A survey of quality assurance practices in biomedical open source software projects.

PubMed

Koru, Günes; El Emam, Khaled; Neisa, Angelica; Umarji, Medha

2007-05-07

Open source (OS) software is continuously gaining recognition and use in the biomedical domain, for example, in health informatics and bioinformatics. Given the mission critical nature of applications in this domain and their potential impact on patient safety, it is important to understand to what degree and how effectively biomedical OS developers perform standard quality assurance (QA) activities such as peer reviews and testing. This would allow the users of biomedical OS software to better understand the quality risks, if any, and the developers to identify process improvement opportunities to produce higher quality software. A survey of developers working on biomedical OS projects was conducted to examine the QA activities that are performed. We took a descriptive approach to summarize the implementation of QA activities and then examined some of the factors that may be related to the implementation of such practices. Our descriptive results show that 63% (95% CI, 54-72) of projects did not include peer reviews in their development process, while 82% (95% CI, 75-89) did include testing. Approximately 74% (95% CI, 67-81) of developers did not have a background in computing, 80% (95% CI, 74-87) were paid for their contributions to the project, and 52% (95% CI, 43-60) had PhDs. A multivariate logistic regression model to predict the implementation of peer reviews was not significant (likelihood ratio test = 16.86, 9 df, P = .051) and neither was a model to predict the implementation of testing (likelihood ratio test = 3.34, 9 df, P = .95). Less attention is paid to peer review than testing. However, the former is a complementary, and necessary, QA practice rather than an alternative. Therefore, one can argue that there are quality risks, at least at this point in time, in transitioning biomedical OS software into any critical settings that may have operational, financial, or safety implications. Developers of biomedical OS applications should invest more effort in implementing systemic peer review practices throughout the development and maintenance processes.

Evaluation of software maintain ability with open EHR - a comparison of architectures.

PubMed

Atalag, Koray; Yang, Hong Yul; Tempero, Ewan; Warren, James R

2014-11-01

To assess whether it is easier to maintain a clinical information system developed using open EHR model driven development versus mainstream methods. A new open source application (GastrOS) has been developed following open EHR's multi-level modelling approach using .Net/C# based on the same requirements of an existing clinically used application developed using Microsoft Visual Basic and Access database. Almost all the domain knowledge was embedded into the software code and data model in the latter. The same domain knowledge has been expressed as a set of open EHR Archetypes in GastrOS. We then introduced eight real-world change requests that had accumulated during live clinical usage, and implemented these in both systems while measuring time for various development tasks and change in software size for each change request. Overall it took half the time to implement changes in GastrOS. However it was the more difficult application to modify for one change request, suggesting the nature of change is also important. It was not possible to implement changes by modelling only. Comparison of relative measures of time and software size change within each application highlights how architectural differences affected maintain ability across change requests. The use of open EHR model driven development can result in better software maintain ability. The degree to which open EHR affects software maintain ability depends on the extent and nature of domain knowledge involved in changes. Although we used relative measures for time and software size, confounding factors could not be totally excluded as a controlled study design was not feasible. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Sandbox for Mac Malware v 1.0

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

Walkup, Elizabeth

This software is an analyzer for automated sandbox analysis of malware on the OS X operating system. It runs inside an OS X virtual machine to collect data about what happens when a given file is opened or run. As of August 2014, there was no sandbox software for Mac OS X malware, as it requires different methods from those used on the Windows OS (which most sandboxes are written for). This software adds OS X analysis capabilities to an existing open-source sandbox, Cuckoo Sandbox (http://cuckoosandbox.org/), which previously only worked for Windows. The analyzer itself can take many different typesmore » of files as input: the traditional Mach-O and FAT executables, .app files, zip files, Python scripts, Java archives, and web pages, as well as PDFs and other documents. While the file is running, the analyzer also simulates rudimentary human interaction with clicks and mouse movements in order to bypass the tests some malware use to see if they are being analyzed. The analyzer outputs several different kinds of data: function call traces, network captures, screenshots, and all created and modified files. This work also includes a static analysis Cuckoo module for Mach-O binary files. It extracts file structures, code library imports and exports, and signatures. This data can be used along with the analyzer results to create signatures for malware.« less

Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics.

PubMed

Bonnal, Raoul J P; Aerts, Jan; Githinji, George; Goto, Naohisa; MacLean, Dan; Miller, Chase A; Mishima, Hiroyuki; Pagani, Massimiliano; Ramirez-Gonzalez, Ricardo; Smant, Geert; Strozzi, Francesco; Syme, Rob; Vos, Rutger; Wennblom, Trevor J; Woodcroft, Ben J; Katayama, Toshiaki; Prins, Pjotr

2012-04-01

Biogem provides a software development environment for the Ruby programming language, which encourages community-based software development for bioinformatics while lowering the barrier to entry and encouraging best practices. Biogem, with its targeted modular and decentralized approach, software generator, tools and tight web integration, is an improved general model for scaling up collaborative open source software development in bioinformatics. Biogem and modules are free and are OSS. Biogem runs on all systems that support recent versions of Ruby, including Linux, Mac OS X and Windows. Further information at http://www.biogems.info. A tutorial is available at http://www.biogems.info/howto.html bonnal@ingm.org.

Dissecting the Re-Os molybdenite geochronometer.

PubMed

Barra, Fernando; Deditius, Artur; Reich, Martin; Kilburn, Matt R; Guagliardo, Paul; Roberts, Malcolm P

2017-11-22

Rhenium and osmium isotopes have been used for decades to date the formation of molybdenite (MoS 2 ), a common mineral in ore deposits and the world's main source of molybdenum and rhenium. Understanding the distribution of parent 187 Re and radiogenic daughter 187 Os isotopes in molybdenite is critical in interpreting isotopic measurements because it can compromise the accurate determination and interpretation of mineralization ages. In order to resolve the controls on the distribution of these elements, chemical and isotope mapping of MoS 2 grains from representative porphyry copper-molybdenum deposits were performed using electron microprobe and nano-scale secondary ion mass spectrometry. Our results show a heterogeneous distribution of 185,187 Re and 192 Os isotopes in MoS 2 , and that both 187 Re and 187 Os isotopes are not decoupled as previously thought. We conclude that Re and Os are structurally bound or present as nanoparticles in or next to molybdenite grains, recording a complex formation history and hindering the use of microbeam techniques for Re-Os molybdenite dating. Our study opens new avenues to explore the effects of isotope nuggeting in geochronometers.

Biomechanical ToolKit: Open-source framework to visualize and process biomechanical data.

PubMed

Barre, Arnaud; Armand, Stéphane

2014-04-01

C3D file format is widely used in the biomechanical field by companies and laboratories to store motion capture systems data. However, few software packages can visualize and modify the integrality of the data in the C3D file. Our objective was to develop an open-source and multi-platform framework to read, write, modify and visualize data from any motion analysis systems using standard (C3D) and proprietary file formats (used by many companies producing motion capture systems). The Biomechanical ToolKit (BTK) was developed to provide cost-effective and efficient tools for the biomechanical community to easily deal with motion analysis data. A large panel of operations is available to read, modify and process data through C++ API, bindings for high-level languages (Matlab, Octave, and Python), and standalone application (Mokka). All these tools are open-source and cross-platform and run on all major operating systems (Windows, Linux, MacOS X). Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Sulfide and whole rock Re-Os systematics of eclogite and pyroxenite xenoliths from the Slave Craton, Canada

NASA Astrophysics Data System (ADS)

Aulbach, Sonja; Creaser, Robert A.; Pearson, Norm J.; Simonetti, Stefanie S.; Heaman, Larry M.; Griffin, William L.; Stachel, Thomas

2009-06-01

We characterized single sulfides in eclogite and pyroxenite xenoliths from the Diavik kimberlites (central Slave Craton, Canada) with regard to their petrography, major-element composition and Re-Os isotope systematics. Together with trace-element and Re-Os isotope compositions of whole rocks, these data allow identification of the major Re-Os host phases and provide constraints on the origin(s) of sulfides in these samples. The majority of sulfide minerals contain 8 to 28 at.% Ni, with intragranular sulfides having on average significantly lower contents (~ 6 at.%) than intergranular sulfides (~ 12 at.%). These high Ni-sulfides are not in equilibrium with an eclogitic assemblage and were likely introduced from a peridotitic source subsequent to eclogite formation. In contrast, their Re-Os abundances and Re/Os ratios (average ~ 825 ppb, 190 ppb and 10, respectively) overlap those of primary eclogitic sulfides. These conflicting compositional characteristics may document open-system disequilibrium processes accompanying the introduction of sulfides into eclogites. The general association of high 187Os/ 188Os with high 187Re/ 188Os of sulfides in three low-temperature eclogite xenoliths suggests that the addition is not young. In contrast, sulfides in a high-temperature eclogite plot on a ~ 90 Ma errorchron with radiogenic initial 187Os/ 188Os, perhaps indicative of young introduction of sulfides from a deep enriched source. Sulfides in a single pyroxenite xenolith have Ni, Re and Os contents intermediate between pristine eclogitic and peridotitic sulfides, and correlated Re-Os isotope systematics defining an age of 1.84 ± 0.14 Ga with a radiogenic 187Os/ 188Os i (0.16 ± 0.01). The age and 187Os/ 188Os i are identical to those obtained for eclogitic sulfide inclusions in diamonds from Diavik, thus supporting a link between eclogite and pyroxenite formation. Several eclogite and pyroxenite whole rocks show evidence for addition of secondary sulfides, but many plot on Paleoproterozoic Re-Os age arrays - particularly so at low Re/Os - coincident with previously determined ages using Lu-Hf and Pb-Pb techniques. They may represent sulfide-poor varieties that did not suffer secondary sulfide addition and that may be best suited to yielding meaningful Re-Os ages.

Comparative composition, diversity, and abundance of oligosaccharides in early lactation milk from commercial dairy and beef cows.

PubMed

Sischo, William M; Short, Diana M; Geissler, Mareen; Bunyatratchata, Apichaya; Barile, Daniela

2017-05-01

Prebiotics are nondigestible dietary ingredients, usually oligosaccharides (OS), that provide a health benefit to the host by directly modulating the gut microbiota. Although there is some information describing OS content in dairy-source milk, no information is available to describe the OS content of beef-source milk. Given the different trait emphasis between dairy and beef for milk production and calf survivability, it is plausible that OS composition, diversity, and abundance differ between production types. The goal of this study was to compare OS in milk from commercial dairy and beef cows in early lactation. Early-lactation multiparous cows (5-12 d in milk) from 5 commercial Holstein dairy herds and 5 Angus or Angus hybrid beef herds were sampled once. Milk was obtained from each enrolled cow and frozen on the farm. Subsequently, each milk sample was assessed for total solids, pH, and OS content and relative abundance. Oligosaccharide diversity and abundance within and between samples was transformed through principal component analysis to reduce data complexity. Factors from principal component analysis were used to create similarity clusters, which were subsequently used in a multivariate logistic regression. In total, 30 OS were identified in early-lactation cow milk, including 21 distinct OS and 9 isomers with unique retention times. The majority of OS detected in the milk samples were present in all individual samples regardless of production type. Two clusters described distribution patterns of OS for the study sample; when median OS abundance was compared between the 2 clusters, we found that overall OS relative abundance was consistently greater in the cluster dominated by beef cows. For several of the structures, including those with known prebiotic effect, the difference in abundance was 2- to 4-fold greater in the beef-dominated cluster. Assuming that beef OS content in milk is the gold standard for cattle, it is likely that preweaning dairy calves are deprived of dietary-source OS. Although supplementing rations with OS is an approach to rectify this deficiency, understanding the health and productivity effects of improving OS abundance being fed to preweaning calves is a necessary next step before recommending supplementation. These studies should account for the observation that OS products are variable for both OS diversity and structural complexity, and some products may not be suitable as prebiotics. The Authors. Published by the Federation of Animal Science Societies and Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/).

A Real-Time Linux for Multicore Platforms

DTIC Science & Technology

2013-12-20

under ARO support) to obtain a fully-functional OS for supporting real-time workloads on multicore platforms. This system, called LITMUS -RT...to be specified as plugin components. LITMUS -RT is open-source software (available at The views, opinions and/or findings contained in this report... LITMUS -RT (LInux Testbed for MUltiprocessor Scheduling in Real-Time systems), allows different multiprocessor real-time scheduling and

GNU Data Language (GDL) - a free and open-source implementation of IDL

NASA Astrophysics Data System (ADS)

Arabas, Sylwester; Schellens, Marc; Coulais, Alain; Gales, Joel; Messmer, Peter

2010-05-01

GNU Data Language (GDL) is developed with the aim of providing an open-source drop-in replacement for the ITTVIS's Interactive Data Language (IDL). It is free software developed by an international team of volunteers led by Marc Schellens - the project's founder (a list of contributors is available on the project's website). The development is hosted on SourceForge where GDL continuously ranks in the 99th percentile of most active projects. GDL with its library routines is designed as a tool for numerical data analysis and visualisation. As its proprietary counterparts (IDL and PV-WAVE), GDL is used particularly in geosciences and astronomy. GDL is dynamically-typed, vectorized and has object-oriented programming capabilities. The library routines handle numerical calculations, data visualisation, signal/image processing, interaction with host OS and data input/output. GDL supports several data formats such as netCDF, HDF4, HDF5, GRIB, PNG, TIFF, DICOM, etc. Graphical output is handled by X11, PostScript, SVG or z-buffer terminals, the last one allowing output to be saved in a variety of raster graphics formats. GDL is an incremental compiler with integrated debugging facilities. It is written in C++ using the ANTLR language-recognition framework. Most of the library routines are implemented as interfaces to open-source packages such as GNU Scientific Library, PLPlot, FFTW, ImageMagick, and others. GDL features a Python bridge (Python code can be called from GDL; GDL can be compiled as a Python module). Extensions to GDL can be written in C++, GDL, and Python. A number of open software libraries written in IDL, such as the NASA Astronomy Library, MPFIT, CMSVLIB and TeXtoIDL are fully or partially functional under GDL. Packaged versions of GDL are available for several Linux distributions and Mac OS X. The source code compiles on some other UNIX systems, including BSD and OpenSolaris. The presentation will cover the current status of the project, the key accomplishments, and the weaknesses - areas where contributions and users' feedback are welcome! While still being in beta-stage of development, GDL proved to be a useful tool for classroom work on data analysis. Its usage for teaching meteorological-data processing at the University of Warsaw will serve as an example.

An open-source framework for testing tracking devices using Lego Mindstorms

NASA Astrophysics Data System (ADS)

Jomier, Julien; Ibanez, Luis; Enquobahrie, Andinet; Pace, Danielle; Cleary, Kevin

2009-02-01

In this paper, we present an open-source framework for testing tracking devices in surgical navigation applications. At the core of image-guided intervention systems is the tracking interface that handles communication with the tracking device and gathers tracking information. Given that the correctness of tracking information is critical for protecting patient safety and for ensuring the successful execution of an intervention, the tracking software component needs to be thoroughly tested on a regular basis. Furthermore, with widespread use of extreme programming methodology that emphasizes continuous and incremental testing of application components, testing design becomes critical. While it is easy to automate most of the testing process, it is often more difficult to test components that require manual intervention such as tracking device. Our framework consists of a robotic arm built from a set of Lego Mindstorms and an open-source toolkit written in C++ to control the robot movements and assess the accuracy of the tracking devices. The application program interface (API) is cross-platform and runs on Windows, Linux and MacOS. We applied this framework for the continuous testing of the Image-Guided Surgery Toolkit (IGSTK), an open-source toolkit for image-guided surgery and shown that regression testing on tracking devices can be performed at low cost and improve significantly the quality of the software.

MARVIN: a medical research application framework based on open source software.

PubMed

Rudolph, Tobias; Puls, Marc; Anderegg, Christoph; Ebert, Lars; Broehan, Martina; Rudin, Adrian; Kowal, Jens

2008-08-01

This paper describes the open source framework MARVIN for rapid application development in the field of biomedical and clinical research. MARVIN applications consist of modules that can be plugged together in order to provide the functionality required for a specific experimental scenario. Application modules work on a common patient database that is used to store and organize medical data as well as derived data. MARVIN provides a flexible input/output system with support for many file formats including DICOM, various 2D image formats and surface mesh data. Furthermore, it implements an advanced visualization system and interfaces to a wide range of 3D tracking hardware. Since it uses only highly portable libraries, MARVIN applications run on Unix/Linux, Mac OS X and Microsoft Windows.

Re-Os geochronology and Os isotope fingerprinting of petroleum sourced from a Type I lacustrine kerogen: Insights from the natural Green River petroleum system in the Uinta Basin and hydrous pyrolysis experiments

NASA Astrophysics Data System (ADS)

Cumming, Vivien M.; Selby, David; Lillis, Paul G.; Lewan, Michael D.

2014-08-01

Rhenium-osmium (Re-Os) geochronology of marine petroleum systems has allowed the determination of the depositional age of source rocks as well as the timing of petroleum generation. In addition, Os isotopes have been applied as a fingerprinting tool to correlate oil to its source unit. To date, only classic marine petroleum systems have been studied. Here we present Re-Os geochronology and Os isotope fingerprinting of different petroleum phases (oils, tar sands and gilsonite) derived from the lacustrine Green River petroleum system in the Uinta Basin, USA. In addition we use an experimental approach, hydrous pyrolysis experiments, to compare to the Re-Os data of naturally generated petroleum in order to further understand the mechanisms of Re and Os transfer to petroleum. The Re-Os geochronology of petroleum from the lacustrine Green River petroleum system (19 ± 14 Ma - all petroleum phases) broadly agrees with previous petroleum generation basin models (∼25 Ma) suggesting that Re-Os geochronology of variable petroleum phases derived from lacustrine Type I kerogen has similar systematics to Type II kerogen (e.g., Selby and Creaser, 2005a,b; Finlay et al., 2010). However, the large uncertainties (over 100% in some cases) produced for the petroleum Re-Os geochronology are a result of multiple generation events occurring through a ∼3000-m thick source unit that creates a mixture of initial Os isotope compositions in the produced petroleum phases. The 187Os/188Os values for the petroleum and source rocks at the time of oil generation vary from 1.4 to 1.9, with the mode at ∼1.6. Oil-to-source correlation using Os isotopes is consistent with previous correlation studies in the Green River petroleum system, and illustrates the potential utility of Os isotopes to characterize the spatial variations within a petroleum system. Hydrous pyrolysis experiments on the Green River Formation source rocks show that Re and Os transfer are mimicking the natural system. This transfer from source to bitumen to oil does not affect source rock Re-Os systematics or Os isotopic compositions. This confirms that Os isotope compositions are transferred intact from source to petroleum during petroleum generation and can be used as a powerful correlation tool. These experiments further confirm that Re-Os systematics in source rocks are not adversely affected by petroleum maturation. Overall this study illustrates that the Re-Os petroleum geochronometer and Os isotope fingerprinting tools can be used on a wide range of petroleum types sourced from variable kerogen types.

Re-Os geochronology and Os isotope fingerprinting of petroleum sourced from a Type I lacustrine kerogen: insights from the natural Green River petroleum system in the Uinta Basin and hydrous pyrolysis experiments

USGS Publications Warehouse

Cumming, Vivien M.; Selby, David; Lillis, Paul G.; Lewan, Michael D.

2014-01-01

Rhenium–osmium (Re–Os) geochronology of marine petroleum systems has allowed the determination of the depositional age of source rocks as well as the timing of petroleum generation. In addition, Os isotopes have been applied as a fingerprinting tool to correlate oil to its source unit. To date, only classic marine petroleum systems have been studied. Here we present Re–Os geochronology and Os isotope fingerprinting of different petroleum phases (oils, tar sands and gilsonite) derived from the lacustrine Green River petroleum system in the Uinta Basin, USA. In addition we use an experimental approach, hydrous pyrolysis experiments, to compare to the Re–Os data of naturally generated petroleum in order to further understand the mechanisms of Re and Os transfer to petroleum. The Re–Os geochronology of petroleum from the lacustrine Green River petroleum system (19 ± 14 Ma – all petroleum phases) broadly agrees with previous petroleum generation basin models (∼25 Ma) suggesting that Re–Os geochronology of variable petroleum phases derived from lacustrine Type I kerogen has similar systematics to Type II kerogen (e.g., Selby and Creaser, 2005a, Selby and Creaser, 2005b and Finlay et al., 2010). However, the large uncertainties (over 100% in some cases) produced for the petroleum Re–Os geochronology are a result of multiple generation events occurring through a ∼3000-m thick source unit that creates a mixture of initial Os isotope compositions in the produced petroleum phases. The 187Os/188Os values for the petroleum and source rocks at the time of oil generation vary from 1.4 to 1.9, with the mode at ∼1.6. Oil-to-source correlation using Os isotopes is consistent with previous correlation studies in the Green River petroleum system, and illustrates the potential utility of Os isotopes to characterize the spatial variations within a petroleum system. Hydrous pyrolysis experiments on the Green River Formation source rocks show that Re and Os transfer are mimicking the natural system. This transfer from source to bitumen to oil does not affect source rock Re–Os systematics or Os isotopic compositions. This confirms that Os isotope compositions are transferred intact from source to petroleum during petroleum generation and can be used as a powerful correlation tool. These experiments further confirm that Re–Os systematics in source rocks are not adversely affected by petroleum maturation. Overall this study illustrates that the Re–Os petroleum geochronometer and Os isotope fingerprinting tools can be used on a wide range of petroleum types sourced from variable kerogen types.

Observational insights into aerosol formation from isoprene.

PubMed

Worton, David R; Surratt, Jason D; Lafranchi, Brian W; Chan, Arthur W H; Zhao, Yunliang; Weber, Robin J; Park, Jeong-Hoo; Gilman, Jessica B; de Gouw, Joost; Park, Changhyoun; Schade, Gunnar; Beaver, Melinda; Clair, Jason M St; Crounse, John; Wennberg, Paul; Wolfe, Glenn M; Harrold, Sara; Thornton, Joel A; Farmer, Delphine K; Docherty, Kenneth S; Cubison, Michael J; Jimenez, Jose-Luis; Frossard, Amanda A; Russell, Lynn M; Kristensen, Kasper; Glasius, Marianne; Mao, Jingqiu; Ren, Xinrong; Brune, William; Browne, Eleanor C; Pusede, Sally E; Cohen, Ronald C; Seinfeld, John H; Goldstein, Allen H

2013-10-15

Atmospheric photooxidation of isoprene is an important source of secondary organic aerosol (SOA) and there is increasing evidence that anthropogenic oxidant emissions can enhance this SOA formation. In this work, we use ambient observations of organosulfates formed from isoprene epoxydiols (IEPOX) and methacrylic acid epoxide (MAE) and a broad suite of chemical measurements to investigate the relative importance of nitrogen oxide (NO/NO2) and hydroperoxyl (HO2) SOA formation pathways from isoprene at a forested site in California. In contrast to IEPOX, the calculated production rate of MAE was observed to be independent of temperature. This is the result of the very fast thermolysis of MPAN at high temperatures that affects the distribution of the MPAN reservoir (MPAN / MPA radical) reducing the fraction that can react with OH to form MAE and subsequently SOA (F(MAE formation)). The strong temperature dependence of F(MAE formation) helps to explain our observations of similar concentrations of IEPOX-derived organosulfates (IEPOX-OS; ~1 ng m(-3)) and MAE-derived organosulfates (MAE-OS; ~1 ng m(-3)) under cooler conditions (lower isoprene concentrations) and much higher IEPOX-OS (~20 ng m(-3)) relative to MAE-OS (<0.0005 ng m(-3)) at higher temperatures (higher isoprene concentrations). A kinetic model of IEPOX and MAE loss showed that MAE forms 10-100 times more ring-opening products than IEPOX and that both are strongly dependent on aerosol water content when aerosol pH is constant. However, the higher fraction of MAE ring opening products does not compensate for the lower MAE production under warmer conditions (higher isoprene concentrations) resulting in lower formation of MAE-derived products relative to IEPOX at the surface. In regions of high NOx, high isoprene emissions and strong vertical mixing the slower MPAN thermolysis rate aloft could increase the fraction of MPAN that forms MAE resulting in a vertically varying isoprene SOA source.

The Hadean upper mantle conundrum: evidence for source depletion and enrichment from Sm-Nd, Re-Os, and Pb isotopic compositions in 3.71 Gy boninite-like metabasalts from the Isua Supracrustal Belt, Greenland

NASA Astrophysics Data System (ADS)

Frei, Robert; Polat, Ali; Meibom, Anders

2004-04-01

Here we present Sm-Nd, Re-Os, and Pb isotopic data of carefully screened, least altered samples of boninite-like metabasalts from the Isua Supracrustal Belt (ISB, W Greenland)that characterize their mantle source at the time of their formation. The principal observations of this study are that by 3.7-3.8 Ga melt source regions existed in the upper mantle with complicated enrichment/depletion histories. Sm-Nd isotopic data define a correlation line with a slope corresponding to an age of 3.69 ± 0.18 Gy and an initial εNd value of +2.0 ± 4.7. This Sm-Nd age is consistent with indirect (but more precise) U-Pb geochronological estimates for their formation between 3.69-3.71 Ga. Relying on the maximum formation age of 3.71 Gy defined by the external age constraints, we calculate an average εNd [T = 3.71 Ga] value of +2.2 ± 0.9 (n = 18, 1σ) for these samples, which is indicative of a strongly depleted mantle source. This is consistent with the high Os concentrations, falling in the range between 1.9-3.4 ppb, which is similar to the estimated Os concentration for the primitive upper mantle. Re-Os isotopic data (excluding three outliers) yield an isochron defining an age of 3.76 ± 0.09 Gy (with an initial γOs value of 3.9 ± 1.2), within error consistent with the Sm-Nd age and the indirect U-Pb age estimates. An average initial γOs [T = 3.71 Ga] value of + 4.4 ± 1.2 (n = 8; 2σ) is indicative of enrichment of their source region during, or prior to, its melting. Thus, this study provides the first observation of an early Archean upper mantle domain with a distinctly radiogenic Os isotopic signature. This requires a mixing component characterized by time-integrated suprachondritic Re/Os evolution and a Os concentration high enough to strongly affect the Os budget of the mantle source; modern sediments, recycled basaltic crust, or the outer core do not constitute suitable candidates. At this point, the nature of the mantle or crustal component responsible for the radiogenic Os isotopic signature is not known. Compared with the Sm-Nd and Re-Os isotope systems, the Pb isotope systematics show evidence for substantial perturbation by postformational hydrothermal-metasomatic alteration processes accompanying an early Archean metamorphic event at 3510 ± 65 Ma and indicate that the U-Th-Pb system was partially opened to Pb-loss on a whole rock scale. Single stage mantle evolution models fail to provide a solution to the Pb isotopic data, which requires that a high-μ component was mixed with the depleted mantle component before or during the extrusion of the basalts. Relatively high 207Pb/204Pb ratios (compared to contemporaneous mantle), support the hypothesis that erosion products of the ancient terrestrial protocrust existed for several hundred My before recycling into the mantle before ∼3.7 Ga. Our results are broadly consistent with models favoring a time-integrated Hadean history of mantle depletion and with the existence of an early Hadean protocrust, the complement to the Hadean depleted mantle, which after establishment of subduction-like processes was, at least locally, recycled into the upper mantle before 3.7 Ga. Thus, already in the Hadean, the upper mantle seems to be characterized by geochemical heterogeneity on a range of length scales; one property that is shared with the modern upper mantle. However, a simple two component mixing scenario between depleted mantle and an enriched-, crustal component with a modern analogue can not account for the complicated and contradictory geochemical properties of this particular Hadean upper mantle source.

A Fault-Oblivious Extreme-Scale Execution Environment (FOX)

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

Van Hensbergen, Eric; Speight, William; Xenidis, Jimi

IBM Research’s contribution to the Fault Oblivious Extreme-scale Execution Environment (FOX) revolved around three core research deliverables: • collaboration with Boston University around the Kittyhawk cloud infrastructure which both enabled a development and deployment platform for the project team and provided a fault-injection testbed to evaluate prototypes • operating systems research focused on exploring role-based operating system technologies through collaboration with Sandia National Labs on the NIX research operating system and collaboration with the broader IBM Research community around a hybrid operating system model which became known as FusedOS • IBM Research also participated in an advisory capacity with themore » Boston University SESA project, the core of which was derived from the K42 operating system research project funded in part by DARPA’s HPCS program. Both of these contributions were built on a foundation of previous operating systems research funding by the Department of Energy’s FastOS Program. Through the course of the X-stack funding we were able to develop prototypes, deploy them on production clusters at scale, and make them available to other researchers. As newer hardware, in the form of BlueGene/Q, came online, we were able to port the prototypes to the new hardware and release the source code for the resulting prototypes as open source to the community. In addition to the open source coded for the Kittyhawk and NIX prototypes, we were able to bring the BlueGene/Q Linux patches up to a more recent kernel and contribute them for inclusion by the broader Linux community. The lasting impact of the IBM Research work on FOX can be seen in its effect on the shift of IBM’s approach to HPC operating systems from Linux and Compute Node Kernels to role-based approaches as prototyped by the NIX and FusedOS work. This impact can be seen beyond IBM in follow-on ideas being incorporated into the proposals for the Exasacale Operating Systems/Runtime program.« less

A Fault Oblivious Extreme-Scale Execution Environment

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

McKie, Jim

The FOX project, funded under the ASCR X-stack I program, developed systems software and runtime libraries for a new approach to the data and work distribution for massively parallel, fault oblivious application execution. Our work was motivated by the premise that exascale computing systems will provide a thousand-fold increase in parallelism and a proportional increase in failure rate relative to today’s machines. To deliver the capability of exascale hardware, the systems software must provide the infrastructure to support existing applications while simultaneously enabling efficient execution of new programming models that naturally express dynamic, adaptive, irregular computation; coupled simulations; and massivemore » data analysis in a highly unreliable hardware environment with billions of threads of execution. Our OS research has prototyped new methods to provide efficient resource sharing, synchronization, and protection in a many-core compute node. We have experimented with alternative task/dataflow programming models and shown scalability in some cases to hundreds of thousands of cores. Much of our software is in active development through open source projects. Concepts from FOX are being pursued in next generation exascale operating systems. Our OS work focused on adaptive, application tailored OS services optimized for multi → many core processors. We developed a new operating system NIX that supports role-based allocation of cores to processes which was released to open source. We contributed to the IBM FusedOS project, which promoted the concept of latency-optimized and throughput-optimized cores. We built a task queue library based on distributed, fault tolerant key-value store and identified scaling issues. A second fault tolerant task parallel library was developed, based on the Linda tuple space model, that used low level interconnect primitives for optimized communication. We designed fault tolerance mechanisms for task parallel computations employing work stealing for load balancing that scaled to the largest existing supercomputers. Finally, we implemented the Elastic Building Blocks runtime, a library to manage object-oriented distributed software components. To support the research, we won two INCITE awards for time on Intrepid (BG/P) and Mira (BG/Q). Much of our work has had impact in the OS and runtime community through the ASCR Exascale OS/R workshop and report, leading to the research agenda of the Exascale OS/R program. Our project was, however, also affected by attrition of multiple PIs. While the PIs continued to participate and offer guidance as time permitted, losing these key individuals was unfortunate both for the project and for the DOE HPC community.« less

The Very Late Eocene Opening of Fram Strait between the Arctic Ocean and the Nordic Seas: Linkages with the Popigai Impact

NASA Astrophysics Data System (ADS)

Hillaire-Marcel, C.; Poirier, A.

2013-12-01

The transition from the Eocene Arctic Lake to the Arctic Ocean through the opening of Fram Strait, initially dated at ca. 18 Ma based on palynological inferences (Moran et al., 2004, Nature 441, 601-605), has been recently assigned to the very late Eocene (~ 36 Ma) based on Os-isotope stratigraphy and Re-Os isochron ages of sediments from the IODP-ACEX core (Lomonosov Ridge) (Poirier & Hillaire-Marcel, 2011, GRL 38, L14607). Here, we examine the potential linkages of this event with the Popigai meteoritic impact from northeastern Siberia, which has been dated independently at 35.7×0.2 Ma (Bottomley et al. 1997, Nature 338, 365-368). Noteworthy is the fact that in the earliest marine sediments of the ACEX core, the Os-isotope stratigraphy records an isotopic excursion which we tentatively assigned to the chondritic impactor of Popigai. Sr and Pb isotope signatures of detrital sediments (i.e., following the removal of exchangeable fractions) were thus used to further document the sources of terrigenous sediments deposited before, during, and after the transition episode. Above and below the lacustrine/marine boundary, we note relatively constant source provenances (or mixture of sources), implying that relative contributions from regional detrital sedimentary sources, thus relative erosion rates over surrounding continents, did not change much at a Ma-long time scale. On the other hand, a sharp change highlights the lacustrine/marine transition, with an abrupt shift to low values in 87Sr/88Sr, also marked by a (smaller) excursion in all three 204Pb-normalised lead isotopes values (corrected for in-situ decay of U). This isotopic excursion might also be due to the Popigai chondritic Impactor. The impact-related ejection over basaltic target materials would have produced the particulate matter of suitable composition (Wooden et al. 1993, GCA 57, 3677-3704) to account for the isotopic excursion observed. A first order estimate of the Popigai impact yields a value of ~ 10^8 megatons, resulting in a potential seismic event in the Fram Strait area with a magnitude > 10, likely to have resulted in major faulting in the area, thus possibly leading to the opening of the Strait. This very late Eocene opening of Fram Strait, would suggest a potential role of the Arctic basin in the inception of the Atlantic Meridional Overturning Circulation. With this new chronology, the entry of the Earth in the "cold house" system of the Early Oligocene, and the early indices for ice-rafting, might have being nearly synchronous in the Arctic and the circum-Antarctica.

Sources of osmium to the modern oceans: New evidence from the 190Pt-186Os system

USGS Publications Warehouse

McDaniel, D.K.; Walker, R.J.; Hemming, S.R.; Horan, M.F.; Becker, H.; Grauch, R.I.

2004-01-01

High precision Os isotope analysis of young marine manganese nodules indicate that whereas the composition of modern seawater is radiogenic with respect to 187Os/188Os, it has 186Os/188Os that is within uncertainty of the chondritic value. Marine Mn nodule compositions thus indicate that the average continental source of Os to modern seawater had long-term high Re/Os compared to Pt/Os. Analyses of loess and freshwater Mn nodules support existing evidence that average upper continental crust (UCC) has resolvably suprachondritic 186Os/188Os, as well as radiogenic 187Os/188Os. Modeling the composition of seawater as a two-component mixture of oceanic/cosmic Os with chondritic Os compositions and continentally-derived Os demonstrates that, insofar as estimates for the composition of average UCC are accurate, congruently weathered average UCC cannot be the sole continental source of Os to seawater. Our analysis of four Cambrian black shales confirm that organic-rich sediments can have 187Os/188Os ratios that are much higher than average UCC, but 186Os/188Os compositions that are generally between those of chondrites and average-UCC. Preferential weathering of black shales can result in dissolved Os discharged to the ocean basins that has a much lower 186Os/188Os than does average upper crust. Modeling the available data demonstrates that augmentation of estimated average UCC compositions with less than 0.1% additional black shale and 1.4% additional ultramafic rock can produce a continental end-member Os isotopic composition that satisfies the requirements imposed by the marine Mn nodule data. The interplay of these two sources provides a mechanism by which the 187Os/188Os of seawater can change as sources and weathering conditions change, yet seawater 186Os/188Os varies only minimally. ?? 2004 Elsevier Ltd.

Study of Adversarial and Defensive Components in an Experimental Machinery Control Systems Laboratory Environment

DTIC Science & Technology

2014-09-01

prevention system (IPS), capable of performing real-time traffic analysis and packet logging on IP networks [25]. Snort’s features include protocol... analysis and content searching/matching. Snort can detect a variety of attacks and network probes, such as buffer overflows, port scans and OS...www.digitalbond.com/tools/the- rack/jtr-s7-password-cracking/ Kismet Mike Kershaw Cross- platform Open source wireless network detector and wireless sniffer

OpenStructure: a flexible software framework for computational structural biology.

PubMed

Biasini, Marco; Mariani, Valerio; Haas, Jürgen; Scheuber, Stefan; Schenk, Andreas D; Schwede, Torsten; Philippsen, Ansgar

2010-10-15

Developers of new methods in computational structural biology are often hampered in their research by incompatible software tools and non-standardized data formats. To address this problem, we have developed OpenStructure as a modular open source platform to provide a powerful, yet flexible general working environment for structural bioinformatics. OpenStructure consists primarily of a set of libraries written in C++ with a cleanly designed application programmer interface. All functionality can be accessed directly in C++ or in a Python layer, meeting both the requirements for high efficiency and ease of use. Powerful selection queries and the notion of entity views to represent these selections greatly facilitate the development and implementation of algorithms on structural data. The modular integration of computational core methods with powerful visualization tools makes OpenStructure an ideal working and development environment. Several applications, such as the latest versions of IPLT and QMean, have been implemented based on OpenStructure-demonstrating its value for the development of next-generation structural biology algorithms. Source code licensed under the GNU lesser general public license and binaries for MacOS X, Linux and Windows are available for download at http://www.openstructure.org. torsten.schwede@unibas.ch Supplementary data are available at Bioinformatics online.

Open source clustering software.

PubMed

de Hoon, M J L; Imoto, S; Nolan, J; Miyano, S

2004-06-12

We have implemented k-means clustering, hierarchical clustering and self-organizing maps in a single multipurpose open-source library of C routines, callable from other C and C++ programs. Using this library, we have created an improved version of Michael Eisen's well-known Cluster program for Windows, Mac OS X and Linux/Unix. In addition, we generated a Python and a Perl interface to the C Clustering Library, thereby combining the flexibility of a scripting language with the speed of C. The C Clustering Library and the corresponding Python C extension module Pycluster were released under the Python License, while the Perl module Algorithm::Cluster was released under the Artistic License. The GUI code Cluster 3.0 for Windows, Macintosh and Linux/Unix, as well as the corresponding command-line program, were released under the same license as the original Cluster code. The complete source code is available at http://bonsai.ims.u-tokyo.ac.jp/mdehoon/software/cluster. Alternatively, Algorithm::Cluster can be downloaded from CPAN, while Pycluster is also available as part of the Biopython distribution.

Tracing Anthropogenic Osmium around Japan using the Osmium Isotopic Composition of Macroalgae

NASA Astrophysics Data System (ADS)

Sproson, A. D.; Selby, D. S.; Suzuki, K.

2016-12-01

The present-day open ocean seawater 187Os/188Os value of 1.06 is seen to reflect the balance between unradiogenic mantle derived osmium (Os) and radiogenic continental Os. However, Os released by anthropogenic activities has been detected in coastal sediments, lakes, estuaries, rain and snow from sources such as sewage sludge, catalytic convertors, smelting, fossil fuel burning and use as a staining reagent, thereby impacting the global Os budget. Despite over two decades of research, contemporary Os inputs into the ocean are believed to be underestimated by a factor of 3, leading to discrepancies in oceanic Os residence times estimated from mass balance calculations. This, in part, is due to the problems associated with directly measuring ultra-low concentrations of Os in seawater. Recently, it has been proposed that the 187Os/188Os of macroalgae (seaweed) reflects that of the seawater in which it lives. This suggests macroalgae can act as a proxy for the Os isotopic composition of seawater. We present Os isotope data for macroalgae collected from Tokyo Bay, Osaka Bay, the Noto Peninsula, Izu Peninsula and Hokkaido. Macroalgae close to the major cities of Tokyo and Osaka exhibit unradiogenic 187Os/188Os values as low as 0.45, in agreement with published sediment data. As you move away from central Tokyo and Osaka, 187Os/188Os values become more radiogenic, reaching values as high as 0.95 due to the entrainment of more radiogenic seawater. Macroalgae from the less urbanised Noto and Izu Peninsulas show a radiogenic 187Os/188Os range of 0.70-0.91, close to global river estimates suggesting little contamination from anthropogenic processes. Deep-water species off the coast of Hokkaido exhibit 187Os/188Os values in agreement with published Pacific Ocean seawater data. We propose macroalgae is recording the influence of anthropogenic processes - in particular sewage sludge production and catalytic convertor exhaust - on the Os budget of Japanese waters. Therefore, macroalgae could become a useful pollution indicator and powerful tracer of continental Os inputs to the ocean.

Comparison of endoscopic and open resection of sinonasal squamous cell carcinoma: a propensity score-matched analysis of 652 patients.

PubMed

Kılıç, Suat; Kılıç, Sarah S; Baredes, Soly; Chan Woo Park, Richard; Mahmoud, Omar; Suh, Jeffrey D; Gray, Stacey T; Eloy, Jean Anderson

2018-03-01

The use of endoscopic resection as an alternative to open surgery for sinonasal malignancies has increased in the past 20 years. The National Cancer Database was queried for cases of sinonasal squamous cell carcinoma (SNSCC) without cervical or distant metastases that were treated surgically between 2010 and 2014. They were split into 2 groups based on surgical approach: open or endoscopic. Demographics, facility and insurance type, stage, tumor characteristics, postoperative treatment, 30-day readmission rate, 30- and 90-day mortality, and overall survival (OS) were compared between the 2 groups. Cox proportional hazard analysis was performed. Propensity score matching (PSM) was used to mimic a randomized, controlled trial. A total of 1,483 patients were identified: 353 (23.8%) received endoscopic and 1130 (76.2%) received open surgery. Age, gender, race, geographic region, tumor size, surgical margins, postoperative chemoradiation, and 30-day readmissions did not vary significantly between the 2 groups. Open surgery was more common in academic centers (62.8% vs 54.2%; p = 0.004), less common for tumors of the ethmoid and sphenoid sinus (p < 0.0001), less common for stage IVB tumors, and associated with longer hospital stay (mean, 4.67 days vs 2.50 days; p < 0.0001). Five-year OS (5Y-OS) was not significantly different between the 2 approaches (p = 0.953; open: 5Y-OS, 56.5%; 95% confidence interval, 51.3% to 61.6%; endoscopic: 5Y-OS, 46.0%; 95% confidence interval, 33.2% to 58.8%). In the PSM cohort of 652 patients, there was also no significant difference in OS (p = 0.850). Endoscopic surgery is an effective alternative to open surgery, even after accounting for confounding factors that may favor its use over the open approach. It is also associated with a shorter hospital stay. © 2017 ARS-AAOA, LLC.

New target prediction and visualization tools incorporating open source molecular fingerprints for TB Mobile 2.0

PubMed Central

2014-01-01

Background We recently developed a freely available mobile app (TB Mobile) for both iOS and Android platforms that displays Mycobacterium tuberculosis (Mtb) active molecule structures and their targets with links to associated data. The app was developed to make target information available to as large an audience as possible. Results We now report a major update of the iOS version of the app. This includes enhancements that use an implementation of ECFP_6 fingerprints that we have made open source. Using these fingerprints, the user can propose compounds with possible anti-TB activity, and view the compounds within a cluster landscape. Proposed compounds can also be compared to existing target data, using a näive Bayesian scoring system to rank probable targets. We have curated an additional 60 new compounds and their targets for Mtb and added these to the original set of 745 compounds. We have also curated 20 further compounds (many without targets in TB Mobile) to evaluate this version of the app with 805 compounds and associated targets. Conclusions TB Mobile can now manage a small collection of compounds that can be imported from external sources, or exported by various means such as email or app-to-app inter-process communication. This means that TB Mobile can be used as a node within a growing ecosystem of mobile apps for cheminformatics. It can also cluster compounds and use internal algorithms to help identify potential targets based on molecular similarity. TB Mobile represents a valuable dataset, data-visualization aid and target prediction tool. PMID:25302078

New target prediction and visualization tools incorporating open source molecular fingerprints for TB Mobile 2.0.

PubMed

Clark, Alex M; Sarker, Malabika; Ekins, Sean

2014-01-01

We recently developed a freely available mobile app (TB Mobile) for both iOS and Android platforms that displays Mycobacterium tuberculosis (Mtb) active molecule structures and their targets with links to associated data. The app was developed to make target information available to as large an audience as possible. We now report a major update of the iOS version of the app. This includes enhancements that use an implementation of ECFP_6 fingerprints that we have made open source. Using these fingerprints, the user can propose compounds with possible anti-TB activity, and view the compounds within a cluster landscape. Proposed compounds can also be compared to existing target data, using a näive Bayesian scoring system to rank probable targets. We have curated an additional 60 new compounds and their targets for Mtb and added these to the original set of 745 compounds. We have also curated 20 further compounds (many without targets in TB Mobile) to evaluate this version of the app with 805 compounds and associated targets. TB Mobile can now manage a small collection of compounds that can be imported from external sources, or exported by various means such as email or app-to-app inter-process communication. This means that TB Mobile can be used as a node within a growing ecosystem of mobile apps for cheminformatics. It can also cluster compounds and use internal algorithms to help identify potential targets based on molecular similarity. TB Mobile represents a valuable dataset, data-visualization aid and target prediction tool.

Characteristics and geological significance of Re-Os isotopic system of evaporites in Mboukoumassi deposit, the Republic of Congo

NASA Astrophysics Data System (ADS)

Zhao, Xianfu; Wang, Zongqi; Liu, Chenglin; Li, Chao; Jiao, Pengcheng; Zhao, Yanjun; Zhang, Fan

2018-02-01

Evaporite dating has been an open problem. The study investigates the Re-Os isotopic system in the organic-rich sedimentary rocks to constrain the infilling of sedimentary basin and related geological events. In the Mboukoumassi potash deposit in the Republic of Congo (Congo-Brazzaville) in West Africa, several layers of organic-rich dark shale were found in the evaporite series. Through drilling core, the dark shale in the evaporite is found to satisfy the requirements of Re-Os isotope test. The result shows that the Re-Os isochron age of the dark shale in the study area ranges from 78.7 ± 1.1 to 96 ± 7 Ma, which is the first precise age of the Mboukoumassi potash deposit in the Republic of Congo (Congo-Brazzaville), West Africa. Therefore, the age of deposition of this set of evaporite may be Cenomanian-Turonian, which is younger than the age previously thought (around 113-125Ma, Aptian). The Re-Os isotopic dating technique used for the pioneering study on the precise dating of the Mboukoumassi potash deposit provides a new approach to the study of the sedimentary age of ancient evaporite deposits. The initial 187Os/188Os value decreasing from 2.02 ± 0.21 to 0.982 ± 0.03 for the core sample reflects the source rock chang along the core, and this is consistent with the geological evolution of the basin.

Osmium Isotopic Evolution of the Mantle Sources of Precambrian Ultramafic Rocks

NASA Astrophysics Data System (ADS)

Gangopadhyay, A.; Walker, R. J.

2006-12-01

The Os isotopic composition of the modern mantle, as recorded collectively by ocean island basalts, mid- oceanic ridge basalts (MORB) and abyssal peridotites, is evidently highly heterogeneous (γ Os(I) ranging from <-10 to >+25). One important question, therefore, is how and when the Earth's mantle developed such large-scale Os isotopic heterogeneities. Previous Os isotopic studies of ancient ultramafic systems, including komatiites and picrites, have shown that the Os isotopic heterogeneity of the terrestrial mantle can be traced as far back as the late-Archean (~ 2.7-2.8 Ga). This observation is based on the initial Os isotopic ratios obtained for the mantle sources of some of the ancient ultramafic rocks determined through analyses of numerous Os-rich whole-rock and/or mineral samples. In some cases, the closed-system behavior of these ancient ultramafic rocks was demonstrated via the generation of isochrons of precise ages, consistent with those obtained from other radiogenic isotopic systems. Thus, a compilation of the published initial ^{187}Os/^{188}Os ratios reported for the mantle sources of komatiitic and picritic rocks is now possible that covers a large range of geologic time spanning from the Mesozoic (ca. 89 Ma Gorgona komatiites) to the Mid-Archean (e.g., ca. 3.3 Ga Commondale komatiites), which provides a comprehensive picture of the Os isotopic evolution of their mantle sources through geologic time. Several Precambrian komatiite/picrite systems are characterized by suprachondritic initial ^{187}Os/^{188}Os ratios (e.g., Belingwe, Kostomuksha, Pechenga). Such long-term enrichments in ^{187}Os of the mantle sources for these rocks may be explained via recycling of old mafic oceanic crust or incorporation of putative suprachondritic outer core materials entrained into their mantle sources. The relative importance of the two processes for some modern mantle-derived systems (e.g., Hawaiian picrites) is an issue of substantial debate. Importantly, however, the high-precision initial Os isotopic compositions of the majority of ultramafic systems show strikingly uniform initial ^{187}Os/^{188}Os ratios, consistent with their derivation from sources that had Os isotopic evolution trajectory very similar to that of carbonaceous chondrites. In addition, the Os isotopic evolution trajectories of the mantle sources for most komatiites show resolvably lower average Re/Os than that estimated for the Primitive Upper Mantle (PUM), yet significantly higher than that obtained in some estimates for the modern convecting upper mantle, as determined via analyses of abyssal peridotites. One possibility is that most of the komatiites sample mantle sources that are unique relative to the sources of abyssal peridotites and MORB. Previous arguments that komatiites originate via large extents of partial melting of relatively deep upper mantle, or even lower mantle materials could, therefore, implicate a source that is different from the convecting upper mantle. If so, this source is remarkably uniform in its long-term Re/Os, and it shows moderate depletion in Re relative to the PUM. Alternatively, if the komatiites are generated within the convective upper mantle through relatively large extents of partial melting, they may provide a better estimate of the Os isotopic composition of the convective upper mantle than that obtained via analyses of MORB, abyssal peridotites and ophiolites.

Posterior Endoscopic Excision of Os Trigonum in Professional National Ballet Dancers.

PubMed

Ballal, Moez S; Roche, Andy; Brodrick, Anna; Williams, R Lloyd; Calder, James D F

2016-01-01

Previous studies have compared the outcomes after open and endoscopic excision of an os trigonum in patients of mixed professions. No studies have compared the differences in outcomes between the 2 procedures in elite ballet dancers. From October 2005 to February 2010, 35 professional ballet dancers underwent excision of a symptomatic os trigonum of the ankle after a failed period of nonoperative treatment. Of the 35 patients, 13 (37.1%) underwent endoscopic excision and 22 (62.9%) open excision. We compared the outcomes, complications, and time to return to dancing. The open excision group experienced a significantly greater incidence of flexor hallucis longus tendon decompression compared with the endoscopic group. The endoscopic release group returned to full dance earlier at a mean of 9.8 (range 6.5 to 16.1) weeks and those undergoing open excision returned to full dance at a mean of 14.9 (range 9 to 20) weeks (p = .001). No major complications developed in either group, such as deep infection or nerve or vessel injury. We have concluded that both techniques are safe and effective in the treatment of symptomatic os trigonum in professional ballet dancers. Endoscopic excision of the os trigonum offers a more rapid return to full dance compared with open excision. Copyright © 2016 American College of Foot and Ankle Surgeons. Published by Elsevier Inc. All rights reserved.

CompactPCI/Linux Platform in FTU Slow Control System

NASA Astrophysics Data System (ADS)

Iannone, F.; Wang, L.; Centioli, C.; Panella, M.; Mazza, G.; Vitale, V.

2004-12-01

In large fusion experiments, such as tokamak devices, there is a common trend for slow control systems. Because of complexity of the plants, the so-called `Standard Model' (SM) in slow control has been adopted on several tokamak machines. This model is based on a three-level hierarchical control: 1) High-Level Control (HLC) with a supervisory function; 2) Medium-Level Control (MLC) to interface and concentrate I/O field equipments; 3) Low-Level Control (LLC) with hard real-time I/O function, often managed by PLCs. FTU control system designed with SM concepts has underwent several stages of developments in its fifteen years duration of runs. The latest evolution was inevitable, due to the obsolescence of the MLC CPUs, based on VME-MOTOROLA 68030 with OS9 operating system. A large amount of C code was developed for that platform to route the data flow from LLC, which is constituted by 24 Westinghouse Numalogic PC-700 PLCs with about 8000 field-points, to HLC, based on a commercial Object-Oriented Real-Time database on Alpha/CompaqTru64 platform. Therefore, we have to look for cost-effective solutions and finally a CompactPCI-Intel x86 platform with Linux operating system was chosen. A software porting has been done, taking into account the differences between OS9 and Linux operating system in terms of Inter/Network Processes Communications and I/O multi-ports serial driver. This paper describes the hardware/software architecture of the new MLC system, emphasizing the reliability and the low costs of the open source solutions. Moreover, a huge amount of software packages available in open source environment will assure a less painful maintenance, and will open the way to further improvements of the system itself.

Osmium isotopes demonstrate distal transport of contaminated sediments in Chesapeake Bay

USGS Publications Warehouse

Helz, G.R.; Adelson, J.M.; Miller, C.V.; Cornwell, J.C.; Hill, J.M.; Horan, M.; Walker, R.J.

2000-01-01

Because the isotopic composition of anthropogenic Os is normally distinctive in comparison to continental crust and is precisely measurable, this platinum-group element is attractive as a tracer of transport pathways for contaminated sediments in estuaries. Evidence herein and elsewhere suggest that biomedical research institutions are the chief source of anthropogenic Os. In the Chesapeake Bay region, uncontaminated sediments bear a crustal 187Os/188Os signature of 0.73 ?? 0.10. Slightly higher 187Os/188Os ratios occur in Re-rich Coastal Plain deposits due to post- Miocene 187Re decay. The upper Susquehanna Basin yields sediments also with higher 187Os/188Os. Beginning in the late 1970s, this signal was overprinted by a low 187Os/188Os (anthropogenic) source in the lower Susquehanna Basin. In the vicinity of Baltimore, which is a major center of heavy industry as well as biomedical research, anthropogenic Os has been found only in sediments impacted by the principal wastewater treatment plant. Surprisingly, a mid-Bay site distant from anthropogenic sources contains the strongest anthropogenic Os signal in the data set, having received anthropogenic Os sporadically since the mid-20th Century. Transport of particles to this site overrode the northward flowing bottom currents. Finding anthropogenic Os at this site cautions that other particle-borne substances, including hazardous ones, could be dispersed broadly in this estuary.Because the isotopic composition of anthropogenic Os is normally distinctive in comparison to continental crust and is precisely measurable, this platinum-group element is attractive as a tracer of transport pathways for contaminated sediments in estuaries. Evidence herein and elsewhere suggest that biomedical research institutions are the chief source of anthropogenic Os. In the Chesapeake Bay region, uncontaminated sediments bear a crustal 187Os/188Os signature of 0.73 ?? 0.10. Slightly higher 187Os/188Os ratios occur in Re-rich Coastal Plain deposits due to post-Miocene 187Re decay. The upper Susquehanna Basin yields sediments also with higher 187Os/188Os. Beginning in the late 1970s, this signal was overprinted by a low 187Os/188Os (anthropogenic) source in the lower Susquehanna Basin. In the vicinity of Baltimore, which is a major center of heavy industry as well as biomedical research, anthropogenic Os has been found only in sediments impacted by the principal wastewater treatment plant. Surprisingly, a mid-Bay site distant from anthropogenic sources contains the strongest anthropogenic Os signal in the data set, having received anthropogenic Os sporadically since the mid-20th Century. Transport of particles to this site overrode the northward flowing bottom currents. Finding anthropogenic Os at this site cautions that other particle-borne substances, including hazardous ones, could be dispersed broadly in this estuary.

Mutation of the OsSAC1 Gene, which Encodes an Endoplasmic Reticulum Protein with an Unknown Function, Causes Sugar Accumulation in Rice Leaves.

PubMed

Zhu, Xiaoyan; Shen, Wenqiang; Huang, Junyang; Zhang, Tianquan; Zhang, Xiaobo; Cui, Yuanjiang; Sang, Xianchun; Ling, Yinghua; Li, Yunfeng; Wang, Nan; Zhao, Fangmin; Zhang, Changwei; Yang, Zhenglin; He, Guanghua

2018-03-01

Sugars are the most abundant organic compounds produced by plants, and can be used to build carbon skeletons and generate energy. The sugar accumulation 1 (OsSAC1) gene encodes a protein with an unknown function that exhibits four N-terminal transmembrane regions and two conserved domains of unknown function, DUF4220 and DUF594. OsSAC1 was found to be poorly and specifically expressed at the bottoms of young leaves and in the developing leaf sheaths. Subcellular location results showed that OsSAC1 was co-localized with ER:mCherry and targeted the endoplasmic reticulum (ER). OsSAC1 has been found to affect sugar partitioning in rice (Oryza sativa). I2/KI starch staining, ultrastructure observations and starch content measurements indicated that more and larger starch granules accumulated in ossac1 source leaves than in wild-type (WT) source leaves. Additionally, higher sucrose and glucose concentrations accumulated in the ossac1 source leaves than in WT source leaves, whereas lower sucrose and glucose concentrations were observed in the ossac1 young leaves and developing leaf sheaths than in those of the WT. Much greater expression of OsAGPL1 and OsAGPS1 (responsible for starch synthesis) and significantly less expression of OscFBP1, OscFBP2, OsSPS1 and OsSPS11 (responsible for sucrose synthesis) and OsSWEET11, OsSWEET14 and OsSUT1 (responsible for sucrose loading) occurred in ossac1 source leaves than in WT source leaves. A greater amount of the rice plasmodesmatal negative regulator OsGSD1 was detected in ossac1 young leaves and developing leaf sheaths than in those of the WT. These results suggest that ER-targeted OsSAC1 may indirectly regulate sugar partitioning in carbon-demanding young leaves and developing leaf sheaths.

Osmium Isotope Compositions of Komatiite Sources Through Time

NASA Astrophysics Data System (ADS)

Walker, R. J.

2001-12-01

Extending Os isotopic measurements to ancient plume sources may help to constrain how and when the well-documented isotopic heterogeneities in modern systems were created. Komatiites and picrites associated with plume-related volcanism are valuable tracers of the Os isotopic composition of plumes because of their typically high Os concentrations and relatively low Re/Os. Re-Os data are now available for a variety of Phanerozoic, Proterozoic and Archean komatiites and picrites. As with modern plumes, the sources of Archean and Proterozoic komatiites exhibit a large range of initial 187Os/188Os ratios. Most komatiites are dominated by sources with chondritic Os isotopic compositions (e.g. Song La; Norseman-Wiluna; Pyke Hill; Alexo), though some (e.g. Gorgona) derive from heterogeneous sources. Of note, however, two ca. 2.7 Ga systems, Kostomuksha (Russia) and Belingwe (Zimbabwe), have initial ratios enriched by 2-3% relative to the contemporary convecting upper mantle. These results suggest that if the 187Os enrichment was due to the incorporation of minor amounts of recycled crust into the mantle source of the rocks, the crust formed very early in Earth history. Thus, the Os results could reflect derivation of melt from hybrid mantle whose composition was modified by the addition of mafic crustal material that would most likely have formed between 4.2 and 4.5 Ga. Alternately, the mantle sources of these komatiites may have derived a portion of their Os from the putative 187Os - and 186Os -enriched outer core. For this hypothesis to be applicable to Archean rocks, an inner core of sufficient mass would have to have crystallized sufficiently early in Earth history to generate an outer core with 187Os enriched by at least 3% relative to the chondritic average. Using the Pt-Re-Os partition coefficients espoused by our earlier work, and assuming linear growth of the inner core started at 4.5 Ga and continued to present, would yield an outer core at 2.7 Ga with a gamma Os value of only +1.2 and a 186Os/188Os enrichment relative to the contemporary upper mantle of only +13 ppm. Greater isotopic enrichments could have been achieved by 2.7 Ga if either the inner core comprised >2.8% of the mass of the core by 2.7 Ga, or if Re and Os solid metal-liquid metal D's for core crystallization were greater that those applied in the initial calculation.

Evolution of open radical retropubic prostatectomy--how have open surgeons responded to the challenge of minimally invasive surgery?

PubMed

Acharya, Sujeet S; Zorn, Kevin C; Shikanov, Sergey; Thong, Alan; Zagaja, Gregory P; Shalhav, Arieh L; Steinberg, Gary D

2009-11-01

With the advent of minimally invasive surgery (MIS) for treating urologic malignancies, emphasis has been placed on reducing patient morbidity and resuming normal activity. We sought to clarify whether open surgeons (OS) have modified their techniques, surgical equipment, and perioperative management in response to this trend. A survey sent to all members of the Society of Urologic Oncology assessed changes that OS performing radical retropubic prostatectomy have made in analgesia, operative technique, perioperative management, and follow-up patterns. We also assessed OS sense of competition from MIS. Surgeon perception of the influence MIS had on these changes was scored from 0 to 4 (0 = not at all, 1 = slightly, 2 = moderately, 3 = greatly, 4 =completely). Overall and major influence by MIS included scores 1-4 and 3-4, respectively. Reduced radical retropubic prostatectomy (RRP) case volume because of MIS competition was reported by 20 OS (24%), with 27 OS (32%) starting to perform MIS, and 20 (24%) doing mostly/exclusively MIS. MIS has influenced OS to reduce incision length (overall influence 56%/major influence 33%), operative time (40%/12%), blood loss (31%/17%), and transfusion rate (33%/14%). MIS has influenced OS to use new instruments (48%/44%) or loupes (20%/9%), modify dissection (45%/31%) or anastomotic technique (14%/12%), and increase the use of hemostatic agents (48%/19%). MIS has reduced convalescence in OS patients by reducing length of stay (52%/28%), time to a regular diet (40%/18%), duration of drain (21%/16%) and Foley (32%/15%), time to return to work (49%/25%), and exercise (44%/21%). MIS has changed follow-up of OS patients by increasing the use of clinical pathways (14%/9%) and validated questionnaires (22%/13%). To date, the influence of MIS on the OS has not been comprehensively assessed. This survey finds that OS report that MIS serves as major competition to the open technique and that it has influenced them to modify their surgical technique, reduce convalescence, and alter follow-up recommendations.

186Os- 187Os systematics of Gorgona Island komatiites: implications for early growth of the inner core

NASA Astrophysics Data System (ADS)

Brandon, Alan D.; Walker, Richard J.; Puchtel, Igor S.; Becker, Harry; Humayun, Munir; Revillon, Sidonie

2003-02-01

The presence of coupled enrichments in 186Os/ 188Os and 187Os/ 188Os in some mantle-derived materials reflects long-term elevation of Pt/Os and Re/Os relative to the primitive upper mantle. New Os data for the 89 Ma Gorgona Island, Colombia komatiites indicate that these lavas are also variably enriched in 186Os and 187Os, with 186Os/ 188Os ranging between 0.1198397±22 and 0.1198470±38, and with γOs correspondingly ranging from +0.15 to +4.4. These data define a linear trend that converges with the previously reported linear trend generated from data for modern Hawaiian picritic lavas and a sample from the ca. 251 Ma Siberian plume, to a common component with a 186Os/ 188Os of approximately 0.119870 and γOs of +17.5. The convergence of these data to this Os isotopic composition may imply a single ubiquitous source in the Earth's interior that mixes with a variety of different mantle compositions distinguished by variations in γOs. The 187Os- and 186Os-enriched component may have been generated via early crystallization of the solid inner core and consequent increases in Pt/Os and Re/Os in the liquid outer core, with time leading to suprachondritic 186Os/ 188Os and γOs in the outer core. The presence of Os from the outer core in certain portions of the mantle would require a mechanism that could transfer Os from the outer core to the lower mantle, and thence to the surface. If this is the process that generated the isotopic enrichments in the mantle sources of these plume-derived systems, then the current understanding of solid metal-liquid metal partitioning of Pt, Re and Os requires that crystallization of the inner core began prior to 3.5 Ga. Thus, the Os isotopic data reported here provide a new source of data to better constrain the timing of inner core formation, complementing magnetic field paleo-intensity measurements as data sources that constrain models based on secular cooling of the Earth.

PRay - A graphical user interface for interactive visualization and modification of rayinvr models

NASA Astrophysics Data System (ADS)

Fromm, T.

2016-01-01

PRay is a graphical user interface for interactive displaying and editing of velocity models for seismic refraction. It is optimized for editing rayinvr models but can also be used as a dynamic viewer for ray tracing results from other software. The main features are the graphical editing of nodes and fast adjusting of the display (stations and phases). It can be extended by user-defined shell scripts and links to phase picking software. PRay is open source software written in the scripting language Perl, runs on Unix-like operating systems including Mac OS X and provides a version controlled source code repository for community development (https://sourceforge.net/projects/pray-plot-rayinvr/).

Real-time control using open source RTOS

NASA Astrophysics Data System (ADS)

Irwin, Philip C.; Johnson, Richard L., Jr.

2002-12-01

Complex telescope systems such as interferometers tend to rely heavily on hard real-time operating systems (RTOS). It has been standard practice at NASA's Jet Propulsion Laboratory (JPL) and many other institutions to use costly commercial RTOSs and hardware. After developing a real-time toolkit for VxWorks on the PowerPC platform (dubbed RTC), the interferometry group at JPL is porting this code to the real-time Application Interface (RTAI), an open source RTOS that is essentially an extension to the Linux kernel. This port has the potential to reduce software and hardware costs for future projects, while increasing the level of performance. The goals of this paper are to briefly describe the RTC toolkit, highlight the successes and pitfalls of porting the toolkit from VxWorks to Linux-RTAI, and to discuss future enhancements that will be implemented as a direct result of this port. The first port of any body of code is always the most difficult since it uncovers the OS-specific calls and forces "red flags" into those portions of the code. For this reason, It has also been a huge benefit that the project chose a generic, platform independent OS extension, ACE, and its CORBA counterpart, TAO. This port of RTC will pave the way for conversions to other environments, the most interesting of which is a non-real-time simulation environment, currently being considered by the Space Interferometry Mission (SIM) and the Terrestrial Planet Finder (TPF) Projects.

Long-Term Outcomes of Laparoscopic Splenectomy Versus Open Splenectomy for Idiopathic Thrombocytopenic Purpura

PubMed Central

Qu, Yikun; Xu, Jian; Jiao, Chengbin; Cheng, Zhuoxin; Ren, Shiyan

2014-01-01

The long-term outcomes of laparoscopic splenectomy (LS) versus open splenectomy (OS) in patients with idiopathic thrombocytopenic purpura (ITP) are not known. A retrospective analysis of 73 patients who underwent splenectomy (32 LS and 41 OS) for refractory ITP between April 2003 and June 2012 was conducted. LS was associated with shorter hospital stay (P = 0.01), less blood loss and blood transfusion during surgery, quicker resumption of oral diet (P < 0.0001), and earlier drain removal (P < 0.01). Conversion to OS was required in 4 patients (12.5%). Operation time was significantly longer in LS (P < 0.0001). Deep venous thrombosis (DVT) was observed in 1 patient after LS and in 4 patients after OS (P = 0.52). One patient died from intraperitoneal bleeding after OS, another patient developed pulmonary embolism. Median follow-up of 36 months was performed in LS group (29 of 32, 91%) and of 46 months in OS group (35 of 41, 85%), 25 patients (86%) in LS group and 32 (91%) in OS group reached sustained complete response (P = 0.792). Kaplan-Meier analysis showed that there was no significant difference in the relapse-free survival rate between the groups (P = 0.777). In conclusion, the long-term outcome of laparoscopic splenectomy is not different from that of open splenectomy for patients with ITP. PMID:24833154

PAPARA(ZZ)I: An open-source software interface for annotating photographs of the deep-sea

NASA Astrophysics Data System (ADS)

Marcon, Yann; Purser, Autun

PAPARA(ZZ)I is a lightweight and intuitive image annotation program developed for the study of benthic megafauna. It offers functionalities such as free, grid and random point annotation. Annotations may be made following existing classification schemes for marine biota and substrata or with the use of user defined, customised lists of keywords, which broadens the range of potential application of the software to other types of studies (e.g. marine litter distribution assessment). If Internet access is available, PAPARA(ZZ)I can also query and use standardised taxa names directly from the World Register of Marine Species (WoRMS). Program outputs include abundances, densities and size calculations per keyword (e.g. per taxon). These results are written into text files that can be imported into spreadsheet programs for further analyses. PAPARA(ZZ)I is open-source and is available at http://papara-zz-i.github.io. Compiled versions exist for most 64-bit operating systems: Windows, Mac OS X and Linux.

Re-Os systematics of komatiites and komatiitic basalts at Dundonald Beach, Ontario, Canada: Evidence for a complex alteration history and implications of a late-Archean chondritic mantle source

NASA Astrophysics Data System (ADS)

Gangopadhyay, A.; Sproule, R. A.; Walker, R. J.; Lesher, C.

2004-12-01

Re-Os concentrations and isotopic compositions have been examined in one komatiite unit and one komatiitic basalt unit at Dundonald Beach, which is part of the spatially-extensive 2.7 Ga Kidd-Munro volcanic assemblage in the Abitibi greenstone belt, Ontario, Canada. The komatiitic rocks in this locality record at least three episodes of alteration of Re-Os elemental and isotope systematics. First, an average of 40% and as much as 75% Re was lost due to shallow degassing during eruption and/or hydrothermal leaching during or immediately after the lava emplacement. Second, the Re-Os isotope systematics of the rocks with 187Re/188Os ratios >1 were reset at ˜2.5 Ga, most likely due to a regional metamorphic event. Finally, there is evidence for relatively recent gain and loss of Re. The variations in Os concentrations in the Dundonald komatiites yield a relative bulk distribution coefficient for Os (DOs solid/liquid) of 2-4, consistent with those obtained for stratigraphically-equivalent komatiites in the nearby Alexo area and in Munro Township. This suggests that Os was moderately compatible during crystal-liquid fractionation of the magma parental to the Kidd-Munro komatiitic rocks. Furthermore, whole-rock samples and chromite separates with low 187Re/188Os ratios (<1) yield a precise chondritic average initial 187Os/188Os ratio of 0.1083 ± 0.0006 (\\gammaOs = 0.0 ± 0.6). The chondritic initial Os isotopic composition of the mantle source for the Dundonald rocks is consistent with that determined for komatiites in the Alexo area and in Munro Township. Our Os isotope results for the Dundonald komatiitic rocks, combined with those in the Alexo and Pyke Hill areas suggest that the mantle source region for the Kidd- Munro volcanic assemblage had evolved along a long-term chondritic Os isotopic trajectory until their eruption at ˜2.7 Ga. The chondritic initial Os isotopic composition of the Kidd-Munro komatiites is indistinguishable from that of the projected contemporaneous convective upper mantle. The uniform chondritic Os isotopic composition of the ˜2.7 Ga mantle source for the Kidd-Munro komatiites contrasts with the typical large-scale Os isotopic heterogeneity in the mantle sources for komatiites from the Gorgona Island, present-day ocean island basalts or arc-related lavas. This suggests a significantly more homogeneous mantle source in the Archean compared to the presentday mantle.

Mousetrap: An integrated, open-source mouse-tracking package.

PubMed

Kieslich, Pascal J; Henninger, Felix

2017-10-01

Mouse-tracking - the analysis of mouse movements in computerized experiments - is becoming increasingly popular in the cognitive sciences. Mouse movements are taken as an indicator of commitment to or conflict between choice options during the decision process. Using mouse-tracking, researchers have gained insight into the temporal development of cognitive processes across a growing number of psychological domains. In the current article, we present software that offers easy and convenient means of recording and analyzing mouse movements in computerized laboratory experiments. In particular, we introduce and demonstrate the mousetrap plugin that adds mouse-tracking to OpenSesame, a popular general-purpose graphical experiment builder. By integrating with this existing experimental software, mousetrap allows for the creation of mouse-tracking studies through a graphical interface, without requiring programming skills. Thus, researchers can benefit from the core features of a validated software package and the many extensions available for it (e.g., the integration with auxiliary hardware such as eye-tracking, or the support of interactive experiments). In addition, the recorded data can be imported directly into the statistical programming language R using the mousetrap package, which greatly facilitates analysis. Mousetrap is cross-platform, open-source and available free of charge from https://github.com/pascalkieslich/mousetrap-os .

NASA World Wind Near Real Time Data for Earth

NASA Astrophysics Data System (ADS)

Hogan, P.

2013-12-01

Innovation requires open standards for data exchange, not to mention ^access to data^ so that value-added, the information intelligence, can be continually created and advanced by the larger community. Likewise, innovation by academia and entrepreneurial enterprise alike, are greatly benefited by an open platform that provides the basic technology for access and visualization of that data. NASA World Wind Java, and now NASA World Wind iOS for the iPhone and iPad, provides that technology. Whether the interest is weather science or climate science, emergency response or supply chain, seeing spatial data in its native context of Earth accelerates understanding and improves decision-making. NASA World Wind open source technology provides the basic elements for 4D visualization, using Open Geospatial Consortium (OGC) protocols, while allowing for customized access to any data, big or small, including support for NetCDF. NASA World Wind includes access to a suite of US Government WMS servers with near real time data. The larger community can readily capitalize on this technology, building their own value-added applications, either open or proprietary. Night lights heat map Glacier National Park

Utilization of and charges for robotic versus laparoscopic versus open surgery for endometrial cancer.

PubMed

Yu, Xinhua; Lum, Deirdre; Kiet, Tuyen K; Fuh, Katherine C; Orr, James; Brooks, Rebecca A; Ueda, Stefanie M; Chen, Lee-May; Kapp, Daniel S; Chan, John K

2013-05-01

To analyze the utilization and hospital charges associated with robotic (RS) versus laparoscopic (LS) versus open surgery (OS) in endometrial cancer patients. Hospital discharge data were extracted from Florida Agency for Health Care Administration between October 2008 and December 2009. Of 2,247 patients (median age: 64 years), 29% had RS, 10% had LS, and 61% had OS. The mean length of hospital stay was 1.6, 1.8, and 3.9 days for RS, LS, and OS, respectively (P < 0.001). The median hospital charge was $51,569, $37,202, and $36,492, for RS, LS, and OS (P < 0.001), with operating room charges ($22,600, $13,684, and $11,272) accounting for the major difference. Robotic surgery utilization increased by 11% (23-34%) over time. In this statewide analysis of endometrial cancer patients, the utilization of robotic surgery increased and is associated with higher hospital charges compared to laparoscopic and open procedures. Copyright © 2012 Wiley Periodicals, Inc.

Defining Success in Open Science

PubMed Central

Ali-Khan, Sarah E.; Jean, Antoine; MacDonald, Emily; Gold, E. Richard

2018-01-01

Mounting evidence indicates that worldwide, innovation systems are increasing unsustainable. Equally, concerns about inequities in the science and innovation process, and in access to its benefits, continue. Against a backdrop of growing health, economic and scientific challenges global stakeholders are urgently seeking to spur innovation and maximize the just distribution of benefits for all. Open Science collaboration (OS) – comprising a variety of approaches to increase open, public, and rapid mobilization of scientific knowledge – is seen to be one of the most promising ways forward. Yet, many decision-makers hesitate to construct policy to support the adoption and implementation of OS without access to substantive, clear and reliable evidence. In October 2017, international thought-leaders gathered at an Open Science Leadership Forum in the Washington DC offices of the Bill and Melinda Gates Foundation to share their views on what successful Open Science looks like. Delegates from developed and developing nations, national governments, science agencies and funding bodies, philanthropy, researchers, patient organizations and the biotechnology, pharma and artificial intelligence (AI) industries discussed the outcomes that would rally them to invest in OS, as well as wider issues of policy and implementation. This first of two reports, summarizes delegates' views on what they believe OS will deliver in terms of research, innovation and social impact in the life sciences. Through open and collaborative process over the next months, we will translate these success outcomes into a toolkit of quantitative and qualitative indicators to assess when, where and how open science collaborations best advance research, innovation and social benefit. Ultimately, this work aims to develop and openly share tools to allow stakeholders to evaluate and re-invent their innovation ecosystems, to maximize value for the global public and patients, and address long-standing questions about the mechanics of innovation. PMID:29553146

Defining Success in Open Science.

PubMed

Ali-Khan, Sarah E; Jean, Antoine; MacDonald, Emily; Gold, E Richard

2018-01-01

Mounting evidence indicates that worldwide, innovation systems are increasing unsustainable. Equally, concerns about inequities in the science and innovation process, and in access to its benefits, continue. Against a backdrop of growing health, economic and scientific challenges global stakeholders are urgently seeking to spur innovation and maximize the just distribution of benefits for all. Open Science collaboration (OS) - comprising a variety of approaches to increase open, public, and rapid mobilization of scientific knowledge - is seen to be one of the most promising ways forward. Yet, many decision-makers hesitate to construct policy to support the adoption and implementation of OS without access to substantive, clear and reliable evidence. In October 2017, international thought-leaders gathered at an Open Science Leadership Forum in the Washington DC offices of the Bill and Melinda Gates Foundation to share their views on what successful Open Science looks like. Delegates from developed and developing nations, national governments, science agencies and funding bodies, philanthropy, researchers, patient organizations and the biotechnology, pharma and artificial intelligence (AI) industries discussed the outcomes that would rally them to invest in OS, as well as wider issues of policy and implementation. This first of two reports, summarizes delegates' views on what they believe OS will deliver in terms of research, innovation and social impact in the life sciences. Through open and collaborative process over the next months, we will translate these success outcomes into a toolkit of quantitative and qualitative indicators to assess when, where and how open science collaborations best advance research, innovation and social benefit. Ultimately, this work aims to develop and openly share tools to allow stakeholders to evaluate and re-invent their innovation ecosystems, to maximize value for the global public and patients, and address long-standing questions about the mechanics of innovation.

Differences in open versus laparoscopic gastric bypass mortality risk using the Obesity Surgery Mortality Risk Score (OS-MRS).

PubMed

Brolin, Robert E; Cody, Ronald P; Marcella, Stephen W

2015-01-01

The Obesity Surgery Mortality Risk Score (OS-MRS) was developed to ascertain preoperative mortality risk of patients having bariatric surgery. To date there has not been a comparison between open and laparoscopic operations using the OS-MRS. To determine whether there are differences in mortality risk between open and laparoscopic Roux-en-Y Gastric Bypass (RYGB) using the OS-MRS. Three university-affiliated hospitals. The 90-day mortality of 2467 consecutive patients who had primary open (1574) or laparoscopic (893) RYGB performed by one surgeon was determined. Univariate and multivariate analysis using 5 OS-MRS risk factors including body mass index (BMI) gender, age>45, presence of hypertension and preoperative deep vein thrombosis (DVT) risk was performed in each group. Each patient was placed in 1 of 3 OS-MRS risk classes based on the number of risks: A (0-1), B (2-3), and C (4-5). Preoperative BMI and DVT risk factors were significantly greater in the open group (OG). Preoperative age was significantly greater in the laparoscopic group (LG). There were significantly more class B and C patients in LG. Ninety-day mortality rates for OG and LG patients were 1.0% and .9%, respectively. Pulmonary embolism was the most common cause of death. All deaths in LG occurred during first 4 years of that experience. Mortality rate by class was A = .1%; B = 1.5%; C = 2.3%. The difference in mortality between class B and C patients was not significant. Univariate analysis in the OG indicated that BMI, age, gender, and DVT risk were significant predictors of mortality. In the LG only BMI and DVT were significant predictors of death. Presence of hypertension was not a significant predictor in either group. Multivariate analysis excluding hypertension found that age was predictive of mortality in the OG while BMI (P = .057) and gender (P = .065) approached statistical significance. Conversely, only BMI was predictive of mortality in the LG with age approaching significance (P = .058). In multivariate analysis DVT risk was not predictive of mortality in either group. There are significant differences in the predictive value of the OS-MRS between open and laparoscopic RYGB. Although laparoscopic patients were significantly older versus the open patients, age was not predictive of mortality after laparoscopic RYGB. BMI trended toward increased mortality risk in both groups. Changes in technique and protocol likely contributed toward no mortality during the last 6 years of our laparoscopic experience. Copyright © 2015 American Society for Bariatric Surgery. Published by Elsevier Inc. All rights reserved.

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.

Terra Harvest Open Source Environment (THOSE): a universal unattended ground sensor controller

NASA Astrophysics Data System (ADS)

Gold, Joshua; Klawon, Kevin; Humeniuk, David; Landoll, Darren

2011-06-01

Under the Terra Harvest Program, the Defense Intelligence Agency (DIA) has the objective of developing a universal Controller for the Unattended Ground Sensor (UGS) community. The mission is to define, implement, and thoroughly document an open architecture that universally supports UGS missions, integrating disparate systems, peripherals, etc. The Controller's inherent interoperability with numerous systems enables the integration of both legacy and future Unattended Ground Sensor System (UGSS) components, while the design's open architecture supports rapid third-party development to ensure operational readiness. The successful accomplishment of these objectives by the program's Phase 3b contractors is demonstrated via integration of the companies' respective plug-'n-play contributions that include various peripherals, such as sensors, cameras, etc., and their associated software drivers. In order to independently validate the Terra Harvest architecture, L-3 Nova Engineering, along with its partner, the University of Dayton Research Institute (UDRI), is developing the Terra Harvest Open Source Environment (THOSE), a Java based system running on an embedded Linux Operating System (OS). The Use Cases on which the software is developed support the full range of UGS operational scenarios such as remote sensor triggering, image capture, and data exfiltration. The Team is additionally developing an ARM microprocessor evaluation platform that is both energyefficient and operationally flexible. The paper describes the overall THOSE architecture, as well as the implementation strategy for some of the key software components. Preliminary integration/test results and the Team's approach for transitioning the THOSE design and source code to the Government are also presented.

OsiriX: an open-source software for navigating in multidimensional DICOM images.

PubMed

Rosset, Antoine; Spadola, Luca; Ratib, Osman

2004-09-01

A multidimensional image navigation and display software was designed for display and interpretation of large sets of multidimensional and multimodality images such as combined PET-CT studies. The software is developed in Objective-C on a Macintosh platform under the MacOS X operating system using the GNUstep development environment. It also benefits from the extremely fast and optimized 3D graphic capabilities of the OpenGL graphic standard widely used for computer games optimized for taking advantage of any hardware graphic accelerator boards available. In the design of the software special attention was given to adapt the user interface to the specific and complex tasks of navigating through large sets of image data. An interactive jog-wheel device widely used in the video and movie industry was implemented to allow users to navigate in the different dimensions of an image set much faster than with a traditional mouse or on-screen cursors and sliders. The program can easily be adapted for very specific tasks that require a limited number of functions, by adding and removing tools from the program's toolbar and avoiding an overwhelming number of unnecessary tools and functions. The processing and image rendering tools of the software are based on the open-source libraries ITK and VTK. This ensures that all new developments in image processing that could emerge from other academic institutions using these libraries can be directly ported to the OsiriX program. OsiriX is provided free of charge under the GNU open-source licensing agreement at http://homepage.mac.com/rossetantoine/osirix.

Himalayan uplift and osmium isotopes in oceans and rivers

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

Sharma, M.; Wasserburg, G.J.; Hofmann, A.W.

1999-12-01

Previous studies have shown that {sup 187}Os/{sup 188}Os in seawater has become increasingly radiogenic over the last 409 Ma in a manner analogous to strontium. This rapid rise in the marine {sup 187}Os/{sup 188}Os over the last 17 Ma has been attributed to an increase in the bulk silicate weathering rates resulting from the rise of the Himalayas and/or selective weathering and erosion of highly radiogenic organic rich ancient sediments. The key test of this hypothesis is the {sup 187}Os/{sup 188}Os and the total osmium concentration of the Himalayan rivers. The authors report the concentration and isotopic composition of osmiummore » in the Ganges, the Brahmaputra, and the Indus rivers. The {sup 187}Os/{sup 188}Os of the Ganges close to its source (at Kaudiyal) is 2.65 and [Os] = 45 fM/kg. A second sample of the lower reaches of the Ganges at Patna gives {sup 187}Os/{sup 188}Os = 1.59 and [Os] = 171 fM/kg. The {sup 187}Os/{sup 188}Os of the Brahmaputra at Guwahati is 1.07 and [Os] = 52 fM/kg. A sample of the Indus (Besham) has a {sup 187}Os/{sup 188}Os of 1.2 and [Os] = 59 fM/kg. The authors infer that the Himalayas do not provide either a high flow of osmium of a highly radiogenic osmium component to the oceans. The overall trend for osmium and strontium could be explained by a regularly increasing input of global continental weathering sources but the Himalayas themselves appear not to be the dominant source.« less

[Identification of Dens Draconis and Os Draconis by XRD method].

PubMed

Chen, Guang-Yun; Wu, Qi-Nan; Shen, Bei; Chen, Rong

2012-04-01

To establish an XRD method for evaluating the quality of Os Draconis and Dens Draconis and applying in judgement of the counterfeit. Dens Draconis, Os Draconis and the counterfeit of Os Draconis were analyzed by XRD. Their diffraction patterns were clustered analysis and evaluated their similarity degree. Established the analytical method of Dens Draconis and Os Draconis basing the features fingerprint information of the 10 common peaks by XRD pattern. Obtained the XRD pattern of the counterfeit of Os Draconis. The similarity degree of separate sources of Dens Draconis was high,while the similarity degree of separate sources of Os Draconis was significant different from each other. This method can be used for identification and evaluation of Os Draconis and Dens Draconis. It also can be used for identification the counterfeit of Os Draconis effectively.

OpenCOR: a modular and interoperable approach to computational biology

PubMed Central

Garny, Alan; Hunter, Peter J.

2015-01-01

Computational biologists have been developing standards and formats for nearly two decades, with the aim of easing the description and exchange of experimental data, mathematical models, simulation experiments, etc. One of those efforts is CellML (cellml.org), an XML-based markup language for the encoding of mathematical models. Early CellML-based environments include COR and OpenCell. However, both of those tools have limitations and were eventually replaced with OpenCOR (opencor.ws). OpenCOR is an open source modeling environment that is supported on Windows, Linux and OS X. It relies on a modular approach, which means that all of its features come in the form of plugins. Those plugins can be used to organize, edit, simulate and analyze models encoded in the CellML format. We start with an introduction to CellML and two of its early adopters, which limitations eventually led to the development of OpenCOR. We then go onto describing the general philosophy behind OpenCOR, as well as describing its openness and its development process. Next, we illustrate various aspects of OpenCOR, such as its user interface and some of the plugins that come bundled with it (e.g., its editing and simulation plugins). Finally, we discuss some of the advantages and limitations of OpenCOR before drawing some concluding remarks. PMID:25705192

Naval Open Architecture Machinery Control Systems for Next Generation Integrated Power Systems

DTIC Science & Technology

2012-05-01

PORTABLE) OS / RTOS ADAPTATION MIDDLEWARE (FOR OS PORTABILITY) MACHINERY CONTROLLER FRAMEWORK MACHINERY CONTROL SYSTEM SERVICES POWER CONTROL SYSTEM...SERVICES SHIP SYSTEM SERVICES TTY 0 TTY N … OPERATING SYSTEM ( OS / RTOS ) COMPUTER HARDWARE UDP IP TCP RAW DEV 0 DEV N … POWER MANAGEMENT CONTROLLER...operating systems (DOS, Windows, Linux, OS /2, QNX, SCO Unix ...) COMPUTERS: ISA compatible motherboards, workstations and portables (Compaq, Dell

Laparoscopic versus conventional open surgery for immune function in patients with colorectal cancer.

PubMed

Liu, Chuanyuan; Liu, Jungang; Zhang, Sen

2011-11-01

To systematically evaluate the immune function in patients with colorectal cancer after laparoscopic surgery (LS) and conventional open surgery (OS). PUBMED, EMBASE, and the Cochrane library were searched and randomized controlled trials (RCTs) comparing the immunological difference between LS and OS were included. Two authors extracted data and assessed trial quality. Eleven studies including 695 patients were analysed. Immune-competent cells demonstrated no significant differences between LS and OS in six trials. Eight trials assessed various perioperative plasma cytokine concentrations with no significant differences in interleukin-6 (IL-6) and C-reactive protein (CRP) levels between LS and OS. However, meta-analysis showed higher T suppressor lymphocytes (CD8+) counts on postoperative days (POD) 1-3 and lower plasma levels of CRP on POD 0-1 in LS group compared with OS group. Although LS groups displayed higher T suppressor lymphocyte (CD8+) counts on postoperative days (POD) 1-3 and lower plasma levels of CRP on POD 0-1, there is no sufficient evidence to support superior preservation of global immune function with LS compared to OS.

Everolimus for the Treatment of Advanced Pancreatic Neuroendocrine Tumors: Overall Survival and Circulating Biomarkers From the Randomized, Phase III RADIANT-3 Study.

PubMed

Yao, James C; Pavel, Marianne; Lombard-Bohas, Catherine; Van Cutsem, Eric; Voi, Maurizio; Brandt, Ulrike; He, Wei; Chen, David; Capdevila, Jaume; de Vries, Elisabeth G E; Tomassetti, Paola; Hobday, Timothy; Pommier, Rodney; Öberg, Kjell

2016-11-10

Purpose Everolimus improved median progression-free survival by 6.4 months in patients with advanced pancreatic neuroendocrine tumors (NET) compared with placebo in the RADIANT-3 study. Here, we present the final overall survival (OS) data and data on the impact of biomarkers on OS from the RADIANT-3 study. Methods Patients with advanced, progressive, low- or intermediate-grade pancreatic NET were randomly assigned to everolimus 10 mg/day (n = 207) or placebo (n = 203). Crossover from placebo to open-label everolimus was allowed on disease progression. Ongoing patients were unblinded after final progression-free survival analysis and could transition to open-label everolimus at the investigator's discretion (extension phase). OS analysis was performed using a stratified log-rank test in the intent-to-treat population. The baseline levels of chromogranin A, neuron-specific enolase, and multiple soluble angiogenic biomarkers were determined and their impact on OS was explored. Results Of 410 patients who were enrolled between July 2007 and March 2014, 225 received open-label everolimus, including 172 patients (85%) randomly assigned initially to the placebo arm. Median OS was 44.0 months (95% CI, 35.6 to 51.8 months) for those randomly assigned to everolimus and 37.7 months (95% CI, 29.1 to 45.8 months) for those randomly assigned to placebo (hazard ratio, 0.94; 95% CI, 0.73 to 1.20; P = .30). Elevated baseline chromogranin A, neuron-specific enolase, placental growth factor, and soluble vascular endothelial growth factor receptor 1 levels were poor prognostic factors for OS. The most common adverse events included stomatitis, rash, and diarrhea. Conclusion Everolimus was associated with a median OS of 44 months in patients with advanced, progressive pancreatic NET, the longest OS reported in a phase III study for this population. Everolimus was associated with a survival benefit of 6.3 months, although this finding was not statistically significant. Crossover of patients likely confounded the OS results.

Apollo: a community resource for genome annotation editing

PubMed Central

Ed, Lee; Nomi, Harris; Mark, Gibson; Raymond, Chetty; Suzanna, Lewis

2009-01-01

Summary: Apollo is a genome annotation-editing tool with an easy to use graphical interface. It is a component of the GMOD project, with ongoing development driven by the community. Recent additions to the software include support for the generic feature format version 3 (GFF3), continuous transcriptome data, a full Chado database interface, integration with remote services for on-the-fly BLAST and Primer BLAST analyses, graphical interfaces for configuring user preferences and full undo of all edit operations. Apollo's user community continues to grow, including its use as an educational tool for college and high-school students. Availability: Apollo is a Java application distributed under a free and open source license. Installers for Windows, Linux, Unix, Solaris and Mac OS X are available at http://apollo.berkeleybop.org, and the source code is available from the SourceForge CVS repository at http://gmod.cvs.sourceforge.net/gmod/apollo. Contact: elee@berkeleybop.org PMID:19439563

Apollo: a community resource for genome annotation editing.

PubMed

Lee, Ed; Harris, Nomi; Gibson, Mark; Chetty, Raymond; Lewis, Suzanna

2009-07-15

Apollo is a genome annotation-editing tool with an easy to use graphical interface. It is a component of the GMOD project, with ongoing development driven by the community. Recent additions to the software include support for the generic feature format version 3 (GFF3), continuous transcriptome data, a full Chado database interface, integration with remote services for on-the-fly BLAST and Primer BLAST analyses, graphical interfaces for configuring user preferences and full undo of all edit operations. Apollo's user community continues to grow, including its use as an educational tool for college and high-school students. Apollo is a Java application distributed under a free and open source license. Installers for Windows, Linux, Unix, Solaris and Mac OS X are available at http://apollo.berkeleybop.org, and the source code is available from the SourceForge CVS repository at http://gmod.cvs.sourceforge.net/gmod/apollo.

Osmium isotope variations in the oceans recorded by Fe-Mn crusts

USGS Publications Warehouse

Burton, K.W.; Bourdon, B.; Birck, J.-L.; Allegre, C.J.; Hein, J.R.

1999-01-01

This study presents osmium (Os) isotope data for recent growth surfaces of hydrogenetic ferromanganese (Fe-Mn) crusts from the Pacific, Atlantic and Indian Oceans. In general, these data indicate a relatively uniform Os isotopic composition for modern seawater, but suggest that North Atlantic seawater is slightly more radiogenic than that of the Pacific and Indian Oceans. The systematic difference in the Os isotopic composition between the major oceans probably reflects a greater input of old continental material with a high Re/Os ratio in the North Atlantic Ocean, consistent with the distribution of Nd and Pb isotopes. This spatial variation in the Os isotope composition in seawater is consistent with a residence time for Os of between 2 and 60 kyr. Indian Ocean samples show no evidence of a local source of radiogenic Os, which suggests that the present-day riverine input from the Himalaya-Tibet region is not a major source for Os. Recently formed Fe-Mn crusts from the TAG hydrothermal field in the North Atlantic yield an Os isotopic composition close to that of modern seawater, which indicates that, in this area, the input of unradiogenic Os from the hydrothermal alteration of oceanic crust is small. However, some samples from the deep Pacific (???4 km) possess a remarkably unradiogenic Os isotope composition (187Os/186Os ratios as low as 4.3). The compositional control of Os incorporation into the crusts and mixing relationships suggest that this unradiogenic composition is most likely due to the direct incorporation of micrometeoritic or abyssal peridotite particles, rather than indicating the presence of an unradiogenic deep-water mass. Moreover, this unradiogenic signal appears to be temporary, and local, and has had little apparent effect on the overall evolution of seawater. These results confirm that input of continental material through erosion is the dominant source of Os in seawater, but it is not clear whether global Os variations are due to the input of mantle or meteoritic material, or simply indicate that the continental source itself is not uniform.

Re-Os isotope and platinum group elements of a FOcal ZOne mantle source, Louisville Seamounts Chain, Pacific ocean

NASA Astrophysics Data System (ADS)

Tejada, Maria Luisa G.; Hanyu, Takeshi; Ishikawa, Akira; Senda, Ryoko; Suzuki, Katsuhiko; Fitton, Godfrey; Williams, Rebecca

2015-02-01

The Louisville Seamount Chain (LSC) is, besides the Hawaiian-Emperor Chain, one of the longest-lived hotspot traces. We report here the first Re-Os isotope and platinum group element (PGE) data for Canopus, Rigil, and Burton Guyots along the chain, which were drilled during IODP Expedition 330. The LSC basalts possess (187Os/188Os)i = 0.1245-0.1314 that are remarkably homogeneous and do not vary with age. A Re-Os isochron age of 64.9 ± 3.2 Ma was obtained for Burton seamount (the youngest of the three seamounts drilled), consistent with 40Ar-39Ar data. Isochron-derived initial 187Os/188Os ratio of 0.1272 ± 0.0008, together with data for olivines (0.1271-0.1275), are within the estimated primitive mantle values. This (187Os/188Os)i range is similar to those of Rarotonga (0.124-0.139) and Samoan shield (0.1276-0.1313) basalts and lower than those of Cook-Austral (0.136-0.155) and Hawaiian shield (0.1283-0.1578) basalts, suggesting little or no recycled component in the LSC mantle source. The PGE data of LSC basalts are distinct from those of oceanic lower crust. Variation in PGE patterns can be largely explained by different low degrees of melting under sulfide-saturated conditions of the same relatively fertile mantle source, consistent with their primitive mantle-like Os and primordial Ne isotope signatures. The PGE patterns and the low 187Os/188Os composition of LSC basalts contrast with those of Ontong Java Plateau (OJP) tholeiites. We conclude that the Re-Os isotope and PGE composition of LSC basalts reflect a relatively pure deep-sourced common mantle sampled by some ocean island basalts but is not discernible in the composition of OJP tholeiites.

GenomeDiagram: a python package for the visualization of large-scale genomic data.

PubMed

Pritchard, Leighton; White, Jennifer A; Birch, Paul R J; Toth, Ian K

2006-03-01

We present GenomeDiagram, a flexible, open-source Python module for the visualization of large-scale genomic, comparative genomic and other data with reference to a single chromosome or other biological sequence. GenomeDiagram may be used to generate publication-quality vector graphics, rastered images and in-line streamed graphics for webpages. The package integrates with datatypes from the BioPython project, and is available for Windows, Linux and Mac OS X systems. GenomeDiagram is freely available as source code (under GNU Public License) at http://bioinf.scri.ac.uk/lp/programs.html, and requires Python 2.3 or higher, and recent versions of the ReportLab and BioPython packages. A user manual, example code and images are available at http://bioinf.scri.ac.uk/lp/programs.html.

Os isotope systematics of La Palma, Canary Islands: Evidence for recycled crust in the mantle source of HIMU ocean islands

NASA Astrophysics Data System (ADS)

Marcantonio, Franco; Zindler, Alan; Elliott, Tim; Staudigel, Hubert

1995-07-01

Sub-aerial lavas from the single ocean island of La Palma, Canary Islands show as large a variation in 187Os/186Os isotope ratios (1.13-1.59) as found across all of French Polynesia [1]. The La Palma lavas, however, display a restricted range of chemical composition and have all been erupted within the last 3.5 Ma. The highest Os isotopic compositions are observed in lavas with low Os concentrations. An uplifted sequence of lavas, that represent the early phase of submarine growth of the island, show extremely heterogeneous 187Os/186Os isotope ratios, from 1.21 to 3.53, with the most radiogenic values found in pillow rinds. Assimilation of these pillow rinds by ascending magma can readily account for highly radiogenic ratios ( 187Os/186Os > 1.3 ) found in lavas with Os concentrations below 30 ppt. Samples with Os concentrations too high to be significantly affected by assimilation still display a range in Os isotope ratios from 1.13 to 1.25. We argue that these radiogenic values reflect a HIMU mantle source that contains ancient recycled oceanic crust. Characteristic incompatible trace element ratios suggest further similarities between the mantle beneath La Palma and other HIMU islands. When potentially contaminated low-Os OIBs are screened from literature data, HIMU islands are found to display the highest Os isotope ratios (up to 1.25). PbOs systematics for uncontaminated OIBs do not define a simple two-component mixing relationship between ambient mantle and recycled oceanic crust of a single composition. We suggest that this is due to variable alteration and subduction-induced perturbation of the U/Pb ratio in the recycled material that forms a component of the HIMU source.

Nucleophilic ring opening of bridging thietanes in open triosmium cluster complexes

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

Adams, R.D.; Belinski, J.A.

1992-07-01

The complexes Os{sub 3}(CO){sub 9}({mu}{sub 3}-S)[{mu}-SCH{sub 2}CMe{sub 2}CMe{sub 2}CH{sub 2}] (1) and Os{sub 3}(CO){sub 9}({mu}{sub 3}-S)[{mu}-SCH{sub 2}CH{sub 2}CH{sub 2}] (2) were obtained from the reactions of Os{sub 3}(CO){sub 10}({mu}{sub 3}-S) with 3,3-dimethylthietane (DMT) and thietane, respectively, at -42 {degree}C in the presence of Me{sub 3}NO. Compound 1 was characterized by a single-crystal X-ray diffraction analysis and was found to contain a DMT group bridging two of the nonbonded metal atoms in the open cluster of three metal atoms by using both lone pairs of electrons on the sulfur atom. Compound 1 reacted with bis(triphenylphosphine)nitrogen(1+) chloride ([PPN]Cl) at 25 {degrees}C tomore » yield the salt [PPN][Os{sub 3}-(CO){sub 9}({mu}-SCH{sub 2}CMe{sub 2}CH{sub 2}Cl)({mu}{sub 3}-S)] (3; 76%), in which the chloride ion was added to one of the methylene groups of the DMT ring in a process that caused the ring to open by cleavage of one of the carbon-sulfur bonds. A 4-chloro-3,3-dimethylpropanethiolate ligand bridges the open edge of the anionic triosmium cluster. Compound 3 was converted to the neutral complex Os{sub 3}(CO){sub 9}[{mu}-SCH{sub 2}CMe{sub 2}CMe{sub 2}CH{sub 2}Cl]({mu}{sub 3}-S)({mu}-H) (4) by reaction with HCl at 25 {degrees}C. Compound 4 is structurally similar to 3, except that is contains a hydride ligand bridging one of the two metal-metal bonds. Compounds 1 and 2 react with HCl in CH{sub 2}Cl{sub 2} solvent to yield the neutral compounds 4 and Os{sub 3}(CO){sub 9}[{mu}-SCH{sub 2}CH{sub 2}CH{sub 2}Cl]({mu}{sub 3}-S)({mu}-H) (5) in 89% and 90% yields, respectively, in one step. 11 refs., 3 figs., 10 tabs.« less

Evaluating Re-Os systematics in organic-rich sedimentary rocks in response to petroleum generation using hydrous pyrolysis experiments

USGS Publications Warehouse

Rooney, A.D.; Selby, D.; Lewan, M.D.; Lillis, P.G.; Houzay, J.-P.

2012-01-01

Successful application of the 187Re–187Os geochronometer has enabled the determination of accurate and precise depositional ages for organic-rich sedimentary rocks (ORS) as well as establishing timing constraints of petroleum generation. However, we do not fully understand the systematics and transfer behaviour of Re and Os between ORS and petroleum products (e.g., bitumen and oil). To more fully understand the behaviour of Re–Os systematics in both source rocks and petroleum products we apply hydrous pyrolysis to two immature hydrocarbon source rocks: the Permian Phosphoria Formation (TOC = 17.4%; Type II-S kerogen) and the Jurassic Staffin Formation (TOC = 2.5%; Type III kerogen). The laboratory-based hydrous pyrolysis experiments were carried out for 72 h at 250, 300, 325 and 350 °C. These experiments provided us with whole rock, extracted rock and bitumen and in some cases expelled oil and asphaltene for evaluation of Re–Os isotopic and elemental abundance. The data from these experiments demonstrate that the majority (>95%) of Re and Os are housed within extracted rock and that thermal maturation does not result in significant transfer of Re or Os from the extracted rock into organic phases. Based on existing thermodynamic data our findings suggest that organic chelating sites have a greater affinity for the quadravalent states of Re and Os than sulphides. Across the temperature range of the hydrous pyrolysis experiments both whole rock and extracted rock 187Re/188Os ratios show small variations (3.3% and 4.7%, for Staffin, respectively and 6.3% and 4.9% for Phosphoria, respectively). Similarly, the 187Os/188Os ratios show only minor variations for the Staffin and Phosphoria whole rock and extracted rock samples (0.6% and 1.4% and 1.3% and 2.2%). These isotopic data strongly suggest that crude oil generation through hydrous pyrolysis experiments does not disturb the Re–Os systematics in ORS as supported by various studies on natural systems. The elemental abundance data reveal limited transfer of Re and Os into the bitumen from a Type III kerogen in comparison to Type II-S kerogen (0.02% vs. 3.7%), suggesting that these metals are very tightly bound in Type III kerogen structure. The 187Os/188Os data from the pyrolysis generated Phosphoria bitumens display minor variation (4%) across the experimental temperatures, with values similar to that of the source rock. This indicates that the isotopic composition of the bitumen reflects the isotopic composition of the source rock at the time of petroleum generation. These data further support the premise that the Os isotopic composition of oils and bitumens can be used to fingerprint petroleum deposits to specific source rocks. Oil generated through the hydrous pyrolysis experiments does not contain appreciable quantities of Re or Os (~120 and ~3 ppt, respectively), in contrast to natural oils (2–50 ppb and 34–288 ppt for Re and Os, respectively), which may suggest that kinetic parameters are fundamental to the transfer of Re and Os from source rocks to oils. From this we hypothesise that, at the temperatures employed in hydrous pyrolysis, Re and Os are assimilated into the extracted rock as a result of cross-linking reactions.

Evaluating Re-Os systematics in organic-rich sedimentary rocks in response to petroleum generation using hydrous pyrolysis experiments

NASA Astrophysics Data System (ADS)

Rooney, Alan D.; Selby, David; Lewan, Michael D.; Lillis, Paul G.; Houzay, Jean-Pierre

2012-01-01

Successful application of the 187Re-187Os geochronometer has enabled the determination of accurate and precise depositional ages for organic-rich sedimentary rocks (ORS) as well as establishing timing constraints of petroleum generation. However, we do not fully understand the systematics and transfer behaviour of Re and Os between ORS and petroleum products (e.g., bitumen and oil). To more fully understand the behaviour of Re-Os systematics in both source rocks and petroleum products we apply hydrous pyrolysis to two immature hydrocarbon source rocks: the Permian Phosphoria Formation (TOC = 17.4%; Type II-S kerogen) and the Jurassic Staffin Formation (TOC = 2.5%; Type III kerogen). The laboratory-based hydrous pyrolysis experiments were carried out for 72 h at 250, 300, 325 and 350 °C. These experiments provided us with whole rock, extracted rock and bitumen and in some cases expelled oil and asphaltene for evaluation of Re-Os isotopic and elemental abundance. The data from these experiments demonstrate that the majority (>95%) of Re and Os are housed within extracted rock and that thermal maturation does not result in significant transfer of Re or Os from the extracted rock into organic phases. Based on existing thermodynamic data our findings suggest that organic chelating sites have a greater affinity for the quadravalent states of Re and Os than sulphides. Across the temperature range of the hydrous pyrolysis experiments both whole rock and extracted rock 187Re/188Os ratios show small variations (3.3% and 4.7%, for Staffin, respectively and 6.3% and 4.9% for Phosphoria, respectively). Similarly, the 187Os/188Os ratios show only minor variations for the Staffin and Phosphoria whole rock and extracted rock samples (0.6% and 1.4% and 1.3% and 2.2%). These isotopic data strongly suggest that crude oil generation through hydrous pyrolysis experiments does not disturb the Re-Os systematics in ORS as supported by various studies on natural systems. The elemental abundance data reveal limited transfer of Re and Os into the bitumen from a Type III kerogen in comparison to Type II-S kerogen (0.02% vs. 3.7%), suggesting that these metals are very tightly bound in Type III kerogen structure. The 187Os/188Os data from the pyrolysis generated Phosphoria bitumens display minor variation (4%) across the experimental temperatures, with values similar to that of the source rock. This indicates that the isotopic composition of the bitumen reflects the isotopic composition of the source rock at the time of petroleum generation. These data further support the premise that the Os isotopic composition of oils and bitumens can be used to fingerprint petroleum deposits to specific source rocks. Oil generated through the hydrous pyrolysis experiments does not contain appreciable quantities of Re or Os (∼120 and ∼3 ppt, respectively), in contrast to natural oils (2-50 ppb and 34-288 ppt for Re and Os, respectively), which may suggest that kinetic parameters are fundamental to the transfer of Re and Os from source rocks to oils. From this we hypothesise that, at the temperatures employed in hydrous pyrolysis, Re and Os are assimilated into the extracted rock as a result of cross-linking reactions.

Osmium isotopic tracing of atmospheric emissions from an aluminum smelter

NASA Astrophysics Data System (ADS)

Gogot, Julien; Poirier, André; Boullemant, Amiel

2015-09-01

We present for the first time the use of osmium isotopic composition as a tracer of atmospheric emissions from an aluminum smelter, where alumina (extracted from bauxite) is reduced through electrolysis into metallic aluminum using carbonaceous anodes. These anodes are consumed in the process; they are made of petroleum coke and pitch and have high Re/Os elementary ratio. Due to the relatively large geological age of their source material, their osmium shows a high content of radiogenic 187Os produced from in situ187Re radioactive decay. The radiogenic isotopic composition (187Os/188Os ∼ 2.5) of atmospheric particulate emissions from this smelter is different from that of other typical anthropogenic osmium sources (that come from ultramafic geological contexts with unradiogenic Os isotopes, e.g., 187Os/188Os < 0.2) and also different from average eroding continental crust 187Os/188Os ratios (ca. 1.2). This study demonstrates the capacity of osmium measurements to monitor particulate matter emissions from the Al-producing industry.

Re-Os isotopic systematics of primitive lavas from the Lassen region of the Cascade arc, California

USGS Publications Warehouse

Borg, L.E.; Brandon, A.D.; Clynne, M.A.; Walker, R.J.

2000-01-01

Rhenium-osmium isotopic systematics of primitive calc-alkaline lavas from the Lassen region appear to be controlled by mantle wedge processes. Lavas with a large proportion of slab component have relatively low Re and Os abundances, and have radiogenic Os and mid ocean ridge basalt-like Sr and Pb isotopic compositions. Lavas with a small proportion of slab component have higher Re and Os elemental abundances and display mantle-like Os, Sr, Nd, and Pb isotopic compositions. Assimilation with fractional crystallization can only generate the Re-Os systematics of the Lassen lavas from a common parent if the distribution coefficient for Re in sulfide is ~40-1100 times higher than most published estimates and if most incompatible element abundances decrease during differentiation. High Re/Os ratios in mid ocean ridge basalts makes subducted oceanic crust a potential source of radiogenic Os in volcanic arcs. The slab beneath the southernmost Cascades is estimated to have 187Os/188Os ratios as high as 1.4. Mixing between a slab component and mantle wedge peridotite can generate the Os isotopic systematics of the Lassen lavas provided the slab component has a Sr/Os ratio of ~7.5X105 and Os abundances that are 100-600 times higher than mid ocean ridge basalts. For this model to be correct, Os must be readily mobilized and concentrated in the slab component, perhaps as a result of high water and HCl fugacities in this subduction environment. Another possible mechanism to account for the correlation between the magnitude of the subduction geochemical signature and Os isotopic composition involves increasing the stability of an Os-bearing phase in mantle wedge peridotites as a result of fluxing with the slab component. Melting of such a source could yield low Os magmas that are more susceptible to crustal contamination, and hence have more radiogenic Os isotopic compositions, than magmas derived from sources with a smaller contribution from the slab. Thus, the addition of the slab component to the mantle wedge appears to result in either the direct or indirect addition of radiogenic Os to arc magmas. (C) 2000 Elsevier Science B.V. All rights reserved.

187Os-enriched domain in an Archean mantle plume: evidence from 2.8 Ga komatiites of the Kostomuksha greenstone belt, NW Baltic Shield

NASA Astrophysics Data System (ADS)

Puchtel, Igor S.; Brügmann, Gerhard E.; Hofmann, Albrecht W.

2001-04-01

The Re-Os data on Archean komatiites from the Kostomuksha greenstone belt in the Baltic Shield are presented. This greenstone belt has been previously interpreted to represent a former oceanic plateau formed by the emplacement of an ancient plume head [Puchtel et al., Earth Planet. Sci. Lett. 155 (1998) 57-74]. Samples of flowtop breccia, spinifex-textured and cumulate komatiites and a chromite separate, all collected from the core of a 300 m deep diamond drill hole, yielded a Re-Os isochron with an age of 2795±40 Ma and an initial 187Os/188Os of 0.1117±0.0011 (γ187Os=+3.6±1.0). The high positive γ187Os(T) implies that the komatiites were derived from a mantle source with a time-integrated suprachondritic Re/Os ratio. Recycling of oceanic lithosphere to produce the enriched 187Os isotope signature is considered unlikely, as 15-25% crustal component is required to be incorporated into the plume source as early as 3.5-4.3 Ga. Such a substantial proportion of mafic material in the source would likely destroy the major and trace element characteristics of the komatiites. Our tentative interpretation is that the 187Os-enrichment in the Kostomuksha plume represents an outer core signature. If confirmed by the ongoing Pt-Os isotope studies, the results would provide evidence for the existence of whole-mantle convection in the late Archean, and might place constraints on the timing of core differentiation in the early Earth.

Using Stellarium to cyber-observe the Great American Eclipse

NASA Astrophysics Data System (ADS)

Prim, Ellie R.; Sitar, David J.

2017-09-01

The Great American Eclipse is over. Somewhat sad, is it not? Individuals who were unable to experience the event on August 21, 2017, can now cyber-observe the eclipse with Stellarium (http://www.stellarium.org). In the authors' opinion, it is fun and has many great applications in the classroom. In addition it is open source and available for Android, iOS, and Linux users. We here at Appalachian use it in our introductory astronomy labs for specific activities such as investigating coordinate systems, discovering differences between solar and sidereal days, as well as determining why your "astrological sign" is most often not your "astronomical sign."

Os-186 and Os-187 Enrichments and High-He-3/He-4 sources in the Earth's Mantle: Evidence from Icelandic Picrites

NASA Technical Reports Server (NTRS)

Brandon, Alan D.; Graham, David W.; Waight, Tod; Gautason, Bjarni

2007-01-01

Picrites from the neovolcanic zones in Iceland display a range in Os-187/Os-188O from 0.1297 to 0.1381 ((gamma)Os = 0.0 to 6.5) and uniform Os-186/Os-188 of 0.1198375+/-32 (2 (sigma)). The value for Os-186/Os-188 is within uncertainty of the present-day value for the primitive upper mantle of 0.1198398+/-16. These Os isotope systematics are best explained by ancient recycled crust or melt enrichment in the mantle source region. If so, then the coupled enrichments displayed in Os-186/Os-188 and Os-187/Os-188 from lavas of other plume systems must result from an independent process, the most viable candidate at present remains core-mantle interaction. While some plumes with high He-3/He-4, such as Hawaii, appear to have been subjected to detectable addition of Os (and possibly He) from the outer core, others such as Iceland do not. A positive correlation between Os-187/Os-188 and He-3/He-4 from 9.6 to 19 RA in Iceland picrites is best modeled as mixtures of 500 Ma or older ancient recycled crust mixed with primitive mantle, creating a hybrid source region that subsequently mixes with the convecting MORB mantle during ascent and melting. This multistage mechanism to explain these isotope systematics is consistent with ancient recycled crust juxtaposed with more primitive, relatively He-rich mantle, in convective isolation from the upper mantle, most likely in the lowermost mantle. This is inconsistent with models that propose random mixing between heterogeneities in the convecting upper mantle as a mechanism to explain the observed isotopic variation in oceanic lavas or models that produce a high He-3/He-4 signature in melt depleted and strongly outgassed, He-poor mantle. Instead these systematics require a deep mantle source to explain the 3He/4He signature in Iceland lavas. The He-3/He-4 of lavas derived from the Iceland plume changed over time, from a maximum of 50 RA at 60 Ma, to approximately 25-27 RA at present. The changes are coupled with distinct compositional gaps between the different aged lavas when H-3/He-4 is plotted versus various geochemical parameters such as Nd-143/Nd-144 and La/Sm. These relationships can be interpreted as an increase in the proportion of ancient recycled crust in the upwelling plume over this time period.

Complex anthropogenic sources of platinum group elements in aerosols on Cape Cod, USA.

PubMed

Sen, Indra S; Peucker-Ehrenbrink, Bernhard; Geboy, Nicholas

2013-09-17

Platinum group elements (PGE) of anthropogenic origin have been reported in rainwater, snow, roadside soil and vegetation, industrial waste, and urban airborne particles around the world. As recent studies have shown that PGE are bioavailable in the environment and pose health risks at chronic levels, the extent of PGE pollution is of global concern. In this study, we report PGE concentrations and osmium isotope ((187)Os/(188)Os) ratios of airborne particles (particulate matter, PM10) collected in Woods Hole, a small coastal village on Cape Cod, Massachusetts, U.S.A. The sampling site is more than 100 km away from the nearest urban centers (Boston, Providence) and has no large industrial emission center within a 30 km radius. The study reveals that, although PGE concentrations in rural airborne particulate matter are orders of magnitude lower than in urban aerosols, 69% of the total osmium is of anthropogenic origin. Anthropogenic PGE signatures in airborne particles are thus not restricted to large cities with high traffic flows and substantial industries; they can also be found in rural environments. We further conclude that the combination of Pt/Rh concentration ratios and (187)Os/(188)Os composition can be used to trace PGE sources. The Pt/Rh and (187)Os/(188)Os composition of Woods Hole aerosols indicate that the anthropogenic PGE fraction is primarily sourced from ore smelting processes, with possible minor contributions from fossil fuel burning and automobile catalyst-derived materials. Our results further substantiate the use of (187)Os/(188)Os in source apportionment studies on continental scales.

Residency of rhenium and osmium in a heavy crude oil

NASA Astrophysics Data System (ADS)

DiMarzio, Jenna M.; Georgiev, Svetoslav V.; Stein, Holly J.; Hannah, Judith L.

2018-01-01

Rhenium-osmium (Re-Os) isotope geochemistry is an emerging tool for the study of oil formation and migration processes, and a new technology for petroleum exploration. Little is known, however, about the residency of Re and Os within asphaltene and maltene sub-fractions of crude oil. This information is crucial for understanding the 187Re-187Os radiometric clock held in petroleum systems and for interpreting geochronology for key processes such as oil formation, migration, and biodegradation. In this study, a heavy crude oil was separated into soluble (maltene, MALT) and insoluble (asphaltene, ASPH) fractions using n-heptane as the asphaltene-precipitating agent. The asphaltenes were separated sequentially into sub-fractions using two different solvent pairs (heptane-dichloromethane and acetone-toluene), and the bulk maltenes were separated into saturate, aromatic, and resin (SAR) fractions using open column chromatography. Each asphaltene and maltene sub-fraction was analyzed for Re and Os. The asphaltene sub-fractions and the bulk ASPH, MALT, and crude oil were analyzed for a suite of trace metals by ICP-MS. Our results show that Re and Os concentrations co-vary between the asphaltene sub-fractions, and that both elements are found mostly in the more polar and aromatic sub-fractions. Significant Re and Os are also present in the aromatic and resin fractions of the maltenes. However, each asphaltene and maltene sub-fraction has a distinct isotopic composition, and sub-fractions are not isochronous. This suggests that asphaltene sub-fractionation separates Re-Os complexes to the point where the isotopic integrity of the geochronometer is compromised. The mobility of individual Re and Os isotopes and the decoupling possibilities between radiogenic 187Os produced from 187Re remain elusive, but their recognition in this study is a critical first step. Re and Os correlate strongly with Mo and Cd in the asphaltene sub-fractions, suggesting that these metals occupy similar sites. Re-Os and Ni-V budgets also show some similarities, indicating that at least some Re (and possibly Os) could be present in metalloporphyrin form. We conclude that progressive asphaltene precipitation during migration and mixing of oils can change the isotopic ratios of the resultant oil. A sense of process is key to interpretation of Re-Os data for tar mats and live oils, whether isochronous or scattered datasets result. Optimally, by combining data from source rocks, oils, and asphaltenes generated along the migration pathway, we can construct temporal histories for whole petroleum systems.

Long-term survival in laparoscopic vs open resection for colorectal liver metastases: inverse probability of treatment weighting using propensity scores.

PubMed

Lewin, Joel W; O'Rourke, Nicholas A; Chiow, Adrian K H; Bryant, Richard; Martin, Ian; Nathanson, Leslie K; Cavallucci, David J

2016-02-01

This study compares long-term outcomes between intention-to-treat laparoscopic and open approaches to colorectal liver metastases (CLM), using inverse probability of treatment weighting (IPTW) based on propensity scores to control for selection bias. Patients undergoing liver resection for CLM by 5 surgeons at 3 institutions from 2000 to early 2014 were analysed. IPTW based on propensity scores were generated and used to assess the marginal treatment effect of the laparoscopic approach via a weighted Cox proportional hazards model. A total of 298 operations were performed in 256 patients. 7 patients with planned two-stage resections were excluded leaving 284 operations in 249 patients for analysis. After IPTW, the population was well balanced. With a median follow up of 36 months, 5-year overall survival (OS) and recurrence-free survival (RFS) for the cohort were 59% and 38%. 146 laparoscopic procedures were performed in 140 patients, with weighted 5-year OS and RFS of 54% and 36% respectively. In the open group, 138 procedures were performed in 122 patients, with a weighted 5-year OS and RFS of 63% and 38% respectively. There was no significant difference between the two groups in terms of OS or RFS. In the Brisbane experience, after accounting for bias in treatment assignment, long term survival after LLR for CLM is equivalent to outcomes in open surgery. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

Long-term survival in laparoscopic vs open resection for colorectal liver metastases: inverse probability of treatment weighting using propensity scores

PubMed Central

Lewin, Joel W.; O'Rourke, Nicholas A.; Chiow, Adrian K.H.; Bryant, Richard; Martin, Ian; Nathanson, Leslie K.; Cavallucci, David J.

2015-01-01

Background This study compares long-term outcomes between intention-to-treat laparoscopic and open approaches to colorectal liver metastases (CLM), using inverse probability of treatment weighting (IPTW) based on propensity scores to control for selection bias. Method Patients undergoing liver resection for CLM by 5 surgeons at 3 institutions from 2000 to early 2014 were analysed. IPTW based on propensity scores were generated and used to assess the marginal treatment effect of the laparoscopic approach via a weighted Cox proportional hazards model. Results A total of 298 operations were performed in 256 patients. 7 patients with planned two-stage resections were excluded leaving 284 operations in 249 patients for analysis. After IPTW, the population was well balanced. With a median follow up of 36 months, 5-year overall survival (OS) and recurrence-free survival (RFS) for the cohort were 59% and 38%. 146 laparoscopic procedures were performed in 140 patients, with weighted 5-year OS and RFS of 54% and 36% respectively. In the open group, 138 procedures were performed in 122 patients, with a weighted 5-year OS and RFS of 63% and 38% respectively. There was no significant difference between the two groups in terms of OS or RFS. Conclusion In the Brisbane experience, after accounting for bias in treatment assignment, long term survival after LLR for CLM is equivalent to outcomes in open surgery. PMID:26902138

Os isotope systematics in ocean island basalts

NASA Astrophysics Data System (ADS)

Reisberg, Laurie; Zindler, Alan; Marcantonio, Franco; White, William; Wyman, Derek; Weaver, Barry

1993-12-01

New Re-Os isotopic results for Os-poor basalts from St. Helena, the Comores, Samoa, Pitcairn and Kerguelen dramatically expand the known range of initial Os-186/Os-187 ratios in Ocean Island Basalts (OIBs) to values as high as 1.7. In contrast to the Os isotopic uniformity of Os-rich basalts from the HIMU islands of Tubuai and Mangaia found by Hauri and Hart, our values for St. Helena span most of the known range of Os isotopic variability in oceanic basalts (initial O-187/Os-186 ranges from 1.2 to 1.7). Generation of such radiogenic Os in the mantle requires melting of source materials that contain large proportions of recycled oceanic crust. The very low Os concentrations of most of the basalts analyzed here, however, leave them susceptible to modification via interaction with materials containing radiogenic Os in the near-surface environment. Thus the high Os-186/Os-187 ratios may result from assimilation of radiogenic Os-rich marine sediments, such as Mn oxides, within the volcanic piles traversed by these magmas en route to the surface. Furthermore, the Os isotopic signatures of Os-rich, olivine-laden OIBs may reflect the accumulation of lithospheric olivine, rather than simply their mantle source characteristics. The extent to which these processes alter the view of the mantle obtained via study of Re-Os systematics in oceanic basalts is uncertain. These effects must be quantified before Re-Os systematics in OIBs can be used with confidence to investigate the nature of mantle heterogeneity and its causes.

Provenance Datasets Highlighting Capture Disparities

DTIC Science & Technology

2014-01-01

Vistrails [20], Taverna [21] or Kepler [6], and an OS -observing system like PASS [18]. In less granular workflow systems, the data files, scripts...run, etc. are capturable as long as they are executed within the workflow system. In more granular OS -observing systems, the actual reads, writes...rolling up” very granular information to less granular information. OS -level capture knows that a socket was opened and that data was sent to a foreign

A Single Oxidosqualene Cyclase Produces the Seco-Triterpenoid α-Onocerin1[OPEN

PubMed Central

Almeida, Aldo; Khakimov, Bekzod; Bassard, Jean-Etienne; Appendino, Giovanni

2018-01-01

8,14-seco-Triterpenoids are characterized by their unusual open C-ring. Their distribution in nature is rare and scattered in taxonomically unrelated plants. The 8,14-seco-triterpenoid α-onocerin is only known from the evolutionarily distant clubmoss genus Lycopodium and the leguminous genus Ononis, which makes the biosynthesis of this seco-triterpenoid intriguing from an evolutionary standpoint. In our experiments with Ononis spinosa, α-onocerin was detected only in the roots. Through transcriptome analysis of the roots, an oxidosqualene cyclase, OsONS1, was identified that produces α-onocerin from squalene-2,3;22,23-dioxide when transiently expressed in Nicotiana bethamiana. In contrast, in Lycopodium clavatum, two sequential cyclases, LcLCC and LcLCD, are required to produce α-onocerin in the N. benthamiana transient expression system. Expression of OsONS1 in the lanosterol synthase knockout yeast strain GIL77, which accumulates squalene-2,3;22,23-dioxide, verified the α-onocerin production. A phylogenetic analysis predicts that OsONS1 branches off from specific lupeol synthases and does not group with the known L. clavatum α-onocerin cyclases. Both the biochemical and phylogenetic analyses of OsONS1 suggest convergent evolution of the α-onocerin pathways. When OsONS1 was coexpressed in N. benthamiana leaves with either of the two O. spinosa squalene epoxidases, OsSQE1 or OsSQE2, α-onocerin production was boosted, most likely because the epoxidases produce higher amounts of squalene-2,3;22,23-dioxide. Fluorescence lifetime imaging microscopy analysis demonstrated specific protein-protein interactions between OsONS1 and both O. spinosa squalene epoxidases. Coexpression of OsONS1 with the two OsSQEs suggests that OsSQE2 is the preferred partner of OsONS1 in planta. Our results provide an example of the convergent evolution of plant specialized metabolism. PMID:29203557

IPeak: An open source tool to combine results from multiple MS/MS search engines.

PubMed

Wen, Bo; Du, Chaoqin; Li, Guilin; Ghali, Fawaz; Jones, Andrew R; Käll, Lukas; Xu, Shaohang; Zhou, Ruo; Ren, Zhe; Feng, Qiang; Xu, Xun; Wang, Jun

2015-09-01

Liquid chromatography coupled tandem mass spectrometry (LC-MS/MS) is an important technique for detecting peptides in proteomics studies. Here, we present an open source software tool, termed IPeak, a peptide identification pipeline that is designed to combine the Percolator post-processing algorithm and multi-search strategy to enhance the sensitivity of peptide identifications without compromising accuracy. IPeak provides a graphical user interface (GUI) as well as a command-line interface, which is implemented in JAVA and can work on all three major operating system platforms: Windows, Linux/Unix and OS X. IPeak has been designed to work with the mzIdentML standard from the Proteomics Standards Initiative (PSI) as an input and output, and also been fully integrated into the associated mzidLibrary project, providing access to the overall pipeline, as well as modules for calling Percolator on individual search engine result files. The integration thus enables IPeak (and Percolator) to be used in conjunction with any software packages implementing the mzIdentML data standard. IPeak is freely available and can be downloaded under an Apache 2.0 license at https://code.google.com/p/mzidentml-lib/. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Concierge: Personal Database Software for Managing Digital Research Resources

PubMed Central

Sakai, Hiroyuki; Aoyama, Toshihiro; Yamaji, Kazutsuna; Usui, Shiro

2007-01-01

This article introduces a desktop application, named Concierge, for managing personal digital research resources. Using simple operations, it enables storage of various types of files and indexes them based on content descriptions. A key feature of the software is a high level of extensibility. By installing optional plug-ins, users can customize and extend the usability of the software based on their needs. In this paper, we also introduce a few optional plug-ins: literature management, electronic laboratory notebook, and XooNlps client plug-ins. XooNIps is a content management system developed to share digital research resources among neuroscience communities. It has been adopted as the standard database system in Japanese neuroinformatics projects. Concierge, therefore, offers comprehensive support from management of personal digital research resources to their sharing in open-access neuroinformatics databases such as XooNIps. This interaction between personal and open-access neuroinformatics databases is expected to enhance the dissemination of digital research resources. Concierge is developed as an open source project; Mac OS X and Windows XP versions have been released at the official site (http://concierge.sourceforge.jp). PMID:18974800

Molecular transformations of phenolic SOA during photochemical aging in the aqueous phase: Competition among oligomerization, functionalization, and fragmentation

DOE PAGES

Yu, Lu; Smith, Jeremy; Laskin, Alexander; ...

2016-04-13

Organic aerosol is formed and transformed in atmospheric aqueous phases (e.g., cloud and fog droplets and deliquesced airborne particles containing small amounts of water) through a multitude of chemical reactions. Understanding these reactions is important for a predictive understanding of atmospheric aging of aerosols and their impacts on climate, air quality, and human health. In this study, we investigate the chemical evolution of aqueous secondary organic aerosol (aqSOA) formed during reactions of phenolic compounds with two oxidants – the triplet excited state of an aromatic carbonyl ( 3C *) and hydroxyl radical ( • OH). Changes in themore » molecular composition of aqSOA as a function of aging time are characterized using an offline nanospray desorption electrospray ionization mass spectrometer (nano-DESI MS) whereas the real-time evolution of SOA mass, elemental ratios, and average carbon oxidation state (OS C) are monitored using an online aerosol mass spectrometer (AMS). Our results indicate that oligomerization is an important aqueous reaction pathway for phenols, especially during the initial stage of photooxidation equivalent to ~2 h irradiation under midday winter solstice sunlight in Northern California. At later reaction times functionalization (i.e., adding polar oxygenated functional groups to the molecule) and fragmentation (i.e., breaking of covalent bonds) become more important processes, forming a large variety of functionalized aromatic and open-ring products with higher OS C values. Fragmentation reactions eventually dominate the photochemical evolution of phenolic aqSOA, forming a large number of highly oxygenated ring-opening molecules with carbon numbers ( n C) below 6. The average n C of phenolic aqSOA decreases while average OS C increases over the course of photochemical aging. In addition, the saturation vapor pressures ( C *) of dozens of the most abundant phenolic aqSOA molecules are estimated. A wide range of C * values is observed, varying from < 10 –20 µg m –3 for functionalized phenolic oligomers to > 10 µg m –3 for small open-ring species. Furthermore, the detection of abundant extremely low-volatile organic compounds (ELVOC) indicates that aqueous reactions of phenolic compounds are likely an important source of ELVOC in the atmosphere.« less

Molecular transformations of phenolic SOA during photochemical aging in the aqueous phase: Competition among oligomerization, functionalization, and fragmentation

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

Yu, Lu; Smith, Jeremy; Laskin, Alexander

Organic aerosol is formed and transformed in atmospheric aqueous phases (e.g., cloud and fog droplets and deliquesced airborne particles containing small amounts of water) through a multitude of chemical reactions. Understanding these reactions is important for a predictive understanding of atmospheric aging of aerosols and their impacts on climate, air quality, and human health. In this study, we investigate the chemical evolution of aqueous secondary organic aerosol (aqSOA) formed during reactions of phenolic compounds with two oxidants – the triplet excited state of an aromatic carbonyl ( 3C *) and hydroxyl radical ( • OH). Changes in themore » molecular composition of aqSOA as a function of aging time are characterized using an offline nanospray desorption electrospray ionization mass spectrometer (nano-DESI MS) whereas the real-time evolution of SOA mass, elemental ratios, and average carbon oxidation state (OS C) are monitored using an online aerosol mass spectrometer (AMS). Our results indicate that oligomerization is an important aqueous reaction pathway for phenols, especially during the initial stage of photooxidation equivalent to ~2 h irradiation under midday winter solstice sunlight in Northern California. At later reaction times functionalization (i.e., adding polar oxygenated functional groups to the molecule) and fragmentation (i.e., breaking of covalent bonds) become more important processes, forming a large variety of functionalized aromatic and open-ring products with higher OS C values. Fragmentation reactions eventually dominate the photochemical evolution of phenolic aqSOA, forming a large number of highly oxygenated ring-opening molecules with carbon numbers ( n C) below 6. The average n C of phenolic aqSOA decreases while average OS C increases over the course of photochemical aging. In addition, the saturation vapor pressures ( C *) of dozens of the most abundant phenolic aqSOA molecules are estimated. A wide range of C * values is observed, varying from < 10 –20 µg m –3 for functionalized phenolic oligomers to > 10 µg m –3 for small open-ring species. Furthermore, the detection of abundant extremely low-volatile organic compounds (ELVOC) indicates that aqueous reactions of phenolic compounds are likely an important source of ELVOC in the atmosphere.« less

Design and implementation of handheld and desktop software for the structured reporting of hepatic masses using the LI-RADS schema.

PubMed

Clark, Toshimasa J; McNeeley, Michael F; Maki, Jeffrey H

2014-04-01

The Liver Imaging Reporting and Data System (LI-RADS) can enhance communication between radiologists and clinicians if applied consistently. We identified an institutional need to improve liver imaging report standardization and developed handheld and desktop software to serve this purpose. We developed two complementary applications that implement the LI-RADS schema. A mobile application for iOS devices written in the Objective-C language allows for rapid characterization of hepatic observations under a variety of circumstances. A desktop application written in the Java language allows for comprehensive observation characterization and standardized report text generation. We chose the applications' languages and feature sets based on the computing resources of target platforms, anticipated usage scenarios, and ease of application installation, deployment, and updating. Our primary results are the publication of the core source code implementing the LI-RADS algorithm and the availability of the applications for use worldwide via our website, http://www.liradsapp.com/. The Java application is free open-source software that can be integrated into nearly any vendor's reporting system. The iOS application is distributed through Apple's iTunes App Store. Observation categorizations of both programs have been manually validated to be correct. The iOS application has been used to characterize liver tumors during multidisciplinary conferences of our institution, and several faculty members, fellows, and residents have adopted the generated text of Java application into their diagnostic reports. Although these two applications were developed for the specific reporting requirements of our liver tumor service, we intend to apply this development model to other diseases as well. Through semiautomated structured report generation and observation characterization, we aim to improve patient care while increasing radiologist efficiency. Published by Elsevier Inc.

Evaluations of laparoscopic proctocolectomy versus traditional technique in patients with rectal cancer.

PubMed

Koulas, Spyridon G; Pappas-Gogos, George; Spirou, Spyridon; Roustanis, Evangelos; Tsimogiannis, Konstantinos E; Tsirves, Georgios; Tsimoyiannis, Evangelos C

2009-01-01

This was a retrospective study that evaluated the surgical outcomes of laparoscopic surgery (LS) for rectal cancer, in comparison with a case control series of open surgery (OS), during an 8-year period. Between October 1998 and December 2006, 203 patients with rectal malignancies underwent colectomy; 146 of them had colectomy with the traditional technique (OS), while 57 underwent resection of rectal cancer laparoscopically (LS). The LS group was compared with 60 patients from the OS group (selected from the 146 OS group patients), matched by size, sex, age, anatomical location of the tumor, type, extent of resection, and pathological stage. Data were obtained from patients' medical records. Statistical analysis was performed with the t test and chi-square test. All data are expressed as mean +/- standard error of the mean (SEM). Mean age of the LS group was 63.7+/-12 years versus 69+/-12 years in the OS group. There were more men than women in both the laparoscopic (33 males, 24 females) and OS groups (35 men, 25 women). The mean follow-up period was 38 months and 78 months for LS and OS groups, respectively. The procedure included low anterior resection (43 in LS and 45 in OS), and 13 patients in both groups underwent abdominoperineal resection and 3 transanal resections (2 in OS and 1 in LS). Mean tumor size was 4.2+/-2.12cm in the LS versus 5.2+/-2.02cm in the OS group. Conversion to an open procedure occurred in 4 patients (6.7%), all in the first 20 cases. Postoperative complications developed in 28 patients (11.7%), 13 in the LS group and 15 in the OS group. Median operative time was longer, but median blood loss was significantly lower in the LS group. The length of hospital stay was significantly shorter for the LS group. Laparoscopic surgery is feasible and safe for patients with rectal cancer and provides benefits during the postoperative period without increased morbidity or mortality.

Comparative composition, diversity, and abundance of oligosaccharides in early lactation milk from commercial dairy and beef cows

PubMed Central

Sischo, William M.; Short, Diana M.; Geissler, Mareen; Bunyatratchata, Apichaya; Barile, Daniela

2017-01-01

Prebiotics are nondigestible dietary ingredients, usually oligosaccharides (OS), that provide a health benefit to the host by directly modulating the gut microbiota. Although there is some information describing OS content in dairy-source milk, no information is available to describe the OS content of beef-source milk. Given the different trait emphasis between dairy and beef for milk production and calf survivability, it is plausible that OS composition, diversity, and abundance differ between production types. The goal of this study was to compare OS in milk from commercial dairy and beef cows in early lactation. Early-lactation multiparous cows (5–12 d in milk) from 5 commercial Holstein dairy herds and 5 Angus or Angus hybrid beef herds were sampled once. Milk was obtained from each enrolled cow and frozen on the farm. Subsequently, each milk sample was assessed for total solids, pH, and OS content and relative abundance. Oligosaccharide diversity and abundance within and between samples was transformed through principal component analysis to reduce data complexity. Factors from principal component analysis were used to create similarity clusters, which were subsequently used in a multivariate logistic regression. In total, 30 OS were identified in early-lactation cow milk, including 21 distinct OS and 9 isomers with unique retention times. The majority of OS detected in the milk samples were present in all individual samples regardless of production type. Two clusters described distribution patterns of OS for the study sample; when median OS abundance was compared between the 2 clusters, we found that overall OS relative abundance was consistently greater in the cluster dominated by beef cows. For several of the structures, including those with known prebiotic effect, the difference in abundance was 2- to 4-fold greater in the beef-dominated cluster. Assuming that beef OS content in milk is the gold standard for cattle, it is likely that preweaning dairy calves are deprived of dietary-source OS. Although supplementing rations with OS is an approach to rectify this deficiency, understanding the health and productivity effects of improving OS abundance being fed to preweaning calves is a necessary next step before recommending supplementation. These studies should account for the observation that OS products are variable for both OS diversity and structural complexity, and some products may not be suitable as prebiotics. PMID:28318588

Counting the dead to determine the source and transmission of the marine herpesvirus OsHV-1 in Crassostrea gigas.

PubMed

Whittington, Richard J; Paul-Pont, Ika; Evans, Olivia; Hick, Paul; Dhand, Navneet K

2018-04-10

Marine herpesviruses are responsible for epizootics in economically, ecologically and culturally significant taxa. The recent emergence of microvariants of Ostreid herpesvirus 1 (OsHV-1) in Pacific oysters Crassostrea gigas has resulted in socioeconomic losses in Europe, New Zealand and Australia however, there is no information on their origin or mode of transmission. These factors need to be understood because they influence the way the disease may be prevented and controlled. Mortality data obtained from experimental populations of C. gigas during natural epizootics of OsHV-1 disease in Australia were analysed qualitatively. In addition we compared actual mortality data with those from a Reed-Frost model of direct transmission and analysed incubation periods using Sartwell's method to test for the type of epizootic, point source or propagating. We concluded that outbreaks were initiated from an unknown environmental source which is unlikely to be farmed oysters in the same estuary. While direct oyster-to-oyster transmission may occur in larger oysters if they are in close proximity (< 40 cm), it did not explain the observed epizootics, point source exposure and indirect transmission being more common and important. A conceptual model is proposed for OsHV-1 index case source and transmission, leading to endemicity with recurrent seasonal outbreaks. The findings suggest that prevention and control of OsHV-1 in C. gigas will require multiple interventions. OsHV-1 in C. gigas, which is a sedentary animal once beyond the larval stage, is an informative model when considering marine host-herpesvirus relationships.

Determination of osmium concentrations and (187)Os/(188)Os of crude oils and source rocks by coupling high-pressure, high-temperature digestion with sparging OsO(4) into a multicollector inductively coupled plasma mass spectrometer.

PubMed

Sen, Indra S; Peucker-Ehrenbrink, Bernhard

2014-03-18

The (187)Os/(188)Os ratio that is based on the β(-)-decay of (187)Re to (187)Os (t1/2 = 41.6 billion years) is widely used to investigate petroleum system processes. Despite its broad applicability to studies of hydrocarbon deposits worldwide, a suitable matrix-matched reference material for Os analysis does not exist. In this study, a method that enables Os isotope measurement of crude oil with in-line Os separation and purification from the sample matrix is proposed. The method to analyze Os concentration and (187)Os/(187)Os involves sample digestion under high pressure and high temperature using a high pressure asher (HPA-S, Anton Paar), sparging of volatile osmium tetroxide from the sample solution, and measurements using multicollector inductively coupled plasma mass spectrometry (MC-ICPMS). This methods significantly reduced the total procedural time compared to conventional Carius tube digestion followed by Os separation and purification using solvent extraction, microdistillation and N-TIMS analysis. The method yields Os concentration (28 ± 4 pg g(-1)) and (187)Os/(188)Os (1.62 ± 0.15) of commercially available crude oil reference material NIST 8505 (1 S.D., n = 6). The reference material NIST 8505 is homogeneous with respect to Os concentration at a test portion size of 0.2 g. Therefore, (187)Os/(188)Os composition and Os concentration of NIST 8505 can serve as a matrix-matched reference material for Os analysis. Data quality was assessed by repeated measurements of the USGS shale reference material SCo-1 (sample matrix similar to petroleum source rock) and the widely used Liquid Os Standard solution (LOsSt). The within-laboratory reproducibility of (187)Os/(188)Os for a 5 pg of LOsSt solution, analyzed with this method over a period of 12 months was ∼1.4% (1 S.D., n = 26), respectively.

Tracking millennial-scale Holocene glacial advance and retreat using osmium isotopes: Insights from the Greenland ice sheet

USGS Publications Warehouse

Rooney, Alan D.; Selby, David; Llyod, Jeremy M.; Roberts, David H.; Luckge, Andreas; Sageman, Bradley B.; Prouty, Nancy G.

2016-01-01

High-resolution Os isotope stratigraphy can aid in reconstructing Pleistocene ice sheet fluctuation and elucidating the role of local and regional weathering fluxes on the marine Os residence time. This paper presents new Os isotope data from ocean cores adjacent to the West Greenland ice sheet that have excellent chronological controls. Cores MSM-520 and DA00-06 represent distal to proximal sites adjacent to two West Greenland ice streams. Core MSM-520 has a steadily decreasing Os signal over the last 10 kyr (187Os/188Os = 1.35–0.81). In contrast, Os isotopes from core DA00-06 (proximal to the calving front of Jakobshavn Isbræ) highlight four stages of ice stream retreat and advance over the past 10 kyr (187Os/188Os = 2.31; 1.68; 2.09; 1.47). Our high-resolution chemostratigraphic records provide vital benchmarks for ice-sheet modelers as we attempt to better constrain the future response of major ice sheets to climate change. Variations in Os isotope composition from sediment and macro-algae (seaweed) sourced from regional and global settings serve to emphasize the overwhelming effect weathering sources have on seawater Os isotope composition. Further, these findings demonstrate that the residence time of Os is shorter than previous estimates of ∼104 yr.

Re — Os isotopic constraints on the origin of volcanic rocks, Gorgona Island, Colombia: Os isotopic evidence for ancient heterogeneities in the mantle

NASA Astrophysics Data System (ADS)

Walker, R. J.; Echeverria, L. M.; Shirey, S. B.; Horan, M. F.

1991-04-01

The Re — Os isotopic systematics of komatiites and spatially associated basalts from Gorgona Island, Colombia, indicate that they were produced at 155±43 Ma. Subsequent episodes of volcanism produced basalts at 88.1±3.8 Ma and picritic and basaltic lavas at ca. 58 Ma. The age for the ultramafic rocks is important because it coincides with the late-Jurassic, early-Cretaceous disassembly of Pangea, when the North- and South-American plates began to pull apart. Deep-seated mantle upwelling possibly precipitated the break-up of these continental plates and caused a tear in the subducting slab west of Gorgona, providing a rare, late-Phanerozoic conduit for the komatiitic melts. Mantle sources for the komatiites were heterogeneous with respect to Os and Pb isotopic compositions, but had homogeneous Nd isotopic compositions (ɛNd+9±1). Initial 187Os/186Os normalized to carbonaceous chondrites at 155 Ma (γOs) ranged from 0 to +22, and model-initial μ values ranged from 8.17 to 8.39. The excess radiogenic Os, compared with an assumed bulk-mantle evolution similar to carbonaceous chondrites, was likely produced in portions of the mantle with long-term elevated Re concentrations. The Os, Pb and Nd isotopic compositions, together with major-element constraints, suggest that the sources of the komatiites were enriched more than 1 Ga ago by low (<20%) and variable amounts of a basalt or komatiite component. This component was added as either subducted oceanic crust or melt derived from greater depths in the mantle. These results suggest that the Re — Os isotope system may be a highly sensitive indicator of the presence of ancient subducted oceanic crust in mantle-source regions.

Re - Os isotopic constraints on the origin of volcanic rocks, Gorgona Island, Colombia: Os isotopic evidence for ancient heterogeneities in the mantle

USGS Publications Warehouse

Walker, R.J.; Echeverria, L.M.; Shirey, S.B.; Horan, M.F.

1991-01-01

The Re - Os isotopic systematics of komatiites and spatially associated basalts from Gorgona Island, Colombia, indicate that they were produced at 155??43 Ma. Subsequent episodes of volcanism produced basalts at 88.1??3.8 Ma and picritic and basaltic lavas at ca. 58 Ma. The age for the ultramafic rocks is important because it coincides with the late-Jurassic, early-Cretaceous disassembly of Pangea, when the North- and South-American plates began to pull apart. Deep-seated mantle upwelling possibly precipitated the break-up of these continental plates and caused a tear in the subducting slab west of Gorgona, providing a rare, late-Phanerozoic conduit for the komatiitic melts. Mantle sources for the komatiites were heterogeneous with respect to Os and Pb isotopic compositions, but had homogeneous Nd isotopic compositions (??Nd+9??1). Initial 187Os/186Os normalized to carbonaceous chondrites at 155 Ma (??Os) ranged from 0 to +22, and model-initial ?? values ranged from 8.17 to 8.39. The excess radiogenic Os, compared with an assumed bulk-mantle evolution similar to carbonaceous chondrites, was likely produced in portions of the mantle with long-term elevated Re concentrations. The Os, Pb and Nd isotopic compositions, together with major-element constraints, suggest that the sources of the komatiites were enriched more than 1 Ga ago by low (<20%) and variable amounts of a basalt or komatiite component. This component was added as either subducted oceanic crust or melt derived from greater depths in the mantle. These results suggest that the Re - Os isotope system may be a highly sensitive indicator of the presence of ancient subducted oceanic crust in mantle-source regions. ?? 1991 Springer-Verlag.

Galaxy Portal: interacting with the galaxy platform through mobile devices.

PubMed

Børnich, Claus; Grytten, Ivar; Hovig, Eivind; Paulsen, Jonas; Čech, Martin; Sandve, Geir Kjetil

2016-06-01

: We present Galaxy Portal app, an open source interface to the Galaxy system through smart phones and tablets. The Galaxy Portal provides convenient and efficient monitoring of job completion, as well as opportunities for inspection of results and execution history. In addition to being useful to the Galaxy community, we believe that the app also exemplifies a useful way of exploiting mobile interfaces for research/high-performance computing resources in general. The source is freely available under a GPL license on GitHub, along with user documentation and pre-compiled binaries and instructions for several platforms: https://github.com/Tarostar/QMLGalaxyPortal It is available for iOS version 7 (and newer) through the Apple App Store, and for Android through Google Play for version 4.1 (API 16) or newer. geirksa@ifi.uio.no. © The Author 2016. Published by Oxford University Press.

esATAC: An Easy-to-use Systematic pipeline for ATAC-seq data analysis.

PubMed

Wei, Zheng; Zhang, Wei; Fang, Huan; Li, Yanda; Wang, Xiaowo

2018-03-07

ATAC-seq is rapidly emerging as one of the major experimental approaches to probe chromatin accessibility genome-wide. Here, we present "esATAC", a highly integrated easy-to-use R/Bioconductor package, for systematic ATAC-seq data analysis. It covers essential steps for full analyzing procedure, including raw data processing, quality control and downstream statistical analysis such as peak calling, enrichment analysis and transcription factor footprinting. esATAC supports one command line execution for preset pipelines, and provides flexible interfaces for building customized pipelines. esATAC package is open source under the GPL-3.0 license. It is implemented in R and C ++. Source code and binaries for Linux, MAC OS X and Windows are available through Bioconductor https://www.bioconductor.org/packages/release/bioc/html/esATAC.html). xwwang@tsinghua.edu.cn. Supplementary data are available at Bioinformatics online.

BioRuby: bioinformatics software for the Ruby programming language.

PubMed

Goto, Naohisa; Prins, Pjotr; Nakao, Mitsuteru; Bonnal, Raoul; Aerts, Jan; Katayama, Toshiaki

2010-10-15

The BioRuby software toolkit contains a comprehensive set of free development tools and libraries for bioinformatics and molecular biology, written in the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO. BioRuby comes with a tutorial, documentation and an interactive environment, which can be used in the shell, and in the web browser. BioRuby is free and open source software, made available under the Ruby license. BioRuby runs on all platforms that support Ruby, including Linux, Mac OS X and Windows. And, with JRuby, BioRuby runs on the Java Virtual Machine. The source code is available from http://www.bioruby.org/. katayama@bioruby.org

187Os-186Os and He Isotope Systematics of Iceland Picrites

NASA Astrophysics Data System (ADS)

Brandon, A. D.; Brandon, A. D.; Graham, D.; Gautason, B.

2001-12-01

Iceland is one of the longest-lived modern plumes, and seismic imaging supports a model where the roots of this plume are at the base of the lower mantle. Hence, Os isotopic data for lavas from this plume are ideal for further testing the role of core-mantle chemical exchange at the site of plume generation in the lower mantle, and for addressing the origin of Os-He isotopic variation in plumes. Recent work has shown that lavas from some plume systems (Hawaii, Noril'sk-Siberia, Gorgona) show coupled enrichments in 186Os/188Os and 187Os/188Os, not observed in upper mantle materials including abyssal peridotites. Picrites from Hawaii display a positive correlation between 186Os/188Os and He isotopes (R/Ra), where range in 186Os/188Os of 0.119834+/-28 to 0.1198475+/-29 and corresponding R/Ra from +7 to +25. These systematics are consistent with a lower mantle source for the radiogenic 186Os signal in the Hawaiian plume. The coupled Os enrichments in these plumes has been attributed to core-mantle chemical exchange, consistent with generation of the Hawaiian plume at the base of the lower mantle in D". Other potentially viable models await additional scrutiny. New He isotope and high precision 186Os/188Os and 187Os/188Os measurements for Iceland picrites show unique systematics compared to Hawaii. These picrites have 187Os/188Os ranging from 0.1297 to 0.1381 and R/Ra of +9 to +18, with generally higher R/Ra correlating with higher 187Os/188Os. Unlike the Hawaiian picrites from Hualalai and Loihi, which have coupled enrichments in 186Os/188Os and 187Os/188Os, the Iceland picrites show no enrichment 186Os/188Os - 0.1198363+/-28 (2s, n=14). Such Os-He isotopic variations require one end-member source that has high R/Ra, coupled with a long term elevated Re/Os and Pt/Os similar to that of the upper mantle. These systematics are inconsistent with either known upper mantle materials or those purported for ancient recycled slabs and may be a previously unidentified component in the lower mantle.

Developing Conceptual Framework for Revising Self-Learning Materials (SLMs) of the Open School (OS) of Bangladesh Open University (BOU) at a Digital Environment

ERIC Educational Resources Information Center

Yeasmin, Sabina; Murthy, C. R. K.

2011-01-01

Bangladesh Open University (BOU) runs school programs as part of its academic activities through open schooling since its inception. As of today, the Open School uses the first generation self-learning materials (SLMs) written, before an era, following an in-house style and template. The concerned faculty member corrects, every year, texts before…

Developing Conceptual Framework for Revising Self-Learning Materials (SLMs) of the Open School (OS) of Bangladesh Open University (BOU) at a Digital Environment

ERIC Educational Resources Information Center

Yeasmin, Sabina; Murthy, C. R. K.

2012-01-01

Bangladesh Open University (BOU) runs school programs as part of its academic activities through open schooling since its inception. As of today, the Open School uses the first generation self-learning materials (SLMs) written, before an era, following an in-house style and template. The concerned faculty member corrects, every year, texts before…

DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony.

PubMed

Wehe, André; Bansal, Mukul S; Burleigh, J Gordon; Eulenstein, Oliver

2008-07-01

DupTree is a new software program for inferring rooted species trees from collections of gene trees using the gene tree parsimony approach. The program implements a novel algorithm that significantly improves upon the run time of standard search heuristics for gene tree parsimony, and enables the first truly genome-scale phylogenetic analyses. In addition, DupTree allows users to examine alternate rootings and to weight the reconciliation costs for gene trees. DupTree is an open source project written in C++. DupTree for Mac OS X, Windows, and Linux along with a sample dataset and an on-line manual are available at http://genome.cs.iastate.edu/CBL/DupTree

MAPPI-DAT: data management and analysis for protein-protein interaction data from the high-throughput MAPPIT cell microarray platform.

PubMed

Gupta, Surya; De Puysseleyr, Veronic; Van der Heyden, José; Maddelein, Davy; Lemmens, Irma; Lievens, Sam; Degroeve, Sven; Tavernier, Jan; Martens, Lennart

2017-05-01

Protein-protein interaction (PPI) studies have dramatically expanded our knowledge about cellular behaviour and development in different conditions. A multitude of high-throughput PPI techniques have been developed to achieve proteome-scale coverage for PPI studies, including the microarray based Mammalian Protein-Protein Interaction Trap (MAPPIT) system. Because such high-throughput techniques typically report thousands of interactions, managing and analysing the large amounts of acquired data is a challenge. We have therefore built the MAPPIT cell microArray Protein Protein Interaction-Data management & Analysis Tool (MAPPI-DAT) as an automated data management and analysis tool for MAPPIT cell microarray experiments. MAPPI-DAT stores the experimental data and metadata in a systematic and structured way, automates data analysis and interpretation, and enables the meta-analysis of MAPPIT cell microarray data across all stored experiments. MAPPI-DAT is developed in Python, using R for data analysis and MySQL as data management system. MAPPI-DAT is cross-platform and can be ran on Microsoft Windows, Linux and OS X/macOS. The source code and a Microsoft Windows executable are freely available under the permissive Apache2 open source license at https://github.com/compomics/MAPPI-DAT. jan.tavernier@vib-ugent.be or lennart.martens@vib-ugent.be. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

An integrated system for rainfall induced shallow landslides modeling

NASA Astrophysics Data System (ADS)

Formetta, Giuseppe; Capparelli, Giovanna; Rigon, Riccardo; Versace, Pasquale

2014-05-01

Rainfall induced shallow landslides (RISL) cause significant damages involving loss of life and properties. Predict susceptible locations for RISL is a complex task that involves many disciplines: hydrology, geotechnical science, geomorphology, statistic. Usually to accomplish this task two main approaches are used: statistical or physically based model. In this work an open source (OS), 3-D, fully distributed hydrological model was integrated in an OS modeling framework (Object Modeling System). The chain is closed by linking the system to a component for safety factor computation with infinite slope approximation able to take into account layered soils and suction contribution to hillslope stability. The model composition was tested for a case study in Calabria (Italy) in order to simulate the triggering of a landslide happened in the Cosenza Province. The integration in OMS allows the use of other components such as a GIS to manage inputs-output processes, and automatic calibration algorithms to estimate model parameters. Finally, model performances were quantified by comparing modelled and simulated trigger time. This research is supported by Ambito/Settore AMBIENTE E SICUREZZA (PON01_01503) project.

General Mission Analysis Tool (GMAT) Architectural Specification. Draft

NASA Technical Reports Server (NTRS)

Hughes, Steven P.; Conway, Darrel, J.

2007-01-01

Early in 2002, Goddard Space Flight Center (GSFC) began to identify requirements for the flight dynamics software needed to fly upcoming missions that use formations of spacecraft to collect data. These requirements ranged from low level modeling features to large scale interoperability requirements. In 2003 we began work on a system designed to meet these requirement; this system is GMAT. The General Mission Analysis Tool (GMAT) is a general purpose flight dynamics modeling tool built on open source principles. The GMAT code is written in C++, and uses modern C++ constructs extensively. GMAT can be run through either a fully functional Graphical User Interface (GUI) or as a command line program with minimal user feedback. The system is built and runs on Microsoft Windows, Linux, and Macintosh OS X platforms. The GMAT GUI is written using wxWidgets, a cross platform library of components that streamlines the development and extension of the user interface Flight dynamics modeling is performed in GMAT by building components that represent the players in the analysis problem that is being modeled. These components interact through the sequential execution of instructions, embodied in the GMAT Mission Sequence. A typical Mission Sequence will model the trajectories of a set of spacecraft evolving over time, calculating relevant parameters during this propagation, and maneuvering individual spacecraft to maintain a set of mission constraints as established by the mission analyst. All of the elements used in GMAT for mission analysis can be viewed in the GMAT GUI or through a custom scripting language. Analysis problems modeled in GMAT are saved as script files, and these files can be read into GMAT. When a script is read into the GMAT GUI, the corresponding user interface elements are constructed in the GMAT GUI. The GMAT system was developed from the ground up to run in a platform agnostic environment. The source code compiles on numerous different platforms, and is regularly exercised running on Windows, Linux and Macintosh computers by the development and analysis teams working on the project. The system can be run using either a graphical user interface, written using the open source wxWidgets framework, or from a text console. The GMAT source code was written using open source tools. GSFC has released the code using the NASA open source license.

Implications of 187Os isotopic heterogeneities in a mantle plume: evidence from Gorgona Island and Curaçao

NASA Astrophysics Data System (ADS)

Walker, Richard J.; Storey, Michael; Kerr, Andrew C.; Tarney, John; Arndt, Nicholas T.

1999-03-01

Recent work has suggested that the mafic-ultramafic volcanism in evidence throughout portions of the Caribbean, Central America, and northern South America, including the islands of Gorgona and Curaçao, was generated as part of a middle-Cretaceous, large igneous province. New Re-Os isochron results for tholeiitic basalts from Gorgona and Curaçao indicate crystallization ages of 89.2 ± 5.2 and 85.6 ± 8.1 Ma, respectively, consistent with reported Ar ages. The Gorgona ultramafic suite shows a large range in initial Os isotopic composition, with γ Os values ranging from -0.5 to +12.4. This large range reflects isotopic heterogeneities in the mantle source similar to those observed for modern ocean island basalts. In contrast to ocean island basalts, however, Os isotopic compositions do not correlate with variations in Nd, Sr, or Pb isotopic compositions, which are within the range of depleted mid-ocean ridge basalts. The processes that produced these rocks evidently resulted in the decoupling of Os isotopes from the Nd, Sr, and Pb isotopic systems. Picrites from Curaçao have very uniform, chondritic initial Os isotopic compositions, with initial γ Os values ranging only from -0.4 to ±1.4. Basalts from Curaçao, however, define an isochron with a 187Os-enriched initial isotopic composition (γ Os = +9.5). In contrast to the 187Os-enriched ultramafic rocks from Gorgona, the enrichment in these basalts could have resulted from lithospheric contamination. If the Gorgona and Curaçao rocks were derived from the same plume, Os results, combined with Sr, Nd, and Pb data indicate a heterogeneous plume, with multiple compositionally and isotopically distinct domains. The Os isotopic results require derivation of Os from a minimum of two distinct reservoirs, one with a composition very similar to the chondritic average and one with long-term enriched Re/Os. Oceanic crustal recycling has been invoked to explain most of the 187Os enrichments that have been observed in ocean island basalt sources and could potentially apply to the Gorgona suite. Crustal recycling, however, requires large proportions of very ancient recycled basaltic crust in the sources of the 187Os-enriched ultramafic rocks to explain the magnitude of 187Os enrichments observed. For example, addition of 20% oceanic crust to fertile mantle, and nearly 3 billion years are necessary to generate a reservoir with the Os isotopic composition of the most radiogenic komatiites. If the recycled oceanic crust was added to basalt-depleted mantle, as may be indicated by ɛ Nd values for the komatiites averaging about +10, even larger proportions of older crust are required. Large proportions of oceanic mafic crust in the sources of the 187Os-enriched komatiites, although petrologically conceivable under certain melting conditions, is unlikely here given the limited trace element and lithophile isotope system variations. These results raise questions about the efficacy of using Os isotopes to constrain the proportion of recycled oceanic crust in other plumes. Other possible mechanisms for generating 187Os-enriched mantle include invoking the existence of a 187Os-enriched lower mantle, and minor outer core-lower mantle interactions.

Time-Dependent Density Functional Theory for Open Systems and Its Applications.

PubMed

Chen, Shuguang; Kwok, YanHo; Chen, GuanHua

2018-02-20

Photovoltaic devices, electrochemical cells, catalysis processes, light emitting diodes, scanning tunneling microscopes, molecular electronics, and related devices have one thing in common: open quantum systems where energy and matter are not conserved. Traditionally quantum chemistry is confined to isolated and closed systems, while quantum dissipation theory studies open quantum systems. The key quantity in quantum dissipation theory is the reduced system density matrix. As the reduced system density matrix is an O(M! × M!) matrix, where M is the number of the particles of the system of interest, quantum dissipation theory can only be employed to simulate systems of a few particles or degrees of freedom. It is thus important to combine quantum chemistry and quantum dissipation theory so that realistic open quantum systems can be simulated from first-principles. We have developed a first-principles method to simulate the dynamics of open electronic systems, the time-dependent density functional theory for open systems (TDDFT-OS). Instead of the reduced system density matrix, the key quantity is the reduced single-electron density matrix, which is an N × N matrix where N is the number of the atomic bases of the system of interest. As the dimension of the key quantity is drastically reduced, the TDDFT-OS can thus be used to simulate the dynamics of realistic open electronic systems and efficient numerical algorithms have been developed. As an application, we apply the method to study how quantum interference develops in a molecular transistor in time domain. We include electron-phonon interaction in our simulation and show that quantum interference in the given system is robust against nuclear vibration not only in the steady state but also in the transient dynamics. As another application, by combining TDDFT-OS with Ehrenfest dynamics, we study current-induced dissociation of water molecules under scanning tunneling microscopy and follow its time dependent dynamics. Given the rapid development in ultrafast experiments with atomic resolution in recent years, time dependent simulation of open electronic systems will be useful to gain insight and understanding of such experiments. This Account will mainly focus on the practical aspects of the TDDFT-OS method, describing the numerical implementation and demonstrating the method with applications.

Evaluation of the rhenium-osmium geochronometer in the Phosphoria petroleum system, Bighorn Basin of Wyoming and Montana, USA

USGS Publications Warehouse

Lillis, Paul G.; Selby, David

2013-01-01

Rhenium-osmium (Re-Os) geochronometry is applied to crude oils derived from the Permian Phosphoria Formation of the Bighorn Basin in Wyoming and Montana to determine whether the radiogenic age reflects the timing of petroleum generation, timing of migration, age of the source rock, or the timing of thermochemical sulfate reduction (TSR). The oils selected for this study are interpreted to be derived from the Meade Peak Phosphatic Shale and Retort Phosphatic Shale Members of the Phosphoria Formation based on oil-oil and oil-source rock correlations utilizing bulk properties, elemental composition, δ13C and δ34S values, and biomarker distributions. The δ34S values of the oils range from -6.2‰ to +5.7‰, with oils heavier than -2‰ interpreted to be indicative of TSR. The Re and Os isotope data of the Phosphoria oils plot in two general trends: (1) the main trend (n = 15 oils) yielding a Triassic age (239 ± 43 Ma) with an initial 187Os/188Os value of 0.85 ± 0.42 and a mean square weighted deviation (MSWD) of 1596, and (2) the Torchlight trend (n = 4 oils) yielding a Miocene age (9.24 ± 0.39 Ma) with an initial 187Os/188Os value of 1.88 ± 0.01 and a MSWD of 0.05. The scatter (high MSWD) in the main-trend regression is due, in part, to TSR in reservoirs along the eastern margin of the basin. Excluding oils that have experienced TSR, the regression is significantly improved, yielding an age of 211 ± 21 Ma with a MSWD of 148. This revised age is consistent with some studies that have proposed Late Triassic as the beginning of Phosphoria oil generation and migration, and does not seem to reflect the source rock age (Permian) or the timing of re-migration (Late Cretaceous to Eocene) associated with the Laramide orogeny. The low precision of the revised regression (±21 Ma) is not unexpected for this oil family given the long duration of generation from a large geographic area of mature Phosphoria source rock, and the possible range in the initial 187Os/188Os values of the Meade Peak and Retort source units. Effects of re-migration may have contributed to the scatter, but thermal cracking and biodegradation likely have had minimal or no effect on the main-trend regression. The four Phosphoria-sourced oils from Torchlight and Lamb fields yield a precise Miocene age Re-Os isochron that may reflect the end of TSR in the reservoir due to cooling below a threshold temperature in the last 10 m.y. from uplift and erosion of overlying rocks. The mechanism for the formation of a Re-Os isotopic relationship in a family of crude oils may involve multiple steps in the petroleum generation process. Bitumen generation from the source rock kerogen may provide a reset of the isotopic chronometer, and incremental expulsion of oil over the duration of the oil window may provide some of the variation seen in 187Re/188Os values from an oil family.

Comparative health technology assessment of robotic-assisted, direct manual laparoscopic and open surgery: a prospective study.

PubMed

Turchetti, Giuseppe; Pierotti, Francesca; Palla, Ilaria; Manetti, Stefania; Freschi, Cinzia; Ferrari, Vincenzo; Cuschieri, Alfred

2017-02-01

Despite many publications reporting on the increased hospital cost of robotic-assisted surgery (RAS) compared to direct manual laparoscopic surgery (DMLS) and open surgery (OS), the reported health economic studies lack details on clinical outcome, precluding valid health technology assessment (HTA). The present prospective study reports total cost analysis on 699 patients undergoing general surgical, gynecological and thoracic operations between 2011 and 2014 in the Italian Public Health Service, during which period eight major teaching hospitals treated the patients. The study compared total healthcare costs of RAS, DMLS and OS based on prospectively collected data on patient outcome in addition to healthcare costs incurred by the three approaches. The cost of RAS operations was significantly higher than that of OS and DMLS for both gynecological and thoracic operations (p < 0.001). The study showed no significant difference in total costs between OS and DMLS. Total costs of general surgery RAS were significantly higher than those of OS (p < 0.001), but not against DMLS general surgery. Indirect costs were significantly lower in RAS compared to both DMLS general surgery and OS gynecological surgery due to the shorter length of hospital stay of RAS approach (p < 0.001). Additionally, in all specialties compared to OS, patients treated by RAS experienced a quicker recovery and significantly less pain during the hospitalization and after discharge. The present HTA while confirming higher total healthcare costs for RAS operations identified significant clinical benefits which may justify the increased expenditure incurred by this approach.

Os isotopes in SNC meteorites and their implications to the early evolution of Mars and Earth

NASA Technical Reports Server (NTRS)

Jagoutz, E.; Luck, J. M.; Othman, D. Ben; Wanke, H.

1993-01-01

A new development on the measurement of the Os isotopic composition by mass spectrometry using negative ions opened a new field of applications. The Re-Os systematic provides time information on the differentiation of the nobel metals. The nobel metals are strongly partitioned into metal and sulphide phases, but also the generation of silicate melts might fractionate the Re-Os system. Compared to the other isotopic systems which are mainly dating the fractionation of the alkalis and alkali-earth elements, the Re-Os system is expected to disclose entirely new information about the geochemistry. Especially the differentiation and early evolution of the planets such as the formation of the core will be elucidated with this method.

Evaluating intraocular pressure-lowering solutions for the treatment of open-angle glaucoma: comparison between bimatoprost 0.03% and bimatoprost 0.01% - an observational switch study.

PubMed

Deshpande, Sarita S; Sonty, Sriram; Ahmad, Afzal

2017-01-01

The purpose of this study is to evaluate the intraocular pressure (IOP)-lowering efficacy of bimatoprost 0.01% solution in patients with primary open-angle glaucoma (POAG), who were switched from bimatoprost 0.03% solution, compared to patients with POAG who continued on bimatoprost 0.03% solution. A retrospective review evaluated 35 patients (35 right eyes [OD], 34 left eyes [OS]) who remained on bimatoprost 0.03% and 30 patients (27 OD, 30 OS) who were switched to bimatoprost 0.01% during the period January 8, 2010 to December 26, 2012. Mean IOP was measured 6 and 3 months before the switch, at switch, and 3, 6, and 12 months after the switch. Hyperemia scores were recorded before and after the switch and were compared to a picture scale. Mean IOP in the group that switched was 16.96±5.03 mmHg in OD and 17.67±5.33 mmHg in OS at baseline. Mean IOP postswitch to bimatoprost 0.01% solution was 17.60±4.34 mmHg in OD and 17.00±3.37 mmHg in OS. IOP was not significantly reduced in either OD or OS postswitch to bimatoprost 0.01% ( P 1 =0.5 OD, P 2 =0.2 OS). The hyperemia scores improved remarkably when bimatoprost 0.03% solution was switched to bimatoprost 0.01% solution ( P <0.001). To our knowledge, this is the first switch study evaluating the hypotensive efficacy and tolerability of bimatoprost in a group of patients with open-angle glaucoma. In this study comparing bimatoprost 0.03% and 0.01% solution, we found improved tolerability postswitch to 0.01% from 0.03% bimatoprost, similar efficacy between the two concentrations before and after switch in the same patient population, and similar IOPs comparable to nonswitch bimatoprost 0.03% solution.

Connecting to HPC VPN | High-Performance Computing | NREL

Science.gov Websites

and password will match your NREL network account login/password. From OS X or Linux, open a terminal finalized. Open a Remote Desktop connection using server name WINHPC02 (this is the login node). Mac Mac

Sniffing position combined with mouth opening improves facemask ventilation in children with adenotonsillar hypertrophy.

PubMed

Cuvas, O; Dikmen, B; Yucel, F

2011-05-01

This study evaluates the influence of sniffing position combined with mouth opening on the effectiveness of facemask ventilation in paralyzed pediatric patients undergoing adenotonsillectomy during sevoflurane-N(2)O anesthesia. After Institutional Ethics Committee approval, 40 children 5-11 years of age who were scheduled for an elective adenotonsillectomy operation were enrolled in this prospective randomized study. After routine monitoring and pre-oxygenation, anesthesia was induced with sevoflurane 8% in a mixture of 50% N(2)O-O(2). Three minutes after the administration of vecuronium, the sequence of the positions was randomized. Three positions were applied during facemask ventilation: Position CN (closed mouth - neutral head and neck position), position CS (closed mouth-sniffing position) and position OS (opened mouth-sniffing position). Volume-controlled ventilation was started. Peak inspiratory pressure (PIP), tidal volume (V(T)), expired tidal volume (V(Texp)) and end-tidal CO(2) pressure were recorded. The percent of leakage was calculated. The primary endpoint of this study was the expired tidal volume (V(Texp)). There was a statistically significant difference among the three positions for V(Texp) and PIP values. The OS resulted in higher V(Texp) values when compared with CN (P=0.022). The OS was significantly better than the other two positions, resulting in lower PIP values (P<0.001 and P=0.004, for CN and CS, respectively). The OS also resulted in less leakage during facemask ventilation when compared with CN and CS. Sniffing position combined with mouth opening improves V(Texp) and PIP values during facemask ventilation during sevoflurane-N(2)O anesthesia in paralyzed pediatric patients with adenotonsillar hypertrophy.

Size distribution and coating thickness of black carbon from the Canadian oil sands operations

NASA Astrophysics Data System (ADS)

Cheng, Yuan; Li, Shao-Meng; Gordon, Mark; Liu, Peter

2018-02-01

Black carbon (BC) plays an important role in the Earth's climate system. However, parameterizations of BC size and mixing state have not been well addressed in aerosol-climate models, introducing substantial uncertainties into the estimation of radiative forcing by BC. In this study, we focused on BC emissions from the oil sands (OS) surface mining activities in northern Alberta, based on an aircraft campaign conducted over the Athabasca OS region in 2013. A total of 14 flights were made over the OS source area, in which the aircraft was typically flown in a four- or five-sided polygon pattern along flight tracks encircling an OS facility. Another 3 flights were performed downwind of the OS source area, each of which involved at least three intercepting locations where the well-mixed OS plume was measured along flight tracks perpendicular to the wind direction. Comparable size distributions were observed for refractory black carbon (rBC) over and downwind of the OS facilities, with rBC mass median diameters (MMDs) between ˜ 135 and 145 nm that were characteristic of fresh urban emissions. This MMD range corresponded to rBC number median diameters (NMDs) of ˜ 60-70 nm, approximately 100 % higher than the NMD settings in some aerosol-climate models. The typical in- and out-of-plume segments of a flight, which had different rBC concentrations and photochemical ages, showed consistent rBC size distributions in terms of MMD, NMD and the corresponding distribution widths. Moreover, rBC size distributions remained unchanged at different downwind distances from the source area, suggesting that atmospheric aging would not necessarily change rBC size distribution. However, aging indeed influenced rBC mixing state. Coating thickness for rBC cores in the diameter range of 130-160 nm was nearly doubled (from ˜ 20 to 40 nm) within 3 h when the OS plume was transported over a distance of 90 km from the source area.

Oncologic outcomes following robot-assisted radical cystectomy with minimum 5-year follow-up: the Roswell Park cancer institute experience.

PubMed

Raza, Syed Johar; Al-Daghmin, Ali; Zhuo, Sharon; Mehboob, Zayn; Wang, Katy; Wilding, Gregory; Kauffman, Eric; Guru, Khurshid A

2014-11-01

Long-term oncologic outcomes following robot-assisted radical cystectomy (RARC) remain scarce. To report long-term oncologic outcomes following RARC at a single institution. Retrospective review of 99 patients who underwent RARC for urothelial carcinoma of bladder between 2005 and 2009. RARC was performed. Primary outcomes included recurrence-free survival (RFS), cancer-specific survival (CSS), and overall survival (OS), measured by the Kaplan-Meier method. The association between primary outcomes and perioperative and pathologic factors was assessed using a multivariable Cox proportional hazards model. Fifty-one (52%) patients had stage pT3 or higher disease. Eight (8%) patients had positive margins and 30 (30%) had positive lymph nodes (LNs), with a median of 21 LNs removed. Median follow-up for patients alive was 74 mo. The 5-yr RFS, CSS, and OS rates were 52.5%, 67.8%, and 42.4%, respectively. Tumor stage, LN stage, and margin status were each significantly associated with RFS, CSS, and OS. On multivariable analysis, tumor and LN stage were independent predictors of RFS, CSS, and OS, while positive margin status and Charlson comorbidity index predicted worse OS and CSS. Adjuvant chemotherapy predicted RFS only. Retrospective design and lack of open comparison are main limitations of this study. Long-term oncologic outcomes following RARC demonstrate RFS and CSS estimates similar to those reported in literature for open radical cystectomy. Randomized controlled trials can better define outcomes of any alternative technique. Survival data 5 yr after RARC for bladder cancer demonstrate that survival outcomes are dependent on the same oncologic parameters as previously reported for open surgery. Copyright © 2014 European Association of Urology. Published by Elsevier B.V. All rights reserved.

Cloning and characterization of an RNase-related protein gene preferentially expressed in rice stems.

PubMed

Wei, Jun-Ya; Li, An-Ming; Li, Yin; Wang, Jing; Liu, Xiao-Bin; Liu, Liang-Shi; Xu, Zeng-Fu

2006-04-01

RNase-related proteins (RRPs) are S- and S-like RNase homologs lacking the active site required for RNase activity. Here we describe the cloning and characterization of the rice (Oryza sativa) RRP gene (OsRRP). A single copy of OsRRP occurs in the rice genome. OsRRP contains three introns and an open reading frame encoding 252 amino acids, with the replacement of two histidines involved in the active site of RNase by lysine and tyrosine respectively. OsRRP is preferentially expressed in stems of wild-type rice and is significantly down-regulated in an increased tillering dwarf mutant ext37.

Subduction-modified oceanic crust in the sources of continental picrite dikes from the Karoo LIP?

NASA Astrophysics Data System (ADS)

Heinonen, J. S.; Carlson, R. W.; Riley, T. R.; Luttinen, A. V.; Horan, M. F.

2013-12-01

The Ahlmannryggen mountain range in East Antarctica hosts unusual LILE-depleted, but Fe- and Ti-enriched ultramafic dikes (Group 3) that belong to the Jurassic (~180 Ma) Karoo continental flood basalt (CFB) province. Their high initial ɛNd (+5 to +9) indicates their origin within the sublithospheric mantle beneath the Gondwana supercontinent. Using the new Pb and Os isotopic data and previously published geochemical and mineral chemical data, we try to constrain their mantle sources. The dikes that lack evidence of crustal contamination exhibit very radiogenic ɛNd (+8.6 to +9.0), relatively radiogenic 206Pb/204Pb (18.2-18.4) and 87Sr/86Sr (0.7035-0.7037), and unradiogenic 187Os/188Os (0.124-0.125) at 180 Ma. These isotopic compositions are unlike those typical of MORBs, excluding depleted mantle as the sole source contributor. The Pb isotopic composition of the dikes plots close to the 4.43 Ga geochron and hence is compatible with derivation from an early-depleted reservoir (EDR), recently suggested to be a major source component in CFBs. However, the high ɛNd of the dikes exceeds the ɛNd estimated for EDR (+4.9 to +8.5 at 180 Ma) and the relative Nb, Fe, and Ti enrichment (pyroxenite fingerprint) of the dikes is not readily ascribed to EDR source. Based on our isotopic and trace element modeling, we regard that the mantle source of the picrite dikes contained seawater-altered and subduction-modified MORB with a recycling age of 0.8 Ga. Such a source component would explain the unusual combination of elevated initial 87Sr/86Sr, ɛNd, and 206Pb/204Pb, relative depletion in fluid-mobile LILE, U, Th, Pb, and LREE, and relative enrichment in Nb, Fe, Ti, and other HFSE. Behavior of Re and Os in subduction environments is not well constrained, but loss of Re from recycled MORB, as observed in some subduction-associated eclogites and blueschists, and predominant contribution of Os from depleted peridotite matrix could have produced the observed low 187Os/188Os. Pyroxenite sources also are consistent with mineral chemical data (e.g., high-Ni olivine) for the picrite dikes. Such peculiar sources were likely not a predominant component in Karoo magmatism in general. Nevertheless, less subduction-modified or more enriched (e.g., additional sediment component) recycled crustal signatures would be difficult to distinguish from the 'lithospheric signatures' of many common CFBs. In addition to depleted mantle or EDR components that have been identified in the high-Mg dikes of the adjacent Vestfjella mountain range, a variety of recycled source components could thus be hiding in the geochemical jungle of the Karoo (and other) CFBs.

The Latina/o Pathway to the Ph.D.: Abriendo Caminos

ERIC Educational Resources Information Center

Castellanos, Jeanett, Ed.; Gloria, Alberta M., Ed.; Kamimura, Mark, Ed.

2005-01-01

This is the first book specifically to engage with the absence of Latinas/os in doctoral studies. It proposes educational and administrative strategies to open up the pipeline, and institutional practices to ensure access, support, models and training for Latinas/os aspiring to the Ph.D. The under-education of Latina/o youth begins early. Given…

Rewards and Costs in Adolescent Other-Sex Friendships: Comparisons to Same-Sex Friendships and Romantic Relationships

ERIC Educational Resources Information Center

Hand, Laura Shaffer; Furman, Wyndol

2009-01-01

This study used a social exchange framework to examine the features of non-romantic other-sex (OS) friendships compared with same-sex (SS) friendships and romantic relationships. High school seniors (N = 141) completed open-ended interviews about the benefits and costs of having OS friendships, SS friendships, and romantic relationships in…

An open source, wireless capable miniature microscope system

NASA Astrophysics Data System (ADS)

Liberti, William A., III; Perkins, L. Nathan; Leman, Daniel P.; Gardner, Timothy J.

2017-08-01

Objective. Fluorescence imaging through head-mounted microscopes in freely behaving animals is becoming a standard method to study neural circuit function. Flexible, open-source designs are needed to spur evolution of the method. Approach. We describe a miniature microscope for single-photon fluorescence imaging in freely behaving animals. The device is made from 3D printed parts and off-the-shelf components. These microscopes weigh less than 1.8 g, can be configured to image a variety of fluorophores, and can be used wirelessly or in conjunction with active commutators. Microscope control software, based in Swift for macOS, provides low-latency image processing capabilities for closed-loop, or BMI, experiments. Main results. Miniature microscopes were deployed in the songbird premotor region HVC (used as a proper name), in singing zebra finches. Individual neurons yield temporally precise patterns of calcium activity that are consistent over repeated renditions of song. Several cells were tracked over timescales of weeks and months, providing an opportunity to study learning related changes in HVC. Significance. 3D printed miniature microscopes, composed completely of consumer grade components, are a cost-effective, modular option for head-mounting imaging. These easily constructed and customizable tools provide access to cell-type specific neural ensembles over timescales of weeks.

SET: a pupil detection method using sinusoidal approximation

PubMed Central

Javadi, Amir-Homayoun; Hakimi, Zahra; Barati, Morteza; Walsh, Vincent; Tcheang, Lili

2015-01-01

Mobile eye-tracking in external environments remains challenging, despite recent advances in eye-tracking software and hardware engineering. Many current methods fail to deal with the vast range of outdoor lighting conditions and the speed at which these can change. This confines experiments to artificial environments where conditions must be tightly controlled. Additionally, the emergence of low-cost eye tracking devices calls for the development of analysis tools that enable non-technical researchers to process the output of their images. We have developed a fast and accurate method (known as “SET”) that is suitable even for natural environments with uncontrolled, dynamic and even extreme lighting conditions. We compared the performance of SET with that of two open-source alternatives by processing two collections of eye images: images of natural outdoor scenes with extreme lighting variations (“Natural”); and images of less challenging indoor scenes (“CASIA-Iris-Thousand”). We show that SET excelled in outdoor conditions and was faster, without significant loss of accuracy, indoors. SET offers a low cost eye-tracking solution, delivering high performance even in challenging outdoor environments. It is offered through an open-source MATLAB toolkit as well as a dynamic-link library (“DLL”), which can be imported into many programming languages including C# and Visual Basic in Windows OS (www.eyegoeyetracker.co.uk). PMID:25914641

Re-Os dating of maltenes and asphaltenes within single samples of crude oil

NASA Astrophysics Data System (ADS)

Georgiev, Svetoslav V.; Stein, Holly J.; Hannah, Judith L.; Galimberti, Roberto; Nali, Micaela; Yang, Gang; Zimmerman, Aaron

2016-04-01

Re-Os geochronology of oil may constrain the timing of oil formation and improve oil-source and oil-oil correlations. Typically, asphaltene (ASPH), the heaviest and most Re-Os rich oil fraction, from multiple oils within an oil field or a larger petroleum system are analyzed to obtain sufficient spread in Re-Os isotopic ratios, a mathematical necessity for precise Re-Os isochrons. Here we offer a new approach for Re-Os geochronology of oil based on isotopic analyses of different fractions within a single sample of crude oil. We studied three oils from the Gela oil field, southern Sicily, Italy, recovered from Triassic-Jurassic stratigraphic intervals (Streppenosa, Noto, and Sciacca Formations) within the Gela-1 well. ASPH (insoluble in n-alkane) and maltene (MALT, soluble in n-alkane) fractions of oil were separated using n-pentane, n-hexane, n-heptane and n-decane solvents. The ASPH contents of the Sciacca and Noto oils (26-33 wt%) are notably higher compared to the Streppenosa oil (7-12 wt% ASPH). We present an optimized Re-Os procedure with sample digestion in a high-pressure asher, followed by isotopic measurements using negative thermal ionization mass spectrometry. Very high metal contents of Gela oils allowed acquisition of precise Re-Os data. Systematic variations between the type of solvent used for ASPH precipitation and the ASPH content of the oil (also known from the literature) and the Re-Os contents of the ASPH and MALT fractions (first observed in this study) provide important practical applications for Re-Os analyses of oil. Most Re and Os (∼96-98%) in the Noto oil are hosted in the ASPH fraction. In contrast, a significant portion of Re and Os (∼33-34%) is stored in the MALT fraction of the lighter, but heavily biodegraded Streppenosa oil. Collectively, our new data on alkane distribution, hopane and sterane biomarkers, major and trace element contents, and Re-Os concentrations and isotopic ratios of the oils and their fractions support the presence of two oil families. Streppenosa oil, a heavily biodegraded oil generated at an early stage of thermal maturation from a shaly source rock, is clearly distinct from the Noto and Sciacca oils, both generated at peak maturation from a carbonate source rock with no subsequent biodegradation. Two Re-Os ages were obtained. Crude oil and ASPH from Noto and Sciacca oil yield a Model 1 isochron age of 27.5 ± 4.6 Ma with an initial 187Os/188Os of 3.89 ± 0.43 (MSWD = 1.6, n = 19). We interpret this Oligocene age as the time of initial oil generation, that was probably related to the onset of regional collisional tectonics in southern Sicily. ASPH and crude oil from the Streppenosa oil yield scattered data, perhaps related to effects of biodegradation. Streppenosa MALT yield a Model 1 age of 200.0 ± 5.2 Ma and initial 187Os/188Os of 1.39 ± 0.11 (MSWD = 0.52; n = 4). This age and initial Os-isotopic composition are consistent with rapid oil generation shortly after Late Triassic source-rock formation, perhaps driven by magmatic-related heating. Here we document a potentially powerful geochronological tool that can be applied to single samples of crude oil. Within each oil, the 187Os/188Os and most of the 187Re/188Os ratios in the MALT fractions are lower than in the corresponding ASPH fractions. Crude oils, being physical mixtures of ASPH and MALT, have intermediate Re-Os isotopic ratios. Hence, the needed spread in data points for a Re-Os isochron is obtained by analyzing components of a single crude oil. This approach eliminates pitfalls in interpretation of Re-Os data from multiple oils with possibly different generation, migration, or reservoir modification history.

The Os-AKT1 Channel Is Critical for K+ Uptake in Rice Roots and Is Modulated by the Rice CBL1-CIPK23 Complex[W][OPEN

PubMed Central

Li, Juan; Long, Yu; Qi, Guo-Ning; Li, Juan; Xu, Zi-Jian; Wu, Wei-Hua; Wang, Yi

2014-01-01

Potassium (K+) is one of the essential nutrient elements for plant growth and development. Plants absorb K+ ions from the environment via root cell K+ channels and/or transporters. In this study, the Shaker K+ channel Os-AKT1 was characterized for its function in K+ uptake in rice (Oryza sativa) roots, and its regulation by Os-CBL1 (Calcineurin B-Like protein1) and Os-CIPK23 (CBL-Interacting Protein Kinase23) was investigated. As an inward K+ channel, Os-AKT1 could carry out K+ uptake and rescue the low-K+-sensitive phenotype of Arabidopsis thaliana akt1 mutant plants. Rice Os-akt1 mutant plants showed decreased K+ uptake and displayed an obvious low-K+-sensitive phenotype. Disruption of Os-AKT1 significantly reduced the K+ content, which resulted in inhibition of plant growth and development. Similar to the AKT1 regulation in Arabidopsis, Os-CBL1 and Os-CIPK23 were identified as the upstream regulators of Os-AKT1 in rice. The Os-CBL1-Os-CIPK23 complex could enhance Os-AKT1-mediated K+ uptake. A phenotype test confirmed that Os-CIPK23 RNAi lines exhibited similar K+-deficient symptoms as the Os-akt1 mutant under low K+ conditions. These findings demonstrate that Os-AKT1-mediated K+ uptake in rice roots is modulated by the Os-CBL1-Os-CIPK23 complex. PMID:25096783

Re-Os isotopic evidence for an enriched-mantle source for the Noril'sk-type, ore-bearing intrusions, Siberia

USGS Publications Warehouse

Walker, R.J.; Morgan, J.W.; Horan, M.F.; Czamanske, G.K.; Krogstad, E.J.; Fedorenko, V.A.; Kunilov, V.E.

1994-01-01

Magmatic Cu-Ni sulfide ores and spatially associated ultramafic and mafic rocks from the Noril'sk I, Talnakh, and Kharaelakh intrusions are examined for Re-Os isotopic systematics. Neodymium and lead isotopic data also are reported for the ultramafic and mafic rocks. The Re-Os data for most samples indicate closed-system behavior since the ca. 250 Ma igneous crystallization age of the intrusions. There are small but significant differences in the initial osmium isotopic compositions of samples from the three intrusions. Ores from the Noril'sk I intrusion have ??Os values that vary from +0.4 to +8.8, but average +5.8. Ores from the Talnakh intrusion have ??Os values that range from +6.7 to +8.2, averaging +7.7. Ores from the Kharaelakh intrusion have ??Os values that range from +7.8 to +12.9, with an average value of +10.4. The osmium isotopic compositions of the ore samples from the Main Kharaelakh orebody exhibit minimal overlap with those for the Noril'sk I and Talnakh intrusions, indicating that these Kharaelakh ores were derived from a more radiogenic source of osmium than the other ores. Combined osmium and lead data for major orebodies in the three intrusions plot in three distinct fields, indicating derivation of osmium and lead from at least three isotopically distinct sources. Some of the variation in lead isotopic compositions may be the result of minor lower-crustal contamination. However, in contrast to most other isotopic and trace element data, Os-Pb variations are generally inconsistent with significant crustal contamination or interaction with the subcontinental lithosphere. Thus, the osmium and lead isotopic compositions of these intrusions probably reflect quite closely the compositions of their mantle source, and suggest that these two isotope systems were insensitive to lithospheric interaction. Ultramafic and mafic rocks have osmium and lead isotopic compositions that range only slightly beyond the compositions of the ores. These rocks also have relatively uniform ??{lunate}Nd values that range only from -0.8 to + 1.1. This limited variation in neodymium isotopic composition may reflect the characteristics of the mantle sources of the rocks, or it may indicate that somehow similar proportions of crust contaminated the parental melts. The osmium, lead, and neodymium isotopic data for these rocks most closely resemble the mantle sources of certain ocean island basalts (OIB), such as some Hawaiian basalts. Hence, these data are consistent with derivation of primary melts from a mantle source similar to that of some types of hotspot activity. The long-term Re/Os enrichment of this and similar mantle sources, relative to chondritic upper mantle, may reflect 1. (1) incorporation of recycled oceanic crust into the source more than 1 Ga ago, 2. (2) derivation from a mantle plume that originated at the outer core-lower mantle interface, or 3. (3) persistence of primordial stratification of rhenium and osmium in the mantle. ?? 1994.

Earth science big data at users' fingertips: the EarthServer Science Gateway Mobile

NASA Astrophysics Data System (ADS)

Barbera, Roberto; Bruno, Riccardo; Calanducci, Antonio; Fargetta, Marco; Pappalardo, Marco; Rundo, Francesco

2014-05-01

The EarthServer project (www.earthserver.eu), funded by the European Commission under its Seventh Framework Program, aims at establishing open access and ad-hoc analytics on extreme-size Earth Science data, based on and extending leading-edge Array Database technology. The core idea is to use database query languages as client/server interface to achieve barrier-free "mix & match" access to multi-source, any-size, multi-dimensional space-time data -- in short: "Big Earth Data Analytics" - based on the open standards of the Open Geospatial Consortium Web Coverage Processing Service (OGC WCPS) and the W3C XQuery. EarthServer combines both, thereby achieving a tight data/metadata integration. Further, the rasdaman Array Database System (www.rasdaman.com) is extended with further space-time coverage data types. On server side, highly effective optimizations - such as parallel and distributed query processing - ensure scalability to Exabyte volumes. In this contribution we will report on the EarthServer Science Gateway Mobile, an app for both iOS and Android-based devices that allows users to seamlessly access some of the EarthServer applications using SAML-based federated authentication and fine-grained authorisation mechanisms.

Factors associated with the effect of open splenectomy for immune thrombocytopenic purpura.

PubMed

Li, Ying; Zhang, Dawei; Hua, Fanli; Gao, Song; Wu, Yangjiong; Xu, Jianmin

2017-01-01

To assess the effect and complications of open splenectomy (OS) for immune thrombocytopenic purpura (ITP) and determine preoperative factors associated with surgical effect. This was a retrospective analysis of ITP patients who failed medical therapy and were treated with OS between 1997 and 2014 at the Jinshan Hospital, China. Follow-up was 60 months. Surgical effect was determined from platelet counts and bleeding episodes. Complications were assessed including bleeding episodes. Preoperative factors were identified by logistic regression analysis. Fifty-six patients (48.2 ± 16.2 yr old; 39 females) were included. Disease course was 31.2 ± 48.2 months; 91.1% patients had preoperative platelet count <20 × 10 9 /L. OS effect at 1 wk, 1 month, 1 yr, and 5 yrs was in 91.1%, 92.9%, 91.1%, and 89.3% patients, respectively. Pneumonia or lower extremity thrombosis occurred in 7.1% patients. Postoperative mild, moderate, and severe bleeding occurred in 33.9%, 50.0%, and 16.1% patients, respectively. No patients required blood transfusion. Mortality was zero. Larger spleen size associated with surgical effect at 1 wk, 1 month, and 1 yr, and lower preoperative minimum platelet count associated with effect at 5 yrs (P < 0.05). Open splenectomy is an effective treatment with less complications for the management of ITP. Lower preoperative minimum platelet count associated with successful OS at 5 yrs. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Major and Trace Element Geochemistry and Os Isotopic Compositions of Komatiites From Dundonald Beach, Abitibi Greenstone Belt, Canada

NASA Astrophysics Data System (ADS)

Gangopadhyay, A.; Walker, R. J.; Sproule, R. A.; Lesher, C.

2003-12-01

We have examined the major and trace elements, and Os isotopic compositions of a suite of cumulate and spinifex textured komatiitic rocks from the Dundonald Beach area, part of the ˜2.7 Ga Abitibi greenstone Belt, Ontario, Canada. This suite of rocks forms a series from peridotitic komatiites (MgO ˜ 42 wt.% on a volatile-free basis) to komatiitic basalts (MgO ˜8 wt.%). Based on major element oxide ratios (e.g. Al2O3/TiO2 ˜21-26 and CaO/Al2O3 typically <= 1) and unfractionated HREE characteristics (e.g. (Gd/Yb)N ˜0.9-1.1), these rocks are similar to the spatially associated Al-undepleted komatiites from Alexo and Munro Townships. Also, these rocks are strongly LREE-depleted ((La/Sm)N = 0.41-0.67; (Ce/Yb)N = 0.41-0.70)) and have variable total REE (4-22 ppm). A strong negative correlation between Mg# and total REEs suggests that the REE patterns of these rocks are primary features of their mantle source. The Re-Os isotope results for whole-rock komatiites and chromite separates from a single flow yield a model 3 isochron age of 2606 +/- 55 Ma. This age is slightly younger ( ˜50 Ma) compared to the U-Pb zircon ages of the associated volcanics reported from the presumed extension of the same Kidd-Munro assemblage in Alexo and Munro Townships. The initial 187Os/188Os ratio (0.1090 +/- 0.0019) obtained from the regression is essentially chondritic (γ Os(T) = -0.2 +/- 1.7). The peridotitic komatiites have the highest Os concentrations and low 187Re/188Os ratios (up to ˜4.2 ppb and < 0.5, respectively) among the whole rocks, whereas the komatiitic basalts have relatively low Os concentrations ( ˜0.3 ppb) and high 187Re/188Os ratios ( ˜3.1-11.9). For these komatiites, Os was compatible with the mantle residue (DOsmantle-melt ˜7.6), whereas Re was moderately incompatible (DRe ˜0.6), typical of most komatiitic magmas. The absence of a strong correlation between Os and Ni concentrations in the whole-rocks suggests that the distribution of Os in these rocks is not primarily controlled by fractionation of olivine. The apparent DReol+chmt/liq. ( ˜0.7), on the other hand, suggests that Re was moderately incompatible in olivine and/or chromite during the differentiation of komatiitic magmas. A chondritic initial Os isotopic composition for the mantle source for these komatiites is consistent with that previously reported for the komatiites from Alexo and Munro Townships. Our Os isotopic results for Dundonald komatiites, combined with those reported for Alexo and Pyke Hill komatiites, therefore, suggest that a major portion of the ˜2.7 Ga mantle source for the komatiites in the Abitibi greenstone belt was dominated by Os with chondritic isotopic compositions. Also, the LREE-depleted, yet chondritic Os isotopic composition for the mantle source of these komatiites is indistinguishable from the projected chondritic composition of the contemporaneous depleted convective upper mantle.

Temporal record of osmium concentrations and 187Os/188Os in organic-rich mudrocks: Implications for the osmium geochemical cycle and the use of osmium as a paleoceanographic tracer

NASA Astrophysics Data System (ADS)

Lu, Xinze; Kendall, Brian; Stein, Holly J.; Hannah, Judith L.

2017-11-01

We present a compilation of 192Os concentrations (representing non-radiogenic Os) and initial 187Os/188Os isotope ratios from organic-rich mudrocks (ORM) to explore the evolution of the Os geochemical cycle during the past three billion years. The initial 187Os/188Os isotope ratio of a Re-Os isochron regression for ORM constrains the local paleo-seawater 187Os/188Os, which is governed by the relative magnitudes of radiogenic Os (old continental crust) and unradiogenic Os (mantle, extraterrestrial, and juvenile/mafic/ultramafic crust) fluxes to seawater. A first-order increase in seawater 187Os/188Os ratios occurs from the Archean to the Phanerozoic, and may reflect a combination of increasing atmosphere-ocean oxygenation and weathering of progressively more radiogenic continental crust due to in-growth of 187Os from radioactive decay of 187Re. Superimposed on this long-term trend are shorter-term fluctuations in seawater 187Os/188Os ratios as a result of climate change, emplacement of large igneous provinces, bolide impacts, tectonic events, changes in seafloor spreading rates, and lithological changes in crustal terranes proximal to sites of ORM deposition. Ediacaran-Phanerozoic ORM have mildly higher 192Os concentrations overall compared with pre-Ediacaran Proterozoic ORM based on the mean and 95% confidence interval of 10,000 median values derived using a bootstrap analysis for each time bin (insufficient Archean data exist for robust statistical comparisons). However, there are two groups with anomalously high 192Os concentrations that are distinguished by their initial 187Os/188Os isotope ratios. Ediacaran-Cambrian ORM from South China have radiogenic initial 187Os/188Os, suggesting their high 192Os concentrations reflect proximal Os-rich crustal source(s), ultraslow sedimentation rates, and/or other unusual depositional conditions. In contrast, the unradiogenic initial 187Os/188Os and high 192Os concentrations of some Mesozoic ORM can be tied to emplacement of large igneous provinces. Excluding these two anomalous groups and repeating the bootstrap analysis, we find that, overall, the 192Os concentrations for the Ediacaran-Phanerozoic and pre-Ediacaran Proterozoic time bins are not significantly different. An improved understanding of Os geochemical behavior in modern environments is required before our compilation can be fully used to constrain the temporal evolution of the seawater Os reservoir.

Re-Os systematics of early proterozoic ferropicrites, Pechenga Complex, northwestern Russia: Evidence for ancient 187Os-enriched plumes

NASA Astrophysics Data System (ADS)

Walker, Richard J.; Morgan, John W.; Hanski, Eero J.; Smolkin, Valery F.

1997-08-01

The Re-Os isotopic systematics of various ferropicritic flows and sills of the Pechenga Complex, Russia, have been examined. During crystallization about 1.98 Ga ago, many of these bodies became highly differentiated. In addition, some of the larger igneous units are associated with major NiCu ore deposits. The melts that produced these rocks have been termed ferropicritic because of their high FeO and MgO contents. They are also enriched in light rare earth elements (LREEs), TiO 2, Zr, and many other incompatible trace elements. Previous studies have concluded that the ferropicrites were most likely derived from an Fe-rich mantle plume that had a complex history of long-term LREE depletion (initial ɛNd = + 1.4), but that also experienced a LREE enrichment event within 200 Ma of the generation of the rocks. Whole rock samples believed to be most representative of primary melt compositions indicate that initial melt concentrations of rhenium and osmium were approximately 1.1 ppb and 0.5 ppb, respectively. The high primary melt concentrations presumably made the osmium contained in the melts relatively immune to the effects of crustal contamination. Nonetheless, all ore-bearing intrusions examined show osmium isotopic evidence for crustal contamination. For example, the initial γOs for some primary magmatic sulfides from the Pilgujärvi intrusion average +46. Other ore-bearing intrusions, such as the Kammikivi sill, appear to have been similarly contaminated by crustal osmium during the injection of magma, with initial yo, values as high as +251. The seemingly high levels of crustal osmium may be attributed to the rapidly diminishing concentrations of osmium in the melts as the larger bodies differentiated, combined with localized in situ assimilation of the metasedimentary rocks that comprise the country rocks. The Re-Os systematics of some whole rock samples of both mineralized and sulfide-poor intrusions were affected by post-magmatic events, especially the greenschist grade metamorphism that impacted the rocks between about 1.7 and 1.8 Ga ago. The metamorphic effects are reflected in the recrystallization of many of the primary sulfides. As a consequence of this open-system behavior in many whole rock samples, the primary igneous Re-Os systematics of these rocks are best examined via analysis of magmatic phases such as chromite, olivine, clinopyroxene, and primary sulfides. Chromite and ilmenite+sulfide separates from two sulfide-poor lava flows, the Lammas and Keskitunturi, have characteristically low 187Re/ 188Os ( < l), and because of the limited age correction, precisely define the initial γOs of these systems to be +6.0±0.7. Because of the identical initial compositions of the two, spatially distinct lava flows, and the fact that these flows were extruded onto only slightly older volcanic rocks, we conclude that the +6.0 value reflects the composition of the mantle source and not minor crustal contamination. Although 187Os-enriched, plume-derived systems are common during the Phanerozoic, this is the earliest known evidence for the existence of long-term, Re-enriched mantle reservoirs. The most commonly invoked model to explain 187Os enrichments in Phanerozoic systems, oceanic crustal recycling, in this instance requires that very large proportions of oceanic crust were recycled into the mantle source and that the event was likely very ancient. Other options, such as core-mantle interaction and a stratified mantle, are also discussed.

InDEx: Open Source iOS and Android Software for Self-Reporting and Monitoring of Alcohol Consumption.

PubMed

Leightley, Daniel; Puddephatt, Jo-Anne; Goodwin, Laura; Rona, Roberto; Fear, Nicola T

2018-03-23

InDEx is a software package for reporting and monitoring alcohol consumption via a smartphone application. Consumption of alcohol is self-reported by the user, and the app provides a visual representation of drinking behaviour and offers feedback on consumption levels compared to the general population. InDEx is intended as an exemplar app, operating as a standalone smartphone application and is highly customisable for a variety of research domains. InDEx is written in JavaScript, using IONIC framework which is cross-platform and is available under the liberal GNU General Public License (v3). The software is available from GitHub (https://github.com/DrDanL/index-app-public).

InDEx: Open Source iOS and Android Software for Self-Reporting and Monitoring of Alcohol Consumption

PubMed Central

Leightley, Daniel; Puddephatt, Jo-Anne; Goodwin, Laura; Rona, Roberto; Fear, Nicola T.

2018-01-01

InDEx is a software package for reporting and monitoring alcohol consumption via a smartphone application. Consumption of alcohol is self-reported by the user, and the app provides a visual representation of drinking behaviour and offers feedback on consumption levels compared to the general population. InDEx is intended as an exemplar app, operating as a standalone smartphone application and is highly customisable for a variety of research domains. InDEx is written in JavaScript, using IONIC framework which is cross-platform and is available under the liberal GNU General Public License (v3). The software is available from GitHub (https://github.com/DrDanL/index-app-public). PMID:29795769

Harness That S.O.B.: Distributing Remote Sensing Analysis in a Small Office/Business

NASA Astrophysics Data System (ADS)

Kramer, J.; Combe, J.; McCord, T. B.

2009-12-01

Researchers in a small office/business (SOB) operate with limited funding, equipment, and software availability. To mitigate these issues, we developed a distributed computing framework that: 1) leverages open source software to implement functionality otherwise reliant on proprietary software and 2) harnesses the unused power of (semi-)idle office computers with mixed operating systems (OSes). This abstract outlines some reasons for the effort, its conceptual basis and implementation, and provides brief speedup results. The Multiple-Endmember Linear Spectral Unmixing Model (MELSUM)1 processes remote-sensing (hyper-)spectral images. The algorithm is computationally expensive, sometimes taking a full week or more for a 1 million pixel/100 wavelength image. Analysis of pixels is independent, so a large benefit can be gained from parallel processing techniques. Job concurrency is limited by the number of active processing units. MELSUM was originally written in the Interactive Data Language (IDL). Despite its multi-threading capabilities, an IDL instance executes on a single machine, and so concurrency is limited by the machine's number of central processing units (CPUs). Network distribution can access more CPUs to provide a greater speedup, while also taking advantage of (often) underutilized extant equipment. appropriately integrating open source software magnifies the impact by avoiding the purchase of additional licenses. Our method of distribution breaks into four conceptual parts: 1) the top- or task-level user interface; 2) a mid-level program that manages hosts and jobs, called the distribution server; 3) a low-level executable for individual pixel calculations; and 4) a control program to synchronize sequential sub-tasks. Each part is a separate OS process, passing information via shell commands and/or temporary files. While the control and low-level executables are short-lived, the top-level program and distribution server run (at least) for the entirety of a task. While any language that supports "spawning" of OS processes can serve as the top-level interface, our solution, d-MELSUM, has been integrated with the IDL code. Doing so extracts the core calculating from IDL, but otherwise preserves IDL features and functionality. The distribution server is an extension of ADE2 mobile robot software, written in Java. Network connections rely on a secure shell (SSH) implementation, whether natively available (e.g., Linux or OS X) or user installed (e.g., OpenSSH available via Cygwin on Windows). Both the low-level and control programs are relatively small C++ programs (~54K, or 1500 lines, total) that were developed in-house, and use GNU's g++ compiler. The low-level code also relies on Linear Algebra PACKage (LAPACK) libraries for pixel calculations. Despite performance being contingent on data size, CPU speed, and network communication rate and latency to some degree, results have generally demonstrated a time reduction of a factor proportional to the number of open connections (one per CPU). For example, the task mentioned above requiring a week to process took 18 hours with d-MELSUM, using 10 CPUs on 2 computers. 1 J.-Ph Combe, et al., PSS 56, 2008. 2 J. Kramer and M. Scheutz, IROS2006, 2006.

Os, Nd and Sr isotope and trace element geochemistry of the Muli picrites: Insights into the mantle source of the Emeishan Large Igneous Province

NASA Astrophysics Data System (ADS)

Li, Jie; Xu, Ji-Feng; Suzuki, Katsuhiko; He, Bin; Xu, Yi-Gang; Ren, Zhong-Yuan

2010-09-01

A suite of picrites and basalts from the Muli area, in the northwestern part of the Emeishan continental flood basalt province, provides new and valuable information on the geochemistry of the Emeishan Large Igneous Province (LIP) and its source. The Muli picrites can be classified as type-1 or type-2. The former shows ocean-island basalt-like trace element characteristics, with γ Os (260 Ma) values and ɛ Nd (260 Ma) values ranging from + 7.5 to + 11.5 and from + 6.0 to + 7.8, respectively. This is the first time that picrites with highly radiogenic Os and high Os contents (up to 3.3 ppb) have been recognized in the Emeishan LIP. These characteristics probably reflect a relatively enriched component in the Emeishan LIP source. The type-2 picrites are characterized by non-radiogenic γ Os (260 Ma) values ranging from - 4.2 to - 0.3, and they may be further subdivided into type-2A and type-2B picrites. Type-2A picrites contain moderate amounts of the light rare earth elements (LREEs), have low Ce N/Yb N values (1.1-2.0), and a relatively high initial ɛ Nd (+ 5.0 to + 6.6). In terms of Os and Nd isotopes, the Muli type-2A picrites are similar to the Song Da komatiites of Vietnam and the Gorgona Island picrites, revealing the existence of a depleted mantle component in the Emeishan LIP source. In contrast with the type-2A picrites, type-2B lavas exhibit a negative Nb anomaly and relatively lower initial ɛ Nd and γ Os values (Nb/La > 1.8; ɛ Nd (260 Ma) = - 5.5 to + 6.4; γ Os (260 Ma) = - 4.2 to - 1.9), suggesting that the type-2B lavas have a depleted mantle source, similar to type-2A, but that the type-2B lavas are also influenced by various degrees of mixing of depleted plume-derived melt, sub-continental lithospheric mantle, and/or continental crust. Given that the basalts in the Muli area show similar geochemical features to those of the type-2B picrites, their origins are inferred to be similar.

Rhenium-osmium isotopes and highly siderophile elements in ultramafic rocks from the Eoarchean Saglek Block, northern Labrador, Canada: implications for Archean mantle evolution

NASA Astrophysics Data System (ADS)

Ishikawa, Akira; Suzuki, Katsuhiko; Collerson, Kenneth D.; Liu, Jingao; Pearson, D. Graham; Komiya, Tsuyoshi

2017-11-01

We determined highly siderophile element (HSE: Os, Ir, Ru, Pt, Pd, and Re) concentrations and 187Os/188Os ratios for ultramafic rocks distributed over the Eoarchean gneiss complex of the Saglek-Hebron area in northern Labrador, Canada in order to constrain to what extent variations in HSE abundances are recorded in Early Archean mantle that have well-resolved 182W isotope anomalies relative to the present-day mantle (∼+11 ppm: Liu et al., 2016). The samples analysed here have been previously classified into two suites: mantle-derived peridotites occurring as tectonically-emplaced slivers of lithospheric mantle, and metakomatiites comprising mostly pyroxenitic layers in supracrustal units dominated by amphibolites. Although previous Sm-Nd and Pb-Pb isotope studies provided whole-rock isochrons indicative of ∼3.8 Ga protolith formation for both suites, our whole-rock Re-Os isotope data on a similar set of samples yield considerably younger errorchrons with ages of 3612 ± 130 Ma (MSWD = 40) and 3096 ± 170 Ma (MSWD = 10.2) for the metakomatiite and lithospheric mantle suites, respectively. The respective initial 187Os/188Os = 0.10200 ± 18 for metakomatiites and 0.1041 ± 18 for lithospheric mantle rocks are within the range of chondrites. Re-depletion Os model ages for unradiogenic samples from the two suites are consistent with the respective Re-Os errorchrons (metakomatiite TRD = 3.4-3.6 Ga; lithospheric mantle TRD = 2.8-3.3 Ga). These observations suggest that the two ultramafic suites are not coeval. However, the estimated mantle sources for the two ultramafics suites are similar in terms of their broadly chondritic evolution of 187Os/188Os and their relative HSE patterns. In detail, both mantle sources show a small excess of Ru/Ir similar to that in modern primitive mantle, but a ∼20% deficit in absolute HSE abundances relative to that in modern primitive mantle (metakomatiite 74 ± 18% of PUM; lithospheric mantle 82 ± 10% of PUM), consistent with the ∼3.8 Ga Isua mantle source and Neoarchean komatiite sources around the world (∼70-86% of PUM). This demonstrates that the lower HSE abundances are not unique to the sources of komatiites, but rather might be a ubiquitous feature of Archean convecting mantle. This tentatively suggests that chondritic late accretion components boosted the convecting mantle HSE inventory after core separation in the Hadean, and that the Eoarchean to Neoarchean convecting mantle was depleted in its HSE content relative to that of today. Further investigation of Archean mantle-derived rocks is required to explore this hypothesis.

Loss of LOFSEP Transcription Factor Function Converts Spikelet to Leaf-Like Structures in Rice1[OPEN

PubMed Central

Zhu, Wanwan

2018-01-01

SEPALLATA (SEP)-like genes, which encode a subfamily of MADS-box transcription factors, are essential for specifying floral organ and meristem identity in angiosperms. Rice (Oryza sativa) has five SEP-like genes with partial redundancy and overlapping expression domains, yet their functions and evolutionary conservation are only partially known. Here, we describe the biological role of one of the SEP genes of rice, OsMADS5, in redundantly controlling spikelet morphogenesis. OsMADS5 belongs to the conserved LOFSEP subgroup along with OsMADS1 and OsMADS34. OsMADS5 was expressed strongly across a broad range of reproductive stages and tissues. No obvious phenotype was observed in the osmads5 single mutants when compared with the wild type, which was largely due to the functional redundancy among the three LOFSEP genes. Genetic and molecular analyses demonstrated that OsMADS1, OsMADS5, and OsMADS34 together regulate floral meristem determinacy and specify the identities of spikelet organs by positively regulating the other MADS-box floral homeotic genes. Experiments conducted in yeast also suggested that OsMADS1, OsMADS5, and OsMADS34 form protein-protein interactions with other MADS-box floral homeotic members, which seems to be a typical, conserved feature of plant SEP proteins. PMID:29217592

Economic impact of switching from an open to a closed enteral nutrition feeding system in an acute care setting.

PubMed

Phillips, Wendy; Roman, Brandis; Glassman, Kendra

2013-08-01

This study compared an open-system (OS) enteral nutrition (EN) delivery system with a closed system (CS). Factors evaluated included nursing time for administration, patient safety factors, and cost of formula and supplies. This study analyzed the cost of formula and supplies in 1 major academic medical center. Data were collected on patients requiring EN in acute care settings. Information collected included formula type and amount of formula ordered and delivered. The average daily cost to feed each adult patient using delivered volume with the OS was $3.84 compared with $4.31 if the patient had been receiving EN from a CS. Considering waste costs, the average cost to feed increased to $4.21 compared with $4.80, respectively. After factoring in increased nursing time with the OS, the cost increased to $9.83. For pediatric patients, formula delivery reached 1 L in only 2% of patient days. The average cost to feed each patient each day using actual delivered volume was $1.89 in the OS and $1.94 in the CS. When factoring in the cost of waste, those costs increased to $2.12 and $3.30, respectively. After factoring in increased nursing time with the OS, the cost increased to $8.92. Due to the higher contract price and increased waste of the CS formulas compared with the OS formulas, a higher daily average cost for formula delivered may be incurred by switching to a CS. However, the CS is more cost-effective when factoring in nursing time.

Rhenium-osmium isotope and highly-siderophile-element abundance systematics of angrite meteorites

NASA Astrophysics Data System (ADS)

Riches, Amy J. V.; Day, James M. D.; Walker, Richard J.; Simonetti, Antonio; Liu, Yang; Neal, Clive R.; Taylor, Lawrence A.

2012-11-01

Coupled 187Os/188Os compositions and highly-siderophile-element (HSE: Os, Ir, Ru, Pt, Pd, and Re) abundance data are reported for eight angrite achondrite meteorites that include quenched- and slowly-cooled textural types. These data are combined with new major- and trace-element concentrations determined for bulk-rock powder fractions and constituent mineral phases, to assess angrite petrogenesis. Angrite meteorites span a wide-range of HSE abundances from <0.005 ppb Os (e.g., Northwest Africa [NWA] 1296; Angra dos Reis) to >100 ppb Os (NWA 4931). Chondritic to supra-chondritic 187Os/188Os (0.1201-0.2127) measured for Angra dos Reis and quenched-angrites correspond to inter- and intra-sample heterogeneities in Re/Os and HSE abundances. Quenched-angrites have chondritic-relative rare-earth-element (REE) abundances at 10-15×CI-chondrite, and their Os-isotope and HSE abundance variations represent mixtures of pristine uncontaminated crustal materials that experienced addition (<0.8%) of exogenous chondritic materials during or after crystallization. Slowly-cooled angrites (NWA 4590 and NWA 4801) have fractionated REE-patterns, chondritic to sub-chondritic 187Os/188Os (0.1056-0.1195), as well as low-Re/Os (0.03-0.13), Pd/Os (0.071-0.946), and relatively low-Pt/Os (0.792-2.640). Sub-chondritic 187Os/188Os compositions in NWA 4590 and NWA 4801 are unusual amongst planetary basalts, and their HSE and REE characteristics may be linked to melting of mantle sources that witnessed prior basaltic melt depletion. Angrite HSE-Yb systematics suggest that the HSE behaved moderately-incompatibly during angrite magma crystallization, implying the presence of metal in the crystallizing assemblage. The new HSE abundance and 187Os/188Os compositions indicate that the silicate mantle of the angrite parent body(ies) (APB) had HSE abundances in chondritic-relative proportions but at variable abundances at the time of angrite crystallization. The HSE systematics of angrites are consistent with protracted post-core formation accretion of materials with chondritic-relative abundances of HSE to the APB, and these accreted materials were rapidly, yet inefficiently, mixed into angrite magma source regions early in Solar System history.

A new synthesis route for Os-complex modified redox polymers for potential biofuel cell applications.

PubMed

Pöller, Sascha; Beyl, Yvonne; Vivekananthan, Jeevanthi; Guschin, Dmitrii A; Schuhmann, Wolfgang

2012-10-01

A new synthesis route for Os-complex modified redox polymers was developed. Instead of ligand exchange reactions for coordinative binding of suitable precursor Os-complexes at the polymer, Os-complexes already exhibiting the final ligand shell containing a suitable functional group were bound to the polymer via an epoxide opening reaction. By separation of the polymer synthesis from the ligand exchange reaction at the Os-complex, the modification of the same polymer backbone with different Os-complexes or the binding of the same Os-complex to a number of different polymer backbones becomes feasible. In addition, the Os-complex can be purified and characterized prior to its binding to the polymer. In order to further understand and optimize suitable enzyme/redox polymer systems concerning their potential application in biosensors or biofuel cells, a series of redox polymers was synthesized and used as immobilization matrix for Trametes hirsuta laccase. The properties of the obtained biofuel cell cathodes were compared with similar biocatalytic interfaces derived from redox polymers obtained via ligand exchange reaction of the parent Os-complex with a ligand integrated into the polymer backbone during the polymer synthesis. Copyright © 2011 Elsevier B.V. All rights reserved.

Tungsten isotope evidence that mantle plumes contain no contribution from the Earth's core

NASA Astrophysics Data System (ADS)

Scherstén, Anders; Elliott, Tim; Hawkesworth, Chris; Norman, Marc

2004-01-01

Osmium isotope ratios provide important constraints on the sources of ocean-island basalts, but two very different models have been put forward to explain such data. One model interprets 187Os-enrichments in terms of a component of recycled oceanic crust within the source material. The other model infers that interaction of the mantle with the Earth's outer core produces the isotope anomalies and, as a result of coupled 186Os-187Os anomalies, put time constraints on inner-core formation. Like osmium, tungsten is a siderophile (`iron-loving') element that preferentially partitioned into the Earth's core during core formation but is also `incompatible' during mantle melting (it preferentially enters the melt phase), which makes it further depleted in the mantle. Tungsten should therefore be a sensitive tracer of core contributions in the source of mantle melts. Here we present high-precision tungsten isotope data from the same set of Hawaiian rocks used to establish the previously interpreted 186Os-187Os anomalies and on selected South African rocks, which have also been proposed to contain a core contribution. None of the samples that we have analysed have a negative tungsten isotope value, as predicted from the core-contribution model. This rules out a simple core-mantle mixing scenario and suggests that the radiogenic osmium in ocean-island basalts can better be explained by the source of such basalts containing a component of recycled crust.

Fast and accurate resonance assignment of small-to-large proteins by combining automated and manual approaches.

PubMed

Niklasson, Markus; Ahlner, Alexandra; Andresen, Cecilia; Marsh, Joseph A; Lundström, Patrik

2015-01-01

The process of resonance assignment is fundamental to most NMR studies of protein structure and dynamics. Unfortunately, the manual assignment of residues is tedious and time-consuming, and can represent a significant bottleneck for further characterization. Furthermore, while automated approaches have been developed, they are often limited in their accuracy, particularly for larger proteins. Here, we address this by introducing the software COMPASS, which, by combining automated resonance assignment with manual intervention, is able to achieve accuracy approaching that from manual assignments at greatly accelerated speeds. Moreover, by including the option to compensate for isotope shift effects in deuterated proteins, COMPASS is far more accurate for larger proteins than existing automated methods. COMPASS is an open-source project licensed under GNU General Public License and is available for download from http://www.liu.se/forskning/foass/tidigare-foass/patrik-lundstrom/software?l=en. Source code and binaries for Linux, Mac OS X and Microsoft Windows are available.

Fast and Accurate Resonance Assignment of Small-to-Large Proteins by Combining Automated and Manual Approaches

PubMed Central

Niklasson, Markus; Ahlner, Alexandra; Andresen, Cecilia; Marsh, Joseph A.; Lundström, Patrik

2015-01-01

The process of resonance assignment is fundamental to most NMR studies of protein structure and dynamics. Unfortunately, the manual assignment of residues is tedious and time-consuming, and can represent a significant bottleneck for further characterization. Furthermore, while automated approaches have been developed, they are often limited in their accuracy, particularly for larger proteins. Here, we address this by introducing the software COMPASS, which, by combining automated resonance assignment with manual intervention, is able to achieve accuracy approaching that from manual assignments at greatly accelerated speeds. Moreover, by including the option to compensate for isotope shift effects in deuterated proteins, COMPASS is far more accurate for larger proteins than existing automated methods. COMPASS is an open-source project licensed under GNU General Public License and is available for download from http://www.liu.se/forskning/foass/tidigare-foass/patrik-lundstrom/software?l=en. Source code and binaries for Linux, Mac OS X and Microsoft Windows are available. PMID:25569628

Detection of Spoofed MAC Addresses in 802.11 Wireless Networks

NASA Astrophysics Data System (ADS)

Tao, Kai; Li, Jing; Sampalli, Srinivas

Medium Access Control (MAC) address spoofing is considered as an important first step in a hacker's attempt to launch a variety of attacks on 802.11 wireless networks. Unfortunately, MAC address spoofing is hard to detect. Most current spoofing detection systems mainly use the sequence number (SN) tracking technique, which has drawbacks. Firstly, it may lead to an increase in the number of false positives. Secondly, such techniques cannot be used in systems with wireless cards that do not follow standard 802.11 sequence number patterns. Thirdly, attackers can forge sequence numbers, thereby causing the attacks to go undetected. We present a new architecture called WISE GUARD (Wireless Security Guard) for detection of MAC address spoofing on 802.11 wireless LANs. It integrates three detection techniques - SN tracking, Operating System (OS) fingerprinting & tracking and Received Signal Strength (RSS) fingerprinting & tracking. It also includes the fingerprinting of Access Point (AP) parameters as an extension to the OS fingerprinting for detection of AP address spoofing. We have implemented WISE GUARD on a test bed using off-the-shelf wireless devices and open source drivers. Experimental results show that the new design enhances the detection effectiveness and reduces the number of false positives in comparison with current approaches.

Resistant Starch Alters the Microbiota-Gut Brain Axis: Implications for Dietary Modulation of Behavior.

PubMed

Lyte, Mark; Chapel, Ashley; Lyte, Joshua M; Ai, Yongfeng; Proctor, Alexandra; Jane, Jay-Lin; Phillips, Gregory J

2016-01-01

The increasing recognition that the gut microbiota plays a central role in behavior and cognition suggests that the manipulation of microbial taxa through diet may provide a means by which behavior may be altered in a reproducible and consistent manner in order to achieve a beneficial outcome for the host. Resistant starch continues to receive attention as a dietary intervention that can benefit the host through mechanisms that include altering the intestinal microbiota. Given the interest in dietary approaches to improve health, the aim of this study was to investigate whether the use of dietary resistant starch in mice to alter the gut microbiota also results in a change in behavior. Forty-eight 6 week-old male Swiss-Webster mice were randomly assigned to 3 treatment groups (n = 16 per group) and fed either a normal corn starch diet (NCS) or diets rich in resistant starches HA7 diet (HA7) or octenyl-succinate HA7 diet (OS-HA7) for 6 week and monitored for weight, behavior and fecal microbiota composition. Animals fed an HA7 diet displayed comparable weight gain over the feeding period to that recorded for NCS-fed animals while OS-HA7 displayed a lower weight gain as compared to either NCS or HA7 animals (ANOVA p = 0.0001; NCS:HA7 p = 0.244; HA7:OS-HA7 p<0.0001; NCS:OS-HA7 p<0.0001). Analysis of fecal microbiota using 16s rRNA gene taxonomic profiling revealed that each diet corresponded with a unique gut microbiota. The distribution of taxonomic classes was dynamic over the 6 week feeding period for each of the diets. At the end of the feeding periods, the distribution of taxa included statistically significant increases in members of the phylum Proteobacteria in OS-HA7 fed mice, while the Verrucomicrobia increased in HA7 fed mice over that of mice fed OS-HA7. At the class level, members of the class Bacilli decreased in the OS-HA7 fed group, and Actinobacteria, which includes the genus Bifidobacteria, was enriched in the HA7 fed group compared to the control diet. Behavioral analysis revealed that animals demonstrated profound anxiety-like behavior as observed by performance on the elevated-plus maze with time spent by the mice in the open arm (ANOVA p = 0.000; NCS:HA7 p = 0.004; NCS:OS-HA7 p = 1.000; HA7:OS-HA7 p = 0.0001) as well as entries in the open arm (ANOVA p = 0.039; NCS:HA7 p = 0.041; HA7:OS-HA7 p = 0.221; NCS:OS-HA7 p = 1.000). Open-field behavior, a measure of general locomotion and exploration, revealed statistically significant differences between groups in locomotion as a measure of transitions across quadrant boundaries. Additionally, the open-field assay revealed decreased exploration as well as decreased rearing in HA7 and OS-HA7 fed mice demonstrating a consistent pattern of increased anxiety-like behavior among these groups. Critically, behavior was not correlated with weight. These results indicate that diets based on resistant starch can be utilized to produce quantifiable changes in the gut microbiota and should be useful to "dial-in" a specific microbiome that is unique to a particular starch composition. However, undesirable effects can also be associated with resistant starch, including lack of weight gain and increased anxiety-like behaviors. These observations warrant careful consideration when developing diets rich in resistant starch in humans and animal models.

Ubiquitous radiogenic Os in Miocene to recent basalts from diverse mantle domains beneath the Colorado Plateau, USA

NASA Astrophysics Data System (ADS)

Schlieder, T.; Reid, M. R.; Widom, E.; Blichert-Toft, J.

2015-12-01

The source of magmatism and mechanisms responsible for the observed geochemical signatures in Miocene to Recent Colorado Plateau (CP) basalts has been a renewed focus of investigation in light of Earthscope results. We report new Os and Nd isotopic data for magnesian basalts (Mg#=62-72) and interpret them in light of previously reported Hf isotope data to help constrain contributions from olivine-poor source lithologies and subduction-derived metasomatism in the genesis of recent CP volcanism. The basalts studied span a large range in Hf isotope compositions and represent melts last equilibrated at a variety of depths beneath the Colorado Plateau and its transition zones. We distinguished at least three mantle domains on the basis of paired Hf-Nd isotope, other isotopic, and geochemical characteristics of CP lavas. Domain 1 likely represents a depleted, variably metasomatized, lithospheric source, with relatively radiogenic ɛHf (+5.2 to +11.8) and highly variable ɛNd (-6.2 to +6.2). Domain 2 could represent either ancient or Farallon subduction-modified mantle and is displaced above the Hf-Nd mantle array (ɛHf=+1.0 to +7.3; ɛNd=-6.1 to -3.5). Domain 3 may be melts of pyroxenite/mica-rich veins or layers within lithospheric mantle and is characterized by unradiogenic Hf and Nd (ɛHf=-12.9 to +0.6; ɛNd=-10.0 to -2.9). The isotopic variability in CP-related lavas can largely be attributed to contributions from these mantle domains. Preliminary Os isotope data show no correlation with proxies for differentiation or crustal contamination. Osmium and Hf isotope compositions are negatively correlated between domains 1 and 2 (187Os/188Os=0.31 to 0.59), whereas the Os isotope ratios in two domain 3 basalts have both lower and higher values (187Os/188Os=0.25 and 0.68). Significantly, Os isotope signatures are highly radiogenic (vs. values of <0.12 for SW US peridotite xenoliths [1]), overlapping and extending the range for inferred melts of pyroxene- and mica-rich veins and/or layers [2]. Thus mafic magmatism associated with the CP appears to ubiquitously tap sources at least locally modified by processes such as recycling of ancient oceanic crust, introduction of terrigenous sediments, or subduction-related metasomatism. [1] Lee et al., Nature, 2001. [2] Carlson and Nowell, G-Cubed, 2001.

Electronic structure and mechanical properties of osmium borides, carbides and nitrides from first principles

NASA Astrophysics Data System (ADS)

Liang, Yongcheng; Zhao, Jianzhi; Zhang, Bin

2008-06-01

The stabilities, mechanical properties and electronic structures of osmium boride (OsB), carbide (OsC) and nitride (OsN), in the tungsten carbide (WC), rocksalt (NaCl), cesium chloride (CsCl) and zinc blende (ZnS) structures respectively, are systematically predicted by calculations from first-principles. Only four phases, namely, OsB(WC), OsB(CsCl), OsC(WC), and OsC(ZnS), are mechanically stable, and none is a superhard compound, contrary to previous speculation. Most importantly, we find that the changing trends of bulk modulus and shear modulus are completely different for OsB, OsC and OsN in same hexagonal WC structure, which indicates that the underlying sources of hardness and incompressibility are fundamentally different: the former is determined by bonding nature while the latter is closely associated with valence electron density.

Re-Os, Sm-Nd, U-Pb, and stepwise lead leaching isotope systematics in shear-zone hosted gold mineralization: genetic tracing and age constraints of crustal hydrothermal activity

NASA Astrophysics Data System (ADS)

Frei, R.; Nägler, Th. F.; Schönberg, R.; Kramers, J. D.

1998-06-01

A combined Re-Os, Sm-Nd, U-Pb, and stepwise Pb leaching (PbSL) isotope study of hydrothermal (Mo-W)-bearing minerals and base metal sulfides from two adjacent shear zone hosted gold deposits (RAN, Kimberley) in the Harare-Shamva greenstone belt (Zimbabwe) constrain the timing of the mineralizing events to two periods. During an initial Late Archean event (2.60 Ga) a first molybdenite-scheelite bearing paragenesis was deposited in both shear zone systems, followed by a local reactivation of the shear systems during an Early Proterozoic (1.96 Ga) tectono-thermal overprint, during which base metal sulfides and most of the gold was (re-)deposited. While PbSL has revealed an open-system behavior of the U-Pb systematics in molybdenite and wolframite from the RAN mine, initial Archean Re-Os ages are still preserved implying that this system in these minerals was more resistant to the overprint. A similar retentivity could be shown for the Sm-Nd system in scheelite and powellite associated with the above ore minerals. Re-Os isotopic data from the Proterozoic mineralization in the Kimberley mine point to a recent gain of Re, most pronouncedly affecting Fe-rich sulfides such as pyrrhotite. A significant Re-loss in powellitic scheelite (an alteration phase of molybdenite-bearing scheelite), coupled with a marked loss of U in W-Mo ore minerals, complements the observation of a major Re uptake in Fe-sulfides during oxidizing conditions in a weathering environment. Pyrrhotite under these conditions behaves as an efficient Re-sink. Lead isotope signatures from PbSL residues of molybdenite, powellite, and quartz indicate a continental crustal source and/or contamination for the mineralizing fluid by interaction of the fluids with older sedimentary material as represented by the direct host country rocks. Our investigation reveals the potential of the Re-Os isotopic system applied to crustal hydrothermal ore minerals for genetic tracing and dating purposes. The simplified chemical separation of Re and Os from geological material used in this study, together with improvements of chemical yields, will enable high precision data to be collected rapidly on crustal material with low Os concentrations in the future.

Osmium uptake, distribution, and 187Os/188Os and 187Re/188Os compositions in Phaeophyceae macroalgae, Fucus vesiculosus: Implications for determining the 187Os/188Os composition of seawater

NASA Astrophysics Data System (ADS)

Racionero-Gómez, B.; Sproson, A. D.; Selby, D.; Gannoun, A.; Gröcke, D. R.; Greenwell, H. C.; Burton, K. W.

2017-02-01

The osmium isotopic composition (187Os/188Os) of seawater reflects the balance of input from mantle-, continental- and anthropogenic-derived sources. This study utilizes the Phaeophyceae, Fucus vesiculosus, to analyse its Os abundance and uptake, as well as to assess if macroalgae records the Os isotope composition of the seawater in which it lives. The data demonstrates that Os is not located in one specific biological structure within macroalgae, but is found throughout the organism. Osmium uptake was measured by culturing F. vesiculosus non-fertile tips with different concentrations of Os with a known 187Os/188Os composition (∼0.16), which is significantly different from the background isotopic composition of local seawater (∼0.94). The Os abundance of cultured non-fertile tips show a positive correlation to the concentration of the Os doped seawater. Moreover, the 187Os/188Os composition of the seaweed equalled that of the culture medium, strongly confirming the possible use of macroalgae as a biological proxy for the Os isotopic composition of the seawater.

The accretion rate of extraterrestrial 3He based on oceanic 230Th flux and the relation to Os isotope variation over the past 200,000 years in an Indian Ocean core

NASA Astrophysics Data System (ADS)

Marcantonio, Franco; Turekian, Karl K.; Higgins, Sean; Anderson, Robert F.; Stute, Martin; Schlosser, Peter

1999-07-01

In the eastern equatorial Indian Ocean, the flux of extraterrestrial 3He, a proxy of interplanetary dust particles (IDPs), has been relatively constant over the past 200 ka. The flux is equal to (1.1±0.4)×10 -12 cm 3 STP cm -2 ka -1, a value obtained using the xs 230Th profiling method. Variations in mass accumulation rates (MARs) derived assuming a constant extraterrestrial 3He flux have a 40-ka periodicity similar to that observed in the δ 18O-derived MARs. This frequency is similar to that of the Earth's obliquity. Measured 187Os/ 188Os ratios are less radiogenic than present-day seawater (0.49-0.98), reflecting the mixing of Os derived from extraterrestrial, terrigenous and hydrogenous sources. When coupled with He data measured on the same samples, Os isotope data yield important information about the terrigenous component supplied to the eastern equatorial Indian Ocean. The amount of Os in the sample derived from the extraterrestrial component can be deduced with the help of the helium systematics. Once corrected for the extraterrestrial component of Os, Os isotope signatures, in conjunction with the 4He concentrations, suggest a supply of terrigenous material from Indonesian ultramafic and Himalayan crustal sources that clearly varies through time.

Helium-oxygen-osmium isotopic and elemental constraints on the mantle sources of the Deccan Traps

NASA Astrophysics Data System (ADS)

Peters, Bradley J.; Day, James M. D.; Greenwood, Richard C.; Hilton, David R.; Gibson, Jennifer; Franchi, Ian A.

2017-11-01

The Deccan Traps, a 65 million-year-old continental flood basalt province located in western India, is the result of one of the largest short-lived magmatic events to have occurred on Earth. The nature and composition of its mantle source(s), however, have been difficult to resolve due to extensive assimilation of continental crust into the ascending Traps magmas. To circumvent this issue, using high-precision electron microprobe analysis, we have analyzed olivine grains from MgO-rich (up to 15.7 wt.%) lavas that likely erupted before substantial crustal assimilation occurred. We compare olivine, pyroxene and plagioclase mineral chemistry and He-O-Os isotope compositions with bulk rock major- and trace-element abundances and 187Os/188Os for both bulk-rocks and mineral separates. Helium isotope compositions for the olivine grains generally show strong influence from crustal assimilation (<3 RA), but one ankaramite from the Pavagadh volcanic complex has a 3He/4He ratio of 10.7 RA, which is slightly lower than the range of 3He/4He measured for present-day Réunion Island volcanism (∼12-14 RA). Olivine-dominated mineral separates span a more restricted range in 187Os/188Os (0.1267 to 0.1443) compared with their host lavas (0.1186 to 0.5010), with the separates reflecting a parental magma composition less affected by lithospheric or crustal interaction than for the bulk-rocks. Despite significant He-Os isotopic variations, Δ17O is relatively invariant (- 0.008 ± 0.014 ‰) and indistinguishable from the bulk mantle, consistent with high-3He/4He hotspots measured to-date. Compositions of olivine grains indicate the presence of up to 25% of a pyroxenite source for Deccan parental magmas, in good agreement with ∼20% predicted from isotopic data for the same samples. Modeled pyroxenite signatures are similar to geochemical signatures expected to arise due to other types of mantle differentiation or due to assimilation of continental crust; however, we show that crustal assimilation cannot account for all of the compositional features of the olivine. Weak correlations exist between a global compilation of Xpx (Deccan: 0.2-0.7) and 3He/4He, δ18O (Deccan olivine: 4.9-5.2‰) and 187Os/188Os. Robust relationships between these parameters may be precluded due to a lack of two-reservoir source mixing, instead involving multiple mantle domains with distinct compositions, or because Xpx may reflect both source features and crustal assimilation. Notwithstanding, geochemical similarities exist between Deccan Traps olivine (3He/4He = 10.7 RA; 187Os/188Osi = 0.1313 ± 45, 2σ) and Réunion igneous rocks (3He/4He = 12-14 RA; 187Os/188Osi = 0.1324 ± 14). These relationships imply that a characteristic geochemical 'fingerprint' may have persisted in the mantle plume that fed the Deccan Traps, since its inception at 65 Ma, to ongoing eruptions occurring on Réunion up to the present-day.

Osmium-Iridium Correlation and Osmium Isotopic Composition in Some Geological Boundaries and Meteorites

NASA Astrophysics Data System (ADS)

Liu, Y. Z.; Wang, J. X.; Mao, X. Y.; Chai, C. F.

1992-07-01

Since the pioneering study of Alvarez et al. on K/T boundary event, Ir has long been considered to be the main indicator of extraterrestrial materials in boundaries, while little work about Os and its isotopic composition have been done. In this work a sophisticated radiochemical separation procedure together with neutron activation analsis (NAA) method was established for the determination of Os in some geological boundaries (P epsilon/epsilon, K/T, D/C, O/S, P/T). Combined with our early work--determination of Ir abundances [1], the sources of boundary events were deciphered by using the Os/Ir ratios. Simultaneously ^184Os/^190Os ratios in K/T boundaries, as well as inclusions of Allende chondrite and acid-insoluble residues of iron meteorites (Nandan, Jianshi, Longchang) were determined to search for the Os isotopic composition anomalies resulted from the extrasolar components by RNAA. The results show that the Os abundances exhibit a positive correlation with the Ir abundances for overall K/T boundary samples, but only the Os/Ir ratios of K/T boundaries, with the average of 0.98 +- 0.55, are in excellent agreement with 1.01 of the solar system [2], Accordingly, it provides new evidence for an extraterrestrial source of the K/T event. The results of ^184Os/^190Os ratios, with uncertainties of less than 1%, indicate there is no remarkable ^184Os/^190Os ratio anomaly in the K/T boundary samples, which implies the impacting matter may be from the solar system not the extrasolar, while no anomaly exists in the inclusions of Allende chondrite and acid-insoluble residues of iron meteorites, which disagree with the results obtained by Goel [3]. REFERENCES [1] Chai Chifang (1988) Isotopenpraxis 24, pp. 257-272. [2] Anders E. and Grevesse N. (l989) Geochim. Cosmochim. Acta 53, 197-214. [3] Goel P.S.(1987) Proc. Indian Acad. Sci. (Earth Planet. Sci), 96, pp. 81-102.

Fluids of the ocular surface: concepts, functions and physics.

PubMed

Cher, Ivan

2012-08-01

General adoption of the ocular surface (OS) concept has advanced the therapy of the external eye. Fresh physical findings have prompted new concepts; examples taken from each section of the text are: (i) ever-present lipid sealant bridges the palpebral fissure capping the three-dimensional 'OS' sac. The muco-aqueous pool (MAP) is thus enclosed, secluded from atmosphere, evaporation mitigated. Hence, the OS is conceptually, a compartment. The term 'dacruon' (otherwise 'tear film') has been coined for the combined fluids of the OS, viz. lipid film and MAP. (ii) Investigative techniques of physics yield data on (say) surface tension and viscosity, and on functions such as anchorage of dacruon base to the varied mucosae of the OS, lubrication, renovation of intermarginal fluid layers as the eye opens after each blink, and refinement of optics and vision by the fluids attached to the cornea. (iii) Physical events in the opening eye produce the unique 'black line' phenomenon in which capillary force induces subsurface flows into thirsty menisci, bringing about parameniscal dark grooves, pupil-ward of each meniscus. Attenuation of fluorescein in the shallowed fluid gaps behind each groove makes the dye appear unilluminated ('black lines') relative to adjacent full-thickness MAP fluid glowing under cobalt-blue illumination. Isolated from cornea by grooves and gaps, the meniscal fluid cannot pass freely over the cornea. It therefore streams through the menisci to nasolacrimal outflow. © 2012 The Author. Clinical and Experimental Ophthalmology © 2012 Royal Australian and New Zealand College of Ophthalmologists.

Anthropogenic Osmium in Airborne Particles from Woods Hole, Massachusetts, USA

NASA Astrophysics Data System (ADS)

Peucker-Ehrenbrink, B.; Sen, I. S.; Geboy, N.

2012-12-01

The global geochemical cycle of osmium has been significantly disturbed by the introduction of automobile exhaust catalysts to convert noxious gas emissions into more benign forms. Anthropogenic osmium has been reported in rainwater, snow, and in the urban airborne particles from around the world to reveal global-scale osmium pollution [1, 2]. In this study, we report on the platinum group element (PGE) concentrations and osmium isotope ratios of airborne particles (PM10) collected in Woods Hole, a small coastal town in Massachusetts to better understand inputs of anthropogenic osmium to rural environments. We further investigate the use of osmium isotopes to track sources of airborne particles and support source apportionment studies on a continental scale. The samples used in this study were collected at Woods Hole Oceanographic Institution over one year (2008-2009). From this collection twelve samples for which the backward air mass trajectories have been determined were selected for osmium isotope analyses. Our results show that the osmium and platinum concentrations are an order of magnitude lower when compared to downtown Boston [2]. The average Os, Pt and Ir concentrations are 0.006±0.012, 0.019±0.023, and 0.685±0.634 pg m-3, respectively. The 187Os/188Os of the aerosols range from 0.275 to 0.788. As continental crust is radiogenic (187Os/188Os >1) and PGE ore bodies generally have unradiogenic 187Os/188Os (~0.2), the unradiogenic 187Os/188Os signature of the aerosols indicates anthropogenic contributions. With 95% of the total osmium mobilization on land being attributed to human activities [3], it is clear that human imprint on airborne particles is not restricted to urban centers with high traffic flows, but also affects rural environments. Aerosol particles that have backward air mass trajectories from the Southwest, the densely populated and industrialized Eastern seaboard, are characterized by unradiogenic osmium, while air masses from the North have radiogenic signatures. Our results suggest that 187Os/188Os has potential for source apportionment studies. [1] Rauch et al. (2005), Environ. Sci. Technol., 39, p. 9464-9470 [2] Chen et al. (2009), PNAS, 106, p. 7724-7728 [3] Sen and Peucker-Ehrenbrink (2012), Environ. Sci. Technol., dx.doi.org/10.102/es301261x

Technological choices for mobile clinical applications.

PubMed

Ehrler, Frederic; Issom, David; Lovis, Christian

2011-01-01

The rise of cheaper and more powerful mobile devices make them a new and attractive platform for clinical applications. The interaction paradigm and portability of the device facilitates bedside human-machine interactions. The better accessibility to information and decision-support anywhere in the hospital improves the efficiency and the safety of care processes. In this study, we attempt to find out what are the most appropriate Operating System (OS) and Software Development Kit (SDK) to support the development of clinical applications on mobile devices. The Android platform is a Linux-based, open source platform that has many advantages. Two main SDKs are available on this platform: the native Android and the Adobe Flex SDK. Both of them have interesting features, but the latter has been preferred due its portability at comparable performance and ease of development.

Software Authority Transition through Multiple Distributors

PubMed Central

Han, Kyusunk; Shon, Taeshik

2014-01-01

The rapid growth in the use of smartphones and tablets has changed the software distribution ecosystem. The trend today is to purchase software through application stores rather than from traditional offline markets. Smartphone and tablet users can install applications easily by purchasing from the online store deployed in their device. Several systems, such as Android or PC-based OS units, allow users to install software from multiple sources. Such openness, however, can promote serious threats, including malware and illegal usage. In order to prevent such threats, several stores use online authentication techniques. These methods can, however, also present a problem whereby even licensed users cannot use their purchased application. In this paper, we discuss these issues and provide an authentication method that will make purchased applications available to the registered user at all times. PMID:25143971

Software authority transition through multiple distributors.

PubMed

Han, Kyusunk; Shon, Taeshik

2014-01-01

The rapid growth in the use of smartphones and tablets has changed the software distribution ecosystem. The trend today is to purchase software through application stores rather than from traditional offline markets. Smartphone and tablet users can install applications easily by purchasing from the online store deployed in their device. Several systems, such as Android or PC-based OS units, allow users to install software from multiple sources. Such openness, however, can promote serious threats, including malware and illegal usage. In order to prevent such threats, several stores use online authentication techniques. These methods can, however, also present a problem whereby even licensed users cannot use their purchased application. In this paper, we discuss these issues and provide an authentication method that will make purchased applications available to the registered user at all times.

Real-time volume rendering of digital medical images on an iOS device

NASA Astrophysics Data System (ADS)

Noon, Christian; Holub, Joseph; Winer, Eliot

2013-03-01

Performing high quality 3D visualizations on mobile devices, while tantalizingly close in many areas, is still a quite difficult task. This is especially true for 3D volume rendering of digital medical images. Allowing this would empower medical personnel a powerful tool to diagnose and treat patients and train the next generation of physicians. This research focuses on performing real time volume rendering of digital medical images on iOS devices using custom developed GPU shaders for orthogonal texture slicing. An interactive volume renderer was designed and developed with several new features including dynamic modification of render resolutions, an incremental render loop, a shader-based clipping algorithm to support OpenGL ES 2.0, and an internal backface culling algorithm for properly sorting rendered geometry with alpha blending. The application was developed using several application programming interfaces (APIs) such as OpenSceneGraph (OSG) as the primary graphics renderer coupled with iOS Cocoa Touch for user interaction, and DCMTK for DICOM I/O. The developed application rendered volume datasets over 450 slices up to 50-60 frames per second, depending on the specific model of the iOS device. All rendering is done locally on the device so no Internet connection is required.

Analysis of the Nuclear Structure of Rhenium-186 Using Neutron-Induced Reactions

DTIC Science & Technology

2015-03-26

5 1.5 Methods ... radioisotope power source for use on the battlefield. 1 Re-Os Cosmochronometer. The isotope 187Re has a half-life in its ground state of 4.35⇥ 1010 years [2...187Os in meteorites permits one to date the nucleosynthesis of rhenium and osmium by high neutron flux events such as supernovae. The Re-Os radioactive

Reoperation after laparoscopic colorectal surgery. Does the laparoscopic approach have any advantages?

PubMed

Ibáñez, Noelia; Abrisqueta, Jesús; Luján, Juan; Sánchez, Pedro; Soriano, María Teresa; Arevalo-Pérez, Julio; Parrilla, Pascual

2018-02-01

The laparoscopic approach in colorectal complications is controversial because of its difficulty. However, it has been proven that it can provide advantages over open surgery. The aim of this study is to compare laparoscopic approach in reoperations for complications after colorectal surgery with the open approach taking into account the severity of the patient prior to reoperation. Patients who underwent laparoscopic colorectal surgery from January 2006 to December 2015 were retrospectively reviewed. Patients requiring urgent surgical procedures for complications in the postoperative period were divided in two groups: laparoscopic surgery (LS) and open surgery (OS). To control clinical severity prior to reoperation, The Mannheim Peritonitis Index (MPI) was calculated. A total of 763 patients were studied, 40 required urgent surgery (24 OS/16 LS). More ileostomies were performed in the LS group (68.7% vs. 29.2%) and more colostomies in the OS group (37.5% vs. 6.2%), p<0.05. MPI was higher in OS group (27.31±6.47 [19-35] vs. 18.36±7.16 [11-24], p<0.001). Hospital stay after re-intervention, oral tolerance and surgical wound infection, were favorable in LS (p<0.05 in all cases). In patients with MPI score ≤26, laparoscopic approach showed shorter hospital stay after re-intervention, less stay in the critical care unit after re-intervention, earlier start of oral tolerance and less surgical wound infection (p<0.05). A laparoscopic approach in re-intervention for complications after laparoscopic colorectal surgery associates a faster recovery reflected in a shorter hospital stay, earlier start of oral tolerance and a lower abdominal wall complication rate in patients with low severity index. Copyright © 2017 AEC. Publicado por Elsevier España, S.L.U. All rights reserved.

Unipro UGENE: a unified bioinformatics toolkit.

PubMed

Okonechnikov, Konstantin; Golosova, Olga; Fursov, Mikhail

2012-04-15

Unipro UGENE is a multiplatform open-source software with the main goal of assisting molecular biologists without much expertise in bioinformatics to manage, analyze and visualize their data. UGENE integrates widely used bioinformatics tools within a common user interface. The toolkit supports multiple biological data formats and allows the retrieval of data from remote data sources. It provides visualization modules for biological objects such as annotated genome sequences, Next Generation Sequencing (NGS) assembly data, multiple sequence alignments, phylogenetic trees and 3D structures. Most of the integrated algorithms are tuned for maximum performance by the usage of multithreading and special processor instructions. UGENE includes a visual environment for creating reusable workflows that can be launched on local resources or in a High Performance Computing (HPC) environment. UGENE is written in C++ using the Qt framework. The built-in plugin system and structured UGENE API make it possible to extend the toolkit with new functionality. UGENE binaries are freely available for MS Windows, Linux and Mac OS X at http://ugene.unipro.ru/download.html. UGENE code is licensed under the GPLv2; the information about the code licensing and copyright of integrated tools can be found in the LICENSE.3rd_party file provided with the source bundle.

ChelomEx: Isotope-assisted discovery of metal chelates in complex media using high-resolution LC-MS.

PubMed

Baars, Oliver; Morel, François M M; Perlman, David H

2014-11-18

Chelating agents can control the speciation and reactivity of trace metals in biological, environmental, and laboratory-derived media. A large number of trace metals (including Fe, Cu, Zn, Hg, and others) show characteristic isotopic fingerprints that can be exploited for the discovery of known and unknown organic metal complexes and related chelating ligands in very complex sample matrices using high-resolution liquid chromatography mass spectrometry (LC-MS). However, there is currently no free open-source software available for this purpose. We present a novel software tool, ChelomEx, which identifies isotope pattern-matched chromatographic features associated with metal complexes along with free ligands and other related adducts in high-resolution LC-MS data. High sensitivity and exclusion of false positives are achieved by evaluation of the chromatographic coherence of the isotope pattern within chromatographic features, which we demonstrate through the analysis of bacterial culture media. A built-in graphical user interface and compound library aid in identification and efficient evaluation of results. ChelomEx is implemented in MatLab. The source code, binaries for MS Windows and MAC OS X as well as test LC-MS data are available for download at SourceForge ( http://sourceforge.net/projects/chelomex ).

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...

Osmium isotopes and mantle convection.

PubMed

Hauri, Erik H

2002-11-15

The decay of (187)Re to (187)Os (with a half-life of 42 billion years) provides a unique isotopic fingerprint for tracing the evolution of crustal materials and mantle residues in the convecting mantle. Ancient subcontinental mantle lithosphere has uniquely low Re/Os and (187)Os/(188)Os ratios due to large-degree melt extraction, recording ancient melt-depletion events as old as 3.2 billion years. Partial melts have Re/Os ratios that are orders of magnitude higher than their sources, and the subduction of oceanic or continental crust introduces into the mantle materials that rapidly accumulate radiogenic (187)Os. Eclogites from the subcontinental lithosphere have extremely high (187)Os/(188)Os ratios, and record ages as old as the oldest peridotites. The data show a near-perfect partitioning of Re/Os and (187)Os/(188)Os ratios between peridotites (low) and eclogites (high). The convecting mantle retains a degree of Os-isotopic heterogeneity similar to the lithospheric mantle, although its amplitude is modulated by convective mixing. Abyssal peridotites from the ocean ridges have low Os isotope ratios, indicating that the upper mantle had undergone episodes of melt depletion prior to the most recent melting events to produce mid-ocean-ridge basalt. The amount of rhenium estimated to be depleted from the upper mantle is 10 times greater than the rhenium budget of the continental crust, requiring a separate reservoir to close the mass balance. A reservoir consisting of 5-10% of the mantle with a rhenium concentration similar to mid-ocean-ridge basalt would balance the rhenium depletion of the upper mantle. This reservoir most likely consists of mafic oceanic crust recycled into the mantle over Earth's history and provides the material that melts at oceanic hotspots to produce ocean-island basalts (OIBs). The ubiquity of high Os isotope ratios in OIB, coupled with other geochemical tracers, indicates that the mantle sources of hotspots contain significant quantities (greater than 10%) of lithologically distinct mafic material which represents ancient oceanic lithosphere cycled through the convecting mantle on a time-scale of 800 million years or more.

Comparison of minimally invasive spine surgery using intraoperative computed tomography integrated navigation, fluoroscopy, and conventional open surgery for lumbar spondylolisthesis: a prospective registry-based cohort study.

PubMed

Wu, Meng-Huang; Dubey, Navneet Kumar; Li, Yen-Yao; Lee, Ching-Yu; Cheng, Chin-Chang; Shi, Chung-Sheng; Huang, Tsung-Jen

2017-08-01

To date, the surgical approaches for the treatment of lumbar spondylolisthesis by transforaminal lumbar interbody fusion (TLIF) using minimally invasive spine surgery assisted with intraoperative computed tomography image-integrated navigation (MISS-iCT), fluoroscopy (MISS-FS), and conventional open surgery (OS) are debatable. This study compared TLIF using MISS-iCT, MISS-FS, and OS for treatment of one-level lumbar spondylolisthesis. This is a prospective, registry-based cohort study that compared surgical approaches for patients who underwent surgical treatment for one-level lumbar spondylolisthesis. One hundred twenty-four patients from January 2010 to March 2012 in a medical center were recruited. The outcome measures were clinical assessments, including Short-Form 12, visual analog scale (VAS), Oswestry Disability Index, Core Outcome Measurement Index, and patient satisfaction, and blood loss, hospital stay, operation time, postoperative pedicle screw accuracy, and superior-level facet violation. All surgeries were performed by two senior surgeons together. Ninety-nine patients (40M, 59F) who had at least 2 years' follow-up were divided into three groups according to the operation methods: MISS-iCT (N=24), MISS-FS (N=23), and OS (N=52) groups. Charts and surgical records along with postoperative CT images were assessed. MISS-iCT and MISS-FS demonstrated a significantly lowered blood loss and hospital stay compared with OS group (p<.01). Operation time was significantly lower in the MISS-iCT and OS groups compared with the MISS-FS group (p=.002). Postoperatively, VAS scores at 1 year and 2 years were significantly improved in the MISS-iCT and MISS-FS groups compared with the OS groups. No significant difference in the number of pedicle screw breach (>2 mm) was found. However, a lower superior-level facet violation rate was observed in the MISS-iCT and OS groups (p=.049). MISS-iCT TLIF demonstrated reduced operation time, blood loss, superior-level facet violation, hospital stay, and improved functional outcomes compared with the MISS-FS and OS approaches. Copyright © 2017 Elsevier Inc. All rights reserved.

Deceased Slabs Drive Oil

NASA Astrophysics Data System (ADS)

Stein, H. J.; Hannah, J. L.

2017-12-01

The application of Re-Os isotope geochemistry to dating single oils is a nascent field [1,2]. Challenges include dissection of oils into asphaltene-maltene (ASPH-MALT) components in a way that preserves meaningful chronologic and source information. Significantly, oil-water mixing rapidly transfers Os to the oil, while Re exchange is sluggish [3]. The Os initial ratio of the oil is shifted in the direction of Os carried in the aqueous fluid, whereas the Re-Os isotopic age is preserved. We show that this phenomenon is operative in natural systems. Further, we show that deserpentinization of old oceanic slabs [4], may be linked to expulsion of Os-enriched waters into overlying sedimentary sections - a process that may be of fundamental importance for oil generation. This conclusion does not diminish the role of traditional organic-rich shales as source rocks for the hydrocarbon, but shows that external fluids are essential to petroleum generation. Moreover, the external fluids may be an important driver for expulsion and migration of oils. We have taken apart several petroleum systems from source rock, to residual oil, to tar mat development, to in situ live oil, through to produced oil. In many cases, a fluid with low 187Os/188Os - unlike that of normal basinal brines - provides a critical component to the oil-water mixture. Funding - CHRONOS project supported by Norwegian petroleum industry (Eni-Norge, Lundin, Aker BP) Acknowledgement - Christine Fichler [4], who first queried us on old slabs and oil, and stimulated ideas. [1] Georgiev, S.V., Stein, H.J., Hannah, J.L., Galimberti, R., Nali, M., Yang, G., and Zimmerman, A. (2016) Re-Os dating of maltenes and asphaltenes within single samples of crude oil: Geochim. Cosmochim. Acta 179: 53-75. [doi.org/10.1016/j.gca.2016.01.016] [2] DiMarzio, J., Georgiev, S.V., Stein, H.J., and Hannah, J.L. (in press) Residency of rhenium and osmium in a heavy crude oil: Geochim. Cosmochim. Acta. [3] Hurtig, N.C., Georgiev, S.V., Stein, H.J., and Hannah, J.L. (in review) Re-Os in oil - in the company of water. [4] Fichler, C., Odinsen, T., Rueslåtten, H., Olesen, O., Vingstad, J.-E., Wienecke, S. (2011) Crustal inhomogenities in the northern North Sea from potential field modeling: inherited structure and serpentinites: Tectonophysics 510: 172-185. [doi:10.1016/j.tecto.2011.06.026

The Systemic Acquired Resistance Regulator OsNPR1 Attenuates Growth by Repressing Auxin Signaling through Promoting IAA-Amido Synthase Expression1[OPEN

PubMed Central

2016-01-01

Systemic acquired resistance is a long-lasting and broad-spectrum disease resistance to pathogens. Our previous study demonstrated that overexpression of NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1 (OsNPR1), a master gene for systemic acquired resistance in rice (Oryza sativa), greatly enhanced resistance to bacterial blight caused by Xanthomonas oryzae pv oryzae. However, the growth and development of the OsNPR1 overexpression (OsNPR1-OX) plants were restrained, and the mechanism remained elusive. In this study, we dissected the OsNPR1-induced growth inhibition. We found that the OsNPR1-OX lines displayed phenotypes mimicking auxin-defective mutants, with decreases in root system, seed number and weight, internode elongation, and tiller number. Whole-genome expression analysis revealed that genes related to the auxin metabolism and signaling pathway were differentially expressed between the OsNPR1-OX and wild-type plants. Consistently, the indole-3-acetic acid (IAA) content was decreased and the auxin distribution pattern was altered in OsNPR1-OX plants. Importantly, we found that some GH3 family members, in particular OsGH3.8 coding IAA-amido synthetase, were constitutively up-regulated in OsNPR1-OX plants. Decreased OsGH3.8 expression by RNA interference could partially restore IAA level and largely rescue the restrained growth and development phenotypes but did not affect the disease resistance of OsNPR1-OX plants. Taken together, we revealed that OsNPR1 affects rice growth and development by disrupting the auxin pathway at least partially through indirectly up-regulating OsGH3.8 expression. PMID:27378815

Multiplexed bovine milk oligosaccharide analysis with aminoxy tandem mass tags

PubMed Central

Poulsen, Nina Aagaard; Barile, Daniela

2018-01-01

Milk oligosaccharides (OS) are a key factor that influences the infant gut microbial composition, and their importance in promoting healthy infant development and disease prevention is becoming increasingly apparent. Investigating the structures, properties, and sources of these compounds requires a host of complementary analytical techniques. Relative compound quantification by mass spectral analysis of isobarically labeled samples is a relatively new technique that has been used mainly in the proteomics field. Glycomics applications have so far focused on analysis of protein-linked glycans, while analysis of free milk OS has previously been conducted only on analytical standards. In this paper, we extend the use of isobaric glycan tags to the analysis of bovine milk OS by presenting a method for separation of labeled OS on a porous graphitized carbon liquid chromatographic column with subsequent analysis by quadrupole time-of-flight tandem mass spectrometry. Abundances for 15 OS extracted from mature bovine milk were measured, with replicate injections providing coefficients of variation below 15% for most OS. Isobaric labeling improved ionization efficiency for low-abundance, high-molecular weight fucosylated OS, which are known to exist in bovine milk but have been only sporadically reported in the literature. We compared the abundances of four fucosylated OS in milk from Holstein and Jersey cattle and found that three of the compounds were more abundant in Jersey milk, which is in general agreement with a previous study. This novel method represents an advancement in our ability to characterize milk OS and provides the advantages associated with isobaric labeling, including reduced instrumental analysis time and increased analyte ionization efficiency. This improved ability to measure differences in bioactive OS abundances in large datasets will facilitate exploration of OS from all food sources for the purpose of developing health-guiding products for infants, immune-compromised elderly, and the population at large. PMID:29698512

OsDMC1 Is Not Required for Homologous Pairing in Rice Meiosis1[OPEN

PubMed Central

Tang, Ding; Liu, Xiaofei; Du, Guijie; Shen, Yi; Li, Yafei; Cheng, Zhukuan

2016-01-01

Meiotic homologous recombination is pivotal to sexual reproduction. DMC1, a conserved recombinase, is involved in directing single-end invasion between interhomologs during meiotic recombination. In this study, we identified OsDMC1A and OsDMC1B, two closely related proteins in rice (Oryza sativa) with high sequence similarity to DMC1 proteins from other species. Analysis of Osdmc1a and Osdmc1b Tos17 insertion mutants indicated that these genes are functionally redundant. Immunolocalization analysis revealed OsDMC1 foci occurred at leptotene, which disappeared from late pachytene chromosomes in wild-type meiocytes. According to cytological analyses, homologous pairing is accomplished in the Osdmc1a Osdmc1b double mutant, but synapsis is seriously disrupted. The reduced number of bivalents and abnormal OsHEI10 foci in Osdmc1a Osdmc1b establishes an essential role for OsDMC1 in crossover formation. In the absence of OsDMC1, early recombination events probably occur normally, leading to normal localization of γH2AX, PAIR3, OsMRE11, OsCOM1, and OsRAD51C. Moreover, OsDMC1 was not detected in pairing-defective mutants, such as pair2, pair3, Oscom1, and Osrad51c, while it was loaded onto meiotic chromosomes in zep1, Osmer3, Oszip4, and Oshei10. Taken together, these results suggest that during meiosis, OsDMC1 is dispensable for homologous pairing in rice, which is quite different from the DMC1 homologs identified so far in other organisms. PMID:26960731

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

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…

Levels of bioactive lipids in cooking oils: olive oil is the richest source of oleoyl serine.

PubMed

Bradshaw, Heather B; Leishman, Emma

2016-05-01

Rates of osteoporosis are significantly lower in regions of the world where olive oil consumption is a dietary cornerstone. Olive oil may represent a source of oleoyl serine (OS), which showed efficacy in animal models of osteoporosis. Here, we tested the hypothesis that OS as well as structurally analogous N-acyl amide and 2-acyl glycerol lipids are present in the following cooking oils: olive, walnut, canola, high heat canola, peanut, safflower, sesame, toasted sesame, grape seed, and smart balance omega. Methanolic lipid extracts from each of the cooking oils were partially purified on C-18 solid-phase extraction columns. Extracts were analyzed with high-performance liquid chromatography-tandem mass spectrometry, and 33 lipids were measured in each sample, including OS and bioactive analogs. Of the oils screened here, walnut oil had the highest number of lipids detected (22/33). Olive oil had the second highest number of lipids detected (20/33), whereas grape-seed and high-heat canola oil were tied for lowest number of detected lipids (6/33). OS was detected in 8 of the 10 oils tested and the levels were highest in olive oil, suggesting that there is something about the olive plant that enriches this lipid. Cooking oils contain varying levels of bioactive lipids from the N-acyl amide and 2-acyl glycerol families. Olive oil is a dietary source of OS, which may contribute to lowered prevalence of osteoporosis in countries with high consumption of this oil.

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

High-precision measurement of (186)Os/(188)Os and (187)Os/(188)Os: isobaric oxide corrections with in-run measured oxygen isotope ratios.

PubMed

Chu, Zhu-Yin; Li, Chao-Feng; Chen, Zhi; Xu, Jun-Jie; Di, Yan-Kun; Guo, Jing-Hui

2015-09-01

We present a novel method for high precision measurement of (186)Os/(188)Os and (187)Os/(188)Os ratios, applying isobaric oxide interference correction based on in-run measurements of oxygen isotopic ratios. For this purpose, we set up a static data collection routine to measure the main Os(16)O3(-) ion beams with Faraday cups connected to conventional 10(11) amplifiers, and (192)Os(16)O2(17)O(-) and (192)Os(16)O2(18)O(-) ion beams with Faraday cups connected to 10(12) amplifiers. Because of the limited number of Faraday cups, we did not measure (184)Os(16)O3(-) and (189)Os(16)O3(-) simultaneously in-run, but the analytical setup had no significant influence on final (186)Os/(188)Os and (187)Os/(188)Os data. By analyzing UMd, DROsS, an in-house Os solution standard, and several rock reference materials, including WPR-1, WMS-1a, and Gpt-5, the in-run measured oxygen isotopic ratios were proven to present accurate Os isotopic data. However, (186)Os/(188)Os and (187)Os/(188)Os data obtained with in-run O isotopic compositions for the solution standards and rock reference materials show minimal improvement in internal and external precision, compared to the conventional oxygen correction method. We concluded that, the small variations of oxygen isotopes during OsO3(-) analytical sessions are probably not the main source of error for high precision Os isotopic analysis. Nevertheless, use of run-specific O isotopic compositions is still a better choice for Os isotopic data reduction and eliminates the requirement of extra measurements of the oxygen isotopic ratios.

Outer Retinal Tubulation in Advanced Age-Related Macular Degeneration: Optical Coherence Tomographic Findings Correspond to Histology

PubMed Central

Schaal, Karen B.; Freund, K. Bailey; Litts, Katie M.; Zhang, Yuhua; Messinger, Jeffrey D.; Curcio, Christine A.

2014-01-01

Purpose To compare optical coherence tomography (OCT) and histology of outer retinal tubulation (ORT) secondary to advanced age-related macular degeneration (AMD) in patients and in post-mortem specimens, with particular attention to the basis of the hyper-reflective border of ORT. Method A private referral practice (imaging) and an academic research laboratory (histology) collaborated on two retrospective case series. High-resolution OCT raster scans of 43 eyes (34 patients) manifesting ORT secondary to advanced AMD were compared to high-resolution histological sections through the fovea and superior perifovea of donor eyes (13 atrophic AMD and 40 neovascular AMD) preserved ≤4 hours after death. Results ORT seen on OCT corresponded to histologic findings of tubular structures comprised largely of cones lacking outer segments (OS) and lacking inner segments (IS). Four phases of cone degeneration were histologically distinguishable in ORT lumenal walls, nascent, mature, degenerate, and end-stage (IS and OS; IS only; no IS; no photoreceptors and only Müller cells forming external limiting membrane, ELM, respectively). Mitochondria, which are normally long and bundled within IS ellipsoids, were small and scattered within shrunken IS and cell bodies of surviving cones. A lumenal border was delimited by an ELM. ORT observed in closed and open configurations were distinguishable from cysts and photoreceptor islands on both OCT and histology. Hyper-reflective lumenal material seen on OCT represents trapped retinal pigment epithelium (RPE) and non-RPE cells. Conclusions The defining OCT features of ORT are location in the outer nuclear layer (ONL), a hyper-reflective band differentiating it from cysts, and RPE that is either dysmorphic or absent. ORT histologic and OCT findings corresponded in regard to composition, location, shape, and stages of formation. The reflectivity of ORT lumenal walls on OCT apparently does not require an OS or an IS/OS junction, indicating an independent reflectivity source, possibly mitochondria, in the IS. PMID:25635579

A Multidisciplinary Tool for Systems Analysis of Planetary Entry, Descent, and Landing (SAPE)

NASA Technical Reports Server (NTRS)

Samareh, Jamshid A.

2009-01-01

SAPE is a Python-based multidisciplinary analysis tool for systems analysis of planetary entry, descent, and landing (EDL) for Venus, Earth, Mars, Jupiter, Saturn, Uranus, Neptune, and Titan. The purpose of SAPE is to provide a variable-fidelity capability for conceptual and preliminary analysis within the same framework. SAPE includes the following analysis modules: geometry, trajectory, aerodynamics, aerothermal, thermal protection system, and structural sizing. SAPE uses the Python language-a platform-independent open-source software for integration and for the user interface. The development has relied heavily on the object-oriented programming capabilities that are available in Python. Modules are provided to interface with commercial and government off-the-shelf software components (e.g., thermal protection systems and finite-element analysis). SAPE runs on Microsoft Windows and Apple Mac OS X and has been partially tested on Linux.

KITTEN Lightweight Kernel 0.1 Beta

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

Pedretti, Kevin; Levenhagen, Michael; Kelly, Suzanne

2007-12-12

The Kitten Lightweight Kernel is a simplified OS (operating system) kernel that is intended to manage a compute node's hardware resources. It provides a set of mechanisms to user-level applications for utilizing hardware resources (e.g., allocating memory, creating processes, accessing the network). Kitten is much simpler than general-purpose OS kernels, such as Linux or Windows, but includes all of the esssential functionality needed to support HPC (high-performance computing) MPI, PGAS and OpenMP applications. Kitten provides unique capabilities such as physically contiguous application memory, transparent large page support, and noise-free tick-less operation, which enable HPC applications to obtain greater efficiency andmore » scalability than with general purpose OS kernels.« less

GeNN: a code generation framework for accelerated brain simulations

NASA Astrophysics Data System (ADS)

Yavuz, Esin; Turner, James; Nowotny, Thomas

2016-01-01

Large-scale numerical simulations of detailed brain circuit models are important for identifying hypotheses on brain functions and testing their consistency and plausibility. An ongoing challenge for simulating realistic models is, however, computational speed. In this paper, we present the GeNN (GPU-enhanced Neuronal Networks) framework, which aims to facilitate the use of graphics accelerators for computational models of large-scale neuronal networks to address this challenge. GeNN is an open source library that generates code to accelerate the execution of network simulations on NVIDIA GPUs, through a flexible and extensible interface, which does not require in-depth technical knowledge from the users. We present performance benchmarks showing that 200-fold speedup compared to a single core of a CPU can be achieved for a network of one million conductance based Hodgkin-Huxley neurons but that for other models the speedup can differ. GeNN is available for Linux, Mac OS X and Windows platforms. The source code, user manual, tutorials, Wiki, in-depth example projects and all other related information can be found on the project website http://genn-team.github.io/genn/.

GeNN: a code generation framework for accelerated brain simulations.

PubMed

Yavuz, Esin; Turner, James; Nowotny, Thomas

2016-01-07

Large-scale numerical simulations of detailed brain circuit models are important for identifying hypotheses on brain functions and testing their consistency and plausibility. An ongoing challenge for simulating realistic models is, however, computational speed. In this paper, we present the GeNN (GPU-enhanced Neuronal Networks) framework, which aims to facilitate the use of graphics accelerators for computational models of large-scale neuronal networks to address this challenge. GeNN is an open source library that generates code to accelerate the execution of network simulations on NVIDIA GPUs, through a flexible and extensible interface, which does not require in-depth technical knowledge from the users. We present performance benchmarks showing that 200-fold speedup compared to a single core of a CPU can be achieved for a network of one million conductance based Hodgkin-Huxley neurons but that for other models the speedup can differ. GeNN is available for Linux, Mac OS X and Windows platforms. The source code, user manual, tutorials, Wiki, in-depth example projects and all other related information can be found on the project website http://genn-team.github.io/genn/.

GeNN: a code generation framework for accelerated brain simulations

PubMed Central

Yavuz, Esin; Turner, James; Nowotny, Thomas

2016-01-01

Large-scale numerical simulations of detailed brain circuit models are important for identifying hypotheses on brain functions and testing their consistency and plausibility. An ongoing challenge for simulating realistic models is, however, computational speed. In this paper, we present the GeNN (GPU-enhanced Neuronal Networks) framework, which aims to facilitate the use of graphics accelerators for computational models of large-scale neuronal networks to address this challenge. GeNN is an open source library that generates code to accelerate the execution of network simulations on NVIDIA GPUs, through a flexible and extensible interface, which does not require in-depth technical knowledge from the users. We present performance benchmarks showing that 200-fold speedup compared to a single core of a CPU can be achieved for a network of one million conductance based Hodgkin-Huxley neurons but that for other models the speedup can differ. GeNN is available for Linux, Mac OS X and Windows platforms. The source code, user manual, tutorials, Wiki, in-depth example projects and all other related information can be found on the project website http://genn-team.github.io/genn/. PMID:26740369

Make Movies out of Your Dynamical Simulations with OGRE!

NASA Astrophysics Data System (ADS)

Tamayo, Daniel; Douglas, R. W.; Ge, H. W.; Burns, J. A.

2013-10-01

We have developed OGRE, the Orbital GRaphics Environment, an open-source project comprising a graphical user interface that allows the user to view the output from several dynamical integrators (e.g., SWIFT) that are commonly used for academic work. One can interactively vary the display speed, rotate the view and zoom the camera. This makes OGRE a great tool for students or the general public to explore accurate orbital histories that may display interesting dynamical features, e.g. the destabilization of Solar System orbits under the Nice model, or interacting pairs of exoplanets. Furthermore, OGRE allows the user to choreograph sequences of transformations as the simulation is played to generate movies for use in public talks or professional presentations. The graphical user interface is coded using Qt to ensure portability across different operating systems. OGRE will run on Linux and Mac OS X. The program is available as a self-contained executable, or as source code that the user can compile. We are continually updating the code, and hope that people who find it useful will contribute to the development of new features.

Make Movies out of Your Dynamical Simulations with OGRE!

NASA Astrophysics Data System (ADS)

Tamayo, Daniel; Douglas, R. W.; Ge, H. W.; Burns, J. A.

2014-01-01

We have developed OGRE, the Orbital GRaphics Environment, an open-source project comprising a graphical user interface that allows the user to view the output from several dynamical integrators (e.g., SWIFT) that are commonly used for academic work. One can interactively vary the display speed, rotate the view and zoom the camera. This makes OGRE a great tool for students or the general public to explore accurate orbital histories that may display interesting dynamical features, e.g. the destabilization of Solar System orbits under the Nice model, or interacting pairs of exoplanets. Furthermore, OGRE allows the user to choreograph sequences of transformations as the simulation is played to generate movies for use in public talks or professional presentations. The graphical user interface is coded using Qt to ensure portability across different operating systems. OGRE will run on Linux and Mac OS X. The program is available as a self-contained executable, or as source code that the user can compile. We are continually updating the code, and hope that people who find it useful will contribute to the development of new features.

Formation of pyroxenite layers in the Totalp ultramafic massif (Swiss Alps) - Insights from highly siderophile elements and Os isotopes

NASA Astrophysics Data System (ADS)

van Acken, David; Becker, Harry; Walker, Richard J.; McDonough, William F.; Wombacher, Frank; Ash, Richard D.; Piccoli, Phil M.

2010-01-01

Pyroxenitic layers are a minor constituent of ultramafic mantle massifs, but are considered important for basalt generation and mantle refertilization. Mafic spinel websterite and garnet-spinel clinopyroxenite layers within Jurassic ocean floor peridotites from the Totalp ultramafic massif (eastern Swiss Alps) were analyzed for their highly siderophile element (HSE) and Os isotope composition. Aluminum-poor pyroxenites (websterites) display chondritic to suprachondritic initial γOs (160 Ma) of -2 to +27. Osmium, Ir and Ru abundances are depleted in websterites relative to the associated peridotites and to mantle lherzolites worldwide, but relative abundances (Os/Ir, Ru/Ir) are similar. Conversely, Pt/Ir, Pd/Ir and Re/Ir are elevated. Aluminum-rich pyroxenites (clinopyroxenites) are characterized by highly radiogenic 187Os/ 188Os with initial γOs (160 Ma) between +20 and +1700. Their HSE composition is similar to that of basalts, as they are more depleted in Os, Ir and Ru compared to Totalp websterites, along with even higher Pt/Ir, Pd/Ir and Re/Ir. The data are most consistent with multiple episodes of reaction of mafic pyroxenite precursor melts with surrounding peridotites, with the highest degree of interaction recorded in the websterites, which typically occur in direct contact to peridotites. Clinopyroxenites, in contrast, represent melt-dominated systems, which retained the precursor melt characteristics to a large extent. The melts may have been derived from a sublithospheric mantle source with high Pd/Ir, Pt/Ir and Re/Os, coupled with highly radiogenic 187Os/ 188Os compositions. Modeling indicates that partial melting of subducted, old oceanic crust in the asthenosphere could be a possible source for such melts. Pentlandite and godlevskite are identified in both types of pyroxenites as the predominant sulfide minerals and HSE carriers. Heterogeneous HSE abundances within these sulfide grains likely reflect subsolidus processes. In contrast, large grain-to-grain variations, and correlated variations of HSE ratios, indicate chemical disequilibrium under high-temperature conditions. This likely reflects multiple events of melt-rock interaction and sulfide precipitation. Notably, sulfides from the same thick section for the pyroxenites may display both residual-peridotite and melt-like HSE signatures. Because Totalp pyroxenites are enriched in Pt and Re, and depleted in Os, they will develop excess radiogenic 187Os and 186Os, compared to ambient mantle. These enrichments, however, do not possess the requisite Pt-Re-Os composition to account for the coupled suprachondritic 186Os- 187Os signatures observed in some Hawaiian picrites, Gorgona komatiites, or the Siberian plume.

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.

TIM, a ray-tracing program for METATOY research and its dissemination

NASA Astrophysics Data System (ADS)

Lambert, Dean; Hamilton, Alasdair C.; Constable, George; Snehanshu, Harsh; Talati, Sharvil; Courtial, Johannes

2012-03-01

TIM (The Interactive METATOY) is a ray-tracing program specifically tailored towards our research in METATOYs, which are optical components that appear to be able to create wave-optically forbidden light-ray fields. For this reason, TIM possesses features not found in other ray-tracing programs. TIM can either be used interactively or by modifying the openly available source code; in both cases, it can easily be run as an applet embedded in a web page. Here we describe the basic structure of TIM's source code and how to extend it, and we give examples of how we have used TIM in our own research. Program summaryProgram title: TIM Catalogue identifier: AEKY_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKY_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License No. of lines in distributed program, including test data, etc.: 124 478 No. of bytes in distributed program, including test data, etc.: 4 120 052 Distribution format: tar.gz Programming language: Java Computer: Any computer capable of running the Java Virtual Machine (JVM) 1.6 Operating system: Any; developed under Mac OS X Version 10.6 RAM: Typically 145 MB (interactive version running under Mac OS X Version 10.6) Classification: 14, 18 External routines: JAMA [1] (source code included) Nature of problem: Visualisation of scenes that include scene objects that create wave-optically forbidden light-ray fields. Solution method: Ray tracing. Unusual features: Specifically designed to visualise wave-optically forbidden light-ray fields; can visualise ray trajectories; can visualise geometric optic transformations; can create anaglyphs (for viewing with coloured "3D glasses") and random-dot autostereograms of the scene; integrable into web pages. Running time: Problem-dependent; typically seconds for a simple scene.

Opening the Duke electronic health record to apps: Implementing SMART on FHIR.

PubMed

Bloomfield, Richard A; Polo-Wood, Felipe; Mandel, Joshua C; Mandl, Kenneth D

2017-03-01

Recognizing a need for our EHR to be highly interoperable, our team at Duke Health enabled our Epic-based electronic health record to be compatible with the Boston Children's project called Substitutable Medical Apps and Reusable Technologies (SMART), which employed Health Level Seven International's (HL7) Fast Healthcare Interoperability Resources (FHIR), commonly known as SMART on FHIR. We created a custom SMART on FHIR-compatible server infrastructure written in Node.js that served two primary functions. First, it handled API management activities such rate-limiting, authorization, auditing, logging, and analytics. Second, it retrieved the EHR data and made it available in a FHIR-compatible format. Finally, we made required changes to the EHR user interface to allow us to integrate several compatible apps into the provider- and patient-facing EHR workflows. After integrating SMART on FHIR into our Epic-based EHR, we demonstrated several types of apps running on the infrastructure. This included both provider- and patient-facing apps as well as apps that are closed source, open source and internally-developed. We integrated the apps into the testing environment of our desktop EHR as well as our patient portal. We also demonstrated the integration of a native iOS app. In this paper, we demonstrate the successful implementation of the SMART and FHIR technologies on our Epic-based EHR and subsequent integration of several compatible provider- and patient-facing apps. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

186Os-187Os and highly siderophile element abundance systematics of the mantle revealed by abyssal peridotites and Os-rich alloys

NASA Astrophysics Data System (ADS)

Day, James M. D.; Walker, Richard J.; Warren, Jessica M.

2017-03-01

Abyssal peridotites are oceanic mantle fragments that were recently processed through ridges and represent residues of both modern and ancient melting. To constrain the nature and timing of melt depletion processes, and the composition of the mantle, we report high-precision Os isotope data for abyssal peridotites from three ocean basins, as well as for Os-rich alloys, primarily from Mesozoic ophiolites. These data are complemented by whole-rock highly siderophile element (HSE: Os, Ir, Ru, Pt, Pd, Re), trace- and major-element abundances for the abyssal peridotites, which are from the Southwest Indian (SWIR), Central Indian (CIR), Mid-Atlantic (MAR) and Gakkel Ridges. The results reveal a limited role for melt refertilization or secondary alteration processes in modifying abyssal peridotite HSE compositions. The abyssal peridotites examined have experienced variable melt depletion (2% to >16%), which occurred >0.5 Ga ago for some samples. Abyssal peridotites typically exhibit low Pd/Ir and, combined with high-degrees of estimated total melt extraction, imply that they were relatively refractory residues prior to incorporation into their present ridge setting. Recent partial melting processes and mid-ocean ridge basalt (MORB) generation therefore played a limited role in the chemical evolution of their precursor mantle domains. The results confirm that many abyssal peridotites are not simple residues of recent MORB source melting, having a more complex and long-lived depletion history. Peridotites from the Gakkel Ridge, SWIR, CIR and MAR indicate that the depleted MORB mantle has 186Os/188Os of 0.1198356 ± 21 (2SD). The Phanerozoic Os-rich alloys yield an average 186Os/188Os within uncertainty of abyssal peridotites (0.1198361 ± 20). Melt depletion trends defined between Os isotopes and melt extraction indices (e.g., Al2O3) allow an estimate of the primitive mantle (PM) composition, using only abyssal peridotites. This yields 187Os/188Os (0.1292 ± 25), and 186Os/188Os of 0.1198388 ± 29, both of which are within uncertainty of previous primitive mantle estimates. The 186Os/188Os composition of the PM is less radiogenic than for some plume-related lavas, with the latter requiring sources with high long-term time-integrated Pt/Os. Estimates of primitive mantle HSE concentrations using abyssal peridotites define chondritic Pd/Ir, which differs from previous supra-chondritic estimates for Pd/Ir based on peridotites from a range of tectonic settings. By contrast, estimates of PM yield supra-chondritic Ru/Ir. The cause of enhanced Ru in the mantle remains enigmatic, but may reflect variable partitioning behavior of Ru at high pressure and temperature.

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…

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 End of Monterey Submarine Canyon Incision and Potential River Source Areas-Os, Nd, and Pb Isotope Constraints from Hydrogenetic Fe-Mn Crusts

NASA Astrophysics Data System (ADS)

Conrad, T. A.; Nielsen, S.; Ehrenbrink, B. P. E.; Blusztajn, J.; Hein, J. R.; Paytan, A.

2015-12-01

The Monterey Canyon off central California is the largest submarine canyon off North America and is comparable in scale to the Grand Canyon. The age and history of the Monterey Canyon are poorly constrained due to thick sediment cover and sediment disruption from turbidity currents. To address this deficit we analyzed isotopic proxies (Os, Pb, Nd) from hydrogenetic ferromanganese (Fe-Mn) crusts, which grow over millions of years on elevated rock surfaces by precipitation of metals from seawater. Fe-Mn crusts were studied from Davidson Seamount near the base of the Monterey submarine fan, the Taney Seamount Chain, and from Hoss Seamount, which serves as a regional control (Fig.). Fe-Mn crusts were dated using Os isotope ratios compared to those that define the Cenozoic Os isotope seawater curve. Four Fe-Mn crust samples from Davidson and Taney Seamounts deviate from the Os isotopic seawater curve towards radiogenic values after 4.5±1 Ma. Osmium is well mixed in the global ocean and is not subject to significant diffusive reequilibration in Fe-Mn crusts. We therefore attribute deviations from the Os isotope seawater curve to large-scale terrestrial input that ended about 4.5±1 Ma. The two Davidson samples also show more radiogenic Nd isotope values from about 4.5±1 Ma. Lead isotopes in one Davidson Seamount crust, measured by LA-ICPMS, deviate from regional values after 4.5±1 Ma for about 500 ka towards terrestrial sources. The Taney Seamount Fe-Mn crust does not deviate from regional Nd nor Pb isotope values due to its greater distance from Monterey Canyon and the shorter marine residence times of Nd and Pb. Isotope plots of our crust data and compiled data for potential source rocks indicate that the river that carved Monterey Canyon carried sediment with values closer to the Sierra Nevada than to a Colorado Plateau source, with cessation of major riverine input occurring approximately 4.5±1 Ma, an age that we interpret as the end of the Monterey Canyon incision.

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.

ESDAPT - APT PROGRAMMING EDITOR AND INTERPRETER

NASA Technical Reports Server (NTRS)

Premack, T.

1994-01-01

ESDAPT is a graphical programming environment for developing APT (Automatically Programmed Tool) programs for controlling numerically controlled machine tools. ESDAPT has a graphical user interface that provides the user with an APT syntax sensitive text editor and windows for displaying geometry and tool paths. APT geometry statement can also be created using menus and screen picks. ESDAPT interprets APT geometry statements and displays the results in its view windows. Tool paths are generated by batching the APT source to an APT processor (COSMIC P-APT recommended). The tool paths are then displayed in the view windows. Hardcopy output of the view windows is in color PostScript format. ESDAPT is written in C-language, yacc, lex, and XView for use on Sun4 series computers running SunOS. ESDAPT requires 4Mb of disk space, 7Mb of RAM, and MIT's X Window System, Version 11 Release 4, or OpenWindows version 3 for execution. Program documentation in PostScript format and an executable for OpenWindows version 3 are provided on the distribution media. The standard distribution medium for ESDAPT is a .25 inch streaming magnetic tape cartridge (Sun QIC-24) in UNIX tar format. This program was developed in 1992.

OsMADS26 Negatively Regulates Resistance to Pathogens and Drought Tolerance in Rice1[OPEN

PubMed Central

Khong, Giang Ngan; Richaud, Frédérique; Parizot, Boris; Mai, Chung Duc; Bès, Martine; Bourrié, Isabelle; Meynard, Donaldo; Beeckman, Tom; Selvaraj, Michael Gomez; Manabu, Ishitani; Brugidou, Christophe; Nang Do, Vinh; Guiderdoni, Emmanuel; Morel, Jean-Benoit; Gantet, Pascal

2015-01-01

Functional analyses of MADS-box transcription factors in plants have unraveled their role in major developmental programs (e.g. flowering and floral organ identity) as well as stress-related developmental processes, such as abscission, fruit ripening, and senescence. Overexpression of the rice (Oryza sativa) MADS26 gene in rice has revealed a possible function related to stress response. Here, we show that OsMADS26-down-regulated plants exhibit enhanced resistance against two major rice pathogens: Magnaporthe oryzae and Xanthomonas oryzae. Despite this enhanced resistance to biotic stresses, OsMADS26-down-regulated plants also displayed enhanced tolerance to water deficit. These phenotypes were observed in both controlled and field conditions. Interestingly, alteration of OsMADS26 expression does not have a strong impact on plant development. Gene expression profiling revealed that a majority of genes misregulated in overexpresser and down-regulated OsMADS26 lines compared with control plants are associated to biotic or abiotic stress response. Altogether, our data indicate that OsMADS26 acts as an upstream regulator of stress-associated genes and thereby, a hub to modulate the response to various stresses in the rice plant. PMID:26424158

OsPRX2 contributes to stomatal closure and improves potassium deficiency tolerance in rice.

PubMed

Mao, Xiaohui; Zheng, Yanmei; Xiao, Kaizhuan; Wei, Yidong; Zhu, Yongsheng; Cai, Qiuhua; Chen, Liping; Xie, Huaan; Zhang, Jianfu

2018-01-01

Peroxiredoxins (Prxs) which are thiol-based peroxidases have been implicated in the toxic reduction and intracellular concentration regulation of hydrogen peroxide. In Arabidopsis thaliana At2-CysPrxB (At5g06290) has been demonstrated to be essential in maintaining the water-water cycle for proper H 2 O 2 scavenging. Although the mechanisms of 2-Cys Prxs have been extensively studied in Arabidopsis thaliana, the function of 2-Cys Prxs in rice is unclear. In this study, a rice homologue gene of At2-CysPrxB, OsPRX2 was investigated aiming to characterize the effect of 2-Cys Prxs on the K + -deficiency tolerance in rice. We found that OsPRX2 was localized in the chloroplast. Overexpressed OsPRX2 causes the stomatal closing and K + -deficiency tolerance increasing, while knockout of OsPRX2 lead to serious defects in leaves phenotype and the stomatal opening under the K + -deficiency tolerance. Detection of K + accumulation, antioxidant activity of transgenic plants under the starvation of potassium, further confirmed that OsPRX2 is a potential target for engineering plants with improved potassium deficiency tolerance. Copyright © 2017 Elsevier Inc. All rights reserved.

Hydrogenetic Ferromanganese Crusts of the California Continental Margin

NASA Astrophysics Data System (ADS)

Conrad, Tracey A.

Hydrogenetic Ferromanganese (Fe-Mn) crusts grow from seawater and in doing so sequester elements of economic interest and serve as archives of past seawater chemistry. Ferromanganese crusts have been extensively studied in open-ocean environments. However, few studies have examined continent-proximal Fe-Mn crusts especially from the northeast Pacific. This thesis addresses Fe-Mn crusts within the northeast Pacific California continental margin (CCM), which is a dynamic geological and oceanographic environment. In the first of three studies, I analyzed the chemical and mineralogical composition of Fe-Mn crusts and show that continental-proximal processes greatly influence the chemistry and mineralogy of CCM Fe-Mn crusts. When compared to global open-ocean Fe-Mn crusts, CCM crusts have higher concentrations of iron, silica, and thorium with lower concentrations of many elements of economic interest including manganese, cobalt, and tellurium, among other elements. The mineralogy of CCM Fe-Mn crusts is also unique with more birnessite and todorokite present than found in open-ocean samples. Unlike open-ocean Fe-Mn crusts, carbonate-fluorapatite is not present in CCM crusts. This lack of phosphatization makes CCM Fe-Mn crusts excellent candidates for robust paleoceanography records. The second and third studies in this thesis use isotope geochemistry on select CCM Fe-Mn crusts from four seamounts in the CCM to study past terrestrial inputs into the CCM and sources and behavior of Pb and Nd isotopes over the past 7 million years along the northeast Pacific margin. The second study focuses on riverine inputs into the Monterey Submarine Canyon System and sources of the continental material. Osmium isotopes in the crusts are compared to the Cenozoic Os seawater curve to develop an age model for the samples that show the crusts range in age of initiation of crust growth from approximately 20 to 6 Myr. Lead and neodymium isotopes measured in select Fe-Mn crusts show that large amounts of terrestrial material entered the CCM via the Monterey Canyon from prior to 6.8+/-0.5 until 4.5 +/-0.5 Myr ago. These data combined with reconstructions of the paleo-coastline indicate that incision of the modern Monterey Canyon started around 7 Myr ago. Isotope plots of potential source regions indicate that the source of the material is the border of the southern Sierra Nevada and western Basin and Range. This answers a long-standing and fundamental question about the timing and formation of the Monterey Canyon, the dominant feature of the Monterey Bay. The third study presented here uses the differences in lead and neodymium isotopic values in CCM Fe-Mn crusts over time compared to open-ocean Pacific, North Pacific, and Arctic Ocean Fe-Mn crusts to identify regional time-series trends and sources for these important oceanographic tracers. I found that sediment fluxes and inputs of terrestrial material from North American rivers effects the lead and neodymium isotope composition of regional seawater.

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.

WavePropaGator: interactive framework for X-ray free-electron laser optics design and simulations.

PubMed

Samoylova, Liubov; Buzmakov, Alexey; Chubar, Oleg; Sinn, Harald

2016-08-01

This article describes the WavePropaGator ( WPG ) package, a new interactive software framework for coherent and partially coherent X-ray wavefront propagation simulations. The package has been developed at European XFEL for users at the existing and emerging free-electron laser (FEL) facilities, as well as at the third-generation synchrotron sources and future diffraction-limited storage rings. The WPG addresses the needs of beamline scientists and user groups to facilitate the design, optimization and improvement of X-ray optics to meet their experimental requirements. The package uses the Synchrotron Radiation Workshop ( SRW ) C/C++ library and its Python binding for numerical wavefront propagation simulations. The framework runs reliably under Linux, Microsoft Windows 7 and Apple Mac OS X and is distributed under an open-source license. The available tools allow for varying source parameters and optics layouts and visualizing the results interactively. The wavefront history structure can be used for tracking changes in every particular wavefront during propagation. The batch propagation mode enables processing of multiple wavefronts in workflow mode. The paper presents a general description of the package and gives some recent application examples, including modeling of full X-ray FEL beamlines and start-to-end simulation of experiments.

CheckMate 141: 1-Year Update and Subgroup Analysis of Nivolumab as First-Line Therapy in Patients with Recurrent/Metastatic Head and Neck Cancer.

PubMed

Gillison, Maura L; Blumenschein, George; Fayette, Jerome; Guigay, Joel; Colevas, A Dimitrios; Licitra, Lisa; Harrington, Kevin J; Kasper, Stefan; Vokes, Everett E; Even, Caroline; Worden, Francis; Saba, Nabil F; Iglesias Docampo, Lara Carmen; Haddad, Robert; Rordorf, Tamara; Kiyota, Naomi; Tahara, Makoto; Monga, Manish; Lynch, Mark; Li, Li; Ferris, Robert L

2018-06-04

Nivolumab significantly improved overall survival (OS) vs investigator's choice (IC) of chemotherapy at the primary analysis of randomized, open-label, phase 3 CheckMate 141 in patients with recurrent or metastatic (R/M) squamous cell carcinoma of the head and neck (SCCHN). Here, we report that OS benefit with nivolumab was maintained at a minimum follow-up of 11.4 months. Further, OS benefit with nivolumab vs IC was also noted among patients who received first-line treatment for R/M SCCHN after progressing on platinum therapy for locally advanced disease in the adjuvant or primary (i.e., with radiation) setting. The Oncologist 2018. © AlphaMed Press 2018.

The Role of a Potassium Transporter OsHAK5 in Potassium Acquisition and Transport from Roots to Shoots in Rice at Low Potassium Supply Levels1[W][OPEN

PubMed Central

Yang, Tianyuan; Zhang, Song; Hu, Yibing; Wu, Fachi; Hu, Qingdi; Chen, Guang; Cai, Jing; Wu, Ting; Moran, Nava; Yu, Ling; Xu, Guohua

2014-01-01

In plants, K transporter (KT)/high affinity K transporter (HAK)/K uptake permease (KUP) is the largest potassium (K) transporter family; however, few of the members have had their physiological functions characterized in planta. Here, we studied OsHAK5 of the KT/HAK/KUP family in rice (Oryza sativa). We determined its cellular and tissue localization and analyzed its functions in rice using both OsHAK5 knockout mutants and overexpression lines in three genetic backgrounds. A β-glucuronidase reporter driven by the OsHAK5 native promoter indicated OsHAK5 expression in various tissue organs from root to seed, abundantly in root epidermis and stele, the vascular tissues, and mesophyll cells. Net K influx rate in roots and K transport from roots to aerial parts were severely impaired by OsHAK5 knockout but increased by OsHAK5 overexpression in 0.1 and 0.3 mm K external solution. The contribution of OsHAK5 to K mobilization within the rice plant was confirmed further by the change of K concentration in the xylem sap and K distribution in the transgenic lines when K was removed completely from the external solution. Overexpression of OsHAK5 increased the K-sodium concentration ratio in the shoots and salt stress tolerance (shoot growth), while knockout of OsHAK5 decreased the K-sodium concentration ratio in the shoots, resulting in sensitivity to salt stress. Taken together, these results demonstrate that OsHAK5 plays a major role in K acquisition by roots faced with low external K and in K upward transport from roots to shoots in K-deficient rice plants. PMID:25157029

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.

K-shell absorption jump factors and jump ratios in elements between Tm ( Z = 69) and Os ( Z = 76) derived from new mass attenuation coefficient measurements

NASA Astrophysics Data System (ADS)

Kaya, Necati; Tıraşoğlu, Engin; Apaydın, Gökhan; Aylıkcı, Volkan; Cengiz, Erhan

2007-08-01

The K-shell absorption jump factors and jump ratios were derived from new mass attenuation coefficients measured using an energy dispersive X-ray fluorescence (EDXRF) spectrometer for Tm, Yb elements being Tm 2O 3, Yb 2O 3 compounds and pure Lu, Hf, Ta, W, Re and Os. The measurements, in the region 56-77 keV, were done in a transmission geometry utilizing the K α1 , K α2 , K β1 and K β2 X- rays from different secondary source targets (Yb, Ta, Os, W, Re and Ir, etc.) excited by the 123.6 keV γ-photons from an 57Co annular source and detected by an Ultra-LEGe solid state detector with a resolution of 150 eV at 5.9 keV. Experimental results have been compared with theoretically calculated values. The measured values of Tm, Yb, Lu, Hf, Ta, W, Re and Os are reported here for the first time.

PathVisio-Faceted Search: an exploration tool for multi-dimensional navigation of large pathways

PubMed Central

Fried, Jake Y.; Luna, Augustin

2013-01-01

Purpose: The PathVisio-Faceted Search plugin helps users explore and understand complex pathways by overlaying experimental data and data from webservices, such as Ensembl BioMart, onto diagrams drawn using formalized notations in PathVisio. The plugin then provides a filtering mechanism, known as a faceted search, to find and highlight diagram nodes (e.g. genes and proteins) of interest based on imported data. The tool additionally provides a flexible scripting mechanism to handle complex queries. Availability: The PathVisio-Faceted Search plugin is compatible with PathVisio 3.0 and above. PathVisio is compatible with Windows, Mac OS X and Linux. The plugin, documentation, example diagrams and Groovy scripts are available at http://PathVisio.org/wiki/PathVisioFacetedSearchHelp. The plugin is free, open-source and licensed by the Apache 2.0 License. Contact: augustin@mail.nih.gov or jakeyfried@gmail.com PMID:23547033

Profex: a graphical user interface for the Rietveld refinement program BGMN.

PubMed

Doebelin, Nicola; Kleeberg, Reinhard

2015-10-01

Profex is a graphical user interface for the Rietveld refinement program BGMN . Its interface focuses on preserving BGMN 's powerful and flexible scripting features by giving direct access to BGMN input files. Very efficient workflows for single or batch refinements are achieved by managing refinement control files and structure files, by providing dialogues and shortcuts for many operations, by performing operations in the background, and by providing import filters for CIF and XML crystal structure files. Refinement results can be easily exported for further processing. State-of-the-art graphical export of diffraction patterns to pixel and vector graphics formats allows the creation of publication-quality graphs with minimum effort. Profex reads and converts a variety of proprietary raw data formats and is thus largely instrument independent. Profex and BGMN are available under an open-source license for Windows, Linux and OS X operating systems.

GIS Mapping and Monitoring of Health Problems Among the Elderly.

PubMed

Dermatis, Zacharias; Tsaloukidis, Nikolaos; Zacharopoulou, Georgia; Lazakidou, Athina

2017-01-01

The electronic survey in conjunction with GIS in the current study aims at presenting the needs and health problems of the elderly in individual Open Elderly Care Centres in Greece. The online GIS survey enables the continuous monitoring and developing of the health problems of the elderly and helps them in their early care by the healthcare units. GIS survey123 is a customizable tool, which can be used to conduct research that is then published on an Android, iOS, and web platform. The ArcGIS software was used for the geographic mapping of data collected from a wide range of sources, so that health care professionals can investigate the factors associated with the onset of the diseases. Also, direct geographic mapping aims at identifying health problems of the elderly in Greece and transferring information to health care professionals in order to impose proper control measures in a very small period of time.

Profex: a graphical user interface for the Rietveld refinement program BGMN

PubMed Central

Doebelin, Nicola; Kleeberg, Reinhard

2015-01-01

Profex is a graphical user interface for the Rietveld refinement program BGMN. Its interface focuses on preserving BGMN’s powerful and flexible scripting features by giving direct access to BGMN input files. Very efficient workflows for single or batch refinements are achieved by managing refinement control files and structure files, by providing dialogues and shortcuts for many operations, by performing operations in the background, and by providing import filters for CIF and XML crystal structure files. Refinement results can be easily exported for further processing. State-of-the-art graphical export of diffraction patterns to pixel and vector graphics formats allows the creation of publication-quality graphs with minimum effort. Profex reads and converts a variety of proprietary raw data formats and is thus largely instrument independent. Profex and BGMN are available under an open-source license for Windows, Linux and OS X operating systems. PMID:26500466

Mapping RNA-seq Reads with STAR

PubMed Central

Dobin, Alexander; Gingeras, Thomas R.

2015-01-01

Mapping of large sets of high-throughput sequencing reads to a reference genome is one of the foundational steps in RNA-seq data analysis. The STAR software package performs this task with high levels of accuracy and speed. In addition to detecting annotated and novel splice junctions, STAR is capable of discovering more complex RNA sequence arrangements, such as chimeric and circular RNA. STAR can align spliced sequences of any length with moderate error rates providing scalability for emerging sequencing technologies. STAR generates output files that can be used for many downstream analyses such as transcript/gene expression quantification, differential gene expression, novel isoform reconstruction, signal visualization, and so forth. In this unit we describe computational protocols that produce various output files, use different RNA-seq datatypes, and utilize different mapping strategies. STAR is Open Source software that can be run on Unix, Linux or Mac OS X systems. PMID:26334920

Mapping RNA-seq Reads with STAR.

PubMed

Dobin, Alexander; Gingeras, Thomas R

2015-09-03

Mapping of large sets of high-throughput sequencing reads to a reference genome is one of the foundational steps in RNA-seq data analysis. The STAR software package performs this task with high levels of accuracy and speed. In addition to detecting annotated and novel splice junctions, STAR is capable of discovering more complex RNA sequence arrangements, such as chimeric and circular RNA. STAR can align spliced sequences of any length with moderate error rates, providing scalability for emerging sequencing technologies. STAR generates output files that can be used for many downstream analyses such as transcript/gene expression quantification, differential gene expression, novel isoform reconstruction, and signal visualization. In this unit, we describe computational protocols that produce various output files, use different RNA-seq datatypes, and utilize different mapping strategies. STAR is open source software that can be run on Unix, Linux, or Mac OS X systems. Copyright © 2015 John Wiley & Sons, Inc.

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…

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.

Behavior of Re and Os during contact between an aqueous solution and oil: Consequences for the application of the Re-Os geochronometer to petroleum

NASA Astrophysics Data System (ADS)

Mahdaoui, Fatima; Michels, Raymond; Reisberg, Laurie; Pujol, Magali; Poirier, Yannick

2015-06-01

Several recent studies have raised the exciting possibility that oils can be dated using the Re-Os radioisotope system. However the exact nature of the events dated by this technique often remains unclear. Geochronologic interpretation of Re-Os data for oils is hampered by our limited knowledge of how these metals behave in petroleum systems. In particular, it is difficult to understand how isotopic homogenization, an essential prerequisite for the development of an isochronal relationship, can be achieved at the scale of a petroleum basin. The mechanisms capable of fractionating the Re/Os ratio in a suite of oils are also poorly understood. For this reason, we have performed an experimental study aimed at investigating the behavior of Re and Os during a particularly widespread phenomenon in petroleum systems, the interaction of formation waters with oils during migration. Contact experiments between natural oils and aqueous solutions enriched in Re and/or Os were carried out for varying lengths of time (6 h to 5 months), at different temperatures (25-150 °C), over a wide range of metal concentrations in the enriched solution (0.001-100 μg/g for Re; 1 and 10 ng/g for Os). In addition, the effect of oil composition on Re-Os exchange at the water-oil interface was examined by testing two oils with very different properties. All of our results demonstrate that Re and Os are transferred massively and very rapidly from the aqueous solution to the organic phase. This is true regardless of temperature or oil composition. It is also true for a very wide range of metal concentrations in the aqueous solution, up to an apparent saturation level that exceeds natural concentrations in oils by several orders of magnitude. Given the efficiency of Re and Os transfer from water to oil demonstrated here, and assuming that our findings are applicable to natural conditions, water/oil ratios of only about 250 would be needed to explain the Re and Os contents of most oils, based on the measured concentrations of Re and Os in groundwaters. Thus transfer of Re and Os from formation waters could plausibly provide a source for these metals in oils. Waters from a given basin may have roughly homogeneous Os isotopic compositions, approximating the average value of the source rocks. On the other hand, variable Re/Os ratios might be expected to develop, as a result of interaction with various phases (e.g. Fe-Mn oxides or authigenic pyrite) encountered by the water as it flows through the reservoir. If homogeneous 187Os/188Os ratios coupled with variable Re/Os ratios are transferred to the oils with which the waters come in contact, the isotopic geochronometer could be reset.

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.

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.

Geochemical markers of sedimentary organic matter in Todos os Santos Bay, Bahia - Brazil. Indicators of sources and preservation.

PubMed

de Souza, José Roberto Bispo; do Rosário Zucchi, Maria; Costa, Alexandre Barreto; de Azevedo, Antonio Expedito Gomes; Spano, Saulo

2017-06-30

Natural stable isotopes, such as carbon (C) and nitrogen (N), are modern tools to assess geochemical processes. C and N in organic matter can carry fingerprints of their hydrologic flows and sedimentary processes, including any anthropogenic modification on the natural system. This study focuses on the determination of aliphatic and polycyclic aromatic hydrocarbons and isotopic ratio in the sediment of Todos os Santos Bay (TSB). The isotopic results of the total organic matter indicate varied contribution marine and terrigenous. Typical rates of PAHs mainly indicate a pyrogenic source and mixture between pyrogenic and petrogenic sources. Typical ratios for the n-alkanes indicate the presence of petroleum hydrocarbons. The isotopic composition of n-alkanes suggests a mixture of sources, with the possible contribution of petrogenic. Copyright © 2017. Published by Elsevier Ltd.

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

Origin of the Mackenzie large igneous province and sourcing of flood basalts from layered intrusions

NASA Astrophysics Data System (ADS)

Day, J. M.; Pearson, D.

2013-12-01

The 1.27 Ga Coppermine continental flood basalt (CFB) in northern Canada represents the extrusive manifestation of the Mackenzie large igneous province (LIP) that includes the Mackenzie dyke swarm and the Muskox layered intrusion. New Re-Os isotope and highly siderophile element (HSE: Re, Pd, Pt, Ru, Ir, Os) abundance data are reported together with whole-rock major- and trace-element abundances and Nd isotopes to examine the behaviour of the HSE during magmatic differentiation and to place constraints on the extent of crustal interaction with mantle-derived melts. Mineral-chemical data are also reported for an unusual andesite glass flow (4.9 wt.% MgO) found in proximity to newly recognised picrites (>20 wt.% MgO) in the lowermost stratigraphy of the Coppermine CFB. Compositions of mineral phases in the andesite are similar to equivalent phases found in Muskox Intrusion chromitites and the melt composition is identical to Muskox chromite melt inclusions. Elevated HSE contents (e.g., 3.8 ppb Os) and the mantle-like initial Os isotope composition of this andesitic glass contrast strongly with oxygen isotope and lithophile element evidence for extensive crustal contamination. These signatures implicate an origin for the glass as a magma mingling product formed within the Muskox Intrusion during chromitite genesis. The combination of crust and mantle signatures define roles for both these reservoirs in chromitite genesis, but the HSE appear to be dominantly mantle-sourced. Combined with Nd isotope data that places the feeder for lower Coppermine CFB picrites and basalts within the Muskox Intrusion, this provides the strongest evidence yet for direct processing of some CFB within upper-crustal magma chambers. Modeling of absolute and relative HSE abundances in CFB reveal that HSE concentrations decrease with increasing fractionation for melts with <8×1 wt.% MgO in the Coppermine CFB, with picrites (>13.5wt.% MgO) from CFB having higher Os abundances than ocean island basalt (OIB) equivalents. The differences between CFB and OIB picrite absolute Os abundances may result from higher degrees of partial melting to form CFB but may also reflect incorporation of trace sulphide in CFB picrites from magmas that reached S-saturation in shallow-level magma chambers. Significant inter-element fractionation between (Re+Pt+Pd)/(Os+Ir+Ru) are generated during magmatic differentiation in response to strongly contrasting partitioning of these two groups of elements into sulphides and/or HSE-rich alloys. Furthermore, fractional crystallization has a greater role on absolute and relative HSE abundances than crustal contamination under conditions of CFB petrogenesis due to the dilution effect of continental crust. The Coppermine CFB define a Re-Os isochron with an age of 1263 +16/-20 Ma and initial gamma Os = +2.2×0.8. Combined data for the basaltic and intrusive portions of the Mackenzie LIP indicate a mantle source broadly within the range of the primitive upper mantle. The majority of Archaean komatiites and Phanerozoic CFB also require mantle sources with primitive upper mantle to chondritic Re/Os evolution, with exceptions typically being from analyses of highly-fractionated MgO-poor basalts.

Rhenium-osmium systematics of calcium-aluminium-rich inclusions in carbonaceous chondrites

USGS Publications Warehouse

Becker, H.; Morgan, J.W.; Walker, R.J.; MacPherson, G.J.; Grossman, J.N.

2001-01-01

The Re-Os isotopic systematics of calcium-aluminium-rich inclusions (CAIs) in chondrites were investigated in order to shed light on the behavior of the Re-Os system in bulk chondrites, and to constrain the timing of chemical fractionation in primitive chondrites. CAIs with relatively unfractionated rare earth element (REE) patterns (groups I, III, V, VI) define a narrow range of 187Re/188Os (0.3764-0.4443) and 187Os/188Os (0.12599-0.12717), and high but variable Re and Os abundances (3209-41,820 ppb Os). In contrast, CAIs that show depletions in highly refractory elements and strongly fractionated REE patterns (group II) also show a much larger range in 187Re/188Os (0.409-0.535) and 187Os/188Os (0.12695-0.13770), and greater than an order of magnitude lower Re and Os abundances than other groups (e.g., 75.7-680.2 ppb Os). Sixteen bulk CAIs and CAI splits plot within analytical uncertainty of a 4558 Ga reference isochron, as is expected for materials of this antiquity. Eight samples, however, plot off the isochron. Several possible reasons for these deviations are discussed. Data for multiple splits of one CAI indicate that the nonisochronous behavior for at least this CAI is the result of Re-Os reequilibration at approximately 1.6 Ga. Thus, the most likely explanation for the deviations of most of the nonisochronous CAIs is late-stage open-system behavior of Re and Os in the asteroidal environment. The 187Os/188Os-Os systematics of CAIs are consistent with previous models that indicate group II CAIs are mixtures of components that lost the bulk of their highly refractory elements in a previous condensation event and a minor second component that provided refractory elements at chondritic relative proportions. The high Re/Os of group II CAIs relative to other CAIs and chondrite bulk rocks may have been caused by variable mobilization of Re and Os during medium- to low-temperature parent body alteration ??4.5 Ga ago. This model is favored over nebular models, which pose several difficulties. The narrow range of 187Os/188Os in group I, III, V, and VI bulk CAIs, and the agreement with 187Os/188Os of whole rock carbonaceous chondrites suggest that on a bulk inclusion scale, secondary alteration only modestly fractionated Re/Os in these CAIs. The average of 187Os/188Os for group I, III, V, and VI CAIs is indistinguishable from average CI chondrites, indicating a modern solar system value for 187Os/188Os of 0.12650, corresponding to a 187Re/188Os of 0.3964. Copyright ?? 2001 Elsevier Science Ltd.

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.

Biophysical mechanism of transient retinal phototropism in rod photoreceptors.

PubMed

Zhao, Xiaohui; Thapa, Damber; Wang, Benquan; Gai, Shaoyan; Yao, Xincheng

2016-02-13

Oblique light stimulation evoked transient retinal phototropism (TRP) has been recently detected in frog and mouse retinas. High resolution microscopy of freshly isolated retinas indicated that the TRP is predominated by rod photoreceptors. Comparative confocal microscopy and optical coherence tomography (OCT) revealed that the TRP predominantly occurred from the photoreceptor outer segment (OS). However, biophysical mechanism of rod OS change is still unknown. In this study, frog retinal slices, which open a cross section of retinal photoreceptor and other functional layers, were used to test the effect of light stimulation on rod OS. Near infrared light microscopy was employed to monitor photoreceptor changes in retinal slices stimulated by a rectangular-shaped visible light flash. Rapid rod OS length change was observed after the stimulation delivery. The magnitude and direction of the rod OS change varied with the position of the rods within the stimulated area. In the center of stimulated region the length of the rod OS shrunk, while in the peripheral region the rod OS tip swung towards center region in the plane perpendicular to the incident stimulus light. Our experimental result and theoretical analysis suggest that the observed TRP may reflect unbalanced disc-shape change due to localized pigment bleaching. Further investigation is required to understand biochemical mechanism of the observed rod OS kinetics. Better study of the TRP may provide a noninvasive biomarker to enable early detection of age-related macular degeneration (AMD) and other diseases that are known to produce retinal photoreceptor dysfunctions.

A novel lymphoid enhancer-binding factor 1-cytoglobin axis promotes extravasation of osteosarcoma cells into the lungs.

PubMed

Pongsuchart, Mongkol; Kuchimaru, Takahiro; Yonezawa, Sakiko; Tran, Diem Thi Phuong; Kha, Nguyen The; Hoang, Ngoc Thi Hong; Kadonosono, Tetsuya; Kizaka-Kondoh, Shinae

2018-06-21

Lung metastasis is a major cause of mortality in patients with osteosarcoma (OS). A better understanding of the molecular mechanism of OS lung metastasis may facilitate development of new therapeutic strategies to prevent the metastasis. We have established high- and low-metastatic sublines (LM8-H and LM8-L respectively) from Dunn OS cell line LM8 by using in vivo image-guided screening. Among the genes whose expression was significantly increased in LM8-H compared to LM8-L, the transcription factor lymphoid enhancer-binding factor 1 (LEF1) was identified as a factor that promotes LM8-H cell extravasation into the lungs. To identify downstream effectors of LEF1 that are involved in OS lung metastasis, 13 genes were selected based on the LM8 microarray data and genome-wide meta-analysis of a public database for OS patients. Among them, the cytoglobin (Cygb) gene was identified as a key effector in promoting OS extravasation into the lungs. CYGB overexpression increased the extravasation ability of LM8-L cells, whereas knocking out the Cygb gene in LM8-H cells reduced this ability. Our results uncovered a novel LEF1-CYGB axis in OS lung metastasis and may open a new avenue for developing therapeutic strategies to prevent OS lung metastasis. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Rice SPX-Major Facility Superfamily3, a Vacuolar Phosphate Efflux Transporter, Is Involved in Maintaining Phosphate Homeostasis in Rice1[OPEN

PubMed Central

Ying, Yinghui; Wang, Shoudong; Secco, David; Liu, Yu; Whelan, James; Tyerman, Stephen D.; Shou, Huixia

2015-01-01

To maintain a stable cytosol phosphate (Pi) concentration, plant cells store Pi in their vacuoles. When the Pi concentration in the cytosol decreases, Pi is exported from the vacuole into the cytosol. This export is mediated by Pi transporters on the tonoplast. In this study, we demonstrate that SYG1, PHO81, and XPR1 (SPX)-Major Facility Superfamily (MFS) proteins have a similar structure with yeast (Saccharomyces cerevisiae) low-affinity Pi transporters Phosphatase87 (PHO87), PHO90, and PHO91. OsSPX-MFS1, OsSPX-MFS2, and OsSPX-MFS3 all localized on the tonoplast of rice (Oryza sativa) protoplasts, even in the absence of the SPX domain. At high external Pi concentration, OsSPX-MFS3 could partially complement the yeast mutant strain EY917 under pH 5.5, which lacks all five Pi transporters present in yeast. In oocytes, OsSPX-MFS3 was shown to facilitate Pi influx or efflux depending on the external pH and Pi concentrations. In contrast to tonoplast localization in plants cells, OsSPX-MFS3 was localized to the plasma membrane when expressed in both yeast and oocytes. Overexpression of OsSPX-MFS3 results in decreased Pi concentration in the vacuole of rice tissues. We conclude that OsSPX-MFS3 is a low-affinity Pi transporter that mediates Pi efflux from the vacuole into cytosol and is coupled to proton movement. PMID:26424157

Two ATP Binding Cassette G Transporters, Rice ATP Binding Cassette G26 and ATP Binding Cassette G15, Collaboratively Regulate Rice Male Reproduction1[OPEN

PubMed Central

Zhao, Guochao; Shi, Jianxin; Liang, Wanqi; Xue, Feiyang; Luo, Qian; Zhu, Lu; Qu, Guorun; Chen, Mingjiao; Schreiber, Lukas; Zhang, Dabing

2015-01-01

Male reproduction in higher plants requires the support of various metabolites, including lipid molecules produced in the innermost anther wall layer (the tapetum), but how the molecules are allocated among different anther tissues remains largely unknown. Previously, rice (Oryza sativa) ATP binding cassette G15 (ABCG15) and its Arabidopsis (Arabidopsis thaliana) ortholog were shown to be required for pollen exine formation. Here, we report the significant role of OsABCG26 in regulating the development of anther cuticle and pollen exine together with OsABCG15 in rice. Cytological and chemical analyses indicate that osabcg26 shows reduced transport of lipidic molecules from tapetal cells for anther cuticle development. Supportively, the localization of OsABCG26 is on the plasma membrane of the anther wall layers. By contrast, OsABCG15 is polarly localized in tapetal plasma membrane facing anther locules. osabcg26 osabcg15 double mutant displays an almost complete absence of anther cuticle and pollen exine, similar to that of osabcg15 single mutant. Taken together, we propose that OsABCG26 and OsABCG15 collaboratively regulate rice male reproduction: OsABCG26 is mainly responsible for the transport of lipidic molecules from tapetal cells to anther wall layers, whereas OsABCG15 mainly is responsible for the export of lipidic molecules from the tapetal cells to anther locules for pollen exine development. PMID:26392263

Biophysical mechanism of transient retinal phototropism in rod photoreceptors

NASA Astrophysics Data System (ADS)

Zhao, Xiaohui; Thapa, Damber; Wang, Benquan; Gai, Shaoyan; Yao, Xincheng

2016-03-01

Oblique light stimulation evoked transient retinal phototropism (TRP) has been recently detected in frog and mouse retinas. High resolution microscopy of freshly isolated retinas indicated that the TRP is predominated by rod photoreceptors. Comparative confocal microscopy and optical coherence tomography (OCT) revealed that the TRP predominantly occurred from the photoreceptor outer segment (OS). However, biophysical mechanism of rod OS change is still unknown. In this study, frog retinal slices, which open a cross section of retinal photoreceptor and other functional layers, were used to test the effect of light stimulation on rod OS. Near infrared light microscopy was employed to monitor photoreceptor changes in retinal slices stimulated by a rectangular-shaped visible light flash. Rapid rod OS length change was observed after the stimulation delivery. The magnitude and direction of the rod OS change varied with the position of the rods within the stimulated area. In the center of stimulated region the length of the rod OS shrunk, while in the peripheral region the rod OS tip swung towards center region in the plane perpendicular to the incident stimulus light. Our experimental result and theoretical analysis suggest that the observed TRP may reflect unbalanced disc-shape change due to localized pigment bleaching. Further investigation is required to understand biochemical mechanism of the observed rod OS kinetics. Better study of the TRP may provide a noninvasive biomarker to enable early detection of age-related macular degeneration (AMD) and other diseases that are known to produce retinal photoreceptor dysfunctions.

Safety of robotic prostatectomy over time: a national study of in-hospital injury.

PubMed

Chughtai, Bilal; Isaacs, Abby J; Mao, Jialin; Lee, Richard; Te, Alexis; Kaplan, Steven; Sedrakyan, Art

2015-02-01

To assess national trends of iatrogenic complications and associated burden of care among patients undergoing open and minimally invasive prostatectomy using a population-based cohort. Using the nationally representative cohort, we identified patients who were diagnosed with prostate cancer, and underwent prostatectomy during 2001 and 2011. We determined the risk of iatrogenic complication and length of stay (LOS) over time among open and minimally invasive surgery (MIS) patients. Hierarchical multivariable logistic regression was performed to assess the changes over time and elucidate independent predictors of iatrogenic complications. We identified 556,932 and 219,434 prostate cancer patients undergoing open and minimally invasive prostatectomy. We found that iatrogenic complications for MIS were less frequent in later years (years 09-11 vs. year 01-02 odds ratio (OR), 0.21; 95% confidence intervals (CI), 0.09-0.40). MIS was associated with higher risk of iatrogenic complications in early period (years 01-02 OR, 3.81; 95% CI, 1.72-8.41), but lower risk in late period (years 09-11 OR 0.72 95% CI 0.61-0.86). Patients who experienced iatrogenic complications tended to have longer LOS (Median: Open vs. MIS, 4 days vs. 3 day) than those who didn't (Median: Open vs. MIS, 2 days vs. 1 day), regardless of procedure type. We found that minimally invasive prostatectomy is associated with lower risk of iatrogenic complications when compared with open surgery (OS). However, as "learning curve" is overcome over time, MIS becomes safer than OS. Iatrogenic complications are not benign and seem to be associated with higher burden of inpatient care.

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.

Osmium isotope evidence for uniform distribution of s- and r-process components in the early solar system

NASA Astrophysics Data System (ADS)

Yokoyama, Tetsuya; Rai, Vinai K.; Alexander, Conel M. O'D.; Lewis, Roy S.; Carlson, Richard W.; Shirey, Steven B.; Thiemens, Mark H.; Walker, Richard J.

2007-07-01

We have precisely measured Os isotopic ratios in bulk samples of five carbonaceous, two enstatite and two ordinary chondrites, as well as the acid-resistant residues of three carbonaceous chondrites. All bulk meteorite samples have uniform 186Os/ 188Os, 188Os/ 189Os and 190Os/ 189Os ratios, when decomposed by an alkaline fusion total digestion technique. These ratios are also identical to estimates for Os in the bulk silicate Earth. Despite Os isotopic homogeneity at the bulk meteorite scale, acid insoluble residues of three carbonaceous chondrites are enriched in 186Os, 188Os and 190Os, isotopes with major contributions from stellar s-process nucleosynthesis. Conversely, these isotopes are depleted in acid soluble portions of the same meteorites. The complementary enriched and depleted fractions indicate the presence of at least two types of Os-rich components in these meteorites, one enriched in Os isotopes produced by s-process nucleosynthesis, the other enriched in isotopes produced by the r-process. Presolar silicon carbide is the most probable host for the s-process-enriched Os present in the acid insoluble residues. Because the enriched and depleted components present in these meteorites are combined in proportions resulting in a uniform chondritic/terrestrial composition, it requires that disparate components were thoroughly mixed within the solar nebula at the time of the initiation of planetesimal accretion. This conclusion contrasts with evidence from the isotopic compositions of some other elements (e.g., Sm, Nd, Ru, Mo) that suggests heterogeneous distribution of matter with disparate nucleosynthetic sources within the nebula.

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.

The role of maintenance thalidomide therapy in multiple myeloma: MRC Myeloma IX results and meta-analysis.

PubMed

Morgan, Gareth J; Gregory, Walter M; Davies, Faith E; Bell, Sue E; Szubert, Alexander J; Brown, Julia M; Coy, Nuria N; Cook, Gordon; Russell, Nigel H; Rudin, Claudius; Roddie, Huw; Drayson, Mark T; Owen, Roger G; Ross, Fiona M; Jackson, Graham H; Child, J Anthony

2012-01-05

Thalidomide maintenance has the potential to modulate residual multiple myeloma (MM) after an initial response. This trial compared the effect of thalidomide maintenance and no maintenance on progression-free survival (PFS) and overall survival (OS) in MM patients. After intensive or nonintensive induction therapy, 820 newly diagnosed MM patients were randomized to open-label thalidomide maintenance until progression, or no maintenance. Interphase FISH (iFISH) analysis was performed at study entry. Median PFS was significantly longer with thalidomide maintenance (log-rank P < .001). Median OS was similar between regimens (log-rank P = .40). Patients with favorable iFISH showed improved PFS (P = .004) and a trend toward a late survival benefit. Patients with adverse iFISH receiving thalidomide showed no significant PFS benefit and worse OS (P = .009). Effective relapse therapy enhanced survival after progression, translating into a significant OS benefit. Meta-analysis of this and other studies show a significant late OS benefit (P < .001, 7-year difference hazard ratio = 12.3; 95% confidence interval, 5.5-19.0). Thalidomide maintenance significantly improves PFS and can be associated with improved OS. iFISH testing is important in assessing the clinical impact of maintenance therapy. Overview analysis demonstrated that thalidomide maintenance was associated with a significant late OS benefit. This trial was registered at www.isrctn.org as #ISRCTN68454111.

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.

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

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.

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

Simultaneous Pure Laparoscopic Resection of Primary Colorectal Cancer and Synchronous Liver Metastases: A Single Institution Experience with Propensity Score Matching Analysis.

PubMed

Ivanecz, Arpad; Krebs, Bojan; Stozer, Andraz; Jagric, Tomaz; Plahuta, Irena; Potrc, Stojan

2018-03-01

The aim of the study was to compare the outcome of pure laparoscopic and open simultaneous resection of both the primary colorectal cancer and synchronous colorectal liver metastases (SCLM). From 2000 to 2016 all patients treated by simultaneous resection were assessed for entry in this single center, clinically nonrandomized trial. A propensity score matching was used to compare the laparoscopic group (LAP) to open surgery group (OPEN). Primary endpoints were perioperative and oncologic outcomes. Secondary endpoints were overall survival (OS) and disease-free survival (DFS). Of the 82 patients identified who underwent simultaneous liver resection for SCLM, 10 patients underwent LAP. All these consecutive patients from LAP were matched to 10 comparable OPEN. LAP reduced the length of hospital stay (P = 0.044) and solid food oral intake was faster (P = 0.006) in this group. No patient undergoing the laparoscopic procedure experienced conversion to the open technique. No difference was observed in operative time, blood loss, transfusion rate, narcotics requirement, clinical risk score, resection margin, R0 resections rate, morbidity, mortality and incisional hernias rate. The two groups did not differ significantly in terms of the 3-year OS rate (90 vs. 75%; P = 0.842) and DFS rate (60 vs. 57%; P = 0.724). LAP reduced the length of hospital stay and offers faster solid food oral intake. Comparable oncologic and survival outcomes can be achieved. LAP is beneficial for well selected patients in high volume centers with appropriate expertise.

Unusual Small Subunit That Is Not Expressed in Photosynthetic Cells Alters the Catalytic Properties of Rubisco in Rice1[C][W][OPEN

PubMed Central

Morita, Koichi; Hatanaka, Tomoko; Misoo, Shuji; Fukayama, Hiroshi

2014-01-01

Rubisco small subunits (RbcSs) are encoded by a nuclear multigene family in plants. Five RbcS genes, OsRbcS1, OsRbcS2, OsRbcS3, OsRbcS4, and OsRbcS5, have been identified in rice (Oryza sativa). Among them, the amino acid sequence of OsRbcS1 differs notably from those of other rice RbcSs. Phylogenetic analysis showed that OsRbcS1 is genetically distant from other rice RbcS genes and more closely related to RbcS from a fern and two woody plants. Reverse transcription-PCR and promoter β-glucuronidase analyses revealed that OsRbcS1 was not expressed in leaf blade, a major photosynthetic organ in rice, but was expressed in leaf sheath, culm, anther, and root central cylinder. In leaf blade of transgenic rice overexpressing OsRbcS1 and leaf sheath of nontransgenic rice, OsRbcS1 was incorporated into the Rubisco holoenzyme. Incorporation of OsRbcS1 into Rubisco increased the catalytic turnover rate and Km for CO2 of the enzyme and slightly decreased the specificity for CO2, indicating that the catalytic properties were shifted to those of a high-activity type Rubisco. The CO2 assimilation rate at low CO2 partial pressure was decreased in overexpression lines but was not changed under ambient and high CO2 partial pressure compared with nontransgenic rice. Although the Rubisco content was increased, Rubisco activation state was decreased in overexpression lines. These results indicate that the catalytic properties of Rubisco can be altered by ectopic expression of OsRbcS1, with substantial effects on photosynthetic performance in rice. We believe this is the first demonstration of organ-specific expression of individual members of the RbcS gene family resulting in marked effects on Rubisco catalytic activity. PMID:24254313

MAOHUZI6/ETHYLENE INSENSITIVE3-LIKE1 and ETHYLENE INSENSITIVE3-LIKE2 Regulate Ethylene Response of Roots and Coleoptiles and Negatively Affect Salt Tolerance in Rice1[OPEN

PubMed Central

Yang, Chao; Ma, Biao; He, Si-Jie; Xiong, Qing; Duan, Kai-Xuan; Yin, Cui-Cui; Chen, Hui; Lu, Xiang; Chen, Shou-Yi; Zhang, Jin-Song

2015-01-01

Ethylene plays important roles in plant growth, development, and stress responses. The ethylene signaling pathway has been studied extensively, mainly in Arabidopsis (Arabidopsis thaliana). However, the molecular mechanism of ethylene signaling is largely unknown in rice (Oryza sativa). Previously, we have isolated a set of rice ethylene-response mutants. Here, we characterized the mutant maohuzi6 (mhz6). Through map-based cloning, we found that MHZ6 encodes ETHYLENE INSENSITIVE3-LIKE1 (OsEIL1), a rice homolog of ETHYLENE INSENSITIVE3 (EIN3), which is the master transcriptional regulator of ethylene signaling in Arabidopsis. Disruption of MHZ6/OsEIL1 caused ethylene insensitivity mainly in roots, whereas silencing of the closely related OsEIL2 led to ethylene insensitivity mainly in coleoptiles of etiolated seedlings. This organ-specific functional divergence is different from the functional features of EIN3 and EIL1, both of which mediate the incomplete ethylene responses of Arabidopsis etiolated seedlings. In Arabidopsis, EIN3 and EIL1 play positive roles in plant salt tolerance. In rice, however, lack of MHZ6/OsEIL1 or OsEIL2 functions improves salt tolerance, whereas the overexpressing lines exhibit salt hypersensitivity at the seedling stage, indicating that MHZ6/OsEIL1 and OsEIL2 negatively regulate salt tolerance in rice. Furthermore, this negative regulation by MHZ6/OsEIL1 and OsEIL2 in salt tolerance is likely attributable in part to the direct regulation of HIGH-AFFINITY K+ TRANSPORTER2;1 expression and Na+ uptake in roots. Additionally, MHZ6/OsEIL1 overexpression promotes grain size and thousand-grain weight. Together, our study provides insights for the functional diversification of MHZ6/OsEIL1 and OsEIL2 in ethylene response and finds a novel mode of ethylene-regulated salt stress response that could be helpful for engineering salt-tolerant crops. PMID:25995326

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.

The COMPASS-Like Complex Promotes Flowering and Panicle Branching in Rice1[OPEN

PubMed Central

Wang, Shiliang; Jiang, Haiyang; Cheng, Beijiu

2018-01-01

Flowering time (heading date) and panicle branch number are important agronomic traits that determine yield in rice (Oryza sativa). The activation of flowering requires histone methylation, but the roles of trimethylation of Lys 4 of histone 3 (H3K4me3) in modulating heading date and panicle development are unclear. Here, we showed that the COMPASS-like complex promotes flowering and panicle branching. The rice (Oryza sativa) WD40 protein OsWDR5a interacts with the TRITHORAX-like protein OsTrx1/SET domain group protein 723 (SDG723) to form the core components of the COMPASS-like complex. Plants in which OsWDR5a or OsTrx1 expression was decreased by RNA interference produced fewer secondary branches and less grain and exhibited a delayed heading date under long-day and short-day conditions, whereas loss of OsWDR5a function resulted in embryo lethality. OsWDR5a binds to Early heading date 1 to regulate its H3K4me3 and expression levels. Together, our results show that the COMPASS-like complex promotes flowering and panicle development and suggest that modulation of H3K4me3 levels by the COMPASS-like complex is critical for rice development. PMID:29440594

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…

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…

Studying the influence of strong meteorological disturbances in the Earth's lower atmosphere on variations of ionospheric parameters in the Asian region of Russia

NASA Astrophysics Data System (ADS)

Chernigovskaya, Marina; Kurkin, Vladimir; Orlov, Igor; Oinats, Alexey; Sharkov, Eugenii

2010-05-01

Short-period temporal variations of ionospheric parameters were analyzed to study probabilities of manifestation of strong meteorological disturbances in the Earth's lower atmosphere in variations of upper atmosphere parameters in a zone far removed from a disturbance source. In the analysis, we used data on maximum observed frequencies (MOF) of oblique sounding (OS) signals along Norilsk-Irkutsk, Magadan-Irkutsk, and Khabarovsk-Irkutsk paths in East Siberia and the Far East. These data were obtained during solar minimum at equinoxes (March, September) in 2008-2009. Analyzing effects of wave disturbances in ionospheric parameters, we take into account helio-geomagnetic and meteorological conditions in regions under study to do an effective separation between disturbances associated with magnetospheric-ionospheric coupling and those induced by the influence of the lower atmosphere on the upper one. The frequency analysis we conducted revealed time intervals with higher intensity of short-period oscillations which may have been interpreted as manifestation of large-scale traveling ionospheric disturbances (TIDs) whose sources were internal gravity waves (IGWs) with periods of 1-5 hours. The complex analysis of helio-geomagnetic, ionospheric, and atmospheric data as well as data on tropical cyclones established that the detected TIDs were unrelated to helio-geomagnetic disturbances (2008-2009 exhibited solar minimum and quiet geomagnetic conditions). The analysis of other potential sources of the observed short-period wave disturbances shows that observed TIDs do not always coincide in time with passage of local meteorological fronts through the region of subionospheric points of OS paths and are not associated with passage of solar terminator. An attempt was made to connect a number of detected TIDs with ionospheric responses to tropical cyclones (TC) which were in active phase in the north-west of the Pacific Ocean during the periods considered. A considerable increase in energy of short-period wave disturbances was observed along Khabarovsk-Irkutsk, Magadan-Irkutsk, and Norilsk-Irkutsk paths during the active tropical cyclogenesis in September 2008-2009. Intensity of the observed TIDs decreased as midpoints of OS paths moved westward away from potential IGW sources. Ionospheric responses to wave disturbance propagation from the same IGW sources differ in the OS paths under analysis. This must be associated with different geometry of the OS paths as well as with the fact that the IGW source under consideration changes in intensity and its coordinates (stages and motion paths of tropical cyclones) during TC development. Thus there is an angular dependence between the wave disturbance propagation direction and the line connecting midpoints of the OS paths. Velocities of wave disturbance propagation (~90-170 m/s) were measured from the delay period of TIDs passage in regions of midpoints of spaced-apart OS paths. Short-period TIDs can also be observed at spring equinox in March 2008-2009 under quiet helio-geomagnetic conditions and in the absence of active tropical cyclones in the north-west of the Pacific Ocean, but TIDs energy is much lower than that in autumn. Authors note it was not possible to identify potential IGW sources for some TIDs within the scope of this work. These TIDs may be related to ionospheric responses to seasonal transitions in the upper atmosphere dynamic regime during the equinoxes under study. Further systematic investigations in this area of study are required to store statistics of observations of ionospheric responses to strong meteorological disturbances. The study was supported by the RFBR grant № 09-05-00760.

Glioblastoma Recurrence Patterns After Radiation Therapy With Regard to the Subventricular Zone

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

Adeberg, Sebastian, E-mail: Sebastian.adeberg@med.uni-heidelberg; König, Laila; Bostel, Tilman

Purpose: We evaluated the influence of tumor location and tumor spread in primary glioblastoma (GBM), with respect to the subventricular zone (SVZ), on recurrence behavior, progression-free survival (PFS), and overall survival (OS). Methods and Materials: 607 patients (376 male and 231 female) with a median age of 61.3 years (range, 3.0-87.9 years) and primary GBM treated with radiation therapy (RT) from 2004 to 2012 at a single institution were included in this retrospective study. Preoperative images and follow-up examination results were assessed to evaluate tumor location. Tumors were classified according to the tumor location in relation to the SVZ. Results: The medianmore » PFS of the study population was 5.2 months (range, 1-91 months), and the median OS was 13.8 months (range, 1-102 months). Kaplan-Meier analysis showed that tumor location in close proximity to the SVZ was associated with a significant decline in PFS and OS (4.8 and 12.3 months, respectively; each P<.001). Furthermore, in cases where tumors were involved with the SVZ, distant cerebral progression (43.8%; P=.005) and multifocal progression (39.8%; P=.008) were more common. Interestingly, opening of the ventricle during the previous surgery showed no impact on PFS and OS. Conclusion: GBM in close proximity to the SVZ was associated with decreased survival and had a higher risk of multifocal or distant progression. Ventricle opening during surgery had no effect on survival rates.« less

Early mantle heterogeneities in the Réunion hotspot source inferred from highly siderophile elements in cumulate xenoliths

NASA Astrophysics Data System (ADS)

Peters, Bradley J.; Day, James M. D.; Taylor, Lawrence A.

2016-08-01

Ultramafic cumulate rocks form during intrusive crystallization of high-MgO magmas, incorporating relatively high abundances of compatible elements, including Cr and Ni, and high abundances of the highly siderophile elements (HSE: Os, Ir, Ru, Pt, Pd, Re). Here, we utilize a suite of cumulate xenoliths from Piton de la Fournaise, La Réunion (Indian Ocean), to examine the mantle source composition of the Réunion hotspot using HSE abundances and Os isotopes. Dunite and wherlite xenoliths and associated lavas from the Piton de la Fournaise volcanic complex span a range of MgO contents (46 to 7 wt.%), yet exhibit remarkably homogeneous 187Os/188Os (0.1324 ± 0.0014, 2σ), representing the Os-isotopic composition of Réunion hotspot primary melts. A significant fraction of the xenoliths also have primitive upper-mantle (PUM) normalized HSE patterns with elevated Ru and Pd (PUM-normalized Ru/Ir and Pd/Ir of 0.8-6.3 and 0.2-7.2, respectively). These patterns are not artifacts of alteration, fractional crystallization, or partial melting processes, but rather require a primary magma with similar relative enrichments. Some highly olivine-phyric (>40 modal percent olivine) Piton de la Fournaise lavas also preserve these relative Ru and Pd enrichments, while others preserve a pattern that is likely related to sulfur saturation in evolved melts. The estimate of HSE abundances in PUM indicates high Ru/Ir and Pd/Pt values relative to carbonaceous, ordinary and enstatite chondrite meteorite groups. Thus, the existence of cumulate rocks with even more fractionated HSE patterns relative to PUM suggests that the Réunion hotspot samples a yet unrecognized mantle source. The origin of fractionated HSE patterns in Réunion melts may arise from sampling of a mantle source that experienced limited late accretion (<0.2% by mass) compared with PUM (0.5-0.8%), possibly involving impactors that were distinct from present-day chondrites, or limited core-mantle interactions. Given the remarkably homogeneous Os, Pb, and noble-gas isotopic signatures of Réunion, which plot near the convergence point of isotopic data for many hotspots, such a conclusion provides evidence for an early differentiated and subsequently isolated mantle domain that may be partially sampled by some ocean island basalts.

Evaluation of nano-ZnOs as a novel Zn source for marine fish: importance of digestive physiology.

PubMed

Wang, Jian; Wang, Aili; Wang, Wen-Xiong

2017-10-01

Waterborne nanotoxicology of zinc oxide nanoparticles (nano-ZnOs) has been extensively studied over the past decade, whereas their potential dietary toxicity and applications were seldom investigated. In the present study, we systematically investigated both short-term bioavailability and chronic effects of nano-ZnOs to two marine fish (marine medaka Oryzias melastigma and red drum Sciaenops ocellatus). At normal supplementary level (80 mg Zn/kg), red drum (with a stomach) had similar assimilation efficiencies of nano-ZnOs and ZnCl 2 . Correspondingly, in vitro digestion experiments showed the continuous dissolution of nano-ZnOs in acid environment. In contrast, nano-ZnOs were more bioavailable than ZnCl 2 to medaka (stomach-less) at 80 mg Zn/kg supplementary level. There results were further validated by using bulk-ZnOs. Chronic dietary exposure to nano-ZnOs (80 mg/kg) significantly enhanced the antioxidative defenses in medaka, with no negative effect on fish growth. Beneficial effects disappeared in the high dietary nano-ZnOs (300 mg/kg) treatment. For the first time, we provided direct evidence that nano-ZnOs was more bioavailable than ZnCl 2 and bulk-ZnOs to stomach-less fish at normal dietary Zn inclusion level (<80 mg/kg), with potential benefits on antioxidative defenses. It is also necessary to pay attention to the dietary nano-ZnOs toxicity on stomach-less fish due to the presence of real 'nano-effects.'

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

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.

The behavior of natural and anthropogenic osmium in Long Island Sound, an urban estuary in the eastern U.S.

NASA Astrophysics Data System (ADS)

Williams, Gwyneth; Marcantonio, Franco; Turekian, Karl K.

1997-04-01

The Os concentration and 187Os/ 186Os distributions in surface sediments of Long Island Sound (eastern U.S.) provide a way of determining the sources and estuarine transport of Os. The contribution of anthropogenic Os from sewer outfalls from the New York City region supplies a tracer with a characteristic 187Os/ 186Os of about 1. The Os concentration of the bulk surface sediment increases steeply moving toward New York City in the westernmost Sound and generally follows the concentration of organic carbon. The 187Os/ 186Os ratio of bulk surface sediment increases from west to east in the westernmost part of the Sound and is effectively constant in the central Sound. We interpret these results as indicating that the surface bulk sediments of the Sound contain a low 187Os/ 186Os component, perhaps as a reduced coating associated with organic remains from sewer outfalls. The acid hydrogen peroxide leach fraction has an average 187Os/ 186Os of 9.5 in the central Sound, significantly higher than both the bulk sediment value and the probable sea water value of about 8. The leach fraction in the westernmost part of the traverse is less radiogenic than the central Sound and follows the Os wsotope trend of the bulk sediment. Liquid effluent from a New York City sewer outfall contains 30 pg l -1 of dissolved Os with a 187Os/ 186Os of about 2.5, consistent with its being an end-member of the west-east sediment pattern recorded in the leach fractions of the westernmost cores. The leachable Os from the central Sound predominantly reflects Os in ferromanganese oxyhydroxide coatings from continentally derived sediments with 187Os/ 186Os ratios more radiogenic than seawater. The distribution patterns of anthropogenic and natural Os, with their characteristic isotopic signatures in the Sound, and the insights gained from the behavior of other particle-reactive species, indicates that very little Os in solution may pass through the estuarine gauntlet.

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.

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…

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

Analysis of vertical marginal discrepancy in feldspathic porcelain crowns manufactured with different CAD/CAM systems: Closed and open.

PubMed

Kricheldorf, Fabio; Bueno, Cleuber Rodrigo de Souza; Amaral, Wilson da Silva; Junior, Joel Ferreira Santiago; Filho, Hugo Nary

2018-01-01

The objective of this study is to compare the marginal adaptation of feldspathic porcelain crowns using two computer-aided design/computer-aided manufacturing systems, one of them is open and the other is closed. Twenty identical titanium abutments were divided into two groups: open system (OS), where ceramic crowns were created using varied equipment and software, and closed system (CS), where ceramic crowns were created using the CEREC system. Through optical microscopy analysis, we assess the marginal adaptation of the prosthetic interfaces. The data were subjected to the distribution of normality and variance. The t -test was used for the analysis of the comparison factor between the groups, and the one-way ANOVA was used to compare the variance of crown analysis regions within the group. A significance level of 5% was considered for the analyses. There was a significant difference between the systems ( P = 0.007), with the CS group having the higher mean (23.75 μm ± 3.05) of marginal discrepancy when compared to the open group (17.94 μm ± 4.77). Furthermore, there were no differences in marginal discrepancy between the different points between the groups ( P ≥ 0.05). The studied groups presented results within the requirements set out in the literature. However, the OS used presented better results in marginal adaptation.

An Android based location service using GSMCellID and GPS to obtain a graphical guide to the nearest cash machine

NASA Astrophysics Data System (ADS)

Jacobsen, Jurma; Edlich, Stefan

2009-02-01

There is a broad range of potential useful mobile location-based applications. One crucial point seems to be to make them available to the public at large. This case illuminates the abilities of Android - the operating system for mobile devices - to fulfill this demand in the mashup way by use of some special geocoding web services and one integrated web service for getting the nearest cash machines data. It shows an exemplary approach for building mobile location-based mashups for everyone: 1. As a basis for reaching as many people as possible the open source Android OS is assumed to spread widely. 2. Everyone also means that the handset has not to be an expensive GPS device. This is realized by re-utilization of the existing GSM infrastructure with the Cell of Origin (COO) method which makes a lookup of the CellID in one of the growing web available CellID databases. Some of these databases are still undocumented and not yet published. Furthermore the Google Maps API for Mobile (GMM) and the open source counterpart OpenCellID are used. The user's current position localization via lookup of the closest cell to which the handset is currently connected to (COO) is not as precise as GPS, but appears to be sufficient for lots of applications. For this reason the GPS user is the most pleased one - for this user the system is fully automated. In contrary there could be some users who doesn't own a GPS cellular. This user should refine his/her location by one click on the map inside of the determined circular region. The users are then shown and guided by a path to the nearest cash machine by integrating Google Maps API with an overlay. Additionally, the GPS user can keep track of him- or herself by getting a frequently updated view via constantly requested precise GPS data for his or her position.

Waggle: A Framework for Intelligent Attentive Sensing and Actuation

NASA Astrophysics Data System (ADS)

Sankaran, R.; Jacob, R. L.; Beckman, P. H.; Catlett, C. E.; Keahey, K.

2014-12-01

Advances in sensor-driven computation and computationally steered sensing will greatly enable future research in fields including environmental and atmospheric sciences. We will present "Waggle," an open-source hardware and software infrastructure developed with two goals: (1) reducing the separation and latency between sensing and computing and (2) improving the reliability and longevity of sensing-actuation platforms in challenging and costly deployments. Inspired by "deep-space probe" systems, the Waggle platform design includes features that can support longitudinal studies, deployments with varying communication links, and remote management capabilities. Waggle lowers the barrier for scientists to incorporate real-time data from their sensors into their computations and to manipulate the sensors or provide feedback through actuators. A standardized software and hardware design allows quick addition of new sensors/actuators and associated software in the nodes and enables them to be coupled with computational codes both insitu and on external compute infrastructure. The Waggle framework currently drives the deployment of two observational systems - a portable and self-sufficient weather platform for study of small-scale effects in Chicago's urban core and an open-ended distributed instrument in Chicago that aims to support several research pursuits across a broad range of disciplines including urban planning, microbiology and computer science. Built around open-source software, hardware, and Linux OS, the Waggle system comprises two components - the Waggle field-node and Waggle cloud-computing infrastructure. Waggle field-node affords a modular, scalable, fault-tolerant, secure, and extensible platform for hosting sensors and actuators in the field. It supports insitu computation and data storage, and integration with cloud-computing infrastructure. The Waggle cloud infrastructure is designed with the goal of scaling to several hundreds of thousands of Waggle nodes. It supports aggregating data from sensors hosted by the nodes, staging computation, relaying feedback to the nodes and serving data to end-users. We will discuss the Waggle design principles and their applicability to various observational research pursuits, and demonstrate its capabilities.

Re-Os systematics and age of pyrite associated with stratiform Zn-Pb mineralization in the Howards Pass district, Yukon and Northwest Territories, Canada

NASA Astrophysics Data System (ADS)

Kelley, Karen D.; Selby, David; Falck, Hendrik; Slack, John F.

2017-03-01

Stratiform Zn-Pb deposits hosted in unmetamorphosed carbonaceous and siliceous mudstones of the Ordovician to Silurian Duo Lake Formation define the Howards Pass district in Yukon Territory and Northwest Territories, western Canada. Collectively, the deposits are amongst the largest in the world, containing drill-indicated and inferred resources of 423 Mt at 4.84 % Zn and 1.59 % Pb. Sulphide textures include (a) fine-scale laminations of sphalerite, galena, and pyrite from <0.05 mm to 1 cm thick, interbedded with carbonaceous sedimentary rock; (b) layers of coarse sulphide that are structurally controlled by microfolds; and (c) veins that cut bedding and sulphide laminations. The finely interlaminated nature of sulphides with mudstone has been used as evidence for syngenetic mineralizing processes, whereas paleomagnetic data determined on coarse layered sulphides suggest a Middle Jurassic age of mineralization. Here, we present new rhenium-osmium (Re-Os) isotopic data for 12 pyrite separates obtained from 4 laminated sulphide-rich samples from the XY Central (XYC) and Don (DON) deposits and for 1 unmineralized organic-rich mudstone ˜20 m stratigraphically below the sulphide-bearing zone. Pyrite separates that lack mudstone inclusions ("pure") from the XYC deposit contain 2.2 to 4.0 ppb Re and 93.4 to 123.4 ppt Os; pure pyrite from the DON deposit is significantly more enriched in Re and Os (34-37 ppb Re; 636.8-694.9 ppt Os). The 187Re/188Os values of pure pyrite separates from the XYC and DON deposits range from 137.6 to 197 and 182.1 to 201.4, respectively. Regression of all pure pyrite Re-Os data from both deposits yields an isochron age of 442 ± 14 Ma (MSWD = 7.4) and an initial 187Os/188Os (Osi) value of 0.71 ± 0.07. The Re-Os age indicates that the early phase of pyrite precipitation (and by inference, sphalerite and galena) occurred during the early Silurian, consistent with biostratigraphic ages of the host rocks. The Osi value of ˜0.8 for earliest Silurian seawater recorded from organic-rich shale in the basal Silurian Global Stratotype Section and Point (GSSP) at Dobs Linn, Scotland is very similar to that provided by the Howards Pass pyrite regression and hence suggests a hydrogenous (seawater) source of Os for the pyrite. Therefore, two possible sources of Os are (1) the Zn- and Pb-bearing hydrothermal fluid that leached Os from footwall sedimentary rocks, which were deposited in seawater, or (2) directly from seawater during precipitation of the pyrite, which suggests that the Os content of the hydrothermal fluid was minor relative to that of seawater.

OsWOX3A is involved in negative feedback regulation of the gibberellic acid biosynthetic pathway in rice (Oryza sativa).

PubMed

Cho, Sung-Hwan; Kang, Kiyoon; Lee, Sang-Hwa; Lee, In-Jung; Paek, Nam-Chon

2016-03-01

The plant-specific WUSCHEL-related homeobox (WOX) nuclear proteins have important roles in the transcriptional regulation of many developmental processes. Among the rice (Oryza sativa) WOX proteins, a loss of OsWOX3A function in narrow leaf2 (nal2) nal3 double mutants (termed nal2/3) causes pleiotropic effects, such as narrow and curly leaves, opened spikelets, narrow grains, more tillers, and fewer lateral roots, but almost normal plant height. To examine OsWOX3A function in more detail, transgenic rice overexpressing OsWOX3A (OsWOX3A-OX) were generated; unexpectedly, all of them consistently exhibited severe dwarfism with very short and wide leaves, a phenotype that resembles that of gibberellic acid (GA)-deficient or GA-insensitive mutants. Exogenous GA3 treatment fully rescued the developmental defects of OsWOX3A-OX plants, suggesting that constitutive overexpression of OsWOX3A downregulates GA biosynthesis. Quantitative analysis of GA intermediates revealed significantly reduced levels of GA20 and bioactive GA1 in OsWOX3A-OX, possibly due to downregulation of the expression of KAO, which encodes ent-kaurenoic acid oxidase, a GA biosynthetic enzyme. Yeast one-hybrid and electrophoretic mobility shift assays revealed that OsWOX3A directly interacts with the KAO promoter. OsWOX3A expression is drastically and temporarily upregulated by GA3 and downregulated by paclobutrazol, a blocker of GA biosynthesis. These data indicate that OsWOX3A is a GA-responsive gene and functions in the negative feedback regulation of the GA biosynthetic pathway for GA homeostasis to maintain the threshold levels of endogenous GA intermediates throughout development. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

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.

OsHAC1;1 and OsHAC1;2 Function as Arsenate Reductases and Regulate Arsenic Accumulation1

PubMed Central

Wang, Tao; Tang, Zhong; Wu, Zhongchang; Salt, David E.; Chao, Dai-Yin

2016-01-01

Rice is a major dietary source of the toxic metalloid arsenic (As). Reducing its accumulation in rice (Oryza sativa) grain is of critical importance to food safety. Rice roots take up arsenate and arsenite depending on the prevailing soil conditions. The first step of arsenate detoxification is its reduction to arsenite, but the enzyme(s) catalyzing this reaction in rice remains unknown. Here, we identify OsHAC1;1 and OsHAC1;2 as arsenate reductases in rice. OsHAC1;1 and OsHAC1;2 are able to complement an Escherichia coli mutant lacking the endogenous arsenate reductase and to reduce arsenate to arsenite. OsHAC1:1 and OsHAC1;2 are predominantly expressed in roots, with OsHAC1;1 being abundant in the epidermis, root hairs, and pericycle cells while OsHAC1;2 is abundant in the epidermis, outer layers of cortex, and endodermis cells. Expression of the two genes was induced by arsenate exposure. Knocking out OsHAC1;1 or OsHAC1;2 decreased the reduction of arsenate to arsenite in roots, reducing arsenite efflux to the external medium. Loss of arsenite efflux was also associated with increased As accumulation in shoots. Greater effects were observed in a double mutant of the two genes. In contrast, overexpression of either OsHAC1;1 or OsHAC1;2 increased arsenite efflux, reduced As accumulation, and enhanced arsenate tolerance. When grown under aerobic soil conditions, overexpression of either OsHAC1;1 or OsHAC1;2 also decreased As accumulation in rice grain, whereas grain As increased in the knockout mutants. We conclude that OsHAC1;1 and OsHAC1;2 are arsenate reductases that play an important role in restricting As accumulation in rice shoots and grain. PMID:27702843

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

Enhanced sensitivity for Os isotope ratios by magnetic sector ICP-MS with a capacitive decoupling Pt guard electrode.

PubMed

Townsend, A T

2000-08-01

A magnetic sector ICP-MS with enhanced sensitivity was used to measure Os isotope ratios in solutions of low Os concentration (approximately 1 ng g(-1) or less). Ratios with 192Os as the basis were determined, while the geologically useful 187Os/188Os ratio was also measured. Sample introduction was via the traditional nebuliser-spray chamber method. A capacitive decoupling Pt shield torch was developed "in-house" and was found to increase Os signals by approximately 5 x under "moderate" plasma conditions (1050 W) over that found during normal operation (1250 W). Sensitivity using the guard electrode for 192Os was approximately 250-350,000 counts s(-1) per ng g(-1) Os. For a I ng g(-1) Os solution with no guard electrode, precisions of the order of 0.2-0.3% (189Os/192Os and 190Os/192Os) to approximately 1% or greater (186Os/192Os, 187Os/192Os and 187Os/188Os) were found (values as 1 sigma for n = 10). With the guard electrode in use, ratio precisions were found to improve to 0.2 to 0.8%. The total amount of Os used in the acquisition of this data was approximately 2.5 ng per measurement per replicate. At the higher concentration of 10 ng g(-1), precisions of the order of 0.15-0.3% were measured (for all ratios), irrespective of whether the shield torch was used. Ratio accuracy was confirmed by comparison with independently obtained NTIMS data. For both Os concentrations considered, the improvement in precision offered by the guard electrode (if any) was small in comparison to calculated theoretical values based on Poisson counting statistics, suggesting noise contributions from other sources (such as the sample introduction system, plasma flicker etc). At lower Os concentrations (to 100 pg g(-1)) no appreciable loss of ratio accuracy was observed, although as expected based on counting statistics, poorer precisions of the order of 0.45-3% (1 sigma, n = 5) were noted. Re was found to have a detrimental effect on the precision of Os ratios involving 187Os, indicating that separation of Re and Os samples is a necessary pre-requisite for highly accurate and precise Os isotope ratio measurements.

A NAP-Family Histone Chaperone Functions in Abiotic Stress Response and Adaptation1[OPEN

PubMed Central

Pareek, Ashwani; Singla-Pareek, Sneh Lata

2016-01-01

Modulation of gene expression is one of the most significant molecular mechanisms of abiotic stress response in plants. Via altering DNA accessibility, histone chaperones affect the transcriptional competence of genomic loci. However, in contrast to other factors affecting chromatin dynamics, the role of plant histone chaperones in abiotic stress response and adaptation remains elusive. Here, we studied the physiological function of a stress-responsive putative rice (Oryza sativa) histone chaperone of the NAP superfamily: OsNAPL6. We show that OsNAPL6 is a nuclear-localized H3/H4 histone chaperone capable of assembling a nucleosome-like structure. Utilizing overexpression and knockdown approaches, we found a positive correlation between OsNAPL6 expression levels and adaptation to multiple abiotic stresses. Results of comparative transcriptome profiling and promoter-recruitment studies indicate that OsNAPL6 functions during stress response via modulation of expression of various genes involved in diverse functions. For instance, we show that OsNAPL6 is recruited to OsRad51 promoter, activating its expression and leading to more efficient DNA repair and abrogation of programmed cell death under salinity and genotoxic stress conditions. These results suggest that the histone chaperone OsNAPL6 may serve a regulatory role in abiotic stress physiology possibly via modulating nucleosome dynamics at various stress-associated genomic loci. Taken together, our findings establish a hitherto unknown link between histone chaperones and abiotic stress response in plants. PMID:27342307

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.

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 ...

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

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

Chondritic late accretion to Mars and the nature of shergottite reservoirs

NASA Astrophysics Data System (ADS)

Tait, Kim T.; Day, James M. D.

2018-07-01

Mars is considered to have formed as a planetary embryo that experienced extensive differentiation early in its history. Shergottite meteorites preserve evidence for this history, and for late accretion events that affected their mantle sources within Mars. Here we report the first coupled 187Re-187Os, 87Sr/86Sr, highly siderophile element (HSE: Os, Ir, Ru, Pt, Pd, Re) and major element abundance dataset for martian shergottites that span a range of MgO contents, from 6.4 to 30.3 wt.%. The shergottites range from picro-basalt to basaltic-andesite compositions, have enriched to depleted incompatible trace-element compositions, and define fractional crystallization trends, enabling the determination of HSE compatibility for martian magmatism in the order: Os > Ir ≥ Ru ≫ Pt ≥ Pd ≥ Re. This order of compatibility is like that defined previously for Earth and the Moon, but the fractionation of strongly compatible Os, Ir and Ru appears to take place at higher MgO contents in martian magmas, due to early onset of sulfide fractionation. In general, enriched shergottites have lower MgO contents than intermediate or depleted shergottites and have fractionated HSE patterns (Re + Pd + Pt > Ru + Ir + Os) and more radiogenic measured 87Sr/86Sr (0.7127-0.7235) and 187Os/188Os (0.140-0.247) than intermediate or depleted shergottite meteorites (87Sr/86Sr = 0.7010-0.7132; 187Os/188Os = 0.127-0.141). Osmium isotope compositions, corrected for crystallization age, define compositions that are implausibly unradiogenic in some enriched shergottites, implying recent mobilization of Re in some samples. Filtering for the effects of alteration and high Re/Os through crystal-liquid fractionation leads to a positive correlation between age-corrected Sr and Os isotope compositions. Mixing between hypothetical martian crustal and mantle reservoirs are unable to generate the observed Sr-Os isotope compositions of shergottites, which require either distinct and discrete long-term incompatible-element depleted and enriched mantle sources, or originate from hybridized melting of deep melts with metasomatized martian lithosphere. Using MgO-regression methods, we obtain a modified estimate of the bulk silicate Mars HSE composition of (in ng g-1) 0.4 [Re], 7.4 [Pd], 9.6 [Pt], 6.2 [Ru], 3.7 [Ir], 4 [Os], and a long-term chondritic 187Os/188Os ratio (∼0.1312). This result does not permit existing models invoking high-pressure and temperature partitioning of the HSE. Instead, our estimate implies 0.6-0.7% by mass of late accretion of broadly chondritic material to Mars. Our results indicate that Mars could have accreted earlier than Earth, but that disproportional accretion of large bodies and a relative constant flux of accretion of available materials in the first 50-100 Ma of Solar System led to the broad similarity in HSE abundances between Earth and Mars.

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.

Open Radio Communications Architecture Core Framework V1.1.0 Volume 1 Software Users Manual

DTIC Science & Technology

2005-02-01

on a PC utilizing the KDE desktop that comes with Red Hat Linux . The default desktop for most Red Hat Linux installations is the GNOME desktop. The...SCA) v2.2. The software was designed for a desktop computer running the Linux operating system (OS). It was developed in C++, uses ACE/TAO for CORBA...middleware, Xerces for the XML parser, and Red Hat Linux for the Operating System. The software is referred to as, Open Radio Communication

MIROS: A Hybrid Real-Time Energy-Efficient Operating System for the Resource-Constrained Wireless Sensor Nodes

PubMed Central

Liu, Xing; Hou, Kun Mean; de Vaulx, Christophe; Shi, Hongling; Gholami, Khalid El

2014-01-01

Operating system (OS) technology is significant for the proliferation of the wireless sensor network (WSN). With an outstanding OS; the constrained WSN resources (processor; memory and energy) can be utilized efficiently. Moreover; the user application development can be served soundly. In this article; a new hybrid; real-time; memory-efficient; energy-efficient; user-friendly and fault-tolerant WSN OS MIROS is designed and implemented. MIROS implements the hybrid scheduler and the dynamic memory allocator. Real-time scheduling can thus be achieved with low memory consumption. In addition; it implements a mid-layer software EMIDE (Efficient Mid-layer Software for User-Friendly Application Development Environment) to decouple the WSN application from the low-level system. The application programming process can consequently be simplified and the application reprogramming performance improved. Moreover; it combines both the software and the multi-core hardware techniques to conserve the energy resources; improve the node reliability; as well as achieve a new debugging method. To evaluate the performance of MIROS; it is compared with the other WSN OSes (TinyOS; Contiki; SOS; openWSN and mantisOS) from different OS concerns. The final evaluation results prove that MIROS is suitable to be used even on the tight resource-constrained WSN nodes. It can support the real-time WSN applications. Furthermore; it is energy efficient; user friendly and fault tolerant. PMID:25248069

MIROS: a hybrid real-time energy-efficient operating system for the resource-constrained wireless sensor nodes.

PubMed

Liu, Xing; Hou, Kun Mean; de Vaulx, Christophe; Shi, Hongling; El Gholami, Khalid

2014-09-22

Operating system (OS) technology is significant for the proliferation of the wireless sensor network (WSN). With an outstanding OS; the constrained WSN resources (processor; memory and energy) can be utilized efficiently. Moreover; the user application development can be served soundly. In this article; a new hybrid; real-time; memory-efficient; energy-efficient; user-friendly and fault-tolerant WSN OS MIROS is designed and implemented. MIROS implements the hybrid scheduler and the dynamic memory allocator. Real-time scheduling can thus be achieved with low memory consumption. In addition; it implements a mid-layer software EMIDE (Efficient Mid-layer Software for User-Friendly Application Development Environment) to decouple the WSN application from the low-level system. The application programming process can consequently be simplified and the application reprogramming performance improved. Moreover; it combines both the software and the multi-core hardware techniques to conserve the energy resources; improve the node reliability; as well as achieve a new debugging method. To evaluate the performance of MIROS; it is compared with the other WSN OSes (TinyOS; Contiki; SOS; openWSN and mantisOS) from different OS concerns. The final evaluation results prove that MIROS is suitable to be used even on the tight resource-constrained WSN nodes. It can support the real-time WSN applications. Furthermore; it is energy efficient; user friendly and fault tolerant.

Effects of mother lode-type gold mineralization on 187Os/188Os and platinum group element concentrations in peridotite: Alleghany District, California

USGS Publications Warehouse

Walker, R.J.; Böhlke, J.K.; McDonough, W.F.; Li, Ji

2007-01-01

Osmium isotope compositions and concentrations of Re, platinum group elements (PGE), and Au were determined for host peridotites (serpentinites and barzburgites) and hydrothermally altered ultramafic wall rocks associated with Mother Lode-type hydrothermal gold-quartz vein mineralization in the Alleghany district, California. The host peridotites have Os isotope compositions and Re, PGE, and Au abundances typical of the upper mantle at their presumed formation age during the late Proterozoic or early Paleozoic. The hydrothermally altered rocks have highly variable initial Os isotope compositions with ??os, values (% deviation of 187OS/188OS from the chondritic average calculated for the approx. 120 Ma time of mineralization) ranging from -1.4 to -8.3. The lowest Os isotope compositions are consistent with Re depletion of a chondritic source (e.g., the upper mantle) at ca. 1.6 Ga. Most of the altered samples are enriched in Au and have depleted and fractionated abundances of Re and PGE relative to their precursor peridotites. Geoehemical characteristics of the altered samples suggest that Re and some PGE were variably removed from the ultramafic rocks during the mineralization event. In addition to Re, the Pt and Pd abundances of the most intensely altered rocks appear to have been most affected by mineralization. The 187Os-depleted isotopic compositions of some altered rocks are interpreted to be a result of preferential 187Os loss via destruction of Re-rich phases during the event. For these rocks, Os evidently is not a useful tracer of the mineralizing fluids. The results do, however, provide evidence for differential mobility of these elements, and mobility of 187Os relative to the initial bulk Os isotope composition during hydrothermal metasomatic alteration of ultramafic rocks. ?? 2007 Society of Economic Geologists, Inc.

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…

Design of Electron-Beam Controlled Switches.

DTIC Science & Technology

1982-11-24

I- HYBRID (OPENING/CLOSING) LO LSW E EBCS(O) 11111 C ESCS(C) T TJL (a) !z 0 TIME E OPEN I IM 0 TIM Fig. 2 - Circuit diagram illustrating the...34 l i iN l II -ItB "i ’ : i = i . • ’ " -.. ~...2 .. .. . * INDUCTIVE (OPENING) (a)(a) LO LSW , io E EBCS(O) III1t RL ___T (a) "ii’ (b) ) IJ.: z 0...switch pressure is given by Eq. (28) with EJ - 20 kV/cm, f. - 2 x lOs cm/V-s for N2-0 2 and ko - 0.25 (Eq. (26)): P -1700 Torr 2.3 atm. (33) The switch

[Comparison of immune response after laparoscopic and open surgery for colorectal carcinoma: a meta-analysis].

PubMed

Song, Hu; Song, Jun; Liang, Yong; Fu, Wei; Xu, Yixin; Zheng, Junnian; Xu, Wei

2014-08-01

To compare the immune function after laparoscopic surgery (LS) and conventional open surgery(OS) for colorectal cancer (CRC). PubMed, EMBASE, the Cochrane Library, China National Knowledge Infrastructure (CNKI), and Wanfang Database were systematically searched for randomized controlled trials published before August 2013 concerning the immunological difference between LS and OS. Data extraction was performed independently by two reviewers and data analysis was performed using Review Manager ver. 4.3.1. Twelve studies including 638 patients (307 in LS group and 331 in OS group) were eligible for analysis. Overall analysis demonstrated that no significant differences were identified for blood C-reactive protein level on postoperative days (POD) 0-1 (P=0.40), plasma lymphocyte count on POD 1-3 (P=0.92) and POD 4-7 (P=0.64), plasma CD4⁺ T cell count on POD 1-7 (P=0.63), plasma CD8⁺ T cell count on POD 4-7 (P=0.09), and plasma NK cell count POD 1-3 (P=0.34) as well as POD 4-7 (P=0.46). Data analysis also showed that a significantly lower serum level of IL-6 on POD 0-1 after LS (WMD=-25.03, 95% CI:-34.06 to -15.99, P=0.000), and a significantly higher plasma level of CD8⁺ T cell count on POD 1-3 after LS(WMD=0.05, 95% CI:0.01 to 0.08, P=0.004). Although postoperatively short-term humoral immune function trends to be better after LS for CRC compared to OS, there is no sufficient evidence to support superior preservation of global immune function after acute reactive phase.

Surface and airborne measurements of organosulfur and methanesulfonate over the western United States and coastal areas

NASA Astrophysics Data System (ADS)

Sorooshian, Armin; Crosbie, Ewan; Maudlin, Lindsay C.; Youn, Jong-Sang; Wang, Zhen; Shingler, Taylor; Ortega, Amber M.; Hersey, Scott; Woods, Roy K.

2015-08-01

This study reports on ambient measurements of organosulfur (OS) and methanesulfonate (MSA) over the western United States and coastal areas. Particulate OS levels are highest in summertime and generally increase as a function of sulfate (a precursor) and sodium (a marine tracer) with peak levels at coastal sites. The ratio of OS to total sulfur is also highest at coastal sites, with increasing values as a function of normalized difference vegetation index and the ratio of organic carbon to elemental carbon. Correlative analysis points to significant relationships between OS and biogenic emissions from marine and continental sources, factors that coincide with secondary production, and vanadium due to a suspected catalytic role. A major OS species, methanesulfonate (MSA), was examined with intensive field measurements, and the resulting data support the case for vanadium's catalytic influence. Mass size distributions reveal a dominant MSA peak between aerodynamic diameters of 0.32-0.56 µm at a desert and coastal site with nearly all MSA mass (≥84%) in submicrometer sizes; MSA:non-sea-salt sulfate ratios vary widely as a function of particle size and proximity to the ocean. Airborne data indicate that relative to the marine boundary layer, particulate MSA levels are enhanced in urban and agricultural areas and also the free troposphere when impacted by biomass burning. Some combination of fires and marine-derived emissions leads to higher MSA levels than either source alone. Finally, MSA differences in cloud water and out-of-cloud aerosol are discussed.

The Seismic Tool-Kit (STK): an open source software for seismology and signal processing.

NASA Astrophysics Data System (ADS)

Reymond, Dominique

2016-04-01

We present an open source software project (GNU public license), named STK: Seismic ToolKit, that is dedicated mainly for seismology and signal processing. The STK project that started in 2007, is hosted by SourceForge.net, and count more than 19 500 downloads at the date of writing. The STK project is composed of two main branches: First, a graphical interface dedicated to signal processing (in the SAC format (SAC_ASCII and SAC_BIN): where the signal can be plotted, zoomed, filtered, integrated, derivated, ... etc. (a large variety of IFR and FIR filter is proposed). The estimation of spectral density of the signal are performed via the Fourier transform, with visualization of the Power Spectral Density (PSD) in linear or log scale, and also the evolutive time-frequency representation (or sonagram). The 3-components signals can be also processed for estimating their polarization properties, either for a given window, or either for evolutive windows along the time. This polarization analysis is useful for extracting the polarized noises, differentiating P waves, Rayleigh waves, Love waves, ... etc. Secondly, a panel of Utilities-Program are proposed for working in a terminal mode, with basic programs for computing azimuth and distance in spherical geometry, inter/auto-correlation, spectral density, time-frequency for an entire directory of signals, focal planes, and main components axis, radiation pattern of P waves, Polarization analysis of different waves (including noize), under/over-sampling the signals, cubic-spline smoothing, and linear/non linear regression analysis of data set. A MINimum library of Linear AlGebra (MIN-LINAG) is also provided for computing the main matrix process like: QR/QL decomposition, Cholesky solve of linear system, finding eigen value/eigen vectors, QR-solve/Eigen-solve of linear equations systems ... etc. STK is developed in C/C++, mainly under Linux OS, and it has been also partially implemented under MS-Windows. Usefull links: http://sourceforge.net/projects/seismic-toolkit/ http://sourceforge.net/p/seismic-toolkit/wiki/browse_pages/

FracPaQ: A MATLAB™ toolbox for the quantification of fracture patterns

NASA Astrophysics Data System (ADS)

Healy, David; Rizzo, Roberto E.; Cornwell, David G.; Farrell, Natalie J. C.; Watkins, Hannah; Timms, Nick E.; Gomez-Rivas, Enrique; Smith, Michael

2017-02-01

The patterns of fractures in deformed rocks are rarely uniform or random. Fracture orientations, sizes, and spatial distributions often exhibit some kind of order. In detail, relationships may exist among the different fracture attributes, e.g. small fractures dominated by one orientation, larger fractures by another. These relationships are important because the mechanical (e.g. strength, anisotropy) and transport (e.g. fluids, heat) properties of rock depend on these fracture attributes and patterns. This paper describes FracPaQ, a new open source, cross-platform toolbox to quantify fracture patterns, including distributions in fracture attributes and their spatial variation. Software has been developed to quantify fracture patterns from 2-D digital images, such as thin section micrographs, geological maps, outcrop or aerial photographs or satellite images. The toolbox comprises a suite of MATLAB™ scripts based on previously published quantitative methods for the analysis of fracture attributes: orientations, lengths, intensity, density and connectivity. An estimate of permeability in 2-D is made using a parallel plate model. The software provides an objective and consistent methodology for quantifying fracture patterns and their variations in 2-D across a wide range of length scales, rock types and tectonic settings. The implemented methods presented are inherently scale independent, and a key task where applicable is analysing and integrating quantitative fracture pattern data from micro-to macro-scales. The toolbox was developed in MATLAB™ and the source code is publicly available on GitHub™ and the Mathworks™ FileExchange. The code runs on any computer with MATLAB installed, including PCs with Microsoft Windows, Apple Macs with Mac OS X, and machines running different flavours of Linux. The application, source code and sample input files are available in open repositories in the hope that other developers and researchers will optimise and extend the functionality for the benefit of the wider community.

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…

Trithorax Group Protein Oryza sativa Trithorax1 Controls Flowering Time in Rice via Interaction with Early heading date31[W][OPEN

PubMed Central

Choi, Sang Chul; Lee, Shinyoung; Kim, Sung-Ryul; Lee, Yang-Seok; Liu, Chunyan; Cao, Xiaofeng; An, Gynheung

2014-01-01

Trithorax group proteins are chromatin-remodeling factors that activate target gene expression by antagonistically functioning against the Polycomb group. In Arabidopsis (Arabidopsis thaliana), Arabidopsis Trithorax protein1 (ATX1) regulates flowering time and floral organ identity. Here, we observed that suppression of Oryza sativa Trithorax1 (OsTrx1), an ortholog of ATX1, delayed flowering time in rice (Oryza sativa). Because the delay occurred only under long-day conditions, we evaluated the flowering signal pathways that specifically function under long-day conditions. Among them, the OsMADS50 and Heading date1 pathways were not affected by the mutation. However, the Grain number, plant height, and heading date7 (Ghd7) pathway was altered in ostrx1. Transcript levels of OsGI, phytochrome genes, and Early heading date3 (Ehd3), which function upstream of Ghd7, were unchanged in the mutant. Because Trx group proteins form a complex with other proteins to modify the chromatin structure of target genes, we investigated whether OsTrx1 interacts with a previously identified protein that functions upstream of Ghd7. We demonstrated that the plant homeodomain motif of OsTrx1 binds to native histone H3 from the calf thymus and that OsTrx1 binds to Ehd3 through the region between the plant homeodomain and SET domains. Finally, we showed that the SET domain at the C-terminal end of OsTrx1 has histone H3 methyltransferase activity when incubated with oligonucleosomes. Our results suggest that OsTrx1 plays an important role in regulating flowering time in rice by modulating chromatin structure. PMID:24420930

Che-1 gene silencing induces osteosarcoma cell apoptosis by inhibiting mutant p53 expression

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

Liu, Ming; Wang, Dan, E-mail: danwangwdd@163.com; Li, Ning

2016-04-22

The transcriptional cofactor Che-1 is an RNA polymerase II (Pol II) which is involved in tumorigenesis, such as breast cancer and multiple myeloma. Che-1 can also regulate mutant p53 expression, which plays roles in many types of cancer. In this study, we aimed to investigate the effects and specific mechanism of Che-1 in the regulation of osteosarcoma (OS) cell growth. We found that Che-1 is highly expressed in several kinds of OS cells compared with osteoblast hFOB1.19 cells. MTT and flow cytometry assays showed that Che-1 depletion by siRNA markedly suppressed MG-63 and U2OS cell proliferation and promoted apoptosis. The chromatinmore » immunoprecipitation (ChIP) assay verified the presence of Che-1 on the p53 promoter in MG-63 and U2OS cells carrying mutant p53. Further studies showed that Che-1 depletion inhibited mutant p53 expression. Notably, our study showed that the loss of Che-1 inhibits proliferation and promotes apoptosis in MG-63 cells by decreasing the level of mutant p53. Therefore, these findings open the possibility that silencing of Che-1 will have therapeutic benefit in OS. - Highlights: • Che-1 is highly expressed in several kinds of OS cells. • Che-1 depletion suppressed MG-63 and U2OS cell growth. • Che-1 is existed in the p53 promoter in MG-63 and U2OS cells. • Che-1 depletion inhibited mutant p53 expression. • Che-1 depletion inhibits cell growth by decreasing the level of mutant p53.« less

OMPC: an Open-Source MATLAB®-to-Python Compiler

PubMed Central

Jurica, Peter; van Leeuwen, Cees

2008-01-01

Free access to scientific information facilitates scientific progress. Open-access scientific journals are a first step in this direction; a further step is to make auxiliary and supplementary materials that accompany scientific publications, such as methodological procedures and data-analysis tools, open and accessible to the scientific community. To this purpose it is instrumental to establish a software base, which will grow toward a comprehensive free and open-source language of technical and scientific computing. Endeavors in this direction are met with an important obstacle. MATLAB®, the predominant computation tool in many fields of research, is a closed-source commercial product. To facilitate the transition to an open computation platform, we propose Open-source MATLAB®-to-Python Compiler (OMPC), a platform that uses syntax adaptation and emulation to allow transparent import of existing MATLAB® functions into Python programs. The imported MATLAB® modules will run independently of MATLAB®, relying on Python's numerical and scientific libraries. Python offers a stable and mature open source platform that, in many respects, surpasses commonly used, expensive commercial closed source packages. The proposed software will therefore facilitate the transparent transition towards a free and general open-source lingua franca for scientific computation, while enabling access to the existing methods and algorithms of technical computing already available in MATLAB®. OMPC is available at http://ompc.juricap.com. PMID:19225577

Hybrid Operations in Patients with Peripheral Arterial Disease

PubMed Central

Murakami, Atsubumi

2018-01-01

In this seminar, I would like to discuss the recent hybrid operations in patients with peripheral arterial diseases. Hybrid is generally defined as combinations of different types of things. In the surgical community, it is loosely defined as therapy combining open surgery (OS) and endovascular therapy (EVT). In practice, combination surgery of diseased inflow vessels by EVT and outflow vessels by OS is a typical example, namely, the combination therapy of thromboendarterectomy (TEA) for common femoral artery and EVT (PTA and stenting) for iliac artery in patients with PAD (ilio-femoral lesions). Also, there is the potential of various combinations of OS and EVT for complex lesions. Unfortunately, we do not have specific guidelines for hybrid therapy of PAD, but in clinical practices, justified decision-making for surgical indication is strictly required. I emphasize that the cardiovascular surgeon (or vascular specialist) must have the ability of decision-making for suitable combination therapy of OS and EVT which adheres to existing specific guidelines. (This is a translation of Jpn J Vasc Surg 2017; 26: 275–283.) PMID:29682108

Open Source Vision

ERIC Educational Resources Information Center

Villano, Matt

2006-01-01

Increasingly, colleges and universities are turning to open source as a way to meet their technology infrastructure and application needs. Open source has changed life for visionary CIOs and their campus communities nationwide. The author discusses what these technologists see as the benefits--and the considerations.

PTT Advisor: A CDC-supported initiative to develop a mobile clinical laboratory decision support application for the iOS platform

PubMed Central

Savel, Thomas G.; Lee, Brian A.; Ledbetter, Greg; Brown, Sara; LaValley, Dale; Taylor, Julie; Thompson, Pam

2013-01-01

Objectives: This manuscript describes the development of PTT (Partial Thromboplastin Time) Advisor, one of the first of a handful of iOS-based mobile applications to be released by the US Centers for Disease Control and Prevention (CDC). PTT Advisor has been a collaboration between two groups at CDC (Informatics R&D and Laboratory Science), and one partner team (Clinical Laboratory Integration into Healthcare Collaborative - CLIHC). The application offers clinicians a resource to quickly select the appropriate follow-up tests to evaluate patients with a prolonged PTT and a normal Prothrombin Time (PT) laboratory result. Methods: The application was designed leveraging an agile methodology, and best practices in user experience (UX) design and mobile application development. Results: As it is an open-source project, the code to PTT Advisor was made available to the public under the Apache Software License. On July 6, 2012, the free app was approved by Apple, and was published to their App Store. Conclusions: Regardless of the complexity of the mobile application, the level of effort required in the development process should not be underestimated. There are several issues that make designing the UI for a mobile phone challenging (not just small screen size): the touchscreen, users' mobile mindset (tasks need to be quick and focused), and the fact that mobile UI conventions/expectations are still being defined and refined (due to the maturity level of the field of mobile application development). PMID:23923100

PTT Advisor: A CDC-supported initiative to develop a mobile clinical laboratory decision support application for the iOS platform.

PubMed

Savel, Thomas G; Lee, Brian A; Ledbetter, Greg; Brown, Sara; Lavalley, Dale; Taylor, Julie; Thompson, Pam

2013-01-01

This manuscript describes the development of PTT (Partial Thromboplastin Time) Advisor, one of the first of a handful of iOS-based mobile applications to be released by the US Centers for Disease Control and Prevention (CDC). PTT Advisor has been a collaboration between two groups at CDC (Informatics R&D and Laboratory Science), and one partner team (Clinical Laboratory Integration into Healthcare Collaborative - CLIHC). The application offers clinicians a resource to quickly select the appropriate follow-up tests to evaluate patients with a prolonged PTT and a normal Prothrombin Time (PT) laboratory result. The application was designed leveraging an agile methodology, and best practices in user experience (UX) design and mobile application development. As it is an open-source project, the code to PTT Advisor was made available to the public under the Apache Software License. On July 6, 2012, the free app was approved by Apple, and was published to their App Store. Regardless of the complexity of the mobile application, the level of effort required in the development process should not be underestimated. There are several issues that make designing the UI for a mobile phone challenging (not just small screen size): the touchscreen, users' mobile mindset (tasks need to be quick and focused), and the fact that mobile UI conventions/expectations are still being defined and refined (due to the maturity level of the field of mobile application development).

A model for osmium isotopic evolution of metallic solids at the core-mantle boundary

NASA Astrophysics Data System (ADS)

Humayun, Munir

2011-03-01

Some plumes are thought to originate at the core-mantle boundary, but geochemical evidence of core-mantle interaction is limited to Os isotopes in samples from Hawaii, Gorgona (89 Ma), and Kostomuksha (2.7 Ga). The Os isotopes have been explained by physical entrainment of Earth's liquid outer core into mantle plumes. This model has come into conflict with geophysical estimates of the timing of core formation, high-pressure experimental determinations of the solid metal-liquid metal partition coefficients (D), and the absence of expected 182W anomalies. A new model is proposed where metallic liquid from the outer core is partially trapped in a compacting cumulate pile of Fe-rich nonmetallic precipitates (FeO, FeS, Fe3Si, etc.) at the top of the core and undergoes fractional crystallization precipitating solid metal grains, followed by expulsion of the residual metallic liquid back to the outer core. The Os isotopic composition of the solids and liquids in the cumulate pile is modeled as a function of the residual liquid remaining and the emplacement age using 1 bar D values, with variable amounts of oxygen (0-10 wt %) as the light element. The precipitated solids evolve Os isotope compositions that match the trends for Hawaii (at an emplacement age of 3.5-4.5 Ga; 5%-10% oxygen) and Gorgona (emplacement age < 1.5 Ga; 0%-5% oxygen). The Fe-rich matrix of the cumulate pile dilutes the precipitated solid metal decoupling the Fe/Mn ratio from Os and W isotopes. The advantages to using precipitated solid metal as the Os host include a lower platinum group element and Ni content to the mantle source region relative to excess iron, miniscule anomalies in 182W (<0.1 ɛ), and no effects for Pb isotopes, etc. A gradual thermomechanical erosion of the cumulate pile results in incorporation of this material into the base of the mantle, where mantle plumes subsequently entrain it. Fractional crystallization of metallic liquids within the CMB provides a consistent explanation of both Os isotope correlations, Os-W isotope systematics, and Fe/Mn evidence for core-mantle interaction over the entire Hawaiian source.

76 FR 34634 - Federal Acquisition Regulation; Prioritizing Sources of Supplies and Services for Use by the...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-14

... contracts before commercial sources in the open market. The proposed rule amends FAR 8.002 as follows: The... requirements for supplies and services from commercial sources in the open market. The proposed FAR 8.004 would... subpart 8.6). (b) Commercial sources (including educational and non-profit institutions) in the open...

Origin and provenance of spherules and magnetic grains at the Younger Dryas boundary

PubMed Central

Wu, Yingzhe; Sharma, Mukul; LeCompte, Malcolm A.; Demitroff, Mark N.; Landis, Joshua D.

2013-01-01

One or more bolide impacts are hypothesized to have triggered the Younger Dryas cooling at ∼12.9 ka. In support of this hypothesis, varying peak abundances of magnetic grains with iridium and magnetic microspherules have been reported at the Younger Dryas boundary (YDB). We show that bulk sediment and/or magnetic grains/microspherules collected from the YDB sites in Arizona, Michigan, New Mexico, New Jersey, and Ohio have 187Os/188Os ratios ≥1.0, similar to average upper continental crust (= 1.3), indicating a terrestrial origin of osmium (Os) in these samples. In contrast, bulk sediments from YDB sites in Belgium and Pennsylvania exhibit 187Os/188Os ratios <<1.0 and at face value suggest mixing with extraterrestrial Os with 187Os/188Os of ∼0.13. However, the Os concentration in bulk sample and magnetic grains from Belgium is 2.8 pg/g and 15 pg/g, respectively, much lower than that in average upper continental crust (=31 pg/g), indicating no meteoritic contribution. The YDB site in Pennsylvania is remarkable in yielding 2- to 5-mm diameter spherules containing minerals such as suessite (Fe-Ni silicide) that form at temperatures in excess of 2000 °C. Gross texture, mineralogy, and age of the spherules appear consistent with their formation as ejecta from an impact 12.9 ka ago. The 187Os/188Os ratios of the spherules and their leachates are often low, but Os in these objects is likely terrestrially derived. The rare earth element patterns and Sr and Nd isotopes of the spherules indicate that their source lies in 1.5-Ga Quebecia terrain in the Grenville Province of northeastern North America. PMID:24009337

FORM version 4.0

NASA Astrophysics Data System (ADS)

Kuipers, J.; Ueda, T.; Vermaseren, J. A. M.; Vollinga, J.

2013-05-01

We present version 4.0 of the symbolic manipulation system FORM. The most important new features are manipulation of rational polynomials and the factorization of expressions. Many other new functions and commands are also added; some of them are very general, while others are designed for building specific high level packages, such as one for Gröbner bases. New is also the checkpoint facility, that allows for periodic backups during long calculations. Finally, FORM 4.0 has become available as open source under the GNU General Public License version 3. Program summaryProgram title: FORM. Catalogue identifier: AEOT_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEOT_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 151599 No. of bytes in distributed program, including test data, etc.: 1 078 748 Distribution format: tar.gz Programming language: The FORM language. FORM itself is programmed in a mixture of C and C++. Computer: All. Operating system: UNIX, LINUX, Mac OS, Windows. Classification: 5. Nature of problem: FORM defines a symbolic manipulation language in which the emphasis lies on fast processing of very large formulas. It has been used successfully for many calculations in Quantum Field Theory and mathematics. In speed and size of formulas that can be handled it outperforms other systems typically by an order of magnitude. Special in this version: The version 4.0 contains many new features. Most important are factorization and rational arithmetic. The program has also become open source under the GPL. The code in CPC is for reference. You are encouraged to upload the most recent sources from www.nikhef.nl/form/formcvs.php because of frequent bug fixes. Solution method: See "Nature of Problem", above. Additional comments: NOTE: The code in CPC is for reference. You are encouraged to upload the most recent sources from www.nikhef.nl/form/formcvs.php because of frequent bug fixes.

Biosecurity and Open-Source Biology: The Promise and Peril of Distributed Synthetic Biological Technologies.

PubMed

Evans, Nicholas G; Selgelid, Michael J

2015-08-01

In this article, we raise ethical concerns about the potential misuse of open-source biology (OSB): biological research and development that progresses through an organisational model of radical openness, deskilling, and innovation. We compare this organisational structure to that of the open-source software model, and detail salient ethical implications of this model. We demonstrate that OSB, in virtue of its commitment to openness, may be resistant to governance attempts.

Ba2NiOsO6: a Dirac-Mott insulator with ferromagnetism near 100 K

NASA Astrophysics Data System (ADS)

Feng, Hl; Calder, S.; Ghimire, M.; Yuan, Yh; Shirako, Y.; Tsujimoto, Y.; Matsushita, Y.; Hu, Z.; Kuo, Cy; Tjeng, Lh; Pi, Tw; Soo, Yl; He, Jf; Tanaka, M.; Katsuya, Y.; Richte, M.; Yamaura, Kazunari

The ferromagnetic semiconductor Ba2NiOsO6(Tmag 100 K) was synthesized at 6 GPa and 1500 ° C. It crystallizes into a double perovskite structure [Fm-3 m; a = 8.0428(1)], where the Ni2+ and Os6+ ions are perfectly ordered at the perovskite B-site. We show that the spin-orbit coupling of Os6+ plays an essential role in opening the charge gap. The magnetic state was investigated by density functional theory calculations and powder neutron diffraction. The latter revealed a collinear ferromagnetic order in a >21-kOe magnetic field at 5 K. The ferromagnetic gapped state is fundamentally different from that of known dilute magnetic semiconductors such as (Ga,Mn)As and (Cd,Mn)Te (Tmag<180 K), the spin-gapless semiconductor Mn2CoAl (Tmag 720 K), and the ferromagnetic insulators EuO (Tmag 70 K) and Bi3Cr3O11(Tmag 220 K). It is also qualitatively different from known ferrimagnetic insulator/semiconductors, which are characterized by an antiparallel spin arrangement. Our report of cubic Ba2NiOsO6 heralds a new class of FM insulator oxides, which may be useful in developing a practical magnetic semiconductor that can be employed in spintronic and quantum magnetic devices.

Using R to implement spatial analysis in open source environment

NASA Astrophysics Data System (ADS)

Shao, Yixi; Chen, Dong; Zhao, Bo

2007-06-01

R is an open source (GPL) language and environment for spatial analysis, statistical computing and graphics which provides a wide variety of statistical and graphical techniques, and is highly extensible. In the Open Source environment it plays an important role in doing spatial analysis. So, to implement spatial analysis in the Open Source environment which we called the Open Source geocomputation is using the R data analysis language integrated with GRASS GIS and MySQL or PostgreSQL. This paper explains the architecture of the Open Source GIS environment and emphasizes the role R plays in the aspect of spatial analysis. Furthermore, one apt illustration of the functions of R is given in this paper through the project of constructing CZPGIS (Cheng Zhou Population GIS) supported by Changzhou Government, China. In this project we use R to implement the geostatistics in the Open Source GIS environment to evaluate the spatial correlation of land price and estimate it by Kriging Interpolation. We also use R integrated with MapServer and php to show how R and other Open Source software cooperate with each other in WebGIS environment, which represents the advantages of using R to implement spatial analysis in Open Source GIS environment. And in the end, we points out that the packages for spatial analysis in R is still scattered and the limited memory is still a bottleneck when large sum of clients connect at the same time. Therefore further work is to group the extensive packages in order or design normative packages and make R cooperate better with other commercial software such as ArcIMS. Also we look forward to developing packages for land price evaluation.

ObsPy: A Python Toolbox for Seismology

NASA Astrophysics Data System (ADS)

Wassermann, J. M.; Krischer, L.; Megies, T.; Barsch, R.; Beyreuther, M.

2013-12-01

Python combines the power of a full-blown programming language with the flexibility and accessibility of an interactive scripting language. Its extensive standard library and large variety of freely available high quality scientific modules cover most needs in developing scientific processing workflows. ObsPy is a community-driven, open-source project extending Python's capabilities to fit the specific needs that arise when working with seismological data. It a) comes with a continuously growing signal processing toolbox that covers most tasks common in seismological analysis, b) provides read and write support for many common waveform, station and event metadata formats and c) enables access to various data centers, webservices and databases to retrieve waveform data and station/event metadata. In combination with mature and free Python packages like NumPy, SciPy, Matplotlib, IPython, Pandas, lxml, and PyQt, ObsPy makes it possible to develop complete workflows in Python, ranging from reading locally stored data or requesting data from one or more different data centers via signal analysis and data processing to visualization in GUI and web applications, output of modified/derived data and the creation of publication-quality figures. All functionality is extensively documented and the ObsPy Tutorial and Gallery give a good impression of the wide range of possible use cases. ObsPy is tested and running on Linux, OS X and Windows and comes with installation routines for these systems. ObsPy is developed in a test-driven approach and is available under the LGPLv3 open source licence. Users are welcome to request help, report bugs, propose enhancements or contribute code via either the user mailing list or the project page on GitHub.

The SCEC Broadband Platform: Open-Source Software for Strong Ground Motion Simulation and Validation

NASA Astrophysics Data System (ADS)

Silva, F.; Goulet, C. A.; Maechling, P. J.; Callaghan, S.; Jordan, T. H.

2016-12-01

The Southern California Earthquake Center (SCEC) Broadband Platform (BBP) is a carefully integrated collection of open-source scientific software programs that can simulate broadband (0-100 Hz) ground motions for earthquakes at regional scales. The BBP can run earthquake rupture and wave propagation modeling software to simulate ground motions for well-observed historical earthquakes and to quantify how well the simulated broadband seismograms match the observed seismograms. The BBP can also run simulations for hypothetical earthquakes. In this case, users input an earthquake location and magnitude description, a list of station locations, and a 1D velocity model for the region of interest, and the BBP software then calculates ground motions for the specified stations. The BBP scientific software modules implement kinematic rupture generation, low- and high-frequency seismogram synthesis using wave propagation through 1D layered velocity structures, several ground motion intensity measure calculations, and various ground motion goodness-of-fit tools. These modules are integrated into a software system that provides user-defined, repeatable, calculation of ground-motion seismograms, using multiple alternative ground motion simulation methods, and software utilities to generate tables, plots, and maps. The BBP has been developed over the last five years in a collaborative project involving geoscientists, earthquake engineers, graduate students, and SCEC scientific software developers. The SCEC BBP software released in 2016 can be compiled and run on recent Linux and Mac OS X systems with GNU compilers. It includes five simulation methods, seven simulation regions covering California, Japan, and Eastern North America, and the ability to compare simulation results against empirical ground motion models (aka GMPEs). The latest version includes updated ground motion simulation methods, a suite of new validation metrics and a simplified command line user interface.

[The use of open source software in graphic anatomic reconstructions and in biomechanic simulations].

PubMed

Ciobanu, O

2009-01-01

The objective of this study was to obtain three-dimensional (3D) images and to perform biomechanical simulations starting from DICOM images obtained by computed tomography (CT). Open source software were used to prepare digitized 2D images of tissue sections and to create 3D reconstruction from the segmented structures. Finally, 3D images were used in open source software in order to perform biomechanic simulations. This study demonstrates the applicability and feasibility of open source software developed in our days for the 3D reconstruction and biomechanic simulation. The use of open source software may improve the efficiency of investments in imaging technologies and in CAD/CAM technologies for implants and prosthesis fabrication which need expensive specialized software.

Inselect: Automating the Digitization of Natural History Collections

PubMed Central

Hudson, Lawrence N.; Blagoderov, Vladimir; Heaton, Alice; Holtzhausen, Pieter; Livermore, Laurence; Price, Benjamin W.; van der Walt, Stéfan; Smith, Vincent S.

2015-01-01

The world’s natural history collections constitute an enormous evidence base for scientific research on the natural world. To facilitate these studies and improve access to collections, many organisations are embarking on major programmes of digitization. This requires automated approaches to mass-digitization that support rapid imaging of specimens and associated data capture, in order to process the tens of millions of specimens common to most natural history collections. In this paper we present Inselect—a modular, easy-to-use, cross-platform suite of open-source software tools that supports the semi-automated processing of specimen images generated by natural history digitization programmes. The software is made up of a Windows, Mac OS X, and Linux desktop application, together with command-line tools that are designed for unattended operation on batches of images. Blending image visualisation algorithms that automatically recognise specimens together with workflows to support post-processing tasks such as barcode reading, label transcription and metadata capture, Inselect fills a critical gap to increase the rate of specimen digitization. PMID:26599208

Inselect: Automating the Digitization of Natural History Collections.

PubMed

Hudson, Lawrence N; Blagoderov, Vladimir; Heaton, Alice; Holtzhausen, Pieter; Livermore, Laurence; Price, Benjamin W; van der Walt, Stéfan; Smith, Vincent S

2015-01-01

The world's natural history collections constitute an enormous evidence base for scientific research on the natural world. To facilitate these studies and improve access to collections, many organisations are embarking on major programmes of digitization. This requires automated approaches to mass-digitization that support rapid imaging of specimens and associated data capture, in order to process the tens of millions of specimens common to most natural history collections. In this paper we present Inselect-a modular, easy-to-use, cross-platform suite of open-source software tools that supports the semi-automated processing of specimen images generated by natural history digitization programmes. The software is made up of a Windows, Mac OS X, and Linux desktop application, together with command-line tools that are designed for unattended operation on batches of images. Blending image visualisation algorithms that automatically recognise specimens together with workflows to support post-processing tasks such as barcode reading, label transcription and metadata capture, Inselect fills a critical gap to increase the rate of specimen digitization.

Web GIS in practice IV: publishing your health maps and connecting to remote WMS sources using the Open Source UMN MapServer and DM Solutions MapLab

PubMed Central

Boulos, Maged N Kamel; Honda, Kiyoshi

2006-01-01

Open Source Web GIS software systems have reached a stage of maturity, sophistication, robustness and stability, and usability and user friendliness rivalling that of commercial, proprietary GIS and Web GIS server products. The Open Source Web GIS community is also actively embracing OGC (Open Geospatial Consortium) standards, including WMS (Web Map Service). WMS enables the creation of Web maps that have layers coming from multiple different remote servers/sources. In this article we present one easy to implement Web GIS server solution that is based on the Open Source University of Minnesota (UMN) MapServer. By following the accompanying step-by-step tutorial instructions, interested readers running mainstream Microsoft® Windows machines and with no prior technical experience in Web GIS or Internet map servers will be able to publish their own health maps on the Web and add to those maps additional layers retrieved from remote WMS servers. The 'digital Asia' and 2004 Indian Ocean tsunami experiences in using free Open Source Web GIS software are also briefly described. PMID:16420699

Rapid development of medical imaging tools with open-source libraries.

PubMed

Caban, Jesus J; Joshi, Alark; Nagy, Paul

2007-11-01

Rapid prototyping is an important element in researching new imaging analysis techniques and developing custom medical applications. In the last ten years, the open source community and the number of open source libraries and freely available frameworks for biomedical research have grown significantly. What they offer are now considered standards in medical image analysis, computer-aided diagnosis, and medical visualization. A cursory review of the peer-reviewed literature in imaging informatics (indeed, in almost any information technology-dependent scientific discipline) indicates the current reliance on open source libraries to accelerate development and validation of processes and techniques. In this survey paper, we review and compare a few of the most successful open source libraries and frameworks for medical application development. Our dual intentions are to provide evidence that these approaches already constitute a vital and essential part of medical image analysis, diagnosis, and visualization and to motivate the reader to use open source libraries and software for rapid prototyping of medical applications and tools.

Open-Source RTOS Space Qualification: An RTEMS Case Study

NASA Technical Reports Server (NTRS)

Zemerick, Scott

2017-01-01

NASA space-qualification of reusable off-the-shelf real-time operating systems (RTOSs) remains elusive due to several factors notably (1) The diverse nature of RTOSs utilized across NASA, (2) No single NASA space-qualification criteria, lack of verification and validation (V&V) analysis, or test beds, and (3) different RTOS heritages, specifically open-source RTOSs and closed vendor-provided RTOSs. As a leader in simulation test beds, the NASA IV&V Program is poised to help jump-start and lead the space-qualification effort of the open source Real-Time Executive for Multiprocessor Systems (RTEMS) RTOS. RTEMS, as a case-study, can be utilized as an example of how to qualify all RTOSs, particularly the reusable non-commercial (open-source) ones that are gaining usage and popularity across NASA. Qualification will improve the overall safety and mission assurance of RTOSs for NASA-agency wide usage. NASA's involvement in space-qualification of an open-source RTOS such as RTEMS will drive the RTOS industry toward a more qualified and mature open-source RTOS product.

Cyberscience and the Knowledge-Based Economy. Open Access and Trade Publishing: From Contradiction to Compatibility with Non-Exclusive Copyright Licensing

ERIC Educational Resources Information Center

Armbruster, Chris

2008-01-01

Open source, open content and open access are set to fundamentally alter the conditions of knowledge production and distribution. Open source, open content and open access are also the most tangible result of the shift towards e-science and digital networking. Yet, widespread misperceptions exist about the impact of this shift on knowledge…

Learning from hackers: open-source clinical trials.

PubMed

Dunn, Adam G; Day, Richard O; Mandl, Kenneth D; Coiera, Enrico

2012-05-02

Open sharing of clinical trial data has been proposed as a way to address the gap between the production of clinical evidence and the decision-making of physicians. A similar gap was addressed in the software industry by their open-source software movement. Here, we examine how the social and technical principles of the movement can guide the growth of an open-source clinical trial community.

Applications of the 190Pt-186Os isotope system to geochemistry and cosmochemistry

USGS Publications Warehouse

Walker, R.J.; Morgan, J.W.; Beary, E.S.; Smoliar, M.I.; Czamanske, G.K.; Horan, M.F.

1997-01-01

Platinum is fractionated from osmium primarily as a consequence of processes involving sulfide and metal crystallization. Consequently, the 190Pt-186Os isotope system (190Pt ??? 186Os + ??) shows promise for dating some types of magmatic sulfide ores and evolved iron meteorites. The first 190Pt-186Os isochrons are presented here for ores from the ca. 251 Ma Noril'sk, Siberia plume, and for group IIAB magmatic iron meteorites. Given the known age of the Noril'sk system, a decay constant for 190Pt is determined to be 1.542 ?? 10-12a-1, with ??1% uncertainty. The isochron generated for the IIAB irons is consistent with this decay constant and the known age of the group. The 186Os/188Os ratios of presumably young, mantle-derived osmiridiums and also the carbonaceous chondrite Allende were measured to high-precision to constrain the composition of the modern upper mantle. These compositions overlap, indicating that the upper mantle is chondritic within the level of resolution now available. Our best estimate for this 186Os/188Os ratio is 0.119834 ?? 2 (2??M). The 190Pt/186Os ratios determined for six enstatite chondrites average 0.001659 ?? 75, which is very similar to published values for carbonaceous chondrites. Using this ratio and the presumed composition of the modern upper mantle and chondrites, a solar system initial 186Os/188Os ratio of 0.119820 is calculated. In comparison to the modern upper mantle composition, the 186Os/188Os ratio of the Noril'sk plume was approximately 0.012% enriched in 186Os. Possible reasons for this heterogeneity include the recycling of Pt-rich crust into the mantle source of the plume and derivation of the osmium from the outer core. Derivation of the osmium from the outer core is our favored model. Copyright ?? 1997 Elsevier Science Ltd.

Thermal stability of hexagonal OsB2

NASA Astrophysics Data System (ADS)

Xie, Zhilin; Blair, Richard G.; Orlovskaya, Nina; Cullen, David A.; Andrew Payzant, E.

2014-11-01

The synthesis of novel hexagonal ReB2-type OsB2 ceramic powder was performed by high energy ball milling of elemental Os and B powders. Two different sources of B powder have been used for this mechanochemical synthesis. One B powder consisted of a mixture of amorphous and crystalline phases and a mixture of 10B and 11B isotopes with a fine particle size, while another B powder was a purely crystalline (rhombohedral) material consisting of enriched 11B isotope with coarse particle size. The same Os powder was used for the synthesis in both cases. It was established that, in the first case, the hexagonal OsB2 phase was the main product of synthesis with a small quantity of Os2B3 phase present after synthesis as an intermediate product. In the second case, where coarse crystalline 11B powder was used as a raw material, only Os2B3 boride was synthesized mechanochemically. The thermal stability of hexagonal OsB2 powder was studied by heating under argon up to 876 °C and cooling in vacuo down to -225 °C. During the heating, the sacrificial reaction 2OsB2+3O2→2Os+2B2O3 took place due to presence of O2/water vapor molecules in the heating chamber, resulting in the oxidation of B atoms and formation of B2O3 and precipitation of Os metal out of the OsB2 lattice. As a result of such phase changes during heating, the lattice parameters of hexagonal OsB2 changed significantly. The shrinkage of the a lattice parameter was recorded in 276-426 °C temperature range upon heating, which was attributed to the removal of B atoms from the OsB2 lattice due to oxidation followed by the precipitation of Os atoms and formation of Os metal. While significant structural changes occurred upon heating due to presence of O2, the hexagonal OsB2 ceramic demonstrated good phase stability upon cooling in vacuo with linear shrinkage of the lattice parameters and no phase changes detected during cooling.

Sensitivity Analysis for some Water Pollution Problem

NASA Astrophysics Data System (ADS)

Le Dimet, François-Xavier; Tran Thu, Ha; Hussaini, Yousuff

2014-05-01

Sensitivity Analysis for Some Water Pollution Problems Francois-Xavier Le Dimet1 & Tran Thu Ha2 & M. Yousuff Hussaini3 1Université de Grenoble, France, 2Vietnamese Academy of Sciences, 3 Florida State University Sensitivity analysis employs some response function and the variable with respect to which its sensitivity is evaluated. If the state of the system is retrieved through a variational data assimilation process, then the observation appears only in the Optimality System (OS). In many cases, observations have errors and it is important to estimate their impact. Therefore, sensitivity analysis has to be carried out on the OS, and in that sense sensitivity analysis is a second order property. The OS can be considered as a generalized model because it contains all the available information. This presentation proposes a method to carry out sensitivity analysis in general. The method is demonstrated with an application to water pollution problem. The model involves shallow waters equations and an equation for the pollutant concentration. These equations are discretized using a finite volume method. The response function depends on the pollutant source, and its sensitivity with respect to the source term of the pollutant is studied. Specifically, we consider: • Identification of unknown parameters, and • Identification of sources of pollution and sensitivity with respect to the sources. We also use a Singular Evolutive Interpolated Kalman Filter to study this problem. The presentation includes a comparison of the results from these two methods. .

Evaluation and selection of open-source EMR software packages based on integrated AHP and TOPSIS.

PubMed

Zaidan, A A; Zaidan, B B; Al-Haiqi, Ahmed; Kiah, M L M; Hussain, Muzammil; Abdulnabi, Mohamed

2015-02-01

Evaluating and selecting software packages that meet the requirements of an organization are difficult aspects of software engineering process. Selecting the wrong open-source EMR software package can be costly and may adversely affect business processes and functioning of the organization. This study aims to evaluate and select open-source EMR software packages based on multi-criteria decision-making. A hands-on study was performed and a set of open-source EMR software packages were implemented locally on separate virtual machines to examine the systems more closely. Several measures as evaluation basis were specified, and the systems were selected based a set of metric outcomes using Integrated Analytic Hierarchy Process (AHP) and TOPSIS. The experimental results showed that GNUmed and OpenEMR software can provide better basis on ranking score records than other open-source EMR software packages. Copyright © 2014 Elsevier Inc. All rights reserved.

OMPC: an Open-Source MATLAB-to-Python Compiler.

PubMed

Jurica, Peter; van Leeuwen, Cees

2009-01-01

Free access to scientific information facilitates scientific progress. Open-access scientific journals are a first step in this direction; a further step is to make auxiliary and supplementary materials that accompany scientific publications, such as methodological procedures and data-analysis tools, open and accessible to the scientific community. To this purpose it is instrumental to establish a software base, which will grow toward a comprehensive free and open-source language of technical and scientific computing. Endeavors in this direction are met with an important obstacle. MATLAB((R)), the predominant computation tool in many fields of research, is a closed-source commercial product. To facilitate the transition to an open computation platform, we propose Open-source MATLAB((R))-to-Python Compiler (OMPC), a platform that uses syntax adaptation and emulation to allow transparent import of existing MATLAB((R)) functions into Python programs. The imported MATLAB((R)) modules will run independently of MATLAB((R)), relying on Python's numerical and scientific libraries. Python offers a stable and mature open source platform that, in many respects, surpasses commonly used, expensive commercial closed source packages. The proposed software will therefore facilitate the transparent transition towards a free and general open-source lingua franca for scientific computation, while enabling access to the existing methods and algorithms of technical computing already available in MATLAB((R)). OMPC is available at http://ompc.juricap.com.

Zinc Isotopes as Tracers of Crust-Mantle Interactions and Mineralization Processes in Layered Intrusions

NASA Astrophysics Data System (ADS)

Day, J. M.; Moynier, F.

2016-12-01

Zinc isotopes are a powerful tool for studying igneous processes and may be useful for distinguishing between mantle or crustal origins for mineralization and for examining crystallization processes. Restricted ranges in δ66Zn for mantle-derived rocks (δ66Zn = 0.28±0.05‰; [{66Zn/64Znsample/66Zn/64ZnJMC-Lyon-1} × 1000] all uncertainties reported are 2SD) contrast the large δ66Zn variations in sedimentary rocks ( 0 to 1‰), or in volcanic and sedimentary hosted ore deposits (e.g., SEDEX; VHMS; MVT = -0.6 to 1.3‰). Here, we use Zn isotopes to investigate magmatic processes in the 1.27 Ga Muskox Intrusion (Canada) and 2.7 Ga Stillwater Intrusion (Montana). The Muskox main chromitite horizon has between 270-330 ppm Zn with δ66Zn ranging from 0.16 to 0.31‰. Zinc isotope compositions negatively correlate with Os isotopes. Chromitite (40a) with the lowest 187Os/188Os (0.132) has δ66Zn of 0.31±0.03‰; indistinguishable from the mantle value. CM19 glass from the co-eval Coppermine Volcanics, which has crust-like O and Nd isotopes but low 187Os/188Os (0.131), has been interpreted as the extrusive manifestation of chromitite genesis. The value of δ66Zn (0.27±0.07‰) for CM19 is within uncertainty of 40A, and permissive of formation during silicic-mafic melt mixing and large-scale chromitite crystallization. Stillwater chromitite seams exhibit a larger range in Zn (166-448 ppm), but generally lower δ66Zn (0.13±0.04‰) than Muskox chromitites, or to a JM Reef bulk sample (69 ppm Zn, δ66Zn = 0.22±0.03‰). These results suggest different sources of Zn for Ultramafic series chromitites versus the JM Reef (Banded series). Correspondingly, variations occur in Os isotopes for PGE poor chromitites (γOs = -2 to +4) versus the PGE-rich JM Reef (γOs = +12 to +34). Zinc isotope variations may be explained by either a mantle source with low δ66Zn that was subsequently contaminated by high δ66Zn crust, or from contamination of the ultramafic series by low δ66Zn continental lithospheric mantle. JM Reef sulphides span a wide range in Zn (1.8-350 ppm) and δ66Zn (-0.03 to 0.68‰) consistent with fractionation of Zn isotopes during sulphide melt-mineral crystallization. These results show promise for using Zn isotopes to study sources of mineralization and to elucidate sulphide crystallization processes.

The validity of open-source data when assessing jail suicides.

PubMed

Thomas, Amanda L; Scott, Jacqueline; Mellow, Jeff

2018-05-09

The Bureau of Justice Statistics' Deaths in Custody Reporting Program is the primary source for jail suicide research, though the data is restricted from general dissemination. This study is the first to examine whether jail suicide data obtained from publicly available sources can help inform our understanding of this serious public health problem. Of the 304 suicides that were reported through the DCRP in 2009, roughly 56 percent (N = 170) of those suicides were identified through the open-source search protocol. Each of the sources was assessed based on how much information was collected on the incident and the types of variables available. A descriptive analysis was then conducted on the variables that were present in both data sources. The four variables present in each data source were: (1) demographic characteristics of the victim, (2) the location of occurrence within the facility, (3) the location of occurrence by state, and (4) the size of the facility. Findings demonstrate that the prevalence and correlates of jail suicides are extremely similar in both open-source and official data. However, for almost every variable measured, open-source data captured as much information as official data did, if not more. Further, variables not found in official data were identified in the open-source database, thus allowing researchers to have a more nuanced understanding of the situational characteristics of the event. This research provides support for the argument in favor of including open-source data in jail suicide research as it illustrates how open-source data can be used to provide additional information not originally found in official data. In sum, this research is vital in terms of possible suicide prevention, which may be directly linked to being able to manipulate environmental factors.

OsCHX14 is Involved in the K+ Homeostasis in Rice (Oryza sativa) Flowers.

PubMed

Chen, Yi; Ma, Jingkun; Miller, Anthony J; Luo, Bingbing; Wang, Mei; Zhu, Zhen; Ouwerkerk, Pieter B F

2016-07-01

Previously we showed in the osjar1 mutants that the lodicule senescence which controls the closing of rice flowers was delayed. This resulted in florets staying open longer when compared with the wild type. The gene OsJAR1 is silenced in osjar1 mutants and is a key member of the jasmonic acid (JA) signaling pathway. We found that K concentrations in lodicules and flowers of osjar1-2 were significantly elevated compared with the wild type, indicating that K + homeostasis may play a role in regulating the closure of rice flowers. The cation/H + exchanger (CHX) family from rice was screened for potential K + transporters involved as many members of this family in Arabidopsis were exclusively or preferentially expressed in flowers. Expression profiling confirmed that among 17 CHX genes in rice, OsCHX14 was the only member that showed an expression polymorphism, not only in osjar1 mutants but also in RNAi (RNA interference) lines of OsCOI1, another key member of the JA signaling pathway. This suggests that the expression of OsCHX14 is regulated by the JA signaling pathway. Green fluorescent protein (GFP)-tagged OsCHX14 protein was preferentially localized to the endoplasmic reticulum. Promoter-β-glucuronidase (GUS) analysis of transgenic rice revealed that OsCHX14 is mainly expressed in lodicules and the region close by throughout the flowering process. Characterization in yeast and Xenopus laevis oocytes verified that OsCHX14 is able to transport K + , Rb + and Cs + in vivo. Our data suggest that OsCHX14 may play an important role in K + homeostasis during flowering in rice. © The Author 2016. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Zircon (U-Th)/He Thermochronometric Constraints on Himalayan Thrust Belt Exhumation, Bedrock Weathering, and Cenozoic Seawater Chemistry

NASA Astrophysics Data System (ADS)

Colleps, Cody L.; McKenzie, N. Ryan; Stockli, Daniel F.; Hughes, Nigel C.; Singh, Birendra P.; Webb, A. Alexander G.; Myrow, Paul M.; Planavsky, Noah J.; Horton, Brian K.

2018-01-01

Shifts in global seawater 187Os/188Os and 87Sr/86Sr are often utilized as proxies to track global weathering processes responsible for CO2 fluctuations in Earth history, particularly climatic cooling during the Cenozoic. It has been proposed, however, that these isotopic records instead reflect the weathering of chemically distinctive Himalayan lithologies exposed at the surface. We present new zircon (U-Th)/He thermochronometric and detrital zircon U-Pb geochronologic evidence from the Himalaya of northwest India to explore these contrasting interpretations concerning the driving mechanisms responsible for these seawater records. Our data demonstrate in-sequence southward thrust propagation with rapid exhumation of Lesser Himalayan strata enriched in labile 187Os and relatively less in radiogenic 87Sr at ˜16 Ma, which directly corresponds with coeval shifts in seawater 187Os/188Os and 87Sr/86Sr. Results presented here provide substantial evidence that the onset of exhumation of 187Os-enriched Lesser Himalayan strata could have significantly impacted the marine 187Os/188Os record at 16 Ma. These results support the hypothesis that regional weathering of isotopically unique source rocks can drive seawater records independently from shifts in global-scale weathering rates, hindering the utility of these records as reliable proxies to track global weathering processes and climate in deep geologic time.

Inferring Roles in Defense from Metabolic Allocation of Rice Diterpenoids.

PubMed

Lu, Xuan; Zhang, Juan; Brown, Benjamin; Li, Riqing; Rodríguez-Romero, Julio; Berasategui, Aileen; Liu, Bo; Xu, Meimei; Luo, Dangping; Pan, Zhiqiang; Baerson, Scott; Gershenzon, Jonathan; Li, Zhaohu; Sesma, Ane; Yang, Bing; Peters, Reuben J

2018-04-24

Among their responses to microbial infection, plants deploy an arsenal of natural antibiotic products. These historically have been identified on the basis of their antibiotic activity in vitro, which leaves open the question of their relevance to defense in planta. The vast majority of such natural products from the important crop plant rice (Oryza sativa) are diterpenoids whose biosynthesis proceeds via either ent- or syn- copalyl diphosphate (CPP) intermediates, and which were isolated on the basis of their antibiotic activity against the fungal blast pathogen Magnaporthe oryzae. However, rice plants in which the gene for the syn-CPP synthase Os-CPS4 is knocked-out do not exhibit increased susceptibility to M. oryzae. Here we show that knocking-out or knocking-down Os-CPS4 actually decreases susceptibility to the bacterial leaf blight pathogen Xanthomonas oryzae. By contrast, genetic manipulation of the gene for the ent-CPP synthase Os-CPS2 alters susceptibility to both M. oryzae and X. oryzae. Despite the secretion of diterpenoids dependent on Os-CPS2 or Os-CPS4 from roots, neither knock-out exhibited significant changes in the composition of their rhizosphere bacterial communities. Nevertheless, rice plants allocate substantial metabolic resources towards syn- and ent-CPP derived diterpenoids upon infection/induction. Further investigation revealed that Os-CPS4 plays a role in fungal non-host disease resistance. Thus, examination of metabolic allocation provides important clues into physiological function. © 2018 American Society of Plant Biologists. All rights reserved.

Expression of the Nitrate Transporter Gene OsNRT1.1A/OsNPF6.3 Confers High Yield and Early Maturation in Rice[OPEN

PubMed Central

Wang, Wei; Hu, Bin; Liu, Yongqiang; Che, Ronghui; Hu, Yingchun; Zhang, Zhihua; Wang, Hongru; Li, Hua; Jiang, Zhimin; Zhang, Zhengli; Gao, Xiaokai; Qiu, Yahong; Meng, Xiangbing; Liu, Yongxin; Bai, Yang; Liang, Yan; Wang, Yiqin; Zhang, Lianhe; Li, Legong; Sodmergen; Jing, Haichun

2018-01-01

Nitrogen (N) is a major driving force for crop yield improvement, but application of high levels of N delays flowering, prolonging maturation and thus increasing the risk of yield losses. Therefore, traits that enable utilization of high levels of N without delaying maturation will be highly desirable for crop breeding. Here, we show that OsNRT1.1A (OsNPF6.3), a member of the rice (Oryza sativa) nitrate transporter 1/peptide transporter family, is involved in regulating N utilization and flowering, providing a target to produce high yield and early maturation simultaneously. OsNRT.1A has functionally diverged from previously reported NRT1.1 genes in plants and functions in upregulating the expression of N utilization-related genes not only for nitrate but also for ammonium, as well as flowering-related genes. Relative to the wild type, osnrt1.1a mutants exhibited reduced N utilization and late flowering. By contrast, overexpression of OsNRT1.1A in rice greatly improved N utilization and grain yield, and maturation time was also significantly shortened. These effects were further confirmed in different rice backgrounds and also in Arabidopsis thaliana. Our study paves a path for the use of a single gene to dramatically increase yield and shorten maturation time for crops, outcomes that promise to substantially increase world food security. PMID:29475937

Diamond ages from Victor (Superior Craton): Intra-mantle cycling of volatiles (C, N, S) during supercontinent reorganisation

NASA Astrophysics Data System (ADS)

Aulbach, S.; Creaser, Robert A.; Stachel, Thomas; Heaman, Larry M.; Chinn, Ingrid L.; Kong, Julie

2018-05-01

The central Superior Craton hosts both the diamondiferous 1.1 Ga Kyle Lake and Jurassic Attawapiskat kimberlites. A major thermal event related to the Midcontinent Rift at ca. 1.1 Ga induced an elevated geothermal gradient that largely destroyed an older generation of diamonds, raising the question of when, and how, the diamond inventory beneath Attawapiskat was formed. We determined Re-Os isotope systematics of sulphides included in diamonds from Victor by isotope dilution negative thermal ionisation mass spectrometry in order to obtain insights into the age and nature of the diamond source in the context of regional tectonothermal evolution. Regression of the peridotitic inclusion data (n = 14 of 16) yields a 718 ± 49 Ma age, with an initial 187Os/188Os ratio of 0.1177 ± 0.0016, i.e. depleted at the time of formation (γOs -3.7 ± 1.3). Consequently, Re depletion model ages calculated for these samples are systematically overestimated. Given that reported 187Os/188Os in olivine from Attawapiskat xenoliths varies strongly (0.1012-0.1821), the low and nearly identical initial Os of sulphide inclusions combined with their high 187Re/188Os (median 0.34) suggest metasomatic formation from a mixed source. This was likely facilitated by percolation of amounts of melt sufficient to homogenise Os, (re)crystallise sulphide and (co)precipitate diamond; that is, the sulphide inclusions and their diamond host are synchronous if not syngenetic. The ∼720 Ma age corresponds to rifting beyond the northern craton margin during Rodinia break-up. This suggests mobilisation of volatiles (C, N, S) and Os due to attendant mantle stretching and metasomatism by initially oxidising and S-undersaturated melts, which ultimately produced lherzolitic diamonds with high N contents compared to older Kyle Lake diamonds. Thus, some rift-influenced settings are prospective with respect to diamond formation. They are also important sites of hidden, intra-lithospheric volatile redistribution that can be revealed by diamond studies. Later emplacement of the Attawapiskat kimberlites, linking the carbon cycle to the surface, was associated with renewed disturbance during passage of the Great Meteor Hotspot. Lherzolitic diamond formation from oxidising small-volume melts may be the expression of an early and deep stage of the lithospheric conditioning required for the successful eruption of kimberlites, which complements the late and shallow emplacement of volatile-rich metasomes after upward displacement of a redox freezing front.

Cyanide Single-Molecule Magnets Exhibiting Solvent Dependent Reversible "On" and "Off" Exchange Bias Behavior.

PubMed

Pinkowicz, Dawid; Southerland, Heather I; Avendaño, Carolina; Prosvirin, Andrey; Sanders, Codi; Wernsdorfer, Wolfgang; Pedersen, Kasper S; Dreiser, Jan; Clérac, Rodolphe; Nehrkorn, Joscha; Simeoni, Giovanna G; Schnegg, Alexander; Holldack, Karsten; Dunbar, Kim R

2015-11-18

The syntheses, structures, and magnetic properties of four new complex salts, (PPN){[Mn(III)(salphen)(MeOH)]2[M(III)(CN)6]}·7MeOH (Mn2M·7MeOH) (M = Fe, Ru, Os and Co; PPN(+) = bis(triphenylphosphoranylidene)ammonium cation; H2salphen = N,N'-bis(salicylidene)-1,2-diaminobenzene), and a mixed metal Co/Os analogue (PPN){[Mn(III)(salphen)(MeOH)]2[Co(III)0.92Os(III)0.08(CN)6]}·7MeOH were undertaken. It was found that all compounds exhibit switchable single-molecule magnet (SMM) and exchange-bias behavior depending on the interstitial methanol content. The pristine (PPN){[Mn(salphen)(MeOH)]2[Os(CN)6]}·7MeOH (Mn2Os·7MeOH) behaves as an SMM with an effective barrier for the magnetization reversal, (Ueff/kB), of 17.1 K. Upon desolvation, Mn2Os exhibits an increase of Ueff/kB to 42.0 K and an opening of the hysteresis loop observable at 1.8 K. Mn2Os·7MeOH shows also exchange-bias behavior with magnetic hysteresis loops exhibiting a shift in the quantum tunneling to 0.25 T from zero-field. The Fe(III) and Ru(III) analogues were prepared as reference compounds for assessing the effect of the 5d versus 4d and 3d metal ions on the SMM properties. These compounds are also SMMs and exhibit similar effects but with lower energy barriers. These findings underscore the importance of introducing heavy transition elements into SMMs to improve their slow relaxation of the magnetization properties. The (PPN){[Mn(III)(salphen)(MeOH)]2[Co(III)(CN)6]}·7MeOH (Mn2Co·7MeOH) analogue with a diamagnetic Co(III) central atom and the mixed Co/Os (PPN){[Mn(III)(salphen)(MeOH)]2[Co(III)0.92Os(III)0.08(CN)6]}·7MeOH (Mn2Co/Os·7MeOH) "magnetically diluted" system with a 9:1 Co/Os metal ratio were prepared in order to further probe the nature of the energy barrier increase upon desolvation of Mn2Os. In addition, inelastic neutron scattering and frequency-domain Fourier-transform THz electron paramagnetic resonance spectra obtained on Mn2Os·7MeOH and Mn2Os in combination with the magnetic data revealed the presence of anisotropic exchange interactions between Mn(III) and Os(III) ions.

Open source tools and toolkits for bioinformatics: significance, and where are we?

PubMed

Stajich, Jason E; Lapp, Hilmar

2006-09-01

This review summarizes important work in open-source bioinformatics software that has occurred over the past couple of years. The survey is intended to illustrate how programs and toolkits whose source code has been developed or released under an Open Source license have changed informatics-heavy areas of life science research. Rather than creating a comprehensive list of all tools developed over the last 2-3 years, we use a few selected projects encompassing toolkit libraries, analysis tools, data analysis environments and interoperability standards to show how freely available and modifiable open-source software can serve as the foundation for building important applications, analysis workflows and resources.

Open Source 2010: Reflections on 2007

ERIC Educational Resources Information Center

Wheeler, Brad

2007-01-01

Colleges and universities and commercial firms have demonstrated great progress in realizing the vision proffered for "Open Source 2007," and 2010 will mark even greater progress. Although much work remains in refining open source for higher education applications, the signals are now clear: the collaborative development of software can provide…

Development and Use of an Open-Source, User-Friendly Package to Simulate Voltammetry Experiments

ERIC Educational Resources Information Center

Wang, Shuo; Wang, Jing; Gao, Yanjing

2017-01-01

An open-source electrochemistry simulation package has been developed that simulates the electrode processes of four reaction mechanisms and two typical electroanalysis techniques: cyclic voltammetry and chronoamperometry. Unlike other open-source simulation software, this package balances the features with ease of learning and implementation and…

Creating Open Source Conversation

ERIC Educational Resources Information Center

Sheehan, Kate

2009-01-01

Darien Library, where the author serves as head of knowledge and learning services, launched a new website on September 1, 2008. The website is built with Drupal, an open source content management system (CMS). In this article, the author describes how she and her colleagues overhauled the library's website to provide an open source content…

Integrating an Automatic Judge into an Open Source LMS

ERIC Educational Resources Information Center

Georgouli, Katerina; Guerreiro, Pedro

2011-01-01

This paper presents the successful integration of the evaluation engine of Mooshak into the open source learning management system Claroline. Mooshak is an open source online automatic judge that has been used for international and national programming competitions. although it was originally designed for programming competitions, Mooshak has also…

76 FR 75875 - Defense Federal Acquisition Regulation Supplement; Open Source Software Public Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-05

... Regulation Supplement; Open Source Software Public Meeting AGENCY: Defense Acquisition Regulations System... initiate a dialogue with industry regarding the use of open source software in DoD contracts. DATES: Public... be held in the General Services Administration (GSA), Central Office Auditorium, 1800 F Street NW...

The open-source movement: an introduction for forestry professionals

Treesearch

Patrick Proctor; Paul C. Van Deusen; Linda S. Heath; Jeffrey H. Gove

2005-01-01

In recent years, the open-source movement has yielded a generous and powerful suite of software and utilities that rivals those developed by many commercial software companies. Open-source programs are available for many scientific needs: operating systems, databases, statistical analysis, Geographic Information System applications, and object-oriented programming....

Open Source Software Development and Lotka's Law: Bibliometric Patterns in Programming.

ERIC Educational Resources Information Center

Newby, Gregory B.; Greenberg, Jane; Jones, Paul

2003-01-01

Applies Lotka's Law to metadata on open source software development. Authoring patterns found in software development productivity are found to be comparable to prior studies of Lotka's Law for scientific and scholarly publishing, and offer promise in predicting aggregate behavior of open source developers. (Author/LRW)

Conceptualization and validation of an open-source closed-loop deep brain stimulation system in rat.

PubMed

Wu, Hemmings; Ghekiere, Hartwin; Beeckmans, Dorien; Tambuyzer, Tim; van Kuyck, Kris; Aerts, Jean-Marie; Nuttin, Bart

2015-04-21

Conventional deep brain stimulation (DBS) applies constant electrical stimulation to specific brain regions to treat neurological disorders. Closed-loop DBS with real-time feedback is gaining attention in recent years, after proved more effective than conventional DBS in terms of pathological symptom control clinically. Here we demonstrate the conceptualization and validation of a closed-loop DBS system using open-source hardware. We used hippocampal theta oscillations as system input, and electrical stimulation in the mesencephalic reticular formation (mRt) as controller output. It is well documented that hippocampal theta oscillations are highly related to locomotion, while electrical stimulation in the mRt induces freezing. We used an Arduino open-source microcontroller between input and output sources. This allowed us to use hippocampal local field potentials (LFPs) to steer electrical stimulation in the mRt. Our results showed that closed-loop DBS significantly suppressed locomotion compared to no stimulation, and required on average only 56% of the stimulation used in open-loop DBS to reach similar effects. The main advantages of open-source hardware include wide selection and availability, high customizability, and affordability. Our open-source closed-loop DBS system is effective, and warrants further research using open-source hardware for closed-loop neuromodulation.

Conceptualization and validation of an open-source closed-loop deep brain stimulation system in rat

PubMed Central

Wu, Hemmings; Ghekiere, Hartwin; Beeckmans, Dorien; Tambuyzer, Tim; van Kuyck, Kris; Aerts, Jean-Marie; Nuttin, Bart

2015-01-01

Conventional deep brain stimulation (DBS) applies constant electrical stimulation to specific brain regions to treat neurological disorders. Closed-loop DBS with real-time feedback is gaining attention in recent years, after proved more effective than conventional DBS in terms of pathological symptom control clinically. Here we demonstrate the conceptualization and validation of a closed-loop DBS system using open-source hardware. We used hippocampal theta oscillations as system input, and electrical stimulation in the mesencephalic reticular formation (mRt) as controller output. It is well documented that hippocampal theta oscillations are highly related to locomotion, while electrical stimulation in the mRt induces freezing. We used an Arduino open-source microcontroller between input and output sources. This allowed us to use hippocampal local field potentials (LFPs) to steer electrical stimulation in the mRt. Our results showed that closed-loop DBS significantly suppressed locomotion compared to no stimulation, and required on average only 56% of the stimulation used in open-loop DBS to reach similar effects. The main advantages of open-source hardware include wide selection and availability, high customizability, and affordability. Our open-source closed-loop DBS system is effective, and warrants further research using open-source hardware for closed-loop neuromodulation. PMID:25897892

Open Source and ROI: 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

A switch to free open source software can minimize cost and allow funding to be diverted to equipment and other programs. For instance, the OpenOffice suite is an alternative to expensive basic application programs offered by major vendors. Many such programs on the market offer features seldom used in education but for which educators must pay.…

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.

Rhenium-osmium and samarium-neodymium isotopic systematics of the stillwater complex

USGS Publications Warehouse

Lambert, D.D.; Morgan, J.W.; Walker, R.J.; Shirey, S.B.; Carlson, R.W.; Zientek, M.L.; Koski, M.S.

1989-01-01

Isotopic data for the Stillwater Complex, Montana , which formed about 2700 Ma (million years ago), were obtained to evaluate the role of magma mixing in the formation of strategic platinum-group element (PGE) ore deposits. Neodymium and osmium isotopic data indicate that the intrusion formed from at least two geochemically distinct magmas. Ultramafic affinity (U-type) magmas had initial ??Nd of -0.8 to -3.2 and a chondritic initial 187Os/186Os ratio of ???0.88, whereas anorthositic affinity (A-type) magmas had ??Nd of -0.7 to +1.7 and an initial 187Os/186Os ratio of ???1.13. These data suggest that U-type magmas were derived from a lithospheric mantle source containing recycled crustal materials whereas A-type magmas originated either by crustal contamination of basaltic magmas or by partial melting of basalt in the lower crust. The Nd and Os isotopic data also suggest that Os, and probably the other PGEs in ore horizons such as the J-M Reef, was derived from A-type magmas. The Nd and Os isotopic heterogeneity observed in rocks below the J-M Reef also suggests that A-type magmas were injected into the Stillwater U-type magma chamber at several stages during the development of the Ultramafic series.

Examining occupational stress, sources of stress and stress management strategies through the eyes of management consultants: a multiple correspondence analysis for latent constructs.

PubMed

von Humboldt, Sofia; Leal, Isabel; Laneiro, Tito; Tavares, Patrícia

2013-12-01

To date, little research has yet focused in broad assessment for management consultancy professionals. This investigation aims to analyse management consultants' self-perceptions of occupational stress (SPoOS), sources of stress (SoS) and stress management strategies (SMS) and to find latent constructs that can work as major determinants in consultants' conceptualization of SPoOS, SoS and SMS. Measures were completed, including demographics and interviews. Complete data were available for 39 management consultants, 53.8% male and aged between 23 and 56 years (M = 38.0; SD = 9.2). The data were subjected to content analysis. Representation of the associations and latent constructs were analysed by a multiple correspondence analysis. Results indicated that 'intellectual disturber' (31.4%) was the most referred SPoOS, 'high workload' (15.1%) was identified as the most prevalent perceived SoS and 'coaching' (19.0%) was the most mentioned SMS. No significant differences between the two gender groups were found regarding the three total scores. SPoOS was explained by a two-factor model: 'organization-oriented' and 'person-oriented'. A three-dimension model formed by 'job concerns', 'organizational constraints' and 'career expectations' was indicated as a best-fit solution for SoS, and SMS was best explained in a three-dimension model by 'group dynamics strategies', 'organizational culture strategies' and 'individual support strategies'. This research makes a unique contribution for a better understanding of what defines SPoOS, SoS and SMS for management consultants. Copyright © 2013 John Wiley & Sons, Ltd.

Surface and Airborne Measurements of Organosulfur and Methanesulfonate Over the Western United States and Coastal Areas

PubMed Central

Sorooshian, Armin; Crosbie, Ewan; Maudlin, Lindsay C.; Youn, Jong-Sang; Wang, Zhen; Shingler, Taylor; Ortega, Amber M.; Hersey, Scott; Woods, Roy K.

2015-01-01

This study reports on ambient measurements of organosulfur (OS) and methanesulfonate (MSA) over the western United States and coastal areas. Particulate OS levels are highest in summertime, and generally increase as a function of sulfate (a precursor) and sodium (a marine tracer) with peak levels at coastal sites. The ratio of OS to total sulfur (TS) is also highest at coastal sites, with increasing values as a function of Normalized Difference Vegetation Index (NDVI) and the ratio of organic carbon to elemental carbon. Correlative analysis points to significant relationships between OS and biogenic emissions from marine and continental sources, factors that coincide with secondary production, and vanadium due to a suspected catalytic role. A major OS species, methanesulfonate (MSA), was examined with intensive field measurements and the resulting data support the case for vanadium’s catalytic influence. Mass size distributions reveal a dominant MSA peak between aerodynamic diameters of 0.32—0.56 μm at a desert and coastal site with nearly all MSA mass (≥ 84%) in sub-micrometer sizes; MSA:non-sea salt sulfate ratios vary widely as a function of particle size and proximity to the ocean. Airborne data indicate that relative to the marine boundary layer, particulate MSA levels are enhanced in urban and agricultural areas, and also the free troposphere when impacted by biomass burning. Some combination of fires and marine-derived emissions leads to higher MSA levels than either source alone. Finally, MSA differences in cloud water and out-of-cloud aerosol are discussed. PMID:26413434

Surface and Airborne Measurements of Organosulfur and Methanesulfonate Over the Western United States and Coastal Areas.

PubMed

Sorooshian, Armin; Crosbie, Ewan; Maudlin, Lindsay C; Youn, Jong-Sang; Wang, Zhen; Shingler, Taylor; Ortega, Amber M; Hersey, Scott; Woods, Roy K

2015-08-27

This study reports on ambient measurements of organosulfur (OS) and methanesulfonate (MSA) over the western United States and coastal areas. Particulate OS levels are highest in summertime, and generally increase as a function of sulfate (a precursor) and sodium (a marine tracer) with peak levels at coastal sites. The ratio of OS to total sulfur (TS) is also highest at coastal sites, with increasing values as a function of Normalized Difference Vegetation Index (NDVI) and the ratio of organic carbon to elemental carbon. Correlative analysis points to significant relationships between OS and biogenic emissions from marine and continental sources, factors that coincide with secondary production, and vanadium due to a suspected catalytic role. A major OS species, methanesulfonate (MSA), was examined with intensive field measurements and the resulting data support the case for vanadium's catalytic influence. Mass size distributions reveal a dominant MSA peak between aerodynamic diameters of 0.32-0.56 μm at a desert and coastal site with nearly all MSA mass (≥ 84%) in sub-micrometer sizes; MSA:non-sea salt sulfate ratios vary widely as a function of particle size and proximity to the ocean. Airborne data indicate that relative to the marine boundary layer, particulate MSA levels are enhanced in urban and agricultural areas, and also the free troposphere when impacted by biomass burning. Some combination of fires and marine-derived emissions leads to higher MSA levels than either source alone. Finally, MSA differences in cloud water and out-of-cloud aerosol are discussed.

Open source drug discovery--a new paradigm of collaborative research in tuberculosis drug development.

PubMed

Bhardwaj, Anshu; Scaria, Vinod; Raghava, Gajendra Pal Singh; Lynn, Andrew Michael; Chandra, Nagasuma; Banerjee, Sulagna; Raghunandanan, Muthukurussi V; Pandey, Vikas; Taneja, Bhupesh; Yadav, Jyoti; Dash, Debasis; Bhattacharya, Jaijit; Misra, Amit; Kumar, Anil; Ramachandran, Srinivasan; Thomas, Zakir; Brahmachari, Samir K

2011-09-01

It is being realized that the traditional closed-door and market driven approaches for drug discovery may not be the best suited model for the diseases of the developing world such as tuberculosis and malaria, because most patients suffering from these diseases have poor paying capacity. To ensure that new drugs are created for patients suffering from these diseases, it is necessary to formulate an alternate paradigm of drug discovery process. The current model constrained by limitations for collaboration and for sharing of resources with confidentiality hampers the opportunities for bringing expertise from diverse fields. These limitations hinder the possibilities of lowering the cost of drug discovery. The Open Source Drug Discovery project initiated by Council of Scientific and Industrial Research, India has adopted an open source model to power wide participation across geographical borders. Open Source Drug Discovery emphasizes integrative science through collaboration, open-sharing, taking up multi-faceted approaches and accruing benefits from advances on different fronts of new drug discovery. Because the open source model is based on community participation, it has the potential to self-sustain continuous development by generating a storehouse of alternatives towards continued pursuit for new drug discovery. Since the inventions are community generated, the new chemical entities developed by Open Source Drug Discovery will be taken up for clinical trial in a non-exclusive manner by participation of multiple companies with majority funding from Open Source Drug Discovery. This will ensure availability of drugs through a lower cost community driven drug discovery process for diseases afflicting people with poor paying capacity. Hopefully what LINUX the World Wide Web have done for the information technology, Open Source Drug Discovery will do for drug discovery. Copyright © 2011 Elsevier Ltd. All rights reserved.

Constraints on the origin of Os-isotope disequilibrium in included and interstitial sulfides in mantle peridotites: Implications for the interpretation of Os-isotope signatures in MORB and Abyssal Peridotites

NASA Astrophysics Data System (ADS)

Lassiter, J. C.

2016-12-01

The use of isotope variations in basalts to probe the composition and evolution of the mantle is predicated on the assumption of local (i.e., grain-scale) isotopic equilibrium during mantle melting (Hofmann & Hart, 1978). However, several studies report Os-isotope disequilibrium in distinct populations of sulfides in some peridotites. In principle, grain-scale isotopic heterogeneity could reflect variable radiogenic ingrowth in ancient sulfides with variable Re/Os, or partial re-equilibration of low-Re/Os sulfides with high-Re/Os silicate phases along grain boundaries during mantle melting (e.g., Alard et al., 2005). Both cases require that sulfides fail to maintain isotopic equilibrium with neighboring phases over geologically long ( Ga) time scales. The preservation of Os-isotope disequilibrium in peridotites has been ascribed to the armoring effect of low-[Os] silicates, which limit diffusive exchange between isolated Os-rich phases. This raises the prospect that peridotite-derived melts may not inherit the Os-isotope composition of their source. The timescale required for diffusive equilibration between separate sulfide grains or between Os-rich sulfides and Os-poor silicates is a function of average sulfide size and spacing, Os diffusivity in armoring silicate minerals, and Os partitioning between silicate and sulfide phases. For typical sulfide abundances and sizes in mantle peridotites, neighboring sulfides are expected to re-equilibrate in less than a few 10s of m.y. at adiabatic mantle temperatures, even for very high (>106) sulfide/silicate KD values. Maintenance of disequilibrium requires very large sulfides (>100 um) separated by several mm and diffusion rates (D < 10-20 m2/s) slower than for most other elements in olivine. Equilibration timescales between sulfides and surrounding silicates are similar, so that large-scale isotopic disequilibrium between sulfides and silicates is also unlikely within the convecting mantle. Instead, observed grain-scale Os-isotope disequilibrium in mantle peridotites likely reflects recent sulfide metasomatism linked to interaction with eclogite- or pyroxenite-derived melts. Interstitial sulfides with radiogenic Os-isotopes provide further evidence for a role of eclogite melting in MORB genesis.

State-of-the-practice and lessons learned on implementing open data and open source policies.

DOT National Transportation Integrated Search

2012-05-01

This report describes the current government, academic, and private sector practices associated with open data and open source application development. These practices are identified; and the potential uses with the ITS Programs Data Capture and M...

Your Personal Analysis Toolkit - An Open Source Solution

NASA Astrophysics Data System (ADS)

Mitchell, T.

2009-12-01

Open source software is commonly known for its web browsers, word processors and programming languages. However, there is a vast array of open source software focused on geographic information management and geospatial application building in general. As geo-professionals, having easy access to tools for our jobs is crucial. Open source software provides the opportunity to add a tool to your tool belt and carry it with you for your entire career - with no license fees, a supportive community and the opportunity to test, adopt and upgrade at your own pace. OSGeo is a US registered non-profit representing more than a dozen mature geospatial data management applications and programming resources. Tools cover areas such as desktop GIS, web-based mapping frameworks, metadata cataloging, spatial database analysis, image processing and more. Learn about some of these tools as they apply to AGU members, as well as how you can join OSGeo and its members in getting the job done with powerful open source tools. If you haven't heard of OSSIM, MapServer, OpenLayers, PostGIS, GRASS GIS or the many other projects under our umbrella - then you need to hear this talk. Invest in yourself - use open source!

All-source Information Management and Integration for Improved Collective Intelligence Production

DTIC Science & Technology

2011-06-01

Intelligence (ELINT) • Open Source Intelligence ( OSINT ) • Technical Intelligence (TECHINT) These intelligence disciplines produce... intelligence , measurement and signature intelligence , signals intelligence , and open - source data, in the production of intelligence . All- source intelligence ...All- Source Information Integration and Management) R&D Project 3 All- Source Intelligence

Osmium Stable Isotope Composition of Chondrites and Iron Meteorites: Implications for Planetary Core Formation

NASA Astrophysics Data System (ADS)

Nanne, J. A. M.; Millet, M. A.; Burton, K. W.; Dale, C. W.; Nowell, G. M.; Williams, H. M.

2016-12-01

Mass-dependent Os stable isotope fractionation is expected to occur during metal-silicate segregation as well as during crystallization of metal alloys due to the different bonding environment between silicate and metals. As such, Os stable isotopes have the potential to resolve questions pertaining to planetary accretion and differentiation. Here, we present stable Os isotope data for a set of chondrites and iron meteorites to examine the processes associated with core solidification. Carbonaceous, ordinary, and enstatite chondrites show no detectable stable isotope variation with a δ190Os weighted average of +0.12±0.04 (n=37). The uniform composition observed for chondrites implies Os stable isotope homogeneity of the bulk solar nebula. Contrary to chondrites, iron meteorites display a large range in Os stable isotope compositions from δ190Os of +0.05 up to +0.49‰. Variation is only observed in the IIAB and IIIAB irons. Type IVB irons display values similar to chondrites (+0.107±0.047 [n=3]) and IVA compositions are slightly different +0.187±0.004 (n=2). The type IIAB and IIIAB groups show values both within the chondritic range and up to heavier values extending up to +0.49‰. Since core formation in small planetary bodies is expected to quantitatively sequester Os in metal phases, bulk planetary cores are expected to display chondritic δ190Os values. Conversely, samples of the IIAB and IIIAB group display significant variation, possibly indicating that stable isotope fractionation occurred during solidification of the parent-body core. However, no covariation is observed between δ190Os and either Os abundance or radiogenic Os isotope ratios. Instead, liquid immiscibility during core crystallization, where the liquid metal splits into separate S- and P-rich liquids, may be a source of Os stable isotope fractionation.

Re-Os isotope evidence from Mesozoic and Cenozoic basalts for secular evolution of the mantle beneath the North China Craton

NASA Astrophysics Data System (ADS)

Huang, Feng; Xu, Ji-Feng; Liu, Yong-Sheng; Li, Jie; Chen, Jian-Lin; Li, Xi-Yao

2017-05-01

The mechanism and process of lithospheric thinning beneath the North China Craton (NCC) are still debated. A key criterion in distinguishing among the proposed mechanisms is whether associated continental basalts were derived from the thinning lithospheric mantle or upwelling asthenosphere. Herein, we investigate the possible mechanisms of lithospheric thinning based on a systematic Re-Os isotopic study of Mesozoic to Cenozoic basalts from the NCC. Our whole-rock Re-Os isotopic results indicate that the Mesozoic basalts generally have high Re and Os concentrations that vary widely from 97.2 to 839.4 ppt and 74.4 to 519.6 ppt, respectively. They have high initial 187Os/188Os ratios ranging from 0.1513 to 0.3805, with corresponding variable γOs(t) values (+20 to +202). In contrast, the Re-Os concentrations and radiogenic Os isotope compositions of the Cenozoic basalts are typically lower than those of the Mesozoic basalts. The lowest initial 187Os/188Os ratios of the Cenozoic basalts are 0.1465 and 0.1479, with corresponding γOs(t) values of +15 and +16, which are within the range of ocean island basalts. These new Re-Os isotopic results, combined with the findings of previous studies, indicate that the Mesozoic basalts were a hybrid product of the melting of pyroxenite and peridotite in ancient lithospheric mantle beneath the NCC. The Cenozoic basalts were derived mainly from upwelling asthenosphere mixed with small amounts of lithospheric materials. The marked differences in geochemistry between the Mesozoic and Cenozoic basalts suggest a greatly reduced involvement of lithospheric mantle as the magma source from the Mesozoic to the Cenozoic. The subsequent lithospheric thinning of the NCC and replacement by upwelling asthenospheric mantle resulted in a change to asthenosphere-derived Cenozoic basalts.

Open source EMR software: profiling, insights and hands-on analysis.

PubMed

Kiah, M L M; Haiqi, Ahmed; Zaidan, B B; Zaidan, A A

2014-11-01

The use of open source software in health informatics is increasingly advocated by authors in the literature. Although there is no clear evidence of the superiority of the current open source applications in the healthcare field, the number of available open source applications online is growing and they are gaining greater prominence. This repertoire of open source options is of a great value for any future-planner interested in adopting an electronic medical/health record system, whether selecting an existent application or building a new one. The following questions arise. How do the available open source options compare to each other with respect to functionality, usability and security? Can an implementer of an open source application find sufficient support both as a user and as a developer, and to what extent? Does the available literature provide adequate answers to such questions? This review attempts to shed some light on these aspects. The objective of this study is to provide more comprehensive guidance from an implementer perspective toward the available alternatives of open source healthcare software, particularly in the field of electronic medical/health records. The design of this study is twofold. In the first part, we profile the published literature on a sample of existent and active open source software in the healthcare area. The purpose of this part is to provide a summary of the available guides and studies relative to the sampled systems, and to identify any gaps in the published literature with respect to our research questions. In the second part, we investigate those alternative systems relative to a set of metrics, by actually installing the software and reporting a hands-on experience of the installation process, usability, as well as other factors. The literature covers many aspects of open source software implementation and utilization in healthcare practice. Roughly, those aspects could be distilled into a basic taxonomy, making the literature landscape more perceivable. Nevertheless, the surveyed articles fall short of fulfilling the targeted objective of providing clear reference to potential implementers. The hands-on study contributed a more detailed comparative guide relative to our set of assessment measures. Overall, no system seems to satisfy an industry-standard measure, particularly in security and interoperability. The systems, as software applications, feel similar from a usability perspective and share a common set of functionality, though they vary considerably in community support and activity. More detailed analysis of popular open source software can benefit the potential implementers of electronic health/medical records systems. The number of examined systems and the measures by which to compare them vary across studies, but still rewarding insights start to emerge. Our work is one step toward that goal. Our overall conclusion is that open source options in the medical field are still far behind the highly acknowledged open source products in other domains, e.g. operating systems market share. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Getting Open Source Software into Schools: Strategies and Challenges

ERIC Educational Resources Information Center

Hepburn, Gary; Buley, Jan

2006-01-01

In this article Gary Hepburn and Jan Buley outline different approaches to implementing open source software (OSS) in schools; they also address the challenges that open source advocates should anticipate as they try to convince educational leaders to adopt OSS. With regard to OSS implementation, they note that schools have a flexible range of…

Open Source Library Management Systems: A Multidimensional Evaluation

ERIC Educational Resources Information Center

Balnaves, Edmund

2008-01-01

Open source library management systems have improved steadily in the last five years. They now present a credible option for small to medium libraries and library networks. An approach to their evaluation is proposed that takes account of three additional dimensions that only open source can offer: the developer and support community, the source…

Open Source as Appropriate Technology for Global Education

ERIC Educational Resources Information Center

Carmichael, Patrick; Honour, Leslie

2002-01-01

Economic arguments for the adoption of "open source" software in business have been widely discussed. In this paper we draw on personal experience in the UK, South Africa and Southeast Asia to forward compelling reasons why open source software should be considered as an appropriate and affordable alternative to the currently prevailing…

Government Technology Acquisition Policy: The Case of Proprietary versus Open Source Software

ERIC Educational Resources Information Center

Hemphill, Thomas A.

2005-01-01

This article begins by explaining the concepts of proprietary and open source software technology, which are now competing in the marketplace. A review of recent individual and cooperative technology development and public policy advocacy efforts, by both proponents of open source software and advocates of proprietary software, subsequently…

Open Source Communities in Technical Writing: Local Exigence, Global Extensibility

ERIC Educational Resources Information Center

Conner, Trey; Gresham, Morgan; McCracken, Jill

2011-01-01

By offering open-source software (OSS)-based networks as an affordable technology alternative, we partnered with a nonprofit community organization. In this article, we narrate the client-based experiences of this partnership, highlighting the ways in which OSS and open-source culture (OSC) transformed our students' and our own expectations of…

Personal Electronic Devices and the ISR Data Explosion: The Impact of Cyber Cameras on the Intelligence Community

DTIC Science & Technology

2015-06-01

ground.aspx?p=1 Texas Tech Security Group, “Automated Open Source Intelligence ( OSINT ) Using APIs.” RaiderSec, Sunday 30 December 2012, http...Open Source Intelligence ( OSINT ) Using APIs,” RaiderSec, Sunday 30 December 2012, http://raidersec.blogspot.com/2012/12/automated-open- source

Open-Source Unionism: New Workers, New Strategies

ERIC Educational Resources Information Center

Schmid, Julie M.

2004-01-01

In "Open-Source Unionism: Beyond Exclusive Collective Bargaining," published in fall 2002 in the journal Working USA, labor scholars Richard B. Freeman and Joel Rogers use the term "open-source unionism" to describe a form of unionization that uses Web technology to organize in hard-to-unionize workplaces. Rather than depend on the traditional…

Perceptions of Open Source versus Commercial Software: Is Higher Education Still on the Fence?

ERIC Educational Resources Information Center

van Rooij, Shahron Williams

2007-01-01

This exploratory study investigated the perceptions of technology and academic decision-makers about open source benefits and risks versus commercial software applications. The study also explored reactions to a concept for outsourcing campus-wide deployment and maintenance of open source. Data collected from telephone interviews were analyzed,…

Open Source for Knowledge and Learning Management: Strategies beyond Tools

ERIC Educational Resources Information Center

Lytras, Miltiadis, Ed.; Naeve, Ambjorn, Ed.

2007-01-01

In the last years, knowledge and learning management have made a significant impact on the IT research community. "Open Source for Knowledge and Learning Management: Strategies Beyond Tools" presents learning and knowledge management from a point of view where the basic tools and applications are provided by open source technologies.…

Open-Source Learning Management Systems: A Predictive Model for Higher Education

ERIC Educational Resources Information Center

van Rooij, S. Williams

2012-01-01

The present study investigated the role of pedagogical, technical, and institutional profile factors in an institution of higher education's decision to select an open-source learning management system (LMS). Drawing on the results of previous research that measured patterns of deployment of open-source software (OSS) in US higher education and…

An Embedded Systems Course for Engineering Students Using Open-Source Platforms in Wireless Scenarios

ERIC Educational Resources Information Center

Rodriguez-Sanchez, M. C.; Torrado-Carvajal, Angel; Vaquero, Joaquin; Borromeo, Susana; Hernandez-Tamames, Juan A.

2016-01-01

This paper presents a case study analyzing the advantages and disadvantages of using project-based learning (PBL) combined with collaborative learning (CL) and industry best practices, integrated with information communication technologies, open-source software, and open-source hardware tools, in a specialized microcontroller and embedded systems…

Technology collaboration by means of an open source government

NASA Astrophysics Data System (ADS)

Berardi, Steven M.

2009-05-01

The idea of open source software originally began in the early 1980s, but it never gained widespread support until recently, largely due to the explosive growth of the Internet. Only the Internet has made this kind of concept possible, bringing together millions of software developers from around the world to pool their knowledge. The tremendous success of open source software has prompted many corporations to adopt the culture of open source and thus share information they previously held secret. The government, and specifically the Department of Defense (DoD), could also benefit from adopting an open source culture. In acquiring satellite systems, the DoD often builds walls between program offices, but installing doors between programs can promote collaboration and information sharing. This paper addresses the challenges and consequences of adopting an open source culture to facilitate technology collaboration for DoD space acquisitions. DISCLAIMER: The views presented here are the views of the author, and do not represent the views of the United States Government, United States Air Force, or the Missile Defense Agency.

Open source software integrated into data services of Japanese planetary explorations

NASA Astrophysics Data System (ADS)

Yamamoto, Y.; Ishihara, Y.; Otake, H.; Imai, K.; Masuda, K.

2015-12-01

Scientific data obtained by Japanese scientific satellites and lunar and planetary explorations are archived in DARTS (Data ARchives and Transmission System). DARTS provides the data with a simple method such as HTTP directory listing for long-term preservation while DARTS tries to provide rich web applications for ease of access with modern web technologies based on open source software. This presentation showcases availability of open source software through our services. KADIAS is a web-based application to search, analyze, and obtain scientific data measured by SELENE(Kaguya), a Japanese lunar orbiter. KADIAS uses OpenLayers to display maps distributed from Web Map Service (WMS). As a WMS server, open source software MapServer is adopted. KAGUYA 3D GIS (KAGUYA 3D Moon NAVI) provides a virtual globe for the SELENE's data. The main purpose of this application is public outreach. NASA World Wind Java SDK is used to develop. C3 (Cross-Cutting Comparisons) is a tool to compare data from various observations and simulations. It uses Highcharts to draw graphs on web browsers. Flow is a tool to simulate a Field-Of-View of an instrument onboard a spacecraft. This tool itself is open source software developed by JAXA/ISAS, and the license is BSD 3-Caluse License. SPICE Toolkit is essential to compile FLOW. SPICE Toolkit is also open source software developed by NASA/JPL, and the website distributes many spacecrafts' data. Nowadays, open source software is an indispensable tool to integrate DARTS services.

Embracing Open Source for NASA's Earth Science Data Systems

NASA Technical Reports Server (NTRS)

Baynes, Katie; Pilone, Dan; Boller, Ryan; Meyer, David; Murphy, Kevin

2017-01-01

The overarching purpose of NASAs Earth Science program is to develop a scientific understanding of Earth as a system. Scientific knowledge is most robust and actionable when resulting from transparent, traceable, and reproducible methods. Reproducibility includes open access to the data as well as the software used to arrive at results. Additionally, software that is custom-developed for NASA should be open to the greatest degree possible, to enable re-use across Federal agencies, reduce overall costs to the government, remove barriers to innovation, and promote consistency through the use of uniform standards. Finally, Open Source Software (OSS) practices facilitate collaboration between agencies and the private sector. To best meet these ends, NASAs Earth Science Division promotes the full and open sharing of not only all data, metadata, products, information, documentation, models, images, and research results but also the source code used to generate, manipulate and analyze them. This talk focuses on the challenges to open sourcing NASA developed software within ESD and the growing pains associated with establishing policies running the gamut of tracking issues, properly documenting build processes, engaging the open source community, maintaining internal compliance, and accepting contributions from external sources. This talk also covers the adoption of existing open source technologies and standards to enhance our custom solutions and our contributions back to the community. Finally, we will be introducing the most recent OSS contributions from NASA Earth Science program and promoting these projects for wider community review and adoption.

Open source Modeling and optimization tools for Planning

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

Peles, S.

Open source modeling and optimization tools for planning The existing tools and software used for planning and analysis in California are either expensive, difficult to use, or not generally accessible to a large number of participants. These limitations restrict the availability of participants for larger scale energy and grid studies in the state. The proposed initiative would build upon federal and state investments in open source software, and create and improve open source tools for use in the state planning and analysis activities. Computational analysis and simulation frameworks in development at national labs and universities can be brought forward tomore » complement existing tools. An open source platform would provide a path for novel techniques and strategies to be brought into the larger community and reviewed by a broad set of stakeholders.« less

Prediction of survival benefits from progression-free survival benefits in advanced non-small-cell lung cancer: evidence from a meta-analysis of 2334 patients from 5 randomised trials

PubMed Central

Laporte, Silvy; Squifflet, Pierre; Baroux, Noémie; Fossella, Frank; Georgoulias, Vassilis; Pujol, Jean-Louis; Douillard, Jean-Yves; Kudoh, Shinzohy; Pignon, Jean-Pierre; Quinaux, Emmanuel; Buyse, Marc

2013-01-01

Objectives To investigate whether progression-free survival (PFS) can be considered a surrogate endpoint for overall survival (OS) in advanced non-small-cell lung cancer (NSCLC). Design Meta-analysis of individual patient data from randomised trials. Setting Five randomised controlled trials comparing docetaxel-based chemotherapy with vinorelbine-based chemotherapy for the first-line treatment of NSCLC. Participants 2331 patients with advanced NSCLC. Primary and secondary outcome measures Surrogacy of PFS for OS was assessed through the association between these endpoints and between the treatment effects on these endpoints. The surrogate threshold effect was the minimum treatment effect on PFS required to predict a non-zero treatment effect on OS. Results The median follow-up of patients still alive was 23.4 months. Median OS was 10 months and median PFS was 5.5 months. The treatment effects on PFS and OS were correlated, whether using centres (R²=0.62, 95% CI 0.52 to 0.72) or prognostic strata (R²=0.72, 95% CI 0.60 to 0.84) as units of analysis. The surrogate threshold effect was a PFS hazard ratio (HR) of 0.49 using centres or 0.53 using prognostic strata. Conclusions These analyses provide only modest support for considering PFS as an acceptable surrogate for OS in patients with advanced NSCLC. Only treatments that have a major impact on PFS (risk reduction of at least 50%) would be expected to also have a significant effect on OS. Whether these results also apply to targeted therapies is an open question that requires independent evaluation. PMID:23485717

Alzheimer’s Toxic Amyloid Beta Oligomers: Unwelcome Visitors to the Na/K ATPase alpha3 Docking Station

PubMed Central

DiChiara, Thomas; DiNunno, Nadia; Clark, Jeffrey; Bu, Riana Lo; Cline, Erika N.; Rollins, Madeline G.; Gong, Yuesong; Brody, David L.; Sligar, Stephen G.; Velasco, Pauline T.; Viola, Kirsten L.; Klein, William L.

2017-01-01

Toxic amyloid beta oligomers (AβOs) are known to accumulate in Alzheimer’s disease (AD) and in animal models of AD. Their structure is heterogeneous, and they are found in both intracellular and extracellular milieu. When given to CNS cultures or injected ICV into non-human primates and other non-transgenic animals, AβOs have been found to cause impaired synaptic plasticity, loss of memory function, tau hyperphosphorylation and tangle formation, synapse elimination, oxidative and ER stress, inflammatory microglial activation, and selective nerve cell death. Memory loss and pathology in transgenic models are prevented by AβO antibodies, while Aducanumab, an antibody that targets AβOs as well as fibrillar Aβ, has provided cognitive benefit to humans in early clinical trials. AβOs have now been investigated in more than 3000 studies and are widely thought to be the major toxic form of Aβ. Although much has been learned about the downstream mechanisms of AβO action, a major gap concerns the earliest steps: How do AβOs initially interact with surface membranes to generate neuron-damaging transmembrane events? Findings from Ohnishi et al (PNAS 2005) combined with new results presented here are consistent with the hypothesis that AβOs act as neurotoxins because they attach to particular membrane protein docks containing Na/K ATPase-α3, where they inhibit ATPase activity and pathologically restructure dock composition and topology in a manner leading to excessive Ca++ build-up. Better understanding of the mechanism that makes attachment of AβOs to vulnerable neurons a neurotoxic phenomenon should open the door to therapeutics and diagnostics targeting the first step of a complex pathway that leads to neural damage and dementia. PMID:28356893

Exposure-response analysis of alectinib in crizotinib-resistant ALK-positive non-small cell lung cancer.

PubMed

Morcos, Peter N; Nueesch, Eveline; Jaminion, Felix; Guerini, Elena; Hsu, Joy C; Bordogna, Walter; Balas, Bogdana; Mercier, Francois

2018-05-10

Alectinib is a selective and potent anaplastic lymphoma kinase (ALK) inhibitor that is active in the central nervous system (CNS). Alectinib demonstrated robust efficacy in a pooled analysis of two single-arm, open-label phase II studies (NP28673, NCT01801111; NP28761, NCT01871805) in crizotinib-resistant ALK-positive non-small-cell lung cancer (NSCLC): median overall survival (OS) 29.1 months (95% confidence interval [CI]: 21.3-39.0) for alectinib 600 mg twice daily (BID). We investigated exposure-response relationships from final pooled phase II OS and safety data to assess alectinib dose selection. A semi-parametric Cox proportional hazards model analyzed relationships between individual median observed steady-state trough concentrations (C trough,ss ) for combined exposure of alectinib and its major metabolite (M4), baseline covariates (demographics and disease characteristics) and OS. Univariate logistic regression analysis analyzed relationships between C trough,ss and incidence of adverse events (AEs: serious and Grade ≥ 3). Overall, 92% of patients (n = 207/225) had C trough,ss data and were included in the analysis. No statistically significant relationship was found between C trough,ss and OS following alectinib treatment. The only baseline covariates that statistically influenced OS were baseline tumor size and prior crizotinib treatment duration. Larger baseline tumor size and shorter prior crizotinib treatment were both associated with shorter OS. Logistic regression confirmed no significant relationship between C trough,ss and AEs. Alectinib 600 mg BID provides systemic exposures at plateau of response for OS while maintaining a well-tolerated safety profile. This analysis confirms alectinib 600 mg BID as the recommended global dose for patients with crizotinib-resistant ALK-positive NSCLC.

Limitations of Phased Array Beamforming in Open Rotor Noise Source Imaging

NASA Technical Reports Server (NTRS)

Horvath, Csaba; Envia, Edmane; Podboy, Gary G.

2013-01-01

Phased array beamforming results of the F31/A31 historical baseline counter-rotating open rotor blade set were investigated for measurement data taken on the NASA Counter-Rotating Open Rotor Propulsion Rig in the 9- by 15-Foot Low-Speed Wind Tunnel of NASA Glenn Research Center as well as data produced using the LINPROP open rotor tone noise code. The planar microphone array was positioned broadside and parallel to the axis of the open rotor, roughly 2.3 rotor diameters away. The results provide insight as to why the apparent noise sources of the blade passing frequency tones and interaction tones appear at their nominal Mach radii instead of at the actual noise sources, even if those locations are not on the blades. Contour maps corresponding to the sound fields produced by the radiating sound waves, taken from the simulations, are used to illustrate how the interaction patterns of circumferential spinning modes of rotating coherent noise sources interact with the phased array, often giving misleading results, as the apparent sources do not always show where the actual noise sources are located. This suggests that a more sophisticated source model would be required to accurately locate the sources of each tone. The results of this study also have implications with regard to the shielding of open rotor sources by airframe empennages.

A Crossover from High Stiffness to High Hardness: The Case of Osmium and Its Borides

NASA Astrophysics Data System (ADS)

Bian, Yongming; Liu, Xiaomei; Li, Anhu; Liang, Yongcheng

2016-09-01

Transition-metal light-element compounds are currently raising great expectations for hard and superhard materials. Using the widely attracting osmium (Os) and its borides (OsB, Os2B3 and OsB2) as prototypes, we demonstrate by first-principles calculations that heavy transition metals, which possess high stiffness but low hardness, can be converted into highly hard materials by incorporating of light elements to form compounds. Such a crossover is a manifestation that the underlying sources of high stiffness and high hardness are fundamentally different. The stiffness is related to elastic deformation that is closely associated with valence electron density, whereas the hardness depends strongly on plastic deformation that is determined by bonding nature. Therefore, the incorporation of light atoms into transition metal should be a valid pathway of designing hard and superhard materials. This strategy is in principle also applicable to other transition-metal borides, carbides, and nitrides.

Comparative biochemical methane potential of paragrass using an unacclimated and an acclimated microbial consortium.

PubMed

Nuchdang, Sasikarn; Khemkhao, Maneerat; Techkarnjanaruk, Somkiet; Phalakornkule, Chantaraporn

2015-05-01

The effect of inoculum sources on the anaerobic digestion of paragrass was investigated. Two types of sludge were used as the inoculums: an anaerobic sludge obtained from a domestic wastewater treatment plant (OS) and a sludge acclimated to fibrous substrates in raw palm oil mill effluent (AMC). Microbial activity assays showed that the AMC had hydrolytic and acetogenic activities two times greater than the activities of the OS. In addition, the production of methane from acetate by the AMC occurred without a lag phase, while it took 8 days for the OS to start producing methane from the same substrate. The biochemical methane potential after 80 days digestion was 316 ml STP/g VS(added) using the AMC, and 277 ml STP/g VS(added) using the OS. The methane potential of the paragrass was estimated to be 3337 Nm(3) CH4/ha a. Copyright © 2015 Elsevier Ltd. All rights reserved.

Develop Direct Geo-referencing System Based on Open Source Software and Hardware Platform

NASA Astrophysics Data System (ADS)

Liu, H. S.; Liao, H. M.

2015-08-01

Direct geo-referencing system uses the technology of remote sensing to quickly grasp images, GPS tracks, and camera position. These data allows the construction of large volumes of images with geographic coordinates. So that users can be measured directly on the images. In order to properly calculate positioning, all the sensor signals must be synchronized. Traditional aerial photography use Position and Orientation System (POS) to integrate image, coordinates and camera position. However, it is very expensive. And users could not use the result immediately because the position information does not embed into image. To considerations of economy and efficiency, this study aims to develop a direct geo-referencing system based on open source software and hardware platform. After using Arduino microcontroller board to integrate the signals, we then can calculate positioning with open source software OpenCV. In the end, we use open source panorama browser, panini, and integrate all these to open source GIS software, Quantum GIS. A wholesome collection of data - a data processing system could be constructed.

Development of an Open Source, Air-Deployable Weather Station

NASA Astrophysics Data System (ADS)

Krejci, A.; Lopez Alcala, J. M.; Nelke, M.; Wagner, J.; Udell, C.; Higgins, C. W.; Selker, J. S.

2017-12-01

We created a packaged weather station intended to be deployed in the air on tethered systems. The device incorporates lightweight sensors and parts and runs for up to 24 hours off of lithium polymer batteries, allowing the entire package to be supported by a thin fiber. As the fiber does not provide a stable platform, additional data (pitch and roll) from typical weather parameters (e.g. temperature, pressure, humidity, wind speed, and wind direction) are determined using an embedded inertial motion unit. All designs are open sourced including electronics, CAD drawings, and descriptions of assembly and can be found on the OPEnS lab website at http://www.open-sensing.org/lowcost-weather-station/. The Openly Published Environmental Sensing Lab (OPEnS: Open-Sensing.org) expands the possibilities of scientific observation of our Earth, transforming the technology, methods, and culture by combining open-source development and cutting-edge technology. New OPEnS labs are now being established in India, France, Switzerland, the Netherlands, and Ghana.

Software for Real-Time Analysis of Subsonic Test Shot Accuracy

DTIC Science & Technology

2014-03-01

used the C++ programming language, the Open Source Computer Vision ( OpenCV ®) software library, and Microsoft Windows® Application Programming...video for comparison through OpenCV image analysis tools. Based on the comparison, the software then computed the coordinates of each shot relative to...DWB researchers wanted to use the Open Source Computer Vision ( OpenCV ) software library for capturing and analyzing frames of video. OpenCV contains

Open source electronic health records and chronic disease management.

PubMed

Goldwater, Jason C; Kwon, Nancy J; Nathanson, Ashley; Muckle, Alison E; Brown, Alexa; Cornejo, Kerri

2014-02-01

To study and report on the use of open source electronic health records (EHR) to assist with chronic care management within safety net medical settings, such as community health centers (CHC). The study was conducted by NORC at the University of Chicago from April to September 2010. The NORC team undertook a comprehensive environmental scan, including a literature review, a dozen key informant interviews using a semistructured protocol, and a series of site visits to CHC that currently use an open source EHR. Two of the sites chosen by NORC were actively using an open source EHR to assist in the redesign of their care delivery system to support more effective chronic disease management. This included incorporating the chronic care model into an CHC and using the EHR to help facilitate its elements, such as care teams for patients, in addition to maintaining health records on indigent populations, such as tuberculosis status on homeless patients. The ability to modify the open-source EHR to adapt to the CHC environment and leverage the ecosystem of providers and users to assist in this process provided significant advantages in chronic care management. Improvements in diabetes management, controlled hypertension and increases in tuberculosis vaccinations were assisted through the use of these open source systems. The flexibility and adaptability of open source EHR demonstrated its utility and viability in the provision of necessary and needed chronic disease care among populations served by CHC.

What an open source clinical trial community can learn from hackers

PubMed Central

Dunn, Adam G.; Day, Richard O.; Mandl, Kenneth D.; Coiera, Enrico

2014-01-01

Summary Open sharing of clinical trial data has been proposed as a way to address the gap between the production of clinical evidence and the decision-making of physicians. Since a similar gap has already been addressed in the software industry by the open source software movement, we examine how the social and technical principles of the movement can be used to guide the growth of an open source clinical trial community. PMID:22553248

B a 2 NiOs O 6 : A Dirac-Mott insulator with ferromagnetism near 100 K

DOE PAGES

Feng, Hai L.; Calder, Stuart; Ghimire, Madhav Prasad; ...

2016-12-28

In this study, the ferromagnetic semiconductor Ba 2NiOsO 6 ( T mag ~ 100 K ) was synthesized at 6 GPa and 1500 °C. It crystallizes into a double perovskite structure [Fm - 3m ; a = 8.0428 ( 1 ) Å], where the Ni 2+ and Os 6+ ions are perfectly ordered at the perovskite B site. We show that the spin-orbit coupling of Os 6+ plays an essential role in opening the charge gap. The magnetic state was investigated by density functional theory calculations and powder neutron diffraction. The latter revealed a collinear ferromagnetic order in a >more » 21 kOe magnetic field at 5 K. The ferromagnetic gapped state is fundamentally different from that of known dilute magnetic semiconductors such as (Ga,Mn)As and (Cd,Mn)Te ( T mag < 180 K ), the spin-gapless semiconductor Mn 2 CoAl ( T mag ~ 720 K ), and the ferromagnetic insulators EuO ( T mag ~ 70 K ) and Bi 3Cr 3O 11 ( T mag ~ 220 K ). It is also qualitatively different from known ferrimagnetic insulators and semiconductors, which are characterized by an antiparallel spin arrangement. Our finding of the ferromagnetic semiconductivity of Ba 2NiOsO 6 should increase interest in the platinum group oxides, because this alternative class of materials should be useful in the development of spintronic, quantum magnetic, and related devices.« less

B a 2 NiOs O 6 : A Dirac-Mott insulator with ferromagnetism near 100 K

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

Feng, Hai L.; Calder, Stuart; Ghimire, Madhav Prasad

In this study, the ferromagnetic semiconductor Ba 2NiOsO 6 ( T mag ~ 100 K ) was synthesized at 6 GPa and 1500 °C. It crystallizes into a double perovskite structure [Fm - 3m ; a = 8.0428 ( 1 ) Å], where the Ni 2+ and Os 6+ ions are perfectly ordered at the perovskite B site. We show that the spin-orbit coupling of Os 6+ plays an essential role in opening the charge gap. The magnetic state was investigated by density functional theory calculations and powder neutron diffraction. The latter revealed a collinear ferromagnetic order in a >more » 21 kOe magnetic field at 5 K. The ferromagnetic gapped state is fundamentally different from that of known dilute magnetic semiconductors such as (Ga,Mn)As and (Cd,Mn)Te ( T mag < 180 K ), the spin-gapless semiconductor Mn 2 CoAl ( T mag ~ 720 K ), and the ferromagnetic insulators EuO ( T mag ~ 70 K ) and Bi 3Cr 3O 11 ( T mag ~ 220 K ). It is also qualitatively different from known ferrimagnetic insulators and semiconductors, which are characterized by an antiparallel spin arrangement. Our finding of the ferromagnetic semiconductivity of Ba 2NiOsO 6 should increase interest in the platinum group oxides, because this alternative class of materials should be useful in the development of spintronic, quantum magnetic, and related devices.« less

Outcomes in 370 patients with mantle cell lymphoma treated with ibrutinib: a pooled analysis from three open-label studies.

PubMed

Rule, Simon; Dreyling, Martin; Goy, Andre; Hess, Georg; Auer, Rebecca; Kahl, Brad; Cavazos, Nora; Liu, Black; Yang, Shiyi; Clow, Fong; Goldberg, Jenna D; Beaupre, Darrin; Vermeulen, Jessica; Wildgust, Mark; Wang, Michael

2017-11-01

Ibrutinib is highly active in treating mantle cell lymphoma (MCL), an aggressive B-cell lymphoma. We pooled data from three ibrutinib studies to explore the impact of baseline patient characteristics on treatment response. Patients with relapsed/refractory MCL (n = 370) treated with ibrutinib had an objective response rate (ORR) of 66% (20% complete response; 46% partial response); median duration of response (DOR), progression-free survival (PFS) and overall survival (OS) were 18·6, 12·8 and 25·0 months, respectively. Univariate analyses showed patients with one versus >one prior line of therapy had longer OS. Multivariate analyses identified that one prior line of therapy affected PFS; Eastern Cooperative Oncology Group (ECOG) performance status, simplified MCL international prognostic index (sMIPI) score, bulky disease, and blastoid histology affected OS and PFS. Patients with blastoid versus non-blastoid histology had similar time to best response, but lower ORR, DOR, PFS and OS. OS and PFS were longer in patients with better sMIPI, patients with ECOG performance status 0-1, non-bulky disease and non-blastoid histology. Additionally, the proportion of patients with poor prognostic factors increased with increasing lines of therapy. Together, results suggest that patient outcomes following treatment failure with ibrutinib are related to the natural biological evolution of the disease. © 2017 John Wiley & Sons Ltd.

An Evaluation of Open Source Learning Management Systems According to Administration Tools and Curriculum Design

ERIC Educational Resources Information Center

Ozdamli, Fezile

2007-01-01

Distance education is becoming more important in the universities and schools. The aim of this research is to evaluate the current existing Open Source Learning Management Systems according to Administration tool and Curriculum Design. For this, seventy two Open Source Learning Management Systems have been subjected to a general evaluation. After…

Evaluating Open Source Software for Use in Library Initiatives: A Case Study Involving Electronic Publishing

ERIC Educational Resources Information Center

Samuels, Ruth Gallegos; Griffy, Henry

2012-01-01

This article discusses best practices for evaluating open source software for use in library projects, based on the authors' experience evaluating electronic publishing solutions. First, it presents a brief review of the literature, emphasizing the need to evaluate open source solutions carefully in order to minimize Total Cost of Ownership. Next,…

A Requirements-Based Exploration of Open-Source Software Development Projects--Towards a Natural Language Processing Software Analysis Framework

ERIC Educational Resources Information Center

Vlas, Radu Eduard

2012-01-01

Open source projects do have requirements; they are, however, mostly informal, text descriptions found in requests, forums, and other correspondence. Understanding such requirements provides insight into the nature of open source projects. Unfortunately, manual analysis of natural language requirements is time-consuming, and for large projects,…

Open Source Meets Virtual Reality--An Instructor's Journey Unearths New Opportunities for Learning, Community, and Academia

ERIC Educational Resources Information Center

O'Connor, Eileen A.

2015-01-01

Opening with the history, recent advances, and emerging ways to use avatar-based virtual reality, an instructor who has used virtual environments since 2007 shares how these environments bring more options to community building, teaching, and education. With the open-source movement, where the source code for virtual environments was made…

The Implications of Incumbent Intellectual Property Strategies for Open Source Software Success and Commercialization

ERIC Educational Resources Information Center

Wen, Wen

2012-01-01

While open source software (OSS) emphasizes open access to the source code and avoids the use of formal appropriability mechanisms, there has been little understanding of how the existence and exercise of formal intellectual property rights (IPR) such as patents influence the direction of OSS innovation. This dissertation seeks to bridge this gap…

Migrations of the Mind: The Emergence of Open Source Education

ERIC Educational Resources Information Center

Glassman, Michael; Bartholomew, Mitchell; Jones, Travis

2011-01-01

The authors describe an Open Source approach to education. They define Open Source Education (OSE) as a teaching and learning framework where the use and presentation of information is non-hierarchical, malleable, and subject to the needs and contributions of students as they become "co-owners" of the course. The course transforms itself into an…

Prepare for Impact

ERIC Educational Resources Information Center

Waters, John K.

2010-01-01

Open source software is poised to make a profound impact on K-12 education. For years industry experts have been predicting the widespread adoption of open source tools by K-12 school districts. They're about to be proved right. The impact may not yet have been profound, but it's fair to say that some open source systems and non-proprietary…

7 Questions to Ask Open Source Vendors

ERIC Educational Resources Information Center

Raths, David

2012-01-01

With their budgets under increasing pressure, many campus IT directors are considering open source projects for the first time. On the face of it, the savings can be significant. Commercial emergency-planning software can cost upward of six figures, for example, whereas the open source Kuali Ready might run as little as $15,000 per year when…

Cognitive Readiness Assessment and Reporting: An Open Source Mobile Framework for Operational Decision Support and Performance Improvement

ERIC Educational Resources Information Center

Heric, Matthew; Carter, Jenn

2011-01-01

Cognitive readiness (CR) and performance for operational time-critical environments are continuing points of focus for military and academic communities. In response to this need, we designed an open source interactive CR assessment application as a highly adaptive and efficient open source testing administration and analysis tool. It is capable…

Self-expandable metallic stent placement plus laparoscopy for acute malignant colorectal obstruction.

PubMed

Zhou, Jia-Min; Yao, Li-Qing; Xu, Jian-Min; Xu, Mei-Dong; Zhou, Ping-Hong; Chen, Wei-Feng; Shi, Qiang; Ren, Zhong; Chen, Tao; Zhong, Yun-Shi

2013-09-07

To investigate the clinical advantages of the stent-laparoscopy approach to treat colorectal cancer (CRC) patients with acute colorectal obstruction (ACO). From April 2008 to April 2012, surgery-related parameters, complications, overall survival (OS), and disease-free survival (DFS) of 74 consecutive patients with left-sided CRC presented with ACO who underwent self-expandable metallic stent (SEMS) placement followed by one-stage open (n = 58) or laparoscopic resection (n = 16) were evaluated retrospectively. The stent-laparoscopy group was also compared with a control group of 96 CRC patients who underwent regular laparoscopy without ACO between January 2010 and December 2011 to explore whether SEMS placement influenced the laparoscopic procedure or reduced long-term survival by influencing CRC oncological characteristics. The characteristics of patients among these groups were comparable. The rate of conversion to open surgery was 12.5% in the stent-laparoscopy group. Bowel function recovery and postoperative hospital stay were significantly shorter (3.3 ± 0.9 d vs 4.2 ± 1.5 d and 6.7 ± 1.1 d vs 9.5 ± 6.7 d, P = 0.016 and P = 0.005), and surgical time was significantly longer (152.1 ± 44.4 min vs 127.4 ± 38.4 min, P = 0.045) in the stent-laparoscopy group than in the stent-open group. Surgery-related complications and the rate of admission to the intensive care unit were lower in the stent-laparoscopy group. There were no significant differences in the interval between stenting and surgery, intraoperative blood loss, OS, and DFS between the two stent groups. Compared with those in the stent-laparoscopy group, all surgery-related parameters, complications, OS, and DFS in the control group were comparable. The stent-laparoscopy approach is a feasible, rapid, and minimally invasive option for patients with ACO caused by left-sided CRC and can achieve a favorable long-term prognosis.

A transgenic study on affecting potato tuber yield by expressing the rice sucrose transporter genes OsSUT5Z and OsSUT2M.

PubMed

Sun, Aijun; Dai, Yan; Zhang, Xinsheng; Li, Chunmin; Meng, Kun; Xu, Honglin; Wei, Xiaoli; Xiao, Guifang; Ouwerkerk, Pieter B F; Wang, Mei; Zhu, Zhen

2011-07-01

In many plants, sucrose transporters are essential for both sucrose exports from sources and imports into sinks, indicating a function in assimilate partitioning. To investigate whether sucrose transporters can improve the yield of starch plant, potato plants (Solanum tuberosum L. cv. Désirée) were transformed with cDNAs of the rice sucrose transporter genes OsSUT5Z and OsSUT2M under the control of a tuber-specific, class-I patatin promoter. Compared to the controls, the average fructose content of OsSUT5Z transgenic tubers significantly increased. However, the content of the sugars and starch in the OsSUT2M transgenic potato tubers showed no obvious difference. Correspondingly, the average tuber yield, average number of tubers per plant and average weight of single tuber showed no significant difference in OsSUT2M transgenic tubers with controls. In the OsSUT5Z transgenic lines, the average tuber yield per plant was 1.9-fold higher than the controls, and the average number of tubers per plant increased by more than 10 tubers on average, whereas the average weight of a single tuber did not increase significantly. These results suggested that the average number of tubers per plant showed more contribution than the average weight of a single tuber to the tuber yield per plant. © 2011 Institute of Botany, Chinese Academy of Sciences.

Open source IPSEC software in manned and unmanned space missions

NASA Astrophysics Data System (ADS)

Edwards, Jacob

Network security is a major topic of research because cyber attackers pose a threat to national security. Securing ground-space communications for NASA missions is important because attackers could endanger mission success and human lives. This thesis describes how an open source IPsec software package was used to create a secure and reliable channel for ground-space communications. A cost efficient, reproducible hardware testbed was also created to simulate ground-space communications. The testbed enables simulation of low-bandwidth and high latency communications links to experiment how the open source IPsec software reacts to these network constraints. Test cases were built that allowed for validation of the testbed and the open source IPsec software. The test cases also simulate using an IPsec connection from mission control ground routers to points of interest in outer space. Tested open source IPsec software did not meet all the requirements. Software changes were suggested to meet requirements.

Upon the Shoulders of Giants: Open-Source Hardware and Software in Analytical Chemistry.

PubMed

Dryden, Michael D M; Fobel, Ryan; Fobel, Christian; Wheeler, Aaron R

2017-04-18

Isaac Newton famously observed that "if I have seen further it is by standing on the shoulders of giants." We propose that this sentiment is a powerful motivation for the "open-source" movement in scientific research, in which creators provide everything needed to replicate a given project online, as well as providing explicit permission for users to use, improve, and share it with others. Here, we write to introduce analytical chemists who are new to the open-source movement to best practices and concepts in this area and to survey the state of open-source research in analytical chemistry. We conclude by considering two examples of open-source projects from our own research group, with the hope that a description of the process, motivations, and results will provide a convincing argument about the benefits that this movement brings to both creators and users.

Open-Source 3-D Platform for Low-Cost Scientific Instrument Ecosystem.

PubMed

Zhang, C; Wijnen, B; Pearce, J M

2016-08-01

The combination of open-source software and hardware provides technically feasible methods to create low-cost, highly customized scientific research equipment. Open-source 3-D printers have proven useful for fabricating scientific tools. Here the capabilities of an open-source 3-D printer are expanded to become a highly flexible scientific platform. An automated low-cost 3-D motion control platform is presented that has the capacity to perform scientific applications, including (1) 3-D printing of scientific hardware; (2) laboratory auto-stirring, measuring, and probing; (3) automated fluid handling; and (4) shaking and mixing. The open-source 3-D platform not only facilities routine research while radically reducing the cost, but also inspires the creation of a diverse array of custom instruments that can be shared and replicated digitally throughout the world to drive down the cost of research and education further. © 2016 Society for Laboratory Automation and Screening.

OpenSesame: an open-source, graphical experiment builder for the social sciences.

PubMed

Mathôt, Sebastiaan; Schreij, Daniel; Theeuwes, Jan

2012-06-01

In the present article, we introduce OpenSesame, a graphical experiment builder for the social sciences. OpenSesame is free, open-source, and cross-platform. It features a comprehensive and intuitive graphical user interface and supports Python scripting for complex tasks. Additional functionality, such as support for eyetrackers, input devices, and video playback, is available through plug-ins. OpenSesame can be used in combination with existing software for creating experiments.

The Privacy and Security Implications of Open Data in Healthcare.

PubMed

Kobayashi, Shinji; Kane, Thomas B; Paton, Chris

2018-04-22

 The International Medical Informatics Association (IMIA) Open Source Working Group (OSWG) initiated a group discussion to discuss current privacy and security issues in the open data movement in the healthcare domain from the perspective of the OSWG membership.  Working group members independently reviewed the recent academic and grey literature and sampled a number of current large-scale open data projects to inform the working group discussion.  This paper presents an overview of open data repositories and a series of short case reports to highlight relevant issues present in the recent literature concerning the adoption of open approaches to sharing healthcare datasets. Important themes that emerged included data standardisation, the inter-connected nature of the open source and open data movements, and how publishing open data can impact on the ethics, security, and privacy of informatics projects.  The open data and open source movements in healthcare share many common philosophies and approaches including developing international collaborations across multiple organisations and domains of expertise. Both movements aim to reduce the costs of advancing scientific research and improving healthcare provision for people around the world by adopting open intellectual property licence agreements and codes of practice. Implications of the increased adoption of open data in healthcare include the need to balance the security and privacy challenges of opening data sources with the potential benefits of open data for improving research and healthcare delivery. Georg Thieme Verlag KG Stuttgart.

Simulation of partially coherent light propagation using parallel computing devices

NASA Astrophysics Data System (ADS)

Magalhães, Tiago C.; Rebordão, José M.

2017-08-01

Light acquires or loses coherence and coherence is one of the few optical observables. Spectra can be derived from coherence functions and understanding any interferometric experiment is also relying upon coherence functions. Beyond the two limiting cases (full coherence or incoherence) the coherence of light is always partial and it changes with propagation. We have implemented a code to compute the propagation of partially coherent light from the source plane to the observation plane using parallel computing devices (PCDs). In this paper, we restrict the propagation in free space only. To this end, we used the Open Computing Language (OpenCL) and the open-source toolkit PyOpenCL, which gives access to OpenCL parallel computation through Python. To test our code, we chose two coherence source models: an incoherent source and a Gaussian Schell-model source. In the former case, we divided into two different source shapes: circular and rectangular. The results were compared to the theoretical values. Our implemented code allows one to choose between the PyOpenCL implementation and a standard one, i.e using the CPU only. To test the computation time for each implementation (PyOpenCL and standard), we used several computer systems with different CPUs and GPUs. We used powers of two for the dimensions of the cross-spectral density matrix (e.g. 324, 644) and a significant speed increase is observed in the PyOpenCL implementation when compared to the standard one. This can be an important tool for studying new source models.

An Open Source Simulation System

NASA Technical Reports Server (NTRS)

Slack, Thomas

2005-01-01

An investigation into the current state of the art of open source real time programming practices. This document includes what technologies are available, how easy is it to obtain, configure, and use them, and some performance measures done on the different systems. A matrix of vendors and their products is included as part of this investigation, but this is not an exhaustive list, and represents only a snapshot of time in a field that is changing rapidly. Specifically, there are three approaches investigated: 1. Completely open source on generic hardware, downloaded from the net. 2. Open source packaged by a vender and provided as free evaluation copy. 3. Proprietary hardware with pre-loaded proprietary source available software provided by the vender as for our evaluation.

Altered Expression of a Malate-Permeable Anion Channel, OsALMT4, Disrupts Mineral Nutrition1[OPEN

PubMed Central

Delhaize, Emmanuel

2017-01-01

Aluminum-activated malate transporters (ALMTs) form a family of anion channels in plants, but little is known about most of its members. This study examined the function of OsALMT4 from rice (Oryza sativa). We show that OsALMT4 is expressed in roots and shoots and that the OsALMT4 protein localizes to the plasma membrane. Transgenic rice lines overexpressing (OX) OsALMT4 released malate from the roots constitutively and had 2-fold higher malate concentrations in the xylem sap than nulls, indicating greater concentrations of malate in the apoplast. OX lines developed brown necrotic spots on the leaves that did not appear on nulls. These symptoms were not associated with altered concentrations of any mineral element in the leaves, although the OX lines had higher concentrations of Mn and B in their grain compared with nulls. While total leaf Mn concentrations were not different between the OX and null lines, Mn concentrations in the apoplast were greater in the OX plants. The OX lines also displayed increased expression of Mn transporters and were more sensitive to Mn toxicity than null plants. We showed that the growth of wild-type rice was unaffected by 100 µm Mn in hydroponics but, when combined with 1 mm malate, this concentration inhibited growth. We conclude that increasing OsALMT4 expression affected malate efflux and compartmentation within the tissues, which increased Mn concentrations in the apoplast of leaves and induced the toxicity symptoms. This study reveals new links between malate transport and mineral nutrition. PMID:29101278

Identification of rice cornichon as a possible cargo receptor for the Golgi-localized sodium transporter OsHKT1;3

PubMed Central

Rosas-Santiago, Paul; Lagunas-Gómez, Daniel; Barkla, Bronwyn J.; Vera-Estrella, Rosario; Lalonde, Sylvie; Jones, Alexander; Frommer, Wolf B.; Zimmermannova, Olga; Sychrová, Hana; Pantoja, Omar

2015-01-01

Membrane proteins are synthesized and folded in the endoplasmic reticulum (ER), and continue their path to their site of residence along the secretory pathway. The COPII system has been identified as a key player for selecting and directing the fate of membrane and secretory cargo proteins. Selection of cargo proteins within the COPII vesicles is achieved by cargo receptors. The cornichon cargo receptor belongs to a conserved protein family found in eukaryotes that has been demonstrated to participate in the selection of integral membrane proteins as cargo for their correct targeting. Here it is demonstrated at the cellular level that rice cornichon OsCNIH1 interacts with OsHKT1;3 and, in yeast cells, enables the expression of the sodium transporter to the Golgi apparatus. Physical and functional HKT–cornichon interactions are confirmed by the mating-based split ubiquitin system, bimolecular fluorescence complementation, and Xenopus oocyte and yeast expression systems. The interaction between the two proteins occurs in the ER of plant cells and their co-expression in oocytes leads to the sequestration of the transporter in the ER. In the yeast cornichon mutant erv14, OsHKT1;3 is mistargeted, preventing the toxic effects of sodium transport in the cell observed in wild-type cells or in the erv14 mutant that co-expressed OsHKT1;3 with either OsCNIH1 or Erv14p. Identification and characterization of rice cornichon as a possible cargo receptor opens up the opportunity to improve our knowledge on membrane protein targeting in plant cells. PMID:25750424

A clinic compatible, open source electrophysiology system.

PubMed

Hermiz, John; Rogers, Nick; Kaestner, Erik; Ganji, Mehran; Cleary, Dan; Snider, Joseph; Barba, David; Dayeh, Shadi; Halgren, Eric; Gilja, Vikash

2016-08-01

Open source electrophysiology (ephys) recording systems have several advantages over commercial systems such as customization and affordability enabling more researchers to conduct ephys experiments. Notable open source ephys systems include Open-Ephys, NeuroRighter and more recently Willow, all of which have high channel count (64+), scalability, and advanced software to develop on top of. However, little work has been done to build an open source ephys system that is clinic compatible, particularly in the operating room where acute human electrocorticography (ECoG) research is performed. We developed an affordable (<; $10,000) and open system for research purposes that features power isolation for patient safety, compact and water resistant enclosures and 256 recording channels sampled up to 20ksam/sec, 16-bit. The system was validated by recording ECoG with a high density, thin film device for an acute, awake craniotomy study at UC San Diego, Thornton Hospital Operating Room.

Freeing Worldview's development process: Open source everything!

NASA Astrophysics Data System (ADS)

Gunnoe, T.

2016-12-01

Freeing your code and your project are important steps for creating an inviting environment for collaboration, with the added side effect of keeping a good relationship with your users. NASA Worldview's codebase was released with the open source NOSA (NASA Open Source Agreement) license in 2014, but this is only the first step. We also have to free our ideas, empower our users by involving them in the development process, and open channels that lead to the creation of a community project. There are many highly successful examples of Free and Open Source Software (FOSS) projects of which we can take note: the Linux kernel, Debian, GNOME, etc. These projects owe much of their success to having a passionate mix of developers/users with a great community and a common goal in mind. This presentation will describe the scope of this openness and how Worldview plans to move forward with a more community-inclusive approach.

OpenFLUID: an open-source software environment for modelling fluxes in landscapes

NASA Astrophysics Data System (ADS)

Fabre, Jean-Christophe; Rabotin, Michaël; Crevoisier, David; Libres, Aline; Dagès, Cécile; Moussa, Roger; Lagacherie, Philippe; Raclot, Damien; Voltz, Marc

2013-04-01

Integrative landscape functioning has become a common concept in environmental management. Landscapes are complex systems where many processes interact in time and space. In agro-ecosystems, these processes are mainly physical processes, including hydrological-processes, biological processes and human activities. Modelling such systems requires an interdisciplinary approach, coupling models coming from different disciplines, developed by different teams. In order to support collaborative works, involving many models coupled in time and space for integrative simulations, an open software modelling platform is a relevant answer. OpenFLUID is an open source software platform for modelling landscape functioning, mainly focused on spatial fluxes. It provides an advanced object-oriented architecture allowing to i) couple models developed de novo or from existing source code, and which are dynamically plugged to the platform, ii) represent landscapes as hierarchical graphs, taking into account multi-scale, spatial heterogeneities and landscape objects connectivity, iii) run and explore simulations in many ways : using the OpenFLUID software interfaces for users (command line interface, graphical user interface), or using external applications such as GNU R through the provided ROpenFLUID package. OpenFLUID is developed in C++ and relies on open source libraries only (Boost, libXML2, GLib/GTK, OGR/GDAL, …). For modelers and developers, OpenFLUID provides a dedicated environment for model development, which is based on an open source toolchain, including the Eclipse editor, the GCC compiler and the CMake build system. OpenFLUID is distributed under the GPLv3 open source license, with a special exception allowing to plug existing models licensed under any license. It is clearly in the spirit of sharing knowledge and favouring collaboration in a community of modelers. OpenFLUID has been involved in many research applications, such as modelling of hydrological network transfer, diagnosis and prediction of water quality taking into account human activities, study of the effect of spatial organization on hydrological fluxes, modelling of surface-subsurface water exchanges, … At LISAH research unit, OpenFLUID is the supporting development platform of the MHYDAS model, which is a distributed model for agrosystems (Moussa et al., 2002, Hydrological Processes, 16, 393-412). OpenFLUID web site : http://www.openfluid-project.org

Interim Open Source Software (OSS) Policy

EPA Pesticide Factsheets

This interim Policy establishes a framework to implement the requirements of the Office of Management and Budget's (OMB) Federal Source Code Policy to achieve efficiency, transparency and innovation through reusable and open source software.

Oxidative Stress and Mitochondrial Dysfunction across Broad-Ranging Pathologies: Toward Mitochondria-Targeted Clinical Strategies

PubMed Central

d'Ischia, Marco; Gadaleta, Maria Nicola; Pallardó, Federico V.; Petrović, Sandra; Tiano, Luca; Zatterale, Adriana

2014-01-01

Beyond the disorders recognized as mitochondrial diseases, abnormalities in function and/or ultrastructure of mitochondria have been reported in several unrelated pathologies. These encompass ageing, malformations, and a number of genetic or acquired diseases, as diabetes and cardiologic, haematologic, organ-specific (e.g., eye or liver), neurologic and psychiatric, autoimmune, and dermatologic disorders. The mechanistic grounds for mitochondrial dysfunction (MDF) along with the occurrence of oxidative stress (OS) have been investigated within the pathogenesis of individual disorders or in groups of interrelated disorders. We attempt to review broad-ranging pathologies that involve mitochondrial-specific deficiencies or rely on cytosol-derived prooxidant states or on autoimmune-induced mitochondrial damage. The established knowledge in these subjects warrants studies aimed at elucidating several open questions that are highlighted in the present review. The relevance of OS and MDF in different pathologies may establish the grounds for chemoprevention trials aimed at compensating OS/MDF by means of antioxidants and mitochondrial nutrients. PMID:24876913

Open Source Molecular Modeling

PubMed Central

Pirhadi, Somayeh; Sunseri, Jocelyn; Koes, David Ryan

2016-01-01

The success of molecular modeling and computational chemistry efforts are, by definition, dependent on quality software applications. Open source software development provides many advantages to users of modeling applications, not the least of which is that the software is free and completely extendable. In this review we categorize, enumerate, and describe available open source software packages for molecular modeling and computational chemistry. PMID:27631126

Open Source Software Development Experiences on the Students' Resumes: Do They Count?--Insights from the Employers' Perspectives

ERIC Educational Resources Information Center

Long, Ju

2009-01-01

Open Source Software (OSS) is a major force in today's Information Technology (IT) landscape. Companies are increasingly using OSS in mission-critical applications. The transparency of the OSS technology itself with openly available source codes makes it ideal for students to participate in the OSS project development. OSS can provide unique…

Open Source Initiative Powers Real-Time Data Streams

NASA Technical Reports Server (NTRS)

2014-01-01

Under an SBIR contract with Dryden Flight Research Center, Creare Inc. developed a data collection tool called the Ring Buffered Network Bus. The technology has now been released under an open source license and is hosted by the Open Source DataTurbine Initiative. DataTurbine allows anyone to stream live data from sensors, labs, cameras, ocean buoys, cell phones, and more.

Xtreme Learning Control: Examples of the Open Source Movement's Impact on Our Educational Practice in a University Setting.

ERIC Educational Resources Information Center

Dunlap, Joanna C.; Wilson, Brent G.; Young, David L.

This paper describes how Open Source philosophy, a movement that has developed in opposition to the proprietary software industry, has influenced educational practice in the pursuit of scholarly freedom and authentic learning activities for students and educators. This paper provides a brief overview of the Open Source movement, and describes…

Adopting Open-Source Software Applications in U. S. Higher Education: A Cross-Disciplinary Review of the Literature

ERIC Educational Resources Information Center

van Rooij, Shahron Williams

2009-01-01

Higher Education institutions in the United States are considering Open Source software applications such as the Moodle and Sakai course management systems and the Kuali financial system to build integrated learning environments that serve both academic and administrative needs. Open Source is presumed to be more flexible and less costly than…

Assessing the Impact of Security Behavior on the Awareness of Open-Source Intelligence: A Quantitative Study of IT Knowledge Workers

ERIC Educational Resources Information Center

Daniels, Daniel B., III

2014-01-01

There is a lack of literature linking end-user behavior to the availability of open-source intelligence (OSINT). Most OSINT literature has been focused on the use and assessment of open-source intelligence, not the proliferation of personally or organizationally identifiable information (PII/OII). Additionally, information security studies have…

Looking toward the Future: A Case Study of Open Source Software in the Humanities

ERIC Educational Resources Information Center

Quamen, Harvey

2006-01-01

In this article Harvey Quamen examines how the philosophy of open source software might be of particular benefit to humanities scholars in the near future--particularly for academic journals with limited financial resources. To this end he provides a case study in which he describes his use of open source technology (MySQL database software and…

Preparing a scientific manuscript in Linux: Today's possibilities and limitations.

PubMed

Tchantchaleishvili, Vakhtang; Schmitto, Jan D

2011-10-22

Increasing number of scientists are enthusiastic about using free, open source software for their research purposes. Authors' specific goal was to examine whether a Linux-based operating system with open source software packages would allow to prepare a submission-ready scientific manuscript without the need to use the proprietary software. Preparation and editing of scientific manuscripts is possible using Linux and open source software. This letter to the editor describes key steps for preparation of a publication-ready scientific manuscript in a Linux-based operating system, as well as discusses the necessary software components. This manuscript was created using Linux and open source programs for Linux.

Open Source Service Agent (OSSA) in the intelligence community's Open Source Architecture

NASA Technical Reports Server (NTRS)

Fiene, Bruce F.

1994-01-01

The Community Open Source Program Office (COSPO) has developed an architecture for the intelligence community's new Open Source Information System (OSIS). The architecture is a multi-phased program featuring connectivity, interoperability, and functionality. OSIS is based on a distributed architecture concept. The system is designed to function as a virtual entity. OSIS will be a restricted (non-public), user configured network employing Internet communications. Privacy and authentication will be provided through firewall protection. Connection to OSIS can be made through any server on the Internet or through dial-up modems provided the appropriate firewall authentication system is installed on the client.

Exploring the Role of Value Networks for Software Innovation

NASA Astrophysics Data System (ADS)

Morgan, Lorraine; Conboy, Kieran

This paper describes a research-in-progress that aims to explore the applicability and implications of open innovation practices in two firms - one that employs agile development methods and another that utilizes open source software. The open innovation paradigm has a lot in common with open source and agile development methodologies. A particular strength of agile approaches is that they move away from 'introverted' development, involving only the development personnel, and intimately involves the customer in all areas of software creation, supposedly leading to the development of a more innovative and hence more valuable information system. Open source software (OSS) development also shares two key elements of the open innovation model, namely the collaborative development of the technology and shared rights to the use of the technology. However, one shortfall with agile development in particular is the narrow focus on a single customer representative. In response to this, we argue that current thinking regarding innovation needs to be extended to include multiple stakeholders both across and outside the organization. Additionally, for firms utilizing open source, it has been found that their position in a network of potential complementors determines the amount of superior value they create for their customers. Thus, this paper aims to get a better understanding of the applicability and implications of open innovation practices in firms that employ open source and agile development methodologies. In particular, a conceptual framework is derived for further testing.

Design and Deployment of a General Purpose, Open Source LoRa to Wi-Fi Hub and Data Logger

NASA Astrophysics Data System (ADS)

DeBell, T. C.; Udell, C.; Kwon, M.; Selker, J. S.; Lopez Alcala, J. M.

2017-12-01

Methods and technologies facilitating internet connectivity and near-real-time status updates for in site environmental sensor data are of increasing interest in Earth Science. However, Open Source, Do-It-Yourself technologies that enable plug and play functionality for web-connected sensors and devices remain largely inaccessible for typical researchers in our community. The Openly Published Environmental Sensing Lab at Oregon State University (OPEnS Lab) constructed an Open Source 900 MHz Long Range Radio (LoRa) receiver hub with SD card data logger, Ethernet and Wi-Fi shield, and 3D printed enclosure that dynamically uploads transmissions from multiple wirelessly-connected environmental sensing devices. Data transmissions may be received from devices up to 20km away. The hub time-stamps, saves to SD card, and uploads all transmissions to a Google Drive spreadsheet to be accessed in near-real-time by researchers and GeoVisualization applications (such as Arc GIS) for access, visualization, and analysis. This research expands the possibilities of scientific observation of our Earth, transforming the technology, methods, and culture by combining open-source development and cutting edge technology. This poster details our methods and evaluates the application of using 3D printing, Arduino Integrated Development Environment (IDE), Adafruit's Open-Hardware Feather development boards, and the WIZNET5500 Ethernet shield for designing this open-source, general purpose LoRa to Wi-Fi data logger.

Musca domestica salivary gland hypertrophy virus, a globally distributed insect virus that infects and sterilizes female houseflies.

PubMed

Prompiboon, Pannipa; Lietze, Verena-Ulrike; Denton, John S S; Geden, Christopher J; Steenberg, Tove; Boucias, Drion G

2010-02-01

The housefly, Musca domestica, is a cosmopolitan pest of livestock and poultry and is of economic, veterinary, and public health importance. Populations of M. domestica are naturally infected with M. domestica salivary gland hypertrophy virus (MdSGHV), a nonoccluded double-stranded DNA virus that inhibits egg production in infected females and is characterized by salivary gland hypertrophy (SGH) symptoms. MdSGHV has been detected in housefly samples from North America, Europe, Asia, the Caribbean, and the southwestern Pacific. In this study, houseflies were collected from various locations and dissected to observe SGH symptoms, and infected gland pairs were collected for MdSGHV isolation and amplification in laboratory-reared houseflies. Differences among the MdSGHV isolates were examined by using molecular and bioassay approaches. Approximately 600-bp nucleotide sequences from each of five open reading frames having homology to genes encoding DNA polymerase and partial homology to the genes encoding four per os infectivity factor proteins (p74, pif-1, pif-2, and pif-3) were selected for phylogenetic analyses. Nucleotide sequences from 16 different geographic isolates were highly homologous, and the polymorphism detected was correlated with geographic source. The virulence of the geographic MdSGHV isolates was evaluated by per os treatment of newly emerged and 24-h-old houseflies with homogenates of infected salivary glands. In all cases, 24-h-old flies displayed a resistance to oral infection that was significantly greater than that displayed by newly eclosed adults. Regardless of the MdSGHV isolate tested, all susceptible insects displayed similar degrees of SGH and complete suppression of oogenesis.

Musca domestica Salivary Gland Hypertrophy Virus, a Globally Distributed Insect Virus That Infects and Sterilizes Female Houseflies▿

PubMed Central

Prompiboon, Pannipa; Lietze, Verena-Ulrike; Denton, John S. S.; Geden, Christopher J.; Steenberg, Tove; Boucias, Drion G.

2010-01-01

The housefly, Musca domestica, is a cosmopolitan pest of livestock and poultry and is of economic, veterinary, and public health importance. Populations of M. domestica are naturally infected with M. domestica salivary gland hypertrophy virus (MdSGHV), a nonoccluded double-stranded DNA virus that inhibits egg production in infected females and is characterized by salivary gland hypertrophy (SGH) symptoms. MdSGHV has been detected in housefly samples from North America, Europe, Asia, the Caribbean, and the southwestern Pacific. In this study, houseflies were collected from various locations and dissected to observe SGH symptoms, and infected gland pairs were collected for MdSGHV isolation and amplification in laboratory-reared houseflies. Differences among the MdSGHV isolates were examined by using molecular and bioassay approaches. Approximately 600-bp nucleotide sequences from each of five open reading frames having homology to genes encoding DNA polymerase and partial homology to the genes encoding four per os infectivity factor proteins (p74, pif-1, pif-2, and pif-3) were selected for phylogenetic analyses. Nucleotide sequences from 16 different geographic isolates were highly homologous, and the polymorphism detected was correlated with geographic source. The virulence of the geographic MdSGHV isolates was evaluated by per os treatment of newly emerged and 24-h-old houseflies with homogenates of infected salivary glands. In all cases, 24-h-old flies displayed a resistance to oral infection that was significantly greater than that displayed by newly eclosed adults. Regardless of the MdSGHV isolate tested, all susceptible insects displayed similar degrees of SGH and complete suppression of oogenesis. PMID:20023109

Ubuntu Core Snaps for Science

NASA Astrophysics Data System (ADS)

Wyngaard, J.

2017-12-01

A key challenge in the burgeoning sector of IoT (Internet of Things) is ensuring device and communication security. Ubuntu Core's approach to this is the use of 'snaps'. Along side this growth, scientists are increasingly utilising the many new low cost sensors now available. This work prototypes the use of snaps as a possible avenue to reducing the barrier to entry for scientific use of these low cost sensors while also ensuring proper meta-data is captured. Snaps are contained applications that have been signed. This means that a snap application is unable to read or write to any area of the system beyond its assigned reach, thereby significantly limiting the possible impact of any break in security higher up the stack. Further, application and system updates are automatically verified as authentic before being applied. Additionally, on an embedded system running Ubuntu Core the hardware interface (Gadget), kernel, and OS (Core) are all also snaps and therefore also have acquired these same gains. The result is an architecture that enables: (1) Secure, robust, remote automatic updates of both the OS and applications. (2) A user friendly deployment mechanism.(3) A easy to maintain means of supporting multiple platforms. The above is primarily targeted at non-academic domains, however, it is proposed that the Scientific community can benefit from it too. This work therefore prototypes a snap for sensors on board a small Unmanned Aircraft System (sUAS). For demonstration purposes this snap specifically targets connecting a popular low cost CO2 meter to a Raspberry Pi3 and the popular open source sUAS autopilot Arducopter.

Improvement of correlation-based centroiding methods for point source Shack-Hartmann wavefront sensor

NASA Astrophysics Data System (ADS)

Li, Xuxu; Li, Xinyang; wang, Caixia

2018-03-01

This paper proposes an efficient approach to decrease the computational costs of correlation-based centroiding methods used for point source Shack-Hartmann wavefront sensors. Four typical similarity functions have been compared, i.e. the absolute difference function (ADF), ADF square (ADF2), square difference function (SDF), and cross-correlation function (CCF) using the Gaussian spot model. By combining them with fast search algorithms, such as three-step search (TSS), two-dimensional logarithmic search (TDL), cross search (CS), and orthogonal search (OS), computational costs can be reduced drastically without affecting the accuracy of centroid detection. Specifically, OS reduces calculation consumption by 90%. A comprehensive simulation indicates that CCF exhibits a better performance than other functions under various light-level conditions. Besides, the effectiveness of fast search algorithms has been verified.

The use of open source electronic health records within the federal safety net.

PubMed

Goldwater, Jason C; Kwon, Nancy J; Nathanson, Ashley; Muckle, Alison E; Brown, Alexa; Cornejo, Kerri

2014-01-01

To conduct a federally funded study that examines the acquisition, implementation and operation of open source electronic health records (EHR) within safety net medical settings, such as federally qualified health centers (FQHC). The study was conducted by the National Opinion Research Center (NORC) at the University of Chicago from April to September 2010. The NORC team undertook a comprehensive environmental scan, including a literature review, a dozen key informant interviews using a semistructured protocol, and a series of site visits to West Virginia, California and Arizona FQHC that were currently using an open source EHR. Five of the six sites that were chosen as part of the study found a number of advantages in the use of their open source EHR system, such as utilizing a large community of users and developers to modify their EHR to fit the needs of their provider and patient communities, and lower acquisition and implementation costs as compared to a commercial system. Despite these advantages, many of the informants and site visit participants felt that widespread dissemination and use of open source was restrained due to a negative connotation regarding this type of software. In addition, a number of participants stated that there is a necessary level of technical acumen needed within the FQHC to make an open source EHR effective. An open source EHR provides advantages for FQHC that have limited resources to acquire and implement an EHR, but additional study is needed to evaluate its overall effectiveness.

Open source electronic health records and chronic disease management

PubMed Central

Goldwater, Jason C; Kwon, Nancy J; Nathanson, Ashley; Muckle, Alison E; Brown, Alexa; Cornejo, Kerri

2014-01-01

Objective To study and report on the use of open source electronic health records (EHR) to assist with chronic care management within safety net medical settings, such as community health centers (CHC). Methods and Materials The study was conducted by NORC at the University of Chicago from April to September 2010. The NORC team undertook a comprehensive environmental scan, including a literature review, a dozen key informant interviews using a semistructured protocol, and a series of site visits to CHC that currently use an open source EHR. Results Two of the sites chosen by NORC were actively using an open source EHR to assist in the redesign of their care delivery system to support more effective chronic disease management. This included incorporating the chronic care model into an CHC and using the EHR to help facilitate its elements, such as care teams for patients, in addition to maintaining health records on indigent populations, such as tuberculosis status on homeless patients. Discussion The ability to modify the open-source EHR to adapt to the CHC environment and leverage the ecosystem of providers and users to assist in this process provided significant advantages in chronic care management. Improvements in diabetes management, controlled hypertension and increases in tuberculosis vaccinations were assisted through the use of these open source systems. Conclusions The flexibility and adaptability of open source EHR demonstrated its utility and viability in the provision of necessary and needed chronic disease care among populations served by CHC. PMID:23813566

A gallery of oil components, their metals and Re-Os signatures

NASA Astrophysics Data System (ADS)

Stein, Holly J.; Hannah, Judith L.

2016-04-01

Most sediment-hosted metallic ore deposits are one degree of freedom from hydrocarbon. That is, sulfide fluid inclusions may contain vestiges of travel in tandem with hydrocarbon-bearing fluids. For metallic ore deposits of stated metamorphic and magmatic origin, the degrees of freedom are several times more or, in some cases, no relationship exists. Still, the fetish for stereotyping and classifying ore types into hardline ore deposit models (or hybrid models when the data are wildly uncooperative) impedes our ability to move toward a better understanding of source rock. Fluids in the deeper earth, fluids in the crust, and the extraterrestrial rain of metals provide the Re-Os template for oil. So, too, this combination ultimately drives the composition of many metallic ore deposits. The world of crude oil and its complex history of maturation, migration, mixing, metal-rich asphaltene precipitation, and subsequent mobility of lighter and metal-poor components, is an untapped resource for students of ore geology. In the same way that Mississippi Valley-type lead and zinc deposits are described as the outcome of two converging and mixing fluids (metal-bearing and sulfur-bearing fluids), asphaltene precipitation can be an outcome of a lighter oil meeting and mixing with a heavier one. In the petroleum industry, this can spell economic disaster if the pore-space becomes clogged with a non-producible heavy oil or solid bitumen. In ore geology, sulfide precipitation on loss of permeability may create a Pb-Zn deposit. Petroleum systems provide a gallery of successive time-integrated Re-Os results. Heavy or biodegraded oils, if intersected by lighter oil or gas, can generate asphaltite or tar mats, and release a reservoir of still lighter oil (or gas). During this process there are opportunities for separation of metal-enriched aqueous fluids that may retain an imprint of their earlier hydrocarbon history, ultimately trapped in fluid inclusions. Salinity, temperature and pH are part of the equation controlling composition of metal-bearing aqueous fluids siphoned from residual hydrocarbons. The Re-Os isotopic behavior of oil components is generally specific to location and may differ within a single oil field, or even within discrete fractions of a single sample of oil [1]. Different fractions in a crude oil, for example maltenes and asphaltenes, can preserve signatures of unique sources. This should not be surprising, since economic geologists have long called upon meeting and mixing of metal-bearing with sulfur-bearing fluids from different sources. A time-integrated geologic history can also be derived from bitumen veins, with the Re-Os age of the metal source cached in these veins. Preservation of early metal and hydrocarbon history, and intact Re-Os systematics preserved in younger-formed systems have enormous potential for the resource industry. Several examples will be presented. [1] Georgiev, S.V., Stein, H.J., Hannah, J.L., Galimberti, R., Nali, M., Yang, G., and Zimmerman, A. (returned post revision, 11 Jan 2016) Re-Os dating of maltenes and asphaltenes within single samples of crude oils: Geochimica et Comochimica Acta. Supported by a consortium of petroleum companies under the CHRONOS project.

OpenCFU, a new free and open-source software to count cell colonies and other circular objects.

PubMed

Geissmann, Quentin

2013-01-01

Counting circular objects such as cell colonies is an important source of information for biologists. Although this task is often time-consuming and subjective, it is still predominantly performed manually. The aim of the present work is to provide a new tool to enumerate circular objects from digital pictures and video streams. Here, I demonstrate that the created program, OpenCFU, is very robust, accurate and fast. In addition, it provides control over the processing parameters and is implemented in an intuitive and modern interface. OpenCFU is a cross-platform and open-source software freely available at http://opencfu.sourceforge.net.

Regulation of glutamine synthetase isoforms in two differentially drought-tolerant rice (Oryza sativa L.) cultivars under water deficit conditions.

PubMed

Singh, Kamal Krishna; Ghosh, Shilpi

2013-02-01

KEY MESSAGE : The regulation of GS isoforms by WD was organ specific. Two GS isoforms i.e. OsGS1;1 and OsGS2 were differentially regulated in IR-64 (drought-sensitive) and Khitish (drought-tolerant) cultivars of rice. Water deficit (WD) has adverse effect on rice (Oryza sativa L.) and acclimation requires essential reactions of primary metabolism to continue. Rice plants utilize ammonium as major nitrogen source, which is assimilated into glutamine by the reaction of Glutamine synthetase (GS, EC 6.3.1.2). Rice plants possess one gene (OsGS2) for chloroplastic GS2 and three genes (OsGS1;1, OsGS1;2 and OsGS1;3) for cytosolic GS1. Here, we report the effect of WD on regulation of GS isoforms in drought-sensitive (cv. IR-64) and drought-tolerant (cv. Khitish) rice cultivars. Under WD, total GS activity in root and leaf decreased significantly in IR-64 seedlings in comparison to Khitish seedlings. The reduced GS activity in IR-64 leaf was mainly due to decrease in GS2 activity, which correlated with decrease in corresponding transcript and polypeptide contents. GS1 transcript and polypeptide accumulated in leaf during WD, however, GS1 activity was maintained at a constant level. Total GS activity in stem of both the varieties was insensitive to WD. Among GS1 genes, OsGS1;1 expression was differently regulated by WD in the two rice varieties. Its transcript accumulated more abundantly in IR-64 leaf than in Khitish leaf. Following WD, OsGS1;1 mRNA level in stem and root tissues declined in IR-64 and enhanced in Khitish. A steady OsGS1;2 expression patterns were noted in leaf, stem and root of both the cultivars. Results suggest that OsGS2 and OsGS1;1 expression may contribute to drought tolerance of Khitish cultivar under WD conditions.

High-pressure structural parameters and equation of state of osmium to 207 GPa

DOE PAGES

Perreault, Christopher S.; Velisavljevic, Nenad; Vohra, Yogesh K.; ...

2017-09-08

We studied the most incompressible transition metal osmium (Os) under high pressure. There is significant interest in Os because of the structural anomalies attributed to topological transitions in the Fermi surface for valence electrons in the hexagonal close-packed phase. We report on measurements of structural parameters and equation of state on Os metal to a pressure of 207 GPa at ambient temperature using platinum as a pressure standard. We also obtained angle-dispersive X-ray diffraction data at a synchrotron source with closely spaced pressure intervals to observe any discontinuities or anomalies in the axial c/a ratio at high pressures. Rietveld refinementsmore » of X-ray diffraction data show a slowly varying axial ratio (c/a) with a broad minimum at 75 GPa. Our data do not provide any evidence of anomalous behavior in the c/a ratio in Os at 25 or 150 GPa as have been reported in previous studies. These experimental results are in agreement with theoretical calculations that do not predict any anomalous behavior in c/a ratio in Os under extreme conditions. We present an equation of state for Os to 207 GPa (V/V 0 = 0.761) at ambient temperature and compare our results with the previously published data.« less

High-pressure structural parameters and equation of state of osmium to 207 GPa

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

Perreault, Christopher S.; Velisavljevic, Nenad; Vohra, Yogesh K.

We studied the most incompressible transition metal osmium (Os) under high pressure. There is significant interest in Os because of the structural anomalies attributed to topological transitions in the Fermi surface for valence electrons in the hexagonal close-packed phase. We report on measurements of structural parameters and equation of state on Os metal to a pressure of 207 GPa at ambient temperature using platinum as a pressure standard. We also obtained angle-dispersive X-ray diffraction data at a synchrotron source with closely spaced pressure intervals to observe any discontinuities or anomalies in the axial c/a ratio at high pressures. Rietveld refinementsmore » of X-ray diffraction data show a slowly varying axial ratio (c/a) with a broad minimum at 75 GPa. Our data do not provide any evidence of anomalous behavior in the c/a ratio in Os at 25 or 150 GPa as have been reported in previous studies. These experimental results are in agreement with theoretical calculations that do not predict any anomalous behavior in c/a ratio in Os under extreme conditions. We present an equation of state for Os to 207 GPa (V/V 0 = 0.761) at ambient temperature and compare our results with the previously published data.« less

Using Open Source Software in Visual Simulation Development

DTIC Science & Technology

2005-09-01

increased the use of the technology in training activities. Using open source/free software tools in the process can expand these possibilities...resulting in even greater cost reduction and allowing the flexibility needed in a training environment. This thesis presents a configuration and architecture...to be used when developing training visual simulations using both personal computers and open source tools. Aspects of the requirements needed in a

Open-Source Intelligence in the Czech Military: Knowledge System and Process Design

DTIC Science & Technology

2002-06-01

in Open-Source Intelligence OSINT, as one of the intelligence disciplines, bears some of the general problems of intelligence " business " OSINT...ADAPTING KNOWLEDGE MANAGEMENT THEORY TO THE CZECH MILITARY INTELLIGENCE Knowledge work is the core business of the military intelligence . As...NAVAL POSTGRADUATE SCHOOL Monterey, California THESIS Approved for public release; distribution is unlimited OPEN-SOURCE INTELLIGENCE IN THE

Writing in the Disciplines versus Corporate Workplaces: On the Importance of Conflicting Disciplinary Discourses in the Open Source Movement and the Value of Intellectual Property

ERIC Educational Resources Information Center

Ballentine, Brian D.

2009-01-01

Writing programs and more specifically, Writing in the Disciplines (WID) initiatives have begun to embrace the use of and the ideology inherent to, open source software. The Conference on College Composition and Communication has passed a resolution stating that whenever feasible educators and their institutions consider open source applications.…

Anatomy of BioJS, an open source community for the life sciences.

PubMed

Yachdav, Guy; Goldberg, Tatyana; Wilzbach, Sebastian; Dao, David; Shih, Iris; Choudhary, Saket; Crouch, Steve; Franz, Max; García, Alexander; García, Leyla J; Grüning, Björn A; Inupakutika, Devasena; Sillitoe, Ian; Thanki, Anil S; Vieira, Bruno; Villaveces, José M; Schneider, Maria V; Lewis, Suzanna; Pettifer, Steve; Rost, Burkhard; Corpas, Manuel

2015-07-08

BioJS is an open source software project that develops visualization tools for different types of biological data. Here we report on the factors that influenced the growth of the BioJS user and developer community, and outline our strategy for building on this growth. The lessons we have learned on BioJS may also be relevant to other open source software projects.

Build, Buy, Open Source, or Web 2.0?: Making an Informed Decision for Your Library

ERIC Educational Resources Information Center

Fagan, Jody Condit; Keach, Jennifer A.

2010-01-01

When improving a web presence, today's libraries have a choice: using a free Web 2.0 application, opting for open source, buying a product, or building a web application. This article discusses how to make an informed decision for one's library. The authors stress that deciding whether to use a free Web 2.0 application, to choose open source, to…

Expanding Human Capabilities through the Adoption and Utilization of Free, Libre, and Open Source Software

ERIC Educational Resources Information Center

Simpson, James Daniel

2014-01-01

Free, libre, and open source software (FLOSS) is software that is collaboratively developed. FLOSS provides end-users with the source code and the freedom to adapt or modify a piece of software to fit their needs (Deek & McHugh, 2008; Stallman, 2010). FLOSS has a 30 year history that dates to the open hacker community at the Massachusetts…

A Framework for the Systematic Collection of Open Source Intelligence

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

Pouchard, Line Catherine; Trien, Joseph P; Dobson, Jonathan D

2009-01-01

Following legislative directions, the Intelligence Community has been mandated to make greater use of Open Source Intelligence (OSINT). Efforts are underway to increase the use of OSINT but there are many obstacles. One of these obstacles is the lack of tools helping to manage the volume of available data and ascertain its credibility. We propose a unique system for selecting, collecting and storing Open Source data from the Web and the Open Source Center. Some data management tasks are automated, document source is retained, and metadata containing geographical coordinates are added to the documents. Analysts are thus empowered to search,more » view, store, and analyze Web data within a single tool. We present ORCAT I and ORCAT II, two implementations of the system.« less

The open-source neutral-mass spectrometer on Atmosphere Explorer-C, -D, and -E.

NASA Technical Reports Server (NTRS)

Nier, A. O.; Potter, W. E.; Hickman, D. R.; Mauersberger, K.

1973-01-01

The open-source mass spectrometer will be used to obtain the number densities of the neutral atmospheric gases in the mass range 1 to 48 amu at the satellite location. The ion source has been designed to allow gas particles to enter the ionizing region with the minimum practicable number of prior collisions with surfaces. This design minimizes the loss of atomic oxygen and other reactive species due to reactions with the walls of the ion source. The principal features of the open-source spectrometer and the laboratory calibration system are discussed.

The behavior of osmium and other siderophile elements during impacts: Insights from the Ries impact structure and central European tektites

NASA Astrophysics Data System (ADS)

Ackerman, Lukáš; Magna, Tomáš; Žák, Karel; Skála, Roman; Jonášová, Šárka; Mizera, Jiří; Řanda, Zdeněk

2017-08-01

Impact processes are natural phenomena that contribute to a variety of physico-chemical mechanisms over an extreme range of shock pressures and temperatures, otherwise seldomly achieved in the Earth's crust through other processes. Under these extreme conditions with transient temperatures and pressures ≥3000 K and ≥100 GPa, followed by their rapid decrease, the behavior of elements has remained poorly understood. Distal glassy ejecta (tektites) were produced in early phases of contact between the Earth's surface and an impacting body. Here we provide evidence for a complex behavior of Os and other highly siderophile elements (HSE; Ir, Ru, Pt, Pd, and Re) during tektite production related to a hyper-velocity impact that formed the Ries structure in Germany. Instead of simple mixing between the surface materials, which are thought to form the major source of central European tektites (moldavites), and impactor matter, the patterns of HSE contents and 187Re/188Os - 187Os/188Os ratios in moldavites, target sediments and impact-related breccias (suevites) can be explained by several sequential and/or contemporary processes. These involve (i) evaporative loss of partially oxidized HSE from the overheated tektite melt, (ii) mixing of target-derived and impactor-derived HSE vapor (plasma) phases, and (iii) early (high-temperature) condensation of a part of the mixed vapor phase back to silicate melt droplets. An almost complete loss of terrestrial Os from the tektite melt and its replacement with extra-terrestrial Os are indicated by low 187Os/188Os ratios in tektites (<0.163) relative to precursor materials (>0.69). This is paralleled by a co-variation between Os and Ni contents in tektites but not in suevites formed later in the impact process.

A Clinician-Centered Evaluation of the Usability of AHLTA and Automated Clinical Practice Guidelines at TAMC

DTIC Science & Technology

2011-03-31

evidence based medicine into clinical practice. It will decrease costs and enable multiple stakeholders to work in an open content/source environment to exchange clinical content, develop and test technology and explore processes in applied CDS. Design: Comparative study between the KMR infrastructure and capabilities developed as an open source, vendor agnostic solution for aCPG execution within AHLTA and the current DoD/MHS standard evaluating: H1: An open source, open standard KMR and Clinical Decision Support Engine can enable organizations to share domain

Preparing a scientific manuscript in Linux: Today's possibilities and limitations

PubMed Central

2011-01-01

Background Increasing number of scientists are enthusiastic about using free, open source software for their research purposes. Authors' specific goal was to examine whether a Linux-based operating system with open source software packages would allow to prepare a submission-ready scientific manuscript without the need to use the proprietary software. Findings Preparation and editing of scientific manuscripts is possible using Linux and open source software. This letter to the editor describes key steps for preparation of a publication-ready scientific manuscript in a Linux-based operating system, as well as discusses the necessary software components. This manuscript was created using Linux and open source programs for Linux. PMID:22018246

Open source bioimage informatics for cell biology.

PubMed

Swedlow, Jason R; Eliceiri, Kevin W

2009-11-01

Significant technical advances in imaging, molecular biology and genomics have fueled a revolution in cell biology, in that the molecular and structural processes of the cell are now visualized and measured routinely. Driving much of this recent development has been the advent of computational tools for the acquisition, visualization, analysis and dissemination of these datasets. These tools collectively make up a new subfield of computational biology called bioimage informatics, which is facilitated by open source approaches. We discuss why open source tools for image informatics in cell biology are needed, some of the key general attributes of what make an open source imaging application successful, and point to opportunities for further operability that should greatly accelerate future cell biology discovery.

Adopting Open Source Software to Address Software Risks during the Scientific Data Life Cycle

NASA Astrophysics Data System (ADS)

Vinay, S.; Downs, R. R.

2012-12-01

Software enables the creation, management, storage, distribution, discovery, and use of scientific data throughout the data lifecycle. However, the capabilities offered by software also present risks for the stewardship of scientific data, since future access to digital data is dependent on the use of software. From operating systems to applications for analyzing data, the dependence of data on software presents challenges for the stewardship of scientific data. Adopting open source software provides opportunities to address some of the proprietary risks of data dependence on software. For example, in some cases, open source software can be deployed to avoid licensing restrictions for using, modifying, and transferring proprietary software. The availability of the source code of open source software also enables the inclusion of modifications, which may be contributed by various community members who are addressing similar issues. Likewise, an active community that is maintaining open source software can be a valuable source of help, providing an opportunity to collaborate to address common issues facing adopters. As part of the effort to meet the challenges of software dependence for scientific data stewardship, risks from software dependence have been identified that exist during various times of the data lifecycle. The identification of these risks should enable the development of plans for mitigating software dependencies, where applicable, using open source software, and to improve understanding of software dependency risks for scientific data and how they can be reduced during the data life cycle.

New insights from old spherules: Os-W isotope and HSE evidence for Paleoarchean meteorite bombardment of the Earth

NASA Astrophysics Data System (ADS)

Schulz, T.; Luguet, A. A.; Koeberl, C.

2014-12-01

Introduction: Although still debated, spherule beds in the Barberton Mountain Land (~3.4 Ga) are suspected to represent remnants of impact-generated and ballistically emplaced silicate melt droplets [e.g. 1]. Such deposits provide the only window into the late stages of the heavy meteorite bombardment on Earth as their source craters have long since been obliterated. In order to identify a possible meteoritic component and, if successful, to discuss potential projectile materials, we are performing a detailed Os-W isotope as well as HSE abundance study on spherule layers from the recently drilled ICDP BARB5 core (grid location 25°30`50.76``S, 31°33`10.08``E). Samples and Methods: Samples were taken from a spherule-containing meta-sedimentary core section discovered between 510 and 512 m depth. About 100 mg of homogenized sample powders were spiked with a mixed 190Os, 185Re, 191Ir and 194Pt tracer and treated in a high pressure asher using inverse aqua regia, followed by conventional extraction schemes for Os and the other HSEs [4]. Chemical and Os isotope measurements (via N-TIMS) were performed in Vienna, whereas HSE measurements were undertaken via ICP MS in Bonn. Results and Discussion: Our preliminary Os isotope data reveal a trend between samples exhibiting high spherule to matrix ratios (187Os/188Os ~0.106 and Os ~0.4 ppm) and samples with lower ones (187Os/188Os up to ~0.304 and Os ~0.008 ppm). Notably, the most unradiogenic samples exhibit carbonaceous-chondrite-like initial 187Os/188Os and HSE ratios, whereas all other samples are clear non-chondritic. These findings support an extraterrestrial contribution in the spherules and can be interpreted compared to conclusions drawn from a Cr isotope study performed on similar samples [3], possibly representing a different impact event and favouring a chondritic projectile. However, further considerations based on precise Os/W ratio determinations and high-precision 182W isotope data, will be presented at the conference. Acknowledgements:We thank W.U. Reimold and T. Mohr-Westheide (Natural History Museum Berlin) for the BARB5 samples, which were obtained in an ICDP project. References: [1] Simonson and Glass, 2004; [2] Lowe et al., 1989; [3] Kyte et al., 2003; [4] Cohen and Waters, 1996; [5] Morel et al., 2002

Open source data assimilation framework for hydrological modeling

NASA Astrophysics Data System (ADS)

Ridler, Marc; Hummel, Stef; van Velzen, Nils; Katrine Falk, Anne; Madsen, Henrik

2013-04-01

An open-source data assimilation framework is proposed for hydrological modeling. Data assimilation (DA) in hydrodynamic and hydrological forecasting systems has great potential to improve predictions and improve model result. The basic principle is to incorporate measurement information into a model with the aim to improve model results by error minimization. Great strides have been made to assimilate traditional in-situ measurements such as discharge, soil moisture, hydraulic head and snowpack into hydrologic models. More recently, remotely sensed data retrievals of soil moisture, snow water equivalent or snow cover area, surface water elevation, terrestrial water storage and land surface temperature have been successfully assimilated in hydrological models. The assimilation algorithms have become increasingly sophisticated to manage measurement and model bias, non-linear systems, data sparsity (time & space) and undetermined system uncertainty. It is therefore useful to use a pre-existing DA toolbox such as OpenDA. OpenDA is an open interface standard for (and free implementation of) a set of tools to quickly implement DA and calibration for arbitrary numerical models. The basic design philosophy of OpenDA is to breakdown DA into a set of building blocks programmed in object oriented languages. To implement DA, a model must interact with OpenDA to create model instances, propagate the model, get/set variables (or parameters) and free the model once DA is completed. An open-source interface for hydrological models exists capable of all these tasks: OpenMI. OpenMI is an open source standard interface already adopted by key hydrological model providers. It defines a universal approach to interact with hydrological models during simulation to exchange data during runtime, thus facilitating the interactions between models and data sources. The interface is flexible enough so that models can interact even if the model is coded in a different language, represent processes from a different domain or have different spatial and temporal resolutions. An open source framework that bridges OpenMI and OpenDA is presented. The framework provides a generic and easy means for any OpenMI compliant model to assimilate observation measurements. An example test case will be presented using MikeSHE, and OpenMI compliant fully coupled integrated hydrological model that can accurately simulate the feedback dynamics of overland flow, unsaturated zone and saturated zone.

High-pressure high-temperature stability of hcp-Ir xOs 1-x (x = 0.50 and 0.55) alloys

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

Yusenko, Kirill V.; Bykova, Elena; Bykov, Maxim

2016-12-23

Hcp-Ir 0.55Os 0.45 and hcp-Ir 0.50Os 0.50 alloys were synthesised by thermal decomposition of single-source precursors in hydrogen atmosphere. Both alloys correspond to a miscibility gap in the Ir–Os binary phase diagram and therefore are metastable at ambient conditions. An in situ powder X-ray diffraction has been used for a monitoring a formation of hcp-Ir0.55Os0.45 alloy from (NH 4) 2[Ir 0.55Os 0.45Cl 6] precursor. A crystalline intermediate compound and nanodimentional metallic particles with a large concentration of defects has been found as key intermediates in the thermal decomposition process in hydrogen flow. High-temperature stability of titled hcp-structured alloys has beenmore » investigated upon compression up to 11 GPa using a multi-anvil press and up to 80 GPa using laser-heated diamond-anvil cells to obtain a phase separation into fcc + hcp mixture. Compressibility curves at room temperature as well as thermal expansion at ambient pressure and under compression up to 80 GPa were collected to obtain thermal expansion coefficients and bulk moduli. hcp-Ir 0.55Os 0.45 alloy shows bulk moduli B0 = 395 GPa. Thermal expansion coefficients were estimated as α = 1.6·10 -5 K -1 at ambient pressure and α = 0.3·10 -5 K -1 at 80 GPa. Obtained high-pressure high-temperature data allowed us to construct the first model for pressure-dependent Ir–Os phase diagram.« less

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

Gearhart, Jared Lee; Adair, Kristin Lynn; Durfee, Justin David.

When developing linear programming models, issues such as budget limitations, customer requirements, or licensing may preclude the use of commercial linear programming solvers. In such cases, one option is to use an open-source linear programming solver. A survey of linear programming tools was conducted to identify potential open-source solvers. From this survey, four open-source solvers were tested using a collection of linear programming test problems and the results were compared to IBM ILOG CPLEX Optimizer (CPLEX) [1], an industry standard. The solvers considered were: COIN-OR Linear Programming (CLP) [2], [3], GNU Linear Programming Kit (GLPK) [4], lp_solve [5] and Modularmore » In-core Nonlinear Optimization System (MINOS) [6]. As no open-source solver outperforms CPLEX, this study demonstrates the power of commercial linear programming software. CLP was found to be the top performing open-source solver considered in terms of capability and speed. GLPK also performed well but cannot match the speed of CLP or CPLEX. lp_solve and MINOS were considerably slower and encountered issues when solving several test problems.« less

Open source OCR framework using mobile devices

NASA Astrophysics Data System (ADS)

Zhou, Steven Zhiying; Gilani, Syed Omer; Winkler, Stefan

2008-02-01

Mobile phones have evolved from passive one-to-one communication device to powerful handheld computing device. Today most new mobile phones are capable of capturing images, recording video, and browsing internet and do much more. Exciting new social applications are emerging on mobile landscape, like, business card readers, sing detectors and translators. These applications help people quickly gather the information in digital format and interpret them without the need of carrying laptops or tablet PCs. However with all these advancements we find very few open source software available for mobile phones. For instance currently there are many open source OCR engines for desktop platform but, to our knowledge, none are available on mobile platform. Keeping this in perspective we propose a complete text detection and recognition system with speech synthesis ability, using existing desktop technology. In this work we developed a complete OCR framework with subsystems from open source desktop community. This includes a popular open source OCR engine named Tesseract for text detection & recognition and Flite speech synthesis module, for adding text-to-speech ability.

Open-source colorimeter.

PubMed

Anzalone, Gerald C; Glover, Alexandra G; Pearce, Joshua M

2013-04-19

The high cost of what have historically been sophisticated research-related sensors and tools has limited their adoption to a relatively small group of well-funded researchers. This paper provides a methodology for applying an open-source approach to design and development of a colorimeter. A 3-D printable, open-source colorimeter utilizing only open-source hardware and software solutions and readily available discrete components is discussed and its performance compared to a commercial portable colorimeter. Performance is evaluated with commercial vials prepared for the closed reflux chemical oxygen demand (COD) method. This approach reduced the cost of reliable closed reflux COD by two orders of magnitude making it an economic alternative for the vast majority of potential users. The open-source colorimeter demonstrated good reproducibility and serves as a platform for further development and derivation of the design for other, similar purposes such as nephelometry. This approach promises unprecedented access to sophisticated instrumentation based on low-cost sensors by those most in need of it, under-developed and developing world laboratories.

Open-Source Colorimeter

PubMed Central

Anzalone, Gerald C.; Glover, Alexandra G.; Pearce, Joshua M.

2013-01-01

The high cost of what have historically been sophisticated research-related sensors and tools has limited their adoption to a relatively small group of well-funded researchers. This paper provides a methodology for applying an open-source approach to design and development of a colorimeter. A 3-D printable, open-source colorimeter utilizing only open-source hardware and software solutions and readily available discrete components is discussed and its performance compared to a commercial portable colorimeter. Performance is evaluated with commercial vials prepared for the closed reflux chemical oxygen demand (COD) method. This approach reduced the cost of reliable closed reflux COD by two orders of magnitude making it an economic alternative for the vast majority of potential users. The open-source colorimeter demonstrated good reproducibility and serves as a platform for further development and derivation of the design for other, similar purposes such as nephelometry. This approach promises unprecedented access to sophisticated instrumentation based on low-cost sensors by those most in need of it, under-developed and developing world laboratories. PMID:23604032

OpenMebius: an open source software for isotopically nonstationary 13C-based metabolic flux analysis.

PubMed

Kajihata, Shuichi; Furusawa, Chikara; Matsuda, Fumio; Shimizu, Hiroshi

2014-01-01

The in vivo measurement of metabolic flux by (13)C-based metabolic flux analysis ((13)C-MFA) provides valuable information regarding cell physiology. Bioinformatics tools have been developed to estimate metabolic flux distributions from the results of tracer isotopic labeling experiments using a (13)C-labeled carbon source. Metabolic flux is determined by nonlinear fitting of a metabolic model to the isotopic labeling enrichment of intracellular metabolites measured by mass spectrometry. Whereas (13)C-MFA is conventionally performed under isotopically constant conditions, isotopically nonstationary (13)C metabolic flux analysis (INST-(13)C-MFA) has recently been developed for flux analysis of cells with photosynthetic activity and cells at a quasi-steady metabolic state (e.g., primary cells or microorganisms under stationary phase). Here, the development of a novel open source software for INST-(13)C-MFA on the Windows platform is reported. OpenMebius (Open source software for Metabolic flux analysis) provides the function of autogenerating metabolic models for simulating isotopic labeling enrichment from a user-defined configuration worksheet. Analysis using simulated data demonstrated the applicability of OpenMebius for INST-(13)C-MFA. Confidence intervals determined by INST-(13)C-MFA were less than those determined by conventional methods, indicating the potential of INST-(13)C-MFA for precise metabolic flux analysis. OpenMebius is the open source software for the general application of INST-(13)C-MFA.

Simulation for Dynamic Situation Awareness and Prediction III

DTIC Science & Technology

2010-03-01

source Java ™ library for capturing and sending network packets; 4) Groovy – an open source, Java -based scripting language (version 1.6 or newer). Open...DMOTH Analyzer application. Groovy is an open source dynamic scripting language for the Java Virtual Machine. It is consistent with Java syntax...between temperature, pressure, wind and relative humidity, and 3) a precipitation editing algorithm. The Editor can be used to prepare scripted changes

Transforming High School Classrooms with Free/Open Source Software: "It's Time for an Open Source Software Revolution"

ERIC Educational Resources Information Center

Pfaffman, Jay

2008-01-01

Free/Open Source Software (FOSS) applications meet many of the software needs of high school science classrooms. In spite of the availability and quality of FOSS tools, they remain unknown to many teachers and utilized by fewer still. In a world where most software has restrictions on copying and use, FOSS is an anomaly, free to use and to…

Managing Digital Archives Using Open Source Software Tools

NASA Astrophysics Data System (ADS)

Barve, S.; Dongare, S.

2007-10-01

This paper describes the use of open source software tools such as MySQL and PHP for creating database-backed websites. Such websites offer many advantages over ones built from static HTML pages. This paper will discuss how OSS tools are used and their benefits, and after the successful implementation of these tools how the library took the initiative in implementing an institutional repository using DSpace open source software.

Open source tools for fluorescent imaging.

PubMed

Hamilton, Nicholas A

2012-01-01

As microscopy becomes increasingly automated and imaging expands in the spatial and time dimensions, quantitative analysis tools for fluorescent imaging are becoming critical to remove both bottlenecks in throughput as well as fully extract and exploit the information contained in the imaging. In recent years there has been a flurry of activity in the development of bio-image analysis tools and methods with the result that there are now many high-quality, well-documented, and well-supported open source bio-image analysis projects with large user bases that cover essentially every aspect from image capture to publication. These open source solutions are now providing a viable alternative to commercial solutions. More importantly, they are forming an interoperable and interconnected network of tools that allow data and analysis methods to be shared between many of the major projects. Just as researchers build on, transmit, and verify knowledge through publication, open source analysis methods and software are creating a foundation that can be built upon, transmitted, and verified. Here we describe many of the major projects, their capabilities, and features. We also give an overview of the current state of open source software for fluorescent microscopy analysis and the many reasons to use and develop open source methods. Copyright © 2012 Elsevier Inc. All rights reserved.

moocRP: Enabling Open Learning Analytics with an Open Source Platform for Data Distribution, Analysis, and Visualization

ERIC Educational Resources Information Center

Pardos, Zachary A.; Whyte, Anthony; Kao, Kevin

2016-01-01

In this paper, we address issues of transparency, modularity, and privacy with the introduction of an open source, web-based data repository and analysis tool tailored to the Massive Open Online Course community. The tool integrates data request/authorization and distribution workflow features as well as provides a simple analytics module upload…

Open Drug Discovery Toolkit (ODDT): a new open-source player in the drug discovery field.

PubMed

Wójcikowski, Maciej; Zielenkiewicz, Piotr; Siedlecki, Pawel

2015-01-01

There has been huge progress in the open cheminformatics field in both methods and software development. Unfortunately, there has been little effort to unite those methods and software into one package. We here describe the Open Drug Discovery Toolkit (ODDT), which aims to fulfill the need for comprehensive and open source drug discovery software. The Open Drug Discovery Toolkit was developed as a free and open source tool for both computer aided drug discovery (CADD) developers and researchers. ODDT reimplements many state-of-the-art methods, such as machine learning scoring functions (RF-Score and NNScore) and wraps other external software to ease the process of developing CADD pipelines. ODDT is an out-of-the-box solution designed to be easily customizable and extensible. Therefore, users are strongly encouraged to extend it and develop new methods. We here present three use cases for ODDT in common tasks in computer-aided drug discovery. Open Drug Discovery Toolkit is released on a permissive 3-clause BSD license for both academic and industrial use. ODDT's source code, additional examples and documentation are available on GitHub (https://github.com/oddt/oddt).

The use of open source electronic health records within the federal safety net

PubMed Central

Goldwater, Jason C; Kwon, Nancy J; Nathanson, Ashley; Muckle, Alison E; Brown, Alexa; Cornejo, Kerri

2014-01-01

Objective To conduct a federally funded study that examines the acquisition, implementation and operation of open source electronic health records (EHR) within safety net medical settings, such as federally qualified health centers (FQHC). Methods and materials The study was conducted by the National Opinion Research Center (NORC) at the University of Chicago from April to September 2010. The NORC team undertook a comprehensive environmental scan, including a literature review, a dozen key informant interviews using a semistructured protocol, and a series of site visits to West Virginia, California and Arizona FQHC that were currently using an open source EHR. Results Five of the six sites that were chosen as part of the study found a number of advantages in the use of their open source EHR system, such as utilizing a large community of users and developers to modify their EHR to fit the needs of their provider and patient communities, and lower acquisition and implementation costs as compared to a commercial system. Discussion Despite these advantages, many of the informants and site visit participants felt that widespread dissemination and use of open source was restrained due to a negative connotation regarding this type of software. In addition, a number of participants stated that there is a necessary level of technical acumen needed within the FQHC to make an open source EHR effective. Conclusions An open source EHR provides advantages for FQHC that have limited resources to acquire and implement an EHR, but additional study is needed to evaluate its overall effectiveness. PMID:23744787

APPLYING OPEN-PATH OPTICAL SPECTROSCOPY TO HEAVY-DUTY DIESEL EMISSIONS

EPA Science Inventory

Non-dispersive infrared absorption has been used to measure gaseous emissions for both stationary and mobile sources. Fourier transform infrared spectroscopy has been used for stationary sources as both extractive and open-path methods. We have applied the open-path method for bo...

The Seismic Tool-Kit (STK): An Open Source Software For Learning the Basis of Signal Processing and Seismology.

NASA Astrophysics Data System (ADS)

Reymond, D.

2016-12-01

We present an open source software project (GNU public license), named STK: Seismic Tool-Kit, that is dedicated mainly for learning signal processing and seismology. The STK project that started in 2007, is hosted by SourceForge.net, and count more than 20000 downloads at the date of writing.The STK project is composed of two main branches:First, a graphical interface dedicated to signal processing (in the SAC format (SAC_ASCII and SAC_BIN): where the signal can be plotted, zoomed, filtered, integrated, derivated, ... etc. (a large variety of IFR and FIR filter is proposed). The passage in the frequency domain via the Fourier transform is used to introduce the estimation of spectral density of the signal , with visualization of the Power Spectral Density (PSD) in linear or log scale, and also the evolutive time-frequency representation (or sonagram). The 3-components signals can be also processed for estimating their polarization properties, either for a given window, or either for evolutive windows along the time. This polarization analysis is useful for extracting the polarized noises, differentiating P waves, Rayleigh waves, Love waves, ... etc. Secondly, a panel of Utilities-Program are proposed for working in a terminal mode, with basic programs for computing azimuth and distance in spherical geometry, inter/auto-correlation, spectral density, time-frequency for an entire directory of signals, focal planes, and main components axis, radiation pattern of P waves, Polarization analysis of different waves (including noise), under/over-sampling the signals, cubic-spline smoothing, and linear/non linear regression analysis of data set. STK is developed in C/C++, mainly under Linux OS, and it has been also partially implemented under MS-Windows. STK has been used in some schools for viewing and plotting seismic records provided by IRIS, and it has been used as a practical support for teaching the basis of signal processing. Useful links:http://sourceforge.net/projects/seismic-toolkit/http://sourceforge.net/p/seismic-toolkit/wiki/browse_pages/

Note: Tormenta: An open source Python-powered control software for camera based optical microscopy.

PubMed

Barabas, Federico M; Masullo, Luciano A; Stefani, Fernando D

2016-12-01

Until recently, PC control and synchronization of scientific instruments was only possible through closed-source expensive frameworks like National Instruments' LabVIEW. Nowadays, efficient cost-free alternatives are available in the context of a continuously growing community of open-source software developers. Here, we report on Tormenta, a modular open-source software for the control of camera-based optical microscopes. Tormenta is built on Python, works on multiple operating systems, and includes some key features for fluorescence nanoscopy based on single molecule localization.

Note: Tormenta: An open source Python-powered control software for camera based optical microscopy

NASA Astrophysics Data System (ADS)

Barabas, Federico M.; Masullo, Luciano A.; Stefani, Fernando D.

2016-12-01

Until recently, PC control and synchronization of scientific instruments was only possible through closed-source expensive frameworks like National Instruments' LabVIEW. Nowadays, efficient cost-free alternatives are available in the context of a continuously growing community of open-source software developers. Here, we report on Tormenta, a modular open-source software for the control of camera-based optical microscopes. Tormenta is built on Python, works on multiple operating systems, and includes some key features for fluorescence nanoscopy based on single molecule localization.

Exploring the "what if?" in geology through a RESTful open-source framework for cloud-based simulation and analysis

NASA Astrophysics Data System (ADS)

Klump, Jens; Robertson, Jess

2016-04-01

The spatial and temporal extent of geological phenomena makes experiments in geology difficult to conduct, if not entirely impossible and collection of data is laborious and expensive - so expensive that most of the time we cannot test a hypothesis. The aim, in many cases, is to gather enough data to build a predictive geological model. Even in a mine, where data are abundant, a model remains incomplete because the information at the level of a blasting block is two orders of magnitude larger than the sample from a drill core, and we have to take measurement errors into account. So, what confidence can we have in a model based on sparse data, uncertainties and measurement error? Our framework consist of two layers: (a) a ground-truth layer that contains geological models, which can be statistically based on historical operations data, and (b) a network of RESTful synthetic sensor microservices which can query the ground-truth for underlying properties and produce a simulated measurement to a control layer, which could be a database or LIMS, a machine learner or a companies' existing data infrastructure. Ground truth data are generated by an implicit geological model which serves as a host for nested models of geological processes as smaller scales. Our two layers are implemented using Flask and Gunicorn, which are open source Python web application framework and server, the PyData stack (numpy, scipy etc) and Rabbit MQ (an open-source queuing library). Sensor data is encoded using a JSON-LD version of the SensorML and Observations and Measurements standards. Containerisation of the synthetic sensors using Docker and CoreOS allows rapid and scalable deployment of large numbers of sensors, as well as sensor discovery to form a self-organized dynamic network of sensors. Real-time simulation of data sources can be used to investigate crucial questions such as the potential information gain from future sensing capabilities, or from new sampling strategies, or the combination of both, and it enables us to test many "what if?" questions, both in geology and in data engineering. What would we be able to see if we could obtain data at higher resolution? How would real-time data analysis change sampling strategies? Does our data infrastructure handle many new real-time data streams? What feature engineering can be deducted for machine learning approaches? By providing a 'data sandbox' able to scale to realistic geological scenarios we hope to start answering some of these questions. Faults happen in real world networks. Future work will investigate the effect of failure on dynamic sensor networks and the impact on the predictive capability of machine learning algorithms.

OpenCFU, a New Free and Open-Source Software to Count Cell Colonies and Other Circular Objects

PubMed Central

Geissmann, Quentin

2013-01-01

Counting circular objects such as cell colonies is an important source of information for biologists. Although this task is often time-consuming and subjective, it is still predominantly performed manually. The aim of the present work is to provide a new tool to enumerate circular objects from digital pictures and video streams. Here, I demonstrate that the created program, OpenCFU, is very robust, accurate and fast. In addition, it provides control over the processing parameters and is implemented in an intuitive and modern interface. OpenCFU is a cross-platform and open-source software freely available at http://opencfu.sourceforge.net. PMID:23457446

Utilization of open source electronic health record around the world: A systematic review.

PubMed

Aminpour, Farzaneh; Sadoughi, Farahnaz; Ahamdi, Maryam

2014-01-01

Many projects on developing Electronic Health Record (EHR) systems have been carried out in many countries. The current study was conducted to review the published data on the utilization of open source EHR systems in different countries all over the world. Using free text and keyword search techniques, six bibliographic databases were searched for related articles. The identified papers were screened and reviewed during a string of stages for the irrelevancy and validity. The findings showed that open source EHRs have been wildly used by source limited regions in all continents, especially in Sub-Saharan Africa and South America. It would create opportunities to improve national healthcare level especially in developing countries with minimal financial resources. Open source technology is a solution to overcome the problems of high-costs and inflexibility associated with the proprietary health information systems.

A New Architecture for Visualization: Open Mission Control Technologies

NASA Technical Reports Server (NTRS)

Trimble, Jay

2017-01-01

Open Mission Control Technologies (MCT) is a new architecture for visualisation of mission data. Driven by requirements for new mission capabilities, including distributed mission operations, access to data anywhere, customization by users, synthesis of multiple data sources, and flexibility for multi-mission adaptation, Open MCT provides users with an integrated customizable environment. Developed at NASAs Ames Research Center (ARC), in collaboration with NASAs Advanced Multimission Operations System (AMMOS) and NASAs Jet Propulsion Laboratory (JPL), Open MCT is getting its first mission use on the Jason 3 Mission, and is also available in the testbed for the Mars 2020 Rover and for development use for NASAs Resource Prospector Lunar Rover. The open source nature of the project provides for use outside of space missions, including open source contributions from a community of users. The defining features of Open MCT for mission users are data integration, end user composition and multiple views. Data integration provides access to mission data across domains in one place, making data such as activities, timelines, telemetry, imagery, event timers and procedures available in one place, without application switching. End user composition provides users with layouts, which act as a canvas to assemble visualisations. Multiple views provide the capability to view the same data in different ways, with live switching of data views in place. Open MCT is browser based, and works on the desktop as well as tablets and phones, providing access to data anywhere. An early use case for mobile data access took place on the Resource Prospector (RP) Mission Distributed Operations Test, in which rover engineers in the field were able to view telemetry on their phones. We envision this capability providing decision support to on console operators from off duty personnel. The plug-in architecture also allows for adaptation for different mission capabilities. Different data types and capabilities may be added or removed using plugins. An API provides a means to write new capabilities and to create data adaptors. Data plugins exist for mission data sources for NASA missions. Adaptors have been written by international and commercial users. Open MCT is open source. Open source enables collaborative development across organizations and also makes the product available outside of the space community, providing a potential source of usage and ideas to drive product design and development. The combination of open source with an Apache 2 license, and distribution on GitHub, has enabled an active community of users and contributors. The spectrum of users for Open MCT is, to our knowledge, unprecedented for mission software. In addition to our NASA users, we have, through open source, had users and inquires on projects ranging from Internet of Things, to radio hobbyists, to farming projects. We have an active community of contributors, enabling a flow of ideas inside and outside of the space community.

An isotopic study of the Ni-Cu-PGE-rich Wellgreen intrusion of the Wrangellia Terrane: Evidence for hydrothermal mobilization of rhenium and osmium

NASA Astrophysics Data System (ADS)

Marcantonio, Franco; Reisberg, Laurie; Zindler, Alan; Wyman, Derek; Hulbert, Larry

1994-01-01

Re-Os, Sm-Nd, Rb-Sr, and oxygen isotope systematics of the Wellgreen intrusion in the Wrangellia terrane were investigated in an effort to deduce the origin of this mafic-ultramafic sill and its attendant Ni-Cu-PGE deposit. Radiogenic initial Os ratios (1.06-1.82) and Sr ratios (0.7044-0.7062), and heavy δ18O (7.3-7.9%.) suggest alteration of the intrusion by hydrothermal fluids that carried radiogenic 187Os and 87Sr from the surrounding country rocks. The great majority (>99%) of the Os, however, and by inference the other PGEs, derived from a mantle-derived magma that suffered little or no interaction with the crust prior to crystallization. Initial Nd isotope ratios are not as variable ( ɛNd( t) ranges from 2.02-4.49) and suggest that the rocks were derived from a light-rare-earth-element depleted mantle source. The Nd results, together with Os data from relatively undisturbed wehrlites, are compatible with either a plume ( RICHARDS et al., 1991) or island arc ( SAMSON et al., 1990) model for Wrangellia. This study contributes to a growing body of evidence that documents the ready mobilization of Os in hydrothermal fluids. The potential effects of this mobility must be carefully evaluated prior to invoking crustal assimilation to explain variable and radiogenic Os initial ratios in layered intrusions.

Detection of ostreid herpesvirus 1 microvariant DNA in aquatic invertebrate species, sediment and other samples collected from the Georges River estuary, New South Wales, Australia.

PubMed

Evans, Olivia; Paul-Pont, Ika; Whittington, Richard J

2017-01-24

Ostreid herpesvirus 1 microvariants (OsHV-1) present a serious threat to the Australian Crassostrea gigas industry. Of great concern is the propensity for mortality due to the virus recurring each season in farmed oysters. However, the source of the virus in recurrent outbreaks remains unclear. Reference strain ostreid herpesvirus 1 (OsHV-1 ref) and other related variants have been detected in several aquatic invertebrate species other than C. gigas in Europe, Asia and the USA. The aim of this study was to confirm the presence or absence of OsHV-1 in a range of opportunistically sampled aquatic invertebrate species inhabiting specific locations within the Georges River estuary in New South Wales, Australia. OsHV-1 DNA was detected in samples of wild C. gigas, Saccostrea glomerata, Anadara trapezia, mussels (Mytilus spp., Trichomya hirsuta), whelks (Batillaria australis or Pyrazus ebeninus) and barnacles Balanus spp. collected from several sites between October 2012 and April 2013. Viral loads in non-ostreid species were consistently low, as was the prevalence of OsHV-1 DNA detection. Viral concentrations were highest in wild C. gigas and S. glomerata; the prevalence of detectable OsHV-1 DNA in these oysters reached approximately 68 and 43%, respectively, at least once during the study. These species may be important to the transmission and/or persistence of OsHV-1 in endemically infected Australian estuaries.

Isolation and Expression analysis of OsPME1, encoding for a putative Pectin Methyl Esterase from Oryza sativa (subsp. indica).

PubMed

Kanneganti, Vydehi; Gupta, Aditya Kumar

2009-04-01

Pectin Methyl Esterases (PMEs) play an essential role during plant development by affecting the mechanical properties of the plant cell walls. Recent studies indicated that PMEs play important role in pollen tube development. In this study, we isolated a 1.3 kb cDNA clone from rice panicle cDNA library. It contained a 1038 bp of open reading frame (ORF) encoding for a putative pectin methyl esterase of 345 aminoacids with a 20 aminoacid signal peptide and was hence designated as OsPME1 (Oryza sativaPectin Methyl Esterase 1). It contained the structural arrangement GXYXE and GXXDFIF, found in the active groups of all PMEs. OsPME1 gene product shared varying identities, ranging from 52 % to 33 % with PMEs from other plant species belonging to Brassicaceae, Fabaceae, Amaranthaceae and Funariaceae. Southern blot analysis indicated that PME1 exists as a single copy in the rice genome. Expression pattern analysis revealed that OsPME1 is expressed only in pollen grains, during the later stages of their development and was also regulated by various abiotic stress treatments and phytohormones. Functional characterization of this pollen specific PME from rice would enable us to understand its role in pollen development.

deepTools2: a next generation web server for deep-sequencing data analysis.

PubMed

Ramírez, Fidel; Ryan, Devon P; Grüning, Björn; Bhardwaj, Vivek; Kilpert, Fabian; Richter, Andreas S; Heyne, Steffen; Dündar, Friederike; Manke, Thomas

2016-07-08

We present an update to our Galaxy-based web server for processing and visualizing deeply sequenced data. Its core tool set, deepTools, allows users to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches. Since we first described our deepTools Galaxy server in 2014, we have implemented new solutions for many requests from the community and our users. Here, we introduce significant enhancements and new tools to further improve data visualization and interpretation. deepTools continue to be open to all users and freely available as a web service at deeptools.ie-freiburg.mpg.de The new deepTools2 suite can be easily deployed within any Galaxy framework via the toolshed repository, and we also provide source code for command line usage under Linux and Mac OS X. A public and documented API for access to deepTools functionality is also available. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking.

PubMed

McMurdie, Paul J; Holmes, Susan

2015-01-15

We have created a Shiny-based Web application, called Shiny-phyloseq, for dynamic interaction with microbiome data that runs on any modern Web browser and requires no programming, increasing the accessibility and decreasing the entrance requirement to using phyloseq and related R tools. Along with a data- and context-aware dynamic interface for exploring the effects of parameter and method choices, Shiny-phyloseq also records the complete user input and subsequent graphical results of a user's session, allowing the user to archive, share and reproduce the sequence of steps that created their result-without writing any new code themselves. Shiny-phyloseq is implemented entirely in the R language. It can be hosted/launched by any system with R installed, including Windows, Mac OS and most Linux distributions. Information technology administrators can also host Shiny--phyloseq from a remote server, in which case users need only have a Web browser installed. Shiny-phyloseq is provided free of charge under a GPL-3 open-source license through GitHub at http://joey711.github.io/shiny-phyloseq/. © The Author 2014. Published by Oxford University Press.

"Just Another Tool for Online Studies” (JATOS): An Easy Solution for Setup and Management of Web Servers Supporting Online Studies

PubMed Central

Lange, Kristian; Kühn, Simone; Filevich, Elisa

2015-01-01

We present here “Just Another Tool for Online Studies” (JATOS): an open source, cross-platform web application with a graphical user interface (GUI) that greatly simplifies setting up and communicating with a web server to host online studies that are written in JavaScript. JATOS is easy to install in all three major platforms (Microsoft Windows, Mac OS X, and Linux), and seamlessly pairs with a database for secure data storage. It can be installed on a server or locally, allowing researchers to try the application and feasibility of their studies within a browser environment, before engaging in setting up a server. All communication with the JATOS server takes place via a GUI (with no need to use a command line interface), making JATOS an especially accessible tool for researchers without a strong IT background. We describe JATOS’ main features and implementation and provide a detailed tutorial along with example studies to help interested researchers to set up their online studies. JATOS can be found under the Internet address: www.jatos.org. PMID:26114751

Real-Time Three-Dimensional Cell Segmentation in Large-Scale Microscopy Data of Developing Embryos.

PubMed

Stegmaier, Johannes; Amat, Fernando; Lemon, William C; McDole, Katie; Wan, Yinan; Teodoro, George; Mikut, Ralf; Keller, Philipp J

2016-01-25

We present the Real-time Accurate Cell-shape Extractor (RACE), a high-throughput image analysis framework for automated three-dimensional cell segmentation in large-scale images. RACE is 55-330 times faster and 2-5 times more accurate than state-of-the-art methods. We demonstrate the generality of RACE by extracting cell-shape information from entire Drosophila, zebrafish, and mouse embryos imaged with confocal and light-sheet microscopes. Using RACE, we automatically reconstructed cellular-resolution tissue anisotropy maps across developing Drosophila embryos and quantified differences in cell-shape dynamics in wild-type and mutant embryos. We furthermore integrated RACE with our framework for automated cell lineaging and performed joint segmentation and cell tracking in entire Drosophila embryos. RACE processed these terabyte-sized datasets on a single computer within 1.4 days. RACE is easy to use, as it requires adjustment of only three parameters, takes full advantage of state-of-the-art multi-core processors and graphics cards, and is available as open-source software for Windows, Linux, and Mac OS. Copyright © 2016 Elsevier Inc. All rights reserved.

Google Sky: A Digital View of the Night Sky

NASA Astrophysics Data System (ADS)

Connolly, A. Scranton, R.; Ornduff, T.

2008-11-01

From its inception Astronomy has been a visual science, from careful observations of the sky using the naked eye, to the use of telescopes and photographs to map the distribution of stars and galaxies, to the current era of digital cameras that can image the sky over many decades of the electromagnetic spectrum. Sky in Google Earth (http://earth.google.com) and Google Sky (http://www.google.com/sky) continue this tradition, providing an intuitive visual interface to some of the largest astronomical imaging surveys of the sky. Streaming multi-color imagery, catalogs, time domain data, as well as annotating interesting astronomical sources and events with placemarks, podcasts and videos, Sky provides a panchromatic view of the universe accessible to anyone with a computer. Beyond a simple exploration of the sky Google Sky enables users to create and share content with others around the world. With an open interface available on Linux, Mac OS X and Windows, and translations of the content into over 20 different languages we present Sky as the embodiment of a virtual telescope for discovery and sharing the excitement of astronomy and science as a whole.

Identification of rice cornichon as a possible cargo receptor for the Golgi-localized sodium transporter OsHKT1;3.

PubMed

Rosas-Santiago, Paul; Lagunas-Gómez, Daniel; Barkla, Bronwyn J; Vera-Estrella, Rosario; Lalonde, Sylvie; Jones, Alexander; Frommer, Wolf B; Zimmermannova, Olga; Sychrová, Hana; Pantoja, Omar

2015-05-01

Membrane proteins are synthesized and folded in the endoplasmic reticulum (ER), and continue their path to their site of residence along the secretory pathway. The COPII system has been identified as a key player for selecting and directing the fate of membrane and secretory cargo proteins. Selection of cargo proteins within the COPII vesicles is achieved by cargo receptors. The cornichon cargo receptor belongs to a conserved protein family found in eukaryotes that has been demonstrated to participate in the selection of integral membrane proteins as cargo for their correct targeting. Here it is demonstrated at the cellular level that rice cornichon OsCNIH1 interacts with OsHKT1;3 and, in yeast cells, enables the expression of the sodium transporter to the Golgi apparatus. Physical and functional HKT-cornichon interactions are confirmed by the mating-based split ubiquitin system, bimolecular fluorescence complementation, and Xenopus oocyte and yeast expression systems. The interaction between the two proteins occurs in the ER of plant cells and their co-expression in oocytes leads to the sequestration of the transporter in the ER. In the yeast cornichon mutant erv14, OsHKT1;3 is mistargeted, preventing the toxic effects of sodium transport in the cell observed in wild-type cells or in the erv14 mutant that co-expressed OsHKT1;3 with either OsCNIH1 or Erv14p. Identification and characterization of rice cornichon as a possible cargo receptor opens up the opportunity to improve our knowledge on membrane protein targeting in plant cells. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.

PRISM Software: Processing and Review Interface for Strong‐Motion Data

USGS Publications Warehouse

Jones, Jeanne M.; Kalkan, Erol; Stephens, Christopher D.; Ng, Peter

2017-01-01

A continually increasing number of high‐quality digital strong‐motion records from stations of the National Strong Motion Project (NSMP) of the U.S. Geological Survey, as well as data from regional seismic networks within the United States, calls for automated processing of strong‐motion records with human review limited to selected significant or flagged records. The NSMP has developed the Processing and Review Interface for Strong Motion data (PRISM) software to meet this need. In combination with the Advanced National Seismic System Quake Monitoring System (AQMS), PRISM automates the processing of strong‐motion records. When used without AQMS, PRISM provides batch‐processing capabilities. The PRISM software is platform independent (coded in Java), open source, and does not depend on any closed‐source or proprietary software. The software consists of two major components: a record processing engine composed of modules for each processing step, and a review tool, which is a graphical user interface for manual review, edit, and processing. To facilitate use by non‐NSMP earthquake engineers and scientists, PRISM (both its processing engine and review tool) is easy to install and run as a stand‐alone system on common operating systems such as Linux, OS X, and Windows. PRISM was designed to be flexible and extensible to accommodate implementation of new processing techniques. All the computing features have been thoroughly tested.

A Re-Os Study of Depleted Trench Peridotites from Northern Mariana

NASA Astrophysics Data System (ADS)

Ghosh, T.; Snow, J. E.; Heri, A. R.; Brandon, A. D.; Ishizuka, O.

2017-12-01

Trench peridotites provide information about the influence of subduction initiation on the extent of mantle wedge melting. They preserve melting records throughout subduction history, and as a result, likely experience multiple melt extraction events leading to successive depletion of melt/fluid mobile major and trace elements. To track melting histories of trench peridotites, Re-Os and PGEs can be used as reliable tracers to constrain early melt extraction or re-fertilization events. The Izu-Bonin-Mariana arc, being the largest intra-oceanic subduction system, provides an excellent area to study the formation of supra-subduction zone mantle and crust. Residual peridotite (harzburgite and dunite) samples were collected by dredging from the landward slope of the northern Mariana Trench. The samples are serpentinized to various extents (typical of abyssal peridotites), leaving behind relict grains of spinel, enstatite and olivine embedded within a serpentine matrix along with occasional interstitial diopside. Major element analyses of primary minerals reveal a wide range of variations in Cr# of spinels from 0.31-0.85 indicating 16-20% of melt fraction with dunites apparently experiencing the highest amount of partial melting. For Re-Os and PGE geochemistry, samples with high amounts of spinel (>4 vol %) and variable Cr# were chosen. Initial results show that bulk rock 187Os/188Os ratios range from 0.1113 to 0.1272. All of the samples are sub-chondritic, but in some cases, they are more radiogenic than average abyssal peridotites. Os abundances vary from 1-9 ppb. Sub-chondritic values can be attributed to the samples having evolved from a Re-depleted mantle source indicating a previous melt-extraction event. The cpx-harzburgites, having lower Cr# ( 0.4) are more radiogenic than ultra depleted dunites (Cr# 0.8), which might indicate preferential removal of Os during an apparent higher degree of partial melting experienced by dunites. The higher 187Os/188Os ratios of cpx-harzburgites possibly imply a late stage melt-rock interaction event, which had refertilized the depleted samples in radiogenic Os. Since there are only trace amounts of sediments in the accretionary prism of N. Mariana, Os ratios of these trench peridotites are not influenced by Os from sediments.

Open source tools for ATR development and performance evaluation

NASA Astrophysics Data System (ADS)

Baumann, James M.; Dilsavor, Ronald L.; Stubbles, James; Mossing, John C.

2002-07-01

Early in almost every engineering project, a decision must be made about tools; should I buy off-the-shelf tools or should I develop my own. Either choice can involve significant cost and risk. Off-the-shelf tools may be readily available, but they can be expensive to purchase and to maintain licenses, and may not be flexible enough to satisfy all project requirements. On the other hand, developing new tools permits great flexibility, but it can be time- (and budget-) consuming, and the end product still may not work as intended. Open source software has the advantages of both approaches without many of the pitfalls. This paper examines the concept of open source software, including its history, unique culture, and informal yet closely followed conventions. These characteristics influence the quality and quantity of software available, and ultimately its suitability for serious ATR development work. We give an example where Python, an open source scripting language, and OpenEV, a viewing and analysis tool for geospatial data, have been incorporated into ATR performance evaluation projects. While this case highlights the successful use of open source tools, we also offer important insight into risks associated with this approach.

Open Source Hbim for Cultural Heritage: a Project Proposal

NASA Astrophysics Data System (ADS)

Diara, F.; Rinaudo, F.

2018-05-01

Actual technologies are changing Cultural Heritage research, analysis, conservation and development ways, allowing new innovative approaches. The possibility of integrating Cultural Heritage data, like archaeological information, inside a three-dimensional environment system (like a Building Information Modelling) involve huge benefits for its management, monitoring and valorisation. Nowadays there are many commercial BIM solutions. However, these tools are thought and developed mostly for architecture design or technical installations. An example of better solution could be a dynamic and open platform that might consider Cultural Heritage needs as priority. Suitable solution for better and complete data usability and accessibility could be guaranteed by open source protocols. This choice would allow adapting software to Cultural Heritage needs and not the opposite, thus avoiding methodological stretches. This work will focus exactly on analysis and experimentations about specific characteristics of these kind of open source software (DBMS, CAD, Servers) applied to a Cultural Heritage example, in order to verifying their flexibility, reliability and then creating a dynamic HBIM open source prototype. Indeed, it might be a starting point for a future creation of a complete HBIM open source solution that we could adapt to others Cultural Heritage researches and analysis.

Open Source Clinical NLP - More than Any Single System.

PubMed

Masanz, James; Pakhomov, Serguei V; Xu, Hua; Wu, Stephen T; Chute, Christopher G; Liu, Hongfang

2014-01-01

The number of Natural Language Processing (NLP) tools and systems for processing clinical free-text has grown as interest and processing capability have surged. Unfortunately any two systems typically cannot simply interoperate, even when both are built upon a framework designed to facilitate the creation of pluggable components. We present two ongoing activities promoting open source clinical NLP. The Open Health Natural Language Processing (OHNLP) Consortium was originally founded to foster a collaborative community around clinical NLP, releasing UIMA-based open source software. OHNLP's mission currently includes maintaining a catalog of clinical NLP software and providing interfaces to simplify the interaction of NLP systems. Meanwhile, Apache cTAKES aims to integrate best-of-breed annotators, providing a world-class NLP system for accessing clinical information within free-text. These two activities are complementary. OHNLP promotes open source clinical NLP activities in the research community and Apache cTAKES bridges research to the health information technology (HIT) practice.

A portable structural analysis library for reaction networks.

PubMed

Bedaso, Yosef; Bergmann, Frank T; Choi, Kiri; Medley, Kyle; Sauro, Herbert M

2018-07-01

The topology of a reaction network can have a significant influence on the network's dynamical properties. Such influences can include constraints on network flows and concentration changes or more insidiously result in the emergence of feedback loops. These effects are due entirely to mass constraints imposed by the network configuration and are important considerations before any dynamical analysis is made. Most established simulation software tools usually carry out some kind of structural analysis of a network before any attempt is made at dynamic simulation. In this paper, we describe a portable software library, libStructural, that can carry out a variety of popular structural analyses that includes conservation analysis, flux dependency analysis and enumerating elementary modes. The library employs robust algorithms that allow it to be used on large networks with more than a two thousand nodes. The library accepts either a raw or fully labeled stoichiometry matrix or models written in SBML format. The software is written in standard C/C++ and comes with extensive on-line documentation and a test suite. The software is available for Windows, Mac OS X, and can be compiled easily on any Linux operating system. A language binding for Python is also available through the pip package manager making it simple to install on any standard Python distribution. The bulk of the source code is licensed under the open source BSD license with other parts using as either the MIT license or more simply public domain. All source is available on GitHub (https://github.com/sys-bio/Libstructural). Copyright © 2018 Elsevier B.V. All rights reserved.

The Use of Open Source Software in the Global Land Ice Measurements From Space (GLIMS) Project, and the Relevance to Institutional Cooperation

Treesearch

Christopher W. Helm

2006-01-01

GLIMS is a NASA funded project that utilizes Open-Source Software to achieve its goal of creating a globally complete inventory of glaciers. The participation of many international institutions and the development of on-line mapping applications to provide access to glacial data have both been enhanced by Open-Source GIS capabilities and play a crucial role in the...

Meteorological Error Budget Using Open Source Data

DTIC Science & Technology

2016-09-01

ARL-TR-7831 ● SEP 2016 US Army Research Laboratory Meteorological Error Budget Using Open- Source Data by J Cogan, J Smith, P...needed. Do not return it to the originator. ARL-TR-7831 ● SEP 2016 US Army Research Laboratory Meteorological Error Budget Using...Error Budget Using Open-Source Data 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) J Cogan, J Smith, P Haines

Open source bioimage informatics for cell biology

PubMed Central

Swedlow, Jason R.; Eliceiri, Kevin W.

2009-01-01

Significant technical advances in imaging, molecular biology and genomics have fueled a revolution in cell biology, in that the molecular and structural processes of the cell are now visualized and measured routinely. Driving much of this recent development has been the advent of computational tools for the acquisition, visualization, analysis and dissemination of these datasets. These tools collectively make up a new subfield of computational biology called bioimage informatics, which is facilitated by open source approaches. We discuss why open source tools for image informatics in cell biology are needed, some of the key general attributes of what make an open source imaging application successful, and point to opportunities for further operability that should greatly accelerate future cell biology discovery. PMID:19833518

Numerical Simulation of Dispersion from Urban Greenhouse Gas Sources

NASA Astrophysics Data System (ADS)

Nottrott, Anders; Tan, Sze; He, Yonggang; Winkler, Renato

2017-04-01

Cities are characterized by complex topography, inhomogeneous turbulence, and variable pollutant source distributions. These features create a scale separation between local sources and urban scale emissions estimates known as the Grey-Zone. Modern computational fluid dynamics (CFD) techniques provide a quasi-deterministic, physically based toolset to bridge the scale separation gap between source level dynamics, local measurements, and urban scale emissions inventories. CFD has the capability to represent complex building topography and capture detailed 3D turbulence fields in the urban boundary layer. This presentation discusses the application of OpenFOAM to urban CFD simulations of natural gas leaks in cities. OpenFOAM is an open source software for advanced numerical simulation of engineering and environmental fluid flows. When combined with free or low cost computer aided drawing and GIS, OpenFOAM generates a detailed, 3D representation of urban wind fields. OpenFOAM was applied to model scalar emissions from various components of the natural gas distribution system, to study the impact of urban meteorology on mobile greenhouse gas measurements. The numerical experiments demonstrate that CH4 concentration profiles are highly sensitive to the relative location of emission sources and buildings. Sources separated by distances of 5-10 meters showed significant differences in vertical dispersion of plumes, due to building wake effects. The OpenFOAM flow fields were combined with an inverse, stochastic dispersion model to quantify and visualize the sensitivity of point sensors to upwind sources in various built environments. The Boussinesq approximation was applied to investigate the effects of canopy layer temperature gradients and convection on sensor footprints.

NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations

NASA Astrophysics Data System (ADS)

Valiev, M.; Bylaska, E. J.; Govind, N.; Kowalski, K.; Straatsma, T. P.; Van Dam, H. J. J.; Wang, D.; Nieplocha, J.; Apra, E.; Windus, T. L.; de Jong, W. A.

2010-09-01

The latest release of NWChem delivers an open-source computational chemistry package with extensive capabilities for large scale simulations of chemical and biological systems. Utilizing a common computational framework, diverse theoretical descriptions can be used to provide the best solution for a given scientific problem. Scalable parallel implementations and modular software design enable efficient utilization of current computational architectures. This paper provides an overview of NWChem focusing primarily on the core theoretical modules provided by the code and their parallel performance. Program summaryProgram title: NWChem Catalogue identifier: AEGI_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGI_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Open Source Educational Community License No. of lines in distributed program, including test data, etc.: 11 709 543 No. of bytes in distributed program, including test data, etc.: 680 696 106 Distribution format: tar.gz Programming language: Fortran 77, C Computer: all Linux based workstations and parallel supercomputers, Windows and Apple machines Operating system: Linux, OS X, Windows Has the code been vectorised or parallelized?: Code is parallelized Classification: 2.1, 2.2, 3, 7.3, 7.7, 16.1, 16.2, 16.3, 16.10, 16.13 Nature of problem: Large-scale atomistic simulations of chemical and biological systems require efficient and reliable methods for ground and excited solutions of many-electron Hamiltonian, analysis of the potential energy surface, and dynamics. Solution method: Ground and excited solutions of many-electron Hamiltonian are obtained utilizing density-functional theory, many-body perturbation approach, and coupled cluster expansion. These solutions or a combination thereof with classical descriptions are then used to analyze potential energy surface and perform dynamical simulations. Additional comments: Full documentation is provided in the distribution file. This includes an INSTALL file giving details of how to build the package. A set of test runs is provided in the examples directory. The distribution file for this program is over 90 Mbytes and therefore is not delivered directly when download or Email is requested. Instead a html file giving details of how the program can be obtained is sent. Running time: Running time depends on the size of the chemical system, complexity of the method, number of cpu's and the computational task. It ranges from several seconds for serial DFT energy calculations on a few atoms to several hours for parallel coupled cluster energy calculations on tens of atoms or ab-initio molecular dynamics simulation on hundreds of atoms.

Application of Open Source Software by the Lunar Mapping and Modeling Project

NASA Astrophysics Data System (ADS)

Ramirez, P.; Goodale, C. E.; Bui, B.; Chang, G.; Kim, R. M.; Law, E.; Malhotra, S.; Rodriguez, L.; Sadaqathullah, S.; Mattmann, C. A.; Crichton, D. J.

2011-12-01

The Lunar Mapping and Modeling Project (LMMP), led by the Marshall Space Flight center (MSFC), is responsible for the development of an information system to support lunar exploration, decision analysis, and release of lunar data to the public. The data available through the lunar portal is predominantly derived from present lunar missions (e.g., the Lunar Reconnaissance Orbiter (LRO)) and from historical missions (e.g., Apollo). This project has created a gold source of data, models, and tools for lunar explorers to exercise and incorporate into their activities. At Jet Propulsion Laboratory (JPL), we focused on engineering and building the infrastructure to support cataloging, archiving, accessing, and delivery of lunar data. We decided to use a RESTful service-oriented architecture to enable us to abstract from the underlying technology choices and focus on interfaces to be used internally and externally. This decision allowed us to leverage several open source software components and integrate them by either writing a thin REST service layer or relying on the API they provided; the approach chosen was dependent on the targeted consumer of a given interface. We will discuss our varying experience using open source products; namely Apache OODT, Oracle Berkley DB XML, Apache Solr, and Oracle OpenSSO (now named OpenAM). Apache OODT, developed at NASA's Jet Propulsion Laboratory and recently migrated over to Apache, provided the means for ingestion and cataloguing of products within the infrastructure. Its usage was based upon team experience with the project and past benefit received on other projects internal and external to JPL. Berkeley DB XML, distributed by Oracle for both commercial and open source use, was the storage technology chosen for our metadata. This decision was in part based on our use Federal Geographic Data Committee (FGDC) Metadata, which is expressed in XML, and the desire to keep it in its native form and exploit other technologies built on top of XML. Apache Solr, an open source search engine, was used to drive our search interface and as way to store references to metadata and data exposed via REST endpoints. As was the case with Apache OODT there was team experience with this component that helped drive this choice. Lastly, OpenSSO, an open source single sign on service, was used to secure and provide access constraints to our REST based services. For this product there was little past experience but given our service based approach seemed to be a natural fit. Given our exposure to open source we will discuss the tradeoffs and benefits received by the choices made. Moreover, we will dive into the context of how the software packages were used and the impact of their design and extensibility had on the construction of the infrastructure. Finally, we will compare our encounter across open source solutions and attributes that can vary the impression one will get. This comprehensive account of our endeavor should aid others in their assessment and use of open source.

Magnaporthe oryzae Induces the Expression of a MicroRNA to Suppress the Immune Response in Rice1[OPEN

PubMed Central

Zhang, Xin; Bao, Yalin; Shan, Deqi; Wang, Zhihui; Song, Xiaoning; Wang, Zhaoyun; Wang, Jiansheng; He, Liqiang; Wu, Liang; Zhang, Zhengguang; Niu, Dongdong

2018-01-01

MicroRNAs play crucial roles in plant responses to pathogen infections. The rice blast disease, caused by the fungus Magnaporthe oryzae, is the most important disease of rice (Oryza sativa). To explore the microRNA species that participate in rice immunity against the rice blast disease, we compared the expression of small RNAs between mock- and M. oryzae-treated rice. We found that infection by M. oryzae strain Guy11 specifically induced the expression of rice miR319 and, consequently, suppressed its target gene TEOSINTE BRANCHED/CYCLOIDEA/PROLIFERATING CELL FACTOR1 (OsTCP21), which encodes a transcription factor. Using transgenic rice that overexpresses miR319b (OE) or expresses OsTCP21-Res (which is resistant to miR319-mediated silencing), we found that OsTCP21 is a positive regulator of the rice defense response against the blast disease. When wild-type and miR319b-OE rice were infected by Guy11, multiple jasmonic acid (JA) synthetic and signaling components were suppressed, indicating that Guy11 suppresses JA signaling through inducing miR319. In particular, we found that LIPOXYGENASE2 (LOX2) and LOX5 were specifically suppressed by miR319 overexpression or by Guy11 infection. LOXs are the key enzymes of JA synthesis, which catalyze the conversion of α-linoleic acid to hydroperoxy-octadecadienoic acid. The application of α-linoleic acid rescued disease symptoms on the OsTCP21-Res rice but not wild-type rice, supporting our hypothesis that OsLOX2 and OsLOX5 are the key JA synthesis genes hijacked by Guy11 to subvert host immunity and facilitate pathogenicity. We propose that induced expression of OsLOX2/5 may improve resistance to the rice blast disease. PMID:29549093

Building CHAOS: An Operating System for Livermore Linux Clusters

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

Garlick, J E; Dunlap, C M

2003-02-21

The Livermore Computing (LC) Linux Integration and Development Project (the Linux Project) produces and supports the Clustered High Availability Operating System (CHAOS), a cluster operating environment based on Red Hat Linux. Each CHAOS release begins with a set of requirements and ends with a formally tested, packaged, and documented release suitable for use on LC's production Linux clusters. One characteristic of CHAOS is that component software packages come from different sources under varying degrees of project control. Some are developed by the Linux Project, some are developed by other LC projects, some are external open source projects, and some aremore » commercial software packages. A challenge to the Linux Project is to adhere to release schedules and testing disciplines in a diverse, highly decentralized development environment. Communication channels are maintained for externally developed packages in order to obtain support, influence development decisions, and coordinate/understand release schedules. The Linux Project embraces open source by releasing locally developed packages under open source license, by collaborating with open source projects where mutually beneficial, and by preferring open source over proprietary software. Project members generally use open source development tools. The Linux Project requires system administrators and developers to work together to resolve problems that arise in production. This tight coupling of production and development is a key strategy for making a product that directly addresses LC's production requirements. It is another challenge to balance support and development activities in such a way that one does not overwhelm the other.« less

10 CFR 39.43 - Inspection, maintenance, and opening of a source or source holder.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 1 2011-01-01 2011-01-01 false Inspection, maintenance, and opening of a source or source holder. 39.43 Section 39.43 Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY..., for defects before each use to ensure that the equipment is in good working condition and that...

10 CFR 39.43 - Inspection, maintenance, and opening of a source or source holder.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 1 2013-01-01 2013-01-01 false Inspection, maintenance, and opening of a source or source holder. 39.43 Section 39.43 Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY..., for defects before each use to ensure that the equipment is in good working condition and that...

10 CFR 39.43 - Inspection, maintenance, and opening of a source or source holder.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 1 2014-01-01 2014-01-01 false Inspection, maintenance, and opening of a source or source holder. 39.43 Section 39.43 Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY..., for defects before each use to ensure that the equipment is in good working condition and that...

10 CFR 39.43 - Inspection, maintenance, and opening of a source or source holder.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 1 2012-01-01 2012-01-01 false Inspection, maintenance, and opening of a source or source holder. 39.43 Section 39.43 Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY..., for defects before each use to ensure that the equipment is in good working condition and that...