Tweeting it off: characteristics of adults who tweet about a weight loss attempt

PubMed Central

Pagoto, Sherry; Schneider, Kristin L; Evans, Martinus; Waring, Molly E; Appelhans, Brad; Busch, Andrew M; Whited, Matthew C; Thind, Herpreet; Ziedonis, Michelle

2014-01-01

Objective The purpose of this study was to describe adults who use Twitter during a weight loss attempt and to compare the positive and negative social influences they experience from their offline friends, online friends, and family members. Materials and methods Participants (N=100, 80% female, mean age=37.65, SD=8.42) were recruited from Twitter. They completed a brief survey about their experiences discussing their weight loss attempt with their online and offline friends and provided responses to open-ended questions on the benefits and drawbacks of discussing weight on Twitter, Facebook, and weight-specific social networks. Results Participants rated their connections on Twitter and weight loss-specific social networks to be significantly greater sources of positive social influence for their weight loss (F(3)=3.47; p<0.001) and significantly lesser sources of negative social influence (F(3)=40.39 and F(3)=33.68 (both p<0.001)) than their offline friends, family, and Facebook friends. Greater positive social influence from Twitter and Facebook friends was associated with greater weight loss in participants’ most recent weight loss attempt (r=0.30, r=0.32; p<0.01). The most commonly reported benefits of tweeting about weight loss include social support, information, and accountability. The most common drawbacks reported are that interactions were too brief and lacked personal connection. Discussion People who discuss their weight loss on Twitter report more social support and less negativity from their Twitter friends than their Facebook friends and in-person relationships. Conclusions Online social networks should be explored as a tool for connecting patients who lack weight loss social support from their in-person relationships. PMID:24928175

pyLIMA : The first open source microlensing modeling software

NASA Astrophysics Data System (ADS)

Bachelet, Etienne; Street, Rachel; Bozza, Valerio

2018-01-01

Microlensing is highly sensitive to planets beyond the snowline and distributed along the line of sight towards the Galactic Bulge. The WFIRST-AFTA mission should detect about 3000 of these planets and significantly improves our knowledge of planet formation and statistics, complementing results found by transit and radial velocity methods. However, the modeling of microlensing event is challenging on different aspects leading to a highly time consuming analysis. After a quick summarize of these different challenges, I will present pyLIMA, the first open source microlensing modeling software. The aimed goal of this software are to be flexible, powerful and user friendly. This presentation will focus on various case and early results.

MyMolDB: a micromolecular database solution with open source and free components.

PubMed

Xia, Bing; Tai, Zheng-Fu; Gu, Yu-Cheng; Li, Bang-Jing; Ding, Li-Sheng; Zhou, Yan

2011-10-01

To manage chemical structures in small laboratories is one of the important daily tasks. Few solutions are available on the internet, and most of them are closed source applications. The open-source applications typically have limited capability and basic cheminformatics functionalities. In this article, we describe an open-source solution to manage chemicals in research groups based on open source and free components. It has a user-friendly interface with the functions of chemical handling and intensive searching. MyMolDB is a micromolecular database solution that supports exact, substructure, similarity, and combined searching. This solution is mainly implemented using scripting language Python with a web-based interface for compound management and searching. Almost all the searches are in essence done with pure SQL on the database by using the high performance of the database engine. Thus, impressive searching speed has been archived in large data sets for no external Central Processing Unit (CPU) consuming languages were involved in the key procedure of the searching. MyMolDB is an open-source software and can be modified and/or redistributed under GNU General Public License version 3 published by the Free Software Foundation (Free Software Foundation Inc. The GNU General Public License, Version 3, 2007. Available at: http://www.gnu.org/licenses/gpl.html). The software itself can be found at http://code.google.com/p/mymoldb/. Copyright © 2011 Wiley Periodicals, Inc.

Assessment of Vision-Based Target Detection and Classification Solutions Using an Indoor Aerial Robot

DTIC Science & Technology

2014-09-01

college student alongside you, little sis! To Jes- xix sika Miller, Lauren Garcia and Caity White , my closest friends and confidants of ten years, who...arena corresponding coverage to the GUI is outlined in white 2.1.3 Challenges in the Model There are inherent challenges with any model that implements...source middleware originally maintained by Willow Garage [36] and now managed by the Open Source Robotics Foundation [37]. It provides a framework for

BioImageXD: an open, general-purpose and high-throughput image-processing platform.

PubMed

Kankaanpää, Pasi; Paavolainen, Lassi; Tiitta, Silja; Karjalainen, Mikko; Päivärinne, Joacim; Nieminen, Jonna; Marjomäki, Varpu; Heino, Jyrki; White, Daniel J

2012-06-28

BioImageXD puts open-source computer science tools for three-dimensional visualization and analysis into the hands of all researchers, through a user-friendly graphical interface tuned to the needs of biologists. BioImageXD has no restrictive licenses or undisclosed algorithms and enables publication of precise, reproducible and modifiable workflows. It allows simple construction of processing pipelines and should enable biologists to perform challenging analyses of complex processes. We demonstrate its performance in a study of integrin clustering in response to selected inhibitors.

Efficient radiologic reading environment by using an open-source macro program as connection software.

PubMed

Lee, Young Han

2012-01-01

The objectives are (1) to introduce an easy open-source macro program as connection software and (2) to illustrate the practical usages in radiologic reading environment by simulating the radiologic reading process. The simulation is a set of radiologic reading process to do a practical task in the radiologic reading room. The principal processes are: (1) to view radiologic images on the Picture Archiving and Communicating System (PACS), (2) to connect the HIS/EMR (Hospital Information System/Electronic Medical Record) system, (3) to make an automatic radiologic reporting system, and (4) to record and recall information of interesting cases. This simulation environment was designed by using open-source macro program as connection software. The simulation performed well on the Window-based PACS workstation. Radiologists practiced the steps of the simulation comfortably by utilizing the macro-powered radiologic environment. This macro program could automate several manual cumbersome steps in the radiologic reading process. This program successfully acts as connection software for the PACS software, EMR/HIS, spreadsheet, and other various input devices in the radiologic reading environment. A user-friendly efficient radiologic reading environment could be established by utilizing open-source macro program as connection software. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

WriteSim TCExam - An open source text simulation environment for training novice researchers in scientific writing

PubMed Central

2010-01-01

Background The ability to write clearly and effectively is of central importance to the scientific enterprise. Encouraged by the success of simulation environments in other biomedical sciences, we developed WriteSim TCExam, an open-source, Web-based, textual simulation environment for teaching effective writing techniques to novice researchers. We shortlisted and modified an existing open source application - TCExam to serve as a textual simulation environment. After testing usability internally in our team, we conducted formal field usability studies with novice researchers. These were followed by formal surveys with researchers fitting the role of administrators and users (novice researchers) Results The development process was guided by feedback from usability tests within our research team. Online surveys and formal studies, involving members of the Research on Research group and selected novice researchers, show that the application is user-friendly. Additionally it has been used to train 25 novice researchers in scientific writing to date and has generated encouraging results. Conclusion WriteSim TCExam is the first Web-based, open-source textual simulation environment designed to complement traditional scientific writing instruction. While initial reviews by students and educators have been positive, a formal study is needed to measure its benefits in comparison to standard instructional methods. PMID:20509946

SNPConvert: SNP Array Standardization and Integration in Livestock Species.

PubMed

Nicolazzi, Ezequiel Luis; Marras, Gabriele; Stella, Alessandra

2016-06-09

One of the main advantages of single nucleotide polymorphism (SNP) array technology is providing genotype calls for a specific number of SNP markers at a relatively low cost. Since its first application in animal genetics, the number of available SNP arrays for each species has been constantly increasing. However, conversely to that observed in whole genome sequence data analysis, SNP array data does not have a common set of file formats or coding conventions for allele calling. Therefore, the standardization and integration of SNP array data from multiple sources have become an obstacle, especially for users with basic or no programming skills. Here, we describe the difficulties related to handling SNP array data, focusing on file formats, SNP allele coding, and mapping. We also present SNPConvert suite, a multi-platform, open-source, and user-friendly set of tools to overcome these issues. This tool, which can be integrated with open-source and open-access tools already available, is a first step towards an integrated system to standardize and integrate any type of raw SNP array data. The tool is available at: https://github. com/nicolazzie/SNPConvert.git.

Design and implementation of an open source indexing solution for a large set of radiological reports and images.

PubMed

Voet, T; Devolder, P; Pynoo, B; Vercruysse, J; Duyck, P

2007-11-01

This paper hopes to share the insights we experienced during designing, building, and running an indexing solution for a large set of radiological reports and images in a production environment for more than 3 years. Several technical challenges were encountered and solved in the course of this project. One hundred four million words in 1.8 million radiological reports from 1989 to the present were indexed and became instantaneously searchable in a user-friendly fashion; the median query duration is only 31 ms. Currently, our highly tuned index holds 332,088 unique words in four languages. The indexing system is feature-rich and language-independent and allows for making complex queries. For research and training purposes it certainly is a valuable and convenient addition to our radiology informatics toolbox. Extended use of open-source technology dramatically reduced both implementation time and cost. All software we developed related to the indexing project has been made available to the open-source community covered by an unrestricted Berkeley Software Distribution-style license.

Genetic and environmental sources of individual religiousness: the roles of individual personality traits and perceived environmental religiousness.

PubMed

Kandler, Christian; Riemann, Rainer

2013-07-01

In the current study, we examined the genetic and environmental sources of the links between individual religiousness and individual personality traits, perceived parental religiousness, and perceived peer religiousness. Data from 870 individuals (incl. 394 twin pairs) were analyzed. Variance in individual religiousness was significantly influenced by genetic effects, environmental influences shared by twins reared together, and individual-specific environmental influences. Individual religiousness showed significant associations with age, sex, specific personality traits (e.g., agreeableness, openness to values), and perceived religiousness of important social interaction partners, such as parents, best friends, and spouses. The links to personality traits were relatively small and primarily genetically mediated. The associations between individual religiousness and parental religiousness were substantial and mediated by shared environmental effects. These links significantly decreased across age accompanying a significant decrease of shared environmental influences on individual religiousness. The correlations between individual religiousness and perceived religiousness of spouses and best friends were relatively moderate but increased with age. These associations were mediated by genetic as well as nonshared environmental sources accompanying an increase of nonshared environmental influences on individual religiousness with age. The results suggest that inter-individual differences in religiousness are due to multiple sources.

Closed Loop Experiment Manager (CLEM)-An Open and Inexpensive Solution for Multichannel Electrophysiological Recordings and Closed Loop Experiments.

PubMed

Hazan, Hananel; Ziv, Noam E

2017-01-01

There is growing need for multichannel electrophysiological systems that record from and interact with neuronal systems in near real-time. Such systems are needed, for example, for closed loop, multichannel electrophysiological/optogenetic experimentation in vivo and in a variety of other neuronal preparations, or for developing and testing neuro-prosthetic devices, to name a few. Furthermore, there is a need for such systems to be inexpensive, reliable, user friendly, easy to set-up, open and expandable, and possess long life cycles in face of rapidly changing computing environments. Finally, they should provide powerful, yet reasonably easy to implement facilities for developing closed-loop protocols for interacting with neuronal systems. Here, we survey commercial and open source systems that address these needs to varying degrees. We then present our own solution, which we refer to as Closed Loop Experiments Manager (CLEM). CLEM is an open source, soft real-time, Microsoft Windows desktop application that is based on a single generic personal computer (PC) and an inexpensive, general-purpose data acquisition board. CLEM provides a fully functional, user-friendly graphical interface, possesses facilities for recording, presenting and logging electrophysiological data from up to 64 analog channels, and facilities for controlling external devices, such as stimulators, through digital and analog interfaces. Importantly, it includes facilities for running closed-loop protocols written in any programming language that can generate dynamic link libraries (DLLs). We describe the application, its architecture and facilities. We then demonstrate, using networks of cortical neurons growing on multielectrode arrays (MEA) that despite its reliance on generic hardware, its performance is appropriate for flexible, closed-loop experimentation at the neuronal network level.

Closed Loop Experiment Manager (CLEM)—An Open and Inexpensive Solution for Multichannel Electrophysiological Recordings and Closed Loop Experiments

PubMed Central

Hazan, Hananel; Ziv, Noam E.

2017-01-01

There is growing need for multichannel electrophysiological systems that record from and interact with neuronal systems in near real-time. Such systems are needed, for example, for closed loop, multichannel electrophysiological/optogenetic experimentation in vivo and in a variety of other neuronal preparations, or for developing and testing neuro-prosthetic devices, to name a few. Furthermore, there is a need for such systems to be inexpensive, reliable, user friendly, easy to set-up, open and expandable, and possess long life cycles in face of rapidly changing computing environments. Finally, they should provide powerful, yet reasonably easy to implement facilities for developing closed-loop protocols for interacting with neuronal systems. Here, we survey commercial and open source systems that address these needs to varying degrees. We then present our own solution, which we refer to as Closed Loop Experiments Manager (CLEM). CLEM is an open source, soft real-time, Microsoft Windows desktop application that is based on a single generic personal computer (PC) and an inexpensive, general-purpose data acquisition board. CLEM provides a fully functional, user-friendly graphical interface, possesses facilities for recording, presenting and logging electrophysiological data from up to 64 analog channels, and facilities for controlling external devices, such as stimulators, through digital and analog interfaces. Importantly, it includes facilities for running closed-loop protocols written in any programming language that can generate dynamic link libraries (DLLs). We describe the application, its architecture and facilities. We then demonstrate, using networks of cortical neurons growing on multielectrode arrays (MEA) that despite its reliance on generic hardware, its performance is appropriate for flexible, closed-loop experimentation at the neuronal network level. PMID:29093659

Sharing Lessons-Learned on Effective Open Data, Open-Source Practices from OpenAQ, a Global Open Air Quality Community.

NASA Astrophysics Data System (ADS)

Hasenkopf, C. A.

2017-12-01

Increasingly, open data, open-source projects are unearthing rich datasets and tools, previously impossible for more traditional avenues to generate. These projects are possible, in part, because of the emergence of online collaborative and code-sharing tools, decreasing costs of cloud-based services to fetch, store, and serve data, and increasing interest of individuals to contribute their time and skills to 'open projects.' While such projects have generated palpable enthusiasm from many sectors, many of these projects face uncharted paths for sustainability, visibility, and acceptance. Our project, OpenAQ, is an example of an open-source, open data community that is currently forging its own uncharted path. OpenAQ is an open air quality data platform that aggregates and universally formats government and research-grade air quality data from 50 countries across the world. To date, we make available more than 76 million air quality (PM2.5, PM10, SO2, NO2, O3, CO and black carbon) data points through an open Application Programming Interface (API) and a user-customizable download interface at https://openaq.org. The goal of the platform is to enable an ecosystem of users to advance air pollution efforts from science to policy to the private sector. The platform is also an open-source project (https://github.com/openaq) and has only been made possible through the coding and data contributions of individuals around the world. In our first two years of existence, we have seen requests for data to our API skyrocket to more than 6 million datapoints per month, and use-cases as varied as ingesting data aggregated from our system into real-time models of wildfires to building open-source statistical packages (e.g. ropenaq and py-openaq) on top of the platform to creating public-friendly apps and chatbots. We will share a whirl-wind trip through our evolution and the many lessons learned so far related to platform structure, community engagement, organizational model type and sustainability.

Kinota: An Open-Source NoSQL implementation of OGC SensorThings for large-scale high-resolution real-time environmental monitoring

NASA Astrophysics Data System (ADS)

Miles, B.; Chepudira, K.; LaBar, W.

2017-12-01

The Open Geospatial Consortium (OGC) SensorThings API (STA) specification, ratified in 2016, is a next-generation open standard for enabling real-time communication of sensor data. Building on over a decade of OGC Sensor Web Enablement (SWE) Standards, STA offers a rich data model that can represent a range of sensor and phenomena types (e.g. fixed sensors sensing fixed phenomena, fixed sensors sensing moving phenomena, mobile sensors sensing fixed phenomena, and mobile sensors sensing moving phenomena) and is data agnostic. Additionally, and in contrast to previous SWE standards, STA is developer-friendly, as is evident from its convenient JSON serialization, and expressive OData-based query language (with support for geospatial queries); with its Message Queue Telemetry Transport (MQTT), STA is also well-suited to efficient real-time data publishing and discovery. All these attributes make STA potentially useful for use in environmental monitoring sensor networks. Here we present Kinota(TM), an Open-Source NoSQL implementation of OGC SensorThings for large-scale high-resolution real-time environmental monitoring. Kinota, which roughly stands for Knowledge from Internet of Things Analyses, relies on Cassandra its underlying data store, which is a horizontally scalable, fault-tolerant open-source database that is often used to store time-series data for Big Data applications (though integration with other NoSQL or rational databases is possible). With this foundation, Kinota can scale to store data from an arbitrary number of sensors collecting data every 500 milliseconds. Additionally, Kinota architecture is very modular allowing for customization by adopters who can choose to replace parts of the existing implementation when desirable. The architecture is also highly portable providing the flexibility to choose between cloud providers like azure, amazon, google etc. The scalable, flexible and cloud friendly architecture of Kinota makes it ideal for use in next-generation large-scale and high-resolution real-time environmental monitoring networks used in domains such as hydrology, geomorphology, and geophysics, as well as management applications such as flood early warning, and regulatory enforcement.

A user-friendly, dynamic web environment for remote data browsing and analysis of multiparametric geophysical data within the MULTIMO project

NASA Astrophysics Data System (ADS)

Carniel, Roberto; Di Cecca, Mauro; Jaquet, Olivier

2006-05-01

In the framework of the EU-funded project "Multi-disciplinary monitoring, modelling and forecasting of volcanic hazard" (MULTIMO), multiparametric data have been recorded at the MULTIMO station in Montserrat. Moreover, several other long time series, recorded at Montserrat and at other volcanoes, have been acquired in order to test stochastic and deterministic methodologies under development. Creating a general framework to handle data efficiently is a considerable task even for homogeneous data. In the case of heterogeneous data, this becomes a major issue. A need for a consistent way of browsing such a heterogeneous dataset in a user-friendly way therefore arose. Additionally, a framework for applying the calculation of the developed dynamical parameters on the data series was also needed in order to easily keep these parameters under control, e.g. for monitoring, research or forecasting purposes. The solution which we present is completely based on Open Source software, including Linux operating system, MySql database management system, Apache web server, Zope application server, Scilab math engine, Plone content management framework, Unified Modelling Language. From the user point of view the main advantage is the possibility of browsing through datasets recorded on different volcanoes, with different instruments, with different sampling frequencies, stored in different formats, all via a consistent, user- friendly interface that transparently runs queries to the database, gets the data from the main storage units, generates the graphs and produces dynamically generated web pages to interact with the user. The involvement of third parties for continuing the development in the Open Source philosophy and/or extending the application fields is now sought.

28 CFR 506.2 - How may family, friends, or other sources deposit funds into an inmate commissary account?

Code of Federal Regulations, 2011 CFR

2011-07-01

... 28 Judicial Administration 2 2011-07-01 2011-07-01 false How may family, friends, or other sources... may family, friends, or other sources deposit funds into an inmate commissary account? (a) Family and friends must mail deposits to the centralized inmate commissary account at the address we provide. (1) The...

28 CFR 506.2 - How may family, friends, or other sources deposit funds into an inmate commissary account?

Code of Federal Regulations, 2010 CFR

2010-07-01

... 28 Judicial Administration 2 2010-07-01 2010-07-01 false How may family, friends, or other sources... may family, friends, or other sources deposit funds into an inmate commissary account? (a) Family and friends must mail deposits to the centralized inmate commissary account at the address we provide. (1) The...

A user-friendly means to scale from the biochemistry of photosynthesis to whole crop canopies and production in time and space - development of Java WIMOVAC.

PubMed

Song, Qingfeng; Chen, Dairui; Long, Stephen P; Zhu, Xin-Guang

2017-01-01

Windows Intuitive Model of Vegetation response to Atmosphere and Climate Change (WIMOVAC) has been used widely as a generic modular mechanistically rich model of plant production. It can predict the responses of leaf and canopy carbon balance, as well as production in different environmental conditions, in particular those relevant to global change. Here, we introduce an open source Java user-friendly version of WIMOVAC. This software is platform independent and can be easily downloaded to a laptop and used without any prior programming skills. In this article, we describe the structure, equations and user guide and illustrate some potential applications of WIMOVAC. © 2016 The Authors Plant, Cell & Environment Published by John Wiley & Sons Ltd.

Web-based spatial analysis with the ILWIS open source GIS software and satellite images from GEONETCast

NASA Astrophysics Data System (ADS)

Lemmens, R.; Maathuis, B.; Mannaerts, C.; Foerster, T.; Schaeffer, B.; Wytzisk, A.

2009-12-01

This paper involves easy accessible integrated web-based analysis of satellite images with a plug-in based open source software. The paper is targeted to both users and developers of geospatial software. Guided by a use case scenario, we describe the ILWIS software and its toolbox to access satellite images through the GEONETCast broadcasting system. The last two decades have shown a major shift from stand-alone software systems to networked ones, often client/server applications using distributed geo-(web-)services. This allows organisations to combine without much effort their own data with remotely available data and processing functionality. Key to this integrated spatial data analysis is a low-cost access to data from within a user-friendly and flexible software. Web-based open source software solutions are more often a powerful option for developing countries. The Integrated Land and Water Information System (ILWIS) is a PC-based GIS & Remote Sensing software, comprising a complete package of image processing, spatial analysis and digital mapping and was developed as commercial software from the early nineties onwards. Recent project efforts have migrated ILWIS into a modular, plug-in-based open source software, and provide web-service support for OGC-based web mapping and processing. The core objective of the ILWIS Open source project is to provide a maintainable framework for researchers and software developers to implement training components, scientific toolboxes and (web-) services. The latest plug-ins have been developed for multi-criteria decision making, water resources analysis and spatial statistics analysis. The development of this framework is done since 2007 in the context of 52°North, which is an open initiative that advances the development of cutting edge open source geospatial software, using the GPL license. GEONETCast, as part of the emerging Global Earth Observation System of Systems (GEOSS), puts essential environmental data at the fingertips of users around the globe. This user-friendly and low-cost information dissemination provides global information as a basis for decision-making in a number of critical areas, including public health, energy, agriculture, weather, water, climate, natural disasters and ecosystems. GEONETCast makes available satellite images via Digital Video Broadcast (DVB) technology. An OGC WMS interface and plug-ins which convert GEONETCast data streams allow an ILWIS user to integrate various distributed data sources with data locally stored on his machine. Our paper describes a use case in which ILWIS is used with GEONETCast satellite imagery for decision making processes in Ghana. We also explain how the ILWIS software can be extended with additional functionality by means of building plug-ins and unfold our plans to implement other OGC standards, such as WCS and WPS in the same context. Especially, the latter one can be seen as a major step forward in terms of moving well-proven desktop based processing functionality to the web. This enables the embedding of ILWIS functionality in Spatial Data Infrastructures or even the execution in scalable and on-demand cloud computing environments.

phylo-node: A molecular phylogenetic toolkit using Node.js.

PubMed

O'Halloran, Damien M

2017-01-01

Node.js is an open-source and cross-platform environment that provides a JavaScript codebase for back-end server-side applications. JavaScript has been used to develop very fast and user-friendly front-end tools for bioinformatic and phylogenetic analyses. However, no such toolkits are available using Node.js to conduct comprehensive molecular phylogenetic analysis. To address this problem, I have developed, phylo-node, which was developed using Node.js and provides a stable and scalable toolkit that allows the user to perform diverse molecular and phylogenetic tasks. phylo-node can execute the analysis and process the resulting outputs from a suite of software options that provides tools for read processing and genome alignment, sequence retrieval, multiple sequence alignment, primer design, evolutionary modeling, and phylogeny reconstruction. Furthermore, phylo-node enables the user to deploy server dependent applications, and also provides simple integration and interoperation with other Node modules and languages using Node inheritance patterns, and a customized piping module to support the production of diverse pipelines. phylo-node is open-source and freely available to all users without sign-up or login requirements. All source code and user guidelines are openly available at the GitHub repository: https://github.com/dohalloran/phylo-node.

WHATIF: an open-source desktop application for extraction and management of the incidental findings from next-generation sequencing variant data

PubMed Central

Ye, Zhan; Kadolph, Christopher; Strenn, Robert; Wall, Daniel; McPherson, Elizabeth; Lin, Simon

2015-01-01

Background Identification and evaluation of incidental findings in patients following whole exome (WGS) or whole genome sequencing (WGS) is challenging for both practicing physicians and researchers. The American College of Medical Genetics and Genomics (ACMG) recently recommended a list of reportable incidental genetic findings. However, no informatics tools are currently available to support evaluation of incidental findings in next-generation sequencing data. Methods The Wisconsin Hierarchical Analysis Tool for Incidental Findings (WHATIF), was developed as a stand-alone Windows-based desktop executable, to support the interactive analysis of incidental findings in the context of the ACMG recommendations. WHATIF integrates the European Bioinformatics Institute Variant Effect Predictor (VEP) tool for biological interpretation and the National Center for Biotechnology Information ClinVar tool for clinical interpretation. Results An open-source desktop program was created to annotate incidental findings and present the results with a user-friendly interface. Further, a meaningful index (WHATIF Index) was devised for each gene to facilitate ranking of the relative importance of the variants and estimate the potential workload associated with further evaluation of the variants. Our WHATIF application is available at: http://tinyurl.com/WHATIF-SOFTWARE Conclusions The WHATIF application offers a user-friendly interface and allows users to investigate the extracted variant information efficiently and intuitively while always accessing the up to date information on variants via application programming interfaces (API) connections. WHATIF’s highly flexible design and straightforward implementation aids users in customizing the source code to meet their own special needs. PMID:25890833

Dugong: a Docker image, based on Ubuntu Linux, focused on reproducibility and replicability for bioinformatics analyses.

PubMed

Menegidio, Fabiano B; Jabes, Daniela L; Costa de Oliveira, Regina; Nunes, Luiz R

2018-02-01

This manuscript introduces and describes Dugong, a Docker image based on Ubuntu 16.04, which automates installation of more than 3500 bioinformatics tools (along with their respective libraries and dependencies), in alternative computational environments. The software operates through a user-friendly XFCE4 graphic interface that allows software management and installation by users not fully familiarized with the Linux command line and provides the Jupyter Notebook to assist in the delivery and exchange of consistent and reproducible protocols and results across laboratories, assisting in the development of open science projects. Source code and instructions for local installation are available at https://github.com/DugongBioinformatics, under the MIT open source license. Luiz.nunes@ufabc.edu.br. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Software-based measurement of thin filament lengths: an open-source GUI for Distributed Deconvolution analysis of fluorescence images

PubMed Central

Gokhin, David S.; Fowler, Velia M.

2016-01-01

The periodically arranged thin filaments within the striated myofibrils of skeletal and cardiac muscle have precisely regulated lengths, which can change in response to developmental adaptations, pathophysiological states, and genetic perturbations. We have developed a user-friendly, open-source ImageJ plugin that provides a graphical user interface (GUI) for super-resolution measurement of thin filament lengths by applying Distributed Deconvolution (DDecon) analysis to periodic line scans collected from fluorescence images. In the workflow presented here, we demonstrate thin filament length measurement using a phalloidin-stained cryosection of mouse skeletal muscle. The DDecon plugin is also capable of measuring distances of any periodically localized fluorescent signal from the Z- or M-line, as well as distances between successive Z- or M-lines, providing a broadly applicable tool for quantitative analysis of muscle cytoarchitecture. These functionalities can also be used to analyze periodic fluorescence signals in nonmuscle cells. PMID:27644080

DStat: A Versatile, Open-Source Potentiostat for Electroanalysis and Integration.

PubMed

Dryden, Michael D M; Wheeler, Aaron R

2015-01-01

Most electroanalytical techniques require the precise control of the potentials in an electrochemical cell using a potentiostat. Commercial potentiostats function as "black boxes," giving limited information about their circuitry and behaviour which can make development of new measurement techniques and integration with other instruments challenging. Recently, a number of lab-built potentiostats have emerged with various design goals including low manufacturing cost and field-portability, but notably lacking is an accessible potentiostat designed for general lab use, focusing on measurement quality combined with ease of use and versatility. To fill this gap, we introduce DStat (http://microfluidics.utoronto.ca/dstat), an open-source, general-purpose potentiostat for use alone or integrated with other instruments. DStat offers picoampere current measurement capabilities, a compact USB-powered design, and user-friendly cross-platform software. DStat is easy and inexpensive to build, may be modified freely, and achieves good performance at low current levels not accessible to other lab-built instruments. In head-to-head tests, DStat's voltammetric measurements are much more sensitive than those of "CheapStat" (a popular open-source potentiostat described previously), and are comparable to those of a compact commercial "black box" potentiostat. Likewise, in head-to-head tests, DStat's potentiometric precision is similar to that of a commercial pH meter. Most importantly, the versatility of DStat was demonstrated through integration with the open-source DropBot digital microfluidics platform. In sum, we propose that DStat is a valuable contribution to the "open source" movement in analytical science, which is allowing users to adapt their tools to their experiments rather than alter their experiments to be compatible with their tools.

A Flexible Method for Producing F.E.M. Analysis of Bone Using Open-Source Software

NASA Technical Reports Server (NTRS)

Boppana, Abhishektha; Sefcik, Ryan; Meyers, Jerry G.; Lewandowski, Beth E.

2016-01-01

This project, performed in support of the NASA GRC Space Academy summer program, sought to develop an open-source workflow methodology that segmented medical image data, created a 3D model from the segmented data, and prepared the model for finite-element analysis. In an initial step, a technological survey evaluated the performance of various existing open-source software that claim to perform these tasks. However, the survey concluded that no single software exhibited the wide array of functionality required for the potential NASA application in the area of bone, muscle and bio fluidic studies. As a result, development of a series of Python scripts provided the bridging mechanism to address the shortcomings of the available open source tools. The implementation of the VTK library provided the most quick and effective means of segmenting regions of interest from the medical images; it allowed for the export of a 3D model by using the marching cubes algorithm to build a surface mesh. To facilitate the development of the model domain from this extracted information required a surface mesh to be processed in the open-source software packages Blender and Gmsh. The Preview program of the FEBio suite proved to be sufficient for volume filling the model with an unstructured mesh and preparing boundaries specifications for finite element analysis. To fully allow FEM modeling, an in house developed Python script allowed assignment of material properties on an element by element basis by performing a weighted interpolation of voxel intensity of the parent medical image correlated to published information of image intensity to material properties, such as ash density. A graphical user interface combined the Python scripts and other software into a user friendly interface. The work using Python scripts provides a potential alternative to expensive commercial software and inadequate, limited open-source freeware programs for the creation of 3D computational models. More work will be needed to validate this approach in creating finite-element models.

Open-Source Development of the Petascale Reactive Flow and Transport Code PFLOTRAN

NASA Astrophysics Data System (ADS)

Hammond, G. E.; Andre, B.; Bisht, G.; Johnson, T.; Karra, S.; Lichtner, P. C.; Mills, R. T.

2013-12-01

Open-source software development has become increasingly popular in recent years. Open-source encourages collaborative and transparent software development and promotes unlimited free redistribution of source code to the public. Open-source development is good for science as it reveals implementation details that are critical to scientific reproducibility, but generally excluded from journal publications. In addition, research funds that would have been spent on licensing fees can be redirected to code development that benefits more scientists. In 2006, the developers of PFLOTRAN open-sourced their code under the U.S. Department of Energy SciDAC-II program. Since that time, the code has gained popularity among code developers and users from around the world seeking to employ PFLOTRAN to simulate thermal, hydraulic, mechanical and biogeochemical processes in the Earth's surface/subsurface environment. PFLOTRAN is a massively-parallel subsurface reactive multiphase flow and transport simulator designed from the ground up to run efficiently on computing platforms ranging from the laptop to leadership-class supercomputers, all from a single code base. The code employs domain decomposition for parallelism and is founded upon the well-established and open-source parallel PETSc and HDF5 frameworks. PFLOTRAN leverages modern Fortran (i.e. Fortran 2003-2008) in its extensible object-oriented design. The use of this progressive, yet domain-friendly programming language has greatly facilitated collaboration in the code's software development. Over the past year, PFLOTRAN's top-level data structures were refactored as Fortran classes (i.e. extendible derived types) to improve the flexibility of the code, ease the addition of new process models, and enable coupling to external simulators. For instance, PFLOTRAN has been coupled to the parallel electrical resistivity tomography code E4D to enable hydrogeophysical inversion while the same code base can be used as a third-party library to provide hydrologic flow, energy transport, and biogeochemical capability to the community land model, CLM, part of the open-source community earth system model (CESM) for climate. In this presentation, the advantages and disadvantages of open source software development in support of geoscience research at government laboratories, universities, and the private sector are discussed. Since the code is open-source (i.e. it's transparent and readily available to competitors), the PFLOTRAN team's development strategy within a competitive research environment is presented. Finally, the developers discuss their approach to object-oriented programming and the leveraging of modern Fortran in support of collaborative geoscience research as the Fortran standard evolves among compiler vendors.

Current trends for customized biomedical software tools.

PubMed

Khan, Haseeb Ahmad

2017-01-01

In the past, biomedical scientists were solely dependent on expensive commercial software packages for various applications. However, the advent of user-friendly programming languages and open source platforms has revolutionized the development of simple and efficient customized software tools for solving specific biomedical problems. Many of these tools are designed and developed by biomedical scientists independently or with the support of computer experts and often made freely available for the benefit of scientific community. The current trends for customized biomedical software tools are highlighted in this short review.

SP-Designer: a user-friendly program for designing species-specific primer pairs from DNA sequence alignments.

PubMed

Villard, Pierre; Malausa, Thibaut

2013-07-01

SP-Designer is an open-source program providing a user-friendly tool for the design of specific PCR primer pairs from a DNA sequence alignment containing sequences from various taxa. SP-Designer selects PCR primer pairs for the amplification of DNA from a target species on the basis of several criteria: (i) primer specificity, as assessed by interspecific sequence polymorphism in the annealing regions, (ii) the biochemical characteristics of the primers and (iii) the intended PCR conditions. SP-Designer generates tables, detailing the primer pair and PCR characteristics, and a FASTA file locating the primer sequences in the original sequence alignment. SP-Designer is Windows-compatible and freely available from http://www2.sophia.inra.fr/urih/sophia_mart/sp_designer/info_sp_designer.php. © 2013 John Wiley & Sons Ltd.

SLIMS--a user-friendly sample operations and inventory management system for genotyping labs.

PubMed

Van Rossum, Thea; Tripp, Ben; Daley, Denise

2010-07-15

We present the Sample-based Laboratory Information Management System (SLIMS), a powerful and user-friendly open source web application that provides all members of a laboratory with an interface to view, edit and create sample information. SLIMS aims to simplify common laboratory tasks with tools such as a user-friendly shopping cart for subjects, samples and containers that easily generates reports, shareable lists and plate designs for genotyping. Further key features include customizable data views, database change-logging and dynamically filled pre-formatted reports. Along with being feature-rich, SLIMS' power comes from being able to handle longitudinal data from multiple time-points and biological sources. This type of data is increasingly common from studies searching for susceptibility genes for common complex diseases that collect thousands of samples generating millions of genotypes and overwhelming amounts of data. LIMSs provide an efficient way to deal with this data while increasing accessibility and reducing laboratory errors; however, professional LIMS are often too costly to be practical. SLIMS gives labs a feasible alternative that is easily accessible, user-centrically designed and feature-rich. To facilitate system customization, and utilization for other groups, manuals have been written for users and developers. Documentation, source code and manuals are available at http://genapha.icapture.ubc.ca/SLIMS/index.jsp. SLIMS was developed using Java 1.6.0, JSPs, Hibernate 3.3.1.GA, DB2 and mySQL, Apache Tomcat 6.0.18, NetBeans IDE 6.5, Jasper Reports 3.5.1 and JasperSoft's iReport 3.5.1.

Electronic data capture for registries and clinical trials in orthopaedic surgery: open source versus commercial systems.

PubMed

Shah, Jatin; Rajgor, Dimple; Pradhan, Shreyasee; McCready, Mariana; Zaveri, Amrapali; Pietrobon, Ricardo

2010-10-01

Collection and analysis of clinical data can help orthopaedic surgeons to practice evidence based medicine. Spreadsheets and offline relational databases are prevalent, but not flexible, secure, workflow friendly and do not support the generation of standardized and interoperable data. Additionally these data collection applications usually do not follow a structured and planned approach which may result in failure to achieve the intended goal. Our purposes are (1) to provide a brief overview of EDC systems, their types, and related pros and cons as well as to describe commonly used EDC platforms and their features; and (2) describe simple steps involved in designing a registry/clinical study in DADOS P, an open source EDC system. WHERE ARE WE NOW?: Electronic data capture systems aimed at addressing these issues are widely being adopted at an institutional/national/international level but are lacking at an individual level. A wide array of features, relative pros and cons and different business models cause confusion and indecision among orthopaedic surgeons interested in implementing EDC systems. WHERE DO WE NEED TO GO?: To answer clinical questions and actively participate in clinical studies, orthopaedic surgeons should collect data in parallel to their clinical activities. Adopting a simple, user-friendly, and robust EDC system can facilitate the data collection process. HOW DO WE GET THERE?: Conducting a balanced evaluation of available options and comparing them with intended goals and requirements can help orthopaedic surgeons to make an informed choice.

PharmTeX: a LaTeX-Based Open-Source Platform for Automated Reporting Workflow.

PubMed

Rasmussen, Christian Hove; Smith, Mike K; Ito, Kaori; Sundararajan, Vijayakumar; Magnusson, Mats O; Niclas Jonsson, E; Fostvedt, Luke; Burger, Paula; McFadyen, Lynn; Tensfeldt, Thomas G; Nicholas, Timothy

2018-03-16

Every year, the pharmaceutical industry generates a large number of scientific reports related to drug research, development, and regulatory submissions. Many of these reports are created using text processing tools such as Microsoft Word. Given the large number of figures, tables, references, and other elements, this is often a tedious task involving hours of copying and pasting and substantial efforts in quality control (QC). In the present article, we present the LaTeX-based open-source reporting platform, PharmTeX, a community-based effort to make reporting simple, reproducible, and user-friendly. The PharmTeX creators put a substantial effort into simplifying the sometimes complex elements of LaTeX into user-friendly functions that rely on advanced LaTeX and Perl code running in the background. Using this setup makes LaTeX much more accessible for users with no prior LaTeX experience. A software collection was compiled for users not wanting to manually install the required software components. The PharmTeX templates allow for inclusion of tables directly from mathematical software output as well and figures from several formats. Code listings can be included directly from source. No previous experience and only a few hours of training are required to start writing reports using PharmTeX. PharmTeX significantly reduces the time required for creating a scientific report fully compliant with regulatory and industry expectations. QC is made much simpler, since there is a direct link between analysis output and report input. PharmTeX makes available to report authors the strengths of LaTeX document processing without the need for extensive training. Graphical Abstract ᅟ.

DStat: A Versatile, Open-Source Potentiostat for Electroanalysis and Integration

PubMed Central

Dryden, Michael D. M.; Wheeler, Aaron R.

2015-01-01

Most electroanalytical techniques require the precise control of the potentials in an electrochemical cell using a potentiostat. Commercial potentiostats function as “black boxes,” giving limited information about their circuitry and behaviour which can make development of new measurement techniques and integration with other instruments challenging. Recently, a number of lab-built potentiostats have emerged with various design goals including low manufacturing cost and field-portability, but notably lacking is an accessible potentiostat designed for general lab use, focusing on measurement quality combined with ease of use and versatility. To fill this gap, we introduce DStat (http://microfluidics.utoronto.ca/dstat), an open-source, general-purpose potentiostat for use alone or integrated with other instruments. DStat offers picoampere current measurement capabilities, a compact USB-powered design, and user-friendly cross-platform software. DStat is easy and inexpensive to build, may be modified freely, and achieves good performance at low current levels not accessible to other lab-built instruments. In head-to-head tests, DStat’s voltammetric measurements are much more sensitive than those of “CheapStat” (a popular open-source potentiostat described previously), and are comparable to those of a compact commercial “black box” potentiostat. Likewise, in head-to-head tests, DStat’s potentiometric precision is similar to that of a commercial pH meter. Most importantly, the versatility of DStat was demonstrated through integration with the open-source DropBot digital microfluidics platform. In sum, we propose that DStat is a valuable contribution to the “open source” movement in analytical science, which is allowing users to adapt their tools to their experiments rather than alter their experiments to be compatible with their tools. PMID:26510100

Information transmission in young children: when social information is more important than nonsocial information.

PubMed

McGuigan, Nicola; Cubillo, Marcus

2013-01-01

The authors' aim was to use a highly novel open diffusion paradigm to investigate the transmission of social information (i.e., gossip) and general knowledge within 2 groups of 10- and 11-year-old children. Four children, 2 from each group, acted as a primed information source, selected on the basis of sex and dominance ranking (high or low) within the group. Each source received 1 piece of gossip and 1 piece of general knowledge from the experimenter during natural class interaction, and the information was allowed to diffuse naturally within the group. Results revealed that gossip was transmitted more frequently than knowledge, and that male sources were more likely to transmit gossip than female sources. The relationship between characteristics of the source, and characteristics of the gossip recipient, also appeared influential with the dominant male source transmitting gossip to exclusively to friends, and the nondominant male source transmitting to individuals of higher peer regard than themselves.

HYDRA Hyperspectral Data Research Application Tom Rink and Tom Whittaker

NASA Astrophysics Data System (ADS)

Rink, T.; Whittaker, T.

2005-12-01

HYDRA is a freely available, easy to install tool for visualization and analysis of large local or remote hyper/multi-spectral datasets. HYDRA is implemented on top of the open source VisAD Java library via Jython - the Java implementation of the user friendly Python programming language. VisAD provides data integration, through its generalized data model, user-display interaction and display rendering. Jython has an easy to read, concise, scripting-like, syntax which eases software development. HYDRA allows data sharing of large datasets through its support of the OpenDAP and OpenADDE server-client protocols. The users can explore and interrogate data, and subset in physical and/or spectral space to isolate key areas of interest for further analysis without having to download an entire dataset. It also has an extensible data input architecture to recognize new instruments and understand different local file formats, currently NetCDF and HDF4 are supported.

Recyclable organic solar cells on cellulose nanocrystal substrates

PubMed Central

Zhou, Yinhua; Fuentes-Hernandez, Canek; Khan, Talha M.; Liu, Jen-Chieh; Hsu, James; Shim, Jae Won; Dindar, Amir; Youngblood, Jeffrey P.; Moon, Robert J.; Kippelen, Bernard

2013-01-01

Solar energy is potentially the largest source of renewable energy at our disposal, but significant advances are required to make photovoltaic technologies economically viable and, from a life-cycle perspective, environmentally friendly, and consequently scalable. Cellulose nanomaterials are emerging high-value nanoparticles extracted from plants that are abundant, renewable, and sustainable. Here, we report on the first demonstration of efficient polymer solar cells fabricated on optically transparent cellulose nanocrystal (CNC) substrates. The solar cells fabricated on the CNC substrates display good rectification in the dark and reach a power conversion efficiency of 2.7%. In addition, we demonstrate that these solar cells can be easily separated and recycled into their major components using low-energy processes at room temperature, opening the door for a truly recyclable solar cell technology. Efficient and easily recyclable organic solar cells on CNC substrates are expected to be an attractive technology for sustainable, scalable, and environmentally-friendly energy production. PMID:23524333

Recyclable organic solar cells on cellulose nanocrystal substrates.

PubMed

Zhou, Yinhua; Fuentes-Hernandez, Canek; Khan, Talha M; Liu, Jen-Chieh; Hsu, James; Shim, Jae Won; Dindar, Amir; Youngblood, Jeffrey P; Moon, Robert J; Kippelen, Bernard

2013-01-01

Solar energy is potentially the largest source of renewable energy at our disposal, but significant advances are required to make photovoltaic technologies economically viable and, from a life-cycle perspective, environmentally friendly, and consequently scalable. Cellulose nanomaterials are emerging high-value nanoparticles extracted from plants that are abundant, renewable, and sustainable. Here, we report on the first demonstration of efficient polymer solar cells fabricated on optically transparent cellulose nanocrystal (CNC) substrates. The solar cells fabricated on the CNC substrates display good rectification in the dark and reach a power conversion efficiency of 2.7%. In addition, we demonstrate that these solar cells can be easily separated and recycled into their major components using low-energy processes at room temperature, opening the door for a truly recyclable solar cell technology. Efficient and easily recyclable organic solar cells on CNC substrates are expected to be an attractive technology for sustainable, scalable, and environmentally-friendly energy production.

Tandem Mass Spectrum Sequencing: An Alternative to Database Search Engines in Shotgun Proteomics.

PubMed

Muth, Thilo; Rapp, Erdmann; Berven, Frode S; Barsnes, Harald; Vaudel, Marc

2016-01-01

Protein identification via database searches has become the gold standard in mass spectrometry based shotgun proteomics. However, as the quality of tandem mass spectra improves, direct mass spectrum sequencing gains interest as a database-independent alternative. In this chapter, the general principle of this so-called de novo sequencing is introduced along with pitfalls and challenges of the technique. The main tools available are presented with a focus on user friendly open source software which can be directly applied in everyday proteomic workflows.

PYCHEM: a multivariate analysis package for python.

PubMed

Jarvis, Roger M; Broadhurst, David; Johnson, Helen; O'Boyle, Noel M; Goodacre, Royston

2006-10-15

We have implemented a multivariate statistical analysis toolbox, with an optional standalone graphical user interface (GUI), using the Python scripting language. This is a free and open source project that addresses the need for a multivariate analysis toolbox in Python. Although the functionality provided does not cover the full range of multivariate tools that are available, it has a broad complement of methods that are widely used in the biological sciences. In contrast to tools like MATLAB, PyChem 2.0.0 is easily accessible and free, allows for rapid extension using a range of Python modules and is part of the growing amount of complementary and interoperable scientific software in Python based upon SciPy. One of the attractions of PyChem is that it is an open source project and so there is an opportunity, through collaboration, to increase the scope of the software and to continually evolve a user-friendly platform that has applicability across a wide range of analytical and post-genomic disciplines. http://sourceforge.net/projects/pychem

OpenTrials: towards a collaborative open database of all available information on all clinical trials.

PubMed

Goldacre, Ben; Gray, Jonathan

2016-04-08

OpenTrials is a collaborative and open database for all available structured data and documents on all clinical trials, threaded together by individual trial. With a versatile and expandable data schema, it is initially designed to host and match the following documents and data for each trial: registry entries; links, abstracts, or texts of academic journal papers; portions of regulatory documents describing individual trials; structured data on methods and results extracted by systematic reviewers or other researchers; clinical study reports; and additional documents such as blank consent forms, blank case report forms, and protocols. The intention is to create an open, freely re-usable index of all such information and to increase discoverability, facilitate research, identify inconsistent data, enable audits on the availability and completeness of this information, support advocacy for better data and drive up standards around open data in evidence-based medicine. The project has phase I funding. This will allow us to create a practical data schema and populate the database initially through web-scraping, basic record linkage techniques, crowd-sourced curation around selected drug areas, and import of existing sources of structured and documents. It will also allow us to create user-friendly web interfaces onto the data and conduct user engagement workshops to optimise the database and interface designs. Where other projects have set out to manually and perfectly curate a narrow range of information on a smaller number of trials, we aim to use a broader range of techniques and attempt to match a very large quantity of information on all trials. We are currently seeking feedback and additional sources of structured data.

The GenABEL Project for statistical genomics.

PubMed

Karssen, Lennart C; van Duijn, Cornelia M; Aulchenko, Yurii S

2016-01-01

Development of free/libre open source software is usually done by a community of people with an interest in the tool. For scientific software, however, this is less often the case. Most scientific software is written by only a few authors, often a student working on a thesis. Once the paper describing the tool has been published, the tool is no longer developed further and is left to its own device. Here we describe the broad, multidisciplinary community we formed around a set of tools for statistical genomics. The GenABEL project for statistical omics actively promotes open interdisciplinary development of statistical methodology and its implementation in efficient and user-friendly software under an open source licence. The software tools developed withing the project collectively make up the GenABEL suite, which currently consists of eleven tools. The open framework of the project actively encourages involvement of the community in all stages, from formulation of methodological ideas to application of software to specific data sets. A web forum is used to channel user questions and discussions, further promoting the use of the GenABEL suite. Developer discussions take place on a dedicated mailing list, and development is further supported by robust development practices including use of public version control, code review and continuous integration. Use of this open science model attracts contributions from users and developers outside the "core team", facilitating agile statistical omics methodology development and fast dissemination.

Relations of Friends' Activities to Friendship Quality

ERIC Educational Resources Information Center

Mathur, Ravisha; Berndt, Thomas J.

2006-01-01

Two studies were conducted to examine age and sex differences in friends' activities and relations of participation in these activities to perceived friendship quality. In Study 1, 52 fourth and eighth graders were asked open-ended questions about activities they do with their best friends. In Study 2, 105 fourth and eighth graders reported both…

Open Source Web-Based Solutions for Disseminating and Analyzing Flood Hazard Information at the Community Level

NASA Astrophysics Data System (ADS)

Santillan, M. M.-M.; Santillan, J. R.; Morales, E. M. O.

2017-09-01

We discuss in this paper the development, including the features and functionalities, of an open source web-based flood hazard information dissemination and analytical system called "Flood EViDEns". Flood EViDEns is short for "Flood Event Visualization and Damage Estimations", an application that was developed by the Caraga State University to address the needs of local disaster managers in the Caraga Region in Mindanao, Philippines in accessing timely and relevant flood hazard information before, during and after the occurrence of flood disasters at the community (i.e., barangay and household) level. The web application made use of various free/open source web mapping and visualization technologies (GeoServer, GeoDjango, OpenLayers, Bootstrap), various geospatial datasets including LiDAR-derived elevation and information products, hydro-meteorological data, and flood simulation models to visualize various scenarios of flooding and its associated damages to infrastructures. The Flood EViDEns application facilitates the release and utilization of this flood-related information through a user-friendly front end interface consisting of web map and tables. A public version of the application can be accessed at http://121.97.192.11:8082/. The application is currently expanded to cover additional sites in Mindanao, Philippines through the "Geo-informatics for the Systematic Assessment of Flood Effects and Risks for a Resilient Mindanao" or the "Geo-SAFER Mindanao" Program.

AMIDE: a free software tool for multimodality medical image analysis.

PubMed

Loening, Andreas Markus; Gambhir, Sanjiv Sam

2003-07-01

Amide's a Medical Image Data Examiner (AMIDE) has been developed as a user-friendly, open-source software tool for displaying and analyzing multimodality volumetric medical images. Central to the package's abilities to simultaneously display multiple data sets (e.g., PET, CT, MRI) and regions of interest is the on-demand data reslicing implemented within the program. Data sets can be freely shifted, rotated, viewed, and analyzed with the program automatically handling interpolation as needed from the original data. Validation has been performed by comparing the output of AMIDE with that of several existing software packages. AMIDE runs on UNIX, Macintosh OS X, and Microsoft Windows platforms, and it is freely available with source code under the terms of the GNU General Public License.

MethLAB

PubMed Central

Kilaru, Varun; Barfield, Richard T; Schroeder, James W; Smith, Alicia K

2012-01-01

Recent evidence suggests that DNA methylation changes may underlie numerous complex traits and diseases. The advent of commercial, array-based methods to interrogate DNA methylation has led to a profusion of epigenetic studies in the literature. Array-based methods, such as the popular Illumina GoldenGate and Infinium platforms, estimate the proportion of DNA methylated at single-base resolution for thousands of CpG sites across the genome. These arrays generate enormous amounts of data, but few software resources exist for efficient and flexible analysis of these data. We developed a software package called MethLAB (http://genetics.emory.edu/conneely/MethLAB) using R, an open source statistical language that can be edited to suit the needs of the user. MethLAB features a graphical user interface (GUI) with a menu-driven format designed to efficiently read in and manipulate array-based methylation data in a user-friendly manner. MethLAB tests for association between methylation and relevant phenotypes by fitting a separate linear model for each CpG site. These models can incorporate both continuous and categorical phenotypes and covariates, as well as fixed or random batch or chip effects. MethLAB accounts for multiple testing by controlling the false discovery rate (FDR) at a user-specified level. Standard output includes a spreadsheet-ready text file and an array of publication-quality figures. Considering the growing interest in and availability of DNA methylation data, there is a great need for user-friendly open source analytical tools. With MethLAB, we present a timely resource that will allow users with no programming experience to implement flexible and powerful analyses of DNA methylation data. PMID:22430798

Mendel,MD: A user-friendly open-source web tool for analyzing WES and WGS in the diagnosis of patients with Mendelian disorders

PubMed Central

D. Linhares, Natália; Pena, Sérgio D. J.

2017-01-01

Whole exome and whole genome sequencing have both become widely adopted methods for investigating and diagnosing human Mendelian disorders. As pangenomic agnostic tests, they are capable of more accurate and agile diagnosis compared to traditional sequencing methods. This article describes new software called Mendel,MD, which combines multiple types of filter options and makes use of regularly updated databases to facilitate exome and genome annotation, the filtering process and the selection of candidate genes and variants for experimental validation and possible diagnosis. This tool offers a user-friendly interface, and leads clinicians through simple steps by limiting the number of candidates to achieve a final diagnosis of a medical genetics case. A useful innovation is the “1-click” method, which enables listing all the relevant variants in genes present at OMIM for perusal by clinicians. Mendel,MD was experimentally validated using clinical cases from the literature and was tested by students at the Universidade Federal de Minas Gerais, at GENE–Núcleo de Genética Médica in Brazil and at the Children’s University Hospital in Dublin, Ireland. We show in this article how it can simplify and increase the speed of identifying the culprit mutation in each of the clinical cases that were received for further investigation. Mendel,MD proved to be a reliable web-based tool, being open-source and time efficient for identifying the culprit mutation in different clinical cases of patients with Mendelian Disorders. It is also freely accessible for academic users on the following URL: https://mendelmd.org. PMID:28594829

APM_GUI: analyzing particle movement on the cell membrane and determining confinement.

PubMed

Menchón, Silvia A; Martín, Mauricio G; Dotti, Carlos G

2012-02-20

Single-particle tracking is a powerful tool for tracking individual particles with high precision. It provides useful information that allows the study of diffusion properties as well as the dynamics of movement. Changes in particle movement behavior, such as transitions between Brownian motion and temporary confinement, can reveal interesting biophysical interactions. Although useful applications exist to determine the paths of individual particles, only a few software implementations are available to analyze these data, and these implementations are generally not user-friendly and do not have a graphical interface,. Here, we present APM_GUI (Analyzing Particle Movement), which is a MatLab-implemented application with a Graphical User Interface. This user-friendly application detects confined movement considering non-random confinement when a particle remains in a region longer than a Brownian diffusant would remain. In addition, APM_GUI exports the results, which allows users to analyze this information using software that they are familiar with. APM_GUI provides an open-source tool that quantifies diffusion coefficients and determines whether trajectories have non-random confinements. It also offers a simple and user-friendly tool that can be used by individuals without programming skills.

Safer scoring? Cryptomarkets, social supply and drug market violence.

PubMed

Barratt, Monica J; Ferris, Jason A; Winstock, Adam R

2016-09-01

Cryptomarkets are digital platforms that use anonymising software (e.g. Tor) and cryptocurrencies (e.g. Bitcoin) to facilitate trade of goods and services, most notably illicit drugs. Cryptomarkets may reduce systemic violence compared with in-person drug trading because no face-to-face contact is required and disputes can be resolved through a neutral third party. In this paper, we describe the purchasing behaviour of cryptomarket users and then compare the self-reported experiences of threats, violence and other drug-market concerns when obtaining drugs from cryptomarkets with obtaining drugs through friends, known dealers and strangers. The Global Drug Survey was completed in late 2014 by a self-selected sample who reported accessing drugs through cryptomarkets in the last 12 months (N=3794). Their median age was 22 years and 82% were male. The drug types most commonly obtained through cryptomarkets were MDMA/Ecstasy (55%), cannabis (43%) and LSD (35%). Cryptomarket users reported using a median of 2 sources in addition to cryptomarkets to access drugs, the most common being in-person friendships (74%), in-person dealers (57%) and open markets/strangers (26%). When asked to nominate the main source they would use if cryptomarkets were unavailable, 49% nominated friends, 34% known dealers and 4% strangers. 'Threats to personal safety' (3%) and 'experiencing physical violence' (1%) were less often reported when using cryptomarkets compared with sourcing through friends (14%; 6%), known dealers (24%; 10%) or strangers (35%; 15%). Concerns about drug impurities and law enforcement were reported more often when using the alternative source, while loss of money, waiting too long and not receiving the product were more often reported when using cryptomarkets. Cryptomarkets are associated with substantially less threats and violence than alternative market types used by cryptomarket customers, even though a large majority of these alternatives were closed networks where violence should be relatively less common. Copyright © 2016 Elsevier B.V. All rights reserved.

compomics-utilities: an open-source Java library for computational proteomics.

PubMed

Barsnes, Harald; Vaudel, Marc; Colaert, Niklaas; Helsens, Kenny; Sickmann, Albert; Berven, Frode S; Martens, Lennart

2011-03-08

The growing interest in the field of proteomics has increased the demand for software tools and applications that process and analyze the resulting data. And even though the purpose of these tools can vary significantly, they usually share a basic set of features, including the handling of protein and peptide sequences, the visualization of (and interaction with) spectra and chromatograms, and the parsing of results from various proteomics search engines. Developers typically spend considerable time and effort implementing these support structures, which detracts from working on the novel aspects of their tool. In order to simplify the development of proteomics tools, we have implemented an open-source support library for computational proteomics, called compomics-utilities. The library contains a broad set of features required for reading, parsing, and analyzing proteomics data. compomics-utilities is already used by a long list of existing software, ensuring library stability and continued support and development. As a user-friendly, well-documented and open-source library, compomics-utilities greatly simplifies the implementation of the basic features needed in most proteomics tools. Implemented in 100% Java, compomics-utilities is fully portable across platforms and architectures. Our library thus allows the developers to focus on the novel aspects of their tools, rather than on the basic functions, which can contribute substantially to faster development, and better tools for proteomics.

MultiElec: A MATLAB Based Application for MEA Data Analysis.

PubMed

Georgiadis, Vassilis; Stephanou, Anastasis; Townsend, Paul A; Jackson, Thomas R

2015-01-01

We present MultiElec, an open source MATLAB based application for data analysis of microelectrode array (MEA) recordings. MultiElec displays an extremely user-friendly graphic user interface (GUI) that allows the simultaneous display and analysis of voltage traces for 60 electrodes and includes functions for activation-time determination, the production of activation-time heat maps with activation time and isoline display. Furthermore, local conduction velocities are semi-automatically calculated along with their corresponding vector plots. MultiElec allows ad hoc signal suppression, enabling the user to easily and efficiently handle signal artefacts and for incomplete data sets to be analysed. Voltage traces and heat maps can be simply exported for figure production and presentation. In addition, our platform is able to produce 3D videos of signal progression over all 60 electrodes. Functions are controlled entirely by a single GUI with no need for command line input or any understanding of MATLAB code. MultiElec is open source under the terms of the GNU General Public License as published by the Free Software Foundation, version 3. Both the program and source code are available to download from http://www.cancer.manchester.ac.uk/MultiElec/.

Environmentally friendly method to grow wide-bandgap semiconductor aluminum nitride crystals: Elementary source vapor phase epitaxy

PubMed Central

Wu, PeiTsen; Funato, Mitsuru; Kawakami, Yoichi

2015-01-01

Aluminum nitride (AlN) has attracted increasing interest as an optoelectronic material in the deep ultraviolet spectral range due to its wide bandgap of 6.0 eV (207 nm wavelength) at room temperature. Because AlN bulk single crystals are ideal device substrates for such applications, the crystal growth of bulky AlN has been extensively studied. Two growth methods seem especially promising: hydride vapor phase epitaxy (HVPE) and sublimation. However, the former requires hazardous gases such as hydrochloric acid and ammonia, while the latter needs extremely high growth temperatures around 2000 °C. Herein we propose a novel vapor-phase-epitaxy-based growth method for AlN that does not use toxic materials; the source precursors are elementary aluminum and nitrogen gas. To prepare our AlN, we constructed a new growth apparatus, which realizes growth of AlN single crystals at a rate of ~18 μm/h at 1550 °C using argon as the source transfer via the simple reaction Al + 1/2N2 → AlN. This growth rate is comparable to that by HVPE, and the growth temperature is much lower than that in sublimation. Thus, this study opens up a novel route to achieve environmentally friendly growth of AlN. PMID:26616203

A state-of-the-art review on nitrous oxide control from waste treatment and industrial sources.

PubMed

Frutos, Osvaldo D; Quijano, Guillermo; Aizpuru, Aitor; Muñoz, Raúl

This review aims at holistically analyzing the environmental problems associated with nitrous oxide (N 2 O) emissions by evaluating the most important sources of N 2 O and its environmental impacts. Emissions from wastewater treatment processes and the industrial production of nitric and adipic acid represent nowadays the most important anthropogenic point sources of N 2 O. Therefore, state-of-the-art strategies to mitigate the generation and release to the atmosphere of this greenhouse and O 3 -depleting gas in the waste treatment and industrial sectors are also reviewed. An updated review of the end-of-the-pipe technologies for N 2 O abatement, both in the waste treatment and industrial sectors, is herein presented and critically discussed for the first time. Despite the consistent efforts recently conducted in the development of cost-efficient and eco-friendly N 2 O abatement technologies, physical/chemical technologies still constitute the most popular treatments for the control of industrial N 2 O emissions at commercial scale. The recent advances achieved on biological N 2 O abatement based on heterotrophic denitrification have opened new opportunities for the development of eco-friendly alternatives for the treatment of N 2 O emissions. Finally, the main limitations and challenges faced by these novel N 2 O abatement biotechnologies are identified in order to pave the way for market implementation. Copyright © 2018 Elsevier Inc. All rights reserved.

Seed: a user-friendly tool for exploring and visualizing microbial community data.

PubMed

Beck, Daniel; Dennis, Christopher; Foster, James A

2015-02-15

In this article we present Simple Exploration of Ecological Data (Seed), a data exploration tool for microbial communities. Seed is written in R using the Shiny library. This provides access to powerful R-based functions and libraries through a simple user interface. Seed allows users to explore ecological datasets using principal coordinate analyses, scatter plots, bar plots, hierarchal clustering and heatmaps. Seed is open source and available at https://github.com/danlbek/Seed. danlbek@gmail.com Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

Canary: An NLP Platform for Clinicians and Researchers.

PubMed

Malmasi, Shervin; Sandor, Nicolae L; Hosomura, Naoshi; Goldberg, Matt; Skentzos, Stephen; Turchin, Alexander

2017-05-03

Information Extraction methods can help discover critical knowledge buried in the vast repositories of unstructured clinical data. However, these methods are underutilized in clinical research, potentially due to the absence of free software geared towards clinicians with little technical expertise. The skills required for developing/using such software constitute a major barrier for medical researchers wishing to employ these methods. To address this, we have developed Canary, a free and open-source solution designed for users without natural language processing (NLP) or software engineering experience. It was designed to be fast and work out of the box via a user-friendly graphical interface.

The GenABEL Project for statistical genomics

PubMed Central

Karssen, Lennart C.; van Duijn, Cornelia M.; Aulchenko, Yurii S.

2016-01-01

Development of free/libre open source software is usually done by a community of people with an interest in the tool. For scientific software, however, this is less often the case. Most scientific software is written by only a few authors, often a student working on a thesis. Once the paper describing the tool has been published, the tool is no longer developed further and is left to its own device. Here we describe the broad, multidisciplinary community we formed around a set of tools for statistical genomics. The GenABEL project for statistical omics actively promotes open interdisciplinary development of statistical methodology and its implementation in efficient and user-friendly software under an open source licence. The software tools developed withing the project collectively make up the GenABEL suite, which currently consists of eleven tools. The open framework of the project actively encourages involvement of the community in all stages, from formulation of methodological ideas to application of software to specific data sets. A web forum is used to channel user questions and discussions, further promoting the use of the GenABEL suite. Developer discussions take place on a dedicated mailing list, and development is further supported by robust development practices including use of public version control, code review and continuous integration. Use of this open science model attracts contributions from users and developers outside the “core team”, facilitating agile statistical omics methodology development and fast dissemination. PMID:27347381

Towards open collaborative health informatics - The Role of free/libre open source principles. Contribution of the IMIA Open Source Health Informatics Working Group.

PubMed

Karopka, T; Schmuhl, H; Marcelo, A; Molin, J Dal; Wright, G

2011-01-01

: To analyze the contribution of Free/Libre Open Source Software in health care (FLOSS-HC) and to give perspectives for future developments. The paper summarizes FLOSS-related trends in health care as anticipated by members of the IMIA Open Source Working Group. Data were obtained through literature review and personal experience and observations of the authors in the last two decades. A status quo is given by a frequency analysis of the database of Medfloss.org, one of the world's largest platforms dedicated to FLOSS-HC. The authors discuss current problems in the field of health care and finally give a prospective roadmap, a projection of the potential influences of FLOSS in health care. FLOSS-HC already exists for more than 2 decades. Several projects have shown that FLOSS may produce highly competitive alternatives to proprietary solutions that are at least equivalent in usability and have a better total cost of ownership ratio. The Medfloss.org database currently lists 221 projects of diverse application types. FLOSS principles hold a great potential for addressing several of the most critical problems in health care IT. The authors argue that an ecosystem perspective is relevant and that FLOSS principles are best suited to create health IT systems that are able to evolve over time as medical knowledge, technologies, insights, workflows etc. continuously change. All these factors that inherently influence the development of health IT systems are changing at an ever growing pace. Traditional models of software engineering are not able to follow these changes and provide up-to-date systems for an acceptable cost/value ratio. To allow FLOSS to positively influence Health IT in the future a "FLOSS-friendly" environment has to be provided. Policy makers should resolve uncertainties in the legal framework that disfavor FLOSS. Certification procedures should be specified in a way that they do not raise additional barriers for FLOSS.

Innovative Ways of Visualising Meta Data in 4D Using Open Source Libaries

NASA Astrophysics Data System (ADS)

Balhar, Jakub; Valach, Pavel; Veselka, Jonas; Voumard, Yann

2016-08-01

There are more and more data being measured by different Earth Observation satellites around the world. Ever increasing amount of these data present new challenges and opportunities for their visualization.In this paper we propose how to visualize the amount, distribution and the structure of the data in a transparent way, which will take into account time-dimensions as well. Our approach allows us to get a global overview as well detailed regional information about distribution of the products from EO observation missions.We focus on introducing our mobile-friendly and easy- to-use web mapping application for 4D visualization of the data. Apart from that we also present the Java application which can read and process the data from various data sources.

MetaboLights: An Open-Access Database Repository for Metabolomics Data.

PubMed

Kale, Namrata S; Haug, Kenneth; Conesa, Pablo; Jayseelan, Kalaivani; Moreno, Pablo; Rocca-Serra, Philippe; Nainala, Venkata Chandrasekhar; Spicer, Rachel A; Williams, Mark; Li, Xuefei; Salek, Reza M; Griffin, Julian L; Steinbeck, Christoph

2016-03-24

MetaboLights is the first general purpose, open-access database repository for cross-platform and cross-species metabolomics research at the European Bioinformatics Institute (EMBL-EBI). Based upon the open-source ISA framework, MetaboLights provides Metabolomics Standard Initiative (MSI) compliant metadata and raw experimental data associated with metabolomics experiments. Users can upload their study datasets into the MetaboLights Repository. These studies are then automatically assigned a stable and unique identifier (e.g., MTBLS1) that can be used for publication reference. The MetaboLights Reference Layer associates metabolites with metabolomics studies in the archive and is extensively annotated with data fields such as structural and chemical information, NMR and MS spectra, target species, metabolic pathways, and reactions. The database is manually curated with no specific release schedules. MetaboLights is also recommended by journals for metabolomics data deposition. This unit provides a guide to using MetaboLights, downloading experimental data, and depositing metabolomics datasets using user-friendly submission tools. Copyright © 2016 John Wiley & Sons, Inc.

ATLAS (Automatic Tool for Local Assembly Structures) - A Comprehensive Infrastructure for Assembly, Annotation, and Genomic Binning of Metagenomic and Metaranscripomic Data

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

White, Richard A.; Brown, Joseph M.; Colby, Sean M.

ATLAS (Automatic Tool for Local Assembly Structures) is a comprehensive multiomics data analysis pipeline that is massively parallel and scalable. ATLAS contains a modular analysis pipeline for assembly, annotation, quantification and genome binning of metagenomics and metatranscriptomics data and a framework for reference metaproteomic database construction. ATLAS transforms raw sequence data into functional and taxonomic data at the microbial population level and provides genome-centric resolution through genome binning. ATLAS provides robust taxonomy based on majority voting of protein coding open reading frames rolled-up at the contig level using modified lowest common ancestor (LCA) analysis. ATLAS provides robust taxonomy based onmore » majority voting of protein coding open reading frames rolled-up at the contig level using modified lowest common ancestor (LCA) analysis. ATLAS is user-friendly, easy install through bioconda maintained as open-source on GitHub, and is implemented in Snakemake for modular customizable workflows.« less

IdentiPy: An Extensible Search Engine for Protein Identification in Shotgun Proteomics.

PubMed

Levitsky, Lev I; Ivanov, Mark V; Lobas, Anna A; Bubis, Julia A; Tarasova, Irina A; Solovyeva, Elizaveta M; Pridatchenko, Marina L; Gorshkov, Mikhail V

2018-06-18

We present an open-source, extensible search engine for shotgun proteomics. Implemented in Python programming language, IdentiPy shows competitive processing speed and sensitivity compared with the state-of-the-art search engines. It is equipped with a user-friendly web interface, IdentiPy Server, enabling the use of a single server installation accessed from multiple workstations. Using a simplified version of X!Tandem scoring algorithm and its novel "autotune" feature, IdentiPy outperforms the popular alternatives on high-resolution data sets. Autotune adjusts the search parameters for the particular data set, resulting in improved search efficiency and simplifying the user experience. IdentiPy with the autotune feature shows higher sensitivity compared with the evaluated search engines. IdentiPy Server has built-in postprocessing and protein inference procedures and provides graphic visualization of the statistical properties of the data set and the search results. It is open-source and can be freely extended to use third-party scoring functions or processing algorithms and allows customization of the search workflow for specialized applications.

MollDE: a homology modeling framework you can click with.

PubMed

Canutescu, Adrian A; Dunbrack, Roland L

2005-06-15

Molecular Integrated Development Environment (MolIDE) is an integrated application designed to provide homology modeling tools and protocols under a uniform, user-friendly graphical interface. Its main purpose is to combine the most frequent modeling steps in a semi-automatic, interactive way, guiding the user from the target protein sequence to the final three-dimensional protein structure. The typical basic homology modeling process is composed of building sequence profiles of the target sequence family, secondary structure prediction, sequence alignment with PDB structures, assisted alignment editing, side-chain prediction and loop building. All of these steps are available through a graphical user interface. MolIDE's user-friendly and streamlined interactive modeling protocol allows the user to focus on the important modeling questions, hiding from the user the raw data generation and conversion steps. MolIDE was designed from the ground up as an open-source, cross-platform, extensible framework. This allows developers to integrate additional third-party programs to MolIDE. http://dunbrack.fccc.edu/molide/molide.php rl_dunbrack@fccc.edu.

BOLDSync: a MATLAB-based toolbox for synchronized stimulus presentation in functional MRI.

PubMed

Joshi, Jitesh; Saharan, Sumiti; Mandal, Pravat K

2014-02-15

Precise and synchronized presentation of paradigm stimuli in functional magnetic resonance imaging (fMRI) is central to obtaining accurate information about brain regions involved in a specific task. In this manuscript, we present a new MATLAB-based toolbox, BOLDSync, for synchronized stimulus presentation in fMRI. BOLDSync provides a user friendly platform for design and presentation of visual, audio, as well as multimodal audio-visual (AV) stimuli in functional imaging experiments. We present simulation experiments that demonstrate the millisecond synchronization accuracy of BOLDSync, and also illustrate the functionalities of BOLDSync through application to an AV fMRI study. BOLDSync gains an advantage over other available proprietary and open-source toolboxes by offering a user friendly and accessible interface that affords both precision in stimulus presentation and versatility across various types of stimulus designs and system setups. BOLDSync is a reliable, efficient, and versatile solution for synchronized stimulus presentation in fMRI study. Copyright © 2013 Elsevier B.V. All rights reserved.

Advanced Cell Classifier: User-Friendly Machine-Learning-Based Software for Discovering Phenotypes in High-Content Imaging Data.

PubMed

Piccinini, Filippo; Balassa, Tamas; Szkalisity, Abel; Molnar, Csaba; Paavolainen, Lassi; Kujala, Kaisa; Buzas, Krisztina; Sarazova, Marie; Pietiainen, Vilja; Kutay, Ulrike; Smith, Kevin; Horvath, Peter

2017-06-28

High-content, imaging-based screens now routinely generate data on a scale that precludes manual verification and interrogation. Software applying machine learning has become an essential tool to automate analysis, but these methods require annotated examples to learn from. Efficiently exploring large datasets to find relevant examples remains a challenging bottleneck. Here, we present Advanced Cell Classifier (ACC), a graphical software package for phenotypic analysis that addresses these difficulties. ACC applies machine-learning and image-analysis methods to high-content data generated by large-scale, cell-based experiments. It features methods to mine microscopic image data, discover new phenotypes, and improve recognition performance. We demonstrate that these features substantially expedite the training process, successfully uncover rare phenotypes, and improve the accuracy of the analysis. ACC is extensively documented, designed to be user-friendly for researchers without machine-learning expertise, and distributed as a free open-source tool at www.cellclassifier.org. Copyright © 2017 Elsevier Inc. All rights reserved.

Detecting Foreign Bodies in a Head Laceration

PubMed Central

Fowler, Thomas R.; Crellin, Steven J.; Greenberg, Marna Rayl

2015-01-01

Open wounds represent a potential area of medicolegal risk if foreign bodies are not identified prior to wound closure. The importance of imaging of lacerations was underscored by a recent case where a 20-year-old male collided with a friend's mouth on a trampoline sustaining a simple, superficial scalp laceration. The wound was evaluated in typical fashion including irrigation and local exploration and was prepared for closure. The friend was then evaluated and noted to have multiple extensive dental fractures. An increased index of suspicion generated further evaluation of the first patient's wound. Plain radiography obtained of the first patient's skull was noted to have bony foreign bodies consistent with teeth, which were then removed after further exploration. Superficial wounds are common and complications arising from retained foreign bodies are a potential source of substantial morbidity and consequently medical litigation. This case serves as a reminder to be vigilant and maintain a high index of suspicion regarding the potential for foreign body. PMID:25802770

Detecting foreign bodies in a head laceration.

PubMed

Fowler, Thomas R; Crellin, Steven J; Greenberg, Marna Rayl

2015-01-01

Open wounds represent a potential area of medicolegal risk if foreign bodies are not identified prior to wound closure. The importance of imaging of lacerations was underscored by a recent case where a 20-year-old male collided with a friend's mouth on a trampoline sustaining a simple, superficial scalp laceration. The wound was evaluated in typical fashion including irrigation and local exploration and was prepared for closure. The friend was then evaluated and noted to have multiple extensive dental fractures. An increased index of suspicion generated further evaluation of the first patient's wound. Plain radiography obtained of the first patient's skull was noted to have bony foreign bodies consistent with teeth, which were then removed after further exploration. Superficial wounds are common and complications arising from retained foreign bodies are a potential source of substantial morbidity and consequently medical litigation. This case serves as a reminder to be vigilant and maintain a high index of suspicion regarding the potential for foreign body.

EEGNET: An Open Source Tool for Analyzing and Visualizing M/EEG Connectome.

PubMed

Hassan, Mahmoud; Shamas, Mohamad; Khalil, Mohamad; El Falou, Wassim; Wendling, Fabrice

2015-01-01

The brain is a large-scale complex network often referred to as the "connectome". Exploring the dynamic behavior of the connectome is a challenging issue as both excellent time and space resolution is required. In this context Magneto/Electroencephalography (M/EEG) are effective neuroimaging techniques allowing for analysis of the dynamics of functional brain networks at scalp level and/or at reconstructed sources. However, a tool that can cover all the processing steps of identifying brain networks from M/EEG data is still missing. In this paper, we report a novel software package, called EEGNET, running under MATLAB (Math works, inc), and allowing for analysis and visualization of functional brain networks from M/EEG recordings. EEGNET is developed to analyze networks either at the level of scalp electrodes or at the level of reconstructed cortical sources. It includes i) Basic steps in preprocessing M/EEG signals, ii) the solution of the inverse problem to localize / reconstruct the cortical sources, iii) the computation of functional connectivity among signals collected at surface electrodes or/and time courses of reconstructed sources and iv) the computation of the network measures based on graph theory analysis. EEGNET is the unique tool that combines the M/EEG functional connectivity analysis and the computation of network measures derived from the graph theory. The first version of EEGNET is easy to use, flexible and user friendly. EEGNET is an open source tool and can be freely downloaded from this webpage: https://sites.google.com/site/eegnetworks/.

EEGNET: An Open Source Tool for Analyzing and Visualizing M/EEG Connectome

PubMed Central

Hassan, Mahmoud; Shamas, Mohamad; Khalil, Mohamad; El Falou, Wassim; Wendling, Fabrice

2015-01-01

The brain is a large-scale complex network often referred to as the “connectome”. Exploring the dynamic behavior of the connectome is a challenging issue as both excellent time and space resolution is required. In this context Magneto/Electroencephalography (M/EEG) are effective neuroimaging techniques allowing for analysis of the dynamics of functional brain networks at scalp level and/or at reconstructed sources. However, a tool that can cover all the processing steps of identifying brain networks from M/EEG data is still missing. In this paper, we report a novel software package, called EEGNET, running under MATLAB (Math works, inc), and allowing for analysis and visualization of functional brain networks from M/EEG recordings. EEGNET is developed to analyze networks either at the level of scalp electrodes or at the level of reconstructed cortical sources. It includes i) Basic steps in preprocessing M/EEG signals, ii) the solution of the inverse problem to localize / reconstruct the cortical sources, iii) the computation of functional connectivity among signals collected at surface electrodes or/and time courses of reconstructed sources and iv) the computation of the network measures based on graph theory analysis. EEGNET is the unique tool that combines the M/EEG functional connectivity analysis and the computation of network measures derived from the graph theory. The first version of EEGNET is easy to use, flexible and user friendly. EEGNET is an open source tool and can be freely downloaded from this webpage: https://sites.google.com/site/eegnetworks/. PMID:26379232

Open Source GIS based integrated watershed management

NASA Astrophysics Data System (ADS)

Byrne, J. M.; Lindsay, J.; Berg, A. A.

2013-12-01

Optimal land and water management to address future and current resource stresses and allocation challenges requires the development of state-of-the-art geomatics and hydrological modelling tools. Future hydrological modelling tools should be of high resolution, process based with real-time capability to assess changing resource issues critical to short, medium and long-term enviromental management. The objective here is to merge two renowned, well published resource modeling programs to create an source toolbox for integrated land and water management applications. This work will facilitate a much increased efficiency in land and water resource security, management and planning. Following an 'open-source' philosophy, the tools will be computer platform independent with source code freely available, maximizing knowledge transfer and the global value of the proposed research. The envisioned set of water resource management tools will be housed within 'Whitebox Geospatial Analysis Tools'. Whitebox, is an open-source geographical information system (GIS) developed by Dr. John Lindsay at the University of Guelph. The emphasis of the Whitebox project has been to develop a user-friendly interface for advanced spatial analysis in environmental applications. The plugin architecture of the software is ideal for the tight-integration of spatially distributed models and spatial analysis algorithms such as those contained within the GENESYS suite. Open-source development extends knowledge and technology transfer to a broad range of end-users and builds Canadian capability to address complex resource management problems with better tools and expertise for managers in Canada and around the world. GENESYS (Generate Earth Systems Science input) is an innovative, efficient, high-resolution hydro- and agro-meteorological model for complex terrain watersheds developed under the direction of Dr. James Byrne. GENESYS is an outstanding research and applications tool to address challenging resource management issues in industry, government and nongovernmental agencies. Current research and analysis tools were developed to manage meteorological, climatological, and land and water resource data efficiently at high resolution in space and time. The deliverable for this work is a Whitebox-GENESYS open-source resource management capacity with routines for GIS based watershed management including water in agriculture and food production. We are adding urban water management routines through GENESYS in 2013-15 with an engineering PhD candidate. Both Whitebox-GAT and GENESYS are already well-established tools. The proposed research will combine these products to create an open-source geomatics based water resource management tool that is revolutionary in both capacity and availability to a wide array of Canadian and global users

MetaNET--a web-accessible interactive platform for biological metabolic network analysis.

PubMed

Narang, Pankaj; Khan, Shawez; Hemrom, Anmol Jaywant; Lynn, Andrew Michael

2014-01-01

Metabolic reactions have been extensively studied and compiled over the last century. These have provided a theoretical base to implement models, simulations of which are used to identify drug targets and optimize metabolic throughput at a systemic level. While tools for the perturbation of metabolic networks are available, their applications are limited and restricted as they require varied dependencies and often a commercial platform for full functionality. We have developed MetaNET, an open source user-friendly platform-independent and web-accessible resource consisting of several pre-defined workflows for metabolic network analysis. MetaNET is a web-accessible platform that incorporates a range of functions which can be combined to produce different simulations related to metabolic networks. These include (i) optimization of an objective function for wild type strain, gene/catalyst/reaction knock-out/knock-down analysis using flux balance analysis. (ii) flux variability analysis (iii) chemical species participation (iv) cycles and extreme paths identification and (v) choke point reaction analysis to facilitate identification of potential drug targets. The platform is built using custom scripts along with the open-source Galaxy workflow and Systems Biology Research Tool as components. Pre-defined workflows are available for common processes, and an exhaustive list of over 50 functions are provided for user defined workflows. MetaNET, available at http://metanet.osdd.net , provides a user-friendly rich interface allowing the analysis of genome-scale metabolic networks under various genetic and environmental conditions. The framework permits the storage of previous results, the ability to repeat analysis and share results with other users over the internet as well as run different tools simultaneously using pre-defined workflows, and user-created custom workflows.

Antibiogramj: A tool for analysing images from disk diffusion tests.

PubMed

Alonso, C A; Domínguez, C; Heras, J; Mata, E; Pascual, V; Torres, C; Zarazaga, M

2017-05-01

Disk diffusion testing, known as antibiogram, is widely applied in microbiology to determine the antimicrobial susceptibility of microorganisms. The measurement of the diameter of the zone of growth inhibition of microorganisms around the antimicrobial disks in the antibiogram is frequently performed manually by specialists using a ruler. This is a time-consuming and error-prone task that might be simplified using automated or semi-automated inhibition zone readers. However, most readers are usually expensive instruments with embedded software that require significant changes in laboratory design and workflow. Based on the workflow employed by specialists to determine the antimicrobial susceptibility of microorganisms, we have designed a software tool that, from images of disk diffusion tests, semi-automatises the process. Standard computer vision techniques are employed to achieve such an automatisation. We present AntibiogramJ, a user-friendly and open-source software tool to semi-automatically determine, measure and categorise inhibition zones of images from disk diffusion tests. AntibiogramJ is implemented in Java and deals with images captured with any device that incorporates a camera, including digital cameras and mobile phones. The fully automatic procedure of AntibiogramJ for measuring inhibition zones achieves an overall agreement of 87% with an expert microbiologist; moreover, AntibiogramJ includes features to easily detect when the automatic reading is not correct and fix it manually to obtain the correct result. AntibiogramJ is a user-friendly, platform-independent, open-source, and free tool that, up to the best of our knowledge, is the most complete software tool for antibiogram analysis without requiring any investment in new equipment or changes in the laboratory. Copyright © 2017 Elsevier B.V. All rights reserved.

MethLAB: a graphical user interface package for the analysis of array-based DNA methylation data.

PubMed

Kilaru, Varun; Barfield, Richard T; Schroeder, James W; Smith, Alicia K; Conneely, Karen N

2012-03-01

Recent evidence suggests that DNA methylation changes may underlie numerous complex traits and diseases. The advent of commercial, array-based methods to interrogate DNA methylation has led to a profusion of epigenetic studies in the literature. Array-based methods, such as the popular Illumina GoldenGate and Infinium platforms, estimate the proportion of DNA methylated at single-base resolution for thousands of CpG sites across the genome. These arrays generate enormous amounts of data, but few software resources exist for efficient and flexible analysis of these data. We developed a software package called MethLAB (http://genetics.emory.edu/conneely/MethLAB) using R, an open source statistical language that can be edited to suit the needs of the user. MethLAB features a graphical user interface (GUI) with a menu-driven format designed to efficiently read in and manipulate array-based methylation data in a user-friendly manner. MethLAB tests for association between methylation and relevant phenotypes by fitting a separate linear model for each CpG site. These models can incorporate both continuous and categorical phenotypes and covariates, as well as fixed or random batch or chip effects. MethLAB accounts for multiple testing by controlling the false discovery rate (FDR) at a user-specified level. Standard output includes a spreadsheet-ready text file and an array of publication-quality figures. Considering the growing interest in and availability of DNA methylation data, there is a great need for user-friendly open source analytical tools. With MethLAB, we present a timely resource that will allow users with no programming experience to implement flexible and powerful analyses of DNA methylation data.

Feeling labeled, judged, lectured, and rejected by family and friends over depression: cautionary results for primary care clinicians from a multi-centered, qualitative study.

PubMed

Fernandez Y-Garcia, Erik; Duberstein, Paul; Paterniti, Debora A; Cipri, Camille S; Kravitz, Richard L; Epstein, Ronald M

2012-06-29

Family and friends may help patients seek out and engage in depression care. However, patients' social networks can also undermine depression treatment and recovery. In an effort to improve depression care in primary care settings, we sought to identify, categorize, and alert primary care clinicians to depression-related messages that patients hear from friends and family that patients perceive as unhelpful or detrimental. We conducted 15 focus groups in 3 cities. Participants (n = 116) with a personal history or knowledge of depression responded to open-ended questions about depression, including self-perceived barriers to care-seeking. Focus group conversations were audio-recorded and analyzed using iterative qualitative analysis. Four themes emerged related to negatively-received depression messages delivered by family and friends. Specifically, participants perceived these messages as making them feel labeled, judged, lectured to, and rejected by family and friends when discussing depression. Some participants also expressed their interpretation of their families' motivations for delivering the messages and described how hearing these messages affected depression care. The richness of our results reflects the complexity of communication within depression sufferers' social networks around this stigmatized issue. To leverage patients' social support networks effectively in depression care, primary care clinicians should be aware of both the potentially beneficial and detrimental aspects of social support. Specifically, clinicians should consider using open-ended queries into patients' experiences with discussing depression with family and friends as an initial step in the process. An open-ended approach may avoid future emotional trauma or stigmatization and assist patients in overcoming self-imposed barriers to depression discussion, symptom disclosure, treatment adherence and follow-up care.

Feeling labeled, judged, lectured, and rejected by family and friends over depression: Cautionary results for primary care clinicians from a multi-centered, qualitative study

PubMed Central

2012-01-01

Background Family and friends may help patients seek out and engage in depression care. However, patients’ social networks can also undermine depression treatment and recovery. In an effort to improve depression care in primary care settings, we sought to identify, categorize, and alert primary care clinicians to depression-related messages that patients hear from friends and family that patients perceive as unhelpful or detrimental. Methods We conducted 15 focus groups in 3 cities. Participants (n = 116) with a personal history or knowledge of depression responded to open-ended questions about depression, including self-perceived barriers to care-seeking. Focus group conversations were audio-recorded and analyzed using iterative qualitative analysis. Results Four themes emerged related to negatively-received depression messages delivered by family and friends. Specifically, participants perceived these messages as making them feel labeled, judged, lectured to, and rejected by family and friends when discussing depression. Some participants also expressed their interpretation of their families’ motivations for delivering the messages and described how hearing these messages affected depression care. Conclusions The richness of our results reflects the complexity of communication within depression sufferers’ social networks around this stigmatized issue. To leverage patients’ social support networks effectively in depression care, primary care clinicians should be aware of both the potentially beneficial and detrimental aspects of social support. Specifically, clinicians should consider using open-ended queries into patients’ experiences with discussing depression with family and friends as an initial step in the process. An open-ended approach may avoid future emotional trauma or stigmatization and assist patients in overcoming self-imposed barriers to depression discussion, symptom disclosure, treatment adherence and follow-up care. PMID:22747989

Comparing sexual-minority and heterosexual young women's friends and parents as sources of support for sexual issues.

PubMed

Friedman, Carly K; Morgan, Elizabeth M

2009-08-01

The present study provides a comparative analysis of sexual-minority and heterosexual emerging adult women's experiences seeking support for sexual issues from parents and friends. Participants included 229 college women (88 sexual-minority women; 141 heterosexual women), ranging from 18 to 25 years of age, who provided written responses to an inquiry about a time they went to friends and parents for support for a issue related to their sexuality. Responses indicated that the majority of participants had sought support from either a parent or a friend and that mothers and female friends were more likely involved than fathers or male friends, respectively. Sexual issues that participants reported discussing with parents and friends were inductively grouped into five categories: dating and romantic relationships, sexual behavior, sexual health, identity negotiation, and discrimination and violence. Issues that were discussed differed based on sexual orientation identity and the source of support (parent or friend); they did not differ by age. Participants generally perceived parents and friends' responses as helpful, though sexual-minority participants perceived both parents and friends' responses as less helpful than did heterosexual participants. Overall, results suggest both similarities and differences between sexual-minority and heterosexual young women's experiences seeking support for sexual issues from parents and friends.

SVAw - a web-based application tool for automated surrogate variable analysis of gene expression studies

PubMed Central

2013-01-01

Background Surrogate variable analysis (SVA) is a powerful method to identify, estimate, and utilize the components of gene expression heterogeneity due to unknown and/or unmeasured technical, genetic, environmental, or demographic factors. These sources of heterogeneity are common in gene expression studies, and failing to incorporate them into the analysis can obscure results. Using SVA increases the biological accuracy and reproducibility of gene expression studies by identifying these sources of heterogeneity and correctly accounting for them in the analysis. Results Here we have developed a web application called SVAw (Surrogate variable analysis Web app) that provides a user friendly interface for SVA analyses of genome-wide expression studies. The software has been developed based on open source bioconductor SVA package. In our software, we have extended the SVA program functionality in three aspects: (i) the SVAw performs a fully automated and user friendly analysis workflow; (ii) It calculates probe/gene Statistics for both pre and post SVA analysis and provides a table of results for the regression of gene expression on the primary variable of interest before and after correcting for surrogate variables; and (iii) it generates a comprehensive report file, including graphical comparison of the outcome for the user. Conclusions SVAw is a web server freely accessible solution for the surrogate variant analysis of high-throughput datasets and facilitates removing all unwanted and unknown sources of variation. It is freely available for use at http://psychiatry.igm.jhmi.edu/sva. The executable packages for both web and standalone application and the instruction for installation can be downloaded from our web site. PMID:23497726

Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes.

PubMed

Winsor, Geoffrey L; Van Rossum, Thea; Lo, Raymond; Khaira, Bhavjinder; Whiteside, Matthew D; Hancock, Robert E W; Brinkman, Fiona S L

2009-01-01

Pseudomonas aeruginosa is a well-studied opportunistic pathogen that is particularly known for its intrinsic antimicrobial resistance, diverse metabolic capacity, and its ability to cause life threatening infections in cystic fibrosis patients. The Pseudomonas Genome Database (http://www.pseudomonas.com) was originally developed as a resource for peer-reviewed, continually updated annotation for the Pseudomonas aeruginosa PAO1 reference strain genome. In order to facilitate cross-strain and cross-species genome comparisons with other Pseudomonas species of importance, we have now expanded the database capabilities to include all Pseudomonas species, and have developed or incorporated methods to facilitate high quality comparative genomics. The database contains robust assessment of orthologs, a novel ortholog clustering method, and incorporates five views of the data at the sequence and annotation levels (Gbrowse, Mauve and custom views) to facilitate genome comparisons. A choice of simple and more flexible user-friendly Boolean search features allows researchers to search and compare annotations or sequences within or between genomes. Other features include more accurate protein subcellular localization predictions and a user-friendly, Boolean searchable log file of updates for the reference strain PAO1. This database aims to continue to provide a high quality, annotated genome resource for the research community and is available under an open source license.

MSiReader: an open-source interface to view and analyze high resolving power MS imaging files on Matlab platform.

PubMed

Robichaud, Guillaume; Garrard, Kenneth P; Barry, Jeremy A; Muddiman, David C

2013-05-01

During the past decade, the field of mass spectrometry imaging (MSI) has greatly evolved, to a point where it has now been fully integrated by most vendors as an optional or dedicated platform that can be purchased with their instruments. However, the technology is not mature and multiple research groups in both academia and industry are still very actively studying the fundamentals of imaging techniques, adapting the technology to new ionization sources, and developing new applications. As a result, there important varieties of data file formats used to store mass spectrometry imaging data and, concurrent to the development of MSi, collaborative efforts have been undertaken to introduce common imaging data file formats. However, few free software packages to read and analyze files of these different formats are readily available. We introduce here MSiReader, a free open source application to read and analyze high resolution MSI data from the most common MSi data formats. The application is built on the Matlab platform (Mathworks, Natick, MA, USA) and includes a large selection of data analysis tools and features. People who are unfamiliar with the Matlab language will have little difficult navigating the user-friendly interface, and users with Matlab programming experience can adapt and customize MSiReader for their own needs.

MSiReader: An Open-Source Interface to View and Analyze High Resolving Power MS Imaging Files on Matlab Platform

NASA Astrophysics Data System (ADS)

Robichaud, Guillaume; Garrard, Kenneth P.; Barry, Jeremy A.; Muddiman, David C.

2013-05-01

During the past decade, the field of mass spectrometry imaging (MSI) has greatly evolved, to a point where it has now been fully integrated by most vendors as an optional or dedicated platform that can be purchased with their instruments. However, the technology is not mature and multiple research groups in both academia and industry are still very actively studying the fundamentals of imaging techniques, adapting the technology to new ionization sources, and developing new applications. As a result, there important varieties of data file formats used to store mass spectrometry imaging data and, concurrent to the development of MSi, collaborative efforts have been undertaken to introduce common imaging data file formats. However, few free software packages to read and analyze files of these different formats are readily available. We introduce here MSiReader, a free open source application to read and analyze high resolution MSI data from the most common MSi data formats. The application is built on the Matlab platform (Mathworks, Natick, MA, USA) and includes a large selection of data analysis tools and features. People who are unfamiliar with the Matlab language will have little difficult navigating the user-friendly interface, and users with Matlab programming experience can adapt and customize MSiReader for their own needs.

CellShape: A user-friendly image analysis tool for quantitative visualization of bacterial cell factories inside.

PubMed

Goñi-Moreno, Ángel; Kim, Juhyun; de Lorenzo, Víctor

2017-02-01

Visualization of the intracellular constituents of individual bacteria while performing as live biocatalysts is in principle doable through more or less sophisticated fluorescence microscopy. Unfortunately, rigorous quantitation of the wealth of data embodied in the resulting images requires bioinformatic tools that are not widely extended within the community-let alone that they are often subject to licensing that impedes software reuse. In this context we have developed CellShape, a user-friendly platform for image analysis with subpixel precision and double-threshold segmentation system for quantification of fluorescent signals stemming from single-cells. CellShape is entirely coded in Python, a free, open-source programming language with widespread community support. For a developer, CellShape enhances extensibility (ease of software improvements) by acting as an interface to access and use existing Python modules; for an end-user, CellShape presents standalone executable files ready to open without installation. We have adopted this platform to analyse with an unprecedented detail the tridimensional distribution of the constituents of the gene expression flow (DNA, RNA polymerase, mRNA and ribosomal proteins) in individual cells of the industrial platform strain Pseudomonas putida KT2440. While the CellShape first release version (v0.8) is readily operational, users and/or developers are enabled to expand the platform further. Copyright © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

ABrox-A user-friendly Python module for approximate Bayesian computation with a focus on model comparison.

PubMed

Mertens, Ulf Kai; Voss, Andreas; Radev, Stefan

2018-01-01

We give an overview of the basic principles of approximate Bayesian computation (ABC), a class of stochastic methods that enable flexible and likelihood-free model comparison and parameter estimation. Our new open-source software called ABrox is used to illustrate ABC for model comparison on two prominent statistical tests, the two-sample t-test and the Levene-Test. We further highlight the flexibility of ABC compared to classical Bayesian hypothesis testing by computing an approximate Bayes factor for two multinomial processing tree models. Last but not least, throughout the paper, we introduce ABrox using the accompanied graphical user interface.

TOPSAN: a dynamic web database for structural genomics.

PubMed

Ellrott, Kyle; Zmasek, Christian M; Weekes, Dana; Sri Krishna, S; Bakolitsa, Constantina; Godzik, Adam; Wooley, John

2011-01-01

The Open Protein Structure Annotation Network (TOPSAN) is a web-based collaboration platform for exploring and annotating structures determined by structural genomics efforts. Characterization of those structures presents a challenge since the majority of the proteins themselves have not yet been characterized. Responding to this challenge, the TOPSAN platform facilitates collaborative annotation and investigation via a user-friendly web-based interface pre-populated with automatically generated information. Semantic web technologies expand and enrich TOPSAN's content through links to larger sets of related databases, and thus, enable data integration from disparate sources and data mining via conventional query languages. TOPSAN can be found at http://www.topsan.org.

COPASI and its applications in biotechnology.

PubMed

Bergmann, Frank T; Hoops, Stefan; Klahn, Brian; Kummer, Ursula; Mendes, Pedro; Pahle, Jürgen; Sahle, Sven

2017-11-10

COPASI is software used for the creation, modification, simulation and computational analysis of kinetic models in various fields. It is open-source, available for all major platforms and provides a user-friendly graphical user interface, but is also controllable via the command line and scripting languages. These are likely reasons for its wide acceptance. We begin this review with a short introduction describing the general approaches and techniques used in computational modeling in the biosciences. Next we introduce the COPASI package, and its capabilities, before looking at typical applications of COPASI in biotechnology. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Trans-oral robotic surgery in oropharyngeal carcinoma - A guide for general practitioners and patients.

PubMed

Liu, Wendy Sijia; Limmer, Alex; Jabbour, Joe; Clark, Jonathan

Trans-oral robotic surgery (TORS) is emerging as a minimally invasive alternative to open surgery, or trans-oral laser surgery, for the treatment of some head and neck pathologies, particularly oropharyngeal carcinoma, which is rapidly increasing in incidence. In this article we review current evidence regarding the use of TORS in head and neck surgery in a manner relevant to general practice. This information may be used to facilitate discussion with patients. Compared with open surgery or trans-oral laser surgery, TORS has numerous advantages, including no scarring, less blood loss, fewer complications, lower rates of admission to the intensive care unit, and reduced length of hospitalisation. The availability of TORS in Australia is currently limited and, therefore, public awareness about TORS is lacking. Details regarding the role of TORS and reliable, up-to-date, patient-friendly information sources are discussed in this article.

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

Krishnamurthy, Dheepak

This paper is an overview of Power System Simulation Toolbox (psst). psst is an open-source Python application for the simulation and analysis of power system models. psst simulates the wholesale market operation by solving a DC Optimal Power Flow (DCOPF), Security Constrained Unit Commitment (SCUC) and a Security Constrained Economic Dispatch (SCED). psst also includes models for the various entities in a power system such as Generator Companies (GenCos), Load Serving Entities (LSEs) and an Independent System Operator (ISO). psst features an open modular object oriented architecture that will make it useful for researchers to customize, expand, experiment beyond solvingmore » traditional problems. psst also includes a web based Graphical User Interface (GUI) that allows for user friendly interaction and for implementation on remote High Performance Computing (HPCs) clusters for parallelized operations. This paper also provides an illustrative application of psst and benchmarks with standard IEEE test cases to show the advanced features and the performance of toolbox.« less

HGDB: A web retrieving cardiovascular-associated gene data.

PubMed

Noorabad-Ghahroodi, Faezeh; Abdi, Samaneh; Zand, Amir Hossein; Najafi, Mohammad

2017-04-01

The use of data obtained from high throughput techniques in genetics studies is an essential subject in biology. The system approaches of networking and enriching may improve the data management. Here, we annotated the molecular features for cardiovascular-associated genes and presented the HGDB search-based database (www.hgdb.ir). The initial seed data was primarily used from Gene Ontology and was automatically enriched with other molecular features. The data was managed in a SQL popular and open source. The search tabs on the HGDB homepage were applied for ID/Name Gene, chromosome, cell organelle and all gene options. The search results were presented on the gene text-based and source link-based descriptions. The HGDB is a friendly website to present gene data in the cardiovascular field. Copyright © 2017 Elsevier B.V. All rights reserved.

College Students' Beliefs about Supporting a Grieving Peer

ERIC Educational Resources Information Center

Tedrick Parikh, Sara J.; Servaty-Seib, Heather L.

2013-01-01

The present study used I. Ajzen's (1991) Theory of Planned Behavior (TBP) to explore college students' beliefs about listening supportively to a grieving friend. Responses to open-ended questions suggested that students ("N" = 23) perceived both benefits and risks, connected with listening supportively, for the grieving friend and for…

S2P: A software tool to quickly carry out reproducible biomedical research projects involving 2D-gel and MALDI-TOF MS protein data.

PubMed

López-Fernández, Hugo; Araújo, José E; Jorge, Susana; Glez-Peña, Daniel; Reboiro-Jato, Miguel; Santos, Hugo M; Fdez-Riverola, Florentino; Capelo, José L

2018-03-01

2D-gel electrophoresis is widely used in combination with MALDI-TOF mass spectrometry in order to analyze the proteome of biological samples. For instance, it can be used to discover proteins that are differentially expressed between two groups (e.g. two disease conditions, case vs. control, etc.) thus obtaining a set of potential biomarkers. This procedure requires a great deal of data processing in order to prepare data for analysis or to merge and integrate data from different sources. This kind of work is usually done manually (e.g. copying and pasting data into spreadsheet files), which is highly time consuming and distracts the researcher from other important, core tasks. Moreover, engaging in a repetitive process in a non-automated, handling-based manner is prone to error, thus threatening reliability and reproducibility. The objective of this paper is to present S2P, an open source software to overcome these drawbacks. S2P is implemented in Java on top of the AIBench framework, and relies on well-established open source libraries to accomplish different tasks. S2P is an AIBench based desktop multiplatform application, specifically aimed to process 2D-gel and MALDI-mass spectrometry protein identification-based data in a computer-aided, reproducible manner. Different case studies are presented in order to show the usefulness of S2P. S2P is open source and free to all users at http://www.sing-group.org/s2p. Through its user-friendly GUI interface, S2P dramatically reduces the time that researchers need to invest in order to prepare data for analysis. Copyright © 2017 Elsevier B.V. All rights reserved.

WImpiBLAST: web interface for mpiBLAST to help biologists perform large-scale annotation using high performance computing.

PubMed

Sharma, Parichit; Mantri, Shrikant S

2014-01-01

The function of a newly sequenced gene can be discovered by determining its sequence homology with known proteins. BLAST is the most extensively used sequence analysis program for sequence similarity search in large databases of sequences. With the advent of next generation sequencing technologies it has now become possible to study genes and their expression at a genome-wide scale through RNA-seq and metagenome sequencing experiments. Functional annotation of all the genes is done by sequence similarity search against multiple protein databases. This annotation task is computationally very intensive and can take days to obtain complete results. The program mpiBLAST, an open-source parallelization of BLAST that achieves superlinear speedup, can be used to accelerate large-scale annotation by using supercomputers and high performance computing (HPC) clusters. Although many parallel bioinformatics applications using the Message Passing Interface (MPI) are available in the public domain, researchers are reluctant to use them due to lack of expertise in the Linux command line and relevant programming experience. With these limitations, it becomes difficult for biologists to use mpiBLAST for accelerating annotation. No web interface is available in the open-source domain for mpiBLAST. We have developed WImpiBLAST, a user-friendly open-source web interface for parallel BLAST searches. It is implemented in Struts 1.3 using a Java backbone and runs atop the open-source Apache Tomcat Server. WImpiBLAST supports script creation and job submission features and also provides a robust job management interface for system administrators. It combines script creation and modification features with job monitoring and management through the Torque resource manager on a Linux-based HPC cluster. Use case information highlights the acceleration of annotation analysis achieved by using WImpiBLAST. Here, we describe the WImpiBLAST web interface features and architecture, explain design decisions, describe workflows and provide a detailed analysis.

WImpiBLAST: Web Interface for mpiBLAST to Help Biologists Perform Large-Scale Annotation Using High Performance Computing

PubMed Central

Sharma, Parichit; Mantri, Shrikant S.

2014-01-01

The function of a newly sequenced gene can be discovered by determining its sequence homology with known proteins. BLAST is the most extensively used sequence analysis program for sequence similarity search in large databases of sequences. With the advent of next generation sequencing technologies it has now become possible to study genes and their expression at a genome-wide scale through RNA-seq and metagenome sequencing experiments. Functional annotation of all the genes is done by sequence similarity search against multiple protein databases. This annotation task is computationally very intensive and can take days to obtain complete results. The program mpiBLAST, an open-source parallelization of BLAST that achieves superlinear speedup, can be used to accelerate large-scale annotation by using supercomputers and high performance computing (HPC) clusters. Although many parallel bioinformatics applications using the Message Passing Interface (MPI) are available in the public domain, researchers are reluctant to use them due to lack of expertise in the Linux command line and relevant programming experience. With these limitations, it becomes difficult for biologists to use mpiBLAST for accelerating annotation. No web interface is available in the open-source domain for mpiBLAST. We have developed WImpiBLAST, a user-friendly open-source web interface for parallel BLAST searches. It is implemented in Struts 1.3 using a Java backbone and runs atop the open-source Apache Tomcat Server. WImpiBLAST supports script creation and job submission features and also provides a robust job management interface for system administrators. It combines script creation and modification features with job monitoring and management through the Torque resource manager on a Linux-based HPC cluster. Use case information highlights the acceleration of annotation analysis achieved by using WImpiBLAST. Here, we describe the WImpiBLAST web interface features and architecture, explain design decisions, describe workflows and provide a detailed analysis. PMID:24979410

Photon-HDF5: An Open File Format for Timestamp-Based Single-Molecule Fluorescence Experiments.

PubMed

Ingargiola, Antonino; Laurence, Ted; Boutelle, Robert; Weiss, Shimon; Michalet, Xavier

2016-01-05

We introduce Photon-HDF5, an open and efficient file format to simplify exchange and long-term accessibility of data from single-molecule fluorescence experiments based on photon-counting detectors such as single-photon avalanche diode, photomultiplier tube, or arrays of such detectors. The format is based on HDF5, a widely used platform- and language-independent hierarchical file format for which user-friendly viewers are available. Photon-HDF5 can store raw photon data (timestamp, channel number, etc.) from any acquisition hardware, but also setup and sample description, information on provenance, authorship and other metadata, and is flexible enough to include any kind of custom data. The format specifications are hosted on a public website, which is open to contributions by the biophysics community. As an initial resource, the website provides code examples to read Photon-HDF5 files in several programming languages and a reference Python library (phconvert), to create new Photon-HDF5 files and convert several existing file formats into Photon-HDF5. To encourage adoption by the academic and commercial communities, all software is released under the MIT open source license. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Photon-HDF5: An Open File Format for Timestamp-Based Single-Molecule Fluorescence Experiments

PubMed Central

Ingargiola, Antonino; Laurence, Ted; Boutelle, Robert; Weiss, Shimon; Michalet, Xavier

2016-01-01

We introduce Photon-HDF5, an open and efficient file format to simplify exchange and long-term accessibility of data from single-molecule fluorescence experiments based on photon-counting detectors such as single-photon avalanche diode, photomultiplier tube, or arrays of such detectors. The format is based on HDF5, a widely used platform- and language-independent hierarchical file format for which user-friendly viewers are available. Photon-HDF5 can store raw photon data (timestamp, channel number, etc.) from any acquisition hardware, but also setup and sample description, information on provenance, authorship and other metadata, and is flexible enough to include any kind of custom data. The format specifications are hosted on a public website, which is open to contributions by the biophysics community. As an initial resource, the website provides code examples to read Photon-HDF5 files in several programming languages and a reference Python library (phconvert), to create new Photon-HDF5 files and convert several existing file formats into Photon-HDF5. To encourage adoption by the academic and commercial communities, all software is released under the MIT open source license. PMID:26745406

Photon-HDF5: an open file format for single-molecule fluorescence experiments using photon-counting detectors

DOE PAGES

Ingargiola, A.; Laurence, T. A.; Boutelle, R.; ...

2015-12-23

We introduce Photon-HDF5, an open and efficient file format to simplify exchange and long term accessibility of data from single-molecule fluorescence experiments based on photon-counting detectors such as single-photon avalanche diode (SPAD), photomultiplier tube (PMT) or arrays of such detectors. The format is based on HDF5, a widely used platform- and language-independent hierarchical file format for which user-friendly viewers are available. Photon-HDF5 can store raw photon data (timestamp, channel number, etc) from any acquisition hardware, but also setup and sample description, information on provenance, authorship and other metadata, and is flexible enough to include any kind of custom data. Themore » format specifications are hosted on a public website, which is open to contributions by the biophysics community. As an initial resource, the website provides code examples to read Photon-HDF5 files in several programming languages and a reference python library (phconvert), to create new Photon-HDF5 files and convert several existing file formats into Photon-HDF5. As a result, to encourage adoption by the academic and commercial communities, all software is released under the MIT open source license.« less

Gang Free: Influencing Friendship Choices in Today's World.

ERIC Educational Resources Information Center

Wiener, Valerie

This book presents information as to how teenagers select their friends. Material was garnered through a review of the literature and hundreds of interviews. The book opens with a focus on how teenagers make friends, and includes such issues as the power of self, finding groups, peer impact, the merging process, seeking significance, and putting…

openBIS: a flexible framework for managing and analyzing complex data in biology research

PubMed Central

2011-01-01

Background Modern data generation techniques used in distributed systems biology research projects often create datasets of enormous size and diversity. We argue that in order to overcome the challenge of managing those large quantitative datasets and maximise the biological information extracted from them, a sound information system is required. Ease of integration with data analysis pipelines and other computational tools is a key requirement for it. Results We have developed openBIS, an open source software framework for constructing user-friendly, scalable and powerful information systems for data and metadata acquired in biological experiments. openBIS enables users to collect, integrate, share, publish data and to connect to data processing pipelines. This framework can be extended and has been customized for different data types acquired by a range of technologies. Conclusions openBIS is currently being used by several SystemsX.ch and EU projects applying mass spectrometric measurements of metabolites and proteins, High Content Screening, or Next Generation Sequencing technologies. The attributes that make it interesting to a large research community involved in systems biology projects include versatility, simplicity in deployment, scalability to very large data, flexibility to handle any biological data type and extensibility to the needs of any research domain. PMID:22151573

Graphic representations: keys to disclose the codex of nature

NASA Astrophysics Data System (ADS)

Caramelo, Liliana; Gonçalves, Norberto; Pereira, Mário; Soares, Armando; Naia, Marco

2010-05-01

Undergraduate and university level students present some difficulties to understand and interpret many of the geosciences concepts, in particular those represented by vector and scalar fields. Our experience reveals that these difficulties are associated with a lack in the development of their abstraction and mental picturing abilities. On the other hand, these students have easy access to communication and information technology software which can be used to built graphic representations of experimental data, time series and vector and scalar fields. This transformation allows an easiest extraction, interpretation and summary of the most important characteristics in the data. There is already commercial and open source software with graphical tools that can be used for this purpose but commercial software packs with user friendly interfaces but their price is not negligible. Open source software can circumvent this difficulty even if, in general, their graphical user interface hasn't reached the desirable level of the commercial ones. We will show a simple procedure to generate an image from the data that characterizes the generation of the suitable images illustrating the key concepts in study, using a freeware code, exactly as it is presented to the students in our open teaching sessions to the general student community. Our experience demonstrated that the students are very enthusiastic using this approach. Furthermore, the use of this software can easily be adopted by teachers and students of secondary schools as part of curricular activities.

The EarthServer Federation: State, Role, and Contribution to GEOSS

NASA Astrophysics Data System (ADS)

Merticariu, Vlad; Baumann, Peter

2016-04-01

The intercontinental EarthServer initiative has established a European datacube platform with proven scalability: known databases exceed 100 TB, and single queries have been split across more than 1,000 cloud nodes. Its service interface being rigorously based on the OGC "Big Geo Data" standards, Web Coverage Service (WCS) and Web Coverage Processing Service (WCPS), a series of clients can dock into the services, ranging from open-source OpenLayers and QGIS over open-source NASA WorldWind to proprietary ESRI ArcGIS. Datacube fusion in a "mix and match" style is supported by the platform technolgy, the rasdaman Array Database System, which transparently federates queries so that users simply approach any node of the federation to access any data item, internally optimized for minimal data transfer. Notably, rasdaman is part of GEOSS GCI. NASA is contributing its Web WorldWind virtual globe for user-friendly data extraction, navigation, and analysis. Integrated datacube / metadata queries are contributed by CITE. Current federation members include ESA (managed by MEEO sr.l.), Plymouth Marine Laboratory (PML), the European Centre for Medium-Range Weather Forecast (ECMWF), Australia's National Computational Infrastructure, and Jacobs University (adding in Planetary Science). Further data centers have expressed interest in joining. We present the EarthServer approach, discuss its underlying technology, and illustrate the contribution this datacube platform can make to GEOSS.

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

Ingargiola, A.; Laurence, T. A.; Boutelle, R.

We introduce Photon-HDF5, an open and efficient file format to simplify exchange and long term accessibility of data from single-molecule fluorescence experiments based on photon-counting detectors such as single-photon avalanche diode (SPAD), photomultiplier tube (PMT) or arrays of such detectors. The format is based on HDF5, a widely used platform- and language-independent hierarchical file format for which user-friendly viewers are available. Photon-HDF5 can store raw photon data (timestamp, channel number, etc) from any acquisition hardware, but also setup and sample description, information on provenance, authorship and other metadata, and is flexible enough to include any kind of custom data. Themore » format specifications are hosted on a public website, which is open to contributions by the biophysics community. As an initial resource, the website provides code examples to read Photon-HDF5 files in several programming languages and a reference python library (phconvert), to create new Photon-HDF5 files and convert several existing file formats into Photon-HDF5. As a result, to encourage adoption by the academic and commercial communities, all software is released under the MIT open source license.« less

Cloudy's Journey from FORTRAN to C, Why and How

NASA Astrophysics Data System (ADS)

Ferland, G. J.

Cloudy is a large-scale plasma simulation code that is widely used across the astronomical community as an aid in the interpretation of spectroscopic data. The cover of the ADAS VI book featured predictions of the code. The FORTRAN 77 source code has always been freely available on the Internet, contributing to its widespread use. The coming of PCs and Linux has fundamentally changed the computing environment. Modern Fortran compilers (F90 and F95) are not freely available. A common-use code must be written in either FORTRAN 77 or C to be Open Source/GNU/Linux friendly. F77 has serious drawbacks - modern language constructs cannot be used, students do not have skills in this language, and it does not contribute to their future employability. It became clear that the code would have to be ported to C to have a viable future. I describe the approach I used to convert Cloudy from FORTRAN 77 with MILSPEC extensions to ANSI/ISO 89 C. Cloudy is now openly available as a C code, and will evolve to C++ as gcc and standard C++ mature. Cloudy looks to a bright future with a modern language.

Pulse sequence programming in a dynamic visual environment: SequenceTree.

PubMed

Magland, Jeremy F; Li, Cheng; Langham, Michael C; Wehrli, Felix W

2016-01-01

To describe SequenceTree, an open source, integrated software environment for implementing MRI pulse sequences and, ideally, exporting them to actual MRI scanners. The software is a user-friendly alternative to vendor-supplied pulse sequence design and editing tools and is suited for programmers and nonprogrammers alike. The integrated user interface was programmed using the Qt4/C++ toolkit. As parameters and code are modified, the pulse sequence diagram is automatically updated within the user interface. Several aspects of pulse programming are handled automatically, allowing users to focus on higher-level aspects of sequence design. Sequences can be simulated using a built-in Bloch equation solver and then exported for use on a Siemens MRI scanner. Ideally, other types of scanners will be supported in the future. SequenceTree has been used for 8 years in our laboratory and elsewhere and has contributed to more than 50 peer-reviewed publications in areas such as cardiovascular imaging, solid state and nonproton NMR, MR elastography, and high-resolution structural imaging. SequenceTree is an innovative, open source, visual pulse sequence environment for MRI combining simplicity with flexibility and is ideal both for advanced users and users with limited programming experience. © 2015 Wiley Periodicals, Inc.

Links between Friends' Physical Aggression and Adolescents' Physical Aggression: What Happens If Gene-Environment Correlations are Controlled?

ERIC Educational Resources Information Center

Vitaro, Frank; Brendgen, Mara; Girard, Alain; Dionne, Ginette; Tremblay, Richard E.; Boivin, Michel

2016-01-01

Exposure to deviant friends has been found to be a powerful source of influence on children's and adolescents' aggressive behavior. However, the contribution of deviant friends may have been overestimated because of a possible non-accounted gene-environment correlation (rGE). In this study, we used a cross-lagged design to test whether friends'…

An Open Catalog for Supernova Data

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

Guillochon, James; Parrent, Jerod; Kelley, Luke Zoltan

We present the Open Supernova Catalog , an online collection of observations and metadata for presently 36,000+ supernovae and related candidates. The catalog is freely available on the web (https://sne.space), with its main interface having been designed to be a user-friendly, rapidly searchable table accessible on desktop and mobile devices. In addition to the primary catalog table containing supernova metadata, an individual page is generated for each supernova, which displays its available metadata, light curves, and spectra spanning X-ray to radio frequencies. The data presented in the catalog is automatically rebuilt on a daily basis and is constructed by parsingmore » several dozen sources, including the data presented in the supernova literature and from secondary sources such as other web-based catalogs. Individual supernova data is stored in the hierarchical, human- and machine-readable JSON format, with the entirety of each supernova’s data being contained within a single JSON file bearing its name. The setup we present here, which is based on open-source software maintained via git repositories hosted on github, enables anyone to download the entirety of the supernova data set to their home computer in minutes, and to make contributions of their own data back to the catalog via git. As the supernova data set continues to grow, especially in the upcoming era of all-sky synoptic telescopes, which will increase the total number of events by orders of magnitude, we hope that the catalog we have designed will be a valuable tool for the community to analyze both historical and contemporary supernovae.« less

An Open Catalog for Supernova Data

NASA Astrophysics Data System (ADS)

Guillochon, James; Parrent, Jerod; Kelley, Luke Zoltan; Margutti, Raffaella

2017-01-01

We present the Open Supernova Catalog, an online collection of observations and metadata for presently 36,000+ supernovae and related candidates. The catalog is freely available on the web (https://sne.space), with its main interface having been designed to be a user-friendly, rapidly searchable table accessible on desktop and mobile devices. In addition to the primary catalog table containing supernova metadata, an individual page is generated for each supernova, which displays its available metadata, light curves, and spectra spanning X-ray to radio frequencies. The data presented in the catalog is automatically rebuilt on a daily basis and is constructed by parsing several dozen sources, including the data presented in the supernova literature and from secondary sources such as other web-based catalogs. Individual supernova data is stored in the hierarchical, human- and machine-readable JSON format, with the entirety of each supernova’s data being contained within a single JSON file bearing its name. The setup we present here, which is based on open-source software maintained via git repositories hosted on github, enables anyone to download the entirety of the supernova data set to their home computer in minutes, and to make contributions of their own data back to the catalog via git. As the supernova data set continues to grow, especially in the upcoming era of all-sky synoptic telescopes, which will increase the total number of events by orders of magnitude, we hope that the catalog we have designed will be a valuable tool for the community to analyze both historical and contemporary supernovae.

National Geothermal Data System: Open Access to Geoscience Data, Maps, and Documents

NASA Astrophysics Data System (ADS)

Caudill, C. M.; Richard, S. M.; Musil, L.; Sonnenschein, A.; Good, J.

2014-12-01

The U.S. National Geothermal Data System (NGDS) provides free open access to millions of geoscience data records, publications, maps, and reports via distributed web services to propel geothermal research, development, and production. NGDS is built on the US Geoscience Information Network (USGIN) data integration framework, which is a joint undertaking of the USGS and the Association of American State Geologists (AASG), and is compliant with international standards and protocols. NGDS currently serves geoscience information from 60+ data providers in all 50 states. Free and open source software is used in this federated system where data owners maintain control of their data. This interactive online system makes geoscience data easily discoverable, accessible, and interoperable at no cost to users. The dynamic project site http://geothermaldata.org serves as the information source and gateway to the system, allowing data and applications discovery and availability of the system's data feed. It also provides access to NGDS specifications and the free and open source code base (on GitHub), a map-centric and library style search interface, other software applications utilizing NGDS services, NGDS tutorials (via YouTube and USGIN site), and user-created tools and scripts. The user-friendly map-centric web-based application has been created to support finding, visualizing, mapping, and acquisition of data based on topic, location, time, provider, or key words. Geographic datasets visualized through the map interface also allow users to inspect the details of individual GIS data points (e.g. wells, geologic units, etc.). In addition, the interface provides the information necessary for users to access the GIS data from third party software applications such as GoogleEarth, UDig, and ArcGIS. A redistributable, free and open source software package called GINstack (USGIN software stack) was also created to give data providers a simple way to release data using interoperable and shareable standards, upload data and documents, and expose those data as a node in the NGDS or any larger data system through a CSW endpoint. The easy-to-use interface is supported by back-end software including Postgres, GeoServer, and custom CKAN extensions among others.

Bayesian inference for psychology. Part II: Example applications with JASP.

PubMed

Wagenmakers, Eric-Jan; Love, Jonathon; Marsman, Maarten; Jamil, Tahira; Ly, Alexander; Verhagen, Josine; Selker, Ravi; Gronau, Quentin F; Dropmann, Damian; Boutin, Bruno; Meerhoff, Frans; Knight, Patrick; Raj, Akash; van Kesteren, Erik-Jan; van Doorn, Johnny; Šmíra, Martin; Epskamp, Sacha; Etz, Alexander; Matzke, Dora; de Jong, Tim; van den Bergh, Don; Sarafoglou, Alexandra; Steingroever, Helen; Derks, Koen; Rouder, Jeffrey N; Morey, Richard D

2018-02-01

Bayesian hypothesis testing presents an attractive alternative to p value hypothesis testing. Part I of this series outlined several advantages of Bayesian hypothesis testing, including the ability to quantify evidence and the ability to monitor and update this evidence as data come in, without the need to know the intention with which the data were collected. Despite these and other practical advantages, Bayesian hypothesis tests are still reported relatively rarely. An important impediment to the widespread adoption of Bayesian tests is arguably the lack of user-friendly software for the run-of-the-mill statistical problems that confront psychologists for the analysis of almost every experiment: the t-test, ANOVA, correlation, regression, and contingency tables. In Part II of this series we introduce JASP ( http://www.jasp-stats.org ), an open-source, cross-platform, user-friendly graphical software package that allows users to carry out Bayesian hypothesis tests for standard statistical problems. JASP is based in part on the Bayesian analyses implemented in Morey and Rouder's BayesFactor package for R. Armed with JASP, the practical advantages of Bayesian hypothesis testing are only a mouse click away.

A user-friendly, open-source tool to project impact and cost of diagnostic tests for tuberculosis

PubMed Central

Dowdy, David W; Andrews, Jason R; Dodd, Peter J; Gilman, Robert H

2014-01-01

Most models of infectious diseases, including tuberculosis (TB), do not provide results customized to local conditions. We created a dynamic transmission model to project TB incidence, TB mortality, multidrug-resistant (MDR) TB prevalence, and incremental costs over 5 years after scale-up of nine alternative diagnostic strategies. A corresponding web-based interface allows users to specify local costs and epidemiology. In settings with little capacity for up-front investment, same-day microscopy had the greatest impact on TB incidence and became cost-saving within 5 years if delivered at $10/test. With greater initial investment, population-level scale-up of Xpert MTB/RIF or microcolony-based culture often averted 10 times more TB cases than narrowly-targeted strategies, at minimal incremental long-term cost. Xpert for smear-positive TB had reasonable impact on MDR-TB incidence, but at substantial price and little impact on overall TB incidence and mortality. This user-friendly modeling framework improves decision-makers' ability to evaluate the local impact of TB diagnostic strategies. DOI: http://dx.doi.org/10.7554/eLife.02565.001 PMID:24898755

The CSSIAR v.1.00 Software: A new tool based on SIAR to assess soil redistribution using Compound Specific Stable Isotopes

NASA Astrophysics Data System (ADS)

Sergio, de los Santos-Villalobos; Claudio, Bravo-Linares; dos Anjos Roberto, Meigikos; Renan, Cardoso; Max, Gibbs; Andrew, Swales; Lionel, Mabit; Gerd, Dercon

Soil erosion is one of the biggest challenges for food production around the world. Many techniques have been used to evaluate and mitigate soil degradation. Nowadays isotopic techniques are becoming a powerful tool to assess soil apportionment. One of the innovative techniques used is the Compound Specific Stable Isotopes (CSSI) analysis, which has been used to track down sediments and specify their sources by the isotopic signature of δ13 C in specific fatty acids. The application of this technique on soil apportionment has been recently developed, however there is a lack of user-friendly Software for data processing and interpretation. The aim of this article is to introduce a new open source tool for working with data sets generated by the use of the CSSI technique to assess soil apportionment, called the CSSIARv1.00 Software

Is it time to tackle PM(2.5) air pollutions in China from biomass-burning emissions?

PubMed

Zhang, Yan-Lin; Cao, Fang

2015-07-01

An increase in haze days has been observed in China over the past two decades due to the rapid industrialization, urbanization and energy consumptions. To address this server issue, Chinese central government has recently released the Action Plan on Prevention and Control of Air Pollution, which mainly focuses on regulation of indusial and transport-related emissions with major energy consumption from fossil fuels. This comprehensive and toughest plan is definitely a major step in the right direction aiming at beautiful and environmental-friendly China; however, based on recent source apportionment results, we suggest that strengthening regulation emissions from biomass-burning sources in both urban and rural areas is needed to meet a rigorous reduction target. Here, household biofuel and open biomass burning are highlighted, as impacts of these emissions can cause local and regional pollution. Copyright © 2015 Elsevier Ltd. All rights reserved.

CellTracker (not only) for dummies.

PubMed

Piccinini, Filippo; Kiss, Alexa; Horvath, Peter

2016-03-15

Time-lapse experiments play a key role in studying the dynamic behavior of cells. Single-cell tracking is one of the fundamental tools for such analyses. The vast majority of the recently introduced cell tracking methods are limited to fluorescently labeled cells. An equally important limitation is that most software cannot be effectively used by biologists without reasonable expertise in image processing. Here we present CellTracker, a user-friendly open-source software tool for tracking cells imaged with various imaging modalities, including fluorescent, phase contrast and differential interference contrast (DIC) techniques. CellTracker is written in MATLAB (The MathWorks, Inc., USA). It works with Windows, Macintosh and UNIX-based systems. Source code and graphical user interface (GUI) are freely available at: http://celltracker.website/ horvath.peter@brc.mta.hu 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.

LocusExplorer: a user-friendly tool for integrated visualization of human genetic association data and biological annotations.

PubMed

Dadaev, Tokhir; Leongamornlert, Daniel A; Saunders, Edward J; Eeles, Rosalind; Kote-Jarai, Zsofia

2016-03-15

: In this article, we present LocusExplorer, a data visualization and exploration tool for genetic association data. LocusExplorer is written in R using the Shiny library, providing access to powerful R-based functions through a simple user interface. LocusExplorer allows users to simultaneously display genetic, statistical and biological data for humans in a single image and allows dynamic zooming and customization of the plot features. Publication quality plots may then be produced in a variety of file formats. LocusExplorer is open source and runs through R and a web browser. It is available at www.oncogenetics.icr.ac.uk/LocusExplorer/ or can be installed locally and the source code accessed from https://github.com/oncogenetics/LocusExplorer tokhir.dadaev@icr.ac.uk. © The Author 2015. Published by Oxford University Press.

bioGUID: resolving, discovering, and minting identifiers for biodiversity informatics

PubMed Central

Page, Roderic DM

2009-01-01

Background Linking together the data of interest to biodiversity researchers (including specimen records, images, taxonomic names, and DNA sequences) requires services that can mint, resolve, and discover globally unique identifiers (including, but not limited to, DOIs, HTTP URIs, and LSIDs). Results bioGUID implements a range of services, the core ones being an OpenURL resolver for bibliographic resources, and a LSID resolver. The LSID resolver supports Linked Data-friendly resolution using HTTP 303 redirects and content negotiation. Additional services include journal ISSN look-up, author name matching, and a tool to monitor the status of biodiversity data providers. Conclusion bioGUID is available at . Source code is available from . PMID:19900301

NOBLAST and JAMBLAST: New Options for BLAST and a Java Application Manager for BLAST results.

PubMed

Lagnel, Jacques; Tsigenopoulos, Costas S; Iliopoulos, Ioannis

2009-03-15

NOBLAST (New Options for BLAST) is an open source program that provides a new user-friendly tabular output format for various NCBI BLAST programs (Blastn, Blastp, Blastx, Tblastn, Tblastx, Mega BLAST and Psi BLAST) without any use of a parser and provides E-value correction in case of use of segmented BLAST database. JAMBLAST using the NOBLAST output allows the user to manage, view and filter the BLAST hits using a number of selection criteria. A distribution package of NOBLAST and JAMBLAST including detailed installation procedure is freely available from http://sourceforge.net/projects/JAMBLAST/ and http://sourceforge.net/projects/NOBLAST. Supplementary data are available at Bioinformatics online.

Community-Led Total Sanitation, Open Defecation Free Status, and Ebola Virus Disease in Lofa County, Liberia.

PubMed

Capps, Jean Meyer; Njiru, Haron; deVries, Pieter

2017-01-01

The Ebola virus disease (EVD) epidemic entered Liberia through Lofa County in February 2014 and spread to two health districts where the nongovernmental organization Global Communities had been implementing community-led total sanitation (CLTS) since 2012. By December 2014 the county had 928 Ebola cases (422 of them confirmed) and 648 deaths. Before the epidemic, CLTS was triggered in 155 communities, and 98 communities were certified as Open Defecation Free (ODF). Using mixed quantitative and qualitative methods, we determined that no cases of EVD were found in ODF communities and in only one CLTS community that had not reached ODF status. No differences were found between EVD and non-EVD communities in tribe, religion, ethnic group, or major sources of Ebola information. Radio was the most common source of information for all communities, but health workers were the most trusted information sources. CLTS ODF communities attributed their avoidance of EVD to Water, Sanitation, and Hygiene behaviors, especially hand washing with soap and disposal of feces that they learned from CLTS prior to the epidemic. Communities that got EVD blamed their strong initial resistance to Ebola response messages on their distrust that Ebola was real and their reliance on friends and family for advice. A strong inverse correlation between EVD and CLTS with or without ODF emerged from the regression analysis (R = -.6).

CoNekT: an open-source framework for comparative genomic and transcriptomic network analyses.

PubMed

Proost, Sebastian; Mutwil, Marek

2018-05-01

The recent accumulation of gene expression data in the form of RNA sequencing creates unprecedented opportunities to study gene regulation and function. Furthermore, comparative analysis of the expression data from multiple species can elucidate which functional gene modules are conserved across species, allowing the study of the evolution of these modules. However, performing such comparative analyses on raw data is not feasible for many biologists. Here, we present CoNekT (Co-expression Network Toolkit), an open source web server, that contains user-friendly tools and interactive visualizations for comparative analyses of gene expression data and co-expression networks. These tools allow analysis and cross-species comparison of (i) gene expression profiles; (ii) co-expression networks; (iii) co-expressed clusters involved in specific biological processes; (iv) tissue-specific gene expression; and (v) expression profiles of gene families. To demonstrate these features, we constructed CoNekT-Plants for green alga, seed plants and flowering plants (Picea abies, Chlamydomonas reinhardtii, Vitis vinifera, Arabidopsis thaliana, Oryza sativa, Zea mays and Solanum lycopersicum) and thus provide a web-tool with the broadest available collection of plant phyla. CoNekT-Plants is freely available from http://conekt.plant.tools, while the CoNekT source code and documentation can be found at https://github.molgen.mpg.de/proost/CoNekT/.

QVAST: a new Quantum GIS plugin for estimating volcanic susceptibility

NASA Astrophysics Data System (ADS)

Bartolini, S.; Cappello, A.; Martí, J.; Del Negro, C.

2013-08-01

One of the most important tasks of modern volcanology is the construction of hazard maps simulating different eruptive scenarios that can be used in risk-based decision-making in land-use planning and emergency management. The first step in the quantitative assessment of volcanic hazards is the development of susceptibility maps, i.e. the spatial probability of a future vent opening given the past eruptive activity of a volcano. This challenging issue is generally tackled using probabilistic methods that use the calculation of a kernel function at each data location to estimate probability density functions (PDFs). The smoothness and the modeling ability of the kernel function are controlled by the smoothing parameter, also known as the bandwidth. Here we present a new tool, QVAST, part of the open-source Geographic Information System Quantum GIS, that is designed to create user-friendly quantitative assessments of volcanic susceptibility. QVAST allows to select an appropriate method for evaluating the bandwidth for the kernel function on the basis of the input parameters and the shapefile geometry, and can also evaluate the PDF with the Gaussian kernel. When different input datasets are available for the area, the total susceptibility map is obtained by assigning different weights to each of the PDFs, which are then combined via a weighted summation and modeled in a non-homogeneous Poisson process. The potential of QVAST, developed in a free and user-friendly environment, is here shown through its application in the volcanic fields of Lanzarote (Canary Islands) and La Garrotxa (NE Spain).

Grade and Gender Differences in Adolescents' Friendship Selection Criteria.

ERIC Educational Resources Information Center

Zook, Joan M.; Repinski, Daniel J.

Noting that when adolescents select friends, they are creating a relationship context that will be an important source of influence, this study examined the criteria adolescents use when choosing friends. Adolescents in grades 7 and 10 were interviewed about the criteria they used when selecting friends, particularly the importance they placed…

Sources of tobacco for youths in communities with strong enforcement of youth access laws.

PubMed

DiFranza, J R; Coleman, M

2001-12-01

To determine how youths obtain tobacco in communities with strong enforcement of tobacco sales laws. Ten communities in Massachusetts with merchant compliance rates at or above 90%. Paper surveys and focus group discussions with 68 adolescent smokers. Parents and friends are the primary sources of tobacco for new smokers. When stealing from parents can no longer satisfy the need for cigarettes, young adolescents ask strangers to buy them tobacco. For high school age smokers, teenage store clerks are a major source. Teenage clerks sell to other teenagers, steal tobacco, and help their friends steal from their employers. Friends who are 18 years of age or over are a second major source for older adolescents. Parents often purchase tobacco for older adolescents. Recommended actions include raising the minimum age for the purchase of tobacco to 21 years, and prohibiting individuals less than 21 years of age from selling tobacco.

Awareness, Openness and Eco-Friendly (AOE) Model Teaches Pre-Service Teachers on How to Be Eco-Friendly

ERIC Educational Resources Information Center

Jena, Ananta Kumar

2012-01-01

This paper studied the empirical pattern to observe the overall attitude of pre service teachers' of different training colleges towards environmental education and practice. Environmental education is a continuous lifelong process, starts at the preschool level and continues up to adulthood via all levels of education. In this context, to know…

The eNanoMapper database for nanomaterial safety information

PubMed Central

Chomenidis, Charalampos; Doganis, Philip; Fadeel, Bengt; Grafström, Roland; Hardy, Barry; Hastings, Janna; Hegi, Markus; Jeliazkov, Vedrin; Kochev, Nikolay; Kohonen, Pekka; Munteanu, Cristian R; Sarimveis, Haralambos; Smeets, Bart; Sopasakis, Pantelis; Tsiliki, Georgia; Vorgrimmler, David; Willighagen, Egon

2015-01-01

Summary Background: The NanoSafety Cluster, a cluster of projects funded by the European Commision, identified the need for a computational infrastructure for toxicological data management of engineered nanomaterials (ENMs). Ontologies, open standards, and interoperable designs were envisioned to empower a harmonized approach to European research in nanotechnology. This setting provides a number of opportunities and challenges in the representation of nanomaterials data and the integration of ENM information originating from diverse systems. Within this cluster, eNanoMapper works towards supporting the collaborative safety assessment for ENMs by creating a modular and extensible infrastructure for data sharing, data analysis, and building computational toxicology models for ENMs. Results: The eNanoMapper database solution builds on the previous experience of the consortium partners in supporting diverse data through flexible data storage, open source components and web services. We have recently described the design of the eNanoMapper prototype database along with a summary of challenges in the representation of ENM data and an extensive review of existing nano-related data models, databases, and nanomaterials-related entries in chemical and toxicogenomic databases. This paper continues with a focus on the database functionality exposed through its application programming interface (API), and its use in visualisation and modelling. Considering the preferred community practice of using spreadsheet templates, we developed a configurable spreadsheet parser facilitating user friendly data preparation and data upload. We further present a web application able to retrieve the experimental data via the API and analyze it with multiple data preprocessing and machine learning algorithms. Conclusion: We demonstrate how the eNanoMapper database is used to import and publish online ENM and assay data from several data sources, how the “representational state transfer” (REST) API enables building user friendly interfaces and graphical summaries of the data, and how these resources facilitate the modelling of reproducible quantitative structure–activity relationships for nanomaterials (NanoQSAR). PMID:26425413

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

NASA Astrophysics Data System (ADS)

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

2013-12-01

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

The eNanoMapper database for nanomaterial safety information.

PubMed

Jeliazkova, Nina; Chomenidis, Charalampos; Doganis, Philip; Fadeel, Bengt; Grafström, Roland; Hardy, Barry; Hastings, Janna; Hegi, Markus; Jeliazkov, Vedrin; Kochev, Nikolay; Kohonen, Pekka; Munteanu, Cristian R; Sarimveis, Haralambos; Smeets, Bart; Sopasakis, Pantelis; Tsiliki, Georgia; Vorgrimmler, David; Willighagen, Egon

2015-01-01

The NanoSafety Cluster, a cluster of projects funded by the European Commision, identified the need for a computational infrastructure for toxicological data management of engineered nanomaterials (ENMs). Ontologies, open standards, and interoperable designs were envisioned to empower a harmonized approach to European research in nanotechnology. This setting provides a number of opportunities and challenges in the representation of nanomaterials data and the integration of ENM information originating from diverse systems. Within this cluster, eNanoMapper works towards supporting the collaborative safety assessment for ENMs by creating a modular and extensible infrastructure for data sharing, data analysis, and building computational toxicology models for ENMs. The eNanoMapper database solution builds on the previous experience of the consortium partners in supporting diverse data through flexible data storage, open source components and web services. We have recently described the design of the eNanoMapper prototype database along with a summary of challenges in the representation of ENM data and an extensive review of existing nano-related data models, databases, and nanomaterials-related entries in chemical and toxicogenomic databases. This paper continues with a focus on the database functionality exposed through its application programming interface (API), and its use in visualisation and modelling. Considering the preferred community practice of using spreadsheet templates, we developed a configurable spreadsheet parser facilitating user friendly data preparation and data upload. We further present a web application able to retrieve the experimental data via the API and analyze it with multiple data preprocessing and machine learning algorithms. We demonstrate how the eNanoMapper database is used to import and publish online ENM and assay data from several data sources, how the "representational state transfer" (REST) API enables building user friendly interfaces and graphical summaries of the data, and how these resources facilitate the modelling of reproducible quantitative structure-activity relationships for nanomaterials (NanoQSAR).

[Having and losing friends: necessary social-emotional competencies in adolescents].

PubMed

von Salisch, Maria; Lüpschen, Nadine; Kanevski, Rimma

2013-01-01

Supportive friendships are an invaluable resource for adolescents because of their various developmental tasks, but establishing and maintaining them requires particular interpersonal skills. In order to identify social-emotional competencies associated with having and losing friends, N = 206 early adolescents (12-14 years of age) were examined longitudinally right after the transition to secondary school in the beginning of grade 7 and again at the end of this school year. Adolescents who had at least one reciprocal friend at both times were compared to those who lost all their friends over the school year. Repeated-measures MANOVAs indicate effects of time (and development) that underline an increase of self-disclosure, explanations and humor as well as a general decrease of openly aggressive behavior when angry at the friend. Interaction effects suggest that adolescents who lost their friend(s) intensified their use of physically and relationally aggressive behavior and of fantasies of revenge over time while continuously befriended adolescents decreased in their aggressive behavior when coping with anger in their friendships. Adolescents who had friends at both times were more willing to disclose private information whereas the self-disclosure of adolescents who lost their friends stagnated. These results are discussed in terms of deficient social-emotional competencies as the cause and the consequence of losing friends.

Evaluating the use of friend or family controls in epidemiologic case-control studies.

PubMed

Zhong, Charlie; Cockburn, Myles; Cozen, Wendy; Voutsinas, Jenna; Lacey, James V; Luo, Jianning; Sullivan-Halley, Jane; Bernstein, Leslie; Wang, Sophia S

2017-02-01

Traditional methodologies for identifying and recruiting controls in epidemiologic case-control studies, such as random digit dialing or neighborhood walk, suffer from declining response rates. Here, we revisit the feasibility and comparability of using alternative sources of controls, specifically friend and family controls. We recruited from a recently completed case-control study of non-Hodgkin lymphoma (NHL) among women in Los Angeles County where controls from the parent study were ascertained by neighborhood walk. We calculated participation rates and compared questionnaire responses between the friend/family controls and the original matched controls from the parent study. Of the 182 NHL case patients contacted, 111 (61%) agreed to participate in our feasibility study. 70 (63%) provided contact information for potential friend and/or family member controls. We were able to successfully contact and recruit a friend/family member for 92% of the case patients. This represented 46 friend controls and 54 family controls. Family controls significantly differed from original matched controls by sex and household income. Other characteristics were similar between friend controls and the original study's neighborhood controls. The apparent comparability of neighborhood controls to friend and family controls among respondents in this study suggests that these alternative methods of control identification can serve as a complementary source of eligible controls in epidemiologic case-control studies. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

22 CFR 71.10 - Emergency medical assistance.

Code of Federal Regulations, 2011 CFR

2011-04-01

... government; (2) All reasonable attempts to obtain private resources (prisoner's family, friends, etc.) have... family or friends who might serve as a source of private funds for medical services, and attempt to...

22 CFR 71.10 - Emergency medical assistance.

Code of Federal Regulations, 2010 CFR

2010-04-01

... government; (2) All reasonable attempts to obtain private resources (prisoner's family, friends, etc.) have... family or friends who might serve as a source of private funds for medical services, and attempt to...

[The relationship between four components of assertiveness and interpersonal behaviors, interpersonal adjustment in high school students' friendship].

PubMed

Watanabe, Asami

2010-04-01

This study examines the relationship between four components of assertiveness ("open expression", "control of emotion", "consideration for others" and "self-direction") and interpersonal behaviors on friends, interpersonal stress events, social anxiety. A questionnaire which included scales to measure the four components of assertiveness, activities with friend, considerate behavior for friends, interpersonal stress events and social anxiety was completed by 177 high school students. The results showed that "self-direction" had curvilinear relations with considerate behavior for friends, interpersonal stress events. An excessively high score for "self-direction" was associated with fewer considerate behavior and interpersonal stress events. An optimum score for "self-direction" was associated with more considerate behavior and interpersonal stress events.

How are curious people viewed and how do they behave in social situations? From the perspectives of self, friends, parents, and unacquainted observers.

PubMed

Kashdan, Todd B; Sherman, Ryne A; Yarbro, Jessica; Funder, David C

2013-04-01

People who are open and curious orient their lives around an appreciation of novelty and a strong urge to explore, discover, and grow. Researchers have recently shown that being an open, curious person is linked to healthy social outcomes. To better understand the benefits (and liabilities) of being a curious person, we used a multimethod design of social behavior to assess the perspectives of multiple informants (including self, friends, and parents) and behavior coded from direct observations in unstructured social interactions. We found an impressive degree of convergence among self, friend, and parent reports of curiosity, and observer-rated behavioral correlates of curiosity. A curious personality was linked to a wide range of adaptive behaviors, including tolerance of anxiety and uncertainty, positive emotional expressiveness, initiation of humor and playfulness, unconventional thinking, and a nondefensive, noncritical attitude. This characterization of curious people provides insights into mechanisms underlying associated healthy social outcomes. © 2012 Wiley Periodicals, Inc.

How are Curious People Viewed and How Do they Behave in Social Situations? From the Perspectives of Self, Friends, Parents, and Unacquainted Observers

PubMed Central

Kashdan, Todd B.; Sherman, Ryne A.; Yarbro, Jessica; Funder, David C.

2012-01-01

Objective People who are open and curious orient their lives around an appreciation of novelty and a strong urge to explore, discover, and grow. Researchers have recently shown that being an open, curious person is linked to healthy social outcomes. Method To better understand the benefits (and liabilities) of being a curious person, we used a multi-method design of social behavior to assess the perspectives of multiple informants including self, friends, and parents, and behavior coded from direct observations in unstructured social interactions. Results We found an impressive degree of convergence among self, friends, and parent reports of curiosity, and observer-rated behavioral correlates of curiosity. A curious personality was linked to a wide range of adaptive behaviors including tolerance of anxiety and uncertainty, positive emotional expressiveness, initiation of humor and playfulness, unconventional thinking, and a non-defensive, non-critical attitude. Conclusions This characterization of curious people provides insights into mechanisms underlying associated healthy social outcomes. PMID:22583101

Use of vendedores (mobile food vendors), pulgas (flea markets), and vecinos o amigos (neighbors or friends) as alternative sources of food for purchase among Mexican-origin households in Texas border colonias.

PubMed

Sharkey, Joseph R; Dean, Wesley R; Johnson, Cassandra M

2012-05-01

There is a paucity of studies acknowledging the existence of alternative food sources, and factors associated with food purchasing from three common alternative sources: vendedores (mobile food vendors), pulgas (flea markets), and vecinos/amigos (neighbors/friends). This analysis aims to examine the use of alternative food sources by Mexican-origin women from Texas-border colonias and determine factors associated with their use. The design was cross-sectional. Promotora-researchers (promotoras de salud trained in research methods) recruited 610 Mexican-origin women from 44 colonias and conducted in-person surveys. Surveys included participant characteristics and measures of food environment use and household food security. Statistical analyses included separate logistic regressions, modeled for food purchase from mobile food vendors, pulgas, or neighbors/friends. Child food insecurity was associated with purchasing food from mobile food vendors, while household food security was associated with using pulgas or neighbors/friends. School nutrition program participants were more likely to live in households that depend on alternative food sources. Efforts to increase healthful food consumption such as fruits and vegetables should acknowledge all potential food sources (traditional, convenience, nontraditional, and alternative), especially those preferred by colonia residents. Current findings support the conceptual broadening of the retail food environment, and the importance of linking use with spatial access (proximity) to more accurately depict access to food sources. Copyright © 2012 Academy of Nutrition and Dietetics. Published by Elsevier Inc. All rights reserved.

Hospital's redesigned Web site patient-friendly, comprehensive. Site one-of-a-kind in Twin Cities market area.

PubMed

Rees, T

2001-01-01

North Memorial Medical Center, Robbinsdale, Minn., has opened a brightly redesigned Web site. It is patient-friendly and features a different approach to provide healthcare information called "care areas," which are organized by condition, such as heart care, cancer care and childbirth. This approach led to the the site being named North Memorial Online Care Center.

Managing research and surveillance projects in real-time with a novel open-source eManagement tool designed for under-resourced countries.

PubMed

Steiner, Andreas; Hella, Jerry; Grüninger, Servan; Mhalu, Grace; Mhimbira, Francis; Cercamondi, Colin I; Doulla, Basra; Maire, Nicolas; Fenner, Lukas

2016-09-01

A software tool is developed to facilitate data entry and to monitor research projects in under-resourced countries in real-time. The eManagement tool "odk_planner" is written in the scripting languages PHP and Python. The odk_planner is lightweight and uses minimal internet resources. It was designed to be used with the open source software Open Data Kit (ODK). The users can easily configure odk_planner to meet their needs, and the online interface displays data collected from ODK forms in a graphically informative way. The odk_planner also allows users to upload pictures and laboratory results and sends text messages automatically. User-defined access rights protect data and privacy. We present examples from four field applications in Tanzania successfully using the eManagement tool: 1) clinical trial; 2) longitudinal Tuberculosis (TB) Cohort Study with a complex visit schedule, where it was used to graphically display missing case report forms, upload digitalized X-rays, and send text message reminders to patients; 3) intervention study to improve TB case detection, carried out at pharmacies: a tablet-based electronic referral system monitored referred patients, and sent automated messages to remind pharmacy clients to visit a TB Clinic; and 4) TB retreatment case monitoring designed to improve drug resistance surveillance: clinicians at four public TB clinics and lab technicians at the TB reference laboratory used a smartphone-based application that tracked sputum samples, and collected clinical and laboratory data. The user friendly, open source odk_planner is a simple, but multi-functional, Web-based eManagement tool with add-ons that helps researchers conduct studies in under-resourced countries. © The Author 2016. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

[Social support and physical activity in adolescents from public schools: the importance of family and friends].

PubMed

Prado, Crisley Vanessa; Lima, Alex Vieira; Fermino, Rogério César; Añez, Ciro Romelio Rodriguez; Reis, Rodrigo Siqueira

2014-04-01

The aim of this study was to verify the association between different types and sources of social support and physical activity among adolescents from Curitiba, Paraná State, Brazil. A school-based survey was conducted with a representative sample of adolescents from public schools (n = 1,469). Multiple regression models were used to test the association between weekly frequency and sources of social support from family and friends and weekly frequency of physical activity. Among boys, frequent company of family (PR: 2.88; 95%CI: 2.00-4.13) and friends (PR: 5.46; 95%CI: 2.33-12.78) and positive reinforcement from friends (PR: 1.81; 95%CI: 1.18-2.77) were positively associated with physical activity. Sporadic invitation by the family was negatively associated with physical activity (PR: 0.66; 95%CI: 0.46-1.14). For girls, frequent company of family (PR: 3.39; 95%CI: 1.49-7.69) and friends (PR: 4.06; 95%CI: 2.22-7.45) increased the likelihood of physical activity. Company of friends was the most important type of social support for physical activity among these adolescents.

KSC-2011-1147

NASA Image and Video Library

2011-01-20

CAPE CANAVERAL, Fla. -- At NASA's Kennedy Space Center in Florida, an audience at the ribbon-cutting ceremony for the new environmentally friendly Propellants North Administration and Maintenance Facility listens to opening remarks made by Frank Kline, a NASA Construction of Facilities project manager. Propellants North consists of two buildings, one to store cryogenic fuel transfer equipment and one to house personnel who support fueling spacecraft. The recently rebuilt buildings will be NASA's first carbon neutral facility, which means it will produce enough energy on site from renewable sources to offset what it requires to operate. The facility also will reach for the U.S. Green Building Council's Leadership in Environmental and Energy Design (LEED) Platinum status, which is the highest LEED rating. Photo credit: NASA/Kim Shiflett

Development of a 3D WebGIS System for Retrieving and Visualizing CityGML Data Based on their Geometric and Semantic Characteristics by Using Free and Open Source Technology

NASA Astrophysics Data System (ADS)

Pispidikis, I.; Dimopoulou, E.

2016-10-01

CityGML is considered as an optimal standard for representing 3D city models. However, international experience has shown that visualization of the latter is quite difficult to be implemented on the web, due to the large size of data and the complexity of CityGML. As a result, in the context of this paper, a 3D WebGIS application is developed in order to successfully retrieve and visualize CityGML data in accordance with their respective geometric and semantic characteristics. Furthermore, the available web technologies and the architecture of WebGIS systems are investigated, as provided by international experience, in order to be utilized in the most appropriate way for the purposes of this paper. Specifically, a PostgreSQL/ PostGIS Database is used, in compliance with the 3DCityDB schema. At Server tier, Apache HTTP Server and GeoServer are utilized, while a Server Side programming language PHP is used. At Client tier, which implemented the interface of the application, the following technologies were used: JQuery, AJAX, JavaScript, HTML5, WebGL and Ol3-Cesium. Finally, it is worth mentioning that the application's primary objectives are a user-friendly interface and a fully open source development.

A resource management tool for public health continuity of operations during disasters.

PubMed

Turner, Anne M; Reeder, Blaine; Wallace, James C

2013-04-01

We developed and validated a user-centered information system to support the local planning of public health continuity of operations for the Community Health Services Division, Public Health - Seattle & King County, Washington. The Continuity of Operations Data Analysis (CODA) system was designed as a prototype developed using requirements identified through participatory design. CODA uses open-source software that links personnel contact and licensing information with needed skills and clinic locations for 821 employees at 14 public health clinics in Seattle and King County. Using a web-based interface, CODA can visualize locations of personnel in relationship to clinics to assist clinic managers in allocating public health personnel and resources under dynamic conditions. Based on user input, the CODA prototype was designed as a low-cost, user-friendly system to inventory and manage public health resources. In emergency conditions, the system can run on a stand-alone battery-powered laptop computer. A formative evaluation by managers of multiple public health centers confirmed the prototype design's usefulness. Emergency management administrators also provided positive feedback about the system during a separate demonstration. Validation of the CODA information design prototype by public health managers and emergency management administrators demonstrates the potential usefulness of building a resource management system using open-source technologies and participatory design principles.

MetaDB a Data Processing Workflow in Untargeted MS-Based Metabolomics Experiments.

PubMed

Franceschi, Pietro; Mylonas, Roman; Shahaf, Nir; Scholz, Matthias; Arapitsas, Panagiotis; Masuero, Domenico; Weingart, Georg; Carlin, Silvia; Vrhovsek, Urska; Mattivi, Fulvio; Wehrens, Ron

2014-01-01

Due to their sensitivity and speed, mass-spectrometry based analytical technologies are widely used to in metabolomics to characterize biological phenomena. To address issues like metadata organization, quality assessment, data processing, data storage, and, finally, submission to public repositories, bioinformatic pipelines of a non-interactive nature are often employed, complementing the interactive software used for initial inspection and visualization of the data. These pipelines often are created as open-source software allowing the complete and exhaustive documentation of each step, ensuring the reproducibility of the analysis of extensive and often expensive experiments. In this paper, we will review the major steps which constitute such a data processing pipeline, discussing them in the context of an open-source software for untargeted MS-based metabolomics experiments recently developed at our institute. The software has been developed by integrating our metaMS R package with a user-friendly web-based application written in Grails. MetaMS takes care of data pre-processing and annotation, while the interface deals with the creation of the sample lists, the organization of the data storage, and the generation of survey plots for quality assessment. Experimental and biological metadata are stored in the ISA-Tab format making the proposed pipeline fully integrated with the Metabolights framework.

Pulse Sequence Programming in a Dynamic Visual Environment: SequenceTree

PubMed Central

Magland, Jeremy F.; Li, Cheng; Langham, Michael C.; Wehrli, Felix W.

2015-01-01

Purpose To describe SequenceTree (ST), an open source. integrated software environment for implementing MRI pulse sequences, and ideally exported them to actual MRI scanners. The software is a user-friendly alternative to vendor-supplied pulse sequence design and editing tools and is suited for non-programmers and programmers alike. Methods The integrated user interface was programmed using the Qt4/C++ toolkit. As parameters and code are modified, the pulse sequence diagram is automatically updated within the user interface. Several aspects of pulse programming are handled automatically allowing users to focus on higher-level aspects of sequence design. Sequences can be simulated using a built-in Bloch equation solver and then exported for use on a Siemens MRI scanner. Ideally other types of scanners will be supported in the future. Results The software has been used for eight years in the authors’ laboratory and elsewhere and has been utilized in more than fifty peer-reviewed publications in areas such as cardiovascular imaging, solid state and non-proton NMR, MR elastography, and high resolution structural imaging. Conclusion ST is an innovative, open source, visual pulse sequence environment for MRI combining simplicity with flexibility and is ideal for both advanced users and those with limited programming experience. PMID:25754837

A Resource Management Tool for Public Health Continuity of Operations During Disasters

PubMed Central

Turner, Anne M.; Reeder, Blaine; Wallace, James C.

2014-01-01

Objective We developed and validated a user-centered information system to support the local planning of public health continuity of operations for the Community Health Services Division, Public Health - Seattle & King County, Washington. Methods The Continuity of Operations Data Analysis (CODA) system was designed as a prototype developed using requirements identified through participatory design. CODA uses open-source software that links personnel contact and licensing information with needed skills and clinic locations for 821 employees at 14 public health clinics in Seattle and King County. Using a web-based interface, CODA can visualize locations of personnel in relationship to clinics to assist clinic managers in allocating public health personnel and resources under dynamic conditions. Results Based on user input, the CODA prototype was designed as a low-cost, user-friendly system to inventory and manage public health resources. In emergency conditions, the system can run on a stand-alone battery-powered laptop computer. A formative evaluation by managers of multiple public health centers confirmed the prototype design’s usefulness. Emergency management administrators also provided positive feedback about the system during a separate demonstration. Conclusions Validation of the CODA information design prototype by public health managers and emergency management administrators demonstrates the potential usefulness of building a resource management system using open-source technologies and participatory design principles. PMID:24618165

Young people, money, and access to tobacco.

PubMed

Wong, Grace; Glover, Marewa; Nosa, Vili; Freeman, Becky; Paynter, Janine; Scragg, Robert

2007-12-14

The social and family processes involved in children's sources and use of money in relation to buying cigarettes are not well understood. Hence this study investigated how Maori, Pacific Island, European, and Asian school students access cigarettes, with a special focus on their disposable income. Students aged 11-15 years, recruited through schools, participated in 12 focus groups run by ethnically matched senior student facilitators and researchers. Topics discussed included sources of student money, parental monitoring of the use of money and student access to cigarettes. Students reported that young people can easily buy cigarettes from tobacco retailers. They could also be bought cheaply (50 cents for a roll-your-own) and/or on an "I owe you" basis from friends and social suppliers. Students used money from family, and money that was earned, "scabbed", and borrowed from friends. Cigarettes were also obtained freely from family members or from adults on the street. Whilst parents monitored students' use of large amounts of money, participants experienced relative freedom to spend small amounts which they saved out of money provided by parents for lunches and other purposes. Students were open to parental advice on how to use money but felt they should have the final say. Cigarettes continue to be accessible to children free or at affordable prices. Adults and family members must be discouraged from supplying cigarettes to children. Parents should be made aware of the way children use small amounts of money and advised to monitor, educate, and guide them to discourage cigarette purchase.

Science and Software

NASA Astrophysics Data System (ADS)

Zelt, C. A.

2017-12-01

Earth science attempts to understand how the earth works. This research often depends on software for modeling, processing, inverting or imaging. Freely sharing open-source software is essential to prevent reinventing the wheel and allows software to be improved and applied in ways the original author may never have envisioned. For young scientists, releasing software can increase their name ID when applying for jobs and funding, and create opportunities for collaborations when scientists who collect data want the software's creator to be involved in their project. However, we frequently hear scientists say software is a tool, it's not science. Creating software that implements a new or better way of earth modeling or geophysical processing, inverting or imaging should be viewed as earth science. Creating software for things like data visualization, format conversion, storage, or transmission, or programming to enhance computational performance, may be viewed as computer science. The former, ideally with an application to real data, can be published in earth science journals, the latter possibly in computer science journals. Citations in either case should accurately reflect the impact of the software on the community. Funding agencies need to support more software development and open-source releasing, and the community should give more high-profile awards for developing impactful open-source software. Funding support and community recognition for software development can have far reaching benefits when the software is used in foreseen and unforeseen ways, potentially for years after the original investment in the software development. For funding, an open-source release that is well documented should be required, with example input and output files. Appropriate funding will provide the incentive and time to release user-friendly software, and minimize the need for others to duplicate the effort. All funded software should be available through a single web site, ideally maintained by someone in a funded position. Perhaps the biggest challenge is the reality that researches who use software, as opposed to develop software, are more attractive university hires because they are more likely to be "big picture" scientists that publish in the highest profile journals, although sometimes the two go together.

Chemical effects in biological systems (CEBS) object model for toxicology data, SysTox-OM: design and application.

PubMed

Xirasagar, Sandhya; Gustafson, Scott F; Huang, Cheng-Cheng; Pan, Qinyan; Fostel, Jennifer; Boyer, Paul; Merrick, B Alex; Tomer, Kenneth B; Chan, Denny D; Yost, Kenneth J; Choi, Danielle; Xiao, Nianqing; Stasiewicz, Stanley; Bushel, Pierre; Waters, Michael D

2006-04-01

The CEBS data repository is being developed to promote a systems biology approach to understand the biological effects of environmental stressors. CEBS will house data from multiple gene expression platforms (transcriptomics), protein expression and protein-protein interaction (proteomics), and changes in low molecular weight metabolite levels (metabolomics) aligned by their detailed toxicological context. The system will accommodate extensive complex querying in a user-friendly manner. CEBS will store toxicological contexts including the study design details, treatment protocols, animal characteristics and conventional toxicological endpoints such as histopathology findings and clinical chemistry measures. All of these data types can be integrated in a seamless fashion to enable data query and analysis in a biologically meaningful manner. An object model, the SysBio-OM (Xirasagar et al., 2004) has been designed to facilitate the integration of microarray gene expression, proteomics and metabolomics data in the CEBS database system. We now report SysTox-OM as an open source systems toxicology model designed to integrate toxicological context into gene expression experiments. The SysTox-OM model is comprehensive and leverages other open source efforts, namely, the Standard for Exchange of Nonclinical Data (http://www.cdisc.org/models/send/v2/index.html) which is a data standard for capturing toxicological information for animal studies and Clinical Data Interchange Standards Consortium (http://www.cdisc.org/models/sdtm/index.html) that serves as a standard for the exchange of clinical data. Such standardization increases the accuracy of data mining, interpretation and exchange. The open source SysTox-OM model, which can be implemented on various software platforms, is presented here. A universal modeling language (UML) depiction of the entire SysTox-OM is available at http://cebs.niehs.nih.gov and the Rational Rose object model package is distributed under an open source license that permits unrestricted academic and commercial use and is available at http://cebs.niehs.nih.gov/cebsdownloads. Currently, the public toxicological data in CEBS can be queried via a web application based on the SysTox-OM at http://cebs.niehs.nih.gov xirasagars@saic.com Supplementary data are available at Bioinformatics online.

Associations among stress, gender, sources of social support, and health in emerging adults.

PubMed

Lee, Chih-Yuan Steven; Dik, Bryan J

2017-10-01

This study aimed to examine how sources of social support intersect with stress and health by testing two theoretical models. Three relationship-specific sources of social support (family, friends, and romantic partners) and two health indicators (self-rated physical health and depressive symptoms) were investigated. The sample consisted of 636 emerging adults attending college (age range: 18-25). Results suggest that only support from family was a stress-buffer, in that it buffered the adverse association between stress and depressive symptoms. Holding stress constant, only support from family was related to self-rated physical health and only support from friends or romantic partners was associated with depressive symptoms. There were no gender differences in the mean levels of self-rated physical health and depressive symptoms. However, gender moderations were found, in that the positive relationship between friends support and physical health was observed only in women, that the association between friends support and depressive symptoms was greater in men than in women, and that family support buffered the negative relationship between stress and physical health only in men. Findings of this study suggest that the associations among stress, social support, and health vary by the sources of support, the health outcome, and gender. Copyright © 2016 John Wiley & Sons, Ltd.

The Wildland Fire Emissions Information System: Providing information for carbon cycle studies with open source geospatial tools

NASA Astrophysics Data System (ADS)

French, N. H.; Erickson, T.; McKenzie, D.

2008-12-01

A major goal of the North American Carbon Program is to resolve uncertainties in understanding and managing the carbon cycle of North America. As carbon modeling tools become more comprehensive and spatially oriented, accurate datasets to spatially quantify carbon emissions from fire are needed, and these data resources need to be accessible to users for decision-making. Under a new NASA Carbon Cycle Science project, Drs. Nancy French and Tyler Erickson, of the Michigan Technological University, Michigan Tech Research Institute (MTRI), are teaming with specialists with the USDA Forest Service Fire and Environmental Research Applications (FERA) team to provide information for mapping fire-derived carbon emissions to users. The project focus includes development of a web-based system to provide spatially resolved fire emissions estimates for North America in a user-friendly environment. The web-based Decision Support System will be based on a variety of open source technologies. The Fuel Characteristic Classification System (FCCS) raster map of fuels and MODIS-derived burned area vector maps will be processed using the Geographic Data Abstraction Library (GDAL) and OGR Simple Features Library. Tabular and spatial project data will be stored in a PostgreSQL/PostGIS, a spatially enabled relational database server. The browser-based user interface will be created using the Django web page framework to allow user input for the decision support system. The OpenLayers mapping framework will be used to provide users with interactive maps within the browser. In addition, the data products will be made available in standard open data formats such as KML, to allow for easy integration into other spatial models and data systems.

Enabling a systems biology knowledgebase with gaggle and firegoose

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

Baliga, Nitin S.

The overall goal of this project was to extend the existing Gaggle and Firegoose systems to develop an open-source technology that runs over the web and links desktop applications with many databases and software applications. This technology would enable researchers to incorporate workflows for data analysis that can be executed from this interface to other online applications. The four specific aims were to (1) provide one-click mapping of genes, proteins, and complexes across databases and species; (2) enable multiple simultaneous workflows; (3) expand sophisticated data analysis for online resources; and enhance open-source development of the Gaggle-Firegoose infrastructure. Gaggle is anmore » open-source Java software system that integrates existing bioinformatics programs and data sources into a user-friendly, extensible environment to allow interactive exploration, visualization, and analysis of systems biology data. Firegoose is an extension to the Mozilla Firefox web browser that enables data transfer between websites and desktop tools including Gaggle. In the last phase of this funding period, we have made substantial progress on development and application of the Gaggle integration framework. We implemented the workspace to the Network Portal. Users can capture data from Firegoose and save them to the workspace. Users can create workflows to start multiple software components programmatically and pass data between them. Results of analysis can be saved to the cloud so that they can be easily restored on any machine. We also developed the Gaggle Chrome Goose, a plugin for the Google Chrome browser in tandem with an opencpu server in the Amazon EC2 cloud. This allows users to interactively perform data analysis on a single web page using the R packages deployed on the opencpu server. The cloud-based framework facilitates collaboration between researchers from multiple organizations. We have made a number of enhancements to the cmonkey2 application to enable and improve the integration within different environments, and we have created a new tools pipeline for generating EGRIN2 models in a largely automated way.« less

MANTA--an open-source, high density electrophysiology recording suite for MATLAB.

PubMed

Englitz, B; David, S V; Sorenson, M D; Shamma, S A

2013-01-01

The distributed nature of nervous systems makes it necessary to record from a large number of sites in order to decipher the neural code, whether single cell, local field potential (LFP), micro-electrocorticograms (μECoG), electroencephalographic (EEG), magnetoencephalographic (MEG) or in vitro micro-electrode array (MEA) data are considered. High channel-count recordings also optimize the yield of a preparation and the efficiency of time invested by the researcher. Currently, data acquisition (DAQ) systems with high channel counts (>100) can be purchased from a limited number of companies at considerable prices. These systems are typically closed-source and thus prohibit custom extensions or improvements by end users. We have developed MANTA, an open-source MATLAB-based DAQ system, as an alternative to existing options. MANTA combines high channel counts (up to 1440 channels/PC), usage of analog or digital headstages, low per channel cost (<$90/channel), feature-rich display and filtering, a user-friendly interface, and a modular design permitting easy addition of new features. MANTA is licensed under the GPL and free of charge. The system has been tested by daily use in multiple setups for >1 year, recording reliably from 128 channels. It offers a growing list of features, including integrated spike sorting, PSTH and CSD display and fully customizable electrode array geometry (including 3D arrays), some of which are not available in commercial systems. MANTA runs on a typical PC and communicates via TCP/IP and can thus be easily integrated with existing stimulus generation/control systems in a lab at a fraction of the cost of commercial systems. With modern neuroscience developing rapidly, MANTA provides a flexible platform that can be rapidly adapted to the needs of new analyses and questions. Being open-source, the development of MANTA can outpace commercial solutions in functionality, while maintaining a low price-point.

Flexible Environmental Modeling with Python and Open - GIS

NASA Astrophysics Data System (ADS)

Pryet, Alexandre; Atteia, Olivier; Delottier, Hugo; Cousquer, Yohann

2015-04-01

Numerical modeling now represents a prominent task of environmental studies. During the last decades, numerous commercial programs have been made available to environmental modelers. These software applications offer user-friendly graphical user interfaces that allow an efficient management of many case studies. However, they suffer from a lack of flexibility and closed-source policies impede source code reviewing and enhancement for original studies. Advanced modeling studies require flexible tools capable of managing thousands of model runs for parameter optimization, uncertainty and sensitivity analysis. In addition, there is a growing need for the coupling of various numerical models associating, for instance, groundwater flow modeling to multi-species geochemical reactions. Researchers have produced hundreds of open-source powerful command line programs. However, there is a need for a flexible graphical user interface allowing an efficient processing of geospatial data that comes along any environmental study. Here, we present the advantages of using the free and open-source Qgis platform and the Python scripting language for conducting environmental modeling studies. The interactive graphical user interface is first used for the visualization and pre-processing of input geospatial datasets. Python scripting language is then employed for further input data processing, call to one or several models, and post-processing of model outputs. Model results are eventually sent back to the GIS program, processed and visualized. This approach combines the advantages of interactive graphical interfaces and the flexibility of Python scripting language for data processing and model calls. The numerous python modules available facilitate geospatial data processing and numerical analysis of model outputs. Once input data has been prepared with the graphical user interface, models may be run thousands of times from the command line with sequential or parallel calls. We illustrate this approach with several case studies in groundwater hydrology and geochemistry and provide links to several python libraries that facilitate pre- and post-processing operations.

MANTA—an open-source, high density electrophysiology recording suite for MATLAB

PubMed Central

Englitz, B.; David, S. V.; Sorenson, M. D.; Shamma, S. A.

2013-01-01

The distributed nature of nervous systems makes it necessary to record from a large number of sites in order to decipher the neural code, whether single cell, local field potential (LFP), micro-electrocorticograms (μECoG), electroencephalographic (EEG), magnetoencephalographic (MEG) or in vitro micro-electrode array (MEA) data are considered. High channel-count recordings also optimize the yield of a preparation and the efficiency of time invested by the researcher. Currently, data acquisition (DAQ) systems with high channel counts (>100) can be purchased from a limited number of companies at considerable prices. These systems are typically closed-source and thus prohibit custom extensions or improvements by end users. We have developed MANTA, an open-source MATLAB-based DAQ system, as an alternative to existing options. MANTA combines high channel counts (up to 1440 channels/PC), usage of analog or digital headstages, low per channel cost (<$90/channel), feature-rich display and filtering, a user-friendly interface, and a modular design permitting easy addition of new features. MANTA is licensed under the GPL and free of charge. The system has been tested by daily use in multiple setups for >1 year, recording reliably from 128 channels. It offers a growing list of features, including integrated spike sorting, PSTH and CSD display and fully customizable electrode array geometry (including 3D arrays), some of which are not available in commercial systems. MANTA runs on a typical PC and communicates via TCP/IP and can thus be easily integrated with existing stimulus generation/control systems in a lab at a fraction of the cost of commercial systems. With modern neuroscience developing rapidly, MANTA provides a flexible platform that can be rapidly adapted to the needs of new analyses and questions. Being open-source, the development of MANTA can outpace commercial solutions in functionality, while maintaining a low price-point. PMID:23653593

Factors Associated with College Students' Responses to Rape-Disclosure Scenarios: Influence of Gender, Rape Characteristics, and Opinions about Health Professionals

ERIC Educational Resources Information Center

Suzuki, Yumi E.; Bonner, Heidi S.

2017-01-01

Few studies examine the role of friends in victims' decisions to seek help from health professionals. This study used a sample of college students (N = 637) to examine the factors that may influence whether students would advise a friend to seek help from health professionals. After providing an open-ended response to a vignette, students answered…

QVAST: a new Quantum GIS plugin for estimating volcanic susceptibility

NASA Astrophysics Data System (ADS)

Bartolini, S.; Cappello, A.; Martí, J.; Del Negro, C.

2013-11-01

One of the most important tasks of modern volcanology is the construction of hazard maps simulating different eruptive scenarios that can be used in risk-based decision making in land-use planning and emergency management. The first step in the quantitative assessment of volcanic hazards is the development of susceptibility maps (i.e., the spatial probability of a future vent opening given the past eruptive activity of a volcano). This challenging issue is generally tackled using probabilistic methods that use the calculation of a kernel function at each data location to estimate probability density functions (PDFs). The smoothness and the modeling ability of the kernel function are controlled by the smoothing parameter, also known as the bandwidth. Here we present a new tool, QVAST, part of the open-source geographic information system Quantum GIS, which is designed to create user-friendly quantitative assessments of volcanic susceptibility. QVAST allows the selection of an appropriate method for evaluating the bandwidth for the kernel function on the basis of the input parameters and the shapefile geometry, and can also evaluate the PDF with the Gaussian kernel. When different input data sets are available for the area, the total susceptibility map is obtained by assigning different weights to each of the PDFs, which are then combined via a weighted summation and modeled in a non-homogeneous Poisson process. The potential of QVAST, developed in a free and user-friendly environment, is here shown through its application in the volcanic fields of Lanzarote (Canary Islands) and La Garrotxa (NE Spain).

22 CFR 71.11 - Short-term full diet program.

Code of Federal Regulations, 2010 CFR

2010-04-01

..., including private funding from family or friends; and (3) If the funds exceed an amount to be established by... sources such as family or friends; (4) Because funds expended by the Department to cover the short-term...

22 CFR 71.11 - Short-term full diet program.

Code of Federal Regulations, 2011 CFR

2011-04-01

..., including private funding from family or friends; and (3) If the funds exceed an amount to be established by... sources such as family or friends; (4) Because funds expended by the Department to cover the short-term...

XSEOS: An Open Software for Chemical Engineering Thermodynamics

ERIC Educational Resources Information Center

Castier, Marcelo

2008-01-01

An Excel add-in--XSEOS--that implements several excess Gibbs free energy models and equations of state has been developed for educational use. Several traditional and modern thermodynamic models are available in the package with a user-friendly interface. XSEOS has open code, is freely available, and should be useful for instructors and students…

Paper-based membraneless hydrogen peroxide fuel cell prepared by micro-fabrication

NASA Astrophysics Data System (ADS)

Mousavi Ehteshami, Seyyed Mohsen; Asadnia, Mohsen; Tan, Swee Ngin; Chan, Siew Hwa

2016-01-01

A paper-based membraneless single-compartment hydrogen peroxide power source prepared by micro-electromechanical systems (MEMS) technology is reported. The cell utilizes hydrogen peroxide as both fuel and oxidant in a low volume cell fabricated on paper. The fabrication method used is a simple method where precise, small-sized patterns are produced which include the hydrophilic paper bounded by hydrophobic resin. Open circuit potentials of 0.61 V and 0.32 V are achieved for the cells fabricated with Prussian Blue as the cathode and aluminium/nickel as the anode materials, respectively. The power produced by the cells is 0.81 mW cm-2 at 0.26 V and 0.38 mW cm-2 at 0.14 V, respectively, even after the cell is bent or distorted. Such a fuel cell provides an easily fabricated, environmentally friendly, flexible and cost saving power source. The cell may be integrated within a self-sustained diagnostic system to provide the on-demand power for future bio-sensing applications.

Your friends know how long you will live: a 75-year study of peer-rated personality traits.

PubMed

Jackson, Joshua J; Connolly, James J; Garrison, S Mason; Leveille, Madeleine M; Connolly, Seamus L

2015-03-01

Although self-rated personality traits predict mortality risk, no study has examined whether one's friends can perceive personality characteristics that predict one's mortality risk. Moreover, it is unclear whether observers' reports (compared with self-reports) provide better or unique information concerning the personal characteristics that result in longer and healthier lives. To test whether friends' reports of personality predict mortality risk, we used data from a 75-year longitudinal study (the Kelly/Connolly Longitudinal Study on Personality and Aging). In that study, 600 participants were observed beginning in 1935 through 1938, when they were in their mid-20s, and continuing through 2013. Male participants seen by their friends as more conscientious and open lived longer, whereas friend-rated emotional stability and agreeableness were protective for women. Friends' ratings were better predictors of longevity than were self-reports of personality, in part because friends' ratings could be aggregated to provide a more reliable assessment. Our findings demonstrate the utility of observers' reports in the study of health and provide insights concerning the pathways by which personality traits influence health. © The Author(s) 2015.

Open Data, Open Specifications and Free and Open Source Software: A powerful mix to create distributed Web-based water information systems

NASA Astrophysics Data System (ADS)

Arias, Carolina; Brovelli, Maria Antonia; Moreno, Rafael

2015-04-01

We are in an age when water resources are increasingly scarce and the impacts of human activities on them are ubiquitous. These problems don't respect administrative or political boundaries and they must be addressed integrating information from multiple sources at multiple spatial and temporal scales. Communication, coordination and data sharing are critical for addressing the water conservation and management issues of the 21st century. However, different countries, provinces, local authorities and agencies dealing with water resources have diverse organizational, socio-cultural, economic, environmental and information technology (IT) contexts that raise challenges to the creation of information systems capable of integrating and distributing information across their areas of responsibility in an efficient and timely manner. Tight and disparate financial resources, and dissimilar IT infrastructures (data, hardware, software and personnel expertise) further complicate the creation of these systems. There is a pressing need for distributed interoperable water information systems that are user friendly, easily accessible and capable of managing and sharing large volumes of spatial and non-spatial data. In a distributed system, data and processes are created and maintained in different locations each with competitive advantages to carry out specific activities. Open Data (data that can be freely distributed) is available in the water domain, and it should be further promoted across countries and organizations. Compliance with Open Specifications for data collection, storage and distribution is the first step toward the creation of systems that are capable of interacting and exchanging data in a seamlessly (interoperable) way. The features of Free and Open Source Software (FOSS) offer low access cost that facilitate scalability and long-term viability of information systems. The World Wide Web (the Web) will be the platform of choice to deploy and access these systems. Geospatial capabilities for mapping, visualization, and spatial analysis will be important components of these new generation of Web-based interoperable information systems in the water domain. The purpose of this presentation is to increase the awareness of scientists, IT personnel and agency managers about the advantages offered by the combined use of Open Data, Open Specifications for geospatial and water-related data collection, storage and sharing, as well as mature FOSS projects for the creation of interoperable Web-based information systems in the water domain. A case study is used to illustrate how these principles and technologies can be integrated to create a system with the previously mentioned characteristics for managing and responding to flood events.

Sources of Nonmedically Used Prescription Stimulants: Differences in Onset, Recency and Severity of Misuse in a Population-Based Study*

PubMed Central

Chen, Lian-Yu; Strain, Eric C.; Crum, Rosa M.; Storr, Carla L.; Mojtabai, Ramin

2014-01-01

Aim Epidemiological data indicate that nonmedical use of prescription stimulants has increased over the past decade. However, little is known regarding the source of the misused stimulants and whether different sources correspond to differences in risk profiles and associated social and health problems. Method Data from the 2006 to 2011 National Survey on Drug Use and Health were used. A total of 4,945 participants who used prescription stimulants nonmedically and also reported their source of misused stimulants were categorized by the source: friend/relative, physician and illegal. Logistic regression models compared the socio-demographic, mental health and behavioral problems, and stimulant use-related problems (onset, recency, frequency, severity) according to the source of the misused stimulants. Results The most common sources of stimulants were friends/relatives, followed by physicians and illegal sources. Compared to participants reporting friends/relatives as the source, participants reporting an illegal source were more likely to be male, unemployed, have less than a high school education, a history of criminal behavior and an earlier age of use onset. Participants reporting a physician source were more likely to have mental health problems and mental health service use. Higher odds of past-month stimulant use, frequent use (≥10 days per year), drug dependence and substance service use were found in individuals reporting physician and illegal sources. Conclusions Identifying the source of misused stimulants may be useful in detecting distinct subgroups of nonmedical prescription stimulant users, which may inform development of tailored prevention and treatment programs and contribute to individual treatment planning. PMID:25454408

The roles of different sources of social support on emotional well-being among Chinese elderly.

PubMed

Li, Haifeng; Ji, Yang; Chen, Tianyong

2014-01-01

Social support has been widely known as a protective factor for the emotional well-being (EWB) of older adults, but less studies have investigated the roles of different sources of social support (i.e., family and friend support) on different facets of EWB (i.e., positive affect and negative affect) simultaneously. In this study, the associations between family/friend support and positive/negative affect were investigated in a sample of 700 Chinese elderly. The EWB and social support were measured with a 12-item affective wordlist (Kahneman et al., 2004) and a self-prepared questionnaire. The results showed that (1) the order of contact frequency and mutual support followed a hierarchical order from spouse, children, to friends; (2) zero-order correlations of both family support and friend support were associated with more positive affect and less negative affect; and when compared with the relative role of family and friend support, (3) spouse (children if spouse is not available) support had greater contribution on decreasing negative affect, while friend support had greater influence on increasing positive affect, even after controlling the demographic, self-rated health and life events variables. Family and friend support play different roles on the two facets of EWB of the elderly. These results were better explained in light of the task specificity model rather than the hierarchical compensatory model. Moreover, positive affect may be enhanced by friend support (based on personal interests and selectable) rather than family support (bonded by kinship and not selectable), which added evidences to the socioemotional selectivity theory.

The Roles of Different Sources of Social Support on Emotional Well-Being among Chinese Elderly

PubMed Central

Li, Haifeng; Ji, Yang; Chen, Tianyong

2014-01-01

Background Social support has been widely known as a protective factor for the emotional well-being (EWB) of older adults, but less studies have investigated the roles of different sources of social support (i.e., family and friend support) on different facets of EWB (i.e., positive affect and negative affect) simultaneously. Methodology and Findings In this study, the associations between family/friend support and positive/negative affect were investigated in a sample of 700 Chinese elderly. The EWB and social support were measured with a 12-item affective wordlist (Kahneman et al., 2004) and a self-prepared questionnaire. The results showed that (1) the order of contact frequency and mutual support followed a hierarchical order from spouse, children, to friends; (2) zero-order correlations of both family support and friend support were associated with more positive affect and less negative affect; and when compared with the relative role of family and friend support, (3) spouse (children if spouse is not available) support had greater contribution on decreasing negative affect, while friend support had greater influence on increasing positive affect, even after controlling the demographic, self-rated health and life events variables. Conclusion Family and friend support play different roles on the two facets of EWB of the elderly. These results were better explained in light of the task specificity model rather than the hierarchical compensatory model. Moreover, positive affect may be enhanced by friend support (based on personal interests and selectable) rather than family support (bonded by kinship and not selectable), which added evidences to the socioemotional selectivity theory. PMID:24594546

Perceived family and friend support and the psychological well-being of American and Chinese elderly persons.

PubMed

Poulin, John; Deng, Rong; Ingersoll, Travis Sky; Witt, Heather; Swain, Melanie

2012-12-01

This study examines two sources of informal support-perceived family and friend support-and the psychological well-being-self-esteem, depression and loneliness-of 150 Chinese and 145 American elders. There were no significant differences between the elderly American and Chinese persons' mean scores on family and friend support. The multiple linear regression analyses with interaction terms (country x family support and country x friend support), however, indicated that the relationship between family support and depression and family support and loneliness was stronger for the Chinese elderly than the US elderly. Conversely, the relationship between friend support and depression and friend support and loneliness is stronger for US elderly than Chinese elderly. The implications of these findings for social work practice in both countries is discussed.

Parental Strategies for Knowledge of Adolescents’ Friends: Distinct from Monitoring?

PubMed Central

Miller, Brenda A.; Duke, Michael R.; Ames, Genevieve M.

2012-01-01

Parental monitoring is defined as a set of behaviors used to gain knowledge about an adolescent’s whereabouts, friends and associates, and activities. However, can knowledge of adolescents’ whereabouts/activities, and friends all be attained through the same strategies? Or do they require their own strategies? This study used qualitative interviews with 173 parents of older adolescents from 100 families. Emergent themes described strategies by which parents gain information about their adolescents’ friends and the substance use of those friends. The strategies included direct interaction with the friend, gaining information from the teen, using second-hand sources, and making assumptions. Some of these strategies were consistent with previous research, while others raise new questions and provide interesting new directions to pursue. Primarily, additional consideration needs to be given to assessments of parental monitoring that include strategies for gaining knowledge of adolescents’ friends and their substance use. PMID:23209361

Narcissists of a Feather Flock Together: Narcissism and the Similarity of Friends.

PubMed

Maaß, Ulrike; Lämmle, Lena; Bensch, Doreen; Ziegler, Matthias

2016-03-01

Who is willing to expose himself or herself to narcissists on a long-term basis? Studies that address the interactions of narcissists focus mainly on their interactions with strangers. Hence, the aim of the present study was to investigate the extent to which two best friends' similarity in narcissism would influence their similarities in other personality profiles. A total of 290 best friends' dyads filled out measurements of the whole Dark Triad as well as the Big Five. For each personality domain, profile similarity and its dependence on the similarity in the Dark Triad were determined. Results showed that the friends' similarity in narcissism significantly predicted similarity in all Big Five domains. For the general Big Five similarity as well as extraversion, the effect of narcissism similarity was stronger for male than female or mixed friends. Similarity in psychopathy and Machiavellianism significantly predicted all domains except for openness and extraversion, respectively. © 2016 by the Society for Personality and Social Psychology, Inc.

TiConverter: A training image converting tool for multiple-point geostatistics

NASA Astrophysics Data System (ADS)

Fadlelmula F., Mohamed M.; Killough, John; Fraim, Michael

2016-11-01

TiConverter is a tool developed to ease the application of multiple-point geostatistics whether by the open source Stanford Geostatistical Modeling Software (SGeMS) or other available commercial software. TiConverter has a user-friendly interface and it allows the conversion of 2D training images into numerical representations in four different file formats without the need for additional code writing. These are the ASCII (.txt), the geostatistical software library (GSLIB) (.txt), the Isatis (.dat), and the VTK formats. It performs the conversion based on the RGB color system. In addition, TiConverter offers several useful tools including image resizing, smoothing, and segmenting tools. The purpose of this study is to introduce the TiConverter, and to demonstrate its application and advantages with several examples from the literature.

Development of a time-variable nuclear pulser for half life measurements

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

Zahn, Guilherme S.; Domienikan, Claudio; Carvalhaes, Roberto P. M.

2013-05-06

In this work a time-variable pulser system with an exponentially-decaying pulse frequency is presented, which was developed using the low-cost, open-source Arduino microcontroler plataform. In this system, the microcontroller produces a TTL signal in the selected rate and a pulse shaper board adjusts it to be entered in an amplifier as a conventional pulser signal; both the decay constant and the initial pulse rate can be adjusted using a user-friendly control software, and the pulse amplitude can be adjusted using a potentiometer in the pulse shaper board. The pulser was tested using several combinations of initial pulse rate and decaymore » constant, and the results show that the system is stable and reliable, and is suitable to be used in half-life measurements.« less

tsiR: An R package for time-series Susceptible-Infected-Recovered models of epidemics.

PubMed

Becker, Alexander D; Grenfell, Bryan T

2017-01-01

tsiR is an open source software package implemented in the R programming language designed to analyze infectious disease time-series data. The software extends a well-studied and widely-applied algorithm, the time-series Susceptible-Infected-Recovered (TSIR) model, to infer parameters from incidence data, such as contact seasonality, and to forward simulate the underlying mechanistic model. The tsiR package aggregates a number of different fitting features previously described in the literature in a user-friendly way, providing support for their broader adoption in infectious disease research. Also included in tsiR are a number of diagnostic tools to assess the fit of the TSIR model. This package should be useful for researchers analyzing incidence data for fully-immunizing infectious diseases.

GBIS (Geodetic Bayesian Inversion Software): Rapid Inversion of InSAR and GNSS Data to Estimate Surface Deformation Source Parameters and Uncertainties

NASA Astrophysics Data System (ADS)

Bagnardi, M.; Hooper, A. J.

2017-12-01

Inversions of geodetic observational data, such as Interferometric Synthetic Aperture Radar (InSAR) and Global Navigation Satellite System (GNSS) measurements, are often performed to obtain information about the source of surface displacements. Inverse problem theory has been applied to study magmatic processes, the earthquake cycle, and other phenomena that cause deformation of the Earth's interior and of its surface. Together with increasing improvements in data resolution, both spatial and temporal, new satellite missions (e.g., European Commission's Sentinel-1 satellites) are providing the unprecedented opportunity to access space-geodetic data within hours from their acquisition. To truly take advantage of these opportunities we must become able to interpret geodetic data in a rapid and robust manner. Here we present the open-source Geodetic Bayesian Inversion Software (GBIS; available for download at http://comet.nerc.ac.uk/gbis). GBIS is written in Matlab and offers a series of user-friendly and interactive pre- and post-processing tools. For example, an interactive function has been developed to estimate the characteristics of noise in InSAR data by calculating the experimental semi-variogram. The inversion software uses a Markov-chain Monte Carlo algorithm, incorporating the Metropolis-Hastings algorithm with adaptive step size, to efficiently sample the posterior probability distribution of the different source parameters. The probabilistic Bayesian approach allows the user to retrieve estimates of the optimal (best-fitting) deformation source parameters together with the associated uncertainties produced by errors in the data (and by scaling, errors in the model). The current version of GBIS (V1.0) includes fast analytical forward models for magmatic sources of different geometry (e.g., point source, finite spherical source, prolate spheroid source, penny-shaped sill-like source, and dipping-dike with uniform opening) and for dipping faults with uniform slip, embedded in a isotropic elastic half-space. However, the software architecture allows the user to easily add any other analytical or numerical forward models to calculate displacements at the surface. GBIS is delivered with a detailed user manual and three synthetic datasets for testing and practical training.

A user-friendly tool to transform large scale administrative data into wide table format using a MapReduce program with a Pig Latin based script.

PubMed

Horiguchi, Hiromasa; Yasunaga, Hideo; Hashimoto, Hideki; Ohe, Kazuhiko

2012-12-22

Secondary use of large scale administrative data is increasingly popular in health services and clinical research, where a user-friendly tool for data management is in great demand. MapReduce technology such as Hadoop is a promising tool for this purpose, though its use has been limited by the lack of user-friendly functions for transforming large scale data into wide table format, where each subject is represented by one row, for use in health services and clinical research. Since the original specification of Pig provides very few functions for column field management, we have developed a novel system called GroupFilterFormat to handle the definition of field and data content based on a Pig Latin script. We have also developed, as an open-source project, several user-defined functions to transform the table format using GroupFilterFormat and to deal with processing that considers date conditions. Having prepared dummy discharge summary data for 2.3 million inpatients and medical activity log data for 950 million events, we used the Elastic Compute Cloud environment provided by Amazon Inc. to execute processing speed and scaling benchmarks. In the speed benchmark test, the response time was significantly reduced and a linear relationship was observed between the quantity of data and processing time in both a small and a very large dataset. The scaling benchmark test showed clear scalability. In our system, doubling the number of nodes resulted in a 47% decrease in processing time. Our newly developed system is widely accessible as an open resource. This system is very simple and easy to use for researchers who are accustomed to using declarative command syntax for commercial statistical software and Structured Query Language. Although our system needs further sophistication to allow more flexibility in scripts and to improve efficiency in data processing, it shows promise in facilitating the application of MapReduce technology to efficient data processing with large scale administrative data in health services and clinical research.

End-of-life dreams and visions: a longitudinal study of hospice patients' experiences.

PubMed

Kerr, Christopher W; Donnelly, James P; Wright, Scott T; Kuszczak, Sarah M; Banas, Anne; Grant, Pei C; Luczkiewicz, Debra L

2014-03-01

End-of-life dreams and visions (ELDVs) have been well documented throughout history and across cultures. The impact of pre-death experiences on dying individuals and their loved ones can be profoundly meaningful. Our aim was to quantify the frequency of dreams/visions experienced by patients nearing the end of life, examine the content and subjective significance of the dreams/visions, and explore the relationship of these factors to time/proximity to death. This mixed-methods study surveyed patients in a hospice inpatient unit using a semi-structured interview. Sixty-six patients admitted to a hospice inpatient unit between January 2011 and July 2012 provided informed consent and participated in the study. The semi-structured interviews contained closed and open-ended questions regarding the content, frequency, and comfort/distress of dreams/visions. Fifty-nine participants comprised the final sample. Most participants reported experiencing at least one dream/vision. Almost half of the dreams/visions occurred while asleep, and nearly all patients indicated that they felt real. The most common dreams/visions included deceased friends/relatives and living friends/relatives. Dreams/visions featuring the deceased (friends, relatives, and animals/pets) were significantly more comforting than those of the living, living and deceased combined, and other people and experiences. As participants approached death, comforting dreams/visions of the deceased became more prevalent. ELDVs are commonly experienced phenomena during the dying process, characterized by a consistent sense of realism and marked emotional significance. These dreams/visions may be a profound source of potential meaning and comfort for the dying, and therefore warrant clinical attention and further research.

GProX, a user-friendly platform for bioinformatics analysis and visualization of quantitative proteomics data.

PubMed

Rigbolt, Kristoffer T G; Vanselow, Jens T; Blagoev, Blagoy

2011-08-01

Recent technological advances have made it possible to identify and quantify thousands of proteins in a single proteomics experiment. As a result of these developments, the analysis of data has become the bottleneck of proteomics experiment. To provide the proteomics community with a user-friendly platform for comprehensive analysis, inspection and visualization of quantitative proteomics data we developed the Graphical Proteomics Data Explorer (GProX)(1). The program requires no special bioinformatics training, as all functions of GProX are accessible within its graphical user-friendly interface which will be intuitive to most users. Basic features facilitate the uncomplicated management and organization of large data sets and complex experimental setups as well as the inspection and graphical plotting of quantitative data. These are complemented by readily available high-level analysis options such as database querying, clustering based on abundance ratios, feature enrichment tests for e.g. GO terms and pathway analysis tools. A number of plotting options for visualization of quantitative proteomics data is available and most analysis functions in GProX create customizable high quality graphical displays in both vector and bitmap formats. The generic import requirements allow data originating from essentially all mass spectrometry platforms, quantitation strategies and software to be analyzed in the program. GProX represents a powerful approach to proteomics data analysis providing proteomics experimenters with a toolbox for bioinformatics analysis of quantitative proteomics data. The program is released as open-source and can be freely downloaded from the project webpage at http://gprox.sourceforge.net.

GProX, a User-Friendly Platform for Bioinformatics Analysis and Visualization of Quantitative Proteomics Data*

PubMed Central

Rigbolt, Kristoffer T. G.; Vanselow, Jens T.; Blagoev, Blagoy

2011-01-01

Recent technological advances have made it possible to identify and quantify thousands of proteins in a single proteomics experiment. As a result of these developments, the analysis of data has become the bottleneck of proteomics experiment. To provide the proteomics community with a user-friendly platform for comprehensive analysis, inspection and visualization of quantitative proteomics data we developed the Graphical Proteomics Data Explorer (GProX)1. The program requires no special bioinformatics training, as all functions of GProX are accessible within its graphical user-friendly interface which will be intuitive to most users. Basic features facilitate the uncomplicated management and organization of large data sets and complex experimental setups as well as the inspection and graphical plotting of quantitative data. These are complemented by readily available high-level analysis options such as database querying, clustering based on abundance ratios, feature enrichment tests for e.g. GO terms and pathway analysis tools. A number of plotting options for visualization of quantitative proteomics data is available and most analysis functions in GProX create customizable high quality graphical displays in both vector and bitmap formats. The generic import requirements allow data originating from essentially all mass spectrometry platforms, quantitation strategies and software to be analyzed in the program. GProX represents a powerful approach to proteomics data analysis providing proteomics experimenters with a toolbox for bioinformatics analysis of quantitative proteomics data. The program is released as open-source and can be freely downloaded from the project webpage at http://gprox.sourceforge.net. PMID:21602510

Bias Correction of Satellite Precipitation Products (SPPs) using a User-friendly Tool: A Step in Enhancing Technical Capacity

NASA Astrophysics Data System (ADS)

Rushi, B. R.; Ellenburg, W. L.; Adams, E. C.; Flores, A.; Limaye, A. S.; Valdés-Pineda, R.; Roy, T.; Valdés, J. B.; Mithieu, F.; Omondi, S.

2017-12-01

SERVIR, a joint NASA-USAID initiative, works to build capacity in Earth observation technologies in developing countries for improved environmental decision making in the arena of: weather and climate, water and disasters, food security and land use/land cover. SERVIR partners with leading regional organizations in Eastern and Southern Africa, Hindu Kush-Himalaya, Mekong region, and West Africa to achieve its objectives. SERVIR develops hydrological applications to address specific needs articulated by key stakeholders and daily rainfall estimates are a vital input for these applications. Satellite-derived rainfall is subjected to systemic biases which need to be corrected before it can be used for any hydrologic application such as real-time or seasonal forecasting. SERVIR and the SWAAT team at the University of Arizona, have co-developed an open-source and user friendly tool of rainfall bias correction approaches for SPPs. Bias correction tools were developed based on Linear Scaling and Quantile Mapping techniques. A set of SPPs, such as PERSIANN-CCS, TMPA-RT, and CMORPH, are bias corrected using Climate Hazards Group InfraRed Precipitation with Station (CHIRPS) data which incorporates ground based precipitation observations. This bias correction tools also contains a component, which is included to improve monthly mean of CHIRPS using precipitation products of the Global Surface Summary of the Day (GSOD) database developed by the National Climatic Data Center (NCDC). This tool takes input from command-line which makes it user-friendly and applicable in any operating platform without prior programming skills. This presentation will focus on this bias-correction tool for SPPs, including application scenarios.

QCloud: A cloud-based quality control system for mass spectrometry-based proteomics laboratories

PubMed Central

Chiva, Cristina; Olivella, Roger; Borràs, Eva; Espadas, Guadalupe; Pastor, Olga; Solé, Amanda

2018-01-01

The increasing number of biomedical and translational applications in mass spectrometry-based proteomics poses new analytical challenges and raises the need for automated quality control systems. Despite previous efforts to set standard file formats, data processing workflows and key evaluation parameters for quality control, automated quality control systems are not yet widespread among proteomics laboratories, which limits the acquisition of high-quality results, inter-laboratory comparisons and the assessment of variability of instrumental platforms. Here we present QCloud, a cloud-based system to support proteomics laboratories in daily quality assessment using a user-friendly interface, easy setup, automated data processing and archiving, and unbiased instrument evaluation. QCloud supports the most common targeted and untargeted proteomics workflows, it accepts data formats from different vendors and it enables the annotation of acquired data and reporting incidences. A complete version of the QCloud system has successfully been developed and it is now open to the proteomics community (http://qcloud.crg.eu). QCloud system is an open source project, publicly available under a Creative Commons License Attribution-ShareAlike 4.0. PMID:29324744

Dose response explorer: an integrated open-source tool for exploring and modelling radiotherapy dose volume outcome relationships

NASA Astrophysics Data System (ADS)

El Naqa, I.; Suneja, G.; Lindsay, P. E.; Hope, A. J.; Alaly, J. R.; Vicic, M.; Bradley, J. D.; Apte, A.; Deasy, J. O.

2006-11-01

Radiotherapy treatment outcome models are a complicated function of treatment, clinical and biological factors. Our objective is to provide clinicians and scientists with an accurate, flexible and user-friendly software tool to explore radiotherapy outcomes data and build statistical tumour control or normal tissue complications models. The software tool, called the dose response explorer system (DREES), is based on Matlab, and uses a named-field structure array data type. DREES/Matlab in combination with another open-source tool (CERR) provides an environment for analysing treatment outcomes. DREES provides many radiotherapy outcome modelling features, including (1) fitting of analytical normal tissue complication probability (NTCP) and tumour control probability (TCP) models, (2) combined modelling of multiple dose-volume variables (e.g., mean dose, max dose, etc) and clinical factors (age, gender, stage, etc) using multi-term regression modelling, (3) manual or automated selection of logistic or actuarial model variables using bootstrap statistical resampling, (4) estimation of uncertainty in model parameters, (5) performance assessment of univariate and multivariate analyses using Spearman's rank correlation and chi-square statistics, boxplots, nomograms, Kaplan-Meier survival plots, and receiver operating characteristics curves, and (6) graphical capabilities to visualize NTCP or TCP prediction versus selected variable models using various plots. DREES provides clinical researchers with a tool customized for radiotherapy outcome modelling. DREES is freely distributed. We expect to continue developing DREES based on user feedback.

a Procedural Solution to Model Roman Masonry Structures

NASA Astrophysics Data System (ADS)

Cappellini, V.; Saleri, R.; Stefani, C.; Nony, N.; De Luca, L.

2013-07-01

The paper will describe a new approach based on the development of a procedural modelling methodology for archaeological data representation. This is a custom-designed solution based on the recognition of the rules belonging to the construction methods used in roman times. We have conceived a tool for 3D reconstruction of masonry structures starting from photogrammetric surveying. Our protocol considers different steps. Firstly we have focused on the classification of opus based on the basic interconnections that can lead to a descriptive system used for their unequivocal identification and design. Secondly, we have chosen an automatic, accurate, flexible and open-source photogrammetric pipeline named Pastis Apero Micmac - PAM, developed by IGN (Paris). We have employed it to generate ortho-images from non-oriented images, using a user-friendly interface implemented by CNRS Marseille (France). Thirdly, the masonry elements are created in parametric and interactive way, and finally they are adapted to the photogrammetric data. The presented application, currently under construction, is developed with an open source programming language called Processing, useful for visual, animated or static, 2D or 3D, interactive creations. Using this computer language, a Java environment has been developed. Therefore, even if the procedural modelling reveals an accuracy level inferior to the one obtained by manual modelling (brick by brick), this method can be useful when taking into account the static evaluation on buildings (requiring quantitative aspects) and metric measures for restoration purposes.

Mining collections of compounds with Screening Assistant 2

PubMed Central

2012-01-01

Background High-throughput screening assays have become the starting point of many drug discovery programs for large pharmaceutical companies as well as academic organisations. Despite the increasing throughput of screening technologies, the almost infinite chemical space remains out of reach, calling for tools dedicated to the analysis and selection of the compound collections intended to be screened. Results We present Screening Assistant 2 (SA2), an open-source JAVA software dedicated to the storage and analysis of small to very large chemical libraries. SA2 stores unique molecules in a MySQL database, and encapsulates several chemoinformatics methods, among which: providers management, interactive visualisation, scaffold analysis, diverse subset creation, descriptors calculation, sub-structure / SMART search, similarity search and filtering. We illustrate the use of SA2 by analysing the composition of a database of 15 million compounds collected from 73 providers, in terms of scaffolds, frameworks, and undesired properties as defined by recently proposed HTS SMARTS filters. We also show how the software can be used to create diverse libraries based on existing ones. Conclusions Screening Assistant 2 is a user-friendly, open-source software that can be used to manage collections of compounds and perform simple to advanced chemoinformatics analyses. Its modular design and growing documentation facilitate the addition of new functionalities, calling for contributions from the community. The software can be downloaded at http://sa2.sourceforge.net/. PMID:23327565

Mining collections of compounds with Screening Assistant 2.

PubMed

Guilloux, Vincent Le; Arrault, Alban; Colliandre, Lionel; Bourg, Stéphane; Vayer, Philippe; Morin-Allory, Luc

2012-08-31

High-throughput screening assays have become the starting point of many drug discovery programs for large pharmaceutical companies as well as academic organisations. Despite the increasing throughput of screening technologies, the almost infinite chemical space remains out of reach, calling for tools dedicated to the analysis and selection of the compound collections intended to be screened. We present Screening Assistant 2 (SA2), an open-source JAVA software dedicated to the storage and analysis of small to very large chemical libraries. SA2 stores unique molecules in a MySQL database, and encapsulates several chemoinformatics methods, among which: providers management, interactive visualisation, scaffold analysis, diverse subset creation, descriptors calculation, sub-structure / SMART search, similarity search and filtering. We illustrate the use of SA2 by analysing the composition of a database of 15 million compounds collected from 73 providers, in terms of scaffolds, frameworks, and undesired properties as defined by recently proposed HTS SMARTS filters. We also show how the software can be used to create diverse libraries based on existing ones. Screening Assistant 2 is a user-friendly, open-source software that can be used to manage collections of compounds and perform simple to advanced chemoinformatics analyses. Its modular design and growing documentation facilitate the addition of new functionalities, calling for contributions from the community. The software can be downloaded at http://sa2.sourceforge.net/.

GRIP Collaboration Portal: Information Management for a Hurricane Field Campaign

NASA Astrophysics Data System (ADS)

Conover, H.; Kulkarni, A.; Garrett, M.; Smith, T.; Goodman, H. M.

2010-12-01

NASA’s Genesis and Rapid Intensification Processes (GRIP) experiment, carried out in August and September of 2010, was a complex operation, involving three aircraft and their crews based at different airports, a dozen instrument teams, mission scientists, weather forecasters, project coordinators and a variety of other participants. In addition, GRIP was coordinated with concurrent airborne missions: NOAA’s IFEX and then NSF-funded PREDICT. The GRIP Collaboration Portal was developed to facilitate communication within and between the different teams and serve as an information repository for the field campaign, providing a single access point for project documents, plans, weather forecasts, flight reports and quicklook data. The portal was developed using the Drupal open source content management framework. This presentation will cover both technology and participation issues. Specific examples include: Drupal’s large and diverse open source developer community is an advantage in that we were able to reuse many modules rather than develop capabilities from scratch, but integrating multiple modules developed by many people adds to the overall complexity of the site. Many of the communication capabilities provided by the site, such as discussion forums and blogs, were not used. Participants were diligent about posting necessary documents, but the favored communication method remained email. Drupal's developer-friendly nature allowed for quick development of the customized functionality needed to accommodate the rapidly changing requirements of GRIP experiment. DC-8 Overflight of Hurricane Earl during GRIP Mission

The Influence of Source of Social Support and Size of Social Network on All-Cause Mortality

PubMed Central

Becofsky, Katie M.; Shook, Robin P.; Sui, Xuemei; Wilcox, Sara; Lavie, Carl J.; Blair, Steven N.

2015-01-01

Objective To examine associations between relative, friend, and partner support, as well as size and source of weekly social network, on mortality risk in the Aerobics Center Longitudinal Study (ACLS). Patients and Methods In a mail-back survey completed between January 1, 1990 and December 31, 1990, adult ACLS participants (n=12,709) answered questions regarding whether they received social support from relatives, friends, and spouse/partner (yes or no for each), and the number of friends and relatives they had contact with at least once per week. Participants were followed until December 31, 2003 or death. Cox proportional hazard regression evaluated the strength of the associations, controlling for covariates. Results Participants (25% women) averaged 53.0 years at baseline. During a median 13.5 years of follow-up, 1,139 deaths occurred. Receiving social support from relatives reduced mortality risk 19% (HR 0.81, 95% CI 0.68–0.95). Receiving spousal/partner support also reduced mortality risk 19% (HR 0.81, 95% CI 0.66-.99). Receiving social support from friends was not associated with mortality risk (HR 0.90, 95% CI 0.75–1.09), however, participants reporting social contact with 6 or 7 friends on a weekly basis had a 24% lower mortality risk than those in contact with ≤ 1 friend (HR 0.76, 95% CI 0.58–0.98). Contact with 2–5 or ≥8 friends was not associated with mortality risk, nor was number of weekly relative contacts. Conclusions Receiving social support from one’s spouse/partner and relatives and maintaining weekly social interaction with 6–7 friends reduced mortality risk. Such data may inform interventions to improve long-term survival. PMID:26055526

"Now I Don't Have to Guess": Using Pamphlets to Encourage Residents and Families/Friends to Engage in Advance Care Planning in Long-Term Care.

PubMed

Sussman, Tamara; Kaasalainen, Sharon; Bui, Matthew; Akhtar-Danesh, Noori; Mintzberg, Susan; Strachan, Patricia

2017-01-01

Objective: This article explores whether access to illness trajectory pamphlets for five conditions with high prevalence in long-term care (LTC) can encourage residents and families/friends to openly engage in advance care planning (ACP) discussions with one another and with health providers. Method: In all, 57 residents and families/friends in LTC completed surveys and 56 participated in seven focus groups that explored whether the pamphlets supported ACP engagement. Results: Survey results suggested that access to pamphlets encouraged residents and families/friends to reflect on future care (48/57, 84%), clarified what questions to ask (40/57, 70%), and increased comfort in talking about end of life (EOL) care (36/57, 63%). Discussions between relatives and friends/families (32/57, 56%) or with health providers (21/57, 37%) were less common. Focus group deliberations illuminated that while reading illness-specific information was validating, a tendency to protect one another from an emotional topic, prevented residents and families/friends from conversing with one another about EOL issues. Discussion: Having access to pamphlets with information about EOL care provides important and welcome opportunities for reflection for both residents in LTC and their families/friends. Moving residents and families/friends from reflecting on issues to discussing them together could require staff support through planned care conferences or staff initiated conversations at the bedside.

How youth-friendly are pharmacies in New Zealand? Surveying aspects of accessibility and the pharmacy environment using a youth participatory approach.

PubMed

Horsfield, Emma; Kelly, Fiona; Clark, Terryann; Sheridan, Janie

2014-01-01

The international youth population has significant unmet health needs, and there have been many calls to increase youth health care access. Community pharmacies may be able to help address these needs, but very little research has investigated this area and it is not known whether the current community pharmacy setting is acceptable or appropriate for youth. 1) To obtain information on physical factors which could affect young people's use of community pharmacies in New Zealand, including accessibility, opening times and the physical youth-friendliness of the pharmacy environment. 2) To involve and utilize young people in the research process, in order to understand their needs and interpretation of survey data. This study applied a cross sectional survey design, informed by a sequential youth participatory approach. A questionnaire was developed in consultation with a youth advisory group (YAG). Questionnaires distributed to pharmacists at 500 randomly selected pharmacies nationwide between May and September 2011 collected information on whether the pharmacy met selected youth-friendly criteria. These included physical aspects of youth-friendliness, such as opening times and the pharmacy environment. The YAG also provided a youth perspective in the interpretation of the results. Three mail shots achieved a response rate of 50.5%. Most respondents reported the pharmacy to be accessible by public transport and many had extended opening hours. Although most pharmacies met some youth-friendly criteria with regards to the pharmacy environment (e.g. having a private consultation area), more specific criteria (such as displaying youth health information) were usually not met. Interpretive feedback from the YAG highlighted areas for improvement. Pharmacies show potential as youth-friendly health care access points and most already meet some youth-friendly criteria. Areas identified for improvement will require a greater youth focus from the profession, and should be undertaken in consultation with young people. We recommend the use of youth participation approaches in future pharmacy practice research into youth health services. Copyright © 2014 Elsevier Inc. All rights reserved.

A LabVIEW model incorporating an open-loop arterial impedance and a closed-loop circulatory system.

PubMed

Cole, R T; Lucas, C L; Cascio, W E; Johnson, T A

2005-11-01

While numerous computer models exist for the circulatory system, many are limited in scope, contain unwanted features or incorporate complex components specific to unique experimental situations. Our purpose was to develop a basic, yet multifaceted, computer model of the left heart and systemic circulation in LabVIEW having universal appeal without sacrificing crucial physiologic features. The program we developed employs Windkessel-type impedance models in several open-loop configurations and a closed-loop model coupling a lumped impedance and ventricular pressure source. The open-loop impedance models demonstrate afterload effects on arbitrary aortic pressure/flow inputs. The closed-loop model catalogs the major circulatory waveforms with changes in afterload, preload, and left heart properties. Our model provides an avenue for expanding the use of the ventricular equations through closed-loop coupling that includes a basic coronary circuit. Tested values used for the afterload components and the effects of afterload parameter changes on various waveforms are consistent with published data. We conclude that this model offers the ability to alter several circulatory factors and digitally catalog the most salient features of the pressure/flow waveforms employing a user-friendly platform. These features make the model a useful instructional tool for students as well as a simple experimental tool for cardiovascular research.

Associations between friends' disordered eating and muscle-enhancing behaviors

PubMed Central

Eisenberg, Marla E.; Wall, Melanie; Shim, Jin Joo; Bruening, Meg; Loth, Katie; Neumark-Sztainer, Dianne

2012-01-01

Dieting, unhealthy weight control and muscle-enhancing behaviors are common among adolescents: friends are a probable source of influence on these behaviors. The present study uses data provided by nominated friends to examine associations between friends' disordered eating and muscle-enhancing behaviors and participants' own behaviors in a diverse sample of American youth. Male and female adolescents (mean age = 14.4) completed surveys and identified their friends from a class roster; friends' survey data were then linked to each participant. Participants (N = 2126) who had at least one nominated friend were included in the analytic sample. Independent variables were created using the same weight control and muscle-enhancing behaviors reported by nominated friends, and were used in logistic regression models to test associations between participants' and their friends' behaviors, stratified by gender. Results indicated that dieting, disordered eating and muscle-enhancing behaviors were common in this sample, and selected friends' behaviors were associated with the same behaviors in participants. For example, girls whose friends reported extreme weight control behaviors had significantly greater odds of using these behaviors than girls whose friends did not report these same behaviors (OR = 2.39). This research suggests that friends' weight- and shape-related behaviors are a feature of social relationships, and is the first report demonstrating these associations for muscle-enhancing behaviors. Capitalizing on the social element may be important to the development of increasingly effective intervention and prevention programs. PMID:23010337

An integrated pipeline of open source software adapted for multi-CPU architectures: use in the large-scale identification of single nucleotide polymorphisms.

PubMed

Jayashree, B; Hanspal, Manindra S; Srinivasan, Rajgopal; Vigneshwaran, R; Varshney, Rajeev K; Spurthi, N; Eshwar, K; Ramesh, N; Chandra, S; Hoisington, David A

2007-01-01

The large amounts of EST sequence data available from a single species of an organism as well as for several species within a genus provide an easy source of identification of intra- and interspecies single nucleotide polymorphisms (SNPs). In the case of model organisms, the data available are numerous, given the degree of redundancy in the deposited EST data. There are several available bioinformatics tools that can be used to mine this data; however, using them requires a certain level of expertise: the tools have to be used sequentially with accompanying format conversion and steps like clustering and assembly of sequences become time-intensive jobs even for moderately sized datasets. We report here a pipeline of open source software extended to run on multiple CPU architectures that can be used to mine large EST datasets for SNPs and identify restriction sites for assaying the SNPs so that cost-effective CAPS assays can be developed for SNP genotyping in genetics and breeding applications. At the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), the pipeline has been implemented to run on a Paracel high-performance system consisting of four dual AMD Opteron processors running Linux with MPICH. The pipeline can be accessed through user-friendly web interfaces at http://hpc.icrisat.cgiar.org/PBSWeb and is available on request for academic use. We have validated the developed pipeline by mining chickpea ESTs for interspecies SNPs, development of CAPS assays for SNP genotyping, and confirmation of restriction digestion pattern at the sequence level.

UManSysProp v1.0: an online and open-source facility for molecular property prediction and atmospheric aerosol calculations

NASA Astrophysics Data System (ADS)

Topping, David; Barley, Mark; Bane, Michael K.; Higham, Nicholas; Aumont, Bernard; Dingle, Nicholas; McFiggans, Gordon

2016-03-01

In this paper we describe the development and application of a new web-based facility, UManSysProp (http://umansysprop.seaes.manchester.ac.uk), for automating predictions of molecular and atmospheric aerosol properties. Current facilities include pure component vapour pressures, critical properties, and sub-cooled densities of organic molecules; activity coefficient predictions for mixed inorganic-organic liquid systems; hygroscopic growth factors and CCN (cloud condensation nuclei) activation potential of mixed inorganic-organic aerosol particles; and absorptive partitioning calculations with/without a treatment of non-ideality. The aim of this new facility is to provide a single point of reference for all properties relevant to atmospheric aerosol that have been checked for applicability to atmospheric compounds where possible. The group contribution approach allows users to upload molecular information in the form of SMILES (Simplified Molecular Input Line Entry System) strings and UManSysProp will automatically extract the relevant information for calculations. Built using open-source chemical informatics, and hosted at the University of Manchester, the facilities are provided via a browser and device-friendly web interface, or can be accessed using the user's own code via a JSON API (application program interface). We also provide the source code for all predictive techniques provided on the site, covered by the GNU GPL (General Public License) license to encourage development of a user community. We have released this via a Github repository (doi:10.5281/zenodo.45143). In this paper we demonstrate its use with specific examples that can be simulated using the web-browser interface.

P-TRAP: a Panicle TRAit Phenotyping tool.

PubMed

A L-Tam, Faroq; Adam, Helene; Anjos, António dos; Lorieux, Mathias; Larmande, Pierre; Ghesquière, Alain; Jouannic, Stefan; Shahbazkia, Hamid Reza

2013-08-29

In crops, inflorescence complexity and the shape and size of the seed are among the most important characters that influence yield. For example, rice panicles vary considerably in the number and order of branches, elongation of the axis, and the shape and size of the seed. Manual low-throughput phenotyping methods are time consuming, and the results are unreliable. However, high-throughput image analysis of the qualitative and quantitative traits of rice panicles is essential for understanding the diversity of the panicle as well as for breeding programs. This paper presents P-TRAP software (Panicle TRAit Phenotyping), a free open source application for high-throughput measurements of panicle architecture and seed-related traits. The software is written in Java and can be used with different platforms (the user-friendly Graphical User Interface (GUI) uses Netbeans Platform 7.3). The application offers three main tools: a tool for the analysis of panicle structure, a spikelet/grain counting tool, and a tool for the analysis of seed shape. The three tools can be used independently or simultaneously for analysis of the same image. Results are then reported in the Extensible Markup Language (XML) and Comma Separated Values (CSV) file formats. Images of rice panicles were used to evaluate the efficiency and robustness of the software. Compared to data obtained by manual processing, P-TRAP produced reliable results in a much shorter time. In addition, manual processing is not repeatable because dry panicles are vulnerable to damage. The software is very useful, practical and collects much more data than human operators. P-TRAP is a new open source software that automatically recognizes the structure of a panicle and the seeds on the panicle in numeric images. The software processes and quantifies several traits related to panicle structure, detects and counts the grains, and measures their shape parameters. In short, P-TRAP offers both efficient results and a user-friendly environment for experiments. The experimental results showed very good accuracy compared to field operator, expert verification and well-known academic methods.

MONALISA for stochastic simulations of Petri net models of biochemical systems.

PubMed

Balazki, Pavel; Lindauer, Klaus; Einloft, Jens; Ackermann, Jörg; Koch, Ina

2015-07-10

The concept of Petri nets (PN) is widely used in systems biology and allows modeling of complex biochemical systems like metabolic systems, signal transduction pathways, and gene expression networks. In particular, PN allows the topological analysis based on structural properties, which is important and useful when quantitative (kinetic) data are incomplete or unknown. Knowing the kinetic parameters, the simulation of time evolution of such models can help to study the dynamic behavior of the underlying system. If the number of involved entities (molecules) is low, a stochastic simulation should be preferred against the classical deterministic approach of solving ordinary differential equations. The Stochastic Simulation Algorithm (SSA) is a common method for such simulations. The combination of the qualitative and semi-quantitative PN modeling and stochastic analysis techniques provides a valuable approach in the field of systems biology. Here, we describe the implementation of stochastic analysis in a PN environment. We extended MONALISA - an open-source software for creation, visualization and analysis of PN - by several stochastic simulation methods. The simulation module offers four simulation modes, among them the stochastic mode with constant firing rates and Gillespie's algorithm as exact and approximate versions. The simulator is operated by a user-friendly graphical interface and accepts input data such as concentrations and reaction rate constants that are common parameters in the biological context. The key features of the simulation module are visualization of simulation, interactive plotting, export of results into a text file, mathematical expressions for describing simulation parameters, and up to 500 parallel simulations of the same parameter sets. To illustrate the method we discuss a model for insulin receptor recycling as case study. We present a software that combines the modeling power of Petri nets with stochastic simulation of dynamic processes in a user-friendly environment supported by an intuitive graphical interface. The program offers a valuable alternative to modeling, using ordinary differential equations, especially when simulating single-cell experiments with low molecule counts. The ability to use mathematical expressions provides an additional flexibility in describing the simulation parameters. The open-source distribution allows further extensions by third-party developers. The software is cross-platform and is licensed under the Artistic License 2.0.

P-TRAP: a Panicle Trait Phenotyping tool

PubMed Central

2013-01-01

Background In crops, inflorescence complexity and the shape and size of the seed are among the most important characters that influence yield. For example, rice panicles vary considerably in the number and order of branches, elongation of the axis, and the shape and size of the seed. Manual low-throughput phenotyping methods are time consuming, and the results are unreliable. However, high-throughput image analysis of the qualitative and quantitative traits of rice panicles is essential for understanding the diversity of the panicle as well as for breeding programs. Results This paper presents P-TRAP software (Panicle TRAit Phenotyping), a free open source application for high-throughput measurements of panicle architecture and seed-related traits. The software is written in Java and can be used with different platforms (the user-friendly Graphical User Interface (GUI) uses Netbeans Platform 7.3). The application offers three main tools: a tool for the analysis of panicle structure, a spikelet/grain counting tool, and a tool for the analysis of seed shape. The three tools can be used independently or simultaneously for analysis of the same image. Results are then reported in the Extensible Markup Language (XML) and Comma Separated Values (CSV) file formats. Images of rice panicles were used to evaluate the efficiency and robustness of the software. Compared to data obtained by manual processing, P-TRAP produced reliable results in a much shorter time. In addition, manual processing is not repeatable because dry panicles are vulnerable to damage. The software is very useful, practical and collects much more data than human operators. Conclusions P-TRAP is a new open source software that automatically recognizes the structure of a panicle and the seeds on the panicle in numeric images. The software processes and quantifies several traits related to panicle structure, detects and counts the grains, and measures their shape parameters. In short, P-TRAP offers both efficient results and a user-friendly environment for experiments. The experimental results showed very good accuracy compared to field operator, expert verification and well-known academic methods. PMID:23987653

Partner Choice in Raven (Corvus corax) Cooperation.

PubMed

Asakawa-Haas, Kenji; Schiestl, Martina; Bugnyar, Thomas; Massen, Jorg J M

2016-01-01

Although social animals frequently make decisions about when or with whom to cooperate, little is known about the underlying mechanisms of partner choice. Most previous studies compared different dyads' performances, though did not allow an actual choice among partners. We tested eleven ravens, Corvus corax, in triads, giving them first the choice to cooperate with either a highly familiar or a rather unfamiliar partner and, second, with either a friend or a non-friend using a cooperative string-pulling task. In either test, the ravens had a second choice and could cooperate with the other partner, given that this one had not pulled the string in the meantime. We show that during the experiments, these partner ravens indeed learn to wait and inhibit pulling, respectively. Moreover, the results of these two experiments show that ravens' preferences for a specific cooperation partner are not based on familiarity. In contrast, the ravens did show a preference based on relationship quality, as they did choose to cooperate significantly more with friends than with non-friends and they were also more proficient when cooperating with a friend. In order to further identify the proximate mechanism of this preference, we designed an open-choice experiment for the whole group where all birds were free to cooperate on two separate apparatuses. This set-up allowed us to distinguish between preferences for close proximity and preferences to cooperate. The results revealed that friends preferred staying close to each other, but did not necessarily cooperate with one another, suggesting that tolerance of proximity and not relationship quality as a whole may be the driving force behind partner choice in raven cooperation. Consequently, we stress the importance of experiments that allow such titrations and, suggest that these results have important implications for the interpretations of cooperation studies that did not include open partner choice.

HIV-Related Sexual Risk among African American Men Preceding Incarceration: Associations with Support from Significant Others, Family, and Friends.

PubMed

Coatsworth, Ashley M; Scheidell, Joy D; Wohl, David A; Whitehead, Nicole E; Golin, Carol E; Judon-Monk, Selena; Khan, Maria R

2017-02-01

We evaluated the association between social support received from significant others, family, and friends and HIV-related sexual risk behaviors among African American men involved in the criminal justice system. Project DISRUPT is a cohort study among African American men released from prison in North Carolina (N = 189). During the baseline (in-prison) survey, we assessed the amount of support men perceived they had received from significant others, family, and friends. We measured associations between low support from each source (

22 CFR 71.10 - Emergency medical assistance.

Code of Federal Regulations, 2012 CFR

2012-04-01

... general criteria: (1) Adequate treatment cannot or will not be provided by prison authorities or the host government; (2) All reasonable attempts to obtain private resources (prisoner's family, friends, etc.) have... family or friends who might serve as a source of private funds for medical services, and attempt to...

Child-Friendly Schools: An Assessment of Secondary Schools

ERIC Educational Resources Information Center

Çobanoglu, Fatma; Ayvaz-Tuncel, Zeynep; Ordu, Aydan

2018-01-01

As education has many variables, essential arrangements are required in different areas to enhance its quality. School buildings, environmental arrangements, teaching and learning process, sources and materials, teachers, principals, health and security are the variables of which come to mind first. The concept of 'child-friendly school' ('CFS')…

A user-friendly model for spray drying to aid pharmaceutical product development.

PubMed

Grasmeijer, Niels; de Waard, Hans; Hinrichs, Wouter L J; Frijlink, Henderik W

2013-01-01

The aim of this study was to develop a user-friendly model for spray drying that can aid in the development of a pharmaceutical product, by shifting from a trial-and-error towards a quality-by-design approach. To achieve this, a spray dryer model was developed in commercial and open source spreadsheet software. The output of the model was first fitted to the experimental output of a Büchi B-290 spray dryer and subsequently validated. The predicted outlet temperatures of the spray dryer model matched the experimental values very well over the entire range of spray dryer settings that were tested. Finally, the model was applied to produce glassy sugars by spray drying, an often used excipient in formulations of biopharmaceuticals. For the production of glassy sugars, the model was extended to predict the relative humidity at the outlet, which is not measured in the spray dryer by default. This extended model was then successfully used to predict whether specific settings were suitable for producing glassy trehalose and inulin by spray drying. In conclusion, a spray dryer model was developed that is able to predict the output parameters of the spray drying process. The model can aid the development of spray dried pharmaceutical products by shifting from a trial-and-error towards a quality-by-design approach.

The association between family and friend integration and physical activity: results from the NHIS.

PubMed

Larsen, Britta A; Strong, David; Linke, Sarah E

2014-06-01

Social integration predicts morbidity and mortality, but its relationships with specific health behaviors that could explain this relationship, such as physical activity, have not been established. Additionally, studies associating social integration with health have not distinguished between sources of social contact (family vs. friends), which could be differentially related to health. The purpose of this study was to examine the association between social integration and physical activity and to explore differences in family and friend social integration. Data came from the 2001 wave of the National Health Interview Survey. Adult participants (N = 33,326) indicated levels of social integration by reporting whether they had seen and/or called friends and/or family in the past 2 weeks and also reported their weekly minutes of physical activity. Logistic regression was used to determine odds of meeting physical activity (PA) guidelines (≥ 150 min/week) and odds of inactivity (0 min/week) based on levels of social integration. Greater integration predicted higher odds of meeting PA guidelines and lower odds of inactivity after controlling for sociodemographic variables. This association was stronger and dose-dependent for integration with friends, whereas moderate family contact predicted greater activity than high levels of family contact. Those who are more socially integrated, particularly with friends rather than family, are also more physically active, which could partially explain the link between social integration and morbidity and mortality. Future studies examining this association should distinguish between sources of integration and explore why and how contact with friends vs. family is differentially associated with health behaviors.

Friends, Family, and Alcohol Abuse: An Examination of General and Alcohol-Specific Social Support

PubMed Central

Groh, David R.; Jason, Leonard A.; Davis, Margaret I.; Olson, Bradley D.; Ferrari, Joseph R.

2010-01-01

Social support may be considered from several different dimensions. While general social support promotes well-being, specific social support is tied to particular functions, such as alcohol use. Not only may the form of social support vary, but also the source (ie, friends vs. family). This study investigated the impact of general and specific support for alcohol use from family versus friends on alcohol use among 897 U.S. residents of abstinent communal-living settings (Oxford Houses). Results indicated that general support from friends and length of stay in Oxford House significantly predicted less alcohol use. Implications for alcohol recovery are discussed. PMID:17364422

Toward better Alzheimer's research information sources for the public.

PubMed

Payne, Perry W

2013-03-01

The National Plan to Address Alzheimer's Disease calls for a new relationship between researchers and members of the public. This relationship is one that provides research information to patients and allows patients to provide ideas to researchers. One way to describe it is a "bidirectional translational relationship." Despite the numerous sources of online and offline information about Alzheimer's disease, there is no information source which currently provides this interaction. This article proposes the creation an Alzheimer's research information source dedicated to monitoring Alzheimer's research literature and providing user friendly, publicly accessible summaries of data written specifically for a lay audience. This information source should contain comprehensive, updated, user friendly, publicly available, reviews of Alzheimer's research and utilize existing online multimedia/social networking tools to provide information in useful formats that help patients, caregivers, and researchers learn rapidly from one another.

Synchronous identification of friendly targets

DOEpatents

Telle, John M.; Roger, Stutz A.

1998-01-01

A synchronous communication targeting system for use in battle. The present invention includes a transceiver having a stabilizing oscillator, a synchronous amplifier and an omnidirectional receiver, all in electrical communication with each other. A remotely located beacon is attached to a blackbody radiation source and has an amplitude modulator in electrical communication with a optical source. The beacon's amplitude modulator is set so that the optical source transmits radiation frequency at approximately the same or lower amplitude than that of the blackbody radiation source to which the beacon is attached. The receiver from the transceiver is adapted to receive frequencies approximately at or below blackbody radiation signals and sends such signals to the synchronous amplifier. The synchronous amplifier then rectifies and amplifies those signals which correspond to the predetermined frequency to therefore identify whether the blackbody radiation source is friendly or not.

The Effect of Social Support on Psychological Flourishing and Distress Among Migrants in Australia.

PubMed

du Plooy, Daniel R; Lyons, Anthony; Kashima, Emiko S

2018-05-04

We examine the access that culturally diverse migrant groups in Australia have to different sources of social support and how this access, or lack thereof, is associated with psychological flourishing and distress. A national online survey was conducted with 1334 migrants in Australia, examining 11 different sources of social support, including family, friends, relationship partner, acquaintances, work colleagues, health professionals, government agencies, community organisations, religious groups, social groups and online groups. We also examined migrants from different cultural groups. All sources of support were significantly associated with mental health, but somewhat differently for the dimensions of distress and flourishing. Flourishing was linked to higher support from all 11 sources, though not for all cultural groups. High psychological distress was linked to lower support only from family, friends, a partner, acquaintances, work colleagues and social groups, and only for some cultural groups. In particular, for distress, there was no link between migrants from Southern Asia and family support, as well as Confucian Asia groups and friend support. Understanding where migrants from different cultural origins draw their support from could help policymakers and support workers improve health and well-being in migrant populations, especially by focusing on sources of support that are linked to lower distress and greater flourishing, as indicated in this study.

Social inequalities in health information seeking among young adults in Montreal.

PubMed

Gagné, Thierry; Ghenadenik, Adrian E; Abel, Thomas; Frohlich, Katherine L

2018-06-01

Over their lifecourse, young adults develop different skills and preferences in relationship to the information sources they seek when having questions about health. Health information seeking behaviour (HISB) includes multiple, unequally accessed sources; yet most studies have focused on single sources and did not examine HISB's association with social inequalities. This study explores 'multiple-source' profiles and their association with socioeconomic characteristics. We analyzed cross-sectional data from the Interdisciplinary Study of Inequalities in Smoking involving 2093 young adults recruited in Montreal, Canada, in 2011-2012. We used latent class analysis to create profiles based on responses to questions regarding whether participants sought health professionals, family, friends or the Internet when having questions about health. Using multinomial logistic regression, we examined the associations between profiles and economic, social and cultural capital indicators: financial difficulties and transportation means, friend satisfaction and network size, and individual, mother's, and father's education. Five profiles were found: 'all sources' (42%), 'health professional centred' (29%), 'family only' (14%), 'Internet centred' (14%) and 'no sources' (2%). Participants with a larger social network and higher friend satisfaction were more likely to be in the 'all sources' group. Participants who experienced financial difficulties and completed college/university were less likely to be in the 'family only' group; those whose mother had completed college/university were more likely to be in this group. Our findings point to the importance of considering multiple sources to study HISB, especially when the capacity to seek multiple sources is unequally distributed. Scholars should acknowledge HISB's implications for health inequalities.

CEBS object model for systems biology data, SysBio-OM.

PubMed

Xirasagar, Sandhya; Gustafson, Scott; Merrick, B Alex; Tomer, Kenneth B; Stasiewicz, Stanley; Chan, Denny D; Yost, Kenneth J; Yates, John R; Sumner, Susan; Xiao, Nianqing; Waters, Michael D

2004-09-01

To promote a systems biology approach to understanding the biological effects of environmental stressors, the Chemical Effects in Biological Systems (CEBS) knowledge base is being developed to house data from multiple complex data streams in a systems friendly manner that will accommodate extensive querying from users. Unified data representation via a single object model will greatly aid in integrating data storage and management, and facilitate reuse of software to analyze and display data resulting from diverse differential expression or differential profile technologies. Data streams include, but are not limited to, gene expression analysis (transcriptomics), protein expression and protein-protein interaction analysis (proteomics) and changes in low molecular weight metabolite levels (metabolomics). To enable the integration of microarray gene expression, proteomics and metabolomics data in the CEBS system, we designed an object model, Systems Biology Object Model (SysBio-OM). The model is comprehensive and leverages other open source efforts, namely the MicroArray Gene Expression Object Model (MAGE-OM) and the Proteomics Experiment Data Repository (PEDRo) object model. SysBio-OM is designed by extending MAGE-OM to represent protein expression data elements (including those from PEDRo), protein-protein interaction and metabolomics data. SysBio-OM promotes the standardization of data representation and data quality by facilitating the capture of the minimum annotation required for an experiment. Such standardization refines the accuracy of data mining and interpretation. The open source SysBio-OM model, which can be implemented on varied computing platforms is presented here. A universal modeling language depiction of the entire SysBio-OM is available at http://cebs.niehs.nih.gov/SysBioOM/. The Rational Rose object model package is distributed under an open source license that permits unrestricted academic and commercial use and is available at http://cebs.niehs.nih.gov/cebsdownloads. The database and interface are being built to implement the model and will be available for public use at http://cebs.niehs.nih.gov.

An open-source solution for advanced imaging flow cytometry data analysis using machine learning.

PubMed

Hennig, Holger; Rees, Paul; Blasi, Thomas; Kamentsky, Lee; Hung, Jane; Dao, David; Carpenter, Anne E; Filby, Andrew

2017-01-01

Imaging flow cytometry (IFC) enables the high throughput collection of morphological and spatial information from hundreds of thousands of single cells. This high content, information rich image data can in theory resolve important biological differences among complex, often heterogeneous biological samples. However, data analysis is often performed in a highly manual and subjective manner using very limited image analysis techniques in combination with conventional flow cytometry gating strategies. This approach is not scalable to the hundreds of available image-based features per cell and thus makes use of only a fraction of the spatial and morphometric information. As a result, the quality, reproducibility and rigour of results are limited by the skill, experience and ingenuity of the data analyst. Here, we describe a pipeline using open-source software that leverages the rich information in digital imagery using machine learning algorithms. Compensated and corrected raw image files (.rif) data files from an imaging flow cytometer (the proprietary .cif file format) are imported into the open-source software CellProfiler, where an image processing pipeline identifies cells and subcellular compartments allowing hundreds of morphological features to be measured. This high-dimensional data can then be analysed using cutting-edge machine learning and clustering approaches using "user-friendly" platforms such as CellProfiler Analyst. Researchers can train an automated cell classifier to recognize different cell types, cell cycle phases, drug treatment/control conditions, etc., using supervised machine learning. This workflow should enable the scientific community to leverage the full analytical power of IFC-derived data sets. It will help to reveal otherwise unappreciated populations of cells based on features that may be hidden to the human eye that include subtle measured differences in label free detection channels such as bright-field and dark-field imagery. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

EarthCollab, building geoscience-centric implementations of the VIVO semantic software suite

NASA Astrophysics Data System (ADS)

Rowan, L. R.; Gross, M. B.; Mayernik, M. S.; Daniels, M. D.; Krafft, D. B.; Kahn, H. J.; Allison, J.; Snyder, C. B.; Johns, E. M.; Stott, D.

2017-12-01

EarthCollab, an EarthCube Building Block project, is extending an existing open-source semantic web application, VIVO, to enable the exchange of information about scientific researchers and resources across institutions. EarthCollab is a collaboration between UNAVCO, a geodetic facility and consortium that supports diverse research projects informed by geodesy, The Bering Sea Project, an interdisciplinary field program whose data archive is hosted by NCAR's Earth Observing Laboratory, and Cornell University. VIVO has been implemented by more than 100 universities and research institutions to highlight research and institutional achievements. This presentation will discuss benefits and drawbacks of working with and extending open source software. Some extensions include plotting georeferenced objects on a map, a mobile-friendly theme, integration of faceting via Elasticsearch, extending the VIVO ontology to capture geoscience-centric objects and relationships, and the ability to cross-link between VIVO instances. Most implementations of VIVO gather information about a single organization. The EarthCollab project created VIVO extensions to enable cross-linking of VIVO instances to reduce the amount of duplicate information about the same people and scientific resources and to enable dynamic linking of related information across VIVO installations. As the list of customizations grows, so does the effort required to maintain compatibility between the EarthCollab forks and the main VIVO code. For example, dozens of libraries and dependencies were updated prior to the VIVO v1.10 release, which introduced conflicts in the EarthCollab cross-linking code. The cross-linking code has been developed to enable sharing of data across different versions of VIVO, however, using a JSON output schema standardized across versions. We will outline lessons learned in working with VIVO and its open source dependencies, which include Jena, Solr, Freemarker, and jQuery and discuss future work by EarthCollab, which includes refining the cross-linking VIVO capabilities by continued integration of persistent and unique identifiers to enable automated lookup and matching across institutional VIVOs.

Alternative energy resources for MoDOT

DOT National Transportation Integrated Search

2011-02-01

This research investigates environmentally friendly alternative energy sources that could be used by MoDOT in various areas, and develops applicable and sustainable strategies to implement those energy sources.

Inattentive listening undermines self-verification in personal storytelling.

PubMed

Pasupathi, Monisha; Rich, Ben

2005-08-01

Two studies explore the narrative construction of self-perceptions in conversational storytelling among pairs of same-sex friends. Specifically, the studies examined how listener behavior can support or undermine attempts to self-verify in personal storytelling. In two studies (n=100 dyads), speakers told attentive, distracted, or disagreeable (Study 1 only) friends about a recent experience. Distracted, but not disagreeable, friends tended to undermine participants' attempts to verify their self-perception of being interested in an activity (Study 1) or their self-perception that an event was typical for them (Study 2). These results support the notion that friends can be an important source of influence on self-perceptions and, perhaps surprisingly, suggest that responsiveness from friends, rather than agreement per se, may be crucial for supporting self-verification processes.

NREL's OpenStudio Helps Design More Efficient Buildings (Fact Sheet)

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

Not Available

2014-07-01

The National Renewable Energy Laboratory (NREL) has created the OpenStudio software platform that makes it easier for architects and engineers to evaluate building energy efficiency measures throughout the design process. OpenStudio makes energy modeling more accessible and affordable, helping professionals to design structures with lower utility bills and less carbon emissions, resulting in a healthier environment. OpenStudio includes a user-friendly application suite that makes the U.S. Department of Energy's EnergyPlus and Radiance simulation engines easier to use for whole building energy and daylighting performance analysis. OpenStudio is freely available and runs on Windows, Mac, and Linux operating systems.

Use of Vendedores (Mobile Food Vendors), Pulgas (Flea Markets), and Vecinos o Amigos (Neighbors or Friends) as Alternative Sources of Food for Purchase among Mexican-origin Households in Texas Border Colonias

PubMed Central

Sharkey, Joseph R.; Dean, Wesley R.; Johnson, Cassandra M.

2012-01-01

There is a paucity of studies acknowledging the existence of alternative food sources, and factors associated with food purchasing from three common alternative sources: vendedores (mobile food vendors), pulgas (flea markets), and vecinos/amigos (neighbors/friends). This analysis aims to examine the use of alternative food sources by Mexican-origin women from Texas-border colonias and determine factors associated with their use. The design was cross-sectional. Promotora-researchers (promotoras de salud trained in research methods) recruited 610 Mexican-origin women from 44 colonias and conducted in-person surveys. Surveys included participant characteristics and measures of food environment use and household food security. Statistical analyses included separate logistic regressions, modeled for food purchase from mobile food vendors, pulgas, or neighbors/friends (NFs). Child food insecurity was associated with purchasing food from mobile food vendors, while household food security was associated with using pulgas or NFs. School nutrition program participants were more likely to live in households that depend on alternative food sources. Efforts to increase healthful food consumption such as fruits and vegetables should acknowledge all potential food sources (traditional, convenience, non-traditional, and alternative), especially those preferred by colonia residents. Current findings support the conceptual broadening of the retail food environment, and the importance of linking use with spatial access (proximity) to more accurately depict access to food sources. PMID:22709775

Heliospotlight: An Information Resource for Heliophysics

NASA Astrophysics Data System (ADS)

Young, C.; Wawro, M.; Schenk, L. C.

2013-12-01

The NASA Goddard Heliophysics Science Division (HSD) EPO and mission websites are rich with content covering the broad subject of heliophysics. This includes detailed information for many age groups, a large range of descriptive imagery and dynamic video and interactive material. The weakness of all this content is that it is scattered over so many websites as opposed to being organized and focused in one user friendly location. The website heliospotlight.org is being developed to address all these concerns, leveraging the vast content already developed while using state-of-the-art web technologies. This will provide a rich user experience simultaneously tailoring to the needs of the broad audience of students, educators, scientists, journalists and the general public. The website will use well supported, open source technologies enabling future flexibility and expansion. HSD EPO will support the development of this information resource.

Development of efficient and cost-effective distributed hydrological modeling tool MWEasyDHM based on open-source MapWindow GIS

NASA Astrophysics Data System (ADS)

Lei, Xiaohui; Wang, Yuhui; Liao, Weihong; Jiang, Yunzhong; Tian, Yu; Wang, Hao

2011-09-01

Many regions are still threatened with frequent floods and water resource shortage problems in China. Consequently, the task of reproducing and predicting the hydrological process in watersheds is hard and unavoidable for reducing the risks of damage and loss. Thus, it is necessary to develop an efficient and cost-effective hydrological tool in China as many areas should be modeled. Currently, developed hydrological tools such as Mike SHE and ArcSWAT (soil and water assessment tool based on ArcGIS) show significant power in improving the precision of hydrological modeling in China by considering spatial variability both in land cover and in soil type. However, adopting developed commercial tools in such a large developing country comes at a high cost. Commercial modeling tools usually contain large numbers of formulas, complicated data formats, and many preprocessing or postprocessing steps that may make it difficult for the user to carry out simulation, thus lowering the efficiency of the modeling process. Besides, commercial hydrological models usually cannot be modified or improved to be suitable for some special hydrological conditions in China. Some other hydrological models are open source, but integrated into commercial GIS systems. Therefore, by integrating hydrological simulation code EasyDHM, a hydrological simulation tool named MWEasyDHM was developed based on open-source MapWindow GIS, the purpose of which is to establish the first open-source GIS-based distributed hydrological model tool in China by integrating modules of preprocessing, model computation, parameter estimation, result display, and analysis. MWEasyDHM provides users with a friendly manipulating MapWindow GIS interface, selectable multifunctional hydrological processing modules, and, more importantly, an efficient and cost-effective hydrological simulation tool. The general construction of MWEasyDHM consists of four major parts: (1) a general GIS module for hydrological analysis, (2) a preprocessing module for modeling inputs, (3) a model calibration module, and (4) a postprocessing module. The general GIS module for hydrological analysis is developed on the basis of totally open-source GIS software, MapWindow, which contains basic GIS functions. The preprocessing module is made up of three submodules including a DEM-based submodule for hydrological analysis, a submodule for default parameter calculation, and a submodule for the spatial interpolation of meteorological data. The calibration module contains parallel computation, real-time computation, and visualization. The postprocessing module includes model calibration and model results spatial visualization using tabular form and spatial grids. MWEasyDHM makes it possible for efficient modeling and calibration of EasyDHM, and promises further development of cost-effective applications in various watersheds.

Post Graduations in Technologies and Computing Applied to Education: From F2F Classes to Multimedia Online Open Courses

ERIC Educational Resources Information Center

Marques, Bertil P.; Carvalho, Piedade; Escudeiro, Paula; Barata, Ana; Silva, Ana; Queiros, Sandra

2017-01-01

Promoted by the significant increase of large scale internet access, many audiences have turned to the web and to its resources for learning and inspiration, with diverse sets of skills and intents. In this context, Multimedia Online Open Courses (MOOC) consist in learning models supported on user-friendly web tools that allow anyone with minimum…

“Now I Don’t Have to Guess”: Using Pamphlets to Encourage Residents and Families/Friends to Engage in Advance Care Planning in Long-Term Care

PubMed Central

Sussman, Tamara; Kaasalainen, Sharon; Bui, Matthew; Akhtar-Danesh, Noori; Mintzberg, Susan; Strachan, Patricia

2017-01-01

Objective: This article explores whether access to illness trajectory pamphlets for five conditions with high prevalence in long-term care (LTC) can encourage residents and families/friends to openly engage in advance care planning (ACP) discussions with one another and with health providers. Method: In all, 57 residents and families/friends in LTC completed surveys and 56 participated in seven focus groups that explored whether the pamphlets supported ACP engagement. Results: Survey results suggested that access to pamphlets encouraged residents and families/friends to reflect on future care (48/57, 84%), clarified what questions to ask (40/57, 70%), and increased comfort in talking about end of life (EOL) care (36/57, 63%). Discussions between relatives and friends/families (32/57, 56%) or with health providers (21/57, 37%) were less common. Focus group deliberations illuminated that while reading illness-specific information was validating, a tendency to protect one another from an emotional topic, prevented residents and families/friends from conversing with one another about EOL issues. Discussion: Having access to pamphlets with information about EOL care provides important and welcome opportunities for reflection for both residents in LTC and their families/friends. Moving residents and families/friends from reflecting on issues to discussing them together could require staff support through planned care conferences or staff initiated conversations at the bedside. PMID:29308424

Integrated Analysis Platform: An Open-Source Information System for High-Throughput Plant Phenotyping1[C][W][OPEN

PubMed Central

Klukas, Christian; Chen, Dijun; Pape, Jean-Michel

2014-01-01

High-throughput phenotyping is emerging as an important technology to dissect phenotypic components in plants. Efficient image processing and feature extraction are prerequisites to quantify plant growth and performance based on phenotypic traits. Issues include data management, image analysis, and result visualization of large-scale phenotypic data sets. Here, we present Integrated Analysis Platform (IAP), an open-source framework for high-throughput plant phenotyping. IAP provides user-friendly interfaces, and its core functions are highly adaptable. Our system supports image data transfer from different acquisition environments and large-scale image analysis for different plant species based on real-time imaging data obtained from different spectra. Due to the huge amount of data to manage, we utilized a common data structure for efficient storage and organization of data for both input data and result data. We implemented a block-based method for automated image processing to extract a representative list of plant phenotypic traits. We also provide tools for build-in data plotting and result export. For validation of IAP, we performed an example experiment that contains 33 maize (Zea mays ‘Fernandez’) plants, which were grown for 9 weeks in an automated greenhouse with nondestructive imaging. Subsequently, the image data were subjected to automated analysis with the maize pipeline implemented in our system. We found that the computed digital volume and number of leaves correlate with our manually measured data in high accuracy up to 0.98 and 0.95, respectively. In summary, IAP provides a multiple set of functionalities for import/export, management, and automated analysis of high-throughput plant phenotyping data, and its analysis results are highly reliable. PMID:24760818

Three-dimensional image reconstruction with free open-source OsiriX software in video-assisted thoracoscopic lobectomy and segmentectomy.

PubMed

Yao, Fei; Wang, Jian; Yao, Ju; Hang, Fangrong; Lei, Xu; Cao, Yongke

2017-03-01

The aim of this retrospective study was to evaluate the practice and the feasibility of Osirix, a free and open-source medical imaging software, in performing accurate video-assisted thoracoscopic lobectomy and segmentectomy. From July 2014 to April 2016, 63 patients received anatomical video-assisted thoracoscopic surgery (VATS), either lobectomy or segmentectomy, in our department. Three-dimensional (3D) reconstruction images of 61 (96.8%) patients were preoperatively obtained with contrast-enhanced computed tomography (CT). Preoperative resection simulations were accomplished with patient-individual reconstructed 3D images. For lobectomy, pulmonary lobar veins, arteries and bronchi were identified meticulously by carefully reviewing the 3D images on the display. For segmentectomy, the intrasegmental veins in the affected segment for division and the intersegmental veins to be preserved were identified on the 3D images. Patient preoperative characteristics, surgical outcomes and postoperative data were reviewed from a prospective database. The study cohort of 63 patients included 33 (52.4%) men and 30 (47.6%) women, of whom 46 (73.0%) underwent VATS lobectomy and 17 (27.0%) underwent VATS segmentectomy. There was 1 conversion from VATS lobectomy to open thoracotomy because of fibrocalcified lymph nodes. A VATS lobectomy was performed in 1 case after completing the segmentectomy because invasive adenocarcinoma was detected by intraoperative frozen-section analysis. There were no 30-day or 90-day operative mortalities CONCLUSIONS: The free, simple, and user-friendly software program Osirix can provide a 3D anatomic structure of pulmonary vessels and a clear vision into the space between the lesion and adjacent tissues, which allows surgeons to make preoperative simulations and improve the accuracy and safety of actual surgery. Copyright © 2017 IJS Publishing Group Ltd. Published by Elsevier Ltd. All rights reserved.

Alternative energy resources for the Missouri Department of Transportation.

DOT National Transportation Integrated Search

2011-01-01

This research investigates environmentally friendly alternative energy sources that could be used by MoDOT in various areas, and develops applicable and sustainable strategies to implement those energy sources.

Sequential Revision of Belief, Trust Type, and the Order Effect.

PubMed

Entin, Elliot E; Serfaty, Daniel

2017-05-01

Objective To investigate how people's sequential adjustments to their position are impacted by the source of the information. Background There is an extensive body of research on how the order in which new information is received affects people's final views and decisions as well as research on how they adjust their views in light of new information. Method Seventy college-aged students, 60% of whom were women, completed one of eight different randomly distributed booklets prepared to create the eight different between-subjects treatment conditions created by crossing the two levels of information source with the four level of order conditions. Based on the information provided, participants estimated the probability of an attack, the dependent measure. Results Confirming information from an expert intelligence officer significantly increased the attack probability from the initial position more than confirming information from a longtime friend. Conversely, disconfirming information from a longtime friend decreased the attack probability significantly more than the same information from an intelligence officer. Conclusion It was confirmed that confirming and disconfirming evidence were differentially affected depending on information source, either an expert or a close friend. The difference appears to be due to the existence of two kinds of trust: cognitive-based imbued to an expert and affective-based imbued to a close friend. Application Purveyors of information need to understand that it is not only the content of a message that counts but that other forces are at work such as the order in which information is received and characteristics of the information source.

NucliTrack: an integrated nuclei tracking application.

PubMed

Cooper, Sam; Barr, Alexis R; Glen, Robert; Bakal, Chris

2017-10-15

Live imaging studies give unparalleled insight into dynamic single cell behaviours and fate decisions. However, the challenge of reliably tracking single cells over long periods of time limits both the throughput and ease with which such studies can be performed. Here, we present NucliTrack, a cross platform solution for automatically segmenting, tracking and extracting features from fluorescently labelled nuclei. NucliTrack performs similarly to other state-of-the-art cell tracking algorithms, but NucliTrack's interactive, graphical interface makes it significantly more user friendly. NucliTrack is available as a free, cross platform application and open source Python package. Installation details and documentation are at: http://nuclitrack.readthedocs.io/en/latest/ A video guide can be viewed online: https://www.youtube.com/watch?v=J6e0D9F-qSU Source code is available through Github: https://github.com/samocooper/nuclitrack. A Matlab toolbox is also available at: https://uk.mathworks.com/matlabcentral/fileexchange/61479-samocooper-nuclitrack-matlab. sam@socooper.com. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Genomes to natural products PRediction Informatics for Secondary Metabolomes (PRISM)

PubMed Central

Skinnider, Michael A.; Dejong, Chris A.; Rees, Philip N.; Johnston, Chad W.; Li, Haoxin; Webster, Andrew L. H.; Wyatt, Morgan A.; Magarvey, Nathan A.

2015-01-01

Microbial natural products are an invaluable source of evolved bioactive small molecules and pharmaceutical agents. Next-generation and metagenomic sequencing indicates untapped genomic potential, yet high rediscovery rates of known metabolites increasingly frustrate conventional natural product screening programs. New methods to connect biosynthetic gene clusters to novel chemical scaffolds are therefore critical to enable the targeted discovery of genetically encoded natural products. Here, we present PRISM, a computational resource for the identification of biosynthetic gene clusters, prediction of genetically encoded nonribosomal peptides and type I and II polyketides, and bio- and cheminformatic dereplication of known natural products. PRISM implements novel algorithms which render it uniquely capable of predicting type II polyketides, deoxygenated sugars, and starter units, making it a comprehensive genome-guided chemical structure prediction engine. A library of 57 tailoring reactions is leveraged for combinatorial scaffold library generation when multiple potential substrates are consistent with biosynthetic logic. We compare the accuracy of PRISM to existing genomic analysis platforms. PRISM is an open-source, user-friendly web application available at http://magarveylab.ca/prism/. PMID:26442528

NucliTrack: an integrated nuclei tracking application

PubMed Central

Cooper, Sam; Barr, Alexis R.; Glen, Robert; Bakal, Chris

2017-01-01

Abstract Summary Live imaging studies give unparalleled insight into dynamic single cell behaviours and fate decisions. However, the challenge of reliably tracking single cells over long periods of time limits both the throughput and ease with which such studies can be performed. Here, we present NucliTrack, a cross platform solution for automatically segmenting, tracking and extracting features from fluorescently labelled nuclei. NucliTrack performs similarly to other state-of-the-art cell tracking algorithms, but NucliTrack’s interactive, graphical interface makes it significantly more user friendly. Availability and implementation NucliTrack is available as a free, cross platform application and open source Python package. Installation details and documentation are at: http://nuclitrack.readthedocs.io/en/latest/ A video guide can be viewed online: https://www.youtube.com/watch?v=J6e0D9F-qSU Source code is available through Github: https://github.com/samocooper/nuclitrack. A Matlab toolbox is also available at: https://uk.mathworks.com/matlabcentral/fileexchange/61479-samocooper-nuclitrack-matlab. Contact sam@socooper.com Supplementary information Supplementary data are available at Bioinformatics online. PMID:28637183

netCDF Operators for Rapid Analysis of Measured and Modeled Swath-like Data

NASA Astrophysics Data System (ADS)

Zender, C. S.

2015-12-01

Swath-like data (hereafter SLD) are defined by non-rectangular and/or time-varying spatial grids in which one or more coordinates are multi-dimensional. It is often challenging and time-consuming to work with SLD, including all Level 2 satellite-retrieved data, non-rectangular subsets of Level 3 data, and model data on curvilinear grids. Researchers and data centers want user-friendly, fast, and powerful methods to specify, extract, serve, manipulate, and thus analyze, SLD. To meet these needs, large research-oriented agencies and modeling center such as NASA, DOE, and NOAA increasingly employ the netCDF Operators (NCO), an open-source scientific data analysis software package applicable to netCDF and HDF data. NCO includes extensive, fast, parallelized regridding features to facilitate analysis and intercomparison of SLD and model data. Remote sensing, weather and climate modeling and analysis communities face similar problems in handling SLD including how to easily: 1. Specify and mask irregular regions such as ocean basins and political boundaries in SLD (and rectangular) grids. 2. Bin, interpolate, average, or re-map SLD to regular grids. 3. Derive secondary data from given quality levels of SLD. These common tasks require a data extraction and analysis toolkit that is SLD-friendly and, like NCO, familiar in all these communities. With NCO users can 1. Quickly project SLD onto the most useful regular grids for intercomparison. 2. Access sophisticated statistical and regridding functions that are robust to missing data and allow easy specification of quality control metrics. These capabilities improve interoperability, software-reuse, and, because they apply to SLD, minimize transmission, storage, and handling of unwanted data. While SLD analysis still poses many challenges compared to regularly gridded, rectangular data, the custom analyses scripts SLD once required are now shorter, more powerful, and user-friendly.

The Integration of CloudStack and OCCI/OpenNebula with DIRAC

NASA Astrophysics Data System (ADS)

Méndez Muñoz, Víctor; Fernández Albor, Víctor; Graciani Diaz, Ricardo; Casajús Ramo, Adriàn; Fernández Pena, Tomás; Merino Arévalo, Gonzalo; José Saborido Silva, Juan

2012-12-01

The increasing availability of Cloud resources is arising as a realistic alternative to the Grid as a paradigm for enabling scientific communities to access large distributed computing resources. The DIRAC framework for distributed computing is an easy way to efficiently access to resources from both systems. This paper explains the integration of DIRAC with two open-source Cloud Managers: OpenNebula (taking advantage of the OCCI standard) and CloudStack. These are computing tools to manage the complexity and heterogeneity of distributed data center infrastructures, allowing to create virtual clusters on demand, including public, private and hybrid clouds. This approach has required to develop an extension to the previous DIRAC Virtual Machine engine, which was developed for Amazon EC2, allowing the connection with these new cloud managers. In the OpenNebula case, the development has been based on the CernVM Virtual Software Appliance with appropriate contextualization, while in the case of CloudStack, the infrastructure has been kept more general, which permits other Virtual Machine sources and operating systems being used. In both cases, CernVM File System has been used to facilitate software distribution to the computing nodes. With the resulting infrastructure, the cloud resources are transparent to the users through a friendly interface, like the DIRAC Web Portal. The main purpose of this integration is to get a system that can manage cloud and grid resources at the same time. This particular feature pushes DIRAC to a new conceptual denomination as interware, integrating different middleware. Users from different communities do not need to care about the installation of the standard software that is available at the nodes, nor the operating system of the host machine which is transparent to the user. This paper presents an analysis of the overhead of the virtual layer, doing some tests to compare the proposed approach with the existing Grid solution. License Notice: Published under licence in Journal of Physics: Conference Series by IOP Publishing Ltd.

Perceived Social Support from Friends and Family and Psychosocial Functioning in Bisexual Young Adult College Students

ERIC Educational Resources Information Center

Sheets, Raymond L., Jr.; Mohr, Jonathan J.

2009-01-01

In this study, the authors investigated the degree to which perceived social support was associated with depression, life satisfaction, and internalized binegativity in a sample of 210 bisexual young adult college students. Two types of social support (general and sexuality specific) and 2 sources of social support (family and friends) were…

Information Expensiveness Perceived by Vietnamese Patients with Respect to Healthcare Provider's Choice.

PubMed

Quan-Hoang, Vuong

2016-10-01

Patients have to acquire information to support their decision on choosing a suitable healthcare provider. But in developing countries like Vietnam, accessibility issues remain an obstacle, thus adversely affect both quality and costliness of healthcare information. Vietnamese use both sources from health professionals and friends/relatives, especially when quality of the Internet-based cheaper sources appear to be still questionable. The search of information from both professionals and friends/relatives incurs some cost, which can be viewed as low or high depending low or high accessibility to the sources. These views potentially affect their choices. To investigate the effects that medical/health services information on perceived expensiveness of patients' labor costs. Two related objectives are a) establishing empirical relations between accessibility to sources and expensiveness; and, b) probabilistic trends of probabilities for perceived expensiveness. There is evidence for established relations among the variables "Convexp" and "Convrel" (all p's < 0.01), indicating that both information sources (experts and friends/relatives) have influence on patients perception of information expensiveness. The use of experts source tends to increase the probability of perceived expensiveness. a) Probabilistic trends show Vietnamese patients have propensity to value healthcare information highly and do not see it as "expensive"; b) The majority of Vietnamese households still take non-professional advices at their own risks; c) There is more for the public healthcare information system to do to reduce costliness and risk of information. The Internet-based health service users communities cannot replace this system.

78 FR 65265 - Materials Technical Advisory Committee; Notice of Open Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2013-10-31

... BIS senior management and export control reform update. 3. Presentation from DuPont on the challenges... friendly. 4. Report of Composite Working Group. 5. Report of Biological and Pump/Valves Working Group. 6...

Influence of the Source of Social Support and Size of Social Network on All-Cause Mortality.

PubMed

Becofsky, Katie M; Shook, Robin P; Sui, Xuemei; Wilcox, Sara; Lavie, Carl J; Blair, Steven N

2015-07-01

To examine associations between relative, friend, and partner support, as well as size and source of weekly social network, and mortality risk in the Aerobics Center Longitudinal Study. In a mail-back survey completed between January 1, 1990, and December 31, 1990, adult participants in the Aerobics Center Longitudinal Study (N=12,709) answered questions on whether they received social support from relatives, friends, and spouse/partner (yes or no for each) and on the number of friends and relatives they had contact with at least once per week. Participants were followed until December 31, 2003, or until the date of death. Cox proportional hazards regression analyses evaluated the strength of the associations, controlling for covariates. Participants (3220 [25%] women) averaged 53.0 ± 11.3 years of age at baseline. During a median follow-up of 13.5 years, 1139 deaths occurred. Receiving social support from relatives reduced mortality risk by 19% (hazard ratio [HR], 0.81; 95% CI, 0.68-0.95). Receiving spousal/partner support also reduced mortality risk by 19% (HR, 0.81; 95% CI, 0.66-0.99). Receiving social support from friends was not associated with mortality risk (HR, 0.90; 95% CI, 0.75-1.09); however, participants reporting social contact with 6 or 7 friends on a weekly basis had a 24% lower mortality risk than did those in contact with 0 or 1 friend (HR, 0.76; 95% CI, 0.58-0.98). Contact with 2 to 5 or 8 or more friends was not associated with mortality risk, nor was the number of weekly contacts with relatives. Receiving social support from one's spouse/partner and relatives and maintaining weekly social interaction with 6 to 7 friends reduced mortality risk. Such data may inform interventions to improve long-term survival. Copyright © 2015 Mayo Foundation for Medical Education and Research. Published by Elsevier Inc. All rights reserved.

KENNEDY SPACE CENTER, FLA. - Center Director Jim Kennedy speaks to attendees at a memorial service honoring the crew of Columbia. He stands in front of the Space Memorial Mirror at the KSC Visitor Complex. Feb. 1 is the one-year anniversary of the loss of the crew and orbiter Columbia in a tragic accident as the ship returned to Earth following mission STS-107. Attended by many friends, co-workers and families, the memorial service was also open to the public.

NASA Image and Video Library

2004-02-01

KENNEDY SPACE CENTER, FLA. - Center Director Jim Kennedy speaks to attendees at a memorial service honoring the crew of Columbia. He stands in front of the Space Memorial Mirror at the KSC Visitor Complex. Feb. 1 is the one-year anniversary of the loss of the crew and orbiter Columbia in a tragic accident as the ship returned to Earth following mission STS-107. Attended by many friends, co-workers and families, the memorial service was also open to the public.

Hybrid Design of Electric Power Generation Systems Including Renewable Sources of Energy

ERIC Educational Resources Information Center

Wang, Lingfeng; Singh, Chanan

2008-01-01

With the stricter environmental regulations and diminishing fossil-fuel reserves, there is now higher emphasis on exploiting various renewable sources of energy. These alternative sources of energy are usually environmentally friendly and emit no pollutants. However, the capital investments for those renewable sources of energy are normally high,…

RICH: OPEN-SOURCE HYDRODYNAMIC SIMULATION ON A MOVING VORONOI MESH

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

Yalinewich, Almog; Steinberg, Elad; Sari, Re’em

2015-02-01

We present here RICH, a state-of-the-art two-dimensional hydrodynamic code based on Godunov’s method, on an unstructured moving mesh (the acronym stands for Racah Institute Computational Hydrodynamics). This code is largely based on the code AREPO. It differs from AREPO in the interpolation and time-advancement schemeS as well as a novel parallelization scheme based on Voronoi tessellation. Using our code, we study the pros and cons of a moving mesh (in comparison to a static mesh). We also compare its accuracy to other codes. Specifically, we show that our implementation of external sources and time-advancement scheme is more accurate and robustmore » than is AREPO when the mesh is allowed to move. We performed a parameter study of the cell rounding mechanism (Lloyd iterations) and its effects. We find that in most cases a moving mesh gives better results than a static mesh, but it is not universally true. In the case where matter moves in one way and a sound wave is traveling in the other way (such that relative to the grid the wave is not moving) a static mesh gives better results than a moving mesh. We perform an analytic analysis for finite difference schemes that reveals that a Lagrangian simulation is better than a Eulerian simulation in the case of a highly supersonic flow. Moreover, we show that Voronoi-based moving mesh schemes suffer from an error, which is resolution independent, due to inconsistencies between the flux calculation and the change in the area of a cell. Our code is publicly available as open source and designed in an object-oriented, user-friendly way that facilitates incorporation of new algorithms and physical processes.« less

OLS Client and OLS Dialog: Open Source Tools to Annotate Public Omics Datasets.

PubMed

Perez-Riverol, Yasset; Ternent, Tobias; Koch, Maximilian; Barsnes, Harald; Vrousgou, Olga; Jupp, Simon; Vizcaíno, Juan Antonio

2017-10-01

The availability of user-friendly software to annotate biological datasets and experimental details is becoming essential in data management practices, both in local storage systems and in public databases. The Ontology Lookup Service (OLS, http://www.ebi.ac.uk/ols) is a popular centralized service to query, browse and navigate biomedical ontologies and controlled vocabularies. Recently, the OLS framework has been completely redeveloped (version 3.0), including enhancements in the data model, like the added support for Web Ontology Language based ontologies, among many other improvements. However, the new OLS is not backwards compatible and new software tools are needed to enable access to this widely used framework now that the previous version is no longer available. We here present the OLS Client as a free, open-source Java library to retrieve information from the new version of the OLS. It enables rapid tool creation by providing a robust, pluggable programming interface and common data model to programmatically access the OLS. The library has already been integrated and is routinely used by several bioinformatics resources and related data annotation tools. Secondly, we also introduce an updated version of the OLS Dialog (version 2.0), a Java graphical user interface that can be easily plugged into Java desktop applications to access the OLS. The software and related documentation are freely available at https://github.com/PRIDE-Utilities/ols-client and https://github.com/PRIDE-Toolsuite/ols-dialog. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

MATtrack: A MATLAB-Based Quantitative Image Analysis Platform for Investigating Real-Time Photo-Converted Fluorescent Signals in Live Cells.

PubMed

Courtney, Jane; Woods, Elena; Scholz, Dimitri; Hall, William W; Gautier, Virginie W

2015-01-01

We introduce here MATtrack, an open source MATLAB-based computational platform developed to process multi-Tiff files produced by a photo-conversion time lapse protocol for live cell fluorescent microscopy. MATtrack automatically performs a series of steps required for image processing, including extraction and import of numerical values from Multi-Tiff files, red/green image classification using gating parameters, noise filtering, background extraction, contrast stretching and temporal smoothing. MATtrack also integrates a series of algorithms for quantitative image analysis enabling the construction of mean and standard deviation images, clustering and classification of subcellular regions and injection point approximation. In addition, MATtrack features a simple user interface, which enables monitoring of Fluorescent Signal Intensity in multiple Regions of Interest, over time. The latter encapsulates a region growing method to automatically delineate the contours of Regions of Interest selected by the user, and performs background and regional Average Fluorescence Tracking, and automatic plotting. Finally, MATtrack computes convenient visualization and exploration tools including a migration map, which provides an overview of the protein intracellular trajectories and accumulation areas. In conclusion, MATtrack is an open source MATLAB-based software package tailored to facilitate the analysis and visualization of large data files derived from real-time live cell fluorescent microscopy using photoconvertible proteins. It is flexible, user friendly, compatible with Windows, Mac, and Linux, and a wide range of data acquisition software. MATtrack is freely available for download at eleceng.dit.ie/courtney/MATtrack.zip.

MATtrack: A MATLAB-Based Quantitative Image Analysis Platform for Investigating Real-Time Photo-Converted Fluorescent Signals in Live Cells

PubMed Central

Courtney, Jane; Woods, Elena; Scholz, Dimitri; Hall, William W.; Gautier, Virginie W.

2015-01-01

We introduce here MATtrack, an open source MATLAB-based computational platform developed to process multi-Tiff files produced by a photo-conversion time lapse protocol for live cell fluorescent microscopy. MATtrack automatically performs a series of steps required for image processing, including extraction and import of numerical values from Multi-Tiff files, red/green image classification using gating parameters, noise filtering, background extraction, contrast stretching and temporal smoothing. MATtrack also integrates a series of algorithms for quantitative image analysis enabling the construction of mean and standard deviation images, clustering and classification of subcellular regions and injection point approximation. In addition, MATtrack features a simple user interface, which enables monitoring of Fluorescent Signal Intensity in multiple Regions of Interest, over time. The latter encapsulates a region growing method to automatically delineate the contours of Regions of Interest selected by the user, and performs background and regional Average Fluorescence Tracking, and automatic plotting. Finally, MATtrack computes convenient visualization and exploration tools including a migration map, which provides an overview of the protein intracellular trajectories and accumulation areas. In conclusion, MATtrack is an open source MATLAB-based software package tailored to facilitate the analysis and visualization of large data files derived from real-time live cell fluorescent microscopy using photoconvertible proteins. It is flexible, user friendly, compatible with Windows, Mac, and Linux, and a wide range of data acquisition software. MATtrack is freely available for download at eleceng.dit.ie/courtney/MATtrack.zip. PMID:26485569

An Update on Electronic Information Sources.

ERIC Educational Resources Information Center

Ackerman, Katherine

1987-01-01

This review of new developments and products in online services discusses trends in travel related services; full text databases; statistical source databases; an emphasis on regional and international business news; and user friendly systems. (Author/CLB)

Malaysians' Preferences and Concerns Regarding Seeking Information About Illegal Drugs.

PubMed

Chie, Qiu Ting; Tam, Cai Lian; Bonn, Gregory

2018-01-01

A brief survey asked Malaysians if they had searched for information about illegal drugs and their thoughts about the information available. Two hundred and eighty participants from four states: Selangor, Penang, Malacca, and Johor filled out a paper-and-pencil survey including both multiple choice and open-ended written questions. Quantitative analyses of closed-ended, and thematic analyses of open-ended data indicated the following: Half of participants had, at some point, actively searched for information about drug use; 28% reported searching at least once per month. Participants generally (79%) preferred to obtain information online, but 62% also reported sharing and obtaining information about drugs in face-to-face interactions with friends and others. Concerns regarding the reliability of information, such as the presence of conflicting or contradictory messages from multiple sources, was a common theme in open ended responses. Of those who searched for information, about 70% reported desiring more detailed information about different drugs, in particular about their various side effects and risks. It is suggested that drug information campaigns, particularly those aimed at university students, might better focus on providing accurate, detailed information about the risks and other issues involved in various types of drug use, rather than one-size-fits-all messages. Given the varied and confusing nature of information already available, overly simplistic anti-drug messages may be ineffective, if not counterproductive.

Green electricity: It`s in the eye of the beholder

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

Rodgers, L.M.

Some people want to know what {open_quotes}green power{close_quotes} means - and, by extension, {open_quotes}environmentally friendly{close_quotes}. Does that mean low emissions, including nuclear energy? Is renewable energy automatically green? Should the simple fact of compliance with all standards imposed by the Environmental Protection Agency afford the right to advertise power generation as green? Consumers, agencies and state and federal officials want truth in advertising. Proponents of alternative generation claim consumers are willing to pay more for cleaner, greener energy. Residential customers of Detroit Edison, for instance, pay more than $6.50 additional per month to support solar energy. In Colorado, the Governor`smore » Office of Energy Conservation is using special funds to help offset the additional cost it takes to power the governors` home with wind. Only clear industry guidelines can ensure that everyone is actually getting what they`re paying for. Green power certification is proceeding on several different fronts. Commissions and legislatures are mandating resource disclosure of generation sources. Legislation at both the state and federal level are investigating the use of renewable portfolio standards. The Federal Trade Commission is considering establishing voluntary guidelines for electricity advertising like those already established for other retail products in the FTCs 1992 {open_quotes}Guides for the Use of Environmental Marketing Claims{close_quotes} (16 CFR 260).« less

Malaysians' Preferences and Concerns Regarding Seeking Information About Illegal Drugs

PubMed Central

Chie, Qiu Ting; Tam, Cai Lian; Bonn, Gregory

2018-01-01

A brief survey asked Malaysians if they had searched for information about illegal drugs and their thoughts about the information available. Two hundred and eighty participants from four states: Selangor, Penang, Malacca, and Johor filled out a paper-and-pencil survey including both multiple choice and open-ended written questions. Quantitative analyses of closed-ended, and thematic analyses of open-ended data indicated the following: Half of participants had, at some point, actively searched for information about drug use; 28% reported searching at least once per month. Participants generally (79%) preferred to obtain information online, but 62% also reported sharing and obtaining information about drugs in face-to-face interactions with friends and others. Concerns regarding the reliability of information, such as the presence of conflicting or contradictory messages from multiple sources, was a common theme in open ended responses. Of those who searched for information, about 70% reported desiring more detailed information about different drugs, in particular about their various side effects and risks. It is suggested that drug information campaigns, particularly those aimed at university students, might better focus on providing accurate, detailed information about the risks and other issues involved in various types of drug use, rather than one-size-fits-all messages. Given the varied and confusing nature of information already available, overly simplistic anti-drug messages may be ineffective, if not counterproductive. PMID:29868548

MilxXplore: a web-based system to explore large imaging datasets.

PubMed

Bourgeat, P; Dore, V; Villemagne, V L; Rowe, C C; Salvado, O; Fripp, J

2013-01-01

As large-scale medical imaging studies are becoming more common, there is an increasing reliance on automated software to extract quantitative information from these images. As the size of the cohorts keeps increasing with large studies, there is a also a need for tools that allow results from automated image processing and analysis to be presented in a way that enables fast and efficient quality checking, tagging and reporting on cases in which automatic processing failed or was problematic. MilxXplore is an open source visualization platform, which provides an interface to navigate and explore imaging data in a web browser, giving the end user the opportunity to perform quality control and reporting in a user friendly, collaborative and efficient way. Compared to existing software solutions that often provide an overview of the results at the subject's level, MilxXplore pools the results of individual subjects and time points together, allowing easy and efficient navigation and browsing through the different acquisitions of a subject over time, and comparing the results against the rest of the population. MilxXplore is fast, flexible and allows remote quality checks of processed imaging data, facilitating data sharing and collaboration across multiple locations, and can be easily integrated into a cloud computing pipeline. With the growing trend of open data and open science, such a tool will become increasingly important to share and publish results of imaging analysis.

You Can't Get Much from Watching the Radio.

ERIC Educational Resources Information Center

Litten, Larry H.

1988-01-01

Examined sources that students preferred for obtaining information on colleges by interviewing students who had taken the Preliminary Scholastic Aptitude Test in 1983. Enrolled friends were most preferred source of basic information, followed by personal visits, published guides, and admission representatives. Also examined sources on…

Fiberfox: facilitating the creation of realistic white matter software phantoms.

PubMed

Neher, Peter F; Laun, Frederik B; Stieltjes, Bram; Maier-Hein, Klaus H

2014-11-01

Phantom-based validation of diffusion-weighted image processing techniques is an important key to innovation in the field and is widely used. Openly available and user friendly tools for the flexible generation of tailor-made datasets for the specific tasks at hand can greatly facilitate the work of researchers around the world. We present an open-source framework, Fiberfox, that enables (1) the intuitive definition of arbitrary artificial white matter fiber tracts, (2) signal generation from those fibers by means of the most recent multi-compartment modeling techniques, and (3) simulation of the actual MR acquisition that allows for the introduction of realistic MRI-related effects into the final image. We show that real acquisitions can be closely approximated by simulating the acquisition of the well-known FiberCup phantom. We further demonstrate the advantages of our framework by evaluating the effects of imaging artifacts and acquisition settings on the outcome of 12 tractography algorithms. Our findings suggest that experiments on a realistic software phantom might change the conclusions drawn from earlier hardware phantom experiments. Fiberfox may find application in validating and further developing methods such as tractography, super-resolution, diffusion modeling or artifact correction. Copyright © 2013 Wiley Periodicals, Inc.

PRGdb: a bioinformatics platform for plant resistance gene analysis

PubMed Central

Sanseverino, Walter; Roma, Guglielmo; De Simone, Marco; Faino, Luigi; Melito, Sara; Stupka, Elia; Frusciante, Luigi; Ercolano, Maria Raffaella

2010-01-01

PRGdb is a web accessible open-source (http://www.prgdb.org) database that represents the first bioinformatic resource providing a comprehensive overview of resistance genes (R-genes) in plants. PRGdb holds more than 16 000 known and putative R-genes belonging to 192 plant species challenged by 115 different pathogens and linked with useful biological information. The complete database includes a set of 73 manually curated reference R-genes, 6308 putative R-genes collected from NCBI and 10463 computationally predicted putative R-genes. Thanks to a user-friendly interface, data can be examined using different query tools. A home-made prediction pipeline called Disease Resistance Analysis and Gene Orthology (DRAGO), based on reference R-gene sequence data, was developed to search for plant resistance genes in public datasets such as Unigene and Genbank. New putative R-gene classes containing unknown domain combinations were discovered and characterized. The development of the PRG platform represents an important starting point to conduct various experimental tasks. The inferred cross-link between genomic and phenotypic information allows access to a large body of information to find answers to several biological questions. The database structure also permits easy integration with other data types and opens up prospects for future implementations. PMID:19906694

phenoVein—A Tool for Leaf Vein Segmentation and Analysis1[OPEN

PubMed Central

Pflugfelder, Daniel; Huber, Gregor; Scharr, Hanno; Hülskamp, Martin; Koornneef, Maarten; Jahnke, Siegfried

2015-01-01

Precise measurements of leaf vein traits are an important aspect of plant phenotyping for ecological and genetic research. Here, we present a powerful and user-friendly image analysis tool named phenoVein. It is dedicated to automated segmenting and analyzing of leaf veins in images acquired with different imaging modalities (microscope, macrophotography, etc.), including options for comfortable manual correction. Advanced image filtering emphasizes veins from the background and compensates for local brightness inhomogeneities. The most important traits being calculated are total vein length, vein density, piecewise vein lengths and widths, areole area, and skeleton graph statistics, like the number of branching or ending points. For the determination of vein widths, a model-based vein edge estimation approach has been implemented. Validation was performed for the measurement of vein length, vein width, and vein density of Arabidopsis (Arabidopsis thaliana), proving the reliability of phenoVein. We demonstrate the power of phenoVein on a set of previously described vein structure mutants of Arabidopsis (hemivenata, ondulata3, and asymmetric leaves2-101) compared with wild-type accessions Columbia-0 and Landsberg erecta-0. phenoVein is freely available as open-source software. PMID:26468519

Acute Therapy: Why Not Over-The-Counter or Other Nonspecific Options?

MedlinePlus

... gatherings or canceling plans with friends, but open communication will help all parties understand that it’s not ... your migraine not only helps you reduce the frequency and intensity of your attacks, but can help ...

Near Real Time Integration of Satellite and Radar Data for Probabilistic Nearcasting of Severe Weather

NASA Astrophysics Data System (ADS)

Pilone, D.; Quinn, P.; Mitchell, A. E.; Baynes, K.; Shum, D.

2014-12-01

This talk introduces the audience to some of the very real challenges associated with visualizing data from disparate data sources as encountered during the development of real world applications. In addition to the fundamental challenges of dealing with the data and imagery, this talk discusses usability problems encountered while trying to provide interactive and user-friendly visualization tools. At the end of this talk the audience will be aware of some of the pitfalls of data visualization along with tools and techniques to help mitigate them. There are many sources of variable resolution visualizations of science data available to application developers including NASA's Global Imagery Browse Services (GIBS), however integrating and leveraging visualizations in modern applications faces a number of challenges, including: - Varying visualized Earth "tile sizes" resulting in challenges merging disparate sources - Multiple visualization frameworks and toolkits with varying strengths and weaknesses - Global composite imagery vs. imagery matching EOSDIS granule distribution - Challenges visualizing geographically overlapping data with different temporal bounds - User interaction with overlapping or collocated data - Complex data boundaries and shapes combined with multi-orbit data and polar projections - Discovering the availability of visualizations and the specific parameters, color palettes, and configurations used to produce them In addition to discussing the challenges and approaches involved in visualizing disparate data, we will discuss solutions and components we'll be making available as open source to encourage reuse and accelerate application development.

Data Visualization Challenges and Opportunities in User-Oriented Application Development

NASA Astrophysics Data System (ADS)

Pilone, D.; Quinn, P.; Mitchell, A. E.; Baynes, K.; Shum, D.

2015-12-01

This talk introduces the audience to some of the very real challenges associated with visualizing data from disparate data sources as encountered during the development of real world applications. In addition to the fundamental challenges of dealing with the data and imagery, this talk discusses usability problems encountered while trying to provide interactive and user-friendly visualization tools. At the end of this talk the audience will be aware of some of the pitfalls of data visualization along with tools and techniques to help mitigate them. There are many sources of variable resolution visualizations of science data available to application developers including NASA's Global Imagery Browse Services (GIBS), however integrating and leveraging visualizations in modern applications faces a number of challenges, including: - Varying visualized Earth "tile sizes" resulting in challenges merging disparate sources - Multiple visualization frameworks and toolkits with varying strengths and weaknesses - Global composite imagery vs. imagery matching EOSDIS granule distribution - Challenges visualizing geographically overlapping data with different temporal bounds - User interaction with overlapping or collocated data - Complex data boundaries and shapes combined with multi-orbit data and polar projections - Discovering the availability of visualizations and the specific parameters, color palettes, and configurations used to produce them In addition to discussing the challenges and approaches involved in visualizing disparate data, we will discuss solutions and components we'll be making available as open source to encourage reuse and accelerate application development.

Friends and social contexts as unshared environments: a discordant sibling analysis of obesity- and health-related behaviors in young adolescents.

PubMed

Salvy, S-J; Feda, D M; Epstein, L H; Roemmich, J N

2017-04-01

This study examines the contribution of best friends' weight and the peer social context (time spent alone versus with friends) as sources of unshared environment associated with variability in weight and health behaviors among weight-discordant siblings. Pairs of same-sex biologic siblings (N=40 pairs; ages 13-17) were originally recruited as part of a study evaluating putative factors contributing to differences in adiposity among weight-discordant siblings. Siblings were asked to bring their best friends to the laboratory and siblings and friends' height and weight were objectively measured. Siblings also completed multi-pass dietary recalls to assess energy intake and sugar sweetened beverage (SSB) consumption. Siblings' physical activity was measured using accelerometry. Experience sampling methodology was used to assess sedentary behaviors/screen time and the number of occasions siblings spent alone and in the presence of friends. Multilevel models were used to estimate the relationships between predictors (best friends' zBMI, time spent alone or with friends) and outcomes (siblings' zBMI and obesity-related health behaviors). Best friends' zBMI was the best predictor of participants' zBMI, even when controlling for child's birth weight. Best friends' weight (zBMI) further predicted participants' SSB intake and time engaged in sedentary behaviors. Being active with friends was positively associated with participants' overall physical activity, whereas spending time alone was negatively associated with accelerometer counts regardless of siblings' adiposity. A friends' weight and the social context are unshared environmental factors associated with variability in adiposity among biologically-related weight-discordant siblings.

Effects of euthanasia on the bereaved family and friends: a cross sectional study.

PubMed

Swarte, Nikkie B; van der Lee, Marije L; van der Bom, Johanna G; van den Bout, Jan; Heintz, A Peter M

2003-07-26

To assess how euthanasia in terminally ill cancer patients affects the grief response of bereaved family and friends. Cross sectional study. Tertiary referral centre for oncology patients in Utrecht, the Netherlands. 189 bereaved family members and close friends of terminally ill cancer patients who died by euthanasia and 316 bereaved family members and close friends of comparable cancer patients who died a natural death between 1992 and 1999. Symptoms of traumatic grief assessed by the inventory of traumatic grief, current feelings of grief assessed by the Texas revised inventory of grief, and post-traumatic stress reactions assessed by the impact of event scale. The bereaved family and friends of cancer patients who died by euthanasia had less traumatic grief symptoms (adjusted difference -5.29 (95% confidence interval -8.44 to -2.15)), less current feeling of grief (adjusted difference 2.93 (0.85 to 5.01)); and less post-traumatic stress reactions (adjusted difference -2.79 (-5.33 to -0.25)) than the family and friends of patients who died of natural causes. These differences were independent of other risk factors. The bereaved family and friends of cancer patients who died by euthanasia coped better with respect to grief symptoms and post-traumatic stress reactions than the bereaved of comparable cancer patients who died a natural death. These results should not be interpreted as a plea for euthanasia, but as a plea for the same level of care and openness in all patients who are terminally ill.

Comparing Sexual-Minority and Heterosexual Young Women's Friends and Parents as Sources of Support for Sexual Issues

ERIC Educational Resources Information Center

Friedman, Carly K.; Morgan, Elizabeth M.

2009-01-01

The present study provides a comparative analysis of sexual-minority and heterosexual emerging adult women's experiences seeking support for sexual issues from parents and friends. Participants included 229 college women (88 sexual-minority women; 141 heterosexual women), ranging from 18 to 25 years of age, who provided written responses to an…

High-resolution Single Particle Analysis from Electron Cryo-microscopy Images Using SPHIRE

PubMed Central

Moriya, Toshio; Saur, Michael; Stabrin, Markus; Merino, Felipe; Voicu, Horatiu; Huang, Zhong; Penczek, Pawel A.; Raunser, Stefan; Gatsogiannis, Christos

2017-01-01

SPHIRE (SPARX for High-Resolution Electron Microscopy) is a novel open-source, user-friendly software suite for the semi-automated processing of single particle electron cryo-microscopy (cryo-EM) data. The protocol presented here describes in detail how to obtain a near-atomic resolution structure starting from cryo-EM micrograph movies by guiding users through all steps of the single particle structure determination pipeline. These steps are controlled from the new SPHIRE graphical user interface and require minimum user intervention. Using this protocol, a 3.5 Å structure of TcdA1, a Tc toxin complex from Photorhabdus luminescens, was derived from only 9500 single particles. This streamlined approach will help novice users without extensive processing experience and a priori structural information, to obtain noise-free and unbiased atomic models of their purified macromolecular complexes in their native state. PMID:28570515

BurnMan: Towards a multidisciplinary toolkit for reproducible deep Earth science

NASA Astrophysics Data System (ADS)

Myhill, R.; Cottaar, S.; Heister, T.; Rose, I.; Unterborn, C. T.; Dannberg, J.; Martin-Short, R.

2016-12-01

BurnMan (www.burnman.org) is an open-source toolbox to compute thermodynamic and thermoelastic properties as a function of pressure and temperature using published mineral physical parameters and equations-of-state. The framework is user-friendly, written in Python, and modular, allowing the user to implement their own equations of state, endmember and solution model libraries, geotherms, and averaging schemes. Here we introduce various new modules, which can be used to: Fit thermodynamic variables to data from high pressure static and shock wave experiments, Calculate equilibrium assemblages given a bulk composition, pressure and temperature, Calculate chemical potentials and oxygen fugacities for given assemblages Compute 3D synthetic seismic models using output from geodynamic models and compare these results with global seismic tomographic models, Create input files for synthetic seismogram codes. Users can contribute scripts that reproduce the results from peer-reviewed articles and practical demonstrations (e.g. Cottaar et al., 2014).

A Python-based interface to examine motions in time series of solar images

NASA Astrophysics Data System (ADS)

Campos-Rozo, J. I.; Vargas Domínguez, S.

2017-10-01

Python is considered to be a mature programming language, besides of being widely accepted as an engaging option for scientific analysis in multiple areas, as will be presented in this work for the particular case of solar physics research. SunPy is an open-source library based on Python that has been recently developed to furnish software tools to solar data analysis and visualization. In this work we present a graphical user interface (GUI) based on Python and Qt to effectively compute proper motions for the analysis of time series of solar data. This user-friendly computing interface, that is intended to be incorporated to the Sunpy library, uses a local correlation tracking technique and some extra tools that allows the selection of different parameters to calculate, vizualize and analyze vector velocity fields of solar data, i.e. time series of solar filtergrams and magnetograms.

A simple method to synthesize modified Fe3O4 for the removal of organic pollutants on water surface

NASA Astrophysics Data System (ADS)

Zhu, Ling; Li, Chuanhao; Wang, Juan; Zhang, Hui; Zhang, Jian; Shen, Yuhua; Li, Cun; Wang, Cuiping; Xie, Anjian

2012-06-01

In this article, a simple, economic and environment-friendly approach is explored to prepare Fe3O4 nanoparticles by using air oxidation at room temperature. Furthermore, the Fe3O4 magnetic nanoparticles (MNPs) have been modified with sodium oleate successfully to form super-hydrophobic surfaces. The alkali source played an important role in controlling the morphologies of Fe3O4 MNPs. Either Fe3O4 MNPs or sodium oleate modified Fe3O4 MNPs possessed good magnetic property, and the as-prepared modified Fe3O4 nanoparticles are both hydrophobic and lipophilic. Therefore, Fe3O4/sodium oleate could be dispersed stable in the oil medium and have been applied in the cleanup engine oil from the water surface. It will open up a potential and broad application in wastewater treatment.

STINGRAY: system for integrated genomic resources and analysis.

PubMed

Wagner, Glauber; Jardim, Rodrigo; Tschoeke, Diogo A; Loureiro, Daniel R; Ocaña, Kary A C S; Ribeiro, Antonio C B; Emmel, Vanessa E; Probst, Christian M; Pitaluga, André N; Grisard, Edmundo C; Cavalcanti, Maria C; Campos, Maria L M; Mattoso, Marta; Dávila, Alberto M R

2014-03-07

The STINGRAY system has been conceived to ease the tasks of integrating, analyzing, annotating and presenting genomic and expression data from Sanger and Next Generation Sequencing (NGS) platforms. STINGRAY includes: (a) a complete and integrated workflow (more than 20 bioinformatics tools) ranging from functional annotation to phylogeny; (b) a MySQL database schema, suitable for data integration and user access control; and (c) a user-friendly graphical web-based interface that makes the system intuitive, facilitating the tasks of data analysis and annotation. STINGRAY showed to be an easy to use and complete system for analyzing sequencing data. While both Sanger and NGS platforms are supported, the system could be faster using Sanger data, since the large NGS datasets could potentially slow down the MySQL database usage. STINGRAY is available at http://stingray.biowebdb.org and the open source code at http://sourceforge.net/projects/stingray-biowebdb/.

PR-PR: Cross-Platform Laboratory Automation System

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

Linshiz, G; Stawski, N; Goyal, G

To enable protocol standardization, sharing, and efficient implementation across laboratory automation platforms, we have further developed the PR-PR open-source high-level biology-friendly robot programming language as a cross-platform laboratory automation system. Beyond liquid-handling robotics, PR-PR now supports microfluidic and microscopy platforms, as well as protocol translation into human languages, such as English. While the same set of basic PR-PR commands and features are available for each supported platform, the underlying optimization and translation modules vary from platform to platform. Here, we describe these further developments to PR-PR, and demonstrate the experimental implementation and validation of PR-PR protocols for combinatorial modified Goldenmore » Gate DNA assembly across liquid-handling robotic, microfluidic, and manual platforms. To further test PR-PR cross-platform performance, we then implement and assess PR-PR protocols for Kunkel DNA mutagenesis and hierarchical Gibson DNA assembly for microfluidic and manual platforms.« less

The LSST metrics analysis framework (MAF)

NASA Astrophysics Data System (ADS)

Jones, R. L.; Yoachim, Peter; Chandrasekharan, Srinivasan; Connolly, Andrew J.; Cook, Kem H.; Ivezic, Željko; Krughoff, K. S.; Petry, Catherine; Ridgway, Stephen T.

2014-07-01

We describe the Metrics Analysis Framework (MAF), an open-source python framework developed to provide a user-friendly, customizable, easily-extensible set of tools for analyzing data sets. MAF is part of the Large Synoptic Survey Telescope (LSST) Simulations effort. Its initial goal is to provide a tool to evaluate LSST Operations Simulation (OpSim) simulated surveys to help understand the effects of telescope scheduling on survey performance, however MAF can be applied to a much wider range of datasets. The building blocks of the framework are Metrics (algorithms to analyze a given quantity of data), Slicers (subdividing the overall data set into smaller data slices as relevant for each Metric), and Database classes (to access the dataset and read data into memory). We describe how these building blocks work together, and provide an example of using MAF to evaluate different dithering strategies. We also outline how users can write their own custom Metrics and use these within the framework.

shinyGISPA: A web application for characterizing phenotype by gene sets using multiple omics data combinations.

PubMed

Dwivedi, Bhakti; Kowalski, Jeanne

2018-01-01

While many methods exist for integrating multi-omics data or defining gene sets, there is no one single tool that defines gene sets based on merging of multiple omics data sets. We present shinyGISPA, an open-source application with a user-friendly web-based interface to define genes according to their similarity in several molecular changes that are driving a disease phenotype. This tool was developed to help facilitate the usability of a previously published method, Gene Integrated Set Profile Analysis (GISPA), among researchers with limited computer-programming skills. The GISPA method allows the identification of multiple gene sets that may play a role in the characterization, clinical application, or functional relevance of a disease phenotype. The tool provides an automated workflow that is highly scalable and adaptable to applications that go beyond genomic data merging analysis. It is available at http://shinygispa.winship.emory.edu/shinyGISPA/.

shinyGISPA: A web application for characterizing phenotype by gene sets using multiple omics data combinations

PubMed Central

Dwivedi, Bhakti

2018-01-01

While many methods exist for integrating multi-omics data or defining gene sets, there is no one single tool that defines gene sets based on merging of multiple omics data sets. We present shinyGISPA, an open-source application with a user-friendly web-based interface to define genes according to their similarity in several molecular changes that are driving a disease phenotype. This tool was developed to help facilitate the usability of a previously published method, Gene Integrated Set Profile Analysis (GISPA), among researchers with limited computer-programming skills. The GISPA method allows the identification of multiple gene sets that may play a role in the characterization, clinical application, or functional relevance of a disease phenotype. The tool provides an automated workflow that is highly scalable and adaptable to applications that go beyond genomic data merging analysis. It is available at http://shinygispa.winship.emory.edu/shinyGISPA/. PMID:29415010

IsoCor: correcting MS data in isotope labeling experiments.

PubMed

Millard, Pierre; Letisse, Fabien; Sokol, Serguei; Portais, Jean-Charles

2012-05-01

Mass spectrometry (MS) is widely used for isotopic labeling studies of metabolism and other biological processes. Quantitative applications-e.g. metabolic flux analysis-require tools to correct the raw MS data for the contribution of all naturally abundant isotopes. IsoCor is a software that allows such correction to be applied to any chemical species. Hence it can be used to exploit any isotopic tracer, from well-known ((13)C, (15)N, (18)O, etc) to unusual ((57)Fe, (77)Se, etc) isotopes. It also provides new features-e.g. correction for the isotopic purity of the tracer-to improve the accuracy of quantitative isotopic studies, and implements an efficient algorithm to process large datasets. Its user-friendly interface makes isotope labeling experiments more accessible to a wider biological community. IsoCor is distributed under OpenSource license at http://metasys.insa-toulouse.fr/software/isocor/

Improving PHENIX search with Solr, Nutch and Drupal.

NASA Astrophysics Data System (ADS)

Morrison, Dave; Sourikova, Irina

2012-12-01

During its 20 years of R&D, construction and operation the PHENIX experiment at the Relativistic Heavy Ion Collider (RHIC) has accumulated large amounts of proprietary collaboration data that is hosted on many servers around the world and is not open for commercial search engines for indexing and searching. The legacy search infrastructure did not scale well with the fast growing PHENIX document base and produced results inadequate in both precision and recall. After considering the possible alternatives that would provide an aggregated, fast, full text search of a variety of data sources and file formats we decided to use Nutch [1] as a web crawler and Solr [2] as a search engine. To present XML-based Solr search results in a user-friendly format we use Drupal [3] as a web interface to Solr. We describe the experience of building a federated search for a heterogeneous collection of 10 million PHENIX documents with Nutch, Solr and Drupal.

STINGRAY: system for integrated genomic resources and analysis

PubMed Central

2014-01-01

Background The STINGRAY system has been conceived to ease the tasks of integrating, analyzing, annotating and presenting genomic and expression data from Sanger and Next Generation Sequencing (NGS) platforms. Findings STINGRAY includes: (a) a complete and integrated workflow (more than 20 bioinformatics tools) ranging from functional annotation to phylogeny; (b) a MySQL database schema, suitable for data integration and user access control; and (c) a user-friendly graphical web-based interface that makes the system intuitive, facilitating the tasks of data analysis and annotation. Conclusion STINGRAY showed to be an easy to use and complete system for analyzing sequencing data. While both Sanger and NGS platforms are supported, the system could be faster using Sanger data, since the large NGS datasets could potentially slow down the MySQL database usage. STINGRAY is available at http://stingray.biowebdb.org and the open source code at http://sourceforge.net/projects/stingray-biowebdb/. PMID:24606808

PR-PR: cross-platform laboratory automation system.

PubMed

Linshiz, Gregory; Stawski, Nina; Goyal, Garima; Bi, Changhao; Poust, Sean; Sharma, Monica; Mutalik, Vivek; Keasling, Jay D; Hillson, Nathan J

2014-08-15

To enable protocol standardization, sharing, and efficient implementation across laboratory automation platforms, we have further developed the PR-PR open-source high-level biology-friendly robot programming language as a cross-platform laboratory automation system. Beyond liquid-handling robotics, PR-PR now supports microfluidic and microscopy platforms, as well as protocol translation into human languages, such as English. While the same set of basic PR-PR commands and features are available for each supported platform, the underlying optimization and translation modules vary from platform to platform. Here, we describe these further developments to PR-PR, and demonstrate the experimental implementation and validation of PR-PR protocols for combinatorial modified Golden Gate DNA assembly across liquid-handling robotic, microfluidic, and manual platforms. To further test PR-PR cross-platform performance, we then implement and assess PR-PR protocols for Kunkel DNA mutagenesis and hierarchical Gibson DNA assembly for microfluidic and manual platforms.

Identification of MS-Cleavable and Non-Cleavable Chemically Crosslinked Peptides with MetaMorpheus.

PubMed

Lu, Lei; Millikin, Robert J; Solntsev, Stefan K; Rolfs, Zach; Scalf, Mark; Shortreed, Michael R; Smith, Lloyd M

2018-05-25

Protein chemical crosslinking combined with mass spectrometry has become an important technique for the analysis of protein structure and protein-protein interactions. A variety of crosslinkers are well developed, but reliable, rapid, and user-friendly tools for large-scale analysis of crosslinked proteins are still in need. Here we report MetaMorpheusXL, a new search module within the MetaMorpheus software suite that identifies both MS-cleavable and non-cleavable crosslinked peptides in MS data. MetaMorpheusXL identifies MS-cleavable crosslinked peptides with an ion-indexing algorithm, which enables an efficient large database search. The identification does not require the presence of signature fragment ions, an advantage compared to similar programs such as XlinkX. One complication associated with the need for signature ions from cleavable crosslinkers such as DSSO (disuccinimidyl sulfoxide) is the requirement for multiple fragmentation types and energy combinations, which is not necessary for MetaMorpheusXL. The ability to perform proteome-wide analysis is another advantage of MetaMorpheusXl compared to such programs as MeroX and DXMSMS. MetaMorpheusXL is also faster than other currently available MS-cleavable crosslink search software programs. It is imbedded in MetaMorpheus, an open-source and freely available software suite that provides a reliable, fast, user-friendly graphical user interface that is readily accessible to researchers.

SimArray: a user-friendly and user-configurable microarray design tool

PubMed Central

Auburn, Richard P; Russell, Roslin R; Fischer, Bettina; Meadows, Lisa A; Sevillano Matilla, Santiago; Russell, Steven

2006-01-01

Background Microarrays were first developed to assess gene expression but are now also used to map protein-binding sites and to assess allelic variation between individuals. Regardless of the intended application, efficient production and appropriate array design are key determinants of experimental success. Inefficient production can make larger-scale studies prohibitively expensive, whereas poor array design makes normalisation and data analysis problematic. Results We have developed a user-friendly tool, SimArray, which generates a randomised spot layout, computes a maximum meta-grid area, and estimates the print time, in response to user-specified design decisions. Selected parameters include: the number of probes to be printed; the microtitre plate format; the printing pin configuration, and the achievable spot density. SimArray is compatible with all current robotic spotters that employ 96-, 384- or 1536-well microtitre plates, and can be configured to reflect most production environments. Print time and maximum meta-grid area estimates facilitate evaluation of each array design for its suitability. Randomisation of the spot layout facilitates correction of systematic biases by normalisation. Conclusion SimArray is intended to help both established researchers and those new to the microarray field to develop microarray designs with randomised spot layouts that are compatible with their specific production environment. SimArray is an open-source program and is available from . PMID:16509966

A User-Friendly Model for Spray Drying to Aid Pharmaceutical Product Development

PubMed Central

Grasmeijer, Niels; de Waard, Hans; Hinrichs, Wouter L. J.; Frijlink, Henderik W.

2013-01-01

The aim of this study was to develop a user-friendly model for spray drying that can aid in the development of a pharmaceutical product, by shifting from a trial-and-error towards a quality-by-design approach. To achieve this, a spray dryer model was developed in commercial and open source spreadsheet software. The output of the model was first fitted to the experimental output of a Büchi B-290 spray dryer and subsequently validated. The predicted outlet temperatures of the spray dryer model matched the experimental values very well over the entire range of spray dryer settings that were tested. Finally, the model was applied to produce glassy sugars by spray drying, an often used excipient in formulations of biopharmaceuticals. For the production of glassy sugars, the model was extended to predict the relative humidity at the outlet, which is not measured in the spray dryer by default. This extended model was then successfully used to predict whether specific settings were suitable for producing glassy trehalose and inulin by spray drying. In conclusion, a spray dryer model was developed that is able to predict the output parameters of the spray drying process. The model can aid the development of spray dried pharmaceutical products by shifting from a trial-and-error towards a quality-by-design approach. PMID:24040240

40 CFR Table 3 to Subpart Wwww of... - Organic HAP Emissions Limits for Existing Open Molding Sources, New Open Molding Sources Emitting...

Code of Federal Regulations, 2010 CFR

2010-07-01

... Existing Open Molding Sources, New Open Molding Sources Emitting Less Than 100 TPY of HAP, and New and... CATEGORIES National Emissions Standards for Hazardous Air Pollutants: Reinforced Plastic Composites... Existing Open Molding Sources, New Open Molding Sources Emitting Less Than 100 TPY of HAP, and New and...

Stakeholder co-development of farm level nutrient management software

NASA Astrophysics Data System (ADS)

Buckley, Cathal; Mechan, Sarah; Macken-Walsh, Aine; Heanue, Kevin

2013-04-01

Over the last number of decades intensification in the use nitrogen (N) and phosphorus (P) in agricultural production has lead to excessive accumulations of these nutrients in soils, groundwaters and surface water bodies (Sutton et al., 2011). According to the European Environment Agency (2012) despite some progress diffuse pollution from agriculture is still significant in more than 40% of Europe's water bodies in rivers and coastal waters, and in one third of the water bodies in lakes and transitional waters. Recently it was estimated that approximately 29% of monitored river channel length is polluted to some degree across the Republic of Ireland. Agricultural sources were suspected in 47 per cent of cases (EPA, 2012). Farm level management practices to reduce nutrient transfers from agricultural land to watercourses can be divided into source reduction and source interception approaches (Ribaudo et al., 2001). Source interception approaches involve capturing nutrients post mobilisation through policy instruments such as riparian buffer zones or wetlands. Conversely, the source reduction approach is preventative in nature and promotes strict management of nutrient at farm and field level to reduce risk of mobilisation in the first instance. This has the potential to deliver a double dividend of reduced nutrient loss to the wider ecosystem while maximising economic return to agricultural production at the field and farm levels. Adoption and use of nutrient management plans among farmers is far from the norm. This research engages key farmer and extension stakeholders to explore how current nutrient management planning software and outputs should be developed to make it more user friendly and usable in a practical way. An open innovation technology co-development approach was adopted to investigate what is demanded by the end users - farm advisors and farmers. Open innovation is a knowledge management strategy that uses the input of stakeholders to improve internal innovation processes. Open innovation incorporates processes such as 'user-led' (farmer and advisor) innovation and the 'co-development' (by technologists and users) of a technology. This strategy is increasingly used by a variety of organisations across sectors to try to ensure that the use of their outputs (products/services/technologies) is optimised by their target customers/clients, by incorporating user insights into the development of outputs. This research use the open innovation co-development framework through farmer and farm advisor focus group sessions to inform the development of a desirable software package for nutrient management planners (farm advisors) and desirable output formats for the end user (farmers). References Sutton, M., Oenema, O., Erisman, J. W., Leip, A., Grinsven, H. & Winiwarter, W. 2011. Too much of a good thing. Nature, 472, 159.161. European Environment Agency, 2012. European waters — assessment of status and pressures. Environmental Protection Agency, 2012. Ireland's Environment: An assessment 2012. Ribaudo, M.O., Heimlich, R., Claassen, R., Peters, M., 2001. Least-cost management of nonpoint source pollution: source reduction versus interception strategies for controlling nitrogen loss in the Mississippi Basin. Ecological Economics, 37, 183-197.

Providing Support to Relatives and Friends Managing Both Chronic Physical Illness and Depression: the Views of a National Sample of U.S. Adults

PubMed Central

Janevic, Mary; Rosland, Ann-Marie; Wiitala, Wyndy; Connell, Cathleen M; Piette, John D.

2012-01-01

Objective To describe how comorbid depression in chronically ill adults affects the willingness of their family and friends to provide them with illness management support. Methods We identified a national sample of U.S. adults (n=1027), all of whom had a close relative or friend with a chronic physical illness. We examined whether respondents were less willing to help their relatives/friends with disease management when they reported that these relatives/friends were also diagnosed with depression. Results In multivariate models, the odds of respondents being willing to provide disease-management support doubled when the relative/friend was depressed (adjusted odds ratio (AOR) = 1.99; 95% C.I=1.31, 3.02). Respondents were willing to perform an equal number of illness support tasks for relatives/friends with and without depression. However, respondents reported 30% more difficulties discussing health issues (incidence rate ratio (IRR)=1.30; 95% C.I=1.11,1.53), and 44% more barriers to providing support (IRR=1.44; 95% C.I=1.18, 1.75) to depressed relatives/friends. Conclusion U.S. adults are more willing to provide disease-management support for chronically ill relatives/friends with depression. However, helping depressed relatives/friends is also more challenging. Practice implications By providing resources for potential supporters, health providers could mobilize an important source of disease-management support for patients with chronic illness and depression. PMID:22748757

Decomposing the components of friendship and friends' influence on adolescent drinking and smoking.

PubMed

Fujimoto, Kayo; Valente, Thomas W

2012-08-01

Friendship networks are an important source of peer influence. However, existing network studies vary in terms of how they operationalize friendship and friend's influence on adolescent substance use. This study uses social network analysis to characterize three types of friendship relations: (1) mutual or reciprocated, (2) directional, and (3) intimate friends. We then examine the relative effects of each friendship type on adolescent drinking and smoking behavior. Using a saturated sample from the Add Health data, a nationally representative sample of high school adolescents (N = 2,533 nested in 12 schools), we computed the level of exposure to drinking and smoking of friends using a network exposure model, and their association with individual drinking and smoking using fixed effect models. Results indicated that the influence from mutual or reciprocated type of friendship relations is stronger on adolescent substance use than directional, especially for smoking. Regarding the directionality of directional type of friendship relations, adolescents are equally influenced by both nominating and nominated friends on their drinking and smoking behavior. Results for intimate friends friendship relations indicated that the influence from "best friends" was weaker than the one from non-"best friends," which indicates that the order of friend nomination may not matter as much as nomination reciprocation. This study demonstrates that considering different features of friendship relationships is important in evaluating friends' influence on adolescent substance use. Related policy implications are discussed. Copyright © 2012 Society for Adolescent Health and Medicine. Published by Elsevier Inc. All rights reserved.

Trusted information sources used during and after Superstorm Sandy: TV and radio were used more often than social media

PubMed Central

Burger, Joanna; Gochfeld, Michael; Jeitner, Christian; Pittfield, Taryn; Donio, Mark

2015-01-01

Health and safety professionals, and the public, are interested in the best methods of providing timely information about disasters. The objective of this study was to examine information sources used for Superstorm Sandy with respect to the storm, evacuation routes, shelters, safety, and health issues. Respondents in Central New Jersey and Jersey Shore communities were differentially impacted by the storm. Jersey shore respondents had higher evacuation rates (47 % vs 13 %), higher flood waters in homes, longer power outages (average 23 vs 6 days), and longer periods without internet (29 vs 6 days). Electricity outages disrupted both sources and receivers of communication. Both groups obtained most of their information regarding safety from television, radio, friends and web/email. Information sources on health varied by location, with central Jersey respondents using mainly TV and the web, and Jersey shore respondents obtaining health information from the radio, and TV (before the storm). For information on evacuation routes, Jersey shore respondents obtained information from many sources, while central Jersey respondents obtained it from TV. Information on mold was largely obtained from friends and the web, since mold issues were dealt with several weeks after Sandy. The reliance on traditional sources of information (TV, radio, friends) found in this study suggests that the extreme power outages rendered web, cell phones, and social media on cell phones less usable, and suggests the need for an integrated communication strategy with redundancies that takes into account prolonged power outages over large geographical areas. PMID:24279815

Information Expensiveness Perceived by Vietnamese Patients with Respect to Healthcare Provider’s Choice

PubMed Central

Quan-Hoang, Vuong

2016-01-01

Background: Patients have to acquire information to support their decision on choosing a suitable healthcare provider. But in developing countries like Vietnam, accessibility issues remain an obstacle, thus adversely affect both quality and costliness of healthcare information. Vietnamese use both sources from health professionals and friends/relatives, especially when quality of the Internet-based cheaper sources appear to be still questionable. The search of information from both professionals and friends/relatives incurs some cost, which can be viewed as low or high depending low or high accessibility to the sources. These views potentially affect their choices. Aim and Objectives: To investigate the effects that medical/health services information on perceived expensiveness of patients’ labor costs. Two related objectives are a) establishing empirical relations between accessibility to sources and expensiveness; and, b) probabilistic trends of probabilities for perceived expensiveness. Results: There is evidence for established relations among the variables “Convexp” and “Convrel” (all p’s < 0.01), indicating that both information sources (experts and friends/relatives) have influence on patients perception of information expensiveness. The use of experts source tends to increase the probability of perceived expensiveness. Conclusion: a) Probabilistic trends show Vietnamese patients have propensity to value healthcare information highly and do not see it as “expensive”; b) The majority of Vietnamese households still take non-professional advices at their own risks; c) There is more for the public healthcare information system to do to reduce costliness and risk of information. The Internet-based health service users communities cannot replace this system. PMID:28077894

Trusted information sources used during and after Superstorm Sandy: TV and radio were used more often than social media.

PubMed

Burger, Joanna; Gochfeld, Michael; Jeitner, Christian; Pittfield, Taryn; Donio, Mark

2013-01-01

Health and safety professionals and the public are interested in the best methods of providing timely information about disasters. The objective of this study was to examine information sources used for Superstorm Sandy with respect to the storm, evacuation routes, shelters, safety, and health issues. Respondents in central New Jersey and Jersey shore communities were differentially impacted by the storm. Jersey shore respondents had higher evacuation rates (47% vs. 13%), higher flood waters in homes, longer power outages (average 23 vs. 6 d), and longer periods without Internet (29 vs. 6 d). Electricity outages disrupted both sources and receivers of communication. Both groups obtained most of their information regarding safety from television, radio, friends, and Web/e-mail. Information sources on health varied by location, with central Jersey respondents using mainly TV and the Web, and Jersey shore respondents obtaining health information from the radio and TV (before the storm). For information on evacuation routes, Jersey shore respondents obtained information from many sources, while central Jersey respondents obtained it from TV. Information on mold was largely obtained from friends and the Web, since mold issues were dealt with several weeks after Sandy. The reliance on traditional sources of information (TV, radio, friends) found in this study suggests that the extreme power outages rendered Web, cell phones, and social media on cell phones less usable, and suggests the need for an integrated communication strategy with redundancies that takes into account prolonged power outages over large geographical areas.

First year medical student experiences with being discouraged from entering medical school.

PubMed

Imperato, P J; Nayeri, K

1991-06-01

Three hundred and fourteen first year medical students from two consecutive classes were surveyed for their experiences with being discouraged from entering medical school. Sixty-eight percent (215) had been discouraged from becoming physicians. The sources of discouragement were varied, with 43% citing physician acquaintances and 40% friends and neighbors. Parents were the principal source of encouragement (58%) followed by friends and neighbors (47%). More students (34%) were encouraged by undergraduate professors and advisors than by their family doctor (23%), a physician relative (18%), or a physician acquaintance (31%). Discouragement centered on three broad areas: diminished financial rewards, increased financial costs, and quality of life.

Sources of Discrimination and Their Associations With Health in Sexual Minority Adults.

PubMed

Figueroa, Wilson S; Zoccola, Peggy M

2016-06-01

Health disparities exist between sexual minorities and heterosexuals. These health disparities may be due to stressful social situations and environments that are created by discrimination. The current study recruited 277 sexual minorities to complete an online survey to examine the effects of discrimination on health. Discrimination from family and friends, compared to non-family and friends, was found to be more strongly associated with poorer health. This effect was partially statistically mediated by perceived stress reactivity. Findings from this study highlight the importance of distinguishing between different sources of discrimination when examining the effect of discrimination on health in sexual minority adults.

Lignin biopolymer based triboelectric nanogenerators

NASA Astrophysics Data System (ADS)

Bao, Yukai; Wang, Ruoxing; Lu, Yunmei; Wu, Wenzhuo

2017-07-01

Ongoing research in triboelectric nanogenerators (TENGs) focuses on increasing power generation, but obstacles concerning economical and eco-friendly utilization of TENGs continue to prevail. Being the second most abundant biopolymer on earth, lignin offers a valuable opportunity for low-cost TENG applications in biomedical devices, benefitting from its biodegradability and biocompatibility. Here, we develop for the first time a lignin biopolymer based TENGs for harvesting mechanical energy in the environment, which shows great potential for self-powered biomedical devices among other applications and opens doors to new technologies that utilize otherwise wasted materials for economically feasible and ecologically friendly production of energy devices.

Sources of strength-training information and strength-training behavior among Japanese older adults.

PubMed

Harada, Kazuhiro; Shibata, Ai; Lee, Euna; Oka, Koichiro; Nakamura, Yoshio

2016-03-01

The promotion of strength training is now recognized as an important component of public health initiatives for older adults. To develop successful communication strategies to increase strength-training behavior among older adults, the identification of effective communication channels to reach older adults is necessary. This study aimed to identify the information sources about strength training that were associated with strength-training behaviors among Japanese older adults. The participants were 1144 adults (60-74 years old) randomly sampled from the registry of residential addresses. A cross-sectional questionnaire survey was conducted. The independent variables were sources of strength-training information (healthcare providers, friends, families, radio, television, newspapers, newsletters, posters, books, magazines, booklets, the Internet, lectures, other sources), and the dependent variable was regular strength-training behavior. Logistic regression analysis was used to identify potential relationships. After adjusting for demographic factors and all other information sources, strength-training information from healthcare providers, friends, books and the Internet were positively related to regular strength-training behavior. The findings of the present study contribute to a better understanding of strength-training behavior and the means of successful communication directed at increasing strength training among older adults. The results suggest that healthcare providers, friends, books and the Internet are effective methods of communication for increasing strength-training behaviors among older adults. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Direct and interactive effects of parent, friend and schoolmate drinking on alcohol use trajectories.

PubMed

Lynch, Alicia Doyle; Coley, Rebekah Levine; Sims, Jacqueline; Lombardi, Caitlin McPherran; Mahalik, James R

2015-01-01

This study considered the unique and interactive roles of social norms from parents, friends and schools in predicting developmental trajectories of adolescent drinking and intoxication. Using data from the National Longitudinal Study of Adolescent Health, which followed adolescents (N = 18,921) for 13 years, we used discrete mixture modelling to identify unique developmental trajectories of drinking and of intoxication. Next, multilevel multinomial regression models examined the role of alcohol-related social norms from parents, friends and schoolmates in the prediction of youths' trajectory group membership. Results demonstrated that social norms from parents, friends and schoolmates that were favourable towards alcohol use uniquely predicted drinking and intoxication trajectory group membership. Interactions between social norms revealed that schoolmate drinking played an important moderating role, frequently augmenting social norms from parents and friends. The current findings suggest that social norms from multiple sources (parents, friends and schools) work both independently and interactively to predict longitudinal trajectories of adolescent alcohol use. Results highlight the need to identify and understand social messages from multiple developmental contexts in efforts to reduce adolescent alcohol consumption and alcohol-related risk-taking.

DESIGNING ENVIRONMENTALLY FRIENDLY CHEMICAL PROCESSES WITH FUGITIVE AND OPEN EMISSIONS

EPA Science Inventory

Designing a chemical process normally includes aspects of economic and environmental disciplines. In this work we describe methods to quickly and easily evaluate the economics and potential environmental impacts of a process, with the hydrodealkylation of toluene as an example. ...

The Emergence of Open-Source Software in China

ERIC Educational Resources Information Center

Pan, Guohua; Bonk, Curtis J.

2007-01-01

The open-source software movement is gaining increasing momentum in China. Of the limited numbers of open-source software in China, "Red Flag Linux" stands out most strikingly, commanding 30 percent share of Chinese software market. Unlike the spontaneity of open-source movement in North America, open-source software development in…

A Study of Clinically Related Open Source Software Projects

PubMed Central

Hogarth, Michael A.; Turner, Stuart

2005-01-01

Open source software development has recently gained significant interest due to several successful mainstream open source projects. This methodology has been proposed as being similarly viable and beneficial in the clinical application domain as well. However, the clinical software development venue differs significantly from the mainstream software venue. Existing clinical open source projects have not been well characterized nor formally studied so the ‘fit’ of open source in this domain is largely unknown. In order to better understand the open source movement in the clinical application domain, we undertook a study of existing open source clinical projects. In this study we sought to characterize and classify existing clinical open source projects and to determine metrics for their viability. This study revealed several findings which we believe could guide the healthcare community in its quest for successful open source clinical software projects. PMID:16779056

Use of natural gas, methanol, and ethanol fuel emulsions as environmentally friendly energy carriers for mobile heat power plants

NASA Astrophysics Data System (ADS)

Likhanov, V. A.; Lopatin, O. P.

2017-12-01

The need for using environmentally friendly energy carriers for mobile heat power plants (HPPs) is grounded. Ecologically friendly sources of energy, such as natural gas as well as renewable methyl and ethyl alcohols, are investigated. In order to develop, determine, and optimize the composition of environmentally friendly energy carriers for an HPP, the latter has been tested when working on diesel fuel (DF), compressed natural gas (CNG), and methanol and ethanol fuel emulsions (MFE, EFE). It has been experimentally established that, for the application of environmentally friendly energy carriers for a 4Ch 11.0/12.5 diesel engine of a mobile fuel and power plant, it is necessary to maintain the following ratio of components when working on CNG: 80% gas and 20% DF primer portion. When working on an alcohol mixture, emulsions of the following composition were used: 25% alcohol (methanol or ethanol), 0.5% detergent-dispersant additive succinimide C-5A, 7% water, and 67.5% DF. When this diesel passed from oil DF to environmentally friendly energy sources, it allowed for the reduction of the content of exhaust gases (EG) (1) when working on CNG with recirculation of exhaust gases (EGR) (recirculation was used to eliminate the increased amount of nitric oxides by using CNG): carbon black by 5.8 times, carbon dioxide by 45.9%, and carbon monoxide by 23.8%; (2) when working on MFE: carbon black by 6.4 times, nitrogen oxides by 29.6%, carbon dioxide by 10.1%, and carbon oxide by 47.6%; (3) when working on EFE: carbon black by 4.8 times; nitrogen oxides by 40.3%, carbon dioxide by 26.6%, and carbon monoxide by 28.6%. The prospects of use of environmentally friendly energy carriers in diesels of mobile HPPs, such as natural gas, ethanol, and methanol, has been determined.

How Sources of Sexual Information Relate to Adolescents' Beliefs about Sex

ERIC Educational Resources Information Center

Bleakley, Amy; Hennessy, Michael; Fishbein, Martin; Jordan, Amy

2009-01-01

Objectives: To examine how sources of sexual information are associated with adolescents' behavioral, normative, and control beliefs about having sexual intercourse using the integrative model of behavior change. Methods: Survey data from a quota sample of 459 youth. Results: The most frequently reported sources were friends, teachers, mothers,…

Open Access, Open Source and Digital Libraries: A Current Trend in University Libraries around the World

ERIC Educational Resources Information Center

Krishnamurthy, M.

2008-01-01

Purpose: The purpose of this paper is to describe the open access and open source movement in the digital library world. Design/methodology/approach: A review of key developments in the open access and open source movement is provided. Findings: Open source software and open access to research findings are of great use to scholars in developing…

New Open-Source Version of FLORIS Released | News | NREL

Science.gov Websites

New Open-Source Version of FLORIS Released New Open-Source Version of FLORIS Released January 26 , 2018 National Renewable Energy Laboratory (NREL) researchers recently released an updated open-source simplified and documented. Because of the living, open-source nature of the newly updated utility, NREL

Marriage work in older couples: Disclosure of marital problems to spouses and friends over time.

PubMed

Jensen, Jakob F; Rauer, Amy J

2015-10-01

This study examined the frequency and impact of "marriage work" (MW), or the act of discussing marital problems with spouses and friends, among a sample of older married couples (N = 64). Using actor-partner interdependence models, we examined how turning to one's spouse and one's friend was linked to changes in both spouses' marital satisfaction and conflict 1 year later. We also investigated whether satisfaction and conflict predicted change in MW for older spouses. Both wives and husbands engaged in more MW with spouses than with friends, and only husbands' MW with spouses decreased over time. Wives' MW with spouses was associated with decreased marital satisfaction for husbands, whereas husbands' MW with spouses was linked with increased satisfaction for husbands. Furthermore, wives' MW with spouses predicted increases in wives' marital conflict over time. When examining effects in the opposite direction, wives' marital satisfaction predicted decreases in wives' MW with spouse. Husbands' satisfaction was linked with increases in wives' MW with spouses, increases in wives' MW with friends, and decreases in husbands' MW with friends. Finally, husbands' conflict predicted increases in husbands' MW with friends. Findings suggest that openly engaging in discussions of marital problems may not be as uniformly helpful for aging couples as it is for their younger counterparts. Given that many older adults tend to actively avoid conflictual interactions in an attempt to maximize emotional rewards, researchers and clinicians should note that traditional approaches to working through romantic conflict may not be ideal for aging couples. (c) 2015 APA, all rights reserved).

Effects of euthanasia on the bereaved family and friends: a cross sectional study

PubMed Central

Swarte, Nikkie B; van der Lee, Marije L; van der Bom, Johanna G; van den Bout, Jan; Heintz, A Peter M

2003-01-01

Objective To assess how euthanasia in terminally ill cancer patients affects the grief response of bereaved family and friends. Design Cross sectional study. Setting Tertiary referral centre for oncology patients in Utrecht, the Netherlands. Participants 189 bereaved family members and close friends of terminally ill cancer patients who died by euthanasia and 316 bereaved family members and close friends of comparable cancer patients who died a natural death between 1992 and 1999. Main outcome measures Symptoms of traumatic grief assessed by the inventory of traumatic grief, current feelings of grief assessed by the Texas revised inventory of grief, and post-traumatic stress reactions assessed by the impact of event scale. Results The bereaved family and friends of cancer patients who died by euthanasia had less traumatic grief symptoms (adjusted difference -5.29 (95% confidence interval -8.44 to -2.15)), less current feeling of grief (adjusted difference 2.93 (0.85 to 5.01)); and less post-traumatic stress reactions (adjusted difference -2.79 (-5.33 to -0.25)) than the family and friends of patients who died of natural causes. These differences were independent of other risk factors. Conclusions The bereaved family and friends of cancer patients who died by euthanasia coped better with respect to grief symptoms and post-traumatic stress reactions than the bereaved of comparable cancer patients who died a natural death. These results should not be interpreted as a plea for euthanasia, but as a plea for the same level of care and openness in all patients who are terminally ill. PMID:12881258

Using simple agent-based modeling to inform and enhance neighborhood walkability.

PubMed

Badland, Hannah; White, Marcus; Macaulay, Gus; Eagleson, Serryn; Mavoa, Suzanne; Pettit, Christopher; Giles-Corti, Billie

2013-12-11

Pedestrian-friendly neighborhoods with proximal destinations and services encourage walking and decrease car dependence, thereby contributing to more active and healthier communities. Proximity to key destinations and services is an important aspect of the urban design decision making process, particularly in areas adopting a transit-oriented development (TOD) approach to urban planning, whereby densification occurs within walking distance of transit nodes. Modeling destination access within neighborhoods has been limited to circular catchment buffers or more sophisticated network-buffers generated using geoprocessing routines within geographical information systems (GIS). Both circular and network-buffer catchment methods are problematic. Circular catchment models do not account for street networks, thus do not allow exploratory 'what-if' scenario modeling; and network-buffering functionality typically exists within proprietary GIS software, which can be costly and requires a high level of expertise to operate. This study sought to overcome these limitations by developing an open-source simple agent-based walkable catchment tool that can be used by researchers, urban designers, planners, and policy makers to test scenarios for improving neighborhood walkable catchments. A simplified version of an agent-based model was ported to a vector-based open source GIS web tool using data derived from the Australian Urban Research Infrastructure Network (AURIN). The tool was developed and tested with end-user stakeholder working group input. The resulting model has proven to be effective and flexible, allowing stakeholders to assess and optimize the walkability of neighborhood catchments around actual or potential nodes of interest (e.g., schools, public transport stops). Users can derive a range of metrics to compare different scenarios modeled. These include: catchment area versus circular buffer ratios; mean number of streets crossed; and modeling of different walking speeds and wait time at intersections. The tool has the capacity to influence planning and public health advocacy and practice, and by using open-access source software, it is available for use locally and internationally. There is also scope to extend this version of the tool from a simple to a complex model, which includes agents (i.e., simulated pedestrians) 'learning' and incorporating other environmental attributes that enhance walkability (e.g., residential density, mixed land use, traffic volume).

Best Friends: Alliances, Friend Ranking, and the MySpace Social Network.

PubMed

DeScioli, Peter; Kurzban, Robert; Koch, Elizabeth N; Liben-Nowell, David

2011-01-01

Like many topics of psychological research, the explanation for friendship is at once intuitive and difficult to address empirically. These difficulties worsen when one seeks, as we do, to go beyond "obvious" explanations ("humans are social creatures") to ask deeper questions, such as "What is the evolved function of human friendship?" In recent years, however, a new window into human behavior has opened as a growing fraction of people's social activity has moved online, leaving a wealth of digital traces behind. One example is a feature of the MySpace social network that allows millions of users to rank their "Top Friends." In this study, we collected over 10 million people's friendship decisions from MySpace to test predictions made by hypotheses about human friendship. We found particular support for the alliance hypothesis, which holds that human friendship is caused by cognitive systems that function to create alliances for potential disputes. Because an ally's support can be undermined by a stronger outside relationship, the alliance model predicts that people will prefer partners who rank them above other friends. Consistent with the alliance model, we found that an individual's choice of best friend in MySpace is strongly predicted by how partners rank that individual. © The Author(s) 2011.

Database Translator (DATALATOR) for Integrated Exploitation

DTIC Science & Technology

2010-10-31

Modelling in Information Systems Engineering. 2007, Berlin : Springer, pp. 39-58. 2. Arnon Rosenthal, Len Seligman . Pragmatics and Open Problems for Inter...2004, Vol. 2938 . 21. Ahuja, S., N. Carriero and D. Gelemte,. Linda and friends. IEEE Computer. August 1986, pp. 26- 32. 40 Next Generation Software

Educational Technology and the Open University.

ERIC Educational Resources Information Center

Sharples, Mike

1982-01-01

Care must be taken to select technology appropriate to the teaching task in distance education. Five principles of media selection are: increasing student-system interaction, matching the medium with the materials, reducing duplication, choosing the most direct channel, and developing user-friendly systems. Interactiveness and efficiency of…

Environmentally friendly elimination of moss from open-graded asphalt pavement.

DOT National Transportation Integrated Search

2011-04-01

Caltrans has discovered moss growing on U.S. Highway 101 in Del Norte and Humboldt counties, U.S. : Highway 199 near the Smith River and other roadways in Caltrans District 1. These areas are heavily : forested, and the heavy tree canopies shielding ...

PACKMAN-Net: A Distributed, Open-Access, and Scalable Network of User-Friendly Space Weather Stations

NASA Astrophysics Data System (ADS)

Zorzano, M.-P.; Martín-Torres, J.; Mathanlal, T.; Vakkada Ramachandran, A.; Ramirez-Luque, J.-A.

2018-04-01

The purpose of this work is to demonstrate the operability of a network of small-sized detectors of the PACKMAN instrument, operated simultaneously to provide real time cosmic ray and solar activity monitoring over the entire planet.

A problem-solving approach to nutrition education with Filipino mothers.

PubMed

Ticao, C J; Aboud, F E

1998-06-01

The study examined Filipino mothers' problem solving on issues related to child feeding, using a dyadic, peer-help approach. The participants were mothers of children under 6 yr of age from a village in the southern Philippines, where malnutrition among children is prevalent. Mothers were paired with a mutual friend (each nominated the other as a best friend) or a unilateral friend (only one nominated the other as a best friend) to discuss a feeding problem to which they initially gave similar solutions (agreed) and one to which they gave different solutions (disagreed). In the final step, they were asked to give privately the solutions they considered best for the problem. The number and quality of these final-step solutions were analyzed as a function of the friend relation, the level of initial agreement with their friend partner, and the source of the solution. Results indicated that the quantity and quality of solutions increased from before to after the dyadic discussion, especially among mothers paired with a mutual friend with whom they agreed. Most of their final-step solutions came from ones they themselves had generated during the discussion, not ones their friend partner had proposed. There was also evidence that high quality solutions were generated by mothers paired with a disagreeing unilateral friend. Implications for nutrition education concern the benefits of a peer-help, dyadic problem-solving approach, taking into account the role of a friend in facilitating a mother's production of new solutions to child feeding problems. The procedure may be used by health promoters who want to build capacities and self-reliance through collective problem solving.

Emerging late adolescent friendship networks and Big Five personality traits: a social network approach.

PubMed

Selfhout, Maarten; Burk, William; Branje, Susan; Denissen, Jaap; van Aken, Marcel; Meeus, Wim

2010-04-01

The current study focuses on the emergence of friendship networks among just-acquainted individuals, investigating the effects of Big Five personality traits on friendship selection processes. Sociometric nominations and self-ratings on personality traits were gathered from 205 late adolescents (mean age=19 years) at 5 time points during the first year of university. SIENA, a novel multilevel statistical procedure for social network analysis, was used to examine effects of Big Five traits on friendship selection. Results indicated that friendship networks between just-acquainted individuals became increasingly more cohesive within the first 3 months and then stabilized. Whereas individuals high on Extraversion tended to select more friends than those low on this trait, individuals high on Agreeableness tended to be selected more as friends. In addition, individuals tended to select friends with similar levels of Agreeableness, Extraversion, and Openness.

Combining high biodiversity with high yields in tropical agroforests.

PubMed

Clough, Yann; Barkmann, Jan; Juhrbandt, Jana; Kessler, Michael; Wanger, Thomas Cherico; Anshary, Alam; Buchori, Damayanti; Cicuzza, Daniele; Darras, Kevin; Putra, Dadang Dwi; Erasmi, Stefan; Pitopang, Ramadhanil; Schmidt, Carsten; Schulze, Christian H; Seidel, Dominik; Steffan-Dewenter, Ingolf; Stenchly, Kathrin; Vidal, Stefan; Weist, Maria; Wielgoss, Arno Christian; Tscharntke, Teja

2011-05-17

Local and landscape-scale agricultural intensification is a major driver of global biodiversity loss. Controversially discussed solutions include wildlife-friendly farming or combining high-intensity farming with land-sparing for nature. Here, we integrate biodiversity and crop productivity data for smallholder cacao in Indonesia to exemplify for tropical agroforests that there is little relationship between yield and biodiversity under current management, opening substantial opportunities for wildlife-friendly management. Species richness of trees, fungi, invertebrates, and vertebrates did not decrease with yield. Moderate shade, adequate labor, and input level can be combined with a complex habitat structure to provide high biodiversity as well as high yields. Although livelihood impacts are held up as a major obstacle for wildlife-friendly farming in the tropics, our results suggest that in some situations, agroforests can be designed to optimize both biodiversity and crop production benefits without adding pressure to convert natural habitat to farmland.

Combining high biodiversity with high yields in tropical agroforests

PubMed Central

Clough, Yann; Barkmann, Jan; Juhrbandt, Jana; Kessler, Michael; Wanger, Thomas Cherico; Anshary, Alam; Buchori, Damayanti; Cicuzza, Daniele; Darras, Kevin; Putra, Dadang Dwi; Erasmi, Stefan; Pitopang, Ramadhanil; Schmidt, Carsten; Schulze, Christian H.; Seidel, Dominik; Steffan-Dewenter, Ingolf; Stenchly, Kathrin; Vidal, Stefan; Weist, Maria; Wielgoss, Arno Christian; Tscharntke, Teja

2011-01-01

Local and landscape-scale agricultural intensification is a major driver of global biodiversity loss. Controversially discussed solutions include wildlife-friendly farming or combining high-intensity farming with land-sparing for nature. Here, we integrate biodiversity and crop productivity data for smallholder cacao in Indonesia to exemplify for tropical agroforests that there is little relationship between yield and biodiversity under current management, opening substantial opportunities for wildlife-friendly management. Species richness of trees, fungi, invertebrates, and vertebrates did not decrease with yield. Moderate shade, adequate labor, and input level can be combined with a complex habitat structure to provide high biodiversity as well as high yields. Although livelihood impacts are held up as a major obstacle for wildlife-friendly farming in the tropics, our results suggest that in some situations, agroforests can be designed to optimize both biodiversity and crop production benefits without adding pressure to convert natural habitat to farmland. PMID:21536873

Genomes to natural products PRediction Informatics for Secondary Metabolomes (PRISM).

PubMed

Skinnider, Michael A; Dejong, Chris A; Rees, Philip N; Johnston, Chad W; Li, Haoxin; Webster, Andrew L H; Wyatt, Morgan A; Magarvey, Nathan A

2015-11-16

Microbial natural products are an invaluable source of evolved bioactive small molecules and pharmaceutical agents. Next-generation and metagenomic sequencing indicates untapped genomic potential, yet high rediscovery rates of known metabolites increasingly frustrate conventional natural product screening programs. New methods to connect biosynthetic gene clusters to novel chemical scaffolds are therefore critical to enable the targeted discovery of genetically encoded natural products. Here, we present PRISM, a computational resource for the identification of biosynthetic gene clusters, prediction of genetically encoded nonribosomal peptides and type I and II polyketides, and bio- and cheminformatic dereplication of known natural products. PRISM implements novel algorithms which render it uniquely capable of predicting type II polyketides, deoxygenated sugars, and starter units, making it a comprehensive genome-guided chemical structure prediction engine. A library of 57 tailoring reactions is leveraged for combinatorial scaffold library generation when multiple potential substrates are consistent with biosynthetic logic. We compare the accuracy of PRISM to existing genomic analysis platforms. PRISM is an open-source, user-friendly web application available at http://magarveylab.ca/prism/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Impact of the social networking applications for health information management for patients and physicians.

PubMed

Sahama, Tony; Liang, Jian; Iannella, Renato

2012-01-01

Most social network users hold more than one social network account and utilize them in different ways depending on the digital context. For example, friendly chat on Facebook, professional discussion on LinkedIn, and health information exchange on PatientsLikeMe. Thus many web users need to manage many disparate profiles across many distributed online sources. Maintaining these profiles is cumbersome, time consuming, inefficient, and leads to lost opportunity. In this paper we propose a framework for multiple profile management of online social networks and showcase a demonstrator utilising an open source platform. The result of the research enables a user to create and manage an integrated profile and share/synchronise their profiles with their social networks. A number of use cases were created to capture the functional requirements and describe the interactions between users and the online services. An innovative application of this project is in public health informatics. We utilize the prototype to examine how the framework can benefit patients and physicians. The framework can greatly enhance health information management for patients and more importantly offer a more comprehensive personal health overview of patients to physicians.

Thermoformed protein based composites in presence of organic acids

USDA-ARS?s Scientific Manuscript database

World industrialization has generated substantial quantities of petroleum-based plastics over many years, which are non biodegradable. There is a growing demand for the use of renewable agricultural sources to develop eco-friendly biobased composites. Agriculture-sourced proteins and starches are b...

Evaluation of the free, open source software WordPress as electronic portfolio system in undergraduate medical education.

PubMed

Avila, Javier; Sostmann, Kai; Breckwoldt, Jan; Peters, Harm

2016-06-03

Electronic portfolios (ePortfolios) are used to document and support learning activities. E-portfolios with mobile capabilities allow even more flexibility. However, the development or acquisition of ePortfolio software is often costly, and at the same time, commercially available systems may not sufficiently fit the institution's needs. The aim of this study was to design and evaluate an ePortfolio system with mobile capabilities using a commercially free and open source software solution. We created an online ePortfolio environment using the blogging software WordPress based on reported capability features of such software by a qualitative weight and sum method. Technical implementation and usability were evaluated by 25 medical students during their clinical training by quantitative and qualitative means using online questionnaires and focus groups. The WordPress ePortfolio environment allowed students a broad spectrum of activities - often documented via mobile devices - like collection of multimedia evidences, posting reflections, messaging, web publishing, ePortfolio searches, collaborative learning, knowledge management in a content management system including a wiki and RSS feeds, and the use of aid tools for studying. The students' experience with WordPress revealed a few technical problems, and this report provides workarounds. The WordPress ePortfolio was rated positively by the students as a content management system (67 % of the students), for exchange with other students (74 %), as a note pad for reflections (53 %) and for its potential as an information source for assessment (48 %) and exchange with a mentor (68 %). On the negative side, 74 % of the students in this pilot study did not find it easy to get started with the system, and 63 % rated the ePortfolio as not being user-friendly. Qualitative analysis indicated a need for more introductory information and training. It is possible to build an advanced ePortfolio system with mobile capabilities with the free and open source software WordPress. This allows institutions without proprietary software to build a sophisticated ePortfolio system adapted to their needs with relatively few resources. The implementation of WordPress should be accompanied by introductory courses in the use of the software and its apps in order to facilitate its usability.

The successes and challenges of open-source biopharmaceutical innovation.

PubMed

Allarakhia, Minna

2014-05-01

Increasingly, open-source-based alliances seek to provide broad access to data, research-based tools, preclinical samples and downstream compounds. The challenge is how to create value from open-source biopharmaceutical innovation. This value creation may occur via transparency and usage of data across the biopharmaceutical value chain as stakeholders move dynamically between open source and open innovation. In this article, several examples are used to trace the evolution of biopharmaceutical open-source initiatives. The article specifically discusses the technological challenges associated with the integration and standardization of big data; the human capacity development challenges associated with skill development around big data usage; and the data-material access challenge associated with data and material access and usage rights, particularly as the boundary between open source and open innovation becomes more fluid. It is the author's opinion that the assessment of when and how value creation will occur, through open-source biopharmaceutical innovation, is paramount. The key is to determine the metrics of value creation and the necessary technological, educational and legal frameworks to support the downstream outcomes of now big data-based open-source initiatives. The continued focus on the early-stage value creation is not advisable. Instead, it would be more advisable to adopt an approach where stakeholders transform open-source initiatives into open-source discovery, crowdsourcing and open product development partnerships on the same platform.

Friendship Repertoires and Care Arrangement: A Praxeological Approach.

PubMed

Hahmann, Julia

2017-01-01

Friends are important companions and serve as sources for diverse dimensions of social support, including elderly care. Rather than researching populations that have already established care arrangements including friends, the author seeks to understand relationship systems with a focus on the inner logic friendship to consequently describe and understand involved care arrangements, be it with family members or friends. To illustrate the diversity of friendship repertoires, qualitative interviews with older adult Germans are analyzed regarding cognitive concepts of friendships in contrast to familiar ties as well as social practices around relationship systems. While some repertoires successfully include chosen ties in their care arrangements, others not only focus on family, they do not wish to receive care from friends. The article's praxeological approach highlights the need to reflect habitual differences when thinking about elderly informal care arrangements. © The Author(s) 2016.

JMS: An Open Source Workflow Management System and Web-Based Cluster Front-End for High Performance Computing.

PubMed

Brown, David K; Penkler, David L; Musyoka, Thommas M; Bishop, Özlem Tastan

2015-01-01

Complex computational pipelines are becoming a staple of modern scientific research. Often these pipelines are resource intensive and require days of computing time. In such cases, it makes sense to run them over high performance computing (HPC) clusters where they can take advantage of the aggregated resources of many powerful computers. In addition to this, researchers often want to integrate their workflows into their own web servers. In these cases, software is needed to manage the submission of jobs from the web interface to the cluster and then return the results once the job has finished executing. We have developed the Job Management System (JMS), a workflow management system and web interface for high performance computing (HPC). JMS provides users with a user-friendly web interface for creating complex workflows with multiple stages. It integrates this workflow functionality with the resource manager, a tool that is used to control and manage batch jobs on HPC clusters. As such, JMS combines workflow management functionality with cluster administration functionality. In addition, JMS provides developer tools including a code editor and the ability to version tools and scripts. JMS can be used by researchers from any field to build and run complex computational pipelines and provides functionality to include these pipelines in external interfaces. JMS is currently being used to house a number of bioinformatics pipelines at the Research Unit in Bioinformatics (RUBi) at Rhodes University. JMS is an open-source project and is freely available at https://github.com/RUBi-ZA/JMS.

GeolOkit 1.0: a new Open Source, Cross-Platform software for geological data visualization in Google Earth environment

NASA Astrophysics Data System (ADS)

Triantafyllou, Antoine; Bastin, Christophe; Watlet, Arnaud

2016-04-01

GIS software suites are today's essential tools to gather and visualise geological data, to apply spatial and temporal analysis and in fine, to create and share interactive maps for further geosciences' investigations. For these purposes, we developed GeolOkit: an open-source, freeware and lightweight software, written in Python, a high-level, cross-platform programming language. GeolOkit software is accessible through a graphical user interface, designed to run in parallel with Google Earth. It is a super user-friendly toolbox that allows 'geo-users' to import their raw data (e.g. GPS, sample locations, structural data, field pictures, maps), to use fast data analysis tools and to plot these one into Google Earth environment using KML code. This workflow requires no need of any third party software, except Google Earth itself. GeolOkit comes with large number of geosciences' labels, symbols, colours and placemarks and may process : (i) multi-points data, (ii) contours via several interpolations methods, (iii) discrete planar and linear structural data in 2D or 3D supporting large range of structures input format, (iv) clustered stereonets and rose diagram, (v) drawn cross-sections as vertical sections, (vi) georeferenced maps and vectors, (vii) field pictures using either geo-tracking metadata from a camera built-in GPS module, or the same-day track of an external GPS. We are looking for you to discover all the functionalities of GeolOkit software. As this project is under development, we are definitely looking to discussions regarding your proper needs, your ideas and contributions to GeolOkit project.

Microbe-ID: an open source toolbox for microbial genotyping and species identification.

PubMed

Tabima, Javier F; Everhart, Sydney E; Larsen, Meredith M; Weisberg, Alexandra J; Kamvar, Zhian N; Tancos, Matthew A; Smart, Christine D; Chang, Jeff H; Grünwald, Niklaus J

2016-01-01

Development of tools to identify species, genotypes, or novel strains of invasive organisms is critical for monitoring emergence and implementing rapid response measures. Molecular markers, although critical to identifying species or genotypes, require bioinformatic tools for analysis. However, user-friendly analytical tools for fast identification are not readily available. To address this need, we created a web-based set of applications called Microbe-ID that allow for customizing a toolbox for rapid species identification and strain genotyping using any genetic markers of choice. Two components of Microbe-ID, named Sequence-ID and Genotype-ID, implement species and genotype identification, respectively. Sequence-ID allows identification of species by using BLAST to query sequences for any locus of interest against a custom reference sequence database. Genotype-ID allows placement of an unknown multilocus marker in either a minimum spanning network or dendrogram with bootstrap support from a user-created reference database. Microbe-ID can be used for identification of any organism based on nucleotide sequences or any molecular marker type and several examples are provided. We created a public website for demonstration purposes called Microbe-ID (microbe-id.org) and provided a working implementation for the genus Phytophthora (phytophthora-id.org). In Phytophthora-ID, the Sequence-ID application allows identification based on ITS or cox spacer sequences. Genotype-ID groups individuals into clonal lineages based on simple sequence repeat (SSR) markers for the two invasive plant pathogen species P. infestans and P. ramorum. All code is open source and available on github and CRAN. Instructions for installation and use are provided at https://github.com/grunwaldlab/Microbe-ID.

SIGNUM: A Matlab, TIN-based landscape evolution model

NASA Astrophysics Data System (ADS)

Refice, A.; Giachetta, E.; Capolongo, D.

2012-08-01

Several numerical landscape evolution models (LEMs) have been developed to date, and many are available as open source codes. Most are written in efficient programming languages such as Fortran or C, but often require additional code efforts to plug in to more user-friendly data analysis and/or visualization tools to ease interpretation and scientific insight. In this paper, we present an effort to port a common core of accepted physical principles governing landscape evolution directly into a high-level language and data analysis environment such as Matlab. SIGNUM (acronym for Simple Integrated Geomorphological Numerical Model) is an independent and self-contained Matlab, TIN-based landscape evolution model, built to simulate topography development at various space and time scales. SIGNUM is presently capable of simulating hillslope processes such as linear and nonlinear diffusion, fluvial incision into bedrock, spatially varying surface uplift which can be used to simulate changes in base level, thrust and faulting, as well as effects of climate changes. Although based on accepted and well-known processes and algorithms in its present version, it is built with a modular structure, which allows to easily modify and upgrade the simulated physical processes to suite virtually any user needs. The code is conceived as an open-source project, and is thus an ideal tool for both research and didactic purposes, thanks to the high-level nature of the Matlab environment and its popularity among the scientific community. In this paper the simulation code is presented together with some simple examples of surface evolution, and guidelines for development of new modules and algorithms are proposed.

JMS: An Open Source Workflow Management System and Web-Based Cluster Front-End for High Performance Computing

PubMed Central

Brown, David K.; Penkler, David L.; Musyoka, Thommas M.; Bishop, Özlem Tastan

2015-01-01

Complex computational pipelines are becoming a staple of modern scientific research. Often these pipelines are resource intensive and require days of computing time. In such cases, it makes sense to run them over high performance computing (HPC) clusters where they can take advantage of the aggregated resources of many powerful computers. In addition to this, researchers often want to integrate their workflows into their own web servers. In these cases, software is needed to manage the submission of jobs from the web interface to the cluster and then return the results once the job has finished executing. We have developed the Job Management System (JMS), a workflow management system and web interface for high performance computing (HPC). JMS provides users with a user-friendly web interface for creating complex workflows with multiple stages. It integrates this workflow functionality with the resource manager, a tool that is used to control and manage batch jobs on HPC clusters. As such, JMS combines workflow management functionality with cluster administration functionality. In addition, JMS provides developer tools including a code editor and the ability to version tools and scripts. JMS can be used by researchers from any field to build and run complex computational pipelines and provides functionality to include these pipelines in external interfaces. JMS is currently being used to house a number of bioinformatics pipelines at the Research Unit in Bioinformatics (RUBi) at Rhodes University. JMS is an open-source project and is freely available at https://github.com/RUBi-ZA/JMS. PMID:26280450

Development of bio-sourced binder to metal injection moulding

NASA Astrophysics Data System (ADS)

Royer, Alexandre; Barrière, Thierry; Gelin, Jean-Claude

2016-10-01

In the MIM process the binder play the most important role. It provides fluidity of the feedstock mixture for injection molding and adhesion of the powder to keep the molded shape. The binder must provide strength and cohesion for the molded part, must be easy to be removed from the molded part, and must be the recyclable, environmentally friendly and economical ones. The goal of this study is to develop a binder environmentally friendly. For this, a study of formulation based on polyethylene glycol, because of is water debinding properties, was made. Polylactic acid and Polyhydroxyalkanoates were investigated as bio sourced polymers. The chemical, miscibility and rheological behavior of the binder formulation were investigated.

CloudDOE: a user-friendly tool for deploying Hadoop clouds and analyzing high-throughput sequencing data with MapReduce.

PubMed

Chung, Wei-Chun; Chen, Chien-Chih; Ho, Jan-Ming; Lin, Chung-Yen; Hsu, Wen-Lian; Wang, Yu-Chun; Lee, D T; Lai, Feipei; Huang, Chih-Wei; Chang, Yu-Jung

2014-01-01

Explosive growth of next-generation sequencing data has resulted in ultra-large-scale data sets and ensuing computational problems. Cloud computing provides an on-demand and scalable environment for large-scale data analysis. Using a MapReduce framework, data and workload can be distributed via a network to computers in the cloud to substantially reduce computational latency. Hadoop/MapReduce has been successfully adopted in bioinformatics for genome assembly, mapping reads to genomes, and finding single nucleotide polymorphisms. Major cloud providers offer Hadoop cloud services to their users. However, it remains technically challenging to deploy a Hadoop cloud for those who prefer to run MapReduce programs in a cluster without built-in Hadoop/MapReduce. We present CloudDOE, a platform-independent software package implemented in Java. CloudDOE encapsulates technical details behind a user-friendly graphical interface, thus liberating scientists from having to perform complicated operational procedures. Users are guided through the user interface to deploy a Hadoop cloud within in-house computing environments and to run applications specifically targeted for bioinformatics, including CloudBurst, CloudBrush, and CloudRS. One may also use CloudDOE on top of a public cloud. CloudDOE consists of three wizards, i.e., Deploy, Operate, and Extend wizards. Deploy wizard is designed to aid the system administrator to deploy a Hadoop cloud. It installs Java runtime environment version 1.6 and Hadoop version 0.20.203, and initiates the service automatically. Operate wizard allows the user to run a MapReduce application on the dashboard list. To extend the dashboard list, the administrator may install a new MapReduce application using Extend wizard. CloudDOE is a user-friendly tool for deploying a Hadoop cloud. Its smart wizards substantially reduce the complexity and costs of deployment, execution, enhancement, and management. Interested users may collaborate to improve the source code of CloudDOE to further incorporate more MapReduce bioinformatics tools into CloudDOE and support next-generation big data open source tools, e.g., Hadoop BigTop and Spark. CloudDOE is distributed under Apache License 2.0 and is freely available at http://clouddoe.iis.sinica.edu.tw/.

CloudDOE: A User-Friendly Tool for Deploying Hadoop Clouds and Analyzing High-Throughput Sequencing Data with MapReduce

PubMed Central

Chung, Wei-Chun; Chen, Chien-Chih; Ho, Jan-Ming; Lin, Chung-Yen; Hsu, Wen-Lian; Wang, Yu-Chun; Lee, D. T.; Lai, Feipei; Huang, Chih-Wei; Chang, Yu-Jung

2014-01-01

Background Explosive growth of next-generation sequencing data has resulted in ultra-large-scale data sets and ensuing computational problems. Cloud computing provides an on-demand and scalable environment for large-scale data analysis. Using a MapReduce framework, data and workload can be distributed via a network to computers in the cloud to substantially reduce computational latency. Hadoop/MapReduce has been successfully adopted in bioinformatics for genome assembly, mapping reads to genomes, and finding single nucleotide polymorphisms. Major cloud providers offer Hadoop cloud services to their users. However, it remains technically challenging to deploy a Hadoop cloud for those who prefer to run MapReduce programs in a cluster without built-in Hadoop/MapReduce. Results We present CloudDOE, a platform-independent software package implemented in Java. CloudDOE encapsulates technical details behind a user-friendly graphical interface, thus liberating scientists from having to perform complicated operational procedures. Users are guided through the user interface to deploy a Hadoop cloud within in-house computing environments and to run applications specifically targeted for bioinformatics, including CloudBurst, CloudBrush, and CloudRS. One may also use CloudDOE on top of a public cloud. CloudDOE consists of three wizards, i.e., Deploy, Operate, and Extend wizards. Deploy wizard is designed to aid the system administrator to deploy a Hadoop cloud. It installs Java runtime environment version 1.6 and Hadoop version 0.20.203, and initiates the service automatically. Operate wizard allows the user to run a MapReduce application on the dashboard list. To extend the dashboard list, the administrator may install a new MapReduce application using Extend wizard. Conclusions CloudDOE is a user-friendly tool for deploying a Hadoop cloud. Its smart wizards substantially reduce the complexity and costs of deployment, execution, enhancement, and management. Interested users may collaborate to improve the source code of CloudDOE to further incorporate more MapReduce bioinformatics tools into CloudDOE and support next-generation big data open source tools, e.g., Hadoop BigTop and Spark. Availability: CloudDOE is distributed under Apache License 2.0 and is freely available at http://clouddoe.iis.sinica.edu.tw/. PMID:24897343

Influence of parents and friends on children's and adolescents' food intake and food selection.

PubMed

Salvy, Sarah-Jeanne; Elmo, Alison; Nitecki, Lauren A; Kluczynski, Melissa A; Roemmich, James N

2011-01-01

The influence of parents versus friends on youths' eating behavior has not been directly compared, and little is known about the developmental effects of social influences on their eating behavior. The objective was to compare the effects of mothers and friends on children's and adolescents' energy intake from sandwiches and from healthy and unhealthy snacks and dessert foods. Twenty-three children (ages 5-7 y) and 27 adolescents (ages 13-15 y) ate a meal with their mother on one occasion and with a same-sex friend on another occasion. Male and female children consumed less energy from unhealthy snacks when in the presence of their mothers than when in the company of their friends. Conversely, female adolescents consumed less energy from unhealthy snacks and more energy from healthy snacks when they were with their friends than when with their mothers. Food selection is differentially influenced by the source of social influence and the age and sex of the child. Parents may act as an inhibitory influence on unhealthy eating for younger children. Adolescent girls may try to convey a good impression of healthy eating when eating with same-sex friends, but the eating habits of teenage boys are not as influenced by the social context. This trial is registered at clinicaltrials.gov as NCT00875576.

Information Source Preference as a Function of Physical and Psychological Distance from the Information Object.

ERIC Educational Resources Information Center

Paisley, William J.

In this study data were collected on "major" and "most helpful" sources used by high school students (incoming Syracuse University freshmen at the time of data collection) as they gathered information about Syracuse and other colleges. Sources were both interpersonal (family, friends, high school personnel, college representatives) and impersonal…

[Microbial "friend-foe" identification in human intestine microsymbiocenosis].

PubMed

Bukharin, O V; Petrunova, N B

2011-01-01

Development of methodical approach of evaluation of microbial "friend-foe" identification in human intestine microsymbiocenosis. 9 bifidobacteria cultures (dominants) and 18 opportunistic microorganism strains (associants) isolated from patients during examination for intestine dysbiosis and identified by conventional methods were used. Evaluation of microbial "friend-foe" identification in microsymbiocenosis was performed by author developed technique that is based on determination of growth factors (GF), anti-lysozyme activity (ALA) and formation of biofilms (BFF) of associants co-incubated with exometabolites of dominants. GF, ALA, BFF were studied photometrically (Bukharin O.V., 1999, 2009; O'Toole G.A., 2000). The data were statistically analyzed by Fisher-Student criteria. The detected opposite (increase/reduction) phenomenon of the "dominant-associant" pair allowed realization of the "friend-foe" identification in microsymbiocenosis. Associants (E. coli and Enterococcus faecium) were "friend" species, in which bifidobacteria exometabolites did not change growth properties and stimulated ALA (by 17,5--32%) and BFF (by 25 - 39%). Associants (Escherichia coli, Klebsiella pneumoniae, Staphylococcus aureus, Candida albicans) were "foe" microsymbiont species, in which bifidoflora exometabolites decreased GF (by 20,7--68%), ALA (by 22,7--54%) and BFF (by 22,5 --39%). Indigenous microflora during microsymbiocenosis formation can participate in "friend-foe" identification, the basis of which is determined by microsymbiont exometabolites. The data obtained open a perspective of understanding mechanisms of intramicrobial interactions and can be used for both diagnostics and optimal selection of "candidates" during creation of new probiotics and synbiotics.

Dr Google, porn and friend-of-a-friend: where are young men really getting their sexual health information?

PubMed

Litras, Amy; Latreille, Sarah; Temple-Smith, Meredith

2015-11-01

Background Young men are vulnerable when it comes to sexual health. They attend the general practitioner (GP) less often than females and are less likely to be offered testing for sexually transmissible infections. Access to accurate health information and education is a cornerstone of primary prevention, yet we know very little about how, where and why young people obtain information about sexual health. One-on-one semi-structured interviews were conducted with 35 male students aged 16-19 years from two Victorian educational institutions for trade skills until data saturation was reached. Interviews were audio-recorded, transcribed and thematically analysed. The young men were poorly informed about sexual health. Their existing knowledge mainly came from school-based sexual health education, which while valued, was generally poorly recalled and provided only a narrow scope of physiological information. Young men seek sexual health information from various sources including family, the Internet, friends and pornography, with information from the latter three sources perceived as unreliable. GPs were seen as a source of trust-worthy information but were not accessed for this purpose due to embarrassment. Young men preferred the GP to initiate such conversations. A desire for privacy and avoidance of embarrassment heavily influenced young men's preferences and behaviours in relation to sexual health information seeking. The current available sources of sexual health information for young men are failing to meet their needs. Results identify potential improvements to school-based sexual education and online resources, and describe a need for innovative technology-based sources of sexual health education.

Open for Business

ERIC Educational Resources Information Center

Voyles, Bennett

2007-01-01

People know about the Sakai Project (open source course management system); they may even know about Kuali (open source financials). So, what is the next wave in open source software? This article discusses business intelligence (BI) systems. Though open source BI may still be only a rumor in most campus IT departments, some brave early adopters…

MilxXplore: a web-based system to explore large imaging datasets

PubMed Central

Bourgeat, P; Dore, V; Villemagne, V L; Rowe, C C; Salvado, O; Fripp, J

2013-01-01

Objective As large-scale medical imaging studies are becoming more common, there is an increasing reliance on automated software to extract quantitative information from these images. As the size of the cohorts keeps increasing with large studies, there is a also a need for tools that allow results from automated image processing and analysis to be presented in a way that enables fast and efficient quality checking, tagging and reporting on cases in which automatic processing failed or was problematic. Materials and methods MilxXplore is an open source visualization platform, which provides an interface to navigate and explore imaging data in a web browser, giving the end user the opportunity to perform quality control and reporting in a user friendly, collaborative and efficient way. Discussion Compared to existing software solutions that often provide an overview of the results at the subject's level, MilxXplore pools the results of individual subjects and time points together, allowing easy and efficient navigation and browsing through the different acquisitions of a subject over time, and comparing the results against the rest of the population. Conclusions MilxXplore is fast, flexible and allows remote quality checks of processed imaging data, facilitating data sharing and collaboration across multiple locations, and can be easily integrated into a cloud computing pipeline. With the growing trend of open data and open science, such a tool will become increasingly important to share and publish results of imaging analysis. PMID:23775173

The forum as a friend: parental mental illness and communication on open Internet forums.

PubMed

Widemalm, My; Hjärthag, Fredrik

2015-10-01

The aim of this study was to identify how daughters or sons to parents suffering from mental illness perceive their situation. The objective was to provide new knowledge based on what they communicate on open Internet forums. The sample consisted of forum posts written by individuals who reported that they had mentally ill parents. Data collection comprised 301 comments from 35 forum threads on 5 different Swedish Internet forums, and predetermined inclusion criteria were used. Data were analyzed qualitatively using thematic analysis. The analysis generated four themes: "Caregiver burden," "Knowledge seeking," "Support from the forum," and "Frustration and powerlessness over health care." The results showed that parents' mental illness affected the forum writers on several levels, and they often felt stigmatized. The writers often lacked knowledge of their parents' mental illness and sought out Internet forums for information and support from peers in similar situations. The psychiatric care given to the parents was a source of dissatisfaction among the forum writers, who often felt that their parents did not receive adequate care. This study shows that fear of stigmatization and perceived lack of care and support caused forum writers to anonymously seek out Internet forums for information and support from others with similar experiences. The role of social support and the attractiveness of anonymity and availability typical for open Internet forums ought to be considered by health care professionals and researchers when developing new ways for providing support for children or adolescents with a mentally ill parent.

Predictors of Job Search Intensity among College Graduates

ERIC Educational Resources Information Center

Tziner, Aharon; Vered, Efrat; Ophir, Limor

2004-01-01

This study examined the connection between personality traits (extraversion, conscientiousness, openness) and two strategies for job search: networking (family, friends, etc.) and general search (want ads, employment agencies), making use of Costa and McCrae's five-factor model of personality dimensions. The relations between the two strategies…

Undergraduate Researchers and the Poster Session

ERIC Educational Resources Information Center

Johnson, Gail; Green, Raymond

2007-01-01

Undergraduates presented original research in classroom poster sessions open to students, faculty, and friends. We assessed the reaction of the students to the experience and their reported change in their interest in presenting at conferences. Students enjoyed the poster session experience and indicated they preferred this method over other…

Making Critical Friends

ERIC Educational Resources Information Center

Raven, Sara; Klein, Vanessa; Namdar, Bahadir

2016-01-01

Argumentation has long been promoted as a core scientific practice in which students should engage, yet science classrooms still often omit it. One remedy is to incorporate socioscientific issues (SSIs) in the curricula. SSIs are open-ended and complex, typically subject to multiple perspectives and solutions. These issues, influenced by science…

To friend or not to friend: the use of social media in clinical oncology.

PubMed

Wiener, Lori; Crum, Caroline; Grady, Christine; Merchant, Melinda

2012-03-01

Online social networking has replaced more traditional methods of personal and professional communication in many segments of society today. The wide reach and immediacy of social media facilitate dissemination of knowledge in advocacy and cancer education, but the usefulness of social media in personal relationships between patients and providers is still unclear. Although professional guidelines regarding e-mail communication may be relevant to social media, the inherent openness in social networks creates potential boundary and privacy issues in the provider-patient context. This commentary seeks to increase provider awareness of unique issues and challenges raised by the integration of social networking into oncology communications.

Influence of information sources on hepatitis B screening behavior and relevant psychosocial factors among Asian immigrants.

PubMed

Tanaka, Miho; Strong, Carol; Lee, Sunmin; Juon, Hee-Soon

2013-08-01

This study examines how different information sources relate to Health Belief Model constructs, hepatitis B virus (HBV) knowledge, and HBV screening. The Maryland Asian American Liver Cancer Education Program administered a survey of 877 Asian immigrants. The most common sources of information identified by the multiple-answer questions were newspapers (39.8 %), physicians (39.3 %), friends (33.8 %), TV (31.7 %), and the Internet (29.5 %). Path analyses-controlling for age, sex, educational level, English proficiency, proportion of life in U.S., health insurance coverage, and family history of HBV infection-showed that learning about HBV from physicians had the strongest direct effect; friends had a marginal indirect effect. Perceived risk, benefits, and severity played limited roles in mediation effects. Path analysis results differed by ethnicity. Physician-based HBV screening intervention would be effective, but should be complemented with community health campaigns through popular information sources for the uninsured.

ALPHACAL: A new user-friendly tool for the calibration of alpha-particle sources.

PubMed

Timón, A Fernández; Vargas, M Jurado; Gallardo, P Álvarez; Sánchez-Oro, J; Peralta, L

2018-05-01

In this work, we present and describe the program ALPHACAL, specifically developed for the calibration of alpha-particle sources. It is therefore more user-friendly and less time-consuming than multipurpose codes developed for a wide range of applications. The program is based on the recently developed code AlfaMC, which simulates specifically the transport of alpha particles. Both cylindrical and point sources mounted on the surface of polished backings can be simulated, as is the convention in experimental measurements of alpha-particle sources. In addition to the efficiency calculation and determination of the backscattering coefficient, some additional tools are available to the user, like the visualization of energy spectrum, use of energy cut-off or low-energy tail corrections. ALPHACAL has been implemented in C++ language using QT library, so it is available for Windows, MacOs and Linux platforms. It is free and can be provided under request to the authors. Copyright © 2018 Elsevier Ltd. All rights reserved.

Information gathering and technology use among low-income minority men at risk for prostate cancer.

PubMed

Song, Hayeon; Cramer, Emily M; McRoy, Susan

2015-05-01

Health communication researchers, public health workers, and health professionals must learn more about the health information-gathering behavior of low-income minority men at risk for prostate cancer in order to share information effectively with the population. In collaboration with the Milwaukee Health Department Men's Health Referral Network, a total of 90 low-income adult men were recruited to complete a survey gauging information sources, seeking behavior, use of technology, as well as prostate cancer awareness and screening behavior. Results indicated participants primarily relied on health professionals, family, and friends for information about general issues of health as well as prostate cancer. The Internet was the least relied on source of information. A hierarchical regression indicated interpersonal information sources such as family or friends to be the only significant predictor enhancing prostate cancer awareness, controlling for other sources of information. Prostate screening behaviors were predicted by reliance on not only medical professionals but also the Internet. Practical implications of the study are discussed. © The Author(s) 2014.

The Commercial Open Source Business Model

NASA Astrophysics Data System (ADS)

Riehle, Dirk

Commercial open source software projects are open source software projects that are owned by a single firm that derives a direct and significant revenue stream from the software. Commercial open source at first glance represents an economic paradox: How can a firm earn money if it is making its product available for free as open source? This paper presents the core properties of com mercial open source business models and discusses how they work. Using a commercial open source approach, firms can get to market faster with a superior product at lower cost than possible for traditional competitors. The paper shows how these benefits accrue from an engaged and self-supporting user community. Lacking any prior comprehensive reference, this paper is based on an analysis of public statements by practitioners of commercial open source. It forges the various anecdotes into a coherent description of revenue generation strategies and relevant business functions.

The Water SWITCH-ON Spatial Information Platform (SIP)

NASA Astrophysics Data System (ADS)

Sala Calero, J., Sr.; Boot, G., Sr.; Dihé, P., Sr.; Arheimer, B.

2017-12-01

The amount of hydrological open data is continually growing and providing opportunities to the scientific community. Although the existing data portals (GEOSS Portal, INSPIRE community geoportal and others) enable access to open data, many users still find browsing through them difficult. Moreover, the time spent on gathering and preparing data usually is more significant than the time spent on the experiment itself. Thus, any improvement on searching, understanding, accessing or using open data is greatly beneficial. The Spatial Information Platform (SIP) has been developed to tackle these issues within the SWITCH-ON European Commission funded FP7 project. The SIP has been designed as a set of tools based on open standards that provide to the user all the necessary functionalities as described in the Publish-Find-Bind (PFB) pattern. In other words, this means that the SIP helps users to locate relevant and suitable data for their experiments analysis, to access and transform it (filtering, extraction, selection, conversion, aggregation). Moreover, the SIP can be used to provide descriptive information about the data and to publish it so others can find and use it. The SIP is based on existing open data protocols such as the OGC/CSW, OGC/WMS, OpenDAP and open-source components like PostgreSQL/PostGIS, GeoServer and pyCSW. The SIP is divided in three main user interfaces: the BYOD (Browse your open dataset) web interface, the Expert GUI tool and the Upload Data and Metadata web interface. The BYOD HTML5 client is the main entry point for users that want to browse through open data in the SIP. The BYOD has a map interface based on Leaflet JavaScript libraries so that the users can search more efficiently. The web-based Open Data Registration Tool is a user-friendly upload and metadata description interface (geographical extent, license, DOI generation). The Expert GUI is a desktop application that provides full metadata editing capabilities for the metadata moderators of the project. In conclusion, the Spatial Information Platform (SIP) provides to its community a set of tools for better understanding and ease of use of hydrological open-data. Moreover, the SIP has been based on well-known OGC standards that will allow the connection and data harvesting from popular open data portals such as the GEOSS system of systems.

Open Tools for Integrated Modelling to Understand SDG development - The OPTIMUS program

NASA Astrophysics Data System (ADS)

Howells, Mark; Zepeda, Eduardo; Rogner, H. Holger; Sanchez, Marco; Roehrl, Alexander; Cicowiez, Matrin; Mentis, Dimitris; Korkevelos, Alexandros; Taliotis, Constantinos; Broad, Oliver; Alfstad, Thomas

2016-04-01

The recently adopted Sustainable Development Goals (SDGs) - a set of 17 measurable and time-bound goals with 169 associated targets for 2030 - are highly inclusive challenges before the world community ranging from eliminating poverty to human rights, inequality, a secure world and protection of the environment. Each individual goal or target by themselves present enormous tasks, taken together they are overwhelming. There strong and weak interlinkages, hence trade-offs and complementarities among goals and targets. Some targets may affect several goals while other goals and targets may conflict or be mutually exclusive (Ref). Meeting each of these requires the judicious exploitation of resource, with energy playing an important role. Such complexity demands to be addressed in an integrated way using systems analysis tools to support informed policy formulation, planning, allocation of scarce resources, monitoring progress, effectiveness and review at different scales. There is no one size fits all methodology that conceivably could include all goal and targets simultaneously. But there are methodologies encapsulating critical subsets of the goal and targets with strong interlinkages with a 'soft' reflection on the weak interlinkages. Universal food security or sustainable energy for all inherently support goals and targets on human rights and equality but possibly at the cost of biodiversity or desertification. Integrated analysis and planning tools are not yet commonplace at national universities - or indeed in many policy making organs. What is needed is a fundamental realignment of institutions and integrations of their planning processes and decision making. We introduce a series of open source tools to support the SDG planning and implementation process. The Global User-friendly CLEW Open Source (GLUCOSE) tool optimizes resource interactions and constraints; The Global Electrification Tool kit (GETit) provides the first global spatially explicit electrification simulator; A national CLEW tool allows for the optimization of national level integrated resource use and Macro-CLEW presents the same allowing for detailed economic-biophysical interactions. Finally open Model Management Infrastructure (MoManI) is presented that allows for the rapid prototyping of new additions to, or new resource optimization tools. Collectively these tools provide insights to some fifteen of the SDGs and are made publicly available with support to governments and academic institutions.

[Family, friends, and other sources of information associated with the initiation of sexual relations by adolescents in El Salvador].

PubMed

Ruiz-Canela, Miguel; López-Del Burgo, Cristina; Carlos, Silvia; Calatrava, María; Osorio, Alfonso; Irala, Jokin de

2012-01-01

The objective of this study is to verify the influence of messages Salvadorian youth receive about sexuality, affection, and leisure from family, friends, and the media on the initiation of sexual activity. Cross-sectional study based on a representative sample of 2 615 students (from 13 to 19 years of age) in El Salvador. A random systematic sampling was used to select 30 schools. Sociodemographic aspects, lifestyles, and sources of information on sexuality and love used by the young people were collected. The average age of the young people studied was 15 (SD = 1.8). In all, 638 (24.4%) of the young people stated that they had had sexual relations. The following factors are associated with a greater probability of having had sexual relations: a perception that siblings (OR = 1.8, CI 95%: 1.2-2.7) or friends (OR = 1.7, CI 95%: 1.3-2.2) encourage them to have sex. Protective factors were found to be the supervision of parents (OR = 0.5, CI 95%: 0.4-0.7); messages received from friends that encourage abstinence (OR = 0.7, CI 95%: 0.6-1.0) or from siblings (OR = 0.7, CI 95%: 0.5-0.8); and favorable messages related to marriage received from parents (OR = 0.4, CI 95%: 0.3-0.6). Messages from family and friends are factors that seem to influence the initiation of sexual activity by young people. Sexual health promotion programs in El Salvador should take these factors into account.

Women's behaviour, beliefs and information sources about physical exercise in pregnancy.

PubMed

Clarke, Penny E; Gross, Harriet

2004-06-01

To examine the potential effect of low-risk pregnancy on women's recreational activity patterns and to explore pregnant women's beliefs and information sources regarding physical exercise participation. Preliminary, prospective survey Participants' homes in the East Midlands, UK. Fifty-seven nulliparous, pregnant women. Levels of maternal physical activity participation were assessed by semi-structured interview at 16, 25, 34 and 38 weeks gestation. The modified Baecke questionnaire provided a measure of women's habitual sport and leisure activities in the 12 months prior to pregnancy. A 10-item scale assessed maternal beliefs regarding the importance of physical activity in pregnancy. The fetal health locus of control scale measured the extent to which women believed their own behaviour, the behaviour of others and/or chance would influence fetal health. Open-ended questions assessed women's information sources. Fourteen of the 36 (39%) women who reported participating in some form of weekly exercise before pregnancy did not report pursuing any similar activities during pregnancy. Rest and relaxation were perceived as being significantly more important during pregnancy than was regular exercise or the maintenance of an active lifestyle. Fifty-five respondents (96%) indicated that they had received advice about physical activity at least once during pregnancy. At 16 weeks gestation, women obtained most of their information from books and magazines. Between 25 and 38 weeks gestation, most advice came from family and friends. Participants who reported receiving this advice were significantly older, more educated and of a higher activity level pre-pregnancy. Levels of maternal exercise may decline during pregnancy both as a result of the physical changes of pregnancy and from a combination of social and psychological factors. Present health education may be failing to correct inaccurate perceptions of the risks associated with physical exercise in pregnancy. Improving the quantity and quality of information related to physical exercise has the potential to correct inaccurate perceptions and confer several benefits on maternal and fetal health. Effective intervention strategies should focus not only on the pregnant woman but also extend to her family, friends and exercise provider.

The EnzymeTracker: an open-source laboratory information management system for sample tracking.

PubMed

Triplet, Thomas; Butler, Gregory

2012-01-26

In many laboratories, researchers store experimental data on their own workstation using spreadsheets. However, this approach poses a number of problems, ranging from sharing issues to inefficient data-mining. Standard spreadsheets are also error-prone, as data do not undergo any validation process. To overcome spreadsheets inherent limitations, a number of proprietary systems have been developed, which laboratories need to pay expensive license fees for. Those costs are usually prohibitive for most laboratories and prevent scientists from benefiting from more sophisticated data management systems. In this paper, we propose the EnzymeTracker, a web-based laboratory information management system for sample tracking, as an open-source and flexible alternative that aims at facilitating entry, mining and sharing of experimental biological data. The EnzymeTracker features online spreadsheets and tools for monitoring numerous experiments conducted by several collaborators to identify and characterize samples. It also provides libraries of shared data such as protocols, and administration tools for data access control using OpenID and user/team management. Our system relies on a database management system for efficient data indexing and management and a user-friendly AJAX interface that can be accessed over the Internet. The EnzymeTracker facilitates data entry by dynamically suggesting entries and providing smart data-mining tools to effectively retrieve data. Our system features a number of tools to visualize and annotate experimental data, and export highly customizable reports. It also supports QR matrix barcoding to facilitate sample tracking. The EnzymeTracker was designed to be easy to use and offers many benefits over spreadsheets, thus presenting the characteristics required to facilitate acceptance by the scientific community. It has been successfully used for 20 months on a daily basis by over 50 scientists. The EnzymeTracker is freely available online at http://cubique.fungalgenomics.ca/enzymedb/index.html under the GNU GPLv3 license.

The EnzymeTracker: an open-source laboratory information management system for sample tracking

PubMed Central

2012-01-01

Background In many laboratories, researchers store experimental data on their own workstation using spreadsheets. However, this approach poses a number of problems, ranging from sharing issues to inefficient data-mining. Standard spreadsheets are also error-prone, as data do not undergo any validation process. To overcome spreadsheets inherent limitations, a number of proprietary systems have been developed, which laboratories need to pay expensive license fees for. Those costs are usually prohibitive for most laboratories and prevent scientists from benefiting from more sophisticated data management systems. Results In this paper, we propose the EnzymeTracker, a web-based laboratory information management system for sample tracking, as an open-source and flexible alternative that aims at facilitating entry, mining and sharing of experimental biological data. The EnzymeTracker features online spreadsheets and tools for monitoring numerous experiments conducted by several collaborators to identify and characterize samples. It also provides libraries of shared data such as protocols, and administration tools for data access control using OpenID and user/team management. Our system relies on a database management system for efficient data indexing and management and a user-friendly AJAX interface that can be accessed over the Internet. The EnzymeTracker facilitates data entry by dynamically suggesting entries and providing smart data-mining tools to effectively retrieve data. Our system features a number of tools to visualize and annotate experimental data, and export highly customizable reports. It also supports QR matrix barcoding to facilitate sample tracking. Conclusions The EnzymeTracker was designed to be easy to use and offers many benefits over spreadsheets, thus presenting the characteristics required to facilitate acceptance by the scientific community. It has been successfully used for 20 months on a daily basis by over 50 scientists. The EnzymeTracker is freely available online at http://cubique.fungalgenomics.ca/enzymedb/index.html under the GNU GPLv3 license. PMID:22280360

Openly Published Environmental Sensing (OPEnS) | Advancing Open-Source Research, Instrumentation, and Dissemination

NASA Astrophysics Data System (ADS)

Udell, C.; Selker, J. S.

2017-12-01

The increasing availability and functionality of Open-Source software and hardware along with 3D printing, low-cost electronics, and proliferation of open-access resources for learning rapid prototyping are contributing to fundamental transformations and new technologies in environmental sensing. These tools invite reevaluation of time-tested methodologies and devices toward more efficient, reusable, and inexpensive alternatives. Building upon Open-Source design facilitates community engagement and invites a Do-It-Together (DIT) collaborative framework for research where solutions to complex problems may be crowd-sourced. However, barriers persist that prevent researchers from taking advantage of the capabilities afforded by open-source software, hardware, and rapid prototyping. Some of these include: requisite technical skillsets, knowledge of equipment capabilities, identifying inexpensive sources for materials, money, space, and time. A university MAKER space staffed by engineering students to assist researchers is one proposed solution to overcome many of these obstacles. This presentation investigates the unique capabilities the USDA-funded Openly Published Environmental Sensing (OPEnS) Lab affords researchers, within Oregon State and internationally, and the unique functions these types of initiatives support at the intersection of MAKER spaces, Open-Source academic research, and open-access dissemination.

Thyroid Cancer and Tumor Collaborative Registry (TCCR).

PubMed

Shats, Oleg; Goldner, Whitney; Feng, Jianmin; Sherman, Alexander; Smith, Russell B; Sherman, Simon

2016-01-01

A multicenter, web-based Thyroid Cancer and Tumor Collaborative Registry (TCCR, http://tccr.unmc.edu) allows for the collection and management of various data on thyroid cancer (TC) and thyroid nodule (TN) patients. The TCCR is coupled with OpenSpecimen, an open-source biobank management system, to annotate biospecimens obtained from the TCCR subjects. The demographic, lifestyle, physical activity, dietary habits, family history, medical history, and quality of life data are provided and may be entered into the registry by subjects. Information on diagnosis, treatment, and outcome is entered by the clinical personnel. The TCCR uses advanced technical and organizational practices, such as (i) metadata-driven software architecture (design); (ii) modern standards and best practices for data sharing and interoperability (standardization); (iii) Agile methodology (project management); (iv) Software as a Service (SaaS) as a software distribution model (operation); and (v) the confederation principle as a business model (governance). This allowed us to create a secure, reliable, user-friendly, and self-sustainable system for TC and TN data collection and management that is compatible with various end-user devices and easily adaptable to a rapidly changing environment. Currently, the TCCR contains data on 2,261 subjects and data on more than 28,000 biospecimens. Data and biological samples collected by the TCCR are used in developing diagnostic, prevention, treatment, and survivorship strategies against TC.

Open-source software: not quite endsville.

PubMed

Stahl, Matthew T

2005-02-01

Open-source software will never achieve ubiquity. There are environments in which it simply does not flourish. By its nature, open-source development requires free exchange of ideas, community involvement, and the efforts of talented and dedicated individuals. However, pressures can come from several sources that prevent this from happening. In addition, openness and complex licensing issues invite misuse and abuse. Care must be taken to avoid the pitfalls of open-source software.

Developing an Open Source Option for NASA Software

NASA Technical Reports Server (NTRS)

Moran, Patrick J.; Parks, John W. (Technical Monitor)

2003-01-01

We present arguments in favor of developing an Open Source option for NASA software; in particular we discuss how Open Source is compatible with NASA's mission. We compare and contrast several of the leading Open Source licenses, and propose one - the Mozilla license - for use by NASA. We also address some of the related issues for NASA with respect to Open Source. In particular, we discuss some of the elements in the External Release of NASA Software document (NPG 2210.1A) that will likely have to be changed in order to make Open Source a reality withm the agency.

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

Zhao, Xin-Yu; Zhu, Ying-Jie, E-mail: y.j.zhu@mail.sic.ac.cn; Lu, Bing-Qiang

Graphical abstract: Hydroxyapatite nanorods are synthesized using biocompatible biomolecule pyridoxal-5′-phosphate as a new organic phosphorus source by the hydrothermal method. - Highlights: • Hydrothermal synthesis of hydroxyapatite nanorods is reported. • Biocompatible pyridoxal-5′-phosphate is used as an organic phosphorus source. • This method is simple, surfactant-free and environmentally friendly. - Abstract: Hydroxyapatite nanorods are synthesized by the hydrothermal method using biocompatible biomolecule pyridoxal-5′-phosphate (PLP) as a new organic phosphorus source. In this method, PLP biomolecules are hydrolyzed to produce phosphate ions under hydrothermal conditions, and these phosphate ions react with pre-existing calcium ions to form hydroxyapatite nanorods. The effects ofmore » experimental conditions including hydrothermal temperature and time on the morphology and crystal phase of the products are investigated. This method is simple, surfactant-free and environmentally friendly. The products are characterized by X-ray powder diffraction, scanning electron microscopy, transmission electron microscopy, Fourier transform infrared (FTIR) spectroscopy, and thermogravimetric (TG) analysis.« less

Analyzing and Visualizing Cosmological Simulations with ParaView

NASA Astrophysics Data System (ADS)

Woodring, Jonathan; Heitmann, Katrin; Ahrens, James; Fasel, Patricia; Hsu, Chung-Hsing; Habib, Salman; Pope, Adrian

2011-07-01

The advent of large cosmological sky surveys—ushering in the era of precision cosmology—has been accompanied by ever larger cosmological simulations. The analysis of these simulations, which currently encompass tens of billions of particles and up to a trillion particles in the near future, is often as daunting as carrying out the simulations in the first place. Therefore, the development of very efficient analysis tools combining qualitative and quantitative capabilities is a matter of some urgency. In this paper, we introduce new analysis features implemented within ParaView, a fully parallel, open-source visualization toolkit, to analyze large N-body simulations. A major aspect of ParaView is that it can live and operate on the same machines and utilize the same parallel power as the simulation codes themselves. In addition, data movement is in a serious bottleneck now and will become even more of an issue in the future; an interactive visualization and analysis tool that can handle data in situ is fast becoming essential. The new features in ParaView include particle readers and a very efficient halo finder that identifies friends-of-friends halos and determines common halo properties, including spherical overdensity properties. In combination with many other functionalities already existing within ParaView, such as histogram routines or interfaces to programming languages like Python, this enhanced version enables fast, interactive, and convenient analyses of large cosmological simulations. In addition, development paths are available for future extensions.

Chipster: user-friendly analysis software for microarray and other high-throughput data.

PubMed

Kallio, M Aleksi; Tuimala, Jarno T; Hupponen, Taavi; Klemelä, Petri; Gentile, Massimiliano; Scheinin, Ilari; Koski, Mikko; Käki, Janne; Korpelainen, Eija I

2011-10-14

The growth of high-throughput technologies such as microarrays and next generation sequencing has been accompanied by active research in data analysis methodology, producing new analysis methods at a rapid pace. While most of the newly developed methods are freely available, their use requires substantial computational skills. In order to enable non-programming biologists to benefit from the method development in a timely manner, we have created the Chipster software. Chipster (http://chipster.csc.fi/) brings a powerful collection of data analysis methods within the reach of bioscientists via its intuitive graphical user interface. Users can analyze and integrate different data types such as gene expression, miRNA and aCGH. The analysis functionality is complemented with rich interactive visualizations, allowing users to select datapoints and create new gene lists based on these selections. Importantly, users can save the performed analysis steps as reusable, automatic workflows, which can also be shared with other users. Being a versatile and easily extendable platform, Chipster can be used for microarray, proteomics and sequencing data. In this article we describe its comprehensive collection of analysis and visualization tools for microarray data using three case studies. Chipster is a user-friendly analysis software for high-throughput data. Its intuitive graphical user interface enables biologists to access a powerful collection of data analysis and integration tools, and to visualize data interactively. Users can collaborate by sharing analysis sessions and workflows. Chipster is open source, and the server installation package is freely available.

SigmoID: a user-friendly tool for improving bacterial genome annotation through analysis of transcription control signals

PubMed Central

Damienikan, Aliaksandr U.

2016-01-01

The majority of bacterial genome annotations are currently automated and based on a ‘gene by gene’ approach. Regulatory signals and operon structures are rarely taken into account which often results in incomplete and even incorrect gene function assignments. Here we present SigmoID, a cross-platform (OS X, Linux and Windows) open-source application aiming at simplifying the identification of transcription regulatory sites (promoters, transcription factor binding sites and terminators) in bacterial genomes and providing assistance in correcting annotations in accordance with regulatory information. SigmoID combines a user-friendly graphical interface to well known command line tools with a genome browser for visualising regulatory elements in genomic context. Integrated access to online databases with regulatory information (RegPrecise and RegulonDB) and web-based search engines speeds up genome analysis and simplifies correction of genome annotation. We demonstrate some features of SigmoID by constructing a series of regulatory protein binding site profiles for two groups of bacteria: Soft Rot Enterobacteriaceae (Pectobacterium and Dickeya spp.) and Pseudomonas spp. Furthermore, we inferred over 900 transcription factor binding sites and alternative sigma factor promoters in the annotated genome of Pectobacterium atrosepticum. These regulatory signals control putative transcription units covering about 40% of the P. atrosepticum chromosome. Reviewing the annotation in cases where it didn’t fit with regulatory information allowed us to correct product and gene names for over 300 loci. PMID:27257541

Chipster: user-friendly analysis software for microarray and other high-throughput data

PubMed Central

2011-01-01

Background The growth of high-throughput technologies such as microarrays and next generation sequencing has been accompanied by active research in data analysis methodology, producing new analysis methods at a rapid pace. While most of the newly developed methods are freely available, their use requires substantial computational skills. In order to enable non-programming biologists to benefit from the method development in a timely manner, we have created the Chipster software. Results Chipster (http://chipster.csc.fi/) brings a powerful collection of data analysis methods within the reach of bioscientists via its intuitive graphical user interface. Users can analyze and integrate different data types such as gene expression, miRNA and aCGH. The analysis functionality is complemented with rich interactive visualizations, allowing users to select datapoints and create new gene lists based on these selections. Importantly, users can save the performed analysis steps as reusable, automatic workflows, which can also be shared with other users. Being a versatile and easily extendable platform, Chipster can be used for microarray, proteomics and sequencing data. In this article we describe its comprehensive collection of analysis and visualization tools for microarray data using three case studies. Conclusions Chipster is a user-friendly analysis software for high-throughput data. Its intuitive graphical user interface enables biologists to access a powerful collection of data analysis and integration tools, and to visualize data interactively. Users can collaborate by sharing analysis sessions and workflows. Chipster is open source, and the server installation package is freely available. PMID:21999641

pROC: an open-source package for R and S+ to analyze and compare ROC curves.

PubMed

Robin, Xavier; Turck, Natacha; Hainard, Alexandre; Tiberti, Natalia; Lisacek, Frédérique; Sanchez, Jean-Charles; Müller, Markus

2011-03-17

Receiver operating characteristic (ROC) curves are useful tools to evaluate classifiers in biomedical and bioinformatics applications. However, conclusions are often reached through inconsistent use or insufficient statistical analysis. To support researchers in their ROC curves analysis we developed pROC, a package for R and S+ that contains a set of tools displaying, analyzing, smoothing and comparing ROC curves in a user-friendly, object-oriented and flexible interface. With data previously imported into the R or S+ environment, the pROC package builds ROC curves and includes functions for computing confidence intervals, statistical tests for comparing total or partial area under the curve or the operating points of different classifiers, and methods for smoothing ROC curves. Intermediary and final results are visualised in user-friendly interfaces. A case study based on published clinical and biomarker data shows how to perform a typical ROC analysis with pROC. pROC is a package for R and S+ specifically dedicated to ROC analysis. It proposes multiple statistical tests to compare ROC curves, and in particular partial areas under the curve, allowing proper ROC interpretation. pROC is available in two versions: in the R programming language or with a graphical user interface in the S+ statistical software. It is accessible at http://expasy.org/tools/pROC/ under the GNU General Public License. It is also distributed through the CRAN and CSAN public repositories, facilitating its installation.

From Family to Friends: Does Witnessing Interparental Violence Affect Young Adults’ Relationships with Friends?

PubMed Central

Mandal, Mahua; Hindin, Michelle J.

2013-01-01

Purpose Childhood exposure to violence in one’s family of origin has been closely linked to subsequent perpetration and victimization of intimate partner violence. There is, however, little research on the relationship between witnessing violence and subsequent peer violence. This study investigates the effects of witnessing interparental violence among Filipino young adults on their use and experience of psychological aggression with friends. Methods The data source for this study was the Cebu Longitudinal Health and Nutrition Survey. Recent perpetration and victimization of friend psychological aggression among young adults ages 21–22 years was assessed through self-reports from the 2005 survey, and witnessing interparental violence during childhood was assessed through self-reports from the 2002 survey. Multinomial logistic regression was used to examine the effects of witnessing interparental violence on subsequent use and experience of friend psychological aggression. Analyses were stratified by gender. Results About 13% of females and 4% of males perpetrated psychological aggression towards close friends, and about 4% of females and males were victims. Fourteen percent of females and 3% of males experienced bidirectional psychological aggression. About 44% of females and 47% of males had, during childhood, witnessed their parents physically hurt one another. Witnessing maternal and reciprocal interparental violence during childhood significantly predicted bidirectional friend psychological aggression among males. Among females, witnessing interparental violence did not significantly predict involvement with friend psychological aggression. Conclusions Violence prevention programs should consider using family-centered interventions, and apply a gendered lens to their application. Further research on gender differences in friend aggression is recommended. PMID:23697789

Alcohol peer influence of participating in organized school activities: a network approach.

PubMed

Fujimoto, Kayo; Valente, Thomas W

2013-10-01

This study compares the network influences on adolescent substance use from peers who coparticipated in school-sponsored organized activities (affiliation-based peer influence) with the influence both from their "nominated" friends (i.e., the adolescent named the alter as a friend), and only "reciprocated" friends (i.e., both adolescents mutually named each other as friends). The study also attempts to parse affiliation-based peer influence into the influence of both activity members who are also friends and those who are not, to address the potential confounding of these sources of peer influence. The study data consisted of a nationally representative sample of 12,551 adolescents in Grades 7-12 within 106 schools from the Add Health data. Ordinal logistic regression was conducted to estimate the effects of affiliation-based and friends influence on alcohol use and drinking frequency. Peer influence via organized activities (sports or clubs) with drinkers and the influence of friends who drink had significant effects on adolescent drinking. Peer influence through club activities with drinkers had a stronger effect on any drinking behavior than through sports activities with drinkers. After decomposing peer influence through activities by friendship status, influence through sport activities had a significant effect on drinking only when coparticipant drinkers were also reciprocated friends (but not nominated friends), whereas influence through club activities had a significant effect on drinking, regardless of friendship reciprocation. The design and implementation of school based substance use prevention and treatment programs should consider the contextual effects of school-sponsored activities. (PsycINFO Database Record (c) 2013 APA, all rights reserved).

From family to friends: does witnessing interparental violence affect young adults' relationships with friends?

PubMed

Mandal, Mahua; Hindin, Michelle J

2013-08-01

Childhood exposure to violence in one's family of origin has been closely linked to subsequent perpetration and victimization of intimate partner violence. There is, however, little research on the relationship between witnessing violence and subsequent peer violence. This study investigates the effects of witnessing interparental violence among Filipino young adults on their use and experience of psychological aggression with friends. The data source for this study was the Cebu Longitudinal Health and Nutrition Survey. Recent perpetration and victimization of friend psychological aggression among young adults ages 21-22 years was assessed through self-reports from the 2005 survey; witnessing interparental violence during childhood was assessed through self-reports from the 2002 survey. Multinomial logistic regression was used to examine the effects of witnessing interparental violence on subsequent use and experience of friend psychological aggression. Analyses were stratified by gender. About 13% of females and 4% of males perpetrated psychological aggression toward close friends, and about 4% of females and males were victims. Fourteen percent of females and 3% of males experienced bidirectional psychological aggression. About 44% of females and 47% of males had, during childhood, witnessed their parents physically hurt one another. Witnessing maternal and reciprocal interparental violence during childhood significantly predicted bidirectional friend psychological aggression among males. Among females, witnessing interparental violence did not significantly predict involvement with friend psychological aggression. Violence prevention programs should consider using family-centered interventions, and apply a gendered lens to their application. Further research on gender differences in friend aggression is recommended. Copyright © 2013 Society for Adolescent Health and Medicine. Published by Elsevier Inc. All rights reserved.

Alcohol Peer Influence of Participating in Organized School Activities: A Network Approach

PubMed Central

Valente, Thomas W.

2014-01-01

Objective This study compares the network influences on adolescent substance use from peers who co-participated in school-sponsored organized activities (affiliation-based peer influence) with the influence both from their “nominated” friends (i.e., the adolescent named the alter as a friend), and only “reciprocated” friends (i.e., both adolescents mutually named each other as friends). The study also attempts to parse affiliation-based peer influence into the influence of both activity members who are also friends, and those who are not, to address the potential confounding of these sources of peer influence. Methods The study data consisted of a nationally representative sample of 12,551 adolescents in Grades 7–12 within 106 schools from the Add Health data. Ordinal logistic regression was conducted to estimate the effects of affiliation-based and friends influence on alcohol use and drinking frequency. Results Peer influence via organized activities (sports or clubs) with drinkers and the influence of friends who drink had significant effects on adolescent drinking. Peer influence through club activities with drinkers had a stronger effect on any drinking behavior than through sports activities with drinkers. After decomposing peer influence through activities by friendship status, influence through sport activities had a significant effect on drinking only when co-participant drinkers were also “reciprocated” friends (but not “nominated” friends), whereas influence through club activities had a significant effect on drinking, regardless of friendship reciprocation. Conclusions The design and implementation of school based substance use prevention and treatment programs should consider the contextual effects of school-sponsored activities. PMID:22924449

Sensitivity Training in the Classroom.

ERIC Educational Resources Information Center

Cameron, Brent

1970-01-01

Sensitivity training in the classroom can help children cope with and adapt to their environment--family, peer group, friends, school, and teachers--and get them to talk honestly and openly about emotional, social, and intellectual feelings and concepts. Some techniques of encouraging students to explore, to become involved with and aware of…

Opening New Doors. Friends through Writing.

ERIC Educational Resources Information Center

British Columbia Buildings Corp., Victoria.

This publication contains 37 stories, vignettes, and poems written by participants in the British Columbia Buildings Corporation Workplace Language Program. The pieces center on family, work, people, and places and were written by people who decided to learn how to improve their language skills. They represent slices of employees' lives as they…

Overcoming the Financial Aid Barrier for E-Learners

ERIC Educational Resources Information Center

Chaloux, Bruce

2008-01-01

Financial aid systems help make higher education available to all who can benefit. To "adjust" the existing financial aid system to make it more student friendly and open doors currently closed to many part-time learners and students with the greatest financial challenges, state policy changes and greater private sector initiatives…

Making it in a 'saturated' market. How the Spence Center wins women's hearts with grass-roots marketing.

PubMed

Moore, P L

1997-01-01

The Spence Centers, full-service, independent clinics for women, depend on grass-roots outreach to cultivate customers and build brand equity. The Centers have garnered national and international press coverage and made enough friends to open a fourth operation.

Using Online Tone Generators

ERIC Educational Resources Information Center

Lincoln, James

2017-01-01

Online tone generators are free, user friendly, and can make for engaging and meaningful study of many topics in the areas of interference, waves, and the physics of music. By using a website such as OnlineToneGenerator.com, and through opening multiple windows simultaneously, students can immediately perform several experiments. In this article,…

The Management of Nature and Socialization to Outdoor Life.

ERIC Educational Resources Information Center

Dahle, Borge

2001-01-01

A Norwegian study of socialization into friluftsliv (traditional open-air life) found that factors affecting lifelong interest included parents' and friends' relationship to friluftsliv, proximity to suitable areas, outdoor hobbies, access to a summer home, and owning a dog. Educational experiences outdoors were collectively about as influential…

How the Source of Word-of-Mouth Influences Information Processing in the Formation of Brand Attitudes

ERIC Educational Resources Information Center

Herold, Kristiina; Tarkiainen, Anssi; Sundqvist, Sanna

2016-01-01

Word-of-mouth (WOM) can be a powerful, persuasive source of information, but relatively little is understood about how consumers utilize information in service evaluations and how the source of WOM (e.g. friends, family) affects attitudes. The importance of WOM is acknowledged in the services context; however, the research field of higher…

Open-Source Data and the Study of Homicide.

PubMed

Parkin, William S; Gruenewald, Jeff

2015-07-20

To date, no discussion has taken place in the social sciences as to the appropriateness of using open-source data to augment, or replace, official data sources in homicide research. The purpose of this article is to examine whether open-source data have the potential to be used as a valid and reliable data source in testing theory and studying homicide. Official and open-source homicide data were collected as a case study in a single jurisdiction over a 1-year period. The data sets were compared to determine whether open-sources could recreate the population of homicides and variable responses collected in official data. Open-source data were able to replicate the population of homicides identified in the official data. Also, for every variable measured, the open-sources captured as much, or more, of the information presented in the official data. Also, variables not available in official data, but potentially useful for testing theory, were identified in open-sources. The results of the case study show that open-source data are potentially as effective as official data in identifying individual- and situational-level characteristics, provide access to variables not found in official homicide data, and offer geographic data that can be used to link macro-level characteristics to homicide events. © The Author(s) 2015.

Family, friend, and media factors are associated with patterns of weight-control behavior among adolescent girls.

PubMed

Balantekin, Katherine N; Birch, Leann L; Savage, Jennifer S

2018-04-01

To examine the relationship of family, friend, and media factors on weight-control group membership at 15 years separately and in a combined model. Subjects included 166 15 year girls. Latent class analysis identified four patterns of weight-control behaviors: non-dieters, lifestyle, dieters, and extreme dieters. Family (family functioning, priority of the family meals, maternal/paternal weight-teasing, and mother's/father's dieting), friend (weight-teasing and dieting), and media variables (media sensitivity and weekly TV time) were included as predictors of weight-control group membership. Family functioning and priority of family meals predicted membership in the Extreme Dieters group, and maternal weight-teasing predicted membership in both dieters and extreme dieters. Friend's dieting and weight-teasing predicted membership in both dieters and extreme dieters. Media sensitivity was significantly associated with membership in lifestyle, dieters, and extreme dieters. In a combined influence model with family, friend, and media factors included, the following remained significantly associated with weight-control group membership: family functioning, friends' dieting, and media sensitivity. Family, friends, and the media are three sources of sociocultural influence, which play a role in adolescent girls' use of patterns of weight-control behaviors; family functioning was a protective factor, whereas friend's dieting and media sensitivity were risk factors. These findings emphasize the need for multidimensional interventions, addressing risk factors for dieting and use of unhealthy weight-control behaviors at the family, peer, and community (e.g., media) levels.

Enhancement of ionization efficiency of mass spectrometric analysis from non-electrospray ionization friendly solvents with conventional and novel ionization techniques.

PubMed

Jiang, Ping; Lucy, Charles A

2015-10-15

Electrospray ionization mass spectrometry (ESI-MS) has significantly impacted the analysis of complex biological and petroleum samples. However ESI-MS has limited ionization efficiency for samples in low dielectric and low polarity solvents. Addition of a make-up solvent through a T union or electrospray solvent through continuous flow extractive desorption electrospray ionization (CF-EDESI) enable ionization of analytes in non-ESI friendly solvents. A conventional make-up solvent addition setup was used and a CF-EDESI source was built for ionization of nitrogen-containing standards in hexane or hexane/isopropanol. Factors affecting the performance of both sources have been investigated and optimized. Both the make-up solvent addition and CF-EDESI improve the ionization efficiency for heteroatom compounds in non-ESI friendly solvents. Make-up solvent addition provides higher ionization efficiency than CF-EDESI. Neither the make-up solvent addition nor the CF-EDESI eliminates ionization suppression of nitrogen-containing compounds caused by compounds of the same chemical class. Copyright © 2015 Elsevier B.V. All rights reserved.

Chondroitin Sulfate, Hyaluronic Acid and Chitin/Chitosan Production Using Marine Waste Sources: Characteristics, Applications and Eco-Friendly Processes: A Review

PubMed Central

Vázquez, José Antonio; Rodríguez-Amado, Isabel; Montemayor, María Ignacia; Fraguas, Javier; del Pilar González, María; Murado, Miguel Anxo

2013-01-01

In the last decade, an increasing number of glycosaminoglycans (GAGs), chitin and chitosan applications have been reported. Their commercial demands have been extended to different markets, such as cosmetics, medicine, biotechnology, food and textiles. Marine wastes from fisheries and aquaculture are susceptible sources for polymers but optimized processes for their recovery and production must be developed to satisfy such necessities. In the present work, we have reviewed different alternatives reported in the literature to produce and purify chondroitin sulfate (CS), hyaluronic acid (HA) and chitin/chitosan (CH/CHs) with the aim of proposing environmentally friendly processes by combination of various microbial, chemical, enzymatic and membranes strategies and technologies. PMID:23478485

Action Tendency Emotions Evoked by Memorable Breast Cancer Messages and Their Association With Prevention and Detection Behaviors

PubMed Central

Smith, Sandi W.; Hamel, Lauren M; Kotowski, Michael R.; Nazione, Samantha; LaPlante, Carolyn; Atkin, Charles K.; Stohl, Cynthia; Skubisz, Christine

2010-01-01

Memorable messages about breast cancer sent by different sources, such as friends and family members, were analyzed for the action tendency emotions that they evoked. Negative emotions of fear, sadness, and anger, and positive emotions of hope and relief were analyzed for their associations with prevention and detection breast cancer behaviors. Messages that evoked fear were significantly more likely to be associated with detection behaviors, whereas messages that evoked relief were significantly less likely to be associated with detection behaviors than messages that did not evoke these emotions. These results are consistent with control theory and also show that friends and family are important sources of memorable messages about breast cancer. PMID:21153990

The hobbyist phenomenon in physical security.

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

Michaud, E. C.

Pro-Ams (professional amateurs) are groups of people who work on a problem as amateurs or unpaid persons in a given field at professional levels of competence. Astronomy is a good example of Pro-Am activity. At Galaxy Zoo, Pro-Ams evaluate data generated by professional observatories and are able to evaluate the millions of galaxies that have been observed but not classified, and report their findings at professional levels for fun. To allow the archiving of millions of galaxies that have been observed but not classified, the website has been engineered so that the public can view and classify galaxies even ifmore » they are not professional astronomers. In this endeavor, it has been found that amateurs can easily outperform automated vision systems. Today in the world of physical security, Pro-Ams are playing an ever-increasing role. Traditionally, locksmiths, corporations, and government organizations have been largely responsible for developing standards, uncovering vulnerabilities, and devising best security practices. Increasingly, however, nonprofit sporting organizations and clubs are doing this. They can be found all over the world, from Europe to the US and now South East Asia. Examples include TOOOL (The Open Organization of Lockpickers), the Longhorn Lockpicking Club, Sportsfreunde der Sperrtechnik - Deustcheland e.V., though there are many others. Members of these groups have been getting together weekly to discuss many elements of security, with some groups specializing in specific areas of security. When members are asked why they participate in these hobbyist groups, they usually reply (with gusto) that they do it for fun, and that they view defeating locks and other security devices as an interesting and entertaining puzzle. A lot of what happens at these clubs would not be possible if it weren't for 'Super Abundance', the ability to easily acquire (at little or no cost) the products, security tools, technologies, and intellectual resources traditionally limited to corporations, government organizations, or wealthy individuals. With this new access comes new discoveries. For example, hobbyist sport lockpicking groups discovered - and publicized - a number of new vulnerabilities between 2004 and 2009 that resulted in the majority of high-security lock manufacturers having to make changes and improvements to their products. A decade ago, amateur physical security discoveries were rare, at least those discussed publicly. In the interim, Internet sites such as lockpicking.org, lockpicking101.com and others have provided an online meeting place for people to trade tips, find friends with similar interests, and develop tools. The open, public discussion of software vulnerabilities, in contrast, has been going on for a long time. These two industries, physical security and software, have very different upgrade mechanisms. With software, a patch can typically be deployed quickly to fix a serious vulnerability, whereas a hardware fix for a physical security device or system can take upwards of months to implement in the field, especially if (as is often the case) hardware integrators are involved. Even when responding to publicly announced security vulnerabilities, manufacturers of physical security devices such as locks, intrusion detectors, or access control devices rarely view hobbyists as a positive resource. This is most unfortunate. In the field of software, it is common to speak of Open Source versus Closed Source. An Open Source software company may choose to distribute their software with a particular license, and give it away openly, with full details and all the lines of source code made available. Linux is a very popular example of this. A Close Source company, in contrast, chooses not to reveal its source code and will license its software products in a restrictive manor. Slowly, the idea of Open Source is now coming to the world of physical security. In the case of locks, it provides an alternative to the traditional Closed Source world of locksmiths. Now locks are physical objects, and can therefore be disassembled. As such, they have always been Open Source in a limited sense. Secrecy, in fact, is very difficult to maintain for a lock that is widely distributed. Having direct access to the lock design provides the hobbyist with a very open environment for finding security flaws, even if the lock manufacturer attempts to follow a Close Source model. It is clear that the field of physical security is going the digital route with companies such as Medeco, Mul-T-Lock, and Abloy manufacturing electromechanical locks. Various companies have already begun to add microcontrollers, cryptographic chip sets, solid-state sensors, and a number of other high-tech improvements to their product lineup in an effort to thwart people from defeating their security products.« less

Vocational Anticipatory Socialization: College Students' Reports of Encouraging/Discouraging Sources and Messages

ERIC Educational Resources Information Center

Powers, Samantha Rae; Myers, Karen K.

2017-01-01

Framed by social cognitive career theory, this study identified college students' perceptions of the most influential sources and content of encouraging/discouraging career messages (vocational anticipatory socialization [VAS]). A survey of 873 university students found that mothers, followed by teachers/professors, friends, and fathers, were…

Association of gestational weight gain expectations with advice on actual weight gain

USDA-ARS?s Scientific Manuscript database

To examine pregnant women's gestational weight gain expectations/advice from various sources (i.e., self, family/friends, physician) and the impact of these sources of expectations/advice on actual measured gestational weight gain. Pregnant women (n=230, 87.4% Caucasian, second pregnancy) in a cohor...

How Is Open Source Special?

ERIC Educational Resources Information Center

Kapor, Mitchell

2005-01-01

Open source software projects involve the production of goods, but in software projects, the "goods" consist of information. The open source model is an alternative to the conventional centralized, command-and-control way in which things are usually made. In contrast, open source projects are genuinely decentralized and transparent. Transparent…

Feasibility of Using Lasers and Infrared Heaters as UNREP Icing Countermeasures

DTIC Science & Technology

1989-12-29

water lance system out of commission, it is likely that the ship’s machine shop could fabricate the necessary parts for temporary repair. No such back...Sturbridge, MA 01566 High powered C02 laser systems and large inductrial machine tools. Coherent Laser Products (800) 527-3786 3210 Porter Drive P.O...friendly LASAG lasers are for user friendly applications The correct Laser Source for a particular in inoustrial apolications. Machining Task Mair

Common characteristics of open source software development and applicability for drug discovery: a systematic review.

PubMed

Ardal, Christine; Alstadsæter, Annette; Røttingen, John-Arne

2011-09-28

Innovation through an open source model has proven to be successful for software development. This success has led many to speculate if open source can be applied to other industries with similar success. We attempt to provide an understanding of open source software development characteristics for researchers, business leaders and government officials who may be interested in utilizing open source innovation in other contexts and with an emphasis on drug discovery. A systematic review was performed by searching relevant, multidisciplinary databases to extract empirical research regarding the common characteristics and barriers of initiating and maintaining an open source software development project. Common characteristics to open source software development pertinent to open source drug discovery were extracted. The characteristics were then grouped into the areas of participant attraction, management of volunteers, control mechanisms, legal framework and physical constraints. Lastly, their applicability to drug discovery was examined. We believe that the open source model is viable for drug discovery, although it is unlikely that it will exactly follow the form used in software development. Hybrids will likely develop that suit the unique characteristics of drug discovery. We suggest potential motivations for organizations to join an open source drug discovery project. We also examine specific differences between software and medicines, specifically how the need for laboratories and physical goods will impact the model as well as the effect of patents.

The social genome of friends and schoolmates in the National Longitudinal Study of Adolescent to Adult Health

PubMed Central

Boardman, Jason D.; Harris, Kathleen Mullan

2018-01-01

Humans tend to form social relationships with others who resemble them. Whether this sorting of like with like arises from historical patterns of migration, meso-level social structures in modern society, or individual-level selection of similar peers remains unsettled. Recent research has evaluated the possibility that unobserved genotypes may play an important role in the creation of homophilous relationships. We extend this work by using data from 5,500 adolescents from the National Longitudinal Study of Adolescent to Adult Health (Add Health) to examine genetic similarities among pairs of friends. Although there is some evidence that friends have correlated genotypes, both at the whole-genome level as well as at trait-associated loci (via polygenic scores), further analysis suggests that meso-level forces, such as school assignment, are a principal source of genetic similarity between friends. We also observe apparent social–genetic effects in which polygenic scores of an individual’s friends and schoolmates predict the individual’s own educational attainment. In contrast, an individual’s height is unassociated with the height genetics of peers. PMID:29317533

Sensor Networks, Dataloggers, and Other Handy Gadgets Using Open-Source Electronics for the Christina River Basin CZO

NASA Astrophysics Data System (ADS)

Hicks, S. D.; Aufdenkampe, A. K.; Montgomery, D. S.

2011-12-01

The search for biogeochemical "hot spots" and "hot moments" that control ecosystem-level processes requires a rethinking of how we observe the environment. Extensive multi-sensor/measurement arrays are required to realize 2D, 3D, or 4D maps of environmental properties with sufficient spatial and temporal resolution to find and understand hot spots and hot moments. To date, the cost of the data logging and communication infrastructure has been a major limitation to large-scale sensor deployment, especially for near-real-time (NRT) wireless networks. A low-cost, user-friendly alternative is needed so that resources can be prioritized toward sensor hardware rather than data acquisition and communication hardware. A flexible development platform would also allow for easy creation of other useful devices in addition to the already apparent need for economical dataloggers. The recent proliferation of open-source electronics platforms offers an opportunity for environmental observatories to deploy sensors at large scales by reducing data logging and communications costs by more than an order of magnitude. Leading the open-source electronics revolution is the Arduino project, designed to make the process of using electronics in multidisciplinary projects more accessible to hobbyists and professionals alike. A large user community has developed and shared hundreds of practical applications for projects that interface with a variety of sensors and use embedded logic to control external hardware. Likewise, dozens of companies and individuals sell low-cost Arduino-compatible boards that can connect together in a modular framework, allowing the user to quickly create devices for a wide range of applications. Based on these open-source technologies and products, we are designing and building a variety of circuit devices for use in our research watersheds. One Arduino-based device is a multi-channel datalogger that can be used with a variety of analog and digital sensors, such as pressure transducers, conductivity sensors, soil moisture and temperature probes, and redox probes. Radio modules can be added to the loggers to create a self-meshing wireless network for streaming live sensor data. A variation of the logger circuit is a smaller handheld unit with a text display that can be used when testing sensors in the field. Another useful custom device is a remote streamwater sampling system, made up of an Arduino circuit and a prepaid cell phone, allowing a user to remotely control multiple pumps by following interactive voice menus and hearing live sensor value readouts. In the lab, an Arduino circuit is used in a multi-chamber CO2 respiration experiment where it is controlling dozens of solenoid valves and logging the data from the analytical instruments. One of the biggest benefits of open source hardware is the low cost of the components. Each of the devices we have built costs less than $100 and can be assembled in a few hours. These circuits could easily be adapted to other applications or interfaced with other sensors in a variety of configurations, making the Arduino platform an incredibly useful tool for researchers.

Open Source Paradigm: A Synopsis of The Cathedral and the Bazaar for Health and Social Care.

PubMed

Benson, Tim

2016-07-04

Open source software (OSS) is becoming more fashionable in health and social care, although the ideas are not new. However progress has been slower than many had expected. The purpose is to summarise the Free/Libre Open Source Software (FLOSS) paradigm in terms of what it is, how it impacts users and software engineers and how it can work as a business model in health and social care sectors. Much of this paper is a synopsis of Eric Raymond's seminal book The Cathedral and the Bazaar, which was the first comprehensive description of the open source ecosystem, set out in three long essays. Direct quotes from the book are used liberally, without reference to specific passages. The first part contrasts open and closed source approaches to software development and support. The second part describes the culture and practices of the open source movement. The third part considers business models. A key benefit of open source is that users can access and collaborate on improving the software if they wish. Closed source code may be regarded as a strategic business risk that that may be unacceptable if there is an open source alternative. The sharing culture of the open source movement fits well with that of health and social care.

An analytic linear accelerator source model for GPU-based Monte Carlo dose calculations.

PubMed

Tian, Zhen; Li, Yongbao; Folkerts, Michael; Shi, Feng; Jiang, Steve B; Jia, Xun

2015-10-21

Recently, there has been a lot of research interest in developing fast Monte Carlo (MC) dose calculation methods on graphics processing unit (GPU) platforms. A good linear accelerator (linac) source model is critical for both accuracy and efficiency considerations. In principle, an analytical source model should be more preferred for GPU-based MC dose engines than a phase-space file-based model, in that data loading and CPU-GPU data transfer can be avoided. In this paper, we presented an analytical field-independent source model specifically developed for GPU-based MC dose calculations, associated with a GPU-friendly sampling scheme. A key concept called phase-space-ring (PSR) was proposed. Each PSR contained a group of particles that were of the same type, close in energy and reside in a narrow ring on the phase-space plane located just above the upper jaws. The model parameterized the probability densities of particle location, direction and energy for each primary photon PSR, scattered photon PSR and electron PSR. Models of one 2D Gaussian distribution or multiple Gaussian components were employed to represent the particle direction distributions of these PSRs. A method was developed to analyze a reference phase-space file and derive corresponding model parameters. To efficiently use our model in MC dose calculations on GPU, we proposed a GPU-friendly sampling strategy, which ensured that the particles sampled and transported simultaneously are of the same type and close in energy to alleviate GPU thread divergences. To test the accuracy of our model, dose distributions of a set of open fields in a water phantom were calculated using our source model and compared to those calculated using the reference phase-space files. For the high dose gradient regions, the average distance-to-agreement (DTA) was within 1 mm and the maximum DTA within 2 mm. For relatively low dose gradient regions, the root-mean-square (RMS) dose difference was within 1.1% and the maximum dose difference within 1.7%. The maximum relative difference of output factors was within 0.5%. Over 98.5% passing rate was achieved in 3D gamma-index tests with 2%/2 mm criteria in both an IMRT prostate patient case and a head-and-neck case. These results demonstrated the efficacy of our model in terms of accurately representing a reference phase-space file. We have also tested the efficiency gain of our source model over our previously developed phase-space-let file source model. The overall efficiency of dose calculation was found to be improved by ~1.3-2.2 times in water and patient cases using our analytical model.

Weather forecasting with open source software

NASA Astrophysics Data System (ADS)

Rautenhaus, Marc; Dörnbrack, Andreas

2013-04-01

To forecast the weather situation during aircraft-based atmospheric field campaigns, we employ a tool chain of existing and self-developed open source software tools and open standards. Of particular value are the Python programming language with its extension libraries NumPy, SciPy, PyQt4, Matplotlib and the basemap toolkit, the NetCDF standard with the Climate and Forecast (CF) Metadata conventions, and the Open Geospatial Consortium Web Map Service standard. These open source libraries and open standards helped to implement the "Mission Support System", a Web Map Service based tool to support weather forecasting and flight planning during field campaigns. The tool has been implemented in Python and has also been released as open source (Rautenhaus et al., Geosci. Model Dev., 5, 55-71, 2012). In this presentation we discuss the usage of free and open source software for weather forecasting in the context of research flight planning, and highlight how the field campaign work benefits from using open source tools and open standards.

Open Source Software Development

DTIC Science & Technology

2011-01-01

Software, 2002, 149(1), 3-17. 3. DiBona , C., Cooper, D., and Stone, M. (Eds.), Open Sources 2.0, 2005, O’Reilly Media, Sebastopol, CA. Also see, C... DiBona , S. Ockman, and M. Stone (Eds.). Open Sources: Vocides from the Open Source Revolution, 1999. O’Reilly Media, Sebastopol, CA. 4. Ducheneaut, N

Utilization of youth friendly services and associated factors among youth in Harar town, east Ethiopia: a mixed method study.

PubMed

Motuma, Aboma; Syre, Thomas; Egata, Gudina; Kenay, Abera

2016-07-17

Youth friendly services are designed to make health services accommodate the unique needs of youth. Nevertheless, in developing countries like Ethiopia, the level of knowledge about the use of these services is limited. The main aim of this study was to assess the extent of youth friendly service utilization and the associated factors among the youth. A community based- cross sectional quantitative study design supplemented with qualitative inquiry was used from January to February 2011. Data were collected from a random sample of 845 youth using a pretested structured questionnaire. Qualitative data were collected through interview guides. Odds ratios, along with 95 % confidence level, were estimated to measure the strength of association between the study variables using multivariable logistic regression. Level of statistical significance was declared at p-value less than 0.05. Thematic analysis was used to analyze the qualitative data. Nearly 64 % of the youth had already utilized youth friendly services at least once at the time of the survey. In multivariable logistic regression analysis, using friends [AOR = 3.65, 95 % CI (1.81,7.32)], health care providers [AOR = 3.27, 95 % CI (1.18,9.00)], and schools [AOR = 1.79, 95 % CI (1.00,3.19) as source of information, and having knowledge about the youth friendly services [AOR = 2.77,95 % CI (1.93,3.96)] were significantly associated with the utilization of youth friendly services. In contrast, being daily laborer and private worker by occupation [AOR = 0.12, 95 % CI (0.05, 0.92)], having negative perception about counseling [AOR = 0.50, 95 % CI (0.31-0.80)], about reproductive health services [AOR = 0 .13, 95 % CI (0.04-0.46)], and about youth friendly service providers [AOR-0.02, 95 % CI (0.08-0.50)] negatively influenced the outcome variable. The utilization of youth friendly services is moderate in this study. Getting youth related services information from different sources and being knowledgeable about the services have increased the utilization of the services. Efforts should be made by all relevant stakes to create conducive environment for the youth through training of the youth service providers, particularly for those who work in the government institutions, and strengthening of the awareness creation strategies among the youth to increase the utilization of the services.

Open-source hardware for medical devices

PubMed Central

2016-01-01

Open-source hardware is hardware whose design is made publicly available so anyone can study, modify, distribute, make and sell the design or the hardware based on that design. Some open-source hardware projects can potentially be used as active medical devices. The open-source approach offers a unique combination of advantages, including reducing costs and faster innovation. This article compares 10 of open-source healthcare projects in terms of how easy it is to obtain the required components and build the device. PMID:27158528

Open-source hardware for medical devices.

PubMed

Niezen, Gerrit; Eslambolchilar, Parisa; Thimbleby, Harold

2016-04-01

Open-source hardware is hardware whose design is made publicly available so anyone can study, modify, distribute, make and sell the design or the hardware based on that design. Some open-source hardware projects can potentially be used as active medical devices. The open-source approach offers a unique combination of advantages, including reducing costs and faster innovation. This article compares 10 of open-source healthcare projects in terms of how easy it is to obtain the required components and build the device.

The case for open-source software in drug discovery.

PubMed

DeLano, Warren L

2005-02-01

Widespread adoption of open-source software for network infrastructure, web servers, code development, and operating systems leads one to ask how far it can go. Will "open source" spread broadly, or will it be restricted to niches frequented by hopeful hobbyists and midnight hackers? Here we identify reasons for the success of open-source software and predict how consumers in drug discovery will benefit from new open-source products that address their needs with increased flexibility and in ways complementary to proprietary options.

ProtocolNavigator: emulation-based software for the design, documentation and reproduction biological experiments.

PubMed

Khan, Imtiaz A; Fraser, Adam; Bray, Mark-Anthony; Smith, Paul J; White, Nick S; Carpenter, Anne E; Errington, Rachel J

2014-12-01

Experimental reproducibility is fundamental to the progress of science. Irreproducible research decreases the efficiency of basic biological research and drug discovery and impedes experimental data reuse. A major contributing factor to irreproducibility is difficulty in interpreting complex experimental methodologies and designs from written text and in assessing variations among different experiments. Current bioinformatics initiatives either are focused on computational research reproducibility (i.e. data analysis) or laboratory information management systems. Here, we present a software tool, ProtocolNavigator, which addresses the largely overlooked challenges of interpretation and assessment. It provides a biologist-friendly open-source emulation-based tool for designing, documenting and reproducing biological experiments. ProtocolNavigator was implemented in Python 2.7, using the wx module to build the graphical user interface. It is a platform-independent software and freely available from http://protocolnavigator.org/index.html under the GPL v2 license. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

The GNAT: A new tool for processing NMR data.

PubMed

Castañar, Laura; Poggetto, Guilherme Dal; Colbourne, Adam A; Morris, Gareth A; Nilsson, Mathias

2018-06-01

The GNAT (General NMR Analysis Toolbox) is a free and open-source software package for processing, visualising, and analysing NMR data. It supersedes the popular DOSY Toolbox, which has a narrower focus on diffusion NMR. Data import of most common formats from the major NMR platforms is supported, as well as a GNAT generic format. Key basic processing of NMR data (e.g., Fourier transformation, baseline correction, and phasing) is catered for within the program, as well as more advanced techniques (e.g., reference deconvolution and pure shift FID reconstruction). Analysis tools include DOSY and SCORE for diffusion data, ROSY T 1 /T 2 estimation for relaxation data, and PARAFAC for multilinear analysis. The GNAT is written for the MATLAB® language and comes with a user-friendly graphical user interface. The standard version is intended to run with a MATLAB installation, but completely free-standing compiled versions for Windows, Mac, and Linux are also freely available. © 2018 The Authors Magnetic Resonance in Chemistry Published by John Wiley & Sons Ltd.

Computer-assisted identification and volumetric quantification of dynamic contrast enhancement in brain MRI: an interactive system

NASA Astrophysics Data System (ADS)

Wu, Shandong; Avgeropoulos, Nicholas G.; Rippe, David J.

2013-03-01

We present a dedicated segmentation system for tumor identification and volumetric quantification in dynamic contrast brain magnetic resonance (MR) scans. Our goal is to offer a practically useful tool at the end of clinicians in order to boost volumetric tumor assessment. The system is designed to work in an interactive mode such that maximizes the integration of computing capacity and clinical intelligence. We demonstrate the main functions of the system in terms of its functional flow and conduct preliminary validation using a representative pilot dataset. The system is inexpensive, user-friendly, easy to deploy and integrate with picture archiving and communication systems (PACS), and possible to be open-source, which enable it to potentially serve as a useful assistant for radiologists and oncologists. It is anticipated that in the future the system can be integrated into clinical workflow so that become routine available to help clinicians make more objective interpretations of treatment interventions and natural history of disease to best advocate patient needs.

cisTEM, user-friendly software for single-particle image processing.

PubMed

Grant, Timothy; Rohou, Alexis; Grigorieff, Nikolaus

2018-03-07

We have developed new open-source software called cis TEM (computational imaging system for transmission electron microscopy) for the processing of data for high-resolution electron cryo-microscopy and single-particle averaging. cis TEM features a graphical user interface that is used to submit jobs, monitor their progress, and display results. It implements a full processing pipeline including movie processing, image defocus determination, automatic particle picking, 2D classification, ab-initio 3D map generation from random parameters, 3D classification, and high-resolution refinement and reconstruction. Some of these steps implement newly-developed algorithms; others were adapted from previously published algorithms. The software is optimized to enable processing of typical datasets (2000 micrographs, 200 k - 300 k particles) on a high-end, CPU-based workstation in half a day or less, comparable to GPU-accelerated processing. Jobs can also be scheduled on large computer clusters using flexible run profiles that can be adapted for most computing environments. cis TEM is available for download from cistem.org. © 2018, Grant et al.

ERAIZDA: a model for holistic annotation of animal infectious and zoonotic diseases

PubMed Central

Buza, Teresia M.; Jack, Sherman W.; Kirunda, Halid; Khaitsa, Margaret L.; Lawrence, Mark L.; Pruett, Stephen; Peterson, Daniel G.

2015-01-01

There is an urgent need for a unified resource that integrates trans-disciplinary annotations of emerging and reemerging animal infectious and zoonotic diseases. Such data integration will provide wonderful opportunity for epidemiologists, researchers and health policy makers to make data-driven decisions designed to improve animal health. Integrating emerging and reemerging animal infectious and zoonotic disease data from a large variety of sources into a unified open-access resource provides more plausible arguments to achieve better understanding of infectious and zoonotic diseases. We have developed a model for interlinking annotations of these diseases. These diseases are of particular interest because of the threats they pose to animal health, human health and global health security. We demonstrated the application of this model using brucellosis, an infectious and zoonotic disease. Preliminary annotations were deposited into VetBioBase database (http://vetbiobase.igbb.msstate.edu). This database is associated with user-friendly tools to facilitate searching, retrieving and downloading of disease-related information. Database URL: http://vetbiobase.igbb.msstate.edu PMID:26581408

DEIVA: a web application for interactive visual analysis of differential gene expression profiles.

PubMed

Harshbarger, Jayson; Kratz, Anton; Carninci, Piero

2017-01-07

Differential gene expression (DGE) analysis is a technique to identify statistically significant differences in RNA abundance for genes or arbitrary features between different biological states. The result of a DGE test is typically further analyzed using statistical software, spreadsheets or custom ad hoc algorithms. We identified a need for a web-based system to share DGE statistical test results, and locate and identify genes in DGE statistical test results with a very low barrier of entry. We have developed DEIVA, a free and open source, browser-based single page application (SPA) with a strong emphasis on being user friendly that enables locating and identifying single or multiple genes in an immediate, interactive, and intuitive manner. By design, DEIVA scales with very large numbers of users and datasets. Compared to existing software, DEIVA offers a unique combination of design decisions that enable inspection and analysis of DGE statistical test results with an emphasis on ease of use.

CImbinator: a web-based tool for drug synergy analysis in small- and large-scale datasets.

PubMed

Flobak, Åsmund; Vazquez, Miguel; Lægreid, Astrid; Valencia, Alfonso

2017-08-01

Drug synergies are sought to identify combinations of drugs particularly beneficial. User-friendly software solutions that can assist analysis of large-scale datasets are required. CImbinator is a web-service that can aid in batch-wise and in-depth analyzes of data from small-scale and large-scale drug combination screens. CImbinator offers to quantify drug combination effects, using both the commonly employed median effect equation, as well as advanced experimental mathematical models describing dose response relationships. CImbinator is written in Ruby and R. It uses the R package drc for advanced drug response modeling. CImbinator is available at http://cimbinator.bioinfo.cnio.es , the source-code is open and available at https://github.com/Rbbt-Workflows/combination_index . A Docker image is also available at https://hub.docker.com/r/mikisvaz/rbbt-ci_mbinator/ . asmund.flobak@ntnu.no or miguel.vazquez@cnio.es. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Bayesian accrual prediction for interim review of clinical studies: open source R package and smartphone application.

PubMed

Jiang, Yu; Guarino, Peter; Ma, Shuangge; Simon, Steve; Mayo, Matthew S; Raghavan, Rama; Gajewski, Byron J

2016-07-22

Subject recruitment for medical research is challenging. Slow patient accrual leads to increased costs and delays in treatment advances. Researchers need reliable tools to manage and predict the accrual rate. The previously developed Bayesian method integrates researchers' experience on former trials and data from an ongoing study, providing a reliable prediction of accrual rate for clinical studies. In this paper, we present a user-friendly graphical user interface program developed in R. A closed-form solution for the total subjects that can be recruited within a fixed time is derived. We also present a built-in Android system using Java for web browsers and mobile devices. Using the accrual software, we re-evaluated the Veteran Affairs Cooperative Studies Program 558- ROBOTICS study. The application of the software in monitoring and management of recruitment is illustrated for different stages of the trial. This developed accrual software provides a more convenient platform for estimation and prediction of the accrual process.

cisTEM, user-friendly software for single-particle image processing

PubMed Central

2018-01-01

We have developed new open-source software called cisTEM (computational imaging system for transmission electron microscopy) for the processing of data for high-resolution electron cryo-microscopy and single-particle averaging. cisTEM features a graphical user interface that is used to submit jobs, monitor their progress, and display results. It implements a full processing pipeline including movie processing, image defocus determination, automatic particle picking, 2D classification, ab-initio 3D map generation from random parameters, 3D classification, and high-resolution refinement and reconstruction. Some of these steps implement newly-developed algorithms; others were adapted from previously published algorithms. The software is optimized to enable processing of typical datasets (2000 micrographs, 200 k – 300 k particles) on a high-end, CPU-based workstation in half a day or less, comparable to GPU-accelerated processing. Jobs can also be scheduled on large computer clusters using flexible run profiles that can be adapted for most computing environments. cisTEM is available for download from cistem.org. PMID:29513216

3D-Lab: a collaborative web-based platform for molecular modeling.

PubMed

Grebner, Christoph; Norrby, Magnus; Enström, Jonatan; Nilsson, Ingemar; Hogner, Anders; Henriksson, Jonas; Westin, Johan; Faramarzi, Farzad; Werner, Philip; Boström, Jonas

2016-09-01

The use of 3D information has shown impact in numerous applications in drug design. However, it is often under-utilized and traditionally limited to specialists. We want to change that, and present an approach making 3D information and molecular modeling accessible and easy-to-use 'for the people'. A user-friendly and collaborative web-based platform (3D-Lab) for 3D modeling, including a blazingly fast virtual screening capability, was developed. 3D-Lab provides an interface to automatic molecular modeling, like conformer generation, ligand alignments, molecular dockings and simple quantum chemistry protocols. 3D-Lab is designed to be modular, and to facilitate sharing of 3D-information to promote interactions between drug designers. Recent enhancements to our open-source virtual reality tool Molecular Rift are described. The integrated drug-design platform allows drug designers to instantaneously access 3D information and readily apply advanced and automated 3D molecular modeling tasks, with the aim to improve decision-making in drug design projects.

Choosing Open Source ERP Systems: What Reasons Are There For Doing So?

NASA Astrophysics Data System (ADS)

Johansson, Björn; Sudzina, Frantisek

Enterprise resource planning (ERP) systems attract a high attention and open source software does it as well. The question is then if, and if so, when do open source ERP systems take off. The paper describes the status of open source ERP systems. Based on literature review of ERP system selection criteria based on Web of Science articles, it discusses reported reasons for choosing open source or proprietary ERP systems. Last but not least, the article presents some conclusions that could act as input for future research. The paper aims at building up a foundation for the basic question: What are the reasons for an organization to adopt open source ERP systems.

To Friend or Not to Friend: The Use of Social Media in Clinical Oncology

PubMed Central

Wiener, Lori; Crum, Caroline; Grady, Christine; Merchant, Melinda

2012-01-01

Online social networking has replaced more traditional methods of personal and professional communication in many segments of society today. The wide reach and immediacy of social media facilitate dissemination of knowledge in advocacy and cancer education, but the usefulness of social media in personal relationships between patients and providers is still unclear. Although professional guidelines regarding e-mail communication may be relevant to social media, the inherent openness in social networks creates potential boundary and privacy issues in the provider-patient context. This commentary seeks to increase provider awareness of unique issues and challenges raised by the integration of social networking into oncology communications. PMID:23077437

Milestones in chloroplast genetic engineering: an environmentally friendly era in biotechnology.

PubMed

Daniell, Henry; Khan, Muhammad S; Allison, Lori

2002-02-01

Chloroplast genomes defied the laws of Mendelian inheritance at the dawn of plant genetics, and continue to defy the mainstream approach to biotechnology, leading the field in an environmentally friendly direction. Recent success in engineering the chloroplast genome for resistance to herbicides, insects, disease and drought, and for production of biopharmaceuticals, has opened the door to a new era in biotechnology. The successful engineering of tomato chromoplasts for high-level transgene expression in fruits, coupled to hyper-expression of vaccine antigens, and the use of plant-derived antibiotic-free selectable markers, augur well for oral delivery of edible vaccines and biopharmaceuticals that are currently beyond the reach of those who need them most.

Open Astronomy Catalogs API

NASA Astrophysics Data System (ADS)

Guillochon, James; Cowperthwaite, Philip S.

2018-05-01

We announce the public release of the application program interface (API) for the Open Astronomy Catalogs (OACs), the OACAPI. The OACs serve near-complete collections of supernova, tidal disruption, kilonova, and fast stars data (including photometry, spectra, radio, and X-ray observations) via a user-friendly web interface that displays the data interactively and offers full data downloads. The OACAPI, by contrast, enables users to specifically download particular pieces of the OAC dataset via a flexible programmatic syntax, either via URL GET requests, or via a module within the astroquery Python package.

Developing open-source codes for electromagnetic geophysics using industry support

NASA Astrophysics Data System (ADS)

Key, K.

2017-12-01

Funding for open-source software development in academia often takes the form of grants and fellowships awarded by government bodies and foundations where there is no conflict-of-interest between the funding entity and the free dissemination of the open-source software products. Conversely, funding for open-source projects in the geophysics industry presents challenges to conventional business models where proprietary licensing offers value that is not present in open-source software. Such proprietary constraints make it easier to convince companies to fund academic software development under exclusive software distribution agreements. A major challenge for obtaining commercial funding for open-source projects is to offer a value proposition that overcomes the criticism that such funding is a give-away to the competition. This work draws upon a decade of experience developing open-source electromagnetic geophysics software for the oil, gas and minerals exploration industry, and examines various approaches that have been effective for sustaining industry sponsorship.

Behind Linus's Law: Investigating Peer Review Processes in Open Source

ERIC Educational Resources Information Center

Wang, Jing

2013-01-01

Open source software has revolutionized the way people develop software, organize collaborative work, and innovate. The numerous open source software systems that have been created and adopted over the past decade are influential and vital in all aspects of work and daily life. The understanding of open source software development can enhance its…

Implementing Open Source Platform for Education Quality Enhancement in Primary Education: Indonesia Experience

ERIC Educational Resources Information Center

Kisworo, Marsudi Wahyu

2016-01-01

Information and Communication Technology (ICT)-supported learning using free and open source platform draws little attention as open source initiatives were focused in secondary or tertiary educations. This study investigates possibilities of ICT-supported learning using open source platform for primary educations. The data of this study is taken…

An Analysis of Open Source Security Software Products Downloads

ERIC Educational Resources Information Center

Barta, Brian J.

2014-01-01

Despite the continued demand for open source security software, a gap in the identification of success factors related to the success of open source security software persists. There are no studies that accurately assess the extent of this persistent gap, particularly with respect to the strength of the relationships of open source software…

Research on OpenStack of open source cloud computing in colleges and universities’ computer room

NASA Astrophysics Data System (ADS)

Wang, Lei; Zhang, Dandan

2017-06-01

In recent years, the cloud computing technology has a rapid development, especially open source cloud computing. Open source cloud computing has attracted a large number of user groups by the advantages of open source and low cost, have now become a large-scale promotion and application. In this paper, firstly we briefly introduced the main functions and architecture of the open source cloud computing OpenStack tools, and then discussed deeply the core problems of computer labs in colleges and universities. Combining with this research, it is not that the specific application and deployment of university computer rooms with OpenStack tool. The experimental results show that the application of OpenStack tool can efficiently and conveniently deploy cloud of university computer room, and its performance is stable and the functional value is good.

MyGeneFriends: A Social Network Linking Genes, Genetic Diseases, and Researchers

PubMed Central

Allot, Alexis; Chennen, Kirsley; Nevers, Yannis; Poidevin, Laetitia; Kress, Arnaud; Ripp, Raymond; Thompson, Julie Dawn; Poch, Olivier

2017-01-01

Background The constant and massive increase of biological data offers unprecedented opportunities to decipher the function and evolution of genes and their roles in human diseases. However, the multiplicity of sources and flow of data mean that efficient access to useful information and knowledge production has become a major challenge. This challenge can be addressed by taking inspiration from Web 2.0 and particularly social networks, which are at the forefront of big data exploration and human-data interaction. Objective MyGeneFriends is a Web platform inspired by social networks, devoted to genetic disease analysis, and organized around three types of proactive agents: genes, humans, and genetic diseases. The aim of this study was to improve exploration and exploitation of biological, postgenomic era big data. Methods MyGeneFriends leverages conventions popularized by top social networks (Facebook, LinkedIn, etc), such as networks of friends, profile pages, friendship recommendations, affinity scores, news feeds, content recommendation, and data visualization. Results MyGeneFriends provides simple and intuitive interactions with data through evaluation and visualization of connections (friendships) between genes, humans, and diseases. The platform suggests new friends and publications and allows agents to follow the activity of their friends. It dynamically personalizes information depending on the user’s specific interests and provides an efficient way to share information with collaborators. Furthermore, the user’s behavior itself generates new information that constitutes an added value integrated in the network, which can be used to discover new connections between biological agents. Conclusions We have developed MyGeneFriends, a Web platform leveraging conventions from popular social networks to redefine the relationship between humans and biological big data and improve human processing of biomedical data. MyGeneFriends is available at lbgi.fr/mygenefriends. PMID:28623182

Common characteristics of open source software development and applicability for drug discovery: a systematic review

PubMed Central

2011-01-01

Background Innovation through an open source model has proven to be successful for software development. This success has led many to speculate if open source can be applied to other industries with similar success. We attempt to provide an understanding of open source software development characteristics for researchers, business leaders and government officials who may be interested in utilizing open source innovation in other contexts and with an emphasis on drug discovery. Methods A systematic review was performed by searching relevant, multidisciplinary databases to extract empirical research regarding the common characteristics and barriers of initiating and maintaining an open source software development project. Results Common characteristics to open source software development pertinent to open source drug discovery were extracted. The characteristics were then grouped into the areas of participant attraction, management of volunteers, control mechanisms, legal framework and physical constraints. Lastly, their applicability to drug discovery was examined. Conclusions We believe that the open source model is viable for drug discovery, although it is unlikely that it will exactly follow the form used in software development. Hybrids will likely develop that suit the unique characteristics of drug discovery. We suggest potential motivations for organizations to join an open source drug discovery project. We also examine specific differences between software and medicines, specifically how the need for laboratories and physical goods will impact the model as well as the effect of patents. PMID:21955914

Technology Opens New Doors--Literally

ERIC Educational Resources Information Center

Murphy, Patti

2008-01-01

Augmentative and alternative communication (AAC) devices can be of huge benefit to people with verbal communication challenges and is applicable in making a living space more accessible. This article presents the story of Sara Pyszka. Sara, 22, wanted a place where she could dance in her wheelchair with no onlookers and have friends over to watch…

76 FR 4894 - Notice Announcing Preliminary Permit Drawing

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-27

... Drawing January 20, 2011. Lock Hydro Friends Fund XLI Project No. 13736-000 Allegheny 7 Hydro, LLC Project... Secretary of the Commission, or her designee, will, by random drawing, determine the filing priority for the two applicants identified in this notice. The drawing is open to the public and will be held in room...

76 FR 4893 - Notice Announcing Preliminary Permit Drawing

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-27

... Drawing January 20, 2011. Lock Hydro Friends Fund XLIII Project No. 13745-000 FFP Missouri 14, LLC Project... Secretary of the Commission, or her designee, will, by random drawing, determine the filing priority for the three applicants identified in this notice. The drawing is open to the public and will be held in room...

Immunology: Is Actin at the Lytic Synapse a Friend or a Foe?

PubMed

Hammer, John A

2018-02-19

Cytotoxic T cells and natural killer cells defend us against disease by secreting lytic granules. Whether actin facilitates or thwarts lytic granule secretion has been an open question. Recent results now indicate that the answer depends on the maturation stage of the immune cell-target cell contact. Published by Elsevier Ltd.

Family-Friendly Policies and Equal Opportunities: A Contradiction in Terms?

ERIC Educational Resources Information Center

Bagilhole, Barbara

2006-01-01

This paper presents the findings from a research study of one large public sector organisation's strategy to promote gender equality and family friendliness. An examination was made of the organisation's policy documentation in this area and a questionnaire survey containing both closed and open-ended questions was undertaken across all staff in…

UNESCO Institute for Lifelong Learning: Annual Report 2013

ERIC Educational Resources Information Center

UNESCO Institute for Lifelong Learning, 2014

2014-01-01

In the introduction to this report, UNESCO Institute for Lifelong Learning (UIL) Director, Arne Carlsen, announces that UIL is presenting a new design and a new concept, aiming to make the report more reader-friendly. The main activities are highlighted, testimonies from beneficiaries and actors are included, and the report opens with a…

Distress, Stress and Solidarity in Palliative Care.

ERIC Educational Resources Information Center

deMontigny, Johanne

1993-01-01

Notes that role of psychologist on palliative care unit is to be there for terminally ill, their friends, and their families, both during the dying and the bereavement and for the caregiver team. Focuses on work of decoding ordinary words which for many patients hide painful past. Stresses necessity to remain open to unexpected. (Author/NB)

Fostering Character Education in an Urban Early Childhood Setting

ERIC Educational Resources Information Center

Kokoszka, Carla; Smith, Juliette

2016-01-01

This article describes the character education program in Donald Stewart School No. 51, in Elizabeth, NJ, a dual-language preschool serving 300 students that first opened its doors in 2004. Over the years this school has been committed to laying the foundation of character development with its preschoolers. Their pillar "Friends Care, Friends…

Social network profiles as information sources for adolescents' offline relations.

PubMed

Courtois, Cédric; All, Anissa; Vanwynsberghe, Hadewijch

2012-06-01

This article presents the results of a study concerning the use of online profile pages by adolescents to know more about "offline" friends and acquaintances. Previous research has indicated that social networking sites (SNSs) are used to gather information on new online contacts. However, several studies have demonstrated a substantial overlap between offline and online social networks. Hence, we question whether online connections are meaningful in gathering information on offline friends and acquaintances. First, the results indicate that a combination of passive uncertainty reduction (monitoring a target's profile) and interactive uncertainty reduction (communication through the target's profile) explains a considerable amount of variance in the level of uncertainty about both friends and acquaintances. More specifically, adolescents generally get to know much more about their acquaintances. Second, the results of online uncertainty reduction positively affect the degree of self-disclosure, which is imperative in building a solid friend relation. Further, we find that uncertainty reduction strategies positively mediate the effect of social anxiety on the level of certainty about friends. This implies that socially anxious teenagers benefit from SNSs by getting the conditions right to build a more solid relation with their friends. Hence, we conclude that SNSs play a substantial role in today's adolescents' everyday interpersonal communication.

The 2017 Bioinformatics Open Source Conference (BOSC)

PubMed Central

Harris, Nomi L.; Cock, Peter J.A.; Chapman, Brad; Fields, Christopher J.; Hokamp, Karsten; Lapp, Hilmar; Munoz-Torres, Monica; Tzovaras, Bastian Greshake; Wiencko, Heather

2017-01-01

The Bioinformatics Open Source Conference (BOSC) is a meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. The 18th annual BOSC ( http://www.open-bio.org/wiki/BOSC_2017) took place in Prague, Czech Republic in July 2017. The conference brought together nearly 250 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, open and reproducible science, and this year’s theme, open data. As in previous years, the conference was preceded by a two-day collaborative coding event open to the bioinformatics community, called the OBF Codefest. PMID:29118973

The 2017 Bioinformatics Open Source Conference (BOSC).

PubMed

Harris, Nomi L; Cock, Peter J A; Chapman, Brad; Fields, Christopher J; Hokamp, Karsten; Lapp, Hilmar; Munoz-Torres, Monica; Tzovaras, Bastian Greshake; Wiencko, Heather

2017-01-01

The Bioinformatics Open Source Conference (BOSC) is a meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. The 18th annual BOSC ( http://www.open-bio.org/wiki/BOSC_2017) took place in Prague, Czech Republic in July 2017. The conference brought together nearly 250 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, open and reproducible science, and this year's theme, open data. As in previous years, the conference was preceded by a two-day collaborative coding event open to the bioinformatics community, called the OBF Codefest.

KENNEDY SPACE CENTER, FLA. - Winston Scott, executive director of Florida Space Authority, speaks to attendees at a memorial service honoring the crew of Columbia. He stands in front of the Space Memorial Mirror at the KSC Visitor Complex. Feb. 1 is the one-year anniversary of the loss of the crew and orbiter Columbia in a tragic accident as the ship returned to Earth following mission STS-107. Scott is a former astronaut who flew on Columbia in 1997. Attended by many friends, co-workers and families, the memorial service was also open to the public.

NASA Image and Video Library

2004-02-01

KENNEDY SPACE CENTER, FLA. - Winston Scott, executive director of Florida Space Authority, speaks to attendees at a memorial service honoring the crew of Columbia. He stands in front of the Space Memorial Mirror at the KSC Visitor Complex. Feb. 1 is the one-year anniversary of the loss of the crew and orbiter Columbia in a tragic accident as the ship returned to Earth following mission STS-107. Scott is a former astronaut who flew on Columbia in 1997. Attended by many friends, co-workers and families, the memorial service was also open to the public.

The Efficient Utilization of Open Source Information

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

Baty, Samuel R.

These are a set of slides on the efficient utilization of open source information. Open source information consists of a vast set of information from a variety of sources. Not only does the quantity of open source information pose a problem, the quality of such information can hinder efforts. To show this, two case studies are mentioned: Iran and North Korea, in order to see how open source information can be utilized. The huge breadth and depth of open source information can complicate an analysis, especially because open information has no guarantee of accuracy. Open source information can provide keymore » insights either directly or indirectly: looking at supporting factors (flow of scientists, products and waste from mines, government budgets, etc.); direct factors (statements, tests, deployments). Fundamentally, it is the independent verification of information that allows for a more complete picture to be formed. Overlapping sources allow for more precise bounds on times, weights, temperatures, yields or other issues of interest in order to determine capability. Ultimately, a "good" answer almost never comes from an individual, but rather requires the utilization of a wide range of skill sets held by a team of people.« less

Source and Size of Emotional and Financial-Related Social Support Network on Physical Activity Behavior Among Older Adults.

PubMed

Loprinzi, Paul D; Joyner, Chelsea

2016-07-01

To examine the association of source of emotional- and financial-related social support and size of social support network on physical activity behavior among older adults. Data from the 1999-2006 NHANES were used (N = 5616; 60 to 85 yrs). Physical activity and emotional- and financial-related social support were assessed via self-report. Older adults with perceived having emotional social support had a 41% increased odds of meeting physical activity guidelines (OR = 1.41; 95% CI: 1.01-1.97). The only specific sources of social support that were associated with meeting physical activity guidelines was friend emotional support (OR = 1.19; 95% CI: 1.01-1.41) and financial support (OR = 1.28; 95% CI: 1.09-1.49). With regard to size of social support network, a dose-response relationship was observed. Compared with those with 0 close friends, those with 1 to 2, 3 to 4, 5, and 6+ close friends, respectively, had a 1.70-, 2.38-, 2.57-, and 2.71-fold increased odds of meeting physical activity guidelines. There was some evidence of gender- and age-specific associations between social support and physical activity. Emotional- and financial-related social support and size of social support network are associated with higher odds of meeting physical activity guidelines among older adults.

Dogs

MedlinePlus

... source of rabies. Be cautious with unfamiliar animals. Approach dogs with care, even if they seem friendly. ... more than 5 years since your last tetanus shot If you have any concerns about your or ...

The 2015 Bioinformatics Open Source Conference (BOSC 2015).

PubMed

Harris, Nomi L; Cock, Peter J A; Lapp, Hilmar; Chapman, Brad; Davey, Rob; Fields, Christopher; Hokamp, Karsten; Munoz-Torres, Monica

2016-02-01

The Bioinformatics Open Source Conference (BOSC) is organized by the Open Bioinformatics Foundation (OBF), a nonprofit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. Since its inception in 2000, BOSC has provided bioinformatics developers with a forum for communicating the results of their latest efforts to the wider research community. BOSC offers a focused environment for developers and users to interact and share ideas about standards; software development practices; practical techniques for solving bioinformatics problems; and approaches that promote open science and sharing of data, results, and software. BOSC is run as a two-day special interest group (SIG) before the annual Intelligent Systems in Molecular Biology (ISMB) conference. BOSC 2015 took place in Dublin, Ireland, and was attended by over 125 people, about half of whom were first-time attendees. Session topics included "Data Science;" "Standards and Interoperability;" "Open Science and Reproducibility;" "Translational Bioinformatics;" "Visualization;" and "Bioinformatics Open Source Project Updates". In addition to two keynote talks and dozens of shorter talks chosen from submitted abstracts, BOSC 2015 included a panel, titled "Open Source, Open Door: Increasing Diversity in the Bioinformatics Open Source Community," that provided an opportunity for open discussion about ways to increase the diversity of participants in BOSC in particular, and in open source bioinformatics in general. The complete program of BOSC 2015 is available online at http://www.open-bio.org/wiki/BOSC_2015_Schedule.

Reducing Work-Family Conflict through Different Sources of Social Support

ERIC Educational Resources Information Center

van Daalen, Geertje; Willemsen, Tineke M.; Sanders, Karin

2006-01-01

The present study examines the relationship between four sources of social support (i.e., spouse, relatives and friends, supervisor, and colleagues) and time and strain-based work-to-family and family-to-work conflict among 444 dual-earners. Gender differences with respect to the relationship between social support and work-family conflict were…

Open Source, Openness, and Higher Education

ERIC Educational Resources Information Center

Wiley, David

2006-01-01

In this article David Wiley provides an overview of how the general expansion of open source software has affected the world of education in particular. In doing so, Wiley not only addresses the development of open source software applications for teachers and administrators, he also discusses how the fundamental philosophy of the open source…

Microbe-ID: an open source toolbox for microbial genotyping and species identification

PubMed Central

Tabima, Javier F.; Everhart, Sydney E.; Larsen, Meredith M.; Weisberg, Alexandra J.; Kamvar, Zhian N.; Tancos, Matthew A.; Smart, Christine D.; Chang, Jeff H.

2016-01-01

Development of tools to identify species, genotypes, or novel strains of invasive organisms is critical for monitoring emergence and implementing rapid response measures. Molecular markers, although critical to identifying species or genotypes, require bioinformatic tools for analysis. However, user-friendly analytical tools for fast identification are not readily available. To address this need, we created a web-based set of applications called Microbe-ID that allow for customizing a toolbox for rapid species identification and strain genotyping using any genetic markers of choice. Two components of Microbe-ID, named Sequence-ID and Genotype-ID, implement species and genotype identification, respectively. Sequence-ID allows identification of species by using BLAST to query sequences for any locus of interest against a custom reference sequence database. Genotype-ID allows placement of an unknown multilocus marker in either a minimum spanning network or dendrogram with bootstrap support from a user-created reference database. Microbe-ID can be used for identification of any organism based on nucleotide sequences or any molecular marker type and several examples are provided. We created a public website for demonstration purposes called Microbe-ID (microbe-id.org) and provided a working implementation for the genus Phytophthora (phytophthora-id.org). In Phytophthora-ID, the Sequence-ID application allows identification based on ITS or cox spacer sequences. Genotype-ID groups individuals into clonal lineages based on simple sequence repeat (SSR) markers for the two invasive plant pathogen species P. infestans and P. ramorum. All code is open source and available on github and CRAN. Instructions for installation and use are provided at https://github.com/grunwaldlab/Microbe-ID. PMID:27602267

SENR /NRPy + : Numerical relativity in singular curvilinear coordinate systems

NASA Astrophysics Data System (ADS)

Ruchlin, Ian; Etienne, Zachariah B.; Baumgarte, Thomas W.

2018-03-01

We report on a new open-source, user-friendly numerical relativity code package called SENR /NRPy + . Our code extends previous implementations of the BSSN reference-metric formulation to a much broader class of curvilinear coordinate systems, making it ideally suited to modeling physical configurations with approximate or exact symmetries. In the context of modeling black hole dynamics, it is orders of magnitude more efficient than other widely used open-source numerical relativity codes. NRPy + provides a Python-based interface in which equations are written in natural tensorial form and output at arbitrary finite difference order as highly efficient C code, putting complex tensorial equations at the scientist's fingertips without the need for an expensive software license. SENR provides the algorithmic framework that combines the C codes generated by NRPy + into a functioning numerical relativity code. We validate against two other established, state-of-the-art codes, and achieve excellent agreement. For the first time—in the context of moving puncture black hole evolutions—we demonstrate nearly exponential convergence of constraint violation and gravitational waveform errors to zero as the order of spatial finite difference derivatives is increased, while fixing the numerical grids at moderate resolution in a singular coordinate system. Such behavior outside the horizons is remarkable, as numerical errors do not converge to zero near punctures, and all points along the polar axis are coordinate singularities. The formulation addresses such coordinate singularities via cell-centered grids and a simple change of basis that analytically regularizes tensor components with respect to the coordinates. Future plans include extending this formulation to allow dynamical coordinate grids and bispherical-like distribution of points to efficiently capture orbiting compact binary dynamics.

PreSurgMapp: a MATLAB Toolbox for Presurgical Mapping of Eloquent Functional Areas Based on Task-Related and Resting-State Functional MRI.

PubMed

Huang, Huiyuan; Ding, Zhongxiang; Mao, Dewang; Yuan, Jianhua; Zhu, Fangmei; Chen, Shuda; Xu, Yan; Lou, Lin; Feng, Xiaoyan; Qi, Le; Qiu, Wusi; Zhang, Han; Zang, Yu-Feng

2016-10-01

The main goal of brain tumor surgery is to maximize tumor resection while minimizing the risk of irreversible postoperative functional sequelae. Eloquent functional areas should be delineated preoperatively, particularly for patients with tumors near eloquent areas. Functional magnetic resonance imaging (fMRI) is a noninvasive technique that demonstrates great promise for presurgical planning. However, specialized data processing toolkits for presurgical planning remain lacking. Based on several functions in open-source software such as Statistical Parametric Mapping (SPM), Resting-State fMRI Data Analysis Toolkit (REST), Data Processing Assistant for Resting-State fMRI (DPARSF) and Multiple Independent Component Analysis (MICA), here, we introduce an open-source MATLAB toolbox named PreSurgMapp. This toolbox can reveal eloquent areas using comprehensive methods and various complementary fMRI modalities. For example, PreSurgMapp supports both model-based (general linear model, GLM, and seed correlation) and data-driven (independent component analysis, ICA) methods and processes both task-based and resting-state fMRI data. PreSurgMapp is designed for highly automatic and individualized functional mapping with a user-friendly graphical user interface (GUI) for time-saving pipeline processing. For example, sensorimotor and language-related components can be automatically identified without human input interference using an effective, accurate component identification algorithm using discriminability index. All the results generated can be further evaluated and compared by neuro-radiologists or neurosurgeons. This software has substantial value for clinical neuro-radiology and neuro-oncology, including application to patients with low- and high-grade brain tumors and those with epilepsy foci in the dominant language hemisphere who are planning to undergo a temporal lobectomy.

Addressing Hydro-economic Modeling Limitations - A Limited Foresight Sacramento Valley Model and an Open-source Modeling Platform

NASA Astrophysics Data System (ADS)

Harou, J. J.; Hansen, K. M.

2008-12-01

Increased scarcity of world water resources is inevitable given the limited supply and increased human pressures. The idea that "some scarcity is optimal" must be accepted for rational resource use and infrastructure management decisions to be made. Hydro-economic systems models are unique at representing the overlap of economic drivers, socio-political forces and distributed water resource systems. They demonstrate the tangible benefits of cooperation and integrated flexible system management. Further improvement of models, quality control practices and software will be needed for these academic policy tools to become accepted into mainstream water resource practice. Promising features include: calibration methods, limited foresight optimization formulations, linked simulation-optimization approaches (e.g. embedding pre-existing calibrated simulation models), spatial groundwater models, stream-aquifer interactions and stream routing, etc.. Conventional user-friendly decision support systems helped spread simulation models on a massive scale. Hydro-economic models must also find a means to facilitate construction, distribution and use. Some of these issues and model features are illustrated with a hydro-economic optimization model of the Sacramento Valley. Carry-over storage value functions are used to limit hydrologic foresight of the multi- period optimization model. Pumping costs are included in the formulation by tracking regional piezometric head of groundwater sub-basins. To help build and maintain this type of network model, an open-source water management modeling software platform is described and initial project work is discussed. The objective is to generically facilitate the connection of models, such as those developed in a modeling environment (GAMS, MatLab, Octave, "), to a geographic user interface (drag and drop node-link network) and a database (topology, parameters and time series). These features aim to incrementally move hydro- economic models in the direction of more practical implementation.

EuroForMix: An open source software based on a continuous model to evaluate STR DNA profiles from a mixture of contributors with artefacts.

PubMed

Bleka, Øyvind; Storvik, Geir; Gill, Peter

2016-03-01

We have released a software named EuroForMix to analyze STR DNA profiles in a user-friendly graphical user interface. The software implements a model to explain the allelic peak height on a continuous scale in order to carry out weight-of-evidence calculations for profiles which could be from a mixture of contributors. Through a properly parameterized model we are able to do inference on mixture proportions, the peak height properties, stutter proportion and degradation. In addition, EuroForMix includes models for allele drop-out, allele drop-in and sub-population structure. EuroForMix supports two inference approaches for likelihood ratio calculations. The first approach uses maximum likelihood estimation of the unknown parameters. The second approach is Bayesian based which requires prior distributions to be specified for the parameters involved. The user may specify any number of known and unknown contributors in the model, however we find that there is a practical computing time limit which restricts the model to a maximum of four unknown contributors. EuroForMix is the first freely open source, continuous model (accommodating peak height, stutter, drop-in, drop-out, population substructure and degradation), to be reported in the literature. It therefore serves an important purpose to act as an unrestricted platform to compare different solutions that are available. The implementation of the continuous model used in the software showed close to identical results to the R-package DNAmixtures, which requires a HUGIN Expert license to be used. An additional feature in EuroForMix is the ability for the user to adapt the Bayesian inference framework by incorporating their own prior information. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

The Emergence of Open-Source Software in North America

ERIC Educational Resources Information Center

Pan, Guohua; Bonk, Curtis J.

2007-01-01

Unlike conventional models of software development, the open source model is based on the collaborative efforts of users who are also co-developers of the software. Interest in open source software has grown exponentially in recent years. A "Google" search for the phrase open source in early 2005 returned 28.8 million webpage hits, while…

Exercise Key to Keeping Weight Off

MedlinePlus

... find out more about weight control, visit MedlinePlus. Source: NIH Research Matters: Why Exercise is Important in Maintaining Weight ... & Players Friends of the National Library of Medicine (FNLM) top

Proteomics to go: Proteomatic enables the user-friendly creation of versatile MS/MS data evaluation workflows.

PubMed

Specht, Michael; Kuhlgert, Sebastian; Fufezan, Christian; Hippler, Michael

2011-04-15

We present Proteomatic, an operating system independent and user-friendly platform that enables the construction and execution of MS/MS data evaluation pipelines using free and commercial software. Required external programs such as for peptide identification are downloaded automatically in the case of free software. Due to a strict separation of functionality and presentation, and support for multiple scripting languages, new processing steps can be added easily. Proteomatic is implemented in C++/Qt, scripts are implemented in Ruby, Python and PHP. All source code is released under the LGPL. Source code and installers for Windows, Mac OS X, and Linux are freely available at http://www.proteomatic.org. michael.specht@uni-muenster.de Supplementary data are available at Bioinformatics online.

Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on

PubMed Central

2011-01-01

Background The Blue Obelisk movement was established in 2005 as a response to the lack of Open Data, Open Standards and Open Source (ODOSOS) in chemistry. It aims to make it easier to carry out chemistry research by promoting interoperability between chemistry software, encouraging cooperation between Open Source developers, and developing community resources and Open Standards. Results This contribution looks back on the work carried out by the Blue Obelisk in the past 5 years and surveys progress and remaining challenges in the areas of Open Data, Open Standards, and Open Source in chemistry. Conclusions We show that the Blue Obelisk has been very successful in bringing together researchers and developers with common interests in ODOSOS, leading to development of many useful resources freely available to the chemistry community. PMID:21999342

Nuclear Receptor Signaling Atlas: Opening Access to the Biology of Nuclear Receptor Signaling Pathways.

PubMed

Becnel, Lauren B; Darlington, Yolanda F; Ochsner, Scott A; Easton-Marks, Jeremy R; Watkins, Christopher M; McOwiti, Apollo; Kankanamge, Wasula H; Wise, Michael W; DeHart, Michael; Margolis, Ronald N; McKenna, Neil J

2015-01-01

Signaling pathways involving nuclear receptors (NRs), their ligands and coregulators, regulate tissue-specific transcriptomes in diverse processes, including development, metabolism, reproduction, the immune response and neuronal function, as well as in their associated pathologies. The Nuclear Receptor Signaling Atlas (NURSA) is a Consortium focused around a Hub website (www.nursa.org) that annotates and integrates diverse 'omics datasets originating from the published literature and NURSA-funded Data Source Projects (NDSPs). These datasets are then exposed to the scientific community on an Open Access basis through user-friendly data browsing and search interfaces. Here, we describe the redesign of the Hub, version 3.0, to deploy "Web 2.0" technologies and add richer, more diverse content. The Molecule Pages, which aggregate information relevant to NR signaling pathways from myriad external databases, have been enhanced to include resources for basic scientists, such as post-translational modification sites and targeting miRNAs, and for clinicians, such as clinical trials. A portal to NURSA's Open Access, PubMed-indexed journal Nuclear Receptor Signaling has been added to facilitate manuscript submissions. Datasets and information on reagents generated by NDSPs are available, as is information concerning periodic new NDSP funding solicitations. Finally, the new website integrates the Transcriptomine analysis tool, which allows for mining of millions of richly annotated public transcriptomic data points in the field, providing an environment for dataset re-use and citation, bench data validation and hypothesis generation. We anticipate that this new release of the NURSA database will have tangible, long term benefits for both basic and clinical research in this field.

Neither the internist nor the Internet: use of and trust in health information sources by people with schizophrenia.

PubMed

Maguire, Paul A; Reay, Rebecca E; Looi, Jeffrey C L; Cubis, Jeff; Byrne, Gerard J; Raphael, Beverley

2011-06-01

The aim of this study was to explore health information sources accessed by people with schizophrenia and the level of trust invested in them. A cross-sectional survey was performed comparing the responses of 71 adults with schizophrenia (recruited from both community and inpatient settings) with 238 general practice attendees on their use of television, radio, the Internet, newspapers, magazines, family and friends, and doctor to obtain information on health matters, and their levels of trust in these sources. People with schizophrenia most commonly reported using a doctor, family and friends, and television to obtain information on health matters. However, compared with general practice attendees, they gained less health information from doctors and the Internet, and had less trust in doctors. Within-group analysis revealed that in people with schizophrenia: living alone increased the likelihood of obtaining health information from television; a higher level of education increased the odds of trusting the Internet as a health information source; a higher estimated household income was associated with an increased likelihood of trusting newspapers; and women with schizophrenia were considerably more likely than men with schizophrenia to trust family and friends as providers of health information. For both groups, there were significant positive correlations between the amount of health information obtained from a given information source and the level of trust invested in it. There are significant differences in the reported utilization and trust of health information sources between people with schizophrenia and attendees at general practice settings. Those with schizophrenia are less likely to trust and obtain information from a doctor, and less likely to access the Internet. Further research is required to explore this disparity. This is critical given the high rates of comorbid physical illness and reduced longevity in people suffering from schizophrenia.

Open Genetic Code: on open source in the life sciences.

PubMed

Deibel, Eric

2014-01-01

The introduction of open source in the life sciences is increasingly being suggested as an alternative to patenting. This is an alternative, however, that takes its shape at the intersection of the life sciences and informatics. Numerous examples can be identified wherein open source in the life sciences refers to access, sharing and collaboration as informatic practices. This includes open source as an experimental model and as a more sophisticated approach of genetic engineering. The first section discusses the greater flexibly in regard of patenting and the relationship to the introduction of open source in the life sciences. The main argument is that the ownership of knowledge in the life sciences should be reconsidered in the context of the centrality of DNA in informatic formats. This is illustrated by discussing a range of examples of open source models. The second part focuses on open source in synthetic biology as exemplary for the re-materialization of information into food, energy, medicine and so forth. The paper ends by raising the question whether another kind of alternative might be possible: one that looks at open source as a model for an alternative to the commodification of life that is understood as an attempt to comprehensively remove the restrictions from the usage of DNA in any of its formats.

Energy Harvesting from Surface River/Ocean Waves

NASA Astrophysics Data System (ADS)

Cai, Wenzheng

The renewable energy is an important subject especially today as the world is facing the results of the pollution and depletion of the conventional energy resources. Around 70% of the Earth's surface is covered by water where the energy of the waves/tides could be used as alternative source of energy that is sustainable and environmental friendly. Most of the research efforts are focused on the development of the large-scale technologies that can operate in the open Ocean. The potential of the low-frequency and small-amplitude wave condition in shallow rivers and lakes where most of the world wave energy exists has not been explored yet. The objective of the current study is to design and develop new concepts for wave energy extraction, which depend on oscillatory wave motion and have the ability to convert the small and medium waves. The proposed devices are self-generating without any external sources, which makes them lightweight and naturally floating on the surface of the water. Feasibility studies of both designs were performed using numerical modeling and field experiments. The final prototypes achieved power output of 5.0+/-0.6mW and 0.25+/-0.01mW, respectively. Array systems implementing both concepts were also introduced to improve the performance of the devices.

Baseline study of methane emission from anaerobic ponds of palm oil mill effluent treatment.

PubMed

Yacob, Shahrakbah; Ali Hassan, Mohd; Shirai, Yoshihito; Wakisaka, Minato; Subash, Sunderaj

2006-07-31

The world currently obtains its energy from the fossil fuels such as oil, natural gas and coal. However, the international crisis in the Middle East, rapid depletion of fossil fuel reserves as well as climate change have driven the world towards renewable energy sources which are abundant, untapped and environmentally friendly. Malaysia has abundant biomass resources generated from the agricultural industry particularly the large commodity, palm oil. This paper will focus on palm oil mill effluent (POME) as the source of renewable energy from the generation of methane and establish the current methane emission from the anaerobic treatment facility. The emission was measured from two anaerobic ponds in Felda Serting Palm Oil Mill for 52 weeks. The results showed that the methane content was between 35.0% and 70.0% and biogas flow rate ranged between 0.5 and 2.4 L/min/m(2). Total methane emission per anaerobic pond was 1043.1 kg/day. The total methane emission calculated from the two equations derived from relationships between methane emission and total carbon removal and POME discharged were comparable with field measurement. This study also revealed that anaerobic pond system is more efficient than open digesting tank system for POME treatment. Two main factors affecting the methane emission were mill activities and oil palm seasonal cropping.

GPU-powered model analysis with PySB/cupSODA.

PubMed

Harris, Leonard A; Nobile, Marco S; Pino, James C; Lubbock, Alexander L R; Besozzi, Daniela; Mauri, Giancarlo; Cazzaniga, Paolo; Lopez, Carlos F

2017-11-01

A major barrier to the practical utilization of large, complex models of biochemical systems is the lack of open-source computational tools to evaluate model behaviors over high-dimensional parameter spaces. This is due to the high computational expense of performing thousands to millions of model simulations required for statistical analysis. To address this need, we have implemented a user-friendly interface between cupSODA, a GPU-powered kinetic simulator, and PySB, a Python-based modeling and simulation framework. For three example models of varying size, we show that for large numbers of simulations PySB/cupSODA achieves order-of-magnitude speedups relative to a CPU-based ordinary differential equation integrator. The PySB/cupSODA interface has been integrated into the PySB modeling framework (version 1.4.0), which can be installed from the Python Package Index (PyPI) using a Python package manager such as pip. cupSODA source code and precompiled binaries (Linux, Mac OS/X, Windows) are available at github.com/aresio/cupSODA (requires an Nvidia GPU; developer.nvidia.com/cuda-gpus). Additional information about PySB is available at pysb.org. paolo.cazzaniga@unibg.it or c.lopez@vanderbilt.edu. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

ASaiM: a Galaxy-based framework to analyze microbiota data.

PubMed

Batut, Bérénice; Gravouil, Kévin; Defois, Clémence; Hiltemann, Saskia; Brugère, Jean-François; Peyretaillade, Eric; Peyret, Pierre

2018-05-22

New generations of sequencing platforms coupled to numerous bioinformatics tools has led to rapid technological progress in metagenomics and metatranscriptomics to investigate complex microorganism communities. Nevertheless, a combination of different bioinformatic tools remains necessary to draw conclusions out of microbiota studies. Modular and user-friendly tools would greatly improve such studies. We therefore developed ASaiM, an Open-Source Galaxy-based framework dedicated to microbiota data analyses. ASaiM provides an extensive collection of tools to assemble, extract, explore and visualize microbiota information from raw metataxonomic, metagenomic or metatranscriptomic sequences. To guide the analyses, several customizable workflows are included and are supported by tutorials and Galaxy interactive tours, which guide users through the analyses step by step. ASaiM is implemented as a Galaxy Docker flavour. It is scalable to thousands of datasets, but also can be used on a normal PC. The associated source code is available under Apache 2 license at https://github.com/ASaiM/framework and documentation can be found online (http://asaim.readthedocs.io). Based on the Galaxy framework, ASaiM offers a sophisticated environment with a variety of tools, workflows, documentation and training to scientists working on complex microorganism communities. It makes analysis and exploration analyses of microbiota data easy, quick, transparent, reproducible and shareable.

The Open Source Teaching Project (OSTP): Research Note.

ERIC Educational Resources Information Center

Hirst, Tony

The Open Source Teaching Project (OSTP) is an attempt to apply a variant of the successful open source software approach to the development of educational materials. Open source software is software licensed in such a way as to allow anyone the right to modify and use it. From such a simple premise, a whole industry has arisen, most notably in the…

Free for All: Open Source Software

ERIC Educational Resources Information Center

Schneider, Karen

2008-01-01

Open source software has become a catchword in libraryland. Yet many remain unclear about open source's benefits--or even what it is. So what is open source software (OSS)? It's software that is free in every sense of the word: free to download, free to use, and free to view or modify. Most OSS is distributed on the Web and one doesn't need to…

Reflections on the role of open source in health information system interoperability.

PubMed

Sfakianakis, S; Chronaki, C E; Chiarugi, F; Conforti, F; Katehakis, D G

2007-01-01

This paper reflects on the role of open source in health information system interoperability. Open source is a driving force in computer science research and the development of information systems. It facilitates the sharing of information and ideas, enables evolutionary development and open collaborative testing of code, and broadens the adoption of interoperability standards. In health care, information systems have been developed largely ad hoc following proprietary specifications and customized design. However, the wide deployment of integrated services such as Electronic Health Records (EHRs) over regional health information networks (RHINs) relies on interoperability of the underlying information systems and medical devices. This reflection is built on the experiences of the PICNIC project that developed shared software infrastructure components in open source for RHINs and the OpenECG network that offers open source components to lower the implementation cost of interoperability standards such as SCP-ECG, in electrocardiography. Open source components implementing standards and a community providing feedback from real-world use are key enablers of health care information system interoperability. Investing in open source is investing in interoperability and a vital aspect of a long term strategy towards comprehensive health services and clinical research.

Aluminium alloyed iron-silicide/silicon solar cells: A simple approach for low cost environmental-friendly photovoltaic technology.

PubMed

Kumar Dalapati, Goutam; Masudy-Panah, Saeid; Kumar, Avishek; Cheh Tan, Cheng; Ru Tan, Hui; Chi, Dongzhi

2015-12-03

This work demonstrates the fabrication of silicide/silicon based solar cell towards the development of low cost and environmental friendly photovoltaic technology. A heterostructure solar cells using metallic alpha phase (α-phase) aluminum alloyed iron silicide (FeSi(Al)) on n-type silicon is fabricated with an efficiency of 0.8%. The fabricated device has an open circuit voltage and fill-factor of 240 mV and 60%, respectively. Performance of the device was improved by about 7 fold to 5.1% through the interface engineering. The α-phase FeSi(Al)/silicon solar cell devices have promising photovoltaic characteristic with an open circuit voltage, short-circuit current and a fill factor (FF) of 425 mV, 18.5 mA/cm(2), and 64%, respectively. The significant improvement of α-phase FeSi(Al)/n-Si solar cells is due to the formation p(+-)n homojunction through the formation of re-grown crystalline silicon layer (~5-10 nm) at the silicide/silicon interface. Thickness of the regrown silicon layer is crucial for the silicide/silicon based photovoltaic devices. Performance of the α-FeSi(Al)/n-Si solar cells significantly depends on the thickness of α-FeSi(Al) layer and process temperature during the device fabrication. This study will open up new opportunities for the Si based photovoltaic technology using a simple, sustainable, and los cost method.

Open Standards, Open Source, and Open Innovation: Harnessing the Benefits of Openness

ERIC Educational Resources Information Center

Committee for Economic Development, 2006

2006-01-01

Digitization of information and the Internet have profoundly expanded the capacity for openness. This report details the benefits of openness in three areas--open standards, open-source software, and open innovation--and examines the major issues in the debate over whether openness should be encouraged or not. The report explains each of these…

Cissus quadrangularis mediated ecofriendly synthesis of copper oxide nanoparticles and its antifungal studies against Aspergillus niger, Aspergillus flavus.

PubMed

Devipriya, Duraipandi; Roopan, Selvaraj Mohana

2017-11-01

Recently, non-toxic source mediated synthesis of metal and a metal oxide nanoparticle attains more attention due to key applicational responsibilities. This present report stated that the eco-friendly synthesis of copper oxide nanoparticles (CuO NPs) using Cissus quadrangularis (C. quadrangularis) plant extract. Further the eco-friendly synthesized CuO NPs were characterized using a number of analytical techniques. The observed results stated that the synthesized CuO NPs were spherical in shape with 30±2nm. Then the eco-friendly synthesized CuO NPs were subjected for anti-fungal against two strains namely Aspergillus niger (A. niger) resulted in 83% at 500ppm, 86% of inhibition at 1000ppm and Aspergillus flavus (A. flavus) resulted in 81% at 500ppm, 85% of inhibition at 1000ppm respectively. Despite the fact that compared to standard Carbendazim, eco-friendly synthesized CuO NPs exhibits better results were discussed in this manuscript. Copyright © 2017 Elsevier B.V. All rights reserved.

The 2015 Bioinformatics Open Source Conference (BOSC 2015)

PubMed Central

Harris, Nomi L.; Cock, Peter J. A.; Lapp, Hilmar

2016-01-01

The Bioinformatics Open Source Conference (BOSC) is organized by the Open Bioinformatics Foundation (OBF), a nonprofit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. Since its inception in 2000, BOSC has provided bioinformatics developers with a forum for communicating the results of their latest efforts to the wider research community. BOSC offers a focused environment for developers and users to interact and share ideas about standards; software development practices; practical techniques for solving bioinformatics problems; and approaches that promote open science and sharing of data, results, and software. BOSC is run as a two-day special interest group (SIG) before the annual Intelligent Systems in Molecular Biology (ISMB) conference. BOSC 2015 took place in Dublin, Ireland, and was attended by over 125 people, about half of whom were first-time attendees. Session topics included “Data Science;” “Standards and Interoperability;” “Open Science and Reproducibility;” “Translational Bioinformatics;” “Visualization;” and “Bioinformatics Open Source Project Updates”. In addition to two keynote talks and dozens of shorter talks chosen from submitted abstracts, BOSC 2015 included a panel, titled “Open Source, Open Door: Increasing Diversity in the Bioinformatics Open Source Community,” that provided an opportunity for open discussion about ways to increase the diversity of participants in BOSC in particular, and in open source bioinformatics in general. The complete program of BOSC 2015 is available online at http://www.open-bio.org/wiki/BOSC_2015_Schedule. PMID:26914653

Support for an expanded tripartite influence model with gay men.

PubMed

Tylka, Tracy L; Andorka, Michael J

2012-01-01

This study investigated whether an expanded tripartite influence model would represent gay men's experiences. This model was extended by adding partners and gay community involvement as sources of social influence and considering dual body image pathways (muscularity and body fat dissatisfaction) to muscularity enhancement and disordered eating behaviors. Latent variable structural equation modeling analyses upheld this model for 346 gay men. Dual body image pathways to body change behaviors were supported, although three unanticipated interrelationships emerged, suggesting that muscularity and body fat concerns and behaviors may be more integrated for gay men. Internalization of the mesomorphic ideal, appearance comparison, muscularity dissatisfaction, and body fat dissatisfaction were key mediators in the model. Of the sources of social influence, friend and media pressure to be lean, gay community involvement, and partner, friend, media, and family pressures to be muscular made incremental contributions. Unexpectedly, certain sources were directly connected to body change behaviors. Copyright © 2011 Elsevier Ltd. All rights reserved.

The 2016 Bioinformatics Open Source Conference (BOSC).

PubMed

Harris, Nomi L; Cock, Peter J A; Chapman, Brad; Fields, Christopher J; Hokamp, Karsten; Lapp, Hilmar; Muñoz-Torres, Monica; Wiencko, Heather

2016-01-01

Message from the ISCB: The Bioinformatics Open Source Conference (BOSC) is a yearly meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. BOSC has been run since 2000 as a two-day Special Interest Group (SIG) before the annual ISMB conference. The 17th annual BOSC ( http://www.open-bio.org/wiki/BOSC_2016) took place in Orlando, Florida in July 2016. As in previous years, the conference was preceded by a two-day collaborative coding event open to the bioinformatics community. The conference brought together nearly 100 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, and open and reproducible science.

Trust in Sources of Advice about Infant Care Practices: The SAFE Study.

PubMed

Hwang, Sunah S; Rybin, Denis V; Heeren, Timothy C; Colson, Eve R; Corwin, Michael J

2016-09-01

Objectives (1) Determine the prevalence of maternal trust in advice sources on infant care practices; (2) Investigate the association of maternal and infant characteristics with trust in advice sources on infant care practices. Methods Using probability sampling methods, we recruited mothers from 32 U.S. maternity hospitals with oversampling of Black and Hispanic women resulting in a nationally representative sample of mothers of infants aged 2-6 months. Survey questions assessed maternal trust in advice sources (physicians, nurses, family, friends, and media) regarding infant care practices including infant sleep practices (sleep position, bed sharing, and pacifier use), feeding, and vaccination. Weighted frequencies of maternal trust in advice sources were calculated to obtain prevalence estimates. Multivariable logistic regression was used to assess the association of maternal and infant characteristics with maternal trust in advice sources. Results Mothers had the greatest trust in doctors for advice on all infant care practices (56-89 %), while trust was lowest for friends (13-22 %) and the media (10-14 %). In the adjusted analyses, there were significant associations of maternal race/ethnicity, education, and age with trust in advice sources. Conclusions for Practice Maternal trust in advice about infant care practices varied significantly by source. A better understanding of which advice sources are most trusted by mothers, as well as the factors associated with maternal trust, may guide the development of more effective strategies to improve adherence to health promoting infant care practices.

Beyond Open Source: According to Jim Hirsch, Open Technology, Not Open Source, Is the Wave of the Future

ERIC Educational Resources Information Center

Villano, Matt

2006-01-01

This article presents an interview with Jim Hirsch, an associate superintendent for technology at Piano Independent School District in Piano, Texas. Hirsch serves as a liaison for the open technologies committee of the Consortium for School Networking. In this interview, he shares his opinion on the significance of open source in K-12.

EMISSIONS OF ORGANIC AIR TOXICS FROM OPEN ...

EPA Pesticide Factsheets

A detailed literature search was performed to collect and collate available data reporting emissions of toxic organic substances into the air from open burning sources. Availability of data varied according to the source and the class of air toxics of interest. Volatile organic compound (VOC) and polycyclic aromatic hydrocarbon (PAH) data were available for many of the sources. Data on semivolatile organic compounds (SVOCs) that are not PAHs were available for several sources. Carbonyl and polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofuran (PCDD/F) data were available for only a few sources. There were several sources for which no emissions data were available at all. Several observations were made including: 1) Biomass open burning sources typically emitted less VOCs than open burning sources with anthropogenic fuels on a mass emitted per mass burned basis, particularly those where polymers were concerned; 2) Biomass open burning sources typically emitted less SVOCs and PAHs than anthropogenic sources on a mass emitted per mass burned basis. Burning pools of crude oil and diesel fuel produced significant amounts of PAHs relative to other types of open burning. PAH emissions were highest when combustion of polymers was taking place; and 3) Based on very limited data, biomass open burning sources typically produced higher levels of carbonyls than anthropogenic sources on a mass emitted per mass burned basis, probably due to oxygenated structures r

Using simple agent-based modeling to inform and enhance neighborhood walkability

PubMed Central

2013-01-01

Background Pedestrian-friendly neighborhoods with proximal destinations and services encourage walking and decrease car dependence, thereby contributing to more active and healthier communities. Proximity to key destinations and services is an important aspect of the urban design decision making process, particularly in areas adopting a transit-oriented development (TOD) approach to urban planning, whereby densification occurs within walking distance of transit nodes. Modeling destination access within neighborhoods has been limited to circular catchment buffers or more sophisticated network-buffers generated using geoprocessing routines within geographical information systems (GIS). Both circular and network-buffer catchment methods are problematic. Circular catchment models do not account for street networks, thus do not allow exploratory ‘what-if’ scenario modeling; and network-buffering functionality typically exists within proprietary GIS software, which can be costly and requires a high level of expertise to operate. Methods This study sought to overcome these limitations by developing an open-source simple agent-based walkable catchment tool that can be used by researchers, urban designers, planners, and policy makers to test scenarios for improving neighborhood walkable catchments. A simplified version of an agent-based model was ported to a vector-based open source GIS web tool using data derived from the Australian Urban Research Infrastructure Network (AURIN). The tool was developed and tested with end-user stakeholder working group input. Results The resulting model has proven to be effective and flexible, allowing stakeholders to assess and optimize the walkability of neighborhood catchments around actual or potential nodes of interest (e.g., schools, public transport stops). Users can derive a range of metrics to compare different scenarios modeled. These include: catchment area versus circular buffer ratios; mean number of streets crossed; and modeling of different walking speeds and wait time at intersections. Conclusions The tool has the capacity to influence planning and public health advocacy and practice, and by using open-access source software, it is available for use locally and internationally. There is also scope to extend this version of the tool from a simple to a complex model, which includes agents (i.e., simulated pedestrians) ‘learning’ and incorporating other environmental attributes that enhance walkability (e.g., residential density, mixed land use, traffic volume). PMID:24330721

JUICE: a data management system that facilitates the analysis of large volumes of information in an EST project workflow.

PubMed

Latorre, Mariano; Silva, Herman; Saba, Juan; Guziolowski, Carito; Vizoso, Paula; Martinez, Veronica; Maldonado, Jonathan; Morales, Andrea; Caroca, Rodrigo; Cambiazo, Veronica; Campos-Vargas, Reinaldo; Gonzalez, Mauricio; Orellana, Ariel; Retamales, Julio; Meisel, Lee A

2006-11-23

Expressed sequence tag (EST) analyses provide a rapid and economical means to identify candidate genes that may be involved in a particular biological process. These ESTs are useful in many Functional Genomics studies. However, the large quantity and complexity of the data generated during an EST sequencing project can make the analysis of this information a daunting task. In an attempt to make this task friendlier, we have developed JUICE, an open source data management system (Apache + PHP + MySQL on Linux), which enables the user to easily upload, organize, visualize and search the different types of data generated in an EST project pipeline. In contrast to other systems, the JUICE data management system allows a branched pipeline to be established, modified and expanded, during the course of an EST project. The web interfaces and tools in JUICE enable the users to visualize the information in a graphical, user-friendly manner. The user may browse or search for sequences and/or sequence information within all the branches of the pipeline. The user can search using terms associated with the sequence name, annotation or other characteristics stored in JUICE and associated with sequences or sequence groups. Groups of sequences can be created by the user, stored in a clipboard and/or downloaded for further analyses. Different user profiles restrict the access of each user depending upon their role in the project. The user may have access exclusively to visualize sequence information, access to annotate sequences and sequence information, or administrative access. JUICE is an open source data management system that has been developed to aid users in organizing and analyzing the large amount of data generated in an EST Project workflow. JUICE has been used in one of the first functional genomics projects in Chile, entitled "Functional Genomics in nectarines: Platform to potentiate the competitiveness of Chile in fruit exportation". However, due to its ability to organize and visualize data from external pipelines, JUICE is a flexible data management system that should be useful for other EST/Genome projects. The JUICE data management system is released under the Open Source GNU Lesser General Public License (LGPL). JUICE may be downloaded from http://genoma.unab.cl/juice_system/ or http://www.genomavegetal.cl/juice_system/.

JUICE: a data management system that facilitates the analysis of large volumes of information in an EST project workflow

PubMed Central

Latorre, Mariano; Silva, Herman; Saba, Juan; Guziolowski, Carito; Vizoso, Paula; Martinez, Veronica; Maldonado, Jonathan; Morales, Andrea; Caroca, Rodrigo; Cambiazo, Veronica; Campos-Vargas, Reinaldo; Gonzalez, Mauricio; Orellana, Ariel; Retamales, Julio; Meisel, Lee A

2006-01-01

Background Expressed sequence tag (EST) analyses provide a rapid and economical means to identify candidate genes that may be involved in a particular biological process. These ESTs are useful in many Functional Genomics studies. However, the large quantity and complexity of the data generated during an EST sequencing project can make the analysis of this information a daunting task. Results In an attempt to make this task friendlier, we have developed JUICE, an open source data management system (Apache + PHP + MySQL on Linux), which enables the user to easily upload, organize, visualize and search the different types of data generated in an EST project pipeline. In contrast to other systems, the JUICE data management system allows a branched pipeline to be established, modified and expanded, during the course of an EST project. The web interfaces and tools in JUICE enable the users to visualize the information in a graphical, user-friendly manner. The user may browse or search for sequences and/or sequence information within all the branches of the pipeline. The user can search using terms associated with the sequence name, annotation or other characteristics stored in JUICE and associated with sequences or sequence groups. Groups of sequences can be created by the user, stored in a clipboard and/or downloaded for further analyses. Different user profiles restrict the access of each user depending upon their role in the project. The user may have access exclusively to visualize sequence information, access to annotate sequences and sequence information, or administrative access. Conclusion JUICE is an open source data management system that has been developed to aid users in organizing and analyzing the large amount of data generated in an EST Project workflow. JUICE has been used in one of the first functional genomics projects in Chile, entitled "Functional Genomics in nectarines: Platform to potentiate the competitiveness of Chile in fruit exportation". However, due to its ability to organize and visualize data from external pipelines, JUICE is a flexible data management system that should be useful for other EST/Genome projects. The JUICE data management system is released under the Open Source GNU Lesser General Public License (LGPL). JUICE may be downloaded from or . PMID:17123449

DigR: a generic model and its open source simulation software to mimic three-dimensional root-system architecture diversity.

PubMed

Barczi, Jean-François; Rey, Hervé; Griffon, Sébastien; Jourdan, Christophe

2018-04-18

Many studies exist in the literature dealing with mathematical representations of root systems, categorized, for example, as pure structure description, partial derivative equations or functional-structural plant models. However, in these studies, root architecture modelling has seldom been carried out at the organ level with the inclusion of environmental influences that can be integrated into a whole plant characterization. We have conducted a multidisciplinary study on root systems including field observations, architectural analysis, and formal and mathematical modelling. This integrative and coherent approach leads to a generic model (DigR) and its software simulator. Architecture analysis applied to root systems helps at root type classification and architectural unit design for each species. Roots belonging to a particular type share dynamic and morphological characteristics which consist of topological and geometric features. The DigR simulator is integrated into the Xplo environment, with a user interface to input parameter values and make output ready for dynamic 3-D visualization, statistical analysis and saving to standard formats. DigR is simulated in a quasi-parallel computing algorithm and may be used either as a standalone tool or integrated into other simulation platforms. The software is open-source and free to download at http://amapstudio.cirad.fr/soft/xplo/download. DigR is based on three key points: (1) a root-system architectural analysis, (2) root type classification and modelling and (3) a restricted set of 23 root type parameters with flexible values indexed in terms of root position. Genericity and botanical accuracy of the model is demonstrated for growth, branching, mortality and reiteration processes, and for different root architectures. Plugin examples demonstrate the model's versatility at simulating plastic responses to environmental constraints. Outputs of the model include diverse root system structures such as tap-root, fasciculate, tuberous, nodulated and clustered root systems. DigR is based on plant architecture analysis which leads to specific root type classification and organization that are directly linked to field measurements. The open source simulator of the model has been included within a friendly user environment. DigR accuracy and versatility are demonstrated for growth simulations of complex root systems for both annual and perennial plants.

OptFlux: an open-source software platform for in silico metabolic engineering.

PubMed

Rocha, Isabel; Maia, Paulo; Evangelista, Pedro; Vilaça, Paulo; Soares, Simão; Pinto, José P; Nielsen, Jens; Patil, Kiran R; Ferreira, Eugénio C; Rocha, Miguel

2010-04-19

Over the last few years a number of methods have been proposed for the phenotype simulation of microorganisms under different environmental and genetic conditions. These have been used as the basis to support the discovery of successful genetic modifications of the microbial metabolism to address industrial goals. However, the use of these methods has been restricted to bioinformaticians or other expert researchers. The main aim of this work is, therefore, to provide a user-friendly computational tool for Metabolic Engineering applications. OptFlux is an open-source and modular software aimed at being the reference computational application in the field. It is the first tool to incorporate strain optimization tasks, i.e., the identification of Metabolic Engineering targets, using Evolutionary Algorithms/Simulated Annealing metaheuristics or the previously proposed OptKnock algorithm. It also allows the use of stoichiometric metabolic models for (i) phenotype simulation of both wild-type and mutant organisms, using the methods of Flux Balance Analysis, Minimization of Metabolic Adjustment or Regulatory on/off Minimization of Metabolic flux changes, (ii) Metabolic Flux Analysis, computing the admissible flux space given a set of measured fluxes, and (iii) pathway analysis through the calculation of Elementary Flux Modes. OptFlux also contemplates several methods for model simplification and other pre-processing operations aimed at reducing the search space for optimization algorithms. The software supports importing/exporting to several flat file formats and it is compatible with the SBML standard. OptFlux has a visualization module that allows the analysis of the model structure that is compatible with the layout information of Cell Designer, allowing the superimposition of simulation results with the model graph. The OptFlux software is freely available, together with documentation and other resources, thus bridging the gap from research in strain optimization algorithms and the final users. It is a valuable platform for researchers in the field that have available a number of useful tools. Its open-source nature invites contributions by all those interested in making their methods available for the community. Given its plug-in based architecture it can be extended with new functionalities. Currently, several plug-ins are being developed, including network topology analysis tools and the integration with Boolean network based regulatory models.

OptFlux: an open-source software platform for in silico metabolic engineering

PubMed Central

2010-01-01

Background Over the last few years a number of methods have been proposed for the phenotype simulation of microorganisms under different environmental and genetic conditions. These have been used as the basis to support the discovery of successful genetic modifications of the microbial metabolism to address industrial goals. However, the use of these methods has been restricted to bioinformaticians or other expert researchers. The main aim of this work is, therefore, to provide a user-friendly computational tool for Metabolic Engineering applications. Results OptFlux is an open-source and modular software aimed at being the reference computational application in the field. It is the first tool to incorporate strain optimization tasks, i.e., the identification of Metabolic Engineering targets, using Evolutionary Algorithms/Simulated Annealing metaheuristics or the previously proposed OptKnock algorithm. It also allows the use of stoichiometric metabolic models for (i) phenotype simulation of both wild-type and mutant organisms, using the methods of Flux Balance Analysis, Minimization of Metabolic Adjustment or Regulatory on/off Minimization of Metabolic flux changes, (ii) Metabolic Flux Analysis, computing the admissible flux space given a set of measured fluxes, and (iii) pathway analysis through the calculation of Elementary Flux Modes. OptFlux also contemplates several methods for model simplification and other pre-processing operations aimed at reducing the search space for optimization algorithms. The software supports importing/exporting to several flat file formats and it is compatible with the SBML standard. OptFlux has a visualization module that allows the analysis of the model structure that is compatible with the layout information of Cell Designer, allowing the superimposition of simulation results with the model graph. Conclusions The OptFlux software is freely available, together with documentation and other resources, thus bridging the gap from research in strain optimization algorithms and the final users. It is a valuable platform for researchers in the field that have available a number of useful tools. Its open-source nature invites contributions by all those interested in making their methods available for the community. Given its plug-in based architecture it can be extended with new functionalities. Currently, several plug-ins are being developed, including network topology analysis tools and the integration with Boolean network based regulatory models. PMID:20403172

Trends in EFL Technology and Educational Coding: A Case Study of an Evaluation Application Developed on LiveCode

ERIC Educational Resources Information Center

Uehara, Suwako; Noriega, Edgar Josafat Martinez

2016-01-01

The availability of user-friendly coding software is increasing, yet teachers might hesitate to use this technology to develop for educational needs. This paper discusses studies related to technology for educational uses and introduces an evaluation application being developed. Through questionnaires by student users and open-ended discussion by…

Computation-Friendly Shape Grammars with Application to Determining the Interior Layout of Buildings from Image Data

ERIC Educational Resources Information Center

Yue, Kui

2009-01-01

A shape grammar is a formalism that has been widely applied, in many different fields, to analyzing designs. Computer implementation of a shape grammar interpreter is vital to both research and application. However, implementing a shape grammar interpreter is hard, especially for parametric shapes defined by open terms. This dissertation…

Heteronormativity in the University Classroom: Novelty Attachment and Content Substitution among Gay-Friendly Students

ERIC Educational Resources Information Center

Ripley, Matthew; Anderson, Eric; McCormack, Mark; Rockett, Ben

2012-01-01

This article explores the complex relationship between an openly gay instructor, homophobia, and heteronormativity in a university classroom. The authors first tabulated the frequency with which the instructor used the lives of heterosexuals and homosexuals as examples of content or as content itself, and then they interviewed 32 students about…

Making Friends and Buying Robots: How to Leverage Collaborations and Collections to Support STEM Learning

ERIC Educational Resources Information Center

Kvenild, Cassandra; Shepherd, Craig E.; Smith, Shannon M.; Thielk, Emma

2017-01-01

In a climate of increased interest in science, technology, engineering, and math (STEM), school libraries have unique opportunities to grow collections and cultivate partnerships in the sciences. At the federal level and in many states, STEM initiatives encourage hands-on exposure to technologies and open the door for student-led discovery of…

Operation Cleansweep in Florida: Extension's Role in an Environmentally Friendly Program Opportunity

ERIC Educational Resources Information Center

Fishel, Fred

2010-01-01

Operation Cleansweep is a free pesticide disposal program that has operated in Florida since 1995. The program is open to commercial facilities, including agricultural production establishments, golf course operators, and pest control companies. Since its inception, the program has had more than 1,700 participants and collected more than 1,000,000…

Operation Cleansweep in Florida: Extension's Role in an Environmental-Friendly Program Opportunity

ERIC Educational Resources Information Center

Fishel, Fred

2010-01-01

Operation Cleansweep is a free pesticide disposal program that has operated in Florida since 1995. The program is open to commercial facilities, including agricultural production establishments, golf course operators, and pest control companies. Since its inception, the program has had more than 1,700 participants and collected more than 1,000,000…

A Capstone on Her Career

ERIC Educational Resources Information Center

Goldman, Jay P.

2005-01-01

Joan Raymond was just six months into a well-earned retirement following 20 demanding years in the superintendency of some of the hottest kitchens in the nation. But when some longtime friends told her about an opening in South Bend, Indiana, Raymond could not ignore the itch to give it one more whirl. Raymond found the school system in far more…

Author as Dialogic Site: A Spatial Metaphor for Authoritative Voice.

ERIC Educational Resources Information Center

Haas, Mark

In a recent debate on authority in the discourse of English Studies scholarship, writers seem to line up on two sides: the "friends of the familiar essay," and those who advocate "the article." The essay/article debate seems to be part of the conflict opened by the Renaissance over writing, selfhood, power, and knowledge. What…

Managing the Openness-Closedness Dialectic: How Graduate Teaching Assistants Handle the Tension

ERIC Educational Resources Information Center

Webb, Nathan G.

2012-01-01

Graduate teaching assistants (GTAs) are a pervasive part of undergraduate education. When interacting with undergraduate students, GTAs must balance a tension of being a friend and an authority figure with students. One of the ways that balance is managed is through GTA self-disclosure. Self-disclosure is defined as, "the act of revealing…

Eco-friendly synthesis of TiO2, Au and Pt doped TiO2 nanoparticles for dye sensitized solar cell applications and evaluation of toxicity

NASA Astrophysics Data System (ADS)

Gopinath, K.; Kumaraguru, S.; Bhakyaraj, K.; Thirumal, S.; Arumugam, A.

2016-04-01

Driven by the demand of pure TiO2, Au and Pt doped TiO2 NPs were successfully synthesized using Terminalia arjuna bark extract. The eco-friendly synthesized NPs were characterized by UV-Vis-DRS, ATR-FT-IR, PL, XRD, Raman, SEM with EDX and TEM analysis. The synthesized NPs were investigation for dye sensitized solar cell applications. UV-Vis-Diffused Reflectance Spectra clearly showed that the expected TiO2 inter band absorption below 306 nm, incorporation of gold shows surface plasma resonant (SPR) near 555 nm and platinum incorporated TiO2 NPs shows absorbance at 460 nm. The energy conversion efficiency for Au doped TiO2 NPs when compared to pure and Pt doped TiO2 NPs. In addition to that, Au noble metal present TiO2 matrix and an improve open-circuit voltage (Voc) of DSSC. Synthesized NPs was evaluated into antibacterial and antifungal activities by disk diffusion method. It is observed that NPs have not shown any activities in all tested bacterial and fungal strains. In this eco-friendly synthesis method to provide non toxic and environmental friendly nanomaterials can be used for solar energy device application.

An Investigation of Social Support and Burnout among Special Education Teachers in the United Arab Emirates

ERIC Educational Resources Information Center

Bataineh, Osamah; Alsagheer, Ahmed

2012-01-01

This study aimed at investigating which source of social support (supervisors, colleagues, friends, spouse, or family) would be most effective in reducing burnout among special education teachers. A sample of 300 special education teachers (50 males and 250 females) completed Burnout and Sources of Social Support questionnaires. Pearson…

Automatic Camera Calibration for Cultural Heritage Applications Using Unstructured Planar Objects

NASA Astrophysics Data System (ADS)

Adam, K.; Kalisperakis, I.; Grammatikopoulos, L.; Karras, G.; Petsa, E.

2013-07-01

As a rule, image-based documentation of cultural heritage relies today on ordinary digital cameras and commercial software. As such projects often involve researchers not familiar with photogrammetry, the question of camera calibration is important. Freely available open-source user-friendly software for automatic camera calibration, often based on simple 2D chess-board patterns, are an answer to the demand for simplicity and automation. However, such tools cannot respond to all requirements met in cultural heritage conservation regarding possible imaging distances and focal lengths. Here we investigate the practical possibility of camera calibration from unknown planar objects, i.e. any planar surface with adequate texture; we have focused on the example of urban walls covered with graffiti. Images are connected pair-wise with inter-image homographies, which are estimated automatically through a RANSAC-based approach after extracting and matching interest points with the SIFT operator. All valid points are identified on all images on which they appear. Provided that the image set includes a "fronto-parallel" view, inter-image homographies with this image are regarded as emulations of image-to-world homographies and allow computing initial estimates for the interior and exterior orientation elements. Following this initialization step, the estimates are introduced into a final self-calibrating bundle adjustment. Measures are taken to discard unsuitable images and verify object planarity. Results from practical experimentation indicate that this method may produce satisfactory results. The authors intend to incorporate the described approach into their freely available user-friendly software tool, which relies on chess-boards, to assist non-experts in their projects with image-based approaches.

Isolating specific cell and tissue compartments from 3D images for quantitative regional distribution analysis using novel computer algorithms.

PubMed

Fenrich, Keith K; Zhao, Ethan Y; Wei, Yuan; Garg, Anirudh; Rose, P Ken

2014-04-15

Isolating specific cellular and tissue compartments from 3D image stacks for quantitative distribution analysis is crucial for understanding cellular and tissue physiology under normal and pathological conditions. Current approaches are limited because they are designed to map the distributions of synapses onto the dendrites of stained neurons and/or require specific proprietary software packages for their implementation. To overcome these obstacles, we developed algorithms to Grow and Shrink Volumes of Interest (GSVI) to isolate specific cellular and tissue compartments from 3D image stacks for quantitative analysis and incorporated these algorithms into a user-friendly computer program that is open source and downloadable at no cost. The GSVI algorithm was used to isolate perivascular regions in the cortex of live animals and cell membrane regions of stained spinal motoneurons in histological sections. We tracked the real-time, intravital biodistribution of injected fluorophores with sub-cellular resolution from the vascular lumen to the perivascular and parenchymal space following a vascular microlesion, and mapped the precise distributions of membrane-associated KCC2 and gephyrin immunolabeling in dendritic and somatic regions of spinal motoneurons. Compared to existing approaches, the GSVI approach is specifically designed for isolating perivascular regions and membrane-associated regions for quantitative analysis, is user-friendly, and free. The GSVI algorithm is useful to quantify regional differences of stained biomarkers (e.g., cell membrane-associated channels) in relation to cell functions, and the effects of therapeutic strategies on the redistributions of biomolecules, drugs, and cells in diseased or injured tissues. Copyright © 2014 Elsevier B.V. All rights reserved.

gPKPDSim: a SimBiology®-based GUI application for PKPD modeling in drug development.

PubMed

Hosseini, Iraj; Gajjala, Anita; Bumbaca Yadav, Daniela; Sukumaran, Siddharth; Ramanujan, Saroja; Paxson, Ricardo; Gadkar, Kapil

2018-04-01

Modeling and simulation (M&S) is increasingly used in drug development to characterize pharmacokinetic-pharmacodynamic (PKPD) relationships and support various efforts such as target feasibility assessment, molecule selection, human PK projection, and preclinical and clinical dose and schedule determination. While model development typically require mathematical modeling expertise, model exploration and simulations could in many cases be performed by scientists in various disciplines to support the design, analysis and interpretation of experimental studies. To this end, we have developed a versatile graphical user interface (GUI) application to enable easy use of any model constructed in SimBiology ® to execute various common PKPD analyses. The MATLAB ® -based GUI application, called gPKPDSim, has a single screen interface and provides functionalities including simulation, data fitting (parameter estimation), population simulation (exploring the impact of parameter variability on the outputs of interest), and non-compartmental PK analysis. Further, gPKPDSim is a user-friendly tool with capabilities including interactive visualization, exporting of results and generation of presentation-ready figures. gPKPDSim was designed primarily for use in preclinical and translational drug development, although broader applications exist. gPKPDSim is a MATLAB ® -based open-source application and is publicly available to download from MATLAB ® Central™. We illustrate the use and features of gPKPDSim using multiple PKPD models to demonstrate the wide applications of this tool in pharmaceutical sciences. Overall, gPKPDSim provides an integrated, multi-purpose user-friendly GUI application to enable efficient use of PKPD models by scientists from various disciplines, regardless of their modeling expertise.

Proteogenomic Analysis of Polymorphisms and Gene Annotation Divergences in Prokaryotes using a Clustered Mass Spectrometry-Friendly Database*

PubMed Central

de Souza, Gustavo A.; Arntzen, Magnus Ø.; Fortuin, Suereta; Schürch, Anita C.; Målen, Hiwa; McEvoy, Christopher R. E.; van Soolingen, Dick; Thiede, Bernd; Warren, Robin M.; Wiker, Harald G.

2011-01-01

Precise annotation of genes or open reading frames is still a difficult task that results in divergence even for data generated from the same genomic sequence. This has an impact in further proteomic studies, and also compromises the characterization of clinical isolates with many specific genetic variations that may not be represented in the selected database. We recently developed software called multistrain mass spectrometry prokaryotic database builder (MSMSpdbb) that can merge protein databases from several sources and be applied on any prokaryotic organism, in a proteomic-friendly approach. We generated a database for the Mycobacterium tuberculosis complex (using three strains of Mycobacterium bovis and five of M. tuberculosis), and analyzed data collected from two laboratory strains and two clinical isolates of M. tuberculosis. We identified 2561 proteins, of which 24 were present in M. tuberculosis H37Rv samples, but not annotated in the M. tuberculosis H37Rv genome. We were also able to identify 280 nonsynonymous single amino acid polymorphisms and confirm 367 translational start sites. As a proof of concept we applied the database to whole-genome DNA sequencing data of one of the clinical isolates, which allowed the validation of 116 predicted single amino acid polymorphisms and the annotation of 131 N-terminal start sites. Moreover we identified regions not present in the original M. tuberculosis H37Rv sequence, indicating strain divergence or errors in the reference sequence. In conclusion, we demonstrated the potential of using a merged database to better characterize laboratory or clinical bacterial strains. PMID:21030493

Developing family rooms in mental health inpatient units: an exploratory descriptive study.

PubMed

Isobel, Sophie; Foster, Kim; Edwards, Clair

2015-06-19

Family-friendly spaces for children and families to visit inpatient mental health units are recommended in international mental health guidelines as one way to provide service delivery that is responsive to the needs of parent-consumers and families. There is a lack of evidence on the implementation of family-friendly spaces or Family Rooms. This study aimed to explore the development, role, and function of Family Rooms in four mental health inpatient units in a local health district in NSW Australia. An exploratory descriptive inductive-deductive design using multiple data sources was employed. Methods included Family Room usage and parental status data over a 12 week period, an open-ended questionnaire, and semi-structured interviews with 20 nurses. Available parental status data indicated that between 8-14 % of inpatients were parents of dependent children under 18. Family Room usage was multipurpose and used specifically for children & families 29 % of the time. As spaces in the units, Family Rooms were perceived as acknowledging of the importance of family, and providing comfortable, secure spaces for parent-consumers and their children and family to maintain connections. Units did not have local policies or guidelines on the development, maintenance, and/or use of the rooms. Despite long-standing recognition of the need to identify consumers' parental status, there remains a lack of systematic processes for identifying parents in mental health inpatient services nationally. Family Rooms as spaces within inpatient units acknowledge the importance of families and are a step towards provision of family-focused mental health care. Recommendations for establishing and maintaining Family Rooms are outlined.

A user-friendly workflow for analysis of Illumina gene expression bead array data available at the arrayanalysis.org portal.

PubMed

Eijssen, Lars M T; Goelela, Varshna S; Kelder, Thomas; Adriaens, Michiel E; Evelo, Chris T; Radonjic, Marijana

2015-06-30

Illumina whole-genome expression bead arrays are a widely used platform for transcriptomics. Most of the tools available for the analysis of the resulting data are not easily applicable by less experienced users. ArrayAnalysis.org provides researchers with an easy-to-use and comprehensive interface to the functionality of R and Bioconductor packages for microarray data analysis. As a modular open source project, it allows developers to contribute modules that provide support for additional types of data or extend workflows. To enable data analysis of Illumina bead arrays for a broad user community, we have developed a module for ArrayAnalysis.org that provides a free and user-friendly web interface for quality control and pre-processing for these arrays. This module can be used together with existing modules for statistical and pathway analysis to provide a full workflow for Illumina gene expression data analysis. The module accepts data exported from Illumina's GenomeStudio, and provides the user with quality control plots and normalized data. The outputs are directly linked to the existing statistics module of ArrayAnalysis.org, but can also be downloaded for further downstream analysis in third-party tools. The Illumina bead arrays analysis module is available at http://www.arrayanalysis.org . A user guide, a tutorial demonstrating the analysis of an example dataset, and R scripts are available. The module can be used as a starting point for statistical evaluation and pathway analysis provided on the website or to generate processed input data for a broad range of applications in life sciences research.

Development of a baby friendly non-contact method for measuring vital signs: First results of clinical measurements in an open incubator at a neonatal intensive care unit

NASA Astrophysics Data System (ADS)

Klaessens, John H.; van den Born, Marlies; van der Veen, Albert; Sikkens-van de Kraats, Janine; van den Dungen, Frank A.; Verdaasdonk, Rudolf M.

2014-02-01

For infants and neonates in an incubator vital signs, such as heart rate, breathing, skin temperature and blood oxygen saturation are measured by sensors and electrodes sticking to the skin. This can damage the vulnerable skin of neonates and cause infections. In addition, the wires interfere with the care and hinder the parents in holding and touching the baby. These problems initiated the search for baby friendly 'non-contact' measurement of vital signs. Using a sensitive color video camera and specially developed software, the heart rate was derived from subtle repetitive color changes. Potentially also respiration and oxygen saturation could be obtained. A thermal camera was used to monitor the temperature distribution of the whole body and detect small temperature variations around the nose revealing the respiration rate. After testing in the laboratory, seven babies were monitored (with parental consent) in the neonatal intensive care unit (NICU) simultaneously with the regular monitoring equipment. From the color video recordings accurate heart rates could be derived and the thermal images provided accurate respiration rates. To correct for the movements of the baby, tracking software could be applied. At present, the image processing was performed off-line. Using narrow band light sources also non-contact blood oxygen saturation could be measured. Non-contact monitoring of vital signs has proven to be feasible and can be developed into a real time system. Besides the application on the NICU non-contact vital function monitoring has large potential for other patient groups.

Public awareness of palliative care in Sweden.

PubMed

Westerlund, Caroline; Tishelman, Carol; Benkel, Inger; Fürst, Carl Johan; Molander, Ulla; Rasmussen, Birgit H; Sauter, Sylvia; Lindqvist, Olav

2018-06-01

The aim of this study was to investigate the awareness of palliative care (PC) in a general Swedish population. We developed an e-survey based on a similar study conducted in Northern Ireland, consisting of 10 questions. Closed questions were primarily analyzed using descriptive statistics. Open questions were subject to inductive qualitative analysis. The study utilized a population sample of 7684 persons aged 18-66, of which 2020 responded, stratified by gender, age and region. Most participants reported 'no' ( n = 827, 41%) or 'some' ( n = 863, 43%) awareness of PC. Being female or older were associated with higher levels of awareness, as was a university-level education, working in a healthcare setting and having a friend or family member receiving PC. Most common sources of knowledge were the media, close friends and relatives receiving PC, as well as working in a healthcare setting. Aims of PC were most frequently identified as 'care before death', 'pain relief', 'dignity' and a 'peaceful death'. The preferred place of care and death was one's own home. The main barriers to raising awareness about PC were fear, shame and taboo, along with perceived lack of information and/or personal relevance. The term 'palliative care' was said to be unfamiliar by many. A number of strategies to enhance awareness and access to PC were suggested, largely reflecting the previously identified barriers. This survey found limited awareness of palliative care in an adult sample of the Swedish general public ≤ 66 years, and points to a more widespread disempowerment surrounding end-of-life issues.

Oxytocin, Social Support and Sleep Quality In Low Income Minority Women Living with HIV

PubMed Central

Fekete, Erin M.; Seay, Julia; Antoni, Michael H.; Mendez, Armando J.; Fletcher, Mary Ann; Szeto, Angela; Schneiderman, Neil

2013-01-01

Sleep disturbances are highly prevalent in women with HIV and few studies examine potential protective factors that may reduce risk for sleep disturbances in this high-risk population. We predicted that HIV-specific social support from various sources (i.e., friends, family, spouses), as well as oxytocin (OT), would explain sleep quality in 71 low income minority women living with HIV. Social support from family members was associated with better sleep quality in women. For women with high OT, support from friends was associated with better sleep quality, while for women with low OT, support from friends was associated with poorer sleep quality. Women with low OT may not effectively interpret and utilize available support resources, which may be associated with sleep disturbances. PMID:23799864

Open-Source 3D-Printable Optics Equipment

PubMed Central

Zhang, Chenlong; Anzalone, Nicholas C.; Faria, Rodrigo P.; Pearce, Joshua M.

2013-01-01

Just as the power of the open-source design paradigm has driven down the cost of software to the point that it is accessible to most people, the rise of open-source hardware is poised to drive down the cost of doing experimental science to expand access to everyone. To assist in this aim, this paper introduces a library of open-source 3-D-printable optics components. This library operates as a flexible, low-cost public-domain tool set for developing both research and teaching optics hardware. First, the use of parametric open-source designs using an open-source computer aided design package is described to customize the optics hardware for any application. Second, details are provided on the use of open-source 3-D printers (additive layer manufacturing) to fabricate the primary mechanical components, which are then combined to construct complex optics-related devices. Third, the use of the open-source electronics prototyping platform are illustrated as control for optical experimental apparatuses. This study demonstrates an open-source optical library, which significantly reduces the costs associated with much optical equipment, while also enabling relatively easily adapted customizable designs. The cost reductions in general are over 97%, with some components representing only 1% of the current commercial investment for optical products of similar function. The results of this study make its clear that this method of scientific hardware development enables a much broader audience to participate in optical experimentation both as research and teaching platforms than previous proprietary methods. PMID:23544104

Open-source 3D-printable optics equipment.

PubMed

Zhang, Chenlong; Anzalone, Nicholas C; Faria, Rodrigo P; Pearce, Joshua M

2013-01-01

Just as the power of the open-source design paradigm has driven down the cost of software to the point that it is accessible to most people, the rise of open-source hardware is poised to drive down the cost of doing experimental science to expand access to everyone. To assist in this aim, this paper introduces a library of open-source 3-D-printable optics components. This library operates as a flexible, low-cost public-domain tool set for developing both research and teaching optics hardware. First, the use of parametric open-source designs using an open-source computer aided design package is described to customize the optics hardware for any application. Second, details are provided on the use of open-source 3-D printers (additive layer manufacturing) to fabricate the primary mechanical components, which are then combined to construct complex optics-related devices. Third, the use of the open-source electronics prototyping platform are illustrated as control for optical experimental apparatuses. This study demonstrates an open-source optical library, which significantly reduces the costs associated with much optical equipment, while also enabling relatively easily adapted customizable designs. The cost reductions in general are over 97%, with some components representing only 1% of the current commercial investment for optical products of similar function. The results of this study make its clear that this method of scientific hardware development enables a much broader audience to participate in optical experimentation both as research and teaching platforms than previous proprietary methods.

Eyes May Be 'Windows to the Brain' in Stroke Patients

MedlinePlus

... their stroke—without the need for an MRI. SOURCE: National Institute of Neurological Disorders and Stroke (NINDS): Stroke Research ... & Players Friends of the National Library of Medicine (FNLM) top

Adolescent, caregiver, and friend preferences for integrating social support and communication features into an asthma self-management app.

PubMed

Roberts, Courtney A; Geryk, Lorie L; Sage, Adam J; Sleath, Betsy L; Tate, Deborah F; Carpenter, Delesha M

2016-11-01

This study examines: 1) adolescent preferences for using asthma self-management mobile applications (apps) to interact with their friends, caregivers, medical providers, and other adolescents with asthma and 2) how caregivers and friends would use mobile apps to communicate with the adolescent and serve as sources of support for asthma management. We recruited 20 adolescents aged 12-16 years with persistent asthma, their caregivers (n = 20), and friends (n = 3) from two suburban pediatric practices in North Carolina. We gave participants iPods with two preloaded asthma apps and asked them to use the apps for 1 week. Adolescents and caregivers provided app feedback during a semi-structured interview at a regularly-scheduled clinic appointment and during a telephone interview one week later. Friends completed one telephone interview. Interviews were audio-recorded and transcribed verbatim. An inductive, theory-driven analysis was used to identify themes and preferences. Adolescents preferred to use apps for instrumental support from caregivers, informational support from friends, and belonging and informational support from others with asthma. The majority of adolescents believed apps could enhance communication with their caregivers and medical providers, and the theme of self-reliance emerged in which caregivers and adolescents believed apps could enable adolescents to better self-manage their asthma. Friends preferred to use apps to provide instrumental and informational support. Given preferences expressed in this study, apps may help adolescents obtain social support to better self-manage their asthma. Future app-based interventions should include features enabling adolescents with asthma to communicate and interact with their caregivers, medical providers, and friends.

Aerostat-Lofted Instrument Platform and Sampling Method for Determination of Emissions from Open Area Sources

EPA Science Inventory

Sampling emissions from open area sources, particularly sources of open burning, is difficult due to fast dilution of emissions and safety concerns for personnel. Representative emission samples can be difficult to obtain with flaming and explosive sources since personnel safety ...

Thyroid Cancer and Tumor Collaborative Registry (TCCR)

PubMed Central

Shats, Oleg; Goldner, Whitney; Feng, Jianmin; Sherman, Alexander; Smith, Russell B.; Sherman, Simon

2016-01-01

A multicenter, web-based Thyroid Cancer and Tumor Collaborative Registry (TCCR, http://tccr.unmc.edu) allows for the collection and management of various data on thyroid cancer (TC) and thyroid nodule (TN) patients. The TCCR is coupled with OpenSpecimen, an open-source biobank management system, to annotate biospecimens obtained from the TCCR subjects. The demographic, lifestyle, physical activity, dietary habits, family history, medical history, and quality of life data are provided and may be entered into the registry by subjects. Information on diagnosis, treatment, and outcome is entered by the clinical personnel. The TCCR uses advanced technical and organizational practices, such as (i) metadata-driven software architecture (design); (ii) modern standards and best practices for data sharing and interoperability (standardization); (iii) Agile methodology (project management); (iv) Software as a Service (SaaS) as a software distribution model (operation); and (v) the confederation principle as a business model (governance). This allowed us to create a secure, reliable, user-friendly, and self-sustainable system for TC and TN data collection and management that is compatible with various end-user devices and easily adaptable to a rapidly changing environment. Currently, the TCCR contains data on 2,261 subjects and data on more than 28,000 biospecimens. Data and biological samples collected by the TCCR are used in developing diagnostic, prevention, treatment, and survivorship strategies against TC. PMID:27168721

The meaning of social support for the critically ill patient.

PubMed

Hupcey, J E

2001-08-01

Social support has been shown to be important for the critically ill patient. However, what constitutes adequate support for these patients has not been investigated. Thus, the purpose of this qualitative study was to investigate patients' perceptions of their need for and adequacy of the social support received while they were critically ill. Thirty adult patients who were critical during some point of their stay in the intensive care unit (ICU) stay were interviewed, once stable. Interviews were tape-recorded and began with an open-ended question regarding the ICU experience. This was followed by open-ended focused questions regarding social support, such as 'Who were your greatest sources of social support while you were critically ill?' 'What did they do that was supportive or unsupportive?' Data were analyzed according to Miles and Huberman (1994). The categories that emerged were need for social support based on patient perceptions (not number of visitors), quality of support (based on perceptions of positive and negative behaviors of supporters) and lack of support. This study found that quality of support was more important than the actual number of visitors. Patients with few visitors may have felt supported, while those with numerous visitors felt unsupported. Patients who felt unsupported also were more critical of the staff and the care they received. Nurses need to individually assess patients regarding their need for support, and assist family/friends to meet these needs.

Evaluation of the influence of family and friends, and the Internet on patient perceptions of long-term topical corticosteroid use.

PubMed

Smith, Saxon D; Farrugia, Lisa L; Harris, Victoria; Lee, Andrew; Carter, Stephen R; Blaszczynski, Alex; Fischer, Gayle

2017-11-01

Topical corticosteroids (TCS) are key to managing chronic inflammatory dermatoses (CID). Parents/patients cite TCS phobia as an impediment to treatment adherence. Family/friends and the Internet are a source of misinformation on TCS which can negatively impact perceptions of TCS safety. To assess information from family/friends and the Internet, as related to and reported by patients/parents using long-term TCS. A multicenter cross-sectional survey of patients (aged >18 years) and parents of patients (aged <18 years) with a history of CID requiring long-term (≥1 month) TCS use assessing messages about TCS received from family/friends and the Internet. A total of 123 patients and 78 parents completed the survey (n = 201). Parents/patients were more likely to be informed by the Internet "[having] my [child's] skin condition means that [I/he/she] will need to use topical corticosteroids" (p < .001) and that "inflamed skin conditions will improve with the topical corticosteroids" (p = .007). Family/friends were more likely to recommend parents/patients "try non-prescription creams/ointments before resorting to the use of prescription topical corticosteroids" (p = .014). High rates of messages about TCS "risk" from family/friends and the Internet may affect patient/parent understanding about TCS safety. This may contribute to treatment non-adherence.

Peer relations of youth with pediatric conditions and health risks: promoting social support and healthy lifestyles.

PubMed

La Greca, Annette M; Bearman, Karen J; Moore, Hannah

2002-08-01

Peer relations and close friendships play important roles in youngsters' emotional development and take on special significance when a child or adolescent has a chronic disease. This article reviews the key ways that peer relations have been examined in youth with chronic pediatric conditions and specifically focuses on (1) the role of peers and close friends as a source of support, (2) friends' influence on treatment adherence, and (3) peers' and friends' impact on health-promoting and health-risk behaviors. In general, youngsters with chronic conditions do not have more problems in their peer relations than other youth, although children with medical conditions that are stigmatizing or that involve the central nervous system (CNS) may encounter peer difficulties. Social support from friends and classmates appears to facilitate youngsters' disease adaptation and may help with the lifestyle aspects of treatment regimens. Adolescent peer-crowd affiliations (e.g., "brains," "jocks") that are linked with health-promoting behaviors may prove beneficial to youngsters' disease management and health. The findings underscore the need for helping children and adolescents disclose their medical condition to peers in positive ways and for including youngsters' close friends in the treatment process and in school-reentry programs after extended medical care. Additional research is needed to develop strategies for incorporating youngsters' peers and friends into the medical management of youth with chronic pediatric conditions.

The Visible Human Data Sets (VHD) and Insight Toolkit (ITk): Experiments in Open Source Software

PubMed Central

Ackerman, Michael J.; Yoo, Terry S.

2003-01-01

From its inception in 1989, the Visible Human Project was designed as an experiment in open source software. In 1994 and 1995 the male and female Visible Human data sets were released by the National Library of Medicine (NLM) as open source data sets. In 2002 the NLM released the first version of the Insight Toolkit (ITk) as open source software. PMID:14728278

Psychological distress in women at risk for hereditary breast cancer: the role of family communication and perceived social support.

PubMed

den Heijer, Mariska; Seynaeve, Caroline; Vanheusden, Kathleen; Duivenvoorden, Hugo J; Bartels, Carina C M; Menke-Pluymers, Marian B E; Tibben, Aad

2011-12-01

Hereditary breast cancer has a profound impact on individual family members and on their mutual communication and interactions. The way at-risk women cope with the threat of hereditary breast cancer may depend on the quality of family communication about hereditary breast cancer and on the perceived social support from family and friends. To examine the associations of family communication and social support with long-term psychological distress in a group of women at risk for hereditary breast cancer, who opted either for regular breast surveillance or prophylactic surgery. The study cohort consisted of 222 women at risk for hereditary breast cancer, who previously participated in a study on the psychological consequences of either regular breast cancer surveillance or prophylactic surgery. General and breast cancer specific distress, hereditary cancer-related family communication, perceived social support, and demographics were assessed. Using structural equation modelling, we found that open communication about hereditary cancer within the family was associated with less general and breast cancer specific distress. In addition, perceived support from family and friends was indirectly associated with less general and breast cancer-specific distress through open communication within the family. These findings indicate that family communication and perceived social support from friends and family are of paramount importance in the long-term adaptation to being at risk for hereditary breast cancer. Attention for these issues needs to be incorporated in the care of women at risk for hereditary breast cancer. Copyright © 2010 John Wiley & Sons, Ltd.

The 2016 Bioinformatics Open Source Conference (BOSC)

PubMed Central

Harris, Nomi L.; Cock, Peter J.A.; Chapman, Brad; Fields, Christopher J.; Hokamp, Karsten; Lapp, Hilmar; Muñoz-Torres, Monica; Wiencko, Heather

2016-01-01

Message from the ISCB: The Bioinformatics Open Source Conference (BOSC) is a yearly meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. BOSC has been run since 2000 as a two-day Special Interest Group (SIG) before the annual ISMB conference. The 17th annual BOSC ( http://www.open-bio.org/wiki/BOSC_2016) took place in Orlando, Florida in July 2016. As in previous years, the conference was preceded by a two-day collaborative coding event open to the bioinformatics community. The conference brought together nearly 100 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, and open and reproducible science. PMID:27781083

Factor analysis of sources of information on organ donation and transplantation in journalism students.

PubMed

Martínez-Alarcón, L; Ríos, A; Ramis, G; López-Navas, A; Febrero, B; Ramírez, P; Parrilla, P

2013-01-01

Journalists and the information they disseminate are essential to promote health and organ donation and transplantation (ODT). The attitude of journalism students toward ODT could influence public opinion and help promote this treatment option. The aim of this study was to determine the media through which journalism students receive information on ODT and to analyze the association between the sources of information and psychosocial variables. We surveyed journalism students (n = 129) recruited in compulsory classes. A validated psychosocial questionnaire (self-administered, anonymous) about ODT was used. Student t test and χ(2) test were applied. Questionnaire completion rate was 98% (n = 126). The medium with the greatest incidence on students was television (TV), followed by press and magazines/books. In the factor analysis to determine the impact of the information by its source, the first factor was talks with friends and family; the second was shared by hoardings/publicity posters, health professionals, and college/school; and the third was TV and radio. In the factor analysis between information sources and psychosocial variables, the associations were between information about organ donation transmitted by friends and family and having spoken about ODT with them; by TV, radio, and hoardings and not having spoken in the family; and by TV/radio and the father's and mother's opinion about ODT. The medium with the greatest incidence on students is TV, and the medium with the greatest impact on broadcasting information was conversations with friends, family, and health professionals. This could be useful for society, because they should be provided with clear and concise information. Copyright © 2013 Elsevier Inc. All rights reserved.

Antenatal depressive symptoms associated with specific life events and sources of social support among Italian women.

PubMed

Agostini, Francesca; Neri, Erica; Salvatori, Paola; Dellabartola, Sara; Bozicevic, Laura; Monti, Fiorella

2015-05-01

This study aimed to identify different kinds of stressful life events and social support associated with antenatal depressive symptoms in a sample of pregnant Italian women. We conducted the study at a primary health-care centre in an urban area (northeast Italy). Mainly recruited at antenatal classes, 404 eligible pregnant women completed a socio-demographic questionnaire that included questions about the present pregnancy, the Edinburgh Depression Scale (EDS) to estimate the prevalence of depressive symptoms, the Multidimensional Scale of Perceived Social Support and List of Threatening Experiences Questionnaire to investigate the quality and nature of social support and recent negative life events. Of the 404 women, 60 (14.9 %) scored 13 or higher on the EDS. This group reported significantly lower social support from various sources-family, friends, and significant others; only in primiparous women were depressive symptoms significantly related to lower support from friends. Women with EDS scores equal or higher than 13 also reported a higher occurrence of recent stressful life events-specifically, death or a serious problem with a close friend or relative, unemployment, financial problems, and moving or housing difficulties. Regression analyses showed that women with high levels of social support or with a positive experience of pregnancy were less likely to experience antenatal depressive symptoms. Our results underscore the associations among antenatal depression, specific life stressors, and low social support from various sources. Clinical attention to these psychosocial correlates is recommended toward detecting vulnerability to antenatal depressive symptoms.

New environmentally-friendly antimicrobials and biocides from Andean and Mexican biodiversity.

PubMed

Cespedes, Carlos L; Alarcon, Julio; Aqueveque, Pedro M; Lobo, Tatiana; Becerra, Julio; Balbontin, Cristian; Avila, Jose G; Kubo, Isao; Seigler, David S

2015-10-01

Persistent application of pesticides often leads to accumulation in the environment and to the development of resistance in various organisms. These chemicals frequently degrade slowly and have the potential to bio-accumulate across the food chain and in top predators. Cancer and neuronal damage at genomic and proteomic levels have been linked to exposure to pesticides in humans. These negative effects encourage search for new sources of biopesticides that are more "environmentally-friendly" to the environment and human health. Many plant or fungal compounds have significant biological activity associated with the presence of secondary metabolites. Plant biotechnology and new molecular methods offer ways to understand regulation and to improve production of secondary metabolites of interest. Naturally occurring crop protection chemicals offer new approaches for pest management by providing new sources of biologically active natural products with biodegradability, low mammalian toxicity and environmentally-friendly qualities. Latin America is one of the world's most biodiverse regions and provide a previously unsuspected reservoir of new and potentially useful molecules. Phytochemicals from a number of families of plants and fungi from the southern Andes and from Mexico have now been evaluated. Andean basidiomycetes are also a great source of scientifically new compounds that are interesting and potentially useful. Use of biopesticides is an important component of integrated pest management (IPM) and can improve the risks and benefits of production of many crops all over the world. Copyright © 2015 Elsevier Inc. All rights reserved.

OpenMx: An Open Source Extended Structural Equation Modeling Framework

ERIC Educational Resources Information Center

Boker, Steven; Neale, Michael; Maes, Hermine; Wilde, Michael; Spiegel, Michael; Brick, Timothy; Spies, Jeffrey; Estabrook, Ryne; Kenny, Sarah; Bates, Timothy; Mehta, Paras; Fox, John

2011-01-01

OpenMx is free, full-featured, open source, structural equation modeling (SEM) software. OpenMx runs within the "R" statistical programming environment on Windows, Mac OS-X, and Linux computers. The rationale for developing OpenMx is discussed along with the philosophy behind the user interface. The OpenMx data structures are…

a Framework for AN Open Source Geospatial Certification Model

NASA Astrophysics Data System (ADS)

Khan, T. U. R.; Davis, P.; Behr, F.-J.

2016-06-01

The geospatial industry is forecasted to have an enormous growth in the forthcoming years and an extended need for well-educated workforce. Hence ongoing education and training play an important role in the professional life. Parallel, in the geospatial and IT arena as well in the political discussion and legislation Open Source solutions, open data proliferation, and the use of open standards have an increasing significance. Based on the Memorandum of Understanding between International Cartographic Association, OSGeo Foundation, and ISPRS this development led to the implementation of the ICA-OSGeo-Lab imitative with its mission "Making geospatial education and opportunities accessible to all". Discussions in this initiative and the growth and maturity of geospatial Open Source software initiated the idea to develop a framework for a worldwide applicable Open Source certification approach. Generic and geospatial certification approaches are already offered by numerous organisations, i.e., GIS Certification Institute, GeoAcademy, ASPRS, and software vendors, i. e., Esri, Oracle, and RedHat. They focus different fields of expertise and have different levels and ways of examination which are offered for a wide range of fees. The development of the certification framework presented here is based on the analysis of diverse bodies of knowledge concepts, i.e., NCGIA Core Curriculum, URISA Body Of Knowledge, USGIF Essential Body Of Knowledge, the "Geographic Information: Need to Know", currently under development, and the Geospatial Technology Competency Model (GTCM). The latter provides a US American oriented list of the knowledge, skills, and abilities required of workers in the geospatial technology industry and influenced essentially the framework of certification. In addition to the theoretical analysis of existing resources the geospatial community was integrated twofold. An online survey about the relevance of Open Source was performed and evaluated with 105 respondents worldwide. 15 interviews (face-to-face or by telephone) with experts in different countries provided additional insights into Open Source usage and certification. The findings led to the development of a certification framework of three main categories with in total eleven sub-categories, i.e., "Certified Open Source Geospatial Data Associate / Professional", "Certified Open Source Geospatial Analyst Remote Sensing & GIS", "Certified Open Source Geospatial Cartographer", "Certified Open Source Geospatial Expert", "Certified Open Source Geospatial Associate Developer / Professional Developer", "Certified Open Source Geospatial Architect". Each certification is described by pre-conditions, scope and objectives, course content, recommended software packages, target group, expected benefits, and the methods of examination. Examinations can be flanked by proofs of professional career paths and achievements which need a peer qualification evaluation. After a couple of years a recertification is required. The concept seeks the accreditation by the OSGeo Foundation (and other bodies) and international support by a group of geospatial scientific institutions to achieve wide and international acceptance for this Open Source geospatial certification model. A business case for Open Source certification and a corresponding SWOT model is examined to support the goals of the Geo-For-All initiative of the ICA-OSGeo pact.

The Case for Open Source: Open Source Has Made Significant Leaps in Recent Years. What Does It Have to Offer Education?

ERIC Educational Resources Information Center

Guhlin, Miguel

2007-01-01

Open source has continued to evolve and in the past three years the development of a graphical user interface has made it increasingly accessible and viable for end users without special training. Open source relies to a great extent on the free software movement. In this context, the term free refers not to cost, but to the freedom users have to…

Associations of a social network typology with physical and mental health risks among older adults in South Korea.

PubMed

Park, N S; Jang, Y; Lee, B S; Chiriboga, D A; Chang, S; Kim, S Y

2018-05-01

The objectives of this study were to (1) develop an empirical typology of social networks in older Koreans; and (2) examine its effect on physical and mental health. A sample of 6900 community-dwelling older adults in South Korea was drawn from the 2014 Korean National Elderly Survey. Latent profile analysis (LPA) was conducted to derive social network types using eight common social network characteristics (marital status, living arrangement, the number and frequency of contact with close family/relatives, the number and frequency of contact with close friends, frequency of participation in social activities, and frequency of having visitors at home). The identified typologies were then regressed on self-rated health and depressive symptoms to explore the health risks posed by the group membership. The LPA identified a model with five types of social network as being most optimal (BIC = 153,848.34, entropy = .90). The groups were named diverse/family (enriched networks with more engagement with family), diverse/friend (enriched networks with more engagement with friends), friend-focused (high engagement with friends), distant (structurally disengaged), and restricted (structurally engaged but disengaged in family/friends networks). A series of regression analyses showed that membership in the restricted type was associated with more health and mental health risks than all types of social networks except the distant type. Findings demonstrate the importance of family and friends as a source of social network and call attention to not only structural but also non-structural aspects of social isolation. Findings and implications are discussed in cultural contexts.

A Cross-Comparative Survey of Information Seeking and Scanning About Drug-Related Sources and Topics Among U.S. and Israeli College Students.

PubMed

Cheng, Ying; Ahn, Jisoo; Lewis, Nehama; Martinez, Lourdes S

2017-08-01

There is an increasing amount of drug-related information that is easily accessible from media and interpersonal sources. Recent research shows significant positive associations between information acquisition and nonmedical drug use intentions among college students. This study examines information about amphetamines and marijuana that was actively searched ("seeking") as well as information that was encountered during routine media use ("scanning"). Data are drawn from a cross-national comparative survey of college students in the United States (N = 734) and in Israel (N = 800). U.S. participants reported seeking and scanning information about marijuana across a broader range of sources than Israeli participants. Among U.S. and Israeli participants, the most frequently searched marijuana-related topics included the benefits of marijuana, negative effects of marijuana use, and political reasons why marijuana should be legal. Participants from both countries reported the benefits of amphetamines, and the negative effects of amphetamine use as the most frequently searched topics about amphetamines. Participants in both countries identified the internet and friends as the most popular sources of drug-related information and noted that physicians, friends, and the internet were the most trusted sources. Implications for research on information seeking and health communication are discussed.

MyGeneFriends: A Social Network Linking Genes, Genetic Diseases, and Researchers.

PubMed

Allot, Alexis; Chennen, Kirsley; Nevers, Yannis; Poidevin, Laetitia; Kress, Arnaud; Ripp, Raymond; Thompson, Julie Dawn; Poch, Olivier; Lecompte, Odile

2017-06-16

The constant and massive increase of biological data offers unprecedented opportunities to decipher the function and evolution of genes and their roles in human diseases. However, the multiplicity of sources and flow of data mean that efficient access to useful information and knowledge production has become a major challenge. This challenge can be addressed by taking inspiration from Web 2.0 and particularly social networks, which are at the forefront of big data exploration and human-data interaction. MyGeneFriends is a Web platform inspired by social networks, devoted to genetic disease analysis, and organized around three types of proactive agents: genes, humans, and genetic diseases. The aim of this study was to improve exploration and exploitation of biological, postgenomic era big data. MyGeneFriends leverages conventions popularized by top social networks (Facebook, LinkedIn, etc), such as networks of friends, profile pages, friendship recommendations, affinity scores, news feeds, content recommendation, and data visualization. MyGeneFriends provides simple and intuitive interactions with data through evaluation and visualization of connections (friendships) between genes, humans, and diseases. The platform suggests new friends and publications and allows agents to follow the activity of their friends. It dynamically personalizes information depending on the user's specific interests and provides an efficient way to share information with collaborators. Furthermore, the user's behavior itself generates new information that constitutes an added value integrated in the network, which can be used to discover new connections between biological agents. We have developed MyGeneFriends, a Web platform leveraging conventions from popular social networks to redefine the relationship between humans and biological big data and improve human processing of biomedical data. MyGeneFriends is available at lbgi.fr/mygenefriends. ©Alexis Allot, Kirsley Chennen, Yannis Nevers, Laetitia Poidevin, Arnaud Kress, Raymond Ripp, Julie Dawn Thompson, Olivier Poch, Odile Lecompte. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 16.06.2017.

SolTrace | Concentrating Solar Power | NREL

Science.gov Websites

NREL packaged distribution or from source code at the SolTrace open source project website. NREL Publications Support FAQs SolTrace open source project The code uses Monte-Carlo ray-tracing methodology. The -tracing capabilities. With the release of the SolTrace open source project, the software has adopted

When Free Isn't Free: The Realities of Running Open Source in School

ERIC Educational Resources Information Center

Derringer, Pam

2009-01-01

Despite the last few years' growth in awareness of open-source software in schools and the potential savings it represents, its widespread adoption is still hampered. Randy Orwin, technology director of the Bainbridge Island School District in Washington State and a strong open-source advocate, cautions that installing an open-source…