Parenting Resource 12–15 Months: Your Child’s Development Download Files Feb 9, 2016 This is a ... who she is. Downloads 12–15 Months: Your Child’s Development PDF 418 KB Read more about: Ages and ...

Generalized Anxiety Disorder: When Worry Gets Out of Control

MedlinePlus

... of Control Download PDF Download ePub Order a free hardcopy What Is GAD? Occasional anxiety is a normal part of life. You might worry about things like health, money, or family problems. But people with generalized anxiety ...

TOMS Tropical Tropospheric Ozone Data Sets at the University of Maryland Website

NASA Technical Reports Server (NTRS)

Kochhar, A. K.; Thompson, A. M.; Hudson, R. D.; Frolov, A. D.; Witte, J. C.; Einaudi, Franco (Technical Monitor)

2001-01-01

Since 1997, shortly after the launch of the Earth-Probe TOMS (Total Ozone Mapping Spectrometer) satellite instrument, we have been processing data in near-real time to post maps of tropical tropospheric ozone at a website: metosrv2.umd.edu/-tropo. Daily, 3-day and 9-day averages of tropical tropospheric ozone column depth (TTO) are viewable from 10N to 10S. Data can be downloaded (running 9-day means) from 20N-30S. Pollution events are trackable along with dynamically-induced variations in tropospheric ozone column. TOMS smoke aerosol (toms.gsfc.nasa.gov) can be used to interpret biomass burning ozone, as for example, during the extreme ozone and smoke pollution period during the ENSO-related fires of August November 1997. During that time plumes of ozone and smoke were frequently decoupled and ozone from Indonesian fires and from Africa merged in one large feature by late October 1997. In addition to the Earth-Probe TOMS record, data as half-month averages and as daily 9-day means from the Nimbus 7 TOMS instrument are at the metosrv2.umd.edu/-tropo website. A guide to the website and examples of ozone time-series and maps will be shown.

Accessing the public MIMIC-II intensive care relational database for clinical research.

PubMed

Scott, Daniel J; Lee, Joon; Silva, Ikaro; Park, Shinhyuk; Moody, George B; Celi, Leo A; Mark, Roger G

2013-01-10

The Multiparameter Intelligent Monitoring in Intensive Care II (MIMIC-II) database is a free, public resource for intensive care research. The database was officially released in 2006, and has attracted a growing number of researchers in academia and industry. We present the two major software tools that facilitate accessing the relational database: the web-based QueryBuilder and a downloadable virtual machine (VM) image. QueryBuilder and the MIMIC-II VM have been developed successfully and are freely available to MIMIC-II users. Simple example SQL queries and the resulting data are presented. Clinical studies pertaining to acute kidney injury and prediction of fluid requirements in the intensive care unit are shown as typical examples of research performed with MIMIC-II. In addition, MIMIC-II has also provided data for annual PhysioNet/Computing in Cardiology Challenges, including the 2012 Challenge "Predicting mortality of ICU Patients". QueryBuilder is a web-based tool that provides easy access to MIMIC-II. For more computationally intensive queries, one can locally install a complete copy of MIMIC-II in a VM. Both publicly available tools provide the MIMIC-II research community with convenient querying interfaces and complement the value of the MIMIC-II relational database.

Full-text, Downloading, & Other Issues.

ERIC Educational Resources Information Center

Tenopir, Carol

1983-01-01

Issues having a possible impact on online search services in libraries are discussed including full text databases, front-end processors which translate user's input into the command language of an appropriate system, downloading to create personal files from commercial databases, and pricing. (EJS)

37 CFR 385.21 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 385.21 Patents, Trademarks, and Copyrights COPYRIGHT ROYALTY BOARD, LIBRARY OF CONGRESS RATES AND... MAKING AND DISTRIBUTING OF PHYSICAL AND DIGITAL PHONORECORDS Limited Offerings, Mixed Service Bundles..., permanent digital downloads, restricted downloads or ringtones; (3) In the case of a music bundle, the...

Delay Differential Equation-Based Modeling of Passively Mode-Locked Quantum Dot Lasers Using Measured Gain and Loss Spectra (Postprint)

DTIC Science & Technology

2013-01-01

semiconductor laser8, 9: ATAe d dA TQiTGi qg 12 11 2 1 (1) 2 0 1 AeeGgd dG GQ (2) Proc. of SPIE Vol. 8255 82551K-2 Downloaded From: http...1 Downloaded From: http://spiedigitallibrary.org/ on 01/14/2013 Terms of Use: http://spiedl.org/terms 1 Approved for public release; distribution...parameters ( 0g and 0q , respectively) have been derived to yield: Gg0 (10) Proc. of SPIE Vol. 8255 82551K-3 Downloaded From: http

Clean Air Status and Trends Network (CASTNET) Download Data Module

EPA Pesticide Factsheets

The CASTNET Download Data module allows users to select, view, and download CASTNET data (Raw, Aggregate, Modeled & Factual Data) based on user selections. CASTNET sites are located in or near rural areas and sensitive ecosystems collecting data on ambient levels of pollutants where urban influences are minimal. CASTNET, which was initiated in 1986, is able to provide data needed to assess and report on geographic patterns and long-term temporal trends in ambient air pollution and dry atmospheric deposition. CASTNET can also be used to track changes in measurements associated with climate change (such as temperature and precipitation).

A Cooperative Downloading Method for VANET Using Distributed Fountain Code.

PubMed

Liu, Jianhang; Zhang, Wenbin; Wang, Qi; Li, Shibao; Chen, Haihua; Cui, Xuerong; Sun, Yi

2016-10-12

Cooperative downloading is one of the effective methods to improve the amount of downloaded data in vehicular ad hoc networking (VANET). However, the poor channel quality and short encounter time bring about a high packet loss rate, which decreases transmission efficiency and fails to satisfy the requirement of high quality of service (QoS) for some applications. Digital fountain code (DFC) can be utilized in the field of wireless communication to increase transmission efficiency. For cooperative forwarding, however, processing delay from frequent coding and decoding as well as single feedback mechanism using DFC cannot adapt to the environment of VANET. In this paper, a cooperative downloading method for VANET using concatenated DFC is proposed to solve the problems above. The source vehicle and cooperative vehicles encodes the raw data using hierarchical fountain code before they send to the client directly or indirectly. Although some packets may be lost, the client can recover the raw data, so long as it receives enough encoded packets. The method avoids data retransmission due to packet loss. Furthermore, the concatenated feedback mechanism in the method reduces the transmission delay effectively. Simulation results indicate the benefits of the proposed scheme in terms of increasing amount of downloaded data and data receiving rate.

Gender analysis of papers published in ACTAS ESPANOLAS DE PSIQUIATRIA (1999-2006).

PubMed

Alonso-Arroyo, A; González-Alcaide, G; Bolaños Pizarro, M; Castelló Cogollos, L; Valderrama-Zurián, J C; Aleixandre-Benavent, R

2008-01-01

The governments and organizations responsible for scientific policies try to encourage equality of gender, among their priorities that of obtaining equal participation and full integration of women in all aspects of the scientific profession. The study analyzes the scientific production of women in the areas of Psychiatry by means of the bibliometric study of the papers published in ACTAS ESPANOLAS DE PSIQUIATRIA. A total of 458 papers published from 1999- 2006 period were downloaded from the Science Citation Index-Expanded database, these including original research papers, review articles and clinical cases. A bibliometric study broken down by gender was carried out to determine the existence or inequalities between men and women regarding scientific productivity, type of document, order of author signatures, on the institutional and geographical level. The papers were published by 1,194 different authors. The gender of 977 authors was identified, 587 (60.08%) men and 390 (39.92%) women. The percentage of women authorship has risen from 29.92% in 1999 to 38.86% in 2006. A total of 42.92% of authors having one published article were women, while (those with more than nine articles) only accounted for 33%. Bibliometric studies on scientific activity provide essential information to promote gender equality. An annual increase over 1% in the number of female authors in the journal has been observed, which if it continues will lead to a parity in coming years.

Questioning the efficacy of 'gold' open access to published articles.

PubMed

Fredericks, Suzanne

2015-07-01

To question the efficacy of 'gold' open access to published articles. Open access is unrestricted access to academic, theoretical and research literature that is scholarly and peer-reviewed. Two models of open access exist: 'gold' and 'green'. Gold open access provides everyone with access to articles during all stages of publication, with processing charges paid by the author(s). Green open access involves placing an already published article into a repository to provide unrestricted access, with processing charges incurred by the publisher. This is a discussion paper. An exploration of the relative benefits and drawbacks of the 'gold' and 'green' open access systems. Green open access is a more economic and efficient means of granting open access to scholarly literature but a large number of researchers select gold open access journals as their first choices for manuscript submissions. This paper questions the efficacy of gold open access models and presents an examination of green open access models to encourage nurse researchers to consider this approach. In the current academic environment, with increased pressures to publish and low funding success rates, it is difficult to understand why gold open access still exists. Green open access enhances the visibility of an academic's work, as increased downloads of articles tend to lead to increased citations. Green open access is the cheaper option, as well as the most beneficial choice, for universities that want to provide unrestricted access to all literature at minimal risk.

Publishing Platform for Aerial Orthophoto Maps, the Complete Stack

NASA Astrophysics Data System (ADS)

Čepický, J.; Čapek, L.

2016-06-01

When creating set of orthophoto maps from mosaic compositions, using airborne systems, such as popular drones, we need to publish results of the work to users. Several steps need to be performed in order get large scale raster data published. As first step, data have to be shared as service (OGC WMS as view service, OGC WCS as download service). But for some applications, OGC WMTS is handy as well, for faster view of the data. Finally the data have to become a part of web mapping application, so that they can be used and evaluated by non-technical users. In this talk, we would like to present automated line of those steps, where user puts in orthophoto image and as a result, OGC Open Web Services are published as well as web mapping application with the data. The web mapping application can be used as standard presentation platform for such type of big raster data to generic user. The publishing platform - Geosense online map information system - can be also used for combination of data from various resources and for creating of unique map compositions and as input for better interpretations of photographed phenomenons. The whole process is successfully tested with eBee drone with raster data resolution 1.5-4 cm/px on many areas and result is also used for creation of derived datasets, usually suited for property management - the records of roads, pavements, traffic signs, public lighting, sewage system, grave locations, and others.

Archive of digital and digitized analog boomer seismic reflection data collected during USGS cruise 96CCT02 in Copano, Corpus Christi, and Nueces Bays and Corpus Christi Bayou, Texas, July 1996

USGS Publications Warehouse

Harrison, Arnell S.; Dadisman, Shawn V.; Kindinger, Jack G.; Morton, Robert A.; Blum, Mike D.; Wiese, Dana S.; Subiño, Janice A.

2007-01-01

In June of 1996, the U.S. Geological Survey conducted geophysical surveys from Nueces to Copano Bays, Texas. This report serves as an archive of unprocessed digital boomer seismic reflection data, trackline maps, navigation files, GIS information, cruise log, and formal FGDC metadata. Filtered and gained digital images of the seismic profiles and high resolution scanned TIFF images of the original paper printouts are also provided. The archived trace data are in standard Society of Exploration Geophysicists (SEG) SEG-Y format (Barry and others, 1975) and may be downloaded and processed with commercial or public domain software such as Seismic Unix (SU). Example SU processing scripts and USGS software for viewing the SEG-Y files (Zihlman, 1992) are also provided.

Archive of Digital Boomer Seismic Reflection Data Collected During USGS Field Activity 08LCA04 in Lakes Cherry, Helen, Hiawassee, Louisa, and Prevatt, Central Florida, September 2008

USGS Publications Warehouse

Harrison, Arnell S.; Dadisman, Shawn V.; Davis, Jeffrey B.; Flocks, James G.; Wiese, Dana S.

2009-01-01

From September 2 through 4, 2008, the U.S. Geological Survey and St. Johns River Water Management District (SJRWMD) conducted geophysical surveys in Lakes Cherry, Helen, Hiawassee, Louisa, and Prevatt, central Florida. This report serves as an archive of unprocessed digital boomer seismic reflection data, trackline maps, navigation files, GIS information, FACS logs, and formal FGDC metadata. Filtered and gained digital images of the seismic profiles are also provided. The archived trace data are in standard Society of Exploration Geophysicists (SEG) SEG-Y format (Barry and others, 1975) and may be downloaded and processed with commercial or public domain software such as Seismic Unix (SU). Example SU processing scripts and USGS software for viewing the SEG-Y files (Zihlman, 1992) are also provided.

Abschätzung des Einflusses von Parameterunsicherheiten bei der Planung und Auswertung von Tracertests unter Verwendung von Ensembleprognosen

NASA Astrophysics Data System (ADS)

Klotzsch, Stephan; Binder, Martin; Händel, Falk

2017-06-01

While planning tracer tests, uncertainties in geohydraulic parameters should be considered as an important factor. Neglecting these uncertainties can lead to missing the tracer breakthrough, for example. One way to consider uncertainties during tracer test design is the so called ensemble forecast. The applicability of this method to geohydrological problems is demonstrated by coupling the method with two analytical solute transport models. The algorithm presented in this article is suitable for prediction as well as parameter estimation. The parameter estimation function can be used in a tracer test for reducing the uncertainties in the measured data which can improve the initial prediction. The algorithm was implemented into a software tool which is freely downloadable from the website of the Institute for Groundwater Management at TU Dresden, Germany.

Informatics application provides instant research to practice benefits.

PubMed Central

Bowles, K. H.; Peng, T.; Qian, R.; Naylor, M. D.

2001-01-01

A web-based research information system was designed to enable our research team to efficiently measure health related quality of life among frail older adults in a variety of health care settings (home care, nursing homes, assisted living, PACE). The structure, process, and outcome data is collected using laptop computers and downloaded to a SQL database. Unique features of this project are the ability to transfer research to practice by instantly sharing individual and aggregate results with the clinicians caring for these elders and directly impacting the quality of their care. Clinicians can also dial in to the database to access standard queries or receive customized reports about the patients in their facilities. This paper will describe the development and implementation of the information system. The conference presentation will include a demonstration and examples of research to practice benefits. PMID:11825156

Systems of fuzzy equations in structural mechanics

NASA Astrophysics Data System (ADS)

Skalna, Iwona; Rama Rao, M. V.; Pownuk, Andrzej

2008-08-01

Systems of linear and nonlinear equations with fuzzy parameters are relevant to many practical problems arising in structure mechanics, electrical engineering, finance, economics and physics. In this paper three methods for solving such equations are discussed: method for outer interval solution of systems of linear equations depending linearly on interval parameters, fuzzy finite element method proposed by Rama Rao and sensitivity analysis method. The performance and advantages of presented methods are described with illustrative examples. Extended version of the present paper can be downloaded from the web page of the UTEP [I. Skalna, M.V. Rama Rao, A. Pownuk, Systems of fuzzy equations in structural mechanics, The University of Texas at El Paso, Department of Mathematical Sciences Research Reports Series, , Texas Research Report No. 2007-01, 2007].

Enhancing Icing Training for Pilots Through Web-Based Multimedia

NASA Technical Reports Server (NTRS)

Fletcher, William; Nolan, Gary; Adanich, Emery; Bond, Thomas H.

2006-01-01

The Aircraft Icing Project of the NASA Aviation Safety Program has developed a number of in-flight icing education and training aids designed to increase pilot awareness about the hazards associated with various icing conditions. The challenges and advantages of transitioning these icing training materials to a Web-based delivery are discussed. Innovative Web-based delivery devices increased course availability to pilots and dispatchers while increasing course flexibility and utility. These courses are customizable for both self-directed and instructor-led learning. Part of our goal was to create training materials with enough flexibility to enable Web-based delivery and downloadable portability while maintaining a rich visual multimedia-based learning experience. Studies suggest that using visually based multimedia techniques increases the effectiveness of icing training materials. This paper describes these concepts, gives examples, and discusses the transitional challenges.

Endogenous versus Exogenous Origins of Crises

NASA Astrophysics Data System (ADS)

Sornette, Didier

Are large biological extinctions such as the Cretaceous/Tertiary KT boundary due to a meteorite, extreme volcanic activity or self-organized critical extinction cascades? Are commercial successes due to a progressive reputation cascade or the result of a well orchestrated advertisement? Determining the chain of causality for Xevents in complex systems requires disentangling interwoven exogenous and endogenous contributions with either no clear signature or too many signatures. Here, I review several efforts carried out with collaborators which suggest a general strategy for understanding the organizations of several complex systems under the dual effect of endogenous and exogenous fluctuations. The studied examples are: internet download shocks, book sale shocks, social shocks, financial volatility shocks, and financial crashes. Simple models are offered to quantitatively relate the endogenous organization to the exogenous response of the system. Suggestions for applications of these ideas to many other systems are offered.

Enrichment of Data Publications in Earth Sciences - Data Reports as a Missing Link

NASA Astrophysics Data System (ADS)

Elger, Kirsten; Bertelmann, Roland; Haberland, Christian; Evans, Peter L.

2015-04-01

During the past decade, the relevance of research data stewardship has been rising significantly. Preservation and publication of scientific data for long-term use, including the storage in adequate repositories has been identified as a key issue by the scientific community as well as by bodies like research agencies. Essential for any kind of re-use is a proper description of the datasets. As a result of the increasing interest, data repositories have been developed and the included research data is accompanied with at least a minimum set of metadata. This metadata is useful for data discovery and a first insight to the content of a dataset. But often data re-use needs more and extended information. Many datasets are accompanied by a small 'readme file' with basic information on the data structure, or other accompanying documents. A source of additional information could be an article published in one of the newly emerging data journals (e.g. Copernicus's ESSD Earth System Science Data or Nature's Scientific Data). Obviously there is an information gap between a 'readme file', that is only accessible after data download (which often leads to less usage of published datasets than if the information was available beforehand) and the much larger effort to prepare an article for a peer-reviewed data journal. For many years, GFZ German Research Centre for Geosciences publishes 'Scientific Technical Reports (STR)' as a report series which is electronically persistently available and citable with assigned DOIs. This series was opened for the description of parallel published datasets as 'STR Data'. These are internally reviewed and offer a flexible publication format describing published data in depth, suitable for different datasets ranging from long-term monitoring time series of observatories to field data, to (meta-)databases, and software publications. STR Data offer a full and consistent overview and description to all relevant parameters of a linked published dataset. These reports are readable and citable on their own, but are, of course, closely connected to the respective datasets. Therefore, they give full insight into the framework of the data before data download. This is especially relevant for large and often heterogeneous datasets, like e.g. controlled-source seismic data gathered with instruments of the 'Geophysical Instrument Pool Potsdam GIPP'. Here, details of the instrumentation, data organization, data format, accuracy, geographical coordinates, timing and data completeness, etc. need to be documented. STR Data are also attractive for the publication of historic datasets, e.g. 30-40 years old seismic experiments. It is also possible for one STR Data to describe several datasets, e.g. from multiple diverse instruments types, or distinct regions of interest. The publication of DOI-assigned data reports is a helpful tool to fill the gap between basic metadata and restricted 'readme' information on the one hand and preparing extended journal articles on the other hand. They open the way for informed re-use and, with their comprehensive data description, may act as 'appetizer' for the re-use of published datasets.

Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV).

PubMed

Lefkowitz, Elliot J; Dempsey, Donald M; Hendrickson, Robert Curtis; Orton, Richard J; Siddell, Stuart G; Smith, Donald B

2018-01-04

The International Committee on Taxonomy of Viruses (ICTV) is charged with the task of developing, refining, and maintaining a universal virus taxonomy. This task encompasses the classification of virus species and higher-level taxa according to the genetic and biological properties of their members; naming virus taxa; maintaining a database detailing the currently approved taxonomy; and providing the database, supporting proposals, and other virus-related information from an open-access, public web site. The ICTV web site (http://ictv.global) provides access to the current taxonomy database in online and downloadable formats, and maintains a complete history of virus taxa back to the first release in 1971. The ICTV has also published the ICTV Report on Virus Taxonomy starting in 1971. This Report provides a comprehensive description of all virus taxa covering virus structure, genome structure, biology and phylogenetics. The ninth ICTV report, published in 2012, is available as an open-access online publication from the ICTV web site. The current, 10th report (http://ictv.global/report/), is being published online, and is replacing the previous hard-copy edition with a completely open access, continuously updated publication. No other database or resource exists that provides such a comprehensive, fully annotated compendium of information on virus taxa and taxonomy. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

MutHTP: Mutations in Human Transmembrane Proteins.

PubMed

A, Kulandaisamy; S, Binny Priya; R, Sakthivel; Tarnovskaya, Svetlana; Bizin, Ilya; Hönigschmid, Peter; Frishman, Dmitrij; Gromiha, M Michael

2018-02-01

We have developed a novel database, MutHTP, which contains information on 183395 disease-associated and 17827 neutral mutations in human transmembrane proteins. For each mutation site MutHTP provides a description of its location with respect to the membrane protein topology, structural environment (if available) and functional features. Comprehensive visualization, search, display and download options are available. The database is publicly available at http://www.iitm.ac.in/bioinfo/MutHTP/. The website is implemented using HTML, PHP and javascript and supports recent versions of all major browsers, such as Firefox, Chrome and Opera. gromiha@iitm.ac.in. Supplementary data are available at Bioinformatics online. © The Author (2018). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Cordova: web-based management of genetic variation data.

PubMed

Ephraim, Sean S; Anand, Nikhil; DeLuca, Adam P; Taylor, Kyle R; Kolbe, Diana L; Simpson, Allen C; Azaiez, Hela; Sloan, Christina M; Shearer, A Eliot; Hallier, Andrea R; Casavant, Thomas L; Scheetz, Todd E; Smith, Richard J H; Braun, Terry A

2014-12-01

Cordova is an out-of-the-box solution for building and maintaining an online database of genetic variations integrated with pathogenicity prediction results from popular algorithms. Our primary motivation for developing this system is to aid researchers and clinician-scientists in determining the clinical significance of genetic variations. To achieve this goal, Cordova provides an interface to review and manually or computationally curate genetic variation data as well as share it for clinical diagnostics and the advancement of research. Cordova is open source under the MIT license and is freely available for download at https://github.com/clcg/cordova. Published by Oxford University Press. This work is written by US Government employees and is in the public domain in the US.

The PMDB Protein Model Database

PubMed Central

Castrignanò, Tiziana; De Meo, Paolo D'Onorio; Cozzetto, Domenico; Talamo, Ivano Giuseppe; Tramontano, Anna

2006-01-01

The Protein Model Database (PMDB) is a public resource aimed at storing manually built 3D models of proteins. The database is designed to provide access to models published in the scientific literature, together with validating experimental data. It is a relational database and it currently contains >74 000 models for ∼240 proteins. The system is accessible at and allows predictors to submit models along with related supporting evidence and users to download them through a simple and intuitive interface. Users can navigate in the database and retrieve models referring to the same target protein or to different regions of the same protein. Each model is assigned a unique identifier that allows interested users to directly access the data. PMID:16381873

Clicks versus Citations: Click Count as a Metric in High Energy Physics Publishing

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

Bitton, Ayelet; /UC, San Diego /SLAC

2011-06-22

High-energy physicists worldwide rely on online resources such as SPIRES and arXiv to perform gather research and share their own publications. SPIRES is a tool designed to search the literature within high-energy physics, while arXiv provides the actual full-text documents of this literature. In high-energy physics, papers are often ranked according to the number of citations they acquire - meaning the number of times a later paper references the original. This paper investigates the correlation between the number of times a paper is clicked in order to be downloaded and the number of citations it receives following the click. Itmore » explores how physicists truly read what they cite.« less

Tibetan Magmatism Database

NASA Astrophysics Data System (ADS)

Chapman, James B.; Kapp, Paul

2017-11-01

A database containing previously published geochronologic, geochemical, and isotopic data on Mesozoic to Quaternary igneous rocks in the Himalayan-Tibetan orogenic system are presented. The database is intended to serve as a repository for new and existing igneous rock data and is publicly accessible through a web-based platform that includes an interactive map and data table interface with search, filtering, and download options. To illustrate the utility of the database, the age, location, and ɛHft composition of magmatism from the central Gangdese batholith in the southern Lhasa terrane are compared. The data identify three high-flux events, which peak at 93, 50, and 15 Ma. They are characterized by inboard arc migration and a temporal and spatial shift to more evolved isotopic compositions.

OPATs: Omnibus P-value association tests.

PubMed

Chen, Chia-Wei; Yang, Hsin-Chou

2017-07-10

Combining statistical significances (P-values) from a set of single-locus association tests in genome-wide association studies is a proof-of-principle method for identifying disease-associated genomic segments, functional genes and biological pathways. We review P-value combinations for genome-wide association studies and introduce an integrated analysis tool, Omnibus P-value Association Tests (OPATs), which provides popular analysis methods of P-value combinations. The software OPATs programmed in R and R graphical user interface features a user-friendly interface. In addition to analysis modules for data quality control and single-locus association tests, OPATs provides three types of set-based association test: window-, gene- and biopathway-based association tests. P-value combinations with or without threshold and rank truncation are provided. The significance of a set-based association test is evaluated by using resampling procedures. Performance of the set-based association tests in OPATs has been evaluated by simulation studies and real data analyses. These set-based association tests help boost the statistical power, alleviate the multiple-testing problem, reduce the impact of genetic heterogeneity, increase the replication efficiency of association tests and facilitate the interpretation of association signals by streamlining the testing procedures and integrating the genetic effects of multiple variants in genomic regions of biological relevance. In summary, P-value combinations facilitate the identification of marker sets associated with disease susceptibility and uncover missing heritability in association studies, thereby establishing a foundation for the genetic dissection of complex diseases and traits. OPATs provides an easy-to-use and statistically powerful analysis tool for P-value combinations. OPATs, examples, and user guide can be downloaded from http://www.stat.sinica.edu.tw/hsinchou/genetics/association/OPATs.htm. © The Author 2017. Published by Oxford University Press.

A suite of R packages for web-enabled modeling and analysis of surface waters

NASA Astrophysics Data System (ADS)

Read, J. S.; Winslow, L. A.; Nüst, D.; De Cicco, L.; Walker, J. I.

2014-12-01

Researchers often create redundant methods for downloading, manipulating, and analyzing data from online resources. Moreover, the reproducibility of science can be hampered by complicated and voluminous data, lack of time for documentation and long-term maintenance of software, and fear of exposing programming skills. The combination of these factors can encourage unshared one-off programmatic solutions instead of openly provided reusable methods. Federal and academic researchers in the water resources and informatics domains have collaborated to address these issues. The result of this collaboration is a suite of modular R packages that can be used independently or as elements in reproducible analytical workflows. These documented and freely available R packages were designed to fill basic needs for the effective use of water data: the retrieval of time-series and spatial data from web resources (dataRetrieval, geoknife), performing quality assurance and quality control checks of these data with robust statistical methods (sensorQC), the creation of useful data derivatives (including physically- and biologically-relevant indices; GDopp, LakeMetabolizer), and the execution and evaluation of models (glmtools, rLakeAnalyzer). Here, we share details and recommendations for the collaborative coding process, and highlight the benefits of an open-source tool development pattern with a popular programming language in the water resources discipline (such as R). We provide examples of reproducible science driven by large volumes of web-available data using these tools, explore benefits of accessing packages as standardized web processing services (WPS) and present a working platform that allows domain experts to publish scientific algorithms in a service-oriented architecture (WPS4R). We assert that in the era of open data, tools that leverage these data should also be freely shared, transparent, and developed in an open innovation environment.

al3c: high-performance software for parameter inference using Approximate Bayesian Computation.

PubMed

Stram, Alexander H; Marjoram, Paul; Chen, Gary K

2015-11-01

The development of Approximate Bayesian Computation (ABC) algorithms for parameter inference which are both computationally efficient and scalable in parallel computing environments is an important area of research. Monte Carlo rejection sampling, a fundamental component of ABC algorithms, is trivial to distribute over multiple processors but is inherently inefficient. While development of algorithms such as ABC Sequential Monte Carlo (ABC-SMC) help address the inherent inefficiencies of rejection sampling, such approaches are not as easily scaled on multiple processors. As a result, current Bayesian inference software offerings that use ABC-SMC lack the ability to scale in parallel computing environments. We present al3c, a C++ framework for implementing ABC-SMC in parallel. By requiring only that users define essential functions such as the simulation model and prior distribution function, al3c abstracts the user from both the complexities of parallel programming and the details of the ABC-SMC algorithm. By using the al3c framework, the user is able to scale the ABC-SMC algorithm in parallel computing environments for his or her specific application, with minimal programming overhead. al3c is offered as a static binary for Linux and OS-X computing environments. The user completes an XML configuration file and C++ plug-in template for the specific application, which are used by al3c to obtain the desired results. Users can download the static binaries, source code, reference documentation and examples (including those in this article) by visiting https://github.com/ahstram/al3c. astram@usc.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

GTRAC: fast retrieval from compressed collections of genomic variants.

PubMed

Tatwawadi, Kedar; Hernaez, Mikel; Ochoa, Idoia; Weissman, Tsachy

2016-09-01

The dramatic decrease in the cost of sequencing has resulted in the generation of huge amounts of genomic data, as evidenced by projects such as the UK10K and the Million Veteran Project, with the number of sequenced genomes ranging in the order of 10 K to 1 M. Due to the large redundancies among genomic sequences of individuals from the same species, most of the medical research deals with the variants in the sequences as compared with a reference sequence, rather than with the complete genomic sequences. Consequently, millions of genomes represented as variants are stored in databases. These databases are constantly updated and queried to extract information such as the common variants among individuals or groups of individuals. Previous algorithms for compression of this type of databases lack efficient random access capabilities, rendering querying the database for particular variants and/or individuals extremely inefficient, to the point where compression is often relinquished altogether. We present a new algorithm for this task, called GTRAC, that achieves significant compression ratios while allowing fast random access over the compressed database. For example, GTRAC is able to compress a Homo sapiens dataset containing 1092 samples in 1.1 GB (compression ratio of 160), while allowing for decompression of specific samples in less than a second and decompression of specific variants in 17 ms. GTRAC uses and adapts techniques from information theory, such as a specialized Lempel-Ziv compressor, and tailored succinct data structures. The GTRAC algorithm is available for download at: https://github.com/kedartatwawadi/GTRAC CONTACT: : kedart@stanford.edu 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.

Cloud-based Jupyter Notebooks for Water Data Analysis

NASA Astrophysics Data System (ADS)

Castronova, A. M.; Brazil, L.; Seul, M.

2017-12-01

The development and adoption of technologies by the water science community to improve our ability to openly collaborate and share workflows will have a transformative impact on how we address the challenges associated with collaborative and reproducible scientific research. Jupyter notebooks offer one solution by providing an open-source platform for creating metadata-rich toolchains for modeling and data analysis applications. Adoption of this technology within the water sciences, coupled with publicly available datasets from agencies such as USGS, NASA, and EPA enables researchers to easily prototype and execute data intensive toolchains. Moreover, implementing this software stack in a cloud-based environment extends its native functionality to provide researchers a mechanism to build and execute toolchains that are too large or computationally demanding for typical desktop computers. Additionally, this cloud-based solution enables scientists to disseminate data processing routines alongside journal publications in an effort to support reproducibility. For example, these data collection and analysis toolchains can be shared, archived, and published using the HydroShare platform or downloaded and executed locally to reproduce scientific analysis. This work presents the design and implementation of a cloud-based Jupyter environment and its application for collecting, aggregating, and munging various datasets in a transparent, sharable, and self-documented manner. The goals of this work are to establish a free and open source platform for domain scientists to (1) conduct data intensive and computationally intensive collaborative research, (2) utilize high performance libraries, models, and routines within a pre-configured cloud environment, and (3) enable dissemination of research products. This presentation will discuss recent efforts towards achieving these goals, and describe the architectural design of the notebook server in an effort to support collaborative and reproducible science.

GAPscreener: an automatic tool for screening human genetic association literature in PubMed using the support vector machine technique.

PubMed

Yu, Wei; Clyne, Melinda; Dolan, Siobhan M; Yesupriya, Ajay; Wulf, Anja; Liu, Tiebin; Khoury, Muin J; Gwinn, Marta

2008-04-22

Synthesis of data from published human genetic association studies is a critical step in the translation of human genome discoveries into health applications. Although genetic association studies account for a substantial proportion of the abstracts in PubMed, identifying them with standard queries is not always accurate or efficient. Further automating the literature-screening process can reduce the burden of a labor-intensive and time-consuming traditional literature search. The Support Vector Machine (SVM), a well-established machine learning technique, has been successful in classifying text, including biomedical literature. The GAPscreener, a free SVM-based software tool, can be used to assist in screening PubMed abstracts for human genetic association studies. The data source for this research was the HuGE Navigator, formerly known as the HuGE Pub Lit database. Weighted SVM feature selection based on a keyword list obtained by the two-way z score method demonstrated the best screening performance, achieving 97.5% recall, 98.3% specificity and 31.9% precision in performance testing. Compared with the traditional screening process based on a complex PubMed query, the SVM tool reduced by about 90% the number of abstracts requiring individual review by the database curator. The tool also ascertained 47 articles that were missed by the traditional literature screening process during the 4-week test period. We examined the literature on genetic associations with preterm birth as an example. Compared with the traditional, manual process, the GAPscreener both reduced effort and improved accuracy. GAPscreener is the first free SVM-based application available for screening the human genetic association literature in PubMed with high recall and specificity. The user-friendly graphical user interface makes this a practical, stand-alone application. The software can be downloaded at no charge.

[From the editor].

PubMed

Dudek, Dominika; Sobański, Jerzy A; Klasa, Katarzyna

2015-01-01

Dear Readers We are happy and proud to announce that we managed to achieve intention announced in the last issue: for the first time in PubMed there is a possibility of direct and free access to the full texts published in Polish Psychiatry (Polish and English language versions are available)!!! For the issue 6/2014 they have been downloaded by Medline users already 500 times. Owing to this, papers by Polish scientists-psychiatrists are more readily available to colleagues from around the world interested in them, and Polish Psychiatry actually becomes journal of international scope. We hope that it will result in a marked improvement in the bibliometric indicators (which, however, is unrealistic to expect in the current or next year) in the following years. Spring issue of Polish Psychiatry touches several important problems. We pay attention to the texts on addiction - behavioural (Internet addiction) and alcohol. Two papers by prof. M. Wojnar's team summarize the issues related to the coexistence of alcohol dependence with other psychiatric disorders. The issue of dual diagnosis has already appeared in our magazine (for example [1]). This is an extremely difficult problem, and patients are a real challenge, both therapeutic and diagnostic. They often require a comprehensive approach: pharmacotherapy of comorbid mental illness, psychoeducation, addiction treatment programmes. For these patients the maintenance of abstinence is particularly difficult, especially in a situation of exacerbation of psychopathological symptoms. An important direction is searching for additional pharmacotherapeutic methods which help to reduce the degree of alcohol abuse and the resulting damage. These include: acamprosate, drugs which are opioid receptor antagonists [2], and in the current issue the authors from the University of Cagliari focused on baclofen. (...).

Inferring the global phylodynamics of influenza A/H3N2 viruses in Taiwan.

PubMed

Gong, Yu-Nong; Tsao, Kuo-Chien; Chen, Guang-Wu

2018-02-20

Influenza A/H3N2 viruses are characterized by highly mutated RNA genomes. In this study, we focused on tracing the phylodynamics of Taiwanese strains over the past four decades. All Taiwanese H3N2 HA1 sequences and references were downloaded from public database. A Bayesian skyline plot (BSP) and phylogenetic tree were used to analyze the evolutionary history, and Bayesian phylogeographic analysis was applied to predict the spatiotemporal migrations of influenza outbreaks. Genetic diversity was found to have peaked near the summer of 2009 in BSP, in addition to the two earlier reported ones in summer of 2005 and 2007. We predicted their spatiotemporal migrations and found the summer epidemic of 2005 from Korea, and 2007 and 2009 from the Western United States. BSP also predicted an elevated genetic diversity in 2015-2017. Quasispecies were found over approximately 20% of the strains included in this time span. In addition, a first-time seen N31S mutation was noted in Taiwan in 2016-2017. We comprehensively investigated the evolutionary history of Taiwanese strains in 1979-2017. An epidemic caution could thus be raised if genetic diversity was found to have peaked. An example showed a newly-discovered cluster in 2016-2017 strains featuring a mutation N31S together with HA-160 quasispecies. Phylogeographic analysis, moreover, provided useful insights in tracing the possible source and migrations of these epidemics around the world. We demonstrated that Asian destinations including Taiwan were the immediate followers, while U.S. continent was predicted the origin of two summer epidemics in 2007 and 2009. Copyright © 2018. Published by Elsevier B.V.

Development of tools and techniques for momentum compression of fast rare isotopes

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

David J. Morrissey; Bradley M. Sherrill; Oleg Tarasov

2010-11-21

As part of our past research and development work, we have created and developed the LISE++ simulation code [Tar04, Tar08]. The LISE++ package was significantly extended with the addition of a Monte Carlo option that includes an option for calculating ion trajectories using a Taylor-series expansion up to fifth order, and implementation of the MOTER Monte Carlo code [Kow87] for ray tracing of the ions into the suite of LISE++ codes. The MOTER code was rewritten from FORTRAN into C++ and transported to the MS-Windows operating system. Extensive work went into the creation of a user-friendly interface for the code.more » An example of the graphical user interface created for the MOTER code is shown in the left panel of Figure 1 and the results of a typical calculation for the trajectories of particles that pass through the A1900 fragment separator are shown in the right panel. The MOTER code is presently included as part of the LISE++ package for downloading without restriction by the worldwide community. The LISE++ was extensively developed and generalized to apply to any projectile fragment separator during the early phase of this grant. In addition to the inclusion of the MOTER code, other important additions to the LISE++ code made during FY08/FY09 are listed. The LISE++ is distributed over the web (http://groups.nscl.msu.edu/lise ) and is available without charge to anyone by anonymous download, thus, the number of individual users is not recorded. The number of 'hits' on the servers that provide the LISE++ code is shown in Figure 3 for the last eight calendar years (left panel) along with the country from the IP address (right panel). The data show an increase in web-activity with the release of the new version of the program during the grant period and a worldwide impact. An important part of the proposed work carried out during FY07, FY08 and FY09 by a graduate student in the MSU Physics program was to benchmark the codes by comparison of detailed measurements to the LISE++ predictions. A large data set was obtained for fission fragments from the reaction of 238U ions at 81 MeV/u in a 92 mg/cm2 beryllium target with the A1900 projectile fragment separator. The data were analyzed and form the bulk of a Ph.D. dissertation that is nearing completion. The rich data set provides a number of benchmarks for the improved LISE++ code and only a few examples can be shown here. The primary information obtained from the measurements is the yield of the products as a function of mass, charge and momentum. Examples of the momentum distributions of individually identified fragments can be seen in Figures 2 and 4 along with comparisons to the predicted distributions. The agreement is remarkably good and indicates the general validity of the model of the nuclear reactions producing these fragments and of the higher order transmission calculations in the LISE++ code. The momentum distributions were integrated to provide the cross sections for the individual isotopes. As shown in Figure 5, there is good agreement with the model predictions although the observed cross sections are a factor of five or so higher in this case. Other comparisons of measured production cross sections from abrasion-fission reactions have been published by our group working at the NSCL during this period [Fol09] and through our collaboration with Japanese researchers working at RIKEN with the BigRIPS separator [Ohn08, Ohn10]. The agreement of the model predictions with the data obtained with two different fragment separators is very good and indicates the usefulness of the new LISE++ code.« less

An experimental and analytical method for approximate determination of the tilt rotor research aircraft rotor/wing download

NASA Technical Reports Server (NTRS)

Jordon, D. E.; Patterson, W.; Sandlin, D. R.

1985-01-01

The XV-15 Tilt Rotor Research Aircraft download phenomenon was analyzed. This phenomenon is a direct result of the two rotor wakes impinging on the wing upper surface when the aircraft is in the hover configuration. For this study the analysis proceeded along tow lines. First was a method whereby results from actual hover tests of the XV-15 aircraft were combined with drag coefficient results from wind tunnel tests of a wing that was representative of the aircraft wing. Second, an analytical method was used that modeled that airflow caused gy the two rotors. Formulas were developed in such a way that acomputer program could be used to calculate the axial velocities were then used in conjunction with the aforementioned wind tunnel drag coefficinet results to produce download values. An attempt was made to validate the analytical results by modeling a model rotor system for which direct download values were determinrd..

Measuring metrics - a 40-year longitudinal cross-validation of citations, downloads, and peer review in astrophysics

NASA Astrophysics Data System (ADS)

Kurtz, Michael J.; Henneken, Edwin A.

2017-03-01

Citation measures, and newer altmetric measures such as downloads are now commonly used to inform personnel decisions. How well do or can these measures measure or predict the past, current, or future scholarly performance of an individual? Using data from the Smithsonian/NASA Astrophysics Data System we analyze the publication, citation, download, and distinction histories of a cohort of 922 individuals who received a U.S. PhD in astronomy in the period 1972-1976. By examining the same and different measures at the same and different times for the same individuals we are able to show the capabilities and limitations of each measure. Because the distributions are lognormal, measurement uncertainties are multiplicative; we show that in order to state with 95% confidence that one person's citations and downloads are significantly higher than another person's, the log difference in the ratio of counts must be at least 0.3dex, which corresponds to a multiplicative factor of 2.

Valuing geospatial information: Using the contingent valuation method to estimate the economic benefits of Landsat satellite imagery

USGS Publications Warehouse

Loomis, John; Koontz, Steve; Miller, Holly M.; Richardson, Leslie A.

2015-01-01

While the U.S. government does not charge for downloading Landsat images, the images have value to users. This paper demonstrates a method that can value Landsat and other imagery to users. A survey of downloaders of Landsat images found: (a) established US users have a mean value of $912 USD per scene; (b) new US users and users returning when imagery became free have a mean value of $367 USD per scene. Total US user benefits for the 2.38 million scenes downloaded is $1.8 billion USD. While these benefits indicate a high willingness-to-pay among many Landsat downloaders, it would be economically inefficient for the US government to charge for Landsat imagery. Charging a price of $100 USD a scene would result in an efficiency loss of $37.5 million a year. This economic information should be useful to policy-makers who must decide about the future of this and similar remote sensing programs.

Use Cases for Combining Web Services with ArcPython Tools for Enabling Quality Control of Land Remote Sensing Data Products.

NASA Astrophysics Data System (ADS)

Krehbiel, C.; Maiersperger, T.; Friesz, A.; Harriman, L.; Quenzer, R.; Impecoven, K.

2016-12-01

Three major obstacles facing big Earth data users include data storage, management, and analysis. As the amount of satellite remote sensing data increases, so does the need for better data storage and management strategies to exploit the plethora of data now available. Standard GIS tools can help big Earth data users whom interact with and analyze increasingly large and diverse datasets. In this presentation we highlight how NASA's Land Processes Distributed Active Archive Center (LP DAAC) is tackling these big Earth data challenges. We provide a real life use case example to describe three tools and services provided by the LP DAAC to more efficiently exploit big Earth data in a GIS environment. First, we describe the Open-source Project for a Network Data Access Protocol (OPeNDAP), which calls to specific data, minimizing the amount of data that a user downloads and improves the efficiency of data downloading and processing. Next, we cover the LP DAAC's Application for Extracting and Exploring Analysis Ready Samples (AppEEARS), a web application interface for extracting and analyzing land remote sensing data. From there, we review an ArcPython toolbox that was developed to provide quality control services to land remote sensing data products. Locating and extracting specific subsets of larger big Earth datasets improves data storage and management efficiency for the end user, and quality control services provides a straightforward interpretation of big Earth data. These tools and services are beneficial to the GIS user community in terms of standardizing workflows and improving data storage, management, and analysis tactics.

The International Space Station Supports International Polar Year (IPY)

NASA Technical Reports Server (NTRS)

Evans, Cynthia A.; Pettit, Donald R.

2007-01-01

Every day, ISS astronauts photograph designated sites and dynamic events on the Earth's surface using digital cameras equipped with a variety of lenses. Depending on observation parameters, astronauts can collect high resolution (4-6 m pixel size) or synoptic views (lower resolution but covering very large areas) digital data in 3 (red-green-blue) color bands. ISS crews have daily opportunities to document a variety of high-latitude phenomena. Although lighting conditions, ground track and other viewing parameters change with orbital precessions and season, the 51.6o orbital inclination and 400 km altitude of the ISS provide the crew an unique vantage point for collecting image-based data of polar phenomena, including surface observations to roughly 65o latitude, and upper atmospheric observations that reach nearly to the poles. During the 2007-2009 timeframe of the IPY, polar observations will become a scientific focus for the CEO experiment; the experiment is designated ISS-IPY. We solicit requests from scientists for observations from the ISS that are coordinated with or complement ground-based polar studies. The CEO imagery website for ISS-IPY provides an on-line form that allows IPY investigators to interact with CEO scientists and define their imagery requests. This information is integrated into daily communications with the ISS astronauts about their Earth Observations targets. All data collected are cataloged and posted on the website for downloading and assimilation into IPY projects. Examples of imagery and detailed information about scientific observations from the ISS can also be downloaded from the ISS-IPY web site.

Construction and completion of flux balance models from pathway databases.

PubMed

Latendresse, Mario; Krummenacker, Markus; Trupp, Miles; Karp, Peter D

2012-02-01

Flux balance analysis (FBA) is a well-known technique for genome-scale modeling of metabolic flux. Typically, an FBA formulation requires the accurate specification of four sets: biochemical reactions, biomass metabolites, nutrients and secreted metabolites. The development of FBA models can be time consuming and tedious because of the difficulty in assembling completely accurate descriptions of these sets, and in identifying errors in the composition of these sets. For example, the presence of a single non-producible metabolite in the biomass will make the entire model infeasible. Other difficulties in FBA modeling are that model distributions, and predicted fluxes, can be cryptic and difficult to understand. We present a multiple gap-filling method to accelerate the development of FBA models using a new tool, called MetaFlux, based on mixed integer linear programming (MILP). The method suggests corrections to the sets of reactions, biomass metabolites, nutrients and secretions. The method generates FBA models directly from Pathway/Genome Databases. Thus, FBA models developed in this framework are easily queried and visualized using the Pathway Tools software. Predicted fluxes are more easily comprehended by visualizing them on diagrams of individual metabolic pathways or of metabolic maps. MetaFlux can also remove redundant high-flux loops, solve FBA models once they are generated and model the effects of gene knockouts. MetaFlux has been validated through construction of FBA models for Escherichia coli and Homo sapiens. Pathway Tools with MetaFlux is freely available to academic users, and for a fee to commercial users. Download from: biocyc.org/download.shtml. mario.latendresse@sri.com Supplementary data are available at Bioinformatics online.

Development of Download System for Waveform Data Observed at Long-Term Borehole Monitoring System installed in the Nankai Trough

NASA Astrophysics Data System (ADS)

Tsuboi, Seiji; Horikawa, Hiroki; Takaesu, Morifumi; Sueki, Kentaro; Araki, Eiichiro; Sonoda, Akira; Takahashi, Narumi

2016-04-01

The Nankai Trough in southwest Japan is one of most active subduction zone in the world. Great mega-thrust earthquakes repeatedly occurred every 100 to 150 years in this area, it's anticipated to occur in the not distant future. For the purpose of elucidation of the history of mega-splay fault activity, the physical properties of the geological strata and the internal structure of the accretionary prism, and monitoring of diastrophism in this area, we have a plan, Nankai Trough Seismogenic Zone Experiments (NanTroSEIZE), as a part of Integrated Ocean Drilling Program (IODP). We have a plan to install the borehole observation system in a few locations by the NanTroSEIZE. This system is called Long-Term Borehole Monitoring System, it consists of various sensors in the borehole such as a broadband seismometer, a tiltmeter, a strainmeter, geophones and accelerometer, thermometer array as well as pressure ports for pore-fluid pressure monitoring. The signal from sensors is transmitted to DONET (Dense Ocean-floor Network System for Earthquake and Tsunamis) in real time. During IODP Exp. 332 in December 2010, the first Long-Term Borehole Monitoring System was installed into the C0002 borehole site located 80 km off the Kii Peninsula, 1938 m water depth in the Nankai Trough. We have developed a web application system for data download, Long-Term Borehole Monitoring Data Site. Based on a term and sensors which user selected on this site, user can download monitoring waveform data (e.g. broadband seismometer data, accelerometer data, strainmeter data, tiltmeter data) in near real-time. This system can make the arbitrary data which user selected a term and sensors, and download it simply. Downloadable continuous data is provided in seed format, which includes sensor informations. In addition, before data download, user can check that data is abailable or not by data check function. In this presentation, we show our web application system and discuss our future plans for developments of monitoring data download system.

Demonstrating the Open Data Repository's Data Publisher: The CheMin Database

NASA Astrophysics Data System (ADS)

Stone, N.; Lafuente, B.; Bristow, T.; Pires, A.; Keller, R. M.; Downs, R. T.; Blake, D.; Dateo, C. E.; Fonda, M.

2018-04-01

The Open Data Repository's Data Publisher aims to provide an easy-to-use software tool that will allow researchers to create and publish database templates and related data. The CheMin Database developed using this framework is shown as an example.

The National Informal STEM Education Network

Science.gov Websites

Evaluation and Research Kits Explore Science: Earth & Space toolkit Building with Biology Kit Explore 2018 toolkits now available for download. Download the 2018 Digital Toolkit! Building with Biology ACTIVITY KIT Building with Biology Conversations and activities about synthetic biology; this emerging

Correcting Inconsistencies and Errors in Bacterial Genome Metadata Using an Automated Curation Tool in Excel (AutoCurE).

PubMed

Schmedes, Sarah E; King, Jonathan L; Budowle, Bruce

2015-01-01

Whole-genome data are invaluable for large-scale comparative genomic studies. Current sequencing technologies have made it feasible to sequence entire bacterial genomes with relative ease and time with a substantially reduced cost per nucleotide, hence cost per genome. More than 3,000 bacterial genomes have been sequenced and are available at the finished status. Publically available genomes can be readily downloaded; however, there are challenges to verify the specific supporting data contained within the download and to identify errors and inconsistencies that may be present within the organizational data content and metadata. AutoCurE, an automated tool for bacterial genome database curation in Excel, was developed to facilitate local database curation of supporting data that accompany downloaded genomes from the National Center for Biotechnology Information. AutoCurE provides an automated approach to curate local genomic databases by flagging inconsistencies or errors by comparing the downloaded supporting data to the genome reports to verify genome name, RefSeq accession numbers, the presence of archaea, BioProject/UIDs, and sequence file descriptions. Flags are generated for nine metadata fields if there are inconsistencies between the downloaded genomes and genomes reports and if erroneous or missing data are evident. AutoCurE is an easy-to-use tool for local database curation for large-scale genome data prior to downstream analyses.

"Just-in-Time" Personal Preparedness: Downloads and Usage Patterns of the American Red Cross Hurricane Application During Hurricane Sandy.

PubMed

Kirsch, Thomas D; Circh, Ryan; Bissell, Richard A; Goldfeder, Matthew

2016-10-01

Personal preparedness is a core activity but has been found to be frequently inadequate. Smart phone applications have many uses for the public, including preparedness. In 2012 the American Red Cross began releasing "disaster" apps for family preparedness and recovery. The Hurricane App was widely used during Hurricane Sandy in 2012. Patterns of download of the application were analyzed by using a download tracking tool by the American Red Cross and Google Analytics. Specific variables included date, time, and location of individual downloads; number of page visits and views; and average time spent on pages. As Hurricane Sandy approached in late October, daily downloads peaked at 152,258 on the day of landfall and by mid-November reached 697,585. Total page views began increasing on October 25 with over 4,000,000 page views during landfall compared to 3.7 million the first 3 weeks of October with a 43,980% increase in views of the "Right Before" page and a 76,275% increase in views of the "During" page. The Hurricane App offered a new type of "just-in-time" training that reached tens of thousands of families in areas affected by Hurricane Sandy. The app allowed these families to access real-time information before and after the storm to help them prepare and recover. (Disaster Med Public Health Preparedness. 2016;page 1 of 6).

Current Status of Cardiovascular Disease-Related Smartphone Apps Downloadable in China.

PubMed

Xiao, Qian; Lu, Sai; Wang, Yanling; Sun, Liu; Wu, Ying

2017-03-01

Smartphone apps present a great opportunity for the management of cardiovascular disease (CVD) as the adoption of apps becomes increasingly popular in China. Yet, little is known about the status of CVD-related Smartphone apps in the country. The aim of this study was to examine the current status of CVD-related smartphone apps available for download in China. Using CVD-related keywords written either in Chinese or English, the top 6 most popular smartphone app online stores in China were searched in September 2015. The information accountability of the selected apps was assessed with the Silberg scale. The key topic areas identified from the European Guidelines on cardiovascular disease prevention served to determine information coverage of the top 5 downloaded apps. The average Silberg score of 151 apps was 2.87 (out of 9) with most apps not revealing authors' qualifications and information references. There was also a lack of sponsorship disclosure and information update. Moreover, none of the top 5 downloaded apps covered all key areas of CVD management as recommended by the European Guidelines on cardiovascular disease prevention. There was little evidence of health professionals' involvement in the formation of the CVD-related apps. This study identified areas for improvement concerning information accountability and the scope of coverage of CVD-related apps downloadable in China. The findings may guide the future advancement of CVD-related apps and benefit CVD management in China.

WILBER and PyWEED: Event-based Seismic Data Request Tools

NASA Astrophysics Data System (ADS)

Falco, N.; Clark, A.; Trabant, C. M.

2017-12-01

WILBER and PyWEED are two user-friendly tools for requesting event-oriented seismic data. Both tools provide interactive maps and other controls for browsing and filtering event and station catalogs, and downloading data for selected event/station combinations, where the data window for each event/station pair may be defined relative to the arrival time of seismic waves from the event to that particular station. Both tools allow data to be previewed visually, and can download data in standard miniSEED, SAC, and other formats, complete with relevant metadata for performing instrument correction. WILBER is a web application requiring only a modern web browser. Once the user has selected an event, WILBER identifies all data available for that time period, and allows the user to select stations based on criteria such as the station's distance and orientation relative to the event. When the user has finalized their request, the data is collected and packaged on the IRIS server, and when it is ready the user is sent a link to download. PyWEED is a downloadable, cross-platform (Macintosh / Windows / Linux) application written in Python. PyWEED allows a user to select multiple events and stations, and will download data for each event/station combination selected. PyWEED is built around the ObsPy seismic toolkit, and allows direct interaction and control of the application through a Python interactive console.

Taiwan Ascii and Idl_save Data Archives (AIDA) for THEMIS

NASA Astrophysics Data System (ADS)

Lee, B.; Hsieh, W.; Shue, J.; Angelopoulos, V.; Glassmeier, K. H.; McFadden, J. P.; Larson, D.

2008-12-01

THEMIS (Time History of Events and their Macroscopic Interactions during Substorms) is a satellite mission that aims to determine where and how substorms are triggered. The space research team in Taiwan has been involved in data promotion and scientific research. Taiwan Ascii and Idl_save Data Archives (AIDA) for THEMIS is the main work of the data promotion. Taiwan AIDA is developed for those who are not familiar with the Interactive Data Language (IDL) data analysis and visualization software, and those who have some basic IDL concepts and techniques and want more flexibilities in reading and plotting the THEMIS data. Two kinds of data format are stored in Taiwan AIDA: one is ASCII format for most users and the other is IDL SAVE format for IDL users. The public can download THEMIS data in either format through the Taiwan AIDA web site, http://themis.ss.ncu.edu.tw/e_data_download.php. Taiwan AIDA provides (1) plasma data including number density, average temperature, and velocity of ions and electrons, (2) magnetic field data, and (3) state information including the position and velocity of five THEMIS probes. On the Taiwan AIDA web site there are two data-downloading options. The public can download a large amount of data for a particular instrument in the FTP equivalent option; the public can also download all the data for a particular date in the Data Search option.

Augmented reality on poster presentations, in the field and in the classroom

NASA Astrophysics Data System (ADS)

Hawemann, Friedrich; Kolawole, Folarin

2017-04-01

Augmented reality (AR) is the direct addition of virtual information through an interface to a real-world environment. In practice, through a mobile device such as a tablet or smartphone, information can be projected onto a target- for example, an image on a poster. Mobile devices are widely distributed today such that augmented reality is easily accessible to almost everyone. Numerous studies have shown that multi-dimensional visualization is essential for efficient perception of the spatial, temporal and geometrical configuration of geological structures and processes. Print media, such as posters and handouts lack the ability to display content in the third and fourth dimensions, which might be in space-domain as seen in three-dimensional (3-D) objects, or time-domain (four-dimensional, 4-D) expressible in the form of videos. Here, we show that augmented reality content can be complimentary to geoscience poster presentations, hands-on material and in the field. In the latter example, location based data is loaded and for example, a virtual geological profile can be draped over a real-world landscape. In object based AR, the application is trained to recognize an image or object through the camera of the user's mobile device, such that specific content is automatically downloaded and displayed on the screen of the device, and positioned relative to the trained image or object. We used ZapWorks, a commercially-available software application to create and present examples of content that is poster-based, in which important supplementary information is presented as interactive virtual images, videos and 3-D models. We suggest that the flexibility and real-time interactivity offered by AR makes it an invaluable tool for effective geoscience poster presentation, class-room and field geoscience learning.

Sharing programming resources between Bio* projects through remote procedure call and native call stack strategies.

PubMed

Prins, Pjotr; Goto, Naohisa; Yates, Andrew; Gautier, Laurent; Willis, Scooter; Fields, Christopher; Katayama, Toshiaki

2012-01-01

Open-source software (OSS) encourages computer programmers to reuse software components written by others. In evolutionary bioinformatics, OSS comes in a broad range of programming languages, including C/C++, Perl, Python, Ruby, Java, and R. To avoid writing the same functionality multiple times for different languages, it is possible to share components by bridging computer languages and Bio* projects, such as BioPerl, Biopython, BioRuby, BioJava, and R/Bioconductor. In this chapter, we compare the two principal approaches for sharing software between different programming languages: either by remote procedure call (RPC) or by sharing a local call stack. RPC provides a language-independent protocol over a network interface; examples are RSOAP and Rserve. The local call stack provides a between-language mapping not over the network interface, but directly in computer memory; examples are R bindings, RPy, and languages sharing the Java Virtual Machine stack. This functionality provides strategies for sharing of software between Bio* projects, which can be exploited more often. Here, we present cross-language examples for sequence translation, and measure throughput of the different options. We compare calling into R through native R, RSOAP, Rserve, and RPy interfaces, with the performance of native BioPerl, Biopython, BioJava, and BioRuby implementations, and with call stack bindings to BioJava and the European Molecular Biology Open Software Suite. In general, call stack approaches outperform native Bio* implementations and these, in turn, outperform RPC-based approaches. To test and compare strategies, we provide a downloadable BioNode image with all examples, tools, and libraries included. The BioNode image can be run on VirtualBox-supported operating systems, including Windows, OSX, and Linux.

Quantifying App Store Dynamics: Longitudinal Tracking of Mental Health Apps

PubMed Central

Nicholas, Jennifer; Christensen, Helen

2016-01-01

Background For many mental health conditions, mobile health apps offer the ability to deliver information, support, and intervention outside the clinical setting. However, there are difficulties with the use of a commercial app store to distribute health care resources, including turnover of apps, irrelevance of apps, and discordance with evidence-based practice. Objective The primary aim of this study was to quantify the longevity and rate of turnover of mental health apps within the official Android and iOS app stores. The secondary aim was to quantify the proportion of apps that were clinically relevant and assess whether the longevity of these apps differed from clinically nonrelevant apps. The tertiary aim was to establish the proportion of clinically relevant apps that included claims of clinical effectiveness. We performed additional subgroup analyses using additional data from the app stores, including search result ranking, user ratings, and number of downloads. Methods We searched iTunes (iOS) and the Google Play (Android) app stores each day over a 9-month period for apps related to depression, bipolar disorder, and suicide. We performed additional app-specific searches if an app no longer appeared within the main search Results On the Android platform, 50% of the search results changed after 130 days (depression), 195 days (bipolar disorder), and 115 days (suicide). Search results were more stable on the iOS platform, with 50% of the search results remaining at the end of the study period. Approximately 75% of Android and 90% of iOS apps were still available to download at the end of the study. We identified only 35.3% (347/982) of apps as being clinically relevant for depression, of which 9 (2.6%) claimed clinical effectiveness. Only 3 included a full citation to a published study. Conclusions The mental health app environment is volatile, with a clinically relevant app for depression becoming unavailable to download every 2.9 days. This poses challenges for consumers and clinicians seeking relevant and long-term apps, as well as for researchers seeking to evaluate the evidence base for publicly available apps. PMID:27507641

Development and validation of MIX: comprehensive free software for meta-analysis of causal research data

PubMed Central

Bax, Leon; Yu, Ly-Mee; Ikeda, Noriaki; Tsuruta, Harukazu; Moons, Karel GM

2006-01-01

Background Meta-analysis has become a well-known method for synthesis of quantitative data from previously conducted research in applied health sciences. So far, meta-analysis has been particularly useful in evaluating and comparing therapies and in assessing causes of disease. Consequently, the number of software packages that can perform meta-analysis has increased over the years. Unfortunately, it can take a substantial amount of time to get acquainted with some of these programs and most contain little or no interactive educational material. We set out to create and validate an easy-to-use and comprehensive meta-analysis package that would be simple enough programming-wise to remain available as a free download. We specifically aimed at students and researchers who are new to meta-analysis, with important parts of the development oriented towards creating internal interactive tutoring tools and designing features that would facilitate usage of the software as a companion to existing books on meta-analysis. Results We took an unconventional approach and created a program that uses Excel as a calculation and programming platform. The main programming language was Visual Basic, as implemented in Visual Basic 6 and Visual Basic for Applications in Excel 2000 and higher. The development took approximately two years and resulted in the 'MIX' program, which can be downloaded from the program's website free of charge. Next, we set out to validate the MIX output with two major software packages as reference standards, namely STATA (metan, metabias, and metatrim) and Comprehensive Meta-Analysis Version 2. Eight meta-analyses that had been published in major journals were used as data sources. All numerical and graphical results from analyses with MIX were identical to their counterparts in STATA and CMA. The MIX program distinguishes itself from most other programs by the extensive graphical output, the click-and-go (Excel) interface, and the educational features. Conclusion The MIX program is a valid tool for performing meta-analysis and may be particularly useful in educational environments. It can be downloaded free of charge via or . PMID:17038197

Development and validation of MIX: comprehensive free software for meta-analysis of causal research data.

PubMed

Bax, Leon; Yu, Ly-Mee; Ikeda, Noriaki; Tsuruta, Harukazu; Moons, Karel G M

2006-10-13

Meta-analysis has become a well-known method for synthesis of quantitative data from previously conducted research in applied health sciences. So far, meta-analysis has been particularly useful in evaluating and comparing therapies and in assessing causes of disease. Consequently, the number of software packages that can perform meta-analysis has increased over the years. Unfortunately, it can take a substantial amount of time to get acquainted with some of these programs and most contain little or no interactive educational material. We set out to create and validate an easy-to-use and comprehensive meta-analysis package that would be simple enough programming-wise to remain available as a free download. We specifically aimed at students and researchers who are new to meta-analysis, with important parts of the development oriented towards creating internal interactive tutoring tools and designing features that would facilitate usage of the software as a companion to existing books on meta-analysis. We took an unconventional approach and created a program that uses Excel as a calculation and programming platform. The main programming language was Visual Basic, as implemented in Visual Basic 6 and Visual Basic for Applications in Excel 2000 and higher. The development took approximately two years and resulted in the 'MIX' program, which can be downloaded from the program's website free of charge. Next, we set out to validate the MIX output with two major software packages as reference standards, namely STATA (metan, metabias, and metatrim) and Comprehensive Meta-Analysis Version 2. Eight meta-analyses that had been published in major journals were used as data sources. All numerical and graphical results from analyses with MIX were identical to their counterparts in STATA and CMA. The MIX program distinguishes itself from most other programs by the extensive graphical output, the click-and-go (Excel) interface, and the educational features. The MIX program is a valid tool for performing meta-analysis and may be particularly useful in educational environments. It can be downloaded free of charge via http://www.mix-for-meta-analysis.info or http://sourceforge.net/projects/meta-analysis.

How Smart are Smartphone Apps for Smoking Cessation? A Content Analysis.

PubMed

Hoeppner, Bettina B; Hoeppner, Susanne S; Seaboyer, Lourah; Schick, Melissa R; Wu, Gwyneth W Y; Bergman, Brandon G; Kelly, John F

2016-05-01

Smartphone technology is ideally suited to provide tailored smoking cessation support, yet it is unclear to what extent currently existing smartphone "apps" use tailoring, and if tailoring is related to app popularity and user-rated quality. We conducted a content analysis of Android smoking cessation apps (n = 225), downloaded between October 1, 2013 to May 31, 2014. We recorded app popularity (>10,000 downloads) and user-rated quality (number of stars) from Google Play, and coded the existence of tailoring features in the apps within the context of using the 5As ("ask," "advise," "assess," "assist," and "arrange follow-up"), as recommended by national clinical practice guidelines. Apps largely provided simplistic tools (eg, calculators, trackers), and used tailoring sparingly: on average, apps addressed 2.1 ± 0.9 of the 5As and used tailoring for 0.7 ± 0.9 of the 5As. Tailoring was positively related to app popularity and user-rated quality: apps that used two-way interactions (odds ratio [OR] = 5.56 [2.45-12.62]), proactive alerts (OR = 3.80 [1.54-9.38]), responsiveness to quit status (OR = 5.28 [2.18-12.79]), addressed more of the 5As (OR = 1.53 [1.10-2.14]), used tailoring for more As (OR = 1.67 [1.21-2.30]), and/or used more ways of tailoring 5As content (OR = 1.35 [1.13-1.62]) were more likely to be frequently downloaded. Higher star ratings were associated with a higher number of 5As addressed (b = 0.16 [0.03-0.30]), a higher number of 5As with any level of tailoring (b = 0.14 [0.01-0.27]), and a higher number of ways of tailoring 5As content (b = 0.08 [0.002-0.15]). Publically available smartphone smoking cessation apps are not particularly "smart": they commonly fall short of providing tailored feedback, despite users' preference for these features. © The Author 2015. 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.

Onsite Systems - Wastewater

Science.gov Websites

can help. Call NESC toll free at (304) 293-4191. or e-mail info@mail.nesc.wvu.edu and ask for different situations. Onsite Technologies for Small Communities Poster - NESC provides free downloads to . Downloads are free. This poster is available to order, charges apply to hard copies only. Pipeline

DOE Research and Development Accomplishments Help

Science.gov Websites

be used to search, locate, access, and electronically download full-text research and development (R Browse Downloading, Viewing, and/or Searching Full-text Documents/Pages Searching the Database Search Features Search allows you to search the OCRed full-text document and bibliographic information, the

Teaching Ethical Copyright Behavior: Assessing the Effects of a University-Sponsored Computing Ethics Program

ERIC Educational Resources Information Center

Siemens, Jennifer Christie; Kopp, Steven W.

2006-01-01

Universities have become sensitized to the potential for students' illegal downloading of copyrighted materials. Education has been advocated as one way to curb downloading of copyrighted digital content. This study investigates the effectiveness of a university-sponsored computing ethics education program. The program positively influenced…

Medical Device Plug-and-Play Interoperability Standards and Technology Leadership

DTIC Science & Technology

2014-10-01

downloads/AboutFDA/CentersOffices/OfficeofMedicalProductsandTobacco/ CDRH /CDRHReports/UCM391521.pdf. Dr. Goldman spoke in multiple panels at this workshop...downloads/AboutFDA/CentersOffices/OfficeofMedicalProductsandTo bacco/ CDRH /CDRHReports/UCM391521.pdf  Arney D, Plourde J, Schrenker R, Mattegunta P

Behavior Change Techniques in Apps for Medication Adherence: A Content Analysis.

PubMed

Morrissey, Eimear C; Corbett, Teresa K; Walsh, Jane C; Molloy, Gerard J

2016-05-01

There are a vast number of smartphone applications (apps) aimed at promoting medication adherence on the market; however, the theory and evidence base in terms of applying established health behavior change techniques underpinning these apps remains unclear. This study aimed to code these apps using the Behavior Change Technique Taxonomy (v1) for the presence or absence of established behavior change techniques. The sample of apps was identified through systematic searches in both the Google Play Store and Apple App Store in February 2015. All apps that fell into the search categories were downloaded for analysis. The downloaded apps were screened with exclusion criteria, and suitable apps were reviewed and coded for behavior change techniques in March 2015. Two researchers performed coding independently. In total, 166 medication adherence apps were identified and coded. The number of behavior change techniques contained in an app ranged from zero to seven (mean=2.77). A total of 12 of a possible 96 behavior change techniques were found to be present across apps. The most commonly included behavior change techniques were "action planning" and "prompt/cues," which were included in 96% of apps, followed by "self-monitoring" (37%) and "feedback on behavior" (36%). The current extent to which established behavior change techniques are used in medication adherence apps is limited. The development of medication adherence apps may not have benefited from advances in the theory and practice of health behavior change. Copyright © 2016 American Journal of Preventive Medicine. Published by Elsevier Inc. All rights reserved.

Economic Recession and Obesity-Related Internet Search Behavior in Taiwan: Analysis of Google Trends Data.

PubMed

Wang, Ho-Wei; Chen, Duan-Rung

2018-04-06

Obesity is highly correlated with the development of chronic diseases and has become a critical public health issue that must be countered by aggressive action. This study determined whether data from Google Trends could provide insight into trends in obesity-related search behaviors in Taiwan. Using Google Trends, we examined how changes in economic conditions-using business cycle indicators as a proxy-were associated with people's internet search behaviors related to obesity awareness, health behaviors, and fast food restaurants. Monthly business cycle indicators were obtained from the Taiwan National Development Council. Weekly Taiwan Stock Exchange (TWSE) weighted index data were accessed and downloaded from Yahoo Finance. The weekly relative search volumes (RSV) of obesity-related terms were downloaded from Google Trends. RSVs of obesity-related terms and the TWSE from January 2007 to December 2011 (60 months) were analyzed using correlation analysis. During an economic recession, the RSV of obesity awareness and health behaviors declined (r=.441, P<.001; r=.593, P<.001, respectively); however, the RSV for fast food restaurants increased (r=-.437, P<.001). Findings indicated that when the economy was faltering, people tended to be less likely to search for information related to health behaviors and obesity awareness; moreover, they were more likely to search for fast food restaurants. Macroeconomic conditions can have an impact on people's health-related internet searches. ©Ho-Wei Wang, Duan-Rung Chen. Originally published in JMIR Public Health and Surveillance (http://publichealth.jmir.org), 06.04.2018.

7 CFR Exhibit C to Subpart B of... - Cooperative Agreement (Example)

Code of Federal Regulations, 2012 CFR

2012-01-01

... 7 Agriculture 14 2012-01-01 2012-01-01 false Cooperative Agreement (Example) C Exhibit C to... Pt. 1955, Subpt. B, Note Exhibit C to Subpart B of Part 1955—Cooperative Agreement (Example) Editorial Note: Exhibit C is not published in the Code of Federal Regulations. It is available in any FmHA...

7 CFR Exhibit C to Subpart B of... - Cooperative Agreement (Example)

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 14 2011-01-01 2011-01-01 false Cooperative Agreement (Example) C Exhibit C to... Pt. 1955, Subpt. B, Note Exhibit C to Subpart B of Part 1955—Cooperative Agreement (Example) Editorial Note: Exhibit C is not published in the Code of Federal Regulations. It is available in any FmHA...

7 CFR Exhibit C to Subpart B of... - Cooperative Agreement (Example)

Code of Federal Regulations, 2014 CFR

2014-01-01

... 7 Agriculture 14 2014-01-01 2014-01-01 false Cooperative Agreement (Example) C Exhibit C to... Pt. 1955, Subpt. B, Note Exhibit C to Subpart B of Part 1955—Cooperative Agreement (Example) Editorial Note: Exhibit C is not published in the Code of Federal Regulations. It is available in any FmHA...

Quality of reporting statistics in two Indian pharmacology journals.

PubMed

Jaykaran; Yadav, Preeti

2011-04-01

To evaluate the reporting of the statistical methods in articles published in two Indian pharmacology journals. All original articles published since 2002 were downloaded from the journals' (Indian Journal of Pharmacology (IJP) and Indian Journal of Physiology and Pharmacology (IJPP)) website. These articles were evaluated on the basis of appropriateness of descriptive statistics and inferential statistics. Descriptive statistics was evaluated on the basis of reporting of method of description and central tendencies. Inferential statistics was evaluated on the basis of fulfilling of assumption of statistical methods and appropriateness of statistical tests. Values are described as frequencies, percentage, and 95% confidence interval (CI) around the percentages. Inappropriate descriptive statistics was observed in 150 (78.1%, 95% CI 71.7-83.3%) articles. Most common reason for this inappropriate descriptive statistics was use of mean ± SEM at the place of "mean (SD)" or "mean ± SD." Most common statistical method used was one-way ANOVA (58.4%). Information regarding checking of assumption of statistical test was mentioned in only two articles. Inappropriate statistical test was observed in 61 (31.7%, 95% CI 25.6-38.6%) articles. Most common reason for inappropriate statistical test was the use of two group test for three or more groups. Articles published in two Indian pharmacology journals are not devoid of statistical errors.

Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV)

PubMed Central

Dempsey, Donald M; Hendrickson, Robert Curtis; Orton, Richard J; Siddell, Stuart G; Smith, Donald B

2018-01-01

Abstract The International Committee on Taxonomy of Viruses (ICTV) is charged with the task of developing, refining, and maintaining a universal virus taxonomy. This task encompasses the classification of virus species and higher-level taxa according to the genetic and biological properties of their members; naming virus taxa; maintaining a database detailing the currently approved taxonomy; and providing the database, supporting proposals, and other virus-related information from an open-access, public web site. The ICTV web site (http://ictv.global) provides access to the current taxonomy database in online and downloadable formats, and maintains a complete history of virus taxa back to the first release in 1971. The ICTV has also published the ICTV Report on Virus Taxonomy starting in 1971. This Report provides a comprehensive description of all virus taxa covering virus structure, genome structure, biology and phylogenetics. The ninth ICTV report, published in 2012, is available as an open-access online publication from the ICTV web site. The current, 10th report (http://ictv.global/report/), is being published online, and is replacing the previous hard-copy edition with a completely open access, continuously updated publication. No other database or resource exists that provides such a comprehensive, fully annotated compendium of information on virus taxa and taxonomy. PMID:29040670

MortalityPredictors.org: a manually-curated database of published biomarkers of human all-cause mortality

PubMed Central

Winslow, Ksenia; Ho, Andrew; Fortney, Kristen; Morgen, Eric

2017-01-01

Biomarkers of all-cause mortality are of tremendous clinical and research interest. Because of the long potential duration of prospective human lifespan studies, such biomarkers can play a key role in quantifying human aging and quickly evaluating any potential therapies. Decades of research into mortality biomarkers have resulted in numerous associations documented across hundreds of publications. Here, we present MortalityPredictors.org, a manually-curated, publicly accessible database, housing published, statistically-significant relationships between biomarkers and all-cause mortality in population-based or generally healthy samples. To gather the information for this database, we searched PubMed for appropriate research papers and then manually curated relevant data from each paper. We manually curated 1,576 biomarker associations, involving 471 distinct biomarkers. Biomarkers ranged in type from hematologic (red blood cell distribution width) to molecular (DNA methylation changes) to physical (grip strength). Via the web interface, the resulting data can be easily browsed, searched, and downloaded for further analysis. MortalityPredictors.org provides comprehensive results on published biomarkers of human all-cause mortality that can be used to compare biomarkers, facilitate meta-analysis, assist with the experimental design of aging studies, and serve as a central resource for analysis. We hope that it will facilitate future research into human mortality and aging. PMID:28858850

MortalityPredictors.org: a manually-curated database of published biomarkers of human all-cause mortality.

PubMed

Peto, Maximus V; De la Guardia, Carlos; Winslow, Ksenia; Ho, Andrew; Fortney, Kristen; Morgen, Eric

2017-08-31

Biomarkers of all-cause mortality are of tremendous clinical and research interest. Because of the long potential duration of prospective human lifespan studies, such biomarkers can play a key role in quantifying human aging and quickly evaluating any potential therapies. Decades of research into mortality biomarkers have resulted in numerous associations documented across hundreds of publications. Here, we present MortalityPredictors.org , a manually-curated, publicly accessible database, housing published, statistically-significant relationships between biomarkers and all-cause mortality in population-based or generally healthy samples. To gather the information for this database, we searched PubMed for appropriate research papers and then manually curated relevant data from each paper. We manually curated 1,576 biomarker associations, involving 471 distinct biomarkers. Biomarkers ranged in type from hematologic (red blood cell distribution width) to molecular (DNA methylation changes) to physical (grip strength). Via the web interface, the resulting data can be easily browsed, searched, and downloaded for further analysis. MortalityPredictors.org provides comprehensive results on published biomarkers of human all-cause mortality that can be used to compare biomarkers, facilitate meta-analysis, assist with the experimental design of aging studies, and serve as a central resource for analysis. We hope that it will facilitate future research into human mortality and aging.

minepath.org: a free interactive pathway analysis web server.

PubMed

Koumakis, Lefteris; Roussos, Panos; Potamias, George

2017-07-03

( www.minepath.org ) is a web-based platform that elaborates on, and radically extends the identification of differentially expressed sub-paths in molecular pathways. Besides the network topology, the underlying MinePath algorithmic processes exploit exact gene-gene molecular relationships (e.g. activation, inhibition) and are able to identify differentially expressed pathway parts. Each pathway is decomposed into all its constituent sub-paths, which in turn are matched with corresponding gene expression profiles. The highly ranked, and phenotype inclined sub-paths are kept. Apart from the pathway analysis algorithm, the fundamental innovation of the MinePath web-server concerns its advanced visualization and interactive capabilities. To our knowledge, this is the first pathway analysis server that introduces and offers visualization of the underlying and active pathway regulatory mechanisms instead of genes. Other features include live interaction, immediate visualization of functional sub-paths per phenotype and dynamic linked annotations for the engaged genes and molecular relations. The user can download not only the results but also the corresponding web viewer framework of the performed analysis. This feature provides the flexibility to immediately publish results without publishing source/expression data, and get all the functionality of a web based pathway analysis viewer. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Our words, our story: a textual analysis of articles published in the Bulletin of the Medical Library Association/Journal of the Medical Library Association from 1961 to 2010.

PubMed

Funk, Mark E

2013-01-01

This lecture explores changes in the medical library profession over the last fifty years, as revealed by individual word usage in a body of literature. I downloaded articles published in the Bulletin of the Medical Library Association and Journal of the Medical Library Association between 1961 and 2000 to create an electronic corpus and tracked annual frequency of individual word usage. I used frequency sparklines of words, matching one of four archetypal shapes (level, rise, fall, and rise-and-fall) to identify significant words. Most significant words fell into the categories of environment, management, technology, and research. Based on word usage changes, the following trends are revealed: Compared to 1961, today's medical librarians are more concerned with digital information, not physical packages. We prefer information to be evidence-based. We focus more on health than medicine. We are reaching out to new constituents, sometimes leaving our building to do so. Teaching has become important for us. We run our libraries more like businesses, using constantly changing technology. We are publishing more research articles. Although these words were chosen by individual authors to tell their particular stories, in the aggregate, our words reveal our story of change in our profession.

Sharing our data—An overview of current (2016) USGS policies and practices for publishing data on ScienceBase and an example interactive mapping application

USGS Publications Warehouse

Chase, Katherine J.; Bock, Andrew R.; Sando, Roy

2017-01-05

This report provides an overview of current (2016) U.S. Geological Survey policies and practices related to publishing data on ScienceBase, and an example interactive mapping application to display those data. ScienceBase is an integrated data sharing platform managed by the U.S. Geological Survey. This report describes resources that U.S. Geological Survey Scientists can use for writing data management plans, formatting data, and creating metadata, as well as for data and metadata review, uploading data and metadata to ScienceBase, and sharing metadata through the U.S. Geological Survey Science Data Catalog. Because data publishing policies and practices are evolving, scientists should consult the resources cited in this paper for definitive policy information.An example is provided where, using the content of a published ScienceBase data release that is associated with an interpretive product, a simple user interface is constructed to demonstrate how the open source capabilities of the R programming language and environment can interact with the properties and objects of the ScienceBase item and be used to generate interactive maps.

Scientometric analysis of published papers in global ophthalmology in the past ten years

PubMed Central

Yu, Zheng-Lu; Hu, Xin-Yue; Wang, Ying-Na; Ma, Zheng

2017-01-01

AIM To investigate the published papers of ophthalmology in past ten years and explore the development of ophthalmology. METHORDS The data of this study retrieved from Science Citation Index Expanded and downloaded online in November 2017, including all the papers with publication year from 2007-2016 were analyzed. The papers were based on the Web of Science category and the journals were based on the Journal Citation Report category. RESULTS The number of ophthalmology papers increased from 7450 to 9089 during 2007 to 2017. The average rate increased 2.2% annually. USA accounts for one thirds of the total and two thirds of the highly cited papers. In Asia, China, Japan and South Korea were in Top 10 by the number of ophthalmology papers. UK, Germany, Japan and Australia also had great impact in global ophthalmology. The hot spots included endothelial growth factor, optical coherence tomography and open-angle glaucoma. CONCLUSION USA is in the leading position in global ophthalmology. Part of Asian countries play an important role in the development of ophthalmology, but the impact needs to be improved. PMID:29259910

Scientometric analysis of published papers in global ophthalmology in the past ten years.

PubMed

Yu, Zheng-Lu; Hu, Xin-Yue; Wang, Ying-Na; Ma, Zheng

2017-01-01

To investigate the published papers of ophthalmology in past ten years and explore the development of ophthalmology. The data of this study retrieved from Science Citation Index Expanded and downloaded online in November 2017, including all the papers with publication year from 2007-2016 were analyzed. The papers were based on the Web of Science category and the journals were based on the Journal Citation Report category. The number of ophthalmology papers increased from 7450 to 9089 during 2007 to 2017. The average rate increased 2.2% annually. USA accounts for one thirds of the total and two thirds of the highly cited papers. In Asia, China, Japan and South Korea were in Top 10 by the number of ophthalmology papers. UK, Germany, Japan and Australia also had great impact in global ophthalmology. The hot spots included endothelial growth factor, optical coherence tomography and open-angle glaucoma. USA is in the leading position in global ophthalmology. Part of Asian countries play an important role in the development of ophthalmology, but the impact needs to be improved.

Sci-Hub provides access to nearly all scholarly literature

PubMed Central

Romero, Ariel Rodriguez; Levernier, Jacob G; Munro, Thomas Anthony; McLaughlin, Stephen Reid; Greshake Tzovaras, Bastian

2018-01-01

The website Sci-Hub enables users to download PDF versions of scholarly articles, including many articles that are paywalled at their journal’s site. Sci-Hub has grown rapidly since its creation in 2011, but the extent of its coverage has been unclear. Here we report that, as of March 2017, Sci-Hub’s database contains 68.9% of the 81.6 million scholarly articles registered with Crossref and 85.1% of articles published in toll access journals. We find that coverage varies by discipline and publisher, and that Sci-Hub preferentially covers popular, paywalled content. For toll access articles, we find that Sci-Hub provides greater coverage than the University of Pennsylvania, a major research university in the United States. Green open access to toll access articles via licit services, on the other hand, remains quite limited. Our interactive browser at https://greenelab.github.io/scihub allows users to explore these findings in more detail. For the first time, nearly all scholarly literature is available gratis to anyone with an Internet connection, suggesting the toll access business model may become unsustainable. PMID:29424689

Effects of the gay publishing boom on classes of titles retrieved under the subject headings "Homosexuality," "Gay Men," and "Gays" in the OCLC WorldCat database.

PubMed

Carmichael, James V

2002-01-01

What do searchers find when they look for literature on homosexuality? This question has profound implications for older as well as younger gays in their coming out, as well as in their subsequent identity development. Library records provide credible data to answer the question, since they represent relatively free sources of information, unlike data from bookstores, publishers, and some World Wide Web sites. The records of WorldCat, the world's largest union database of library records, comprise over 30 million records listed in the Online Computer Library Center. For the purposes of the study, 18,757 records listed under "Homosexuality," "Gay Men," and "Gays" were downloaded; records for "Lesbian" and "Lesbians" were not examined. Findings of the study suggest that while there has indeed been considerable growth in terms of the quantity of gay literature produced since 1969, such gains may be offset by the deteriorating quality of cataloging copy, which makes the experience of browsing records a discouraging and confusing one.

LED-based near infrared sensor for cancer diagnostics

NASA Astrophysics Data System (ADS)

Bogomolov, Andrey; Ageev, Vladimir; Zabarylo, Urszula; Usenov, Iskander; Schulte, Franziska; Kirsanov, Dmitry; Belikova, Valeria; Minet, Olaf; Feliksberger, E.; Meshkovsky, I.; Artyushenko, Viacheslav

2016-03-01

Optical spectroscopic technologies are increasingly used for cancer diagnostics. Feasibility of differentiation between malignant and healthy samples of human kidney using Fluorescence, Raman, MIR and NIR spectroscopy has been recently reported . In the present work, a simplification of NIR spectroscopy method has been studied. Traditional high-resolution NIR spectrometry was replaced by an optical sensor based on a set of light-emitting diodes at selected wavelengths as light sources and a photodiode. Two prototypes of the sensor have been developed and tested using 14 in-vitro samples of seven kidney tumor patients. Statistical evaluation of results using principal component analysis and partial least-squares discriminant analysis has been performed. Despite only partial discrimination between tumor and healthy tissue achieved by the presented new technique, the results evidence benefits of LED-based near-infrared sensing used for oncological diagnostics. Publisher's Note: This paper, originally published on 4 March, 2016, was replaced with a corrected/revised version on 7 April, 2016. If you downloaded the original PDF but are unable to access the revision, please contact SPIE Digital Library Customer Service for assistance.

Standard for the U.S. Geological Survey Historical Topographic Map Collection

USGS Publications Warehouse

Allord, Gregory J.; Fishburn, Kristin A.; Walter, Jennifer L.

2014-01-01

This document defines the digital map product of the U.S. Geological Survey (USGS) Historical Topographic Map Collection (HTMC). The HTMC is a digital archive of about 190,000 printed topographic quadrangle maps published by the USGS from the inception of the topographic mapping program in 1884 until the last paper topographic map using lithographic printing technology was published in 2006. The HTMC provides a comprehensive digital repository of all scales and all editions of USGS printed topographic maps that is easily discovered, browsed, and downloaded by the public at no cost. Each printed topographic map is scanned “as is” and captures the content and condition of each map. The HTMC provides ready access to maps that are no longer available for distribution in print. A new generation of topographic maps called “US Topo” was defined in 2009. US Topo maps, though modeled on the legacy 7.5-minute topographic maps, conform to different standards. For more information on the HTMC, see the project Web site at: http://nationalmap.gov/historical/.

SGDB: a database of synthetic genes re-designed for optimizing protein over-expression.

PubMed

Wu, Gang; Zheng, Yuanpu; Qureshi, Imran; Zin, Htar Thant; Beck, Tyler; Bulka, Blazej; Freeland, Stephen J

2007-01-01

Here we present the Synthetic Gene Database (SGDB): a relational database that houses sequences and associated experimental information on synthetic (artificially engineered) genes from all peer-reviewed studies published to date. At present, the database comprises information from more than 200 published experiments. This resource not only provides reference material to guide experimentalists in designing new genes that improve protein expression, but also offers a dataset for analysis by bioinformaticians who seek to test ideas regarding the underlying factors that influence gene expression. The SGDB was built under MySQL database management system. We also offer an XML schema for standardized data description of synthetic genes. Users can access the database at http://www.evolvingcode.net/codon/sgdb/index.php, or batch downloads all information through XML files. Moreover, users may visually compare the coding sequences of a synthetic gene and its natural counterpart with an integrated web tool at http://www.evolvingcode.net/codon/sgdb/aligner.php, and discuss questions, findings and related information on an associated e-forum at http://www.evolvingcode.net/forum/viewforum.php?f=27.

The Astrophysics Source Code Library: Supporting software publication and citation

NASA Astrophysics Data System (ADS)

Allen, Alice; Teuben, Peter

2018-01-01

The Astrophysics Source Code Library (ASCL, ascl.net), established in 1999, is a free online registry for source codes used in research that has appeared in, or been submitted to, peer-reviewed publications. The ASCL is indexed by the SAO/NASA Astrophysics Data System (ADS) and Web of Science and is citable by using the unique ascl ID assigned to each code. In addition to registering codes, the ASCL can house archive files for download and assign them DOIs. The ASCL advocations for software citation on par with article citation, participates in multidiscipinary events such as Force11, OpenCon, and the annual Workshop on Sustainable Software for Science, works with journal publishers, and organizes Special Sessions and Birds of a Feather meetings at national and international conferences such as Astronomical Data Analysis Software and Systems (ADASS), European Week of Astronomy and Space Science, and AAS meetings. In this presentation, I will discuss some of the challenges of gathering credit for publishing software and ideas and efforts from other disciplines that may be useful to astronomy.

There is a strong need for a single unified textbook even though education in disaster mitigation covers many fields

NASA Astrophysics Data System (ADS)

Sugimoto, M.; Song, Y.

2015-12-01

Areas of scientific specialties have been segmentalized nowadays. Each natural hazard are researched by scientific researchers. A huge variety of textbooks on one or few natural hazard are published by a single researcher in the world. There are possibilities are several natural disaster in one place. People have to learn from each hazard. However such disaster textbook is not unified education publish. Education in disaster mitigation covers many fields. There is a strong need for a single unified textbook. When I teach disaster education to children in kindergartens and schools, I understand students are confused by each different direction in such textbooks. "Doctor, which is right when a earthquake happens, cover my head or go out of a building? " I would like to discuss what the most valuable disaster textbook is as my following disatser handbook with audiences. This is publisehd for developping countries. You can freely download UNESCO disaster handbook following URL:http://www.icharm.pwri.go.jp/publication/pdf/handbook_on_local_disaster_management_experiences.pdf

Wing Download Results from a Test of a 0.658-Scale V-22 Rotor and Wing

NASA Technical Reports Server (NTRS)

Felker, Fort F.

1992-01-01

A test of a 0.658-scale V-22 rotor and wing was conducted in the 40 x 80 Foot Wind Tunnel at Ames Research Center. One of the principal objectives of the test was to measure the wing download in hover for a variety of test configurations. The wing download and surface pressures were measured for a wide range of thrust coefficients, with five different flap angles, two nacelle angles, and both directions or rotor rotation. This paper presents these results, and describes a new method for interpreting wing surface pressure data in hover. This method shows that the wing flap can produce substantial lift loads in hover.

The GLIMS Glacier Database

NASA Astrophysics Data System (ADS)

Raup, B. H.; Khalsa, S. S.; Armstrong, R.

2007-12-01

The Global Land Ice Measurements from Space (GLIMS) project has built a geospatial and temporal database of glacier data, composed of glacier outlines and various scalar attributes. These data are being derived primarily from satellite imagery, such as from ASTER and Landsat. Each "snapshot" of a glacier is from a specific time, and the database is designed to store multiple snapshots representative of different times. We have implemented two web-based interfaces to the database; one enables exploration of the data via interactive maps (web map server), while the other allows searches based on text-field constraints. The web map server is an Open Geospatial Consortium (OGC) compliant Web Map Server (WMS) and Web Feature Server (WFS). This means that other web sites can display glacier layers from our site over the Internet, or retrieve glacier features in vector format. All components of the system are implemented using Open Source software: Linux, PostgreSQL, PostGIS (geospatial extensions to the database), MapServer (WMS and WFS), and several supporting components such as Proj.4 (a geographic projection library) and PHP. These tools are robust and provide a flexible and powerful framework for web mapping applications. As a service to the GLIMS community, the database contains metadata on all ASTER imagery acquired over glacierized terrain. Reduced-resolution of the images (browse imagery) can be viewed either as a layer in the MapServer application, or overlaid on the virtual globe within Google Earth. The interactive map application allows the user to constrain by time what data appear on the map. For example, ASTER or glacier outlines from 2002 only, or from Autumn in any year, can be displayed. The system allows users to download their selected glacier data in a choice of formats. The results of a query based on spatial selection (using a mouse) or text-field constraints can be downloaded in any of these formats: ESRI shapefiles, KML (Google Earth), MapInfo, GML (Geography Markup Language) and GMT (Generic Mapping Tools). This "clip-and-ship" function allows users to download only the data they are interested in. Our flexible web interfaces to the database, which includes various support layers (e.g. a layer to help collaborators identify satellite imagery over their region of expertise) will facilitate enhanced analysis to be undertaken on glacier systems, their distribution, and their impacts on other Earth systems.

Integrating data from biological experiments into metabolic networks with the DBE information system.

PubMed

Borisjuk, Ljudmilla; Hajirezaei, Mohammad-Reza; Klukas, Christian; Rolletschek, Hardy; Schreiber, Falk

2005-01-01

Modern 'omics'-technologies result in huge amounts of data about life processes. For analysis and data mining purposes this data has to be considered in the context of the underlying biological networks. This work presents an approach for integrating data from biological experiments into metabolic networks by mapping the data onto network elements and visualising the data enriched networks automatically. This methodology is implemented in DBE, an information system that supports the analysis and visualisation of experimental data in the context of metabolic networks. It consists of five parts: (1) the DBE-Database for consistent data storage, (2) the Excel-Importer application for the data import, (3) the DBE-Website as the interface for the system, (4) the DBE-Pictures application for the up- and download of binary (e. g. image) files, and (5) DBE-Gravisto, a network analysis and graph visualisation system. The usability of this approach is demonstrated in two examples.

Cyclone: java-based querying and computing with Pathway/Genome databases.

PubMed

Le Fèvre, François; Smidtas, Serge; Schächter, Vincent

2007-05-15

Cyclone aims at facilitating the use of BioCyc, a collection of Pathway/Genome Databases (PGDBs). Cyclone provides a fully extensible Java Object API to analyze and visualize these data. Cyclone can read and write PGDBs, and can write its own data in the CycloneML format. This format is automatically generated from the BioCyc ontology by Cyclone itself, ensuring continued compatibility. Cyclone objects can also be stored in a relational database CycloneDB. Queries can be written in SQL, and in an intuitive and concise object-oriented query language, Hibernate Query Language (HQL). In addition, Cyclone interfaces easily with Java software including the Eclipse IDE for HQL edition, the Jung API for graph algorithms or Cytoscape for graph visualization. Cyclone is freely available under an open source license at: http://sourceforge.net/projects/nemo-cyclone. For download and installation instructions, tutorials, use cases and examples, see http://nemo-cyclone.sourceforge.net.

Molecular Rift: Virtual Reality for Drug Designers.

PubMed

Norrby, Magnus; Grebner, Christoph; Eriksson, Joakim; Boström, Jonas

2015-11-23

Recent advances in interaction design have created new ways to use computers. One example is the ability to create enhanced 3D environments that simulate physical presence in the real world--a virtual reality. This is relevant to drug discovery since molecular models are frequently used to obtain deeper understandings of, say, ligand-protein complexes. We have developed a tool (Molecular Rift), which creates a virtual reality environment steered with hand movements. Oculus Rift, a head-mounted display, is used to create the virtual settings. The program is controlled by gesture-recognition, using the gaming sensor MS Kinect v2, eliminating the need for standard input devices. The Open Babel toolkit was integrated to provide access to powerful cheminformatics functions. Molecular Rift was developed with a focus on usability, including iterative test-group evaluations. We conclude with reflections on virtual reality's future capabilities in chemistry and education. Molecular Rift is open source and can be downloaded from GitHub.

Integrative analysis of environmental sequences using MEGAN4.

PubMed

Huson, Daniel H; Mitra, Suparna; Ruscheweyh, Hans-Joachim; Weber, Nico; Schuster, Stephan C

2011-09-01

A major challenge in the analysis of environmental sequences is data integration. The question is how to analyze different types of data in a unified approach, addressing both the taxonomic and functional aspects. To facilitate such analyses, we have substantially extended MEGAN, a widely used taxonomic analysis program. The new program, MEGAN4, provides an integrated approach to the taxonomic and functional analysis of metagenomic, metatranscriptomic, metaproteomic, and rRNA data. While taxonomic analysis is performed based on the NCBI taxonomy, functional analysis is performed using the SEED classification of subsystems and functional roles or the KEGG classification of pathways and enzymes. A number of examples illustrate how such analyses can be performed, and show that one can also import and compare classification results obtained using others' tools. MEGAN4 is freely available for academic purposes, and installers for all three major operating systems can be downloaded from www-ab.informatik.uni-tuebingen.de/software/megan.

PROVAT: a tool for Voronoi tessellation analysis of protein structures and complexes.

PubMed

Gore, Swanand P; Burke, David F; Blundell, Tom L

2005-08-01

Voronoi tessellation has proved to be a useful tool in protein structure analysis. We have developed PROVAT, a versatile public domain software that enables computation and visualization of Voronoi tessellations of proteins and protein complexes. It is a set of Python scripts that integrate freely available specialized software (Qhull, Pymol etc.) into a pipeline. The calculation component of the tool computes Voronoi tessellation of a given protein system in a way described by a user-supplied XML recipe and stores resulting neighbourhood information as text files with various styles. The Python pickle file generated in the process is used by the visualization component, a Pymol plug-in, that offers a GUI to explore the tessellation visually. PROVAT source code can be downloaded from http://raven.bioc.cam.ac.uk/~swanand/Provat1, which also provides a webserver for its calculation component, documentation and examples.

Mining and Utilizing Dataset Relevancy from Oceanographic Dataset (MUDROD) Metadata, Usage Metrics, and User Feedback to Improve Data Discovery and Access

NASA Astrophysics Data System (ADS)

Jiang, Y.

2015-12-01

Oceanographic resource discovery is a critical step for developing ocean science applications. With the increasing number of resources available online, many Spatial Data Infrastructure (SDI) components (e.g. catalogues and portals) have been developed to help manage and discover oceanographic resources. However, efficient and accurate resource discovery is still a big challenge because of the lack of data relevancy information. In this article, we propose a search engine framework for mining and utilizing dataset relevancy from oceanographic dataset metadata, usage metrics, and user feedback. The objective is to improve discovery accuracy of oceanographic data and reduce time for scientist to discover, download and reformat data for their projects. Experiments and a search example show that the propose engine helps both scientists and general users search for more accurate results with enhanced performance and user experience through a user-friendly interface.

A critical note on the IAGA-endorsed Polar Cap (PC) indices: excessive excursions in the real-time index values

NASA Astrophysics Data System (ADS)

Stauning, Peter

2018-04-01

The Polar Cap (PC) indices were approved by the International Association for Geomagnetism and Aeronomy (IAGA) in 2013 and made available at the web portal http://pcindex.org holding prompt (real-time) as well as archival index values. The present note provides the first reported examination of the validity of the IAGA-endorsed method to generate real-time PC index values. It is demonstrated that features of the derivation procedure defined by Janzhura and Troshichev (2011) may cause considerable excursions in the real-time PC index values compared to the final index values. In examples based on occasional downloads of index values, the differences between real-time and final values of PC indices were found to exceed 3 mV m-1, which is a magnitude level that may indicate (or hide) strong magnetic storm activity.

RAIN: RNA–protein Association and Interaction Networks

PubMed Central

Junge, Alexander; Refsgaard, Jan C.; Garde, Christian; Pan, Xiaoyong; Santos, Alberto; Alkan, Ferhat; Anthon, Christian; von Mering, Christian; Workman, Christopher T.; Jensen, Lars Juhl; Gorodkin, Jan

2017-01-01

Protein association networks can be inferred from a range of resources including experimental data, literature mining and computational predictions. These types of evidence are emerging for non-coding RNAs (ncRNAs) as well. However, integration of ncRNAs into protein association networks is challenging due to data heterogeneity. Here, we present a database of ncRNA–RNA and ncRNA–protein interactions and its integration with the STRING database of protein–protein interactions. These ncRNA associations cover four organisms and have been established from curated examples, experimental data, interaction predictions and automatic literature mining. RAIN uses an integrative scoring scheme to assign a confidence score to each interaction. We demonstrate that RAIN outperforms the underlying microRNA-target predictions in inferring ncRNA interactions. RAIN can be operated through an easily accessible web interface and all interaction data can be downloaded. Database URL: http://rth.dk/resources/rain PMID:28077569

ChoiceKey: a real-time speech recognition program for psychology experiments with a small response set.

PubMed

Donkin, Christopher; Brown, Scott D; Heathcote, Andrew

2009-02-01

Psychological experiments often collect choice responses using buttonpresses. However, spoken responses are useful in many cases-for example, when working with special clinical populations, or when a paradigm demands vocalization, or when accurate response time measurements are desired. In these cases, spoken responses are typically collected using a voice key, which usually involves manual coding by experimenters in a tedious and error-prone manner. We describe ChoiceKey, an open-source speech recognition package for MATLAB. It can be optimized by training for small response sets and different speakers. We show ChoiceKey to be reliable with minimal training for most participants in experiments with two different responses. Problems presented by individual differences, and occasional atypical responses, are examined, and extensions to larger response sets are explored. The ChoiceKey source files and instructions may be downloaded as supplemental materials for this article from brm.psychonomic-journals.org/content/supplemental.

Sampling and counting genome rearrangement scenarios

PubMed Central

2015-01-01

Background Even for moderate size inputs, there are a tremendous number of optimal rearrangement scenarios, regardless what the model is and which specific question is to be answered. Therefore giving one optimal solution might be misleading and cannot be used for statistical inferring. Statistically well funded methods are necessary to sample uniformly from the solution space and then a small number of samples are sufficient for statistical inferring. Contribution In this paper, we give a mini-review about the state-of-the-art of sampling and counting rearrangement scenarios, focusing on the reversal, DCJ and SCJ models. Above that, we also give a Gibbs sampler for sampling most parsimonious labeling of evolutionary trees under the SCJ model. The method has been implemented and tested on real life data. The software package together with example data can be downloaded from http://www.renyi.hu/~miklosi/SCJ-Gibbs/ PMID:26452124

Teaching astronomy and astrophysics at the Valencian International University (VIU): Application and use of Virtual Observatory tools

NASA Astrophysics Data System (ADS)

Diago, P. D.; Gutiérrez-Soto, J.; Ruiz, J. E.; Solano, E.

2013-05-01

The Astronomy and Astrophysics Master, running at the Valencian International University (VIU, http://www.viu.es) since march 2010, is a clear example of how development of infor- mation and communication technologies (ICTs) and new e-learning methods are changing the traditional distance learning. In the context of the European Space for Higher Edu- cation (ESHE) we present how the Virtual Observatory (VO) tools can be an important part in the Astronomy and Astrophysics teaching. The described tasks has been carried out during the last three courses. These tasks are representative of the state of the art in Astrophysics research. We attach a description and a learning results list of each one of the presented tasks. The tasks can be downloaded at the Spanish VO website: http://svo.cab.inta-csic.es/docs/index.php?pagename=Education/VOcases

Detecting double compression of audio signal

NASA Astrophysics Data System (ADS)

Yang, Rui; Shi, Yun Q.; Huang, Jiwu

2010-01-01

MP3 is the most popular audio format nowadays in our daily life, for example music downloaded from the Internet and file saved in the digital recorder are often in MP3 format. However, low bitrate MP3s are often transcoded to high bitrate since high bitrate ones are of high commercial value. Also audio recording in digital recorder can be doctored easily by pervasive audio editing software. This paper presents two methods for the detection of double MP3 compression. The methods are essential for finding out fake-quality MP3 and audio forensics. The proposed methods use support vector machine classifiers with feature vectors formed by the distributions of the first digits of the quantized MDCT (modified discrete cosine transform) coefficients. Extensive experiments demonstrate the effectiveness of the proposed methods. To the best of our knowledge, this piece of work is the first one to detect double compression of audio signal.

Automated ocean color product validation for the Southern California Bight

NASA Astrophysics Data System (ADS)

Davis, Curtiss O.; Tufillaro, Nicholas; Jones, Burt; Arnone, Robert

2012-06-01

Automated match ups allow us to maintain and improve the products of current satellite ocean color sensors (MODIS, MERIS), and new sensors (VIIRS). As part of the VIIRS mission preparation, we have created a web based automated match up tool that provides access to searchable fields for date, site, and products, and creates match-ups between satellite (MODIS, MERIS, VIIRS), and in-situ measurements (HyperPRO and SeaPRISM). The back end of the system is a 'mySQL' database, and the front end is a `php' web portal with pull down menus for searchable fields. Based on selections, graphics are generated showing match-ups and statistics, and ascii files are created for downloads for the matchup data. Examples are shown for matching the satellite data with the data from Platform Eureka SeaPRISM off L.A. Harbor in the Southern California Bight.

Markov Chain Monte Carlo Methods for Bayesian Data Analysis in Astronomy

NASA Astrophysics Data System (ADS)

Sharma, Sanjib

2017-08-01

Markov Chain Monte Carlo based Bayesian data analysis has now become the method of choice for analyzing and interpreting data in almost all disciplines of science. In astronomy, over the last decade, we have also seen a steady increase in the number of papers that employ Monte Carlo based Bayesian analysis. New, efficient Monte Carlo based methods are continuously being developed and explored. In this review, we first explain the basics of Bayesian theory and discuss how to set up data analysis problems within this framework. Next, we provide an overview of various Monte Carlo based methods for performing Bayesian data analysis. Finally, we discuss advanced ideas that enable us to tackle complex problems and thus hold great promise for the future. We also distribute downloadable computer software (available at https://github.com/sanjibs/bmcmc/ ) that implements some of the algorithms and examples discussed here.

I Tune, You Tube, We Rule

NASA Astrophysics Data System (ADS)

Shida, R. Y.; Gater, W.

2007-10-01

The website YouTube was created in 2005 and has rapidly become one of the most popular entertainment websites on the internet. It is riding the online video wave today like few other online companies and is currently more popular than the video sections of either Yahoo or Google. iTunes, a digital media application created by Apple in 2001, where one can download and play music and videos, has had a similar success. There is little doubt that they both represent important communication channels in a world heavily influenced by online media, especially among teenagers and young adults. As science communicators we can use this direct route to a younger audience to our advantage. This article aims to give a taste of these applications with a few selected examples demonstrating that both YouTube and iTunes are excellent tools to teach and inspire the general public.

GRN2SBML: automated encoding and annotation of inferred gene regulatory networks complying with SBML.

PubMed

Vlaic, Sebastian; Hoffmann, Bianca; Kupfer, Peter; Weber, Michael; Dräger, Andreas

2013-09-01

GRN2SBML automatically encodes gene regulatory networks derived from several inference tools in systems biology markup language. Providing a graphical user interface, the networks can be annotated via the simple object access protocol (SOAP)-based application programming interface of BioMart Central Portal and minimum information required in the annotation of models registry. Additionally, we provide an R-package, which processes the output of supported inference algorithms and automatically passes all required parameters to GRN2SBML. Therefore, GRN2SBML closes a gap in the processing pipeline between the inference of gene regulatory networks and their subsequent analysis, visualization and storage. GRN2SBML is freely available under the GNU Public License version 3 and can be downloaded from http://www.hki-jena.de/index.php/0/2/490. General information on GRN2SBML, examples and tutorials are available at the tool's web page.

Method and apparatus for detecting and determining event characteristics with reduced data collection

NASA Technical Reports Server (NTRS)

Totman, Peter D. (Inventor); Everton, Randy L. (Inventor); Egget, Mark R. (Inventor); Macon, David J. (Inventor)

2007-01-01

A method and apparatus for detecting and determining event characteristics such as, for example, the material failure of a component, in a manner which significantly reduces the amount of data collected. A sensor array, including a plurality of individual sensor elements, is coupled to a programmable logic device (PLD) configured to operate in a passive state and an active state. A triggering event is established such that the PLD records information only upon detection of the occurrence of the triggering event which causes a change in state within one or more of the plurality of sensor elements. Upon the occurrence of the triggering event, the change in state of the one or more sensor elements causes the PLD to record in memory which sensor element detected the event and at what time the event was detected. The PLD may be coupled with a computer for subsequent downloading and analysis of the acquired data.

18 CFR 284.13 - Reporting requirements for interstate pipelines.

Code of Federal Regulations, 2011 CFR

2011-04-01

... following information on its Internet web site, and provide the information in downloadable file formats, in... index of customers must also posted on the pipeline's Internet web, in accordance with standards adopted in § 284.12 of this part, and made available from the Internet web site in a downloadable format...

18 CFR 284.13 - Reporting requirements for interstate pipelines.

Code of Federal Regulations, 2014 CFR

2014-04-01

... following information on its Internet web site, and provide the information in downloadable file formats, in... index of customers must also posted on the pipeline's Internet web, in accordance with standards adopted in § 284.12 of this part, and made available from the Internet web site in a downloadable format...

18 CFR 284.13 - Reporting requirements for interstate pipelines.

Code of Federal Regulations, 2013 CFR

2013-04-01

... following information on its Internet web site, and provide the information in downloadable file formats, in... index of customers must also posted on the pipeline's Internet web, in accordance with standards adopted in § 284.12 of this part, and made available from the Internet web site in a downloadable format...

18 CFR 284.13 - Reporting requirements for interstate pipelines.

Code of Federal Regulations, 2012 CFR

2012-04-01

... following information on its Internet web site, and provide the information in downloadable file formats, in... index of customers must also posted on the pipeline's Internet web, in accordance with standards adopted in § 284.12 of this part, and made available from the Internet web site in a downloadable format...

18 CFR 284.13 - Reporting requirements for interstate pipelines.

Code of Federal Regulations, 2010 CFR

2010-04-01

... following information on its Internet web site, and provide the information in downloadable file formats, in... index of customers must also posted on the pipeline's Internet web, in accordance with standards adopted in § 284.12 of this part, and made available from the Internet web site in a downloadable format...

18 CFR 37.7 - Auditing Transmission Service Information.

Code of Federal Regulations, 2011 CFR

2011-04-01

... COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE FEDERAL POWER ACT OPEN ACCESS SAME-TIME INFORMATION... time stamped. (b) Audit data must remain available for download on the OASIS for 90 days, except ATC/TTC postings that must remain available for download on the OASIS for 20 days. The audit data are to...

18 CFR 37.7 - Auditing Transmission Service Information.

Code of Federal Regulations, 2010 CFR

2010-04-01

... COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE FEDERAL POWER ACT OPEN ACCESS SAME-TIME INFORMATION... time stamped. (b) Audit data must remain available for download on the OASIS for 90 days, except ATC/TTC postings that must remain available for download on the OASIS for 20 days. The audit data are to...

Chapter 10: Enclosure--Building enclosure design for cross-laminated timber construction

Treesearch

Samuel V. Glass; Jieying Wang; Steve Easley; Graham Finch

2013-01-01

 Note: Clicking on the \\'View\\' option to download the PDF copy of the publication will redirect you to the web site www.masstimber.com where you will need to register prior to downloading.Cross-laminated timber #CLT# was developed in Europe for the prefabricated construction of wall, roof, and...

18 CFR 37.7 - Auditing Transmission Service Information.

Code of Federal Regulations, 2012 CFR

2012-04-01

... COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE FEDERAL POWER ACT OPEN ACCESS SAME-TIME INFORMATION... time stamped. (b) Audit data must remain available for download on the OASIS for 90 days, except ATC/TTC postings that must remain available for download on the OASIS for 20 days. The audit data are to...

18 CFR 37.7 - Auditing Transmission Service Information.

Code of Federal Regulations, 2014 CFR

2014-04-01

... COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE FEDERAL POWER ACT OPEN ACCESS SAME-TIME INFORMATION... time stamped. (b) Audit data must remain available for download on the OASIS for 90 days, except ATC/TTC postings that must remain available for download on the OASIS for 20 days. The audit data are to...

18 CFR 37.7 - Auditing Transmission Service Information.

Code of Federal Regulations, 2013 CFR

2013-04-01

... COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE FEDERAL POWER ACT OPEN ACCESS SAME-TIME INFORMATION... time stamped. (b) Audit data must remain available for download on the OASIS for 90 days, except ATC/TTC postings that must remain available for download on the OASIS for 20 days. The audit data are to...

Alternative Fuels Data Center: Maps and Data

Science.gov Websites

Fuel Standard Volumes by Year Generated_thumb20150904-8240-13hgnxh Last update August 2012 View Graph product or destination Last update August 2015 View Graph Graph Download Data Custom_thumb U.S. Ethanol , from 1866-2014 Last update August 2015 View Graph Graph Download Data Generated_thumb20160920-21993