Sample records for www.actris.net
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EARLINET: towards an advanced sustainable European aerosol lidar network
NASA Astrophysics Data System (ADS)
Pappalardo, G.; Amodeo, A.; Apituley, A.; Comeron, A.; Freudenthaler, V.; Linné, H.; Ansmann, A.; Bösenberg, J.; D'Amico, G.; Mattis, I.; Mona, L.; Wandinger, U.; Amiridis, V.; Alados-Arboledas, L.; Nicolae, D.; Wiegner, M.
2014-08-01
The European Aerosol Research Lidar Network, EARLINET, was founded in 2000 as a research project for establishing a quantitative, comprehensive, and statistically significant database for the horizontal, vertical, and temporal distribution of aerosols on a continental scale. Since then EARLINET has continued to provide the most extensive collection of ground-based data for the aerosol vertical distribution over Europe. This paper gives an overview of the network's main developments since 2000 and introduces the dedicated EARLINET special issue, which reports on the present innovative and comprehensive technical solutions and scientific results related to the use of advanced lidar remote sensing techniques for the study of aerosol properties as developed within the network in the last 13 years. Since 2000, EARLINET has developed greatly in terms of number of stations and spatial distribution: from 17 stations in 10 countries in 2000 to 27 stations in 16 countries in 2013. EARLINET has developed greatly also in terms of technological advances with the spread of advanced multiwavelength Raman lidar stations in Europe. The developments for the quality assurance strategy, the optimization of instruments and data processing, and the dissemination of data have contributed to a significant improvement of the network towards a more sustainable observing system, with an increase in the observing capability and a reduction of operational costs. Consequently, EARLINET data have already been extensively used for many climatological studies, long-range transport events, Saharan dust outbreaks, plumes from volcanic eruptions, and for model evaluation and satellite data validation and integration. Future plans are aimed at continuous measurements and near-real-time data delivery in close cooperation with other ground-based networks, such as in the ACTRIS (Aerosols, Clouds, and Trace gases Research InfraStructure Network) www.actris.net, and with the modeling and satellite community, linking the research community with the operational world, with the aim of establishing of the atmospheric part of the European component of the integrated global observing system.
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NASA Astrophysics Data System (ADS)
Sciare, Jean; Dulac, François; Crenn, Vincent; Hamonou, Eric; Baisnée, Dominique; Nicolas, José B.; Pont, Véronique; Lambert, Dominique; Gheusi, François; Mallet, Marc; Tison, Emmanuel; Sauvage, Stéphane; Bourrianne, Thierry; Roberts, Gregory; Colomb, Aurélie; Pichon, Jean-Marc; Sellegri, Karine; Savelli, Jean-Luc
2015-04-01
As part of the MISTRALS/ChArMEx (Mediterranean Integrated Studies aT Regional And Local Scales/the Chemistry-Aerosol Mediterranean Experiment; http://www.mistrals-home.org; http://charmex.lsce.ipsl.fr) and the CORSiCA (http://www.obs-mip.fr/corsica) programs, 2-year continuous observations of near real-time chemical composition of submicron aerosols were performed between June 2012 & July 2014 at the Cape Corsica atmospheric supersite (http://gaw.empa.ch/gawsis/reports.asp?StationID=2076203042), a remote marine site in the Western Mediterranean. Submicron organic aerosols (OA) and the major inorganic salts (sulfate, ammonium, nitrate) were monitored every 30 min using a Quadripole Aerosol Chemical Speciation Monitor (Q-ACSM; Aerodyne Res. Inc. MA, USA). Quality control of this large dataset (24-month continuous observations) was performed through closure studies (using co-located SMPS and TEOM-FDMS measurements), direct comparisons with other on-line / off-line instruments running in parallel (filter sampling, OPC, nephelometer …), and large intercomparison of 13 Q-ACSM performed within the EU-FP7 ACTRIS program (http://www.actris.net/). Source apportionment of OA was then performed on a monthly basis using the SourceFinder software (SoFi, http://www.psi.ch/acsm-stations/me-2) allowing the distinction between hydrogen- and oxygen-like organic aerosols (HOA and OOA, respectively). This monthly resolved source apportionment was first compared with co-located real-time tracer measurements (NOx, BC, CO, VOC …) available at the Cape Corsica station. Seasonal patterns of the various properties of (secondary) OOA (OSc, O/C ratio …) were then investigated from monthly resolved source apportionment results (monthly OOA mass spectra) obtained over the period June 2012 - July 2014. Acknowledgements: Atmospheric measurements performed at Cape Corsica Station were funded by CNRS-INSU, ADEME, CEA, and METEO-FRANCE. This work was carried out in the framework of the CORSiCA project funded by the Collectivité Territoriale de Corse through the Fonds Européen de Développement Régional of the European Operational Program 2007-2013 and the Contrat de Plan Etat Région.
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Estimation of aerosol direct radiative forcing in Lecce during the 2013 ADRIMED campaign
NASA Astrophysics Data System (ADS)
Barragan, Ruben; Romano, Salvatore; Sicard, Michaël.; Burlizzi, Pasquale; Perrone, Maria-Rita; Comeron, Adolfo
2015-10-01
In the framework of the ChArMEx (Chemistry-Aerosol Mediterranean Experiment, http://charmex.lsce.ipsl.fr/) initiative, a field campaign took place in the western Mediterranean Basin between 10 June and 5 July 2013 within the ADRIMED (Aerosol Direct Radiative Impact on the regional climate in the MEDiterranean region) project. The scientific objectives of ADRIMED are the characterization of the typical "Mediterranean aerosol" and its direct radiative forcing (column closure and regional scale). This work is focused on the multi-intrusion Saharan dust transport period of moderate intensity that occurred over the western and central Mediterranean Basin during the period 14 - 27 June. The dust plumes were detected by the EARLINET/ACTRIS (European Aerosol Research Lidar Network / Aerosols, Clouds, and Trace gases Research InfraStructure Network, http://www.actris.net/) lidar stations of Barcelona (16 and 17 June) and Lecce (22 June). First, two well-known and robust radiative transfer models, parametrized by lidar profiles for the aerosol vertical distribution, are validated both in the shortwave and longwave spectral range 1) at the surface with down- and up-ward flux measurements from radiometers and 2) at the top of the atmosphere with upward flux measurements from the CERES (Clouds and the Earth's Radiant Energy System) radiometers on board the AQUA and TERRA satellites. The differences between models and their limitations are discussed. The instantaneous and clear-sky direct radiative forcing of mineral dust is then estimated using lidar data for parametrizing the particle vertical distribution at Lecce. The difference between the obtained forcings is discussed in regard to the mineralogy and vertical structure of the dust plume.
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NASA Astrophysics Data System (ADS)
Mona, Lucia; Benedetti, Angela; D'Amico, Giuseppe; Myhre, Cathrine Lund; Schulz, Michael; Wandinger, Ulla; Laj, Paolo; Pappalardo, Gelsomina
2016-04-01
The ACTRIS-2 project, funded by Horizon 2020, addresses the scope of integrating state-of-the-art European ground-based stations for long term observations of aerosols, clouds and short lived gases, capitalizing on the work of FP7-ACTRIS. It aims at achieving the construction of a user-oriented RI, unique in the EU-RI landscape for providing 4-D integrated high-quality data from near-surface to high altitude (vertical profiles and total-column) which are relevant to climate and air-quality research. ACTRIS-2 develops and implements, in a large network of stations in Europe and beyond, observational protocols that permit the harmonization of collected data and their dissemination. ACTRIS secures provision and dissemination of a unique set of data and data-products that would not otherwise be available with the same level of quality and standardization. This results from a 10-year plus effort in constructing a research infrastructure capable of responding to community needs and requirements, and has been engaged since the start of the FP5 EU commission program. ACTRIS ensures compliance with reporting requirements (timing, format, traceability) defined by the major global observing networks. EARLINET (European Aerosol research Lidar NETwork), the aerosol vertical profiling component of ACTRIS, is providing since May 2000 vertical profiles of aerosol extinction and backscatter over Europe. A new structure of the EARLINET database has been designed in a more user oriented approach reporting new data products which are more effective for specific uses of different communities. In particular, a new era is starting with the Copernicus program during which the aerosol vertical profiling capability will be fundamental for assimilation and validation purposes. The new data products have been designed thanks to a strong link with EARLINET data users, first of all modeling and satellite communities, established since the beginning of EARLINET and re-enforced within ACTRIS2. The potentiality of the new EARLINET data products and first examples of integrated studies with models will be presented at the conference. Acknowledgments: ACTRIS2 Research Infrastructure Project is funded by the European Union's Horizon 2020 research and innovation programme under the grant agreement n. 654169 and previously under FP7 grant agreement n. 262254.
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NASA Astrophysics Data System (ADS)
Barragan, Ruben; Sicard, Michaël; Totems, Julien; François Léon, Jean; Baptiste Renard, Jean; Dulac, François; Mallet, Marc; Pelon, Jacques; Alados-Arboledas, Lucas; Amodeo, Aldo; José Granados-Muñoz, María; Boselli, Antonella; Bravo-Aranda, Juan Antonio; Muñoz-Porcar, Constantino; Chazette, Patrick; Comerón, Adolfo; D'Amico, Giuseppe; Wang, Xuan; Mona, Lucia; Pappalardo, Gelsomina
2015-04-01
In the framework of the ChArMEx (Chemistry-Aerosol Mediterranean Experiment, http://charmex.lsce.ipsl.fr/) initiative, a field campaign took place in the western Mediterranean Basin between 10 June and 5 July 2013 within the ADRIMED (Aerosol Direct Radiative Impact on the regional climate in the MEDiterranean region) project. The scientific objectives of the campaign were the characterization of the different aerosol types found over the Mediterranean Sea and the calculation of their direct radiative forcing (column closure and regional scale). Two super-sites (Ersa, Corsica Island, France, and Lampedusa Island, Italy) were equipped with a complete set of instruments to measure in-situ aerosol physical, chemical and optical properties, as well as aerosol mixing state and vertical distribution and radiative fluxes. Four secondary sites were operated in Granada (Spain), Menorca Island (Spain), Rome (Italy) and Lecce (Italy). All sites were equipped with AERONET sunphotometers. The ground observations were supported by airborne measurements including 2 SAFIRE aircraft (ATR-42 equipped with in situ measurements (10 June - 5 July) and Falcon-20 (17 June - 5 July) with the LNG aerosol lidar) and sounding and drifting balloons launched by CNES from Menorca Island and carrying the LOAC particle counter/sizer (16 June - 4 July). Satellite products from MODIS, MSG/SEVIRI and CALIOP provided additional observations. In several occasions corresponding to aerosol loads of different types, the aircraft flew near EARLINET/ACTRIS (European Aerosol Research Lidar Network / Aerosols, Clouds, and Trace gases Research InfraStructure Network, http://www.actris.net/) lidar stations. This work is focused on a moderate multi-intrusion Saharan dust event occurred over the western Mediterranean Basin (WMB) during the period 14 - 27 June. The dust plumes were detected by the EARLINET stations of Granada, Barcelona, Naples, Potenza, Lecce and Serra la Nave (Sicily) and by the ChArMEx lidar stations of Menorca, Ersa and Lampedusa. The dust origin is chronologically identified from northern Morocco, center Algeria and center Tunisia. The multi-intrusion aspect of the event results in aerosol optical depth peaks higher in the eastern part of the WMB (maximum of 0.45 at 440 nm detected in Lecce) than in the western part of the WMB where the event starts (maximum of 0.29 at 440 nm detected in Granada). The spatio-temporal evolution of the plumes during their transport and the differences due to the different dust origins are investigated with multi-wavelength ground-based lidars, sun-photometers, the airborne lidar and balloon-borne aerosol counters. Acknowledgments: EARLINET lidar measurements are supported by the 7th Framework Programme under the project ACTRIS (Aerosols, Clouds, and Trace Gases Research Infrastructure Network; grant agreement no. 262254). The field campaign was performed in the framework of work package 4 on aerosol-radiation-climate interactions of the coordinated programme MISTRALS/ChArMEx) and was also supported by ANR.
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NASA Astrophysics Data System (ADS)
Gilge, Stefan; Plass-Dülmer, Christian; Weyrauch, Dietmar; Rohrer, Franz
2013-04-01
The European ACTRIS (Aerosols, Clouds, and Trace gases Research InfraStructure Network) project, Work Package 4, aims at harmonization and improvement of the measurement of volatile organic carbon and nitrogen oxides. Central tools to assess and compare the performance of European NOx monitoring stations and labs within ACTRIS are a round robin experiment (2012) and side-by-side intercomparisons (Nov 2012). While the first checked the used laboratories' scales versus a common scale, the latter investigated weather same samples are identically and artefact-free analyzed by collocated instruments. The ACTRIS-NOx-side-by-side intercomparison was realised by instruments sampling from a common manifold which was fed by zero gas, synthetic air mixtures, ambient air, and spiked ambient air. Thus, the side-by-side experiments enabled a full characterization of the detection limit, the linear range, the span, and of potential artefacts due to interfering species for each of the contributing instruments. Generally, CLD type NOx instruments were used in the comparisons supplemented by four new optical techniques, comprising LIF and cavity enhanced techniques. In the round robin exercise, some 20 monitoring sites participated, and 14 instruments were running side-by-side in the one week Nov comparison. The results of both experiments will be presented and discussed with respect to the data quality objectives of GAW and ACTRIS.
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ACTRIS Data Centre: An atmospheric data portal
NASA Astrophysics Data System (ADS)
Myhre, C. Lund; Fahre Vik, A.; Logna, R.; Torseth, K.; Linné, H.; O'Connor, E.
2012-04-01
ACTRIS (Aerosols, Clouds, and Trace gases Research InfraStructure Network) is a European Project aiming at integrating European ground-based stations equipped with advanced instrumentation for studying aerosols, clouds, and short-lived gas-phase species. The ACTRIS activities result in improved atmospheric measurements data made at more than 60 European sites, from numerous instruments and includes variables measured by ground based in situ and remote sensing technologies. Core variables are in situ aerosol optical, physical and chemical properties, short-lived trace gases (volatile organic carbon and nitrogen oxides), aerosol scattering and extinction profiles, and cloud properties. The ACTRIS data centre (ACTRIS DC) is giving free and open access to all data resulting from the activities of the infrastructure network, complemented with data from other relevant networks and data bases. The overall goal is to facilitate scientists and other user groups access to atmospheric observational data, and to provide mature products for analysis and interpretation of atmospheric composition change. The ACTRIS DC aims at substantially increasing the number of high-quality data by providing long-term observational data relevant to climate and air quality research produced with standardized or comparable procedures throughout the network. The backbone of the ACTRIS DC is the three core data bases: - EARLINET Data Base hosting aerosol lidar data from more than 30 European sites - EBAS hosting ground based atmospheric in situ data from more than 1000 sites globally - Cloudnet hosting remote sensing cloud data and products from 5 European sites Furthermore, a joint portal is developed combining information from various data sources to gain new information not presently available from standalone databases or networks. The data centre will provide tools and services to facilitate the use of measurements for broad user communities. Higher level and integrated products will be developed stage-by-stage during the project, and user requirements, interactions and feedbacks are essential. The first version of ACTRIS DC is a web portal that allows users to search for atmospheric composition data from a multitude of data archives through a single user interface. Examples of data bases and frameworks included are EMEP, the GAW- world data centres, EARLINET, NDACC, CARIBIC-GEOmon, HTAP, AMAP amongst others. Currently the portal provides an overview of more than 800 000 data sets from more than 20 data bases/frameworks globally. For some of the databases included in the portal, the interface furthermore allows you to download data directly through the portal. A map functionality is implemented facilitating the identification of data and making it possible to search for collocation of observations, variables and sites both in time and space. The data portal can serve as "one-stop-shop" of atmospheric high-quality data, and the portal will also offer a direct interface towards external users like the MACC II project and GMES in-situ. The data dissemination will take into account the principles outlined in SEIS, INSPIRE, WIS and GEOSS.
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2011-05-12
www.epa.gov/nrmrl/pubs/600r09048/600r09048.pdf • http://www.epa.gov/awi/res_rehabilitation.html Net Zero Waste • http://www.army.mil/-news/2011/02...24/52403-net- zero - waste -goal-becoming-a-reality- at-jblm/ • http://www.operationfree.net/2011/04/11/u-s-army-looks-to-net- zero - waste / 27
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ACTRIS Aerosol, Clouds and Trace Gases Research Infrastructure
NASA Astrophysics Data System (ADS)
Pappalardo, Gelsomina
2018-04-01
The Aerosols, Clouds and Trace gases Research Infrastructure (ACTRIS) is a distributed infrastructure dedicated to high-quality observation of aerosols, clouds, trace gases and exploration of their interactions. It will deliver precision data, services and procedures regarding the 4D variability of clouds, short-lived atmospheric species and the physical, optical and chemical properties of aerosols to improve the current capacity to analyse, understand and predict past, current and future evolution of the atmospheric environment.
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NASA Astrophysics Data System (ADS)
Dulac, Francois
2013-04-01
The Chemistry-Aerosol Mediterranean Experiment (ChArMEx, http://charmex.lsce.ipsl.fr/) is a French initiative supported by the MISTRALS program (Mediterranean Integrated Studies at Regional And Locals Scales, http://www.mistrals-home.org). It aims at a scientific assessment of the present and future state of the atmospheric environment in the Mediterranean Basin, and of its impacts on the regional climate, air quality, and marine biogeochemistry. The major stake is an understanding of the future of the Mediterranean region in a context of strong regional anthropogenic and climatic pressures. The target of ChArMEx is short-lived particulate and gaseous tropospheric trace species which are the cause of poor air quality events, have two-way interactions with climate, or impact the marine biogeochemistry. In order to fulfill these objectives, important efforts have been put in 2012 in order to implement the infrastructure and instrumentation for a fully equipped background monitoring station at Ersa, Cape Corsica, a key location at the crossroads of dusty southerly air masses and polluted outflows from the European continent. The observations at this station began in June 2012 (in the context of the EMEP / ACTRIS / PEGASOS / ChArMEx campaigns). A broad spectrum of aerosol properties is also measured at the station, from the chemical composition (off-line daily filter sampling in PM2.5/PM10, on-line Aerosol Chemical Speciation Monitor), ground optical properties (extinction/absorption/light scattering coeff. with 1-? CAPS PMex monitor, 7-? Aethalometer, 3-? Nephelometer), integrated and vertically resolved optical properties (4-? Cimel sunphotometer and LIDAR, respective), size distribution properties (N-AIS, SMPS, APS, and OPS instruments), mass (PM1/PM10 by TEOM/TEOM-FDMS), hygroscopicity (CCN), as well as total insoluble deposition. So far, real-time measurement of reactive gases (O3, CO, NO, NO2), and off-line VOC measurements (cylinders, cartridges) are also performed. A Kipp and Zonen system for monitoring direct and diffuse broadband radiative fluxes will also be in operation soon, as well as an ICOS/RAMCES CO2 and CH4 monitoring instrument. Through this unprecedented effort and with the support from ChArMEx, ADEME, and CORSiCA programs (http://www.obs-mip.fr/corsica), this observatory represents so far the most achieved French atmospheric station having the best set of instruments for measuring in-situ reactive gases and aerosols. It stands out as the station of not one laboratory but of a large number (see list of co-authors). It provides "real time" information useful to the local air quality network (Qualitair Corse, http://www.qualitaircorse.org/) concerning EU regulated parameters (O3, PMx). This station aims providing quality controlled climatically relevant gas/aerosol database following the recommendations of the EU-FP7 ACTRIS infrastructure, EMEP and WMO-GAW programs. Atmospheric datasets are currently available at the MISTRALS database (http://mistrals.sedoo.fr/ChArMEx/) and soon at the ACTRIS & GAW databases. After a brief presentation of the Cape Corsica Station (location, climatology, instrumental settings ...), we present here the first months of aerosols properties (optical / chemical / particle size) obtained at this station. Acknowledgements: the station is mainly supported by ADEME, CNRS-INSU, CEA, CTC, EMD, FEDER, and Météo-France.
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NASA Astrophysics Data System (ADS)
Tsekeri, Alexandra; Amiridis, Vassilis; Lopatin, Anton; Marinou, Eleni; Giannakaki, Eleni; Pikridas, Michael; Sciare, Jean; Liakakou, Eleni; Gerasopoulos, Evangelos; Duesing, Sebastian; Corbin, Joel C.; Gysel, Martin; Bukowiecki, Nicolas; Baars, Holger; Engelmann, Ronny; Wehner, Birgit; Kottas, Michael; Mamali, Dimitra; Kokkalis, Panagiotis; Raptis, Panagiotis I.; Stavroulas, Iasonas; Keleshis, Christos; Müller, Detlef; Solomos, Stavros; Binietoglou, Ioannis; Mihalopoulos, Nikolaos; Papayannis, Alexandros; Stachlewska, Iwona S.; Igloffstein, Julia; Wandinger, Ulla; Ansmann, Albert; Dubovik, Oleg; Goloub, Philippe
2018-04-01
Aerosol absorption profiling is crucial for radiative transfer calculations and climate modelling. Here, we utilize the synergy of lidar with sun-photometer measurements to derive the absorption coefficient and single scattering albedo profiles during the ACTRIS-2 campaigns held in Germany, Greece and Cyprus. The remote sensing techniques are compared with in situ measurements in order to harmonize and validate the different methodologies and reduce the absorption profiling uncertainties.
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The lesson learnt during interact - I and INTERACT - II actris measurement campaigns
NASA Astrophysics Data System (ADS)
Rosoldi, Marco; Madonna, Fabio; Pappalardo, Gelsomina; Vande Hey, Joshua; Zheng, Yunhui
2018-04-01
The INTERACT-II (INTERcomparison of Aerosol and Cloud Tracking) campaign, performed at the CNR-IMAA Atmospheric Observatory (760 m a.s.l., 40.60° N, 15.72° E), aims to evaluate the performances of commercial automatic lidars and ceilometers for atmospheric aerosol profiling, through the comparison with Potenza EARLINET (European Aerosol Research Lidar NETwork) lidars. The results of the campaign and the overall lesson learnt within INTERACT-I and INTERACT-II ACTRIS campaigns will be presented.
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Resources - cancer ... The following organizations are good resources for information on cancer : American Cancer Society -- www.cancer.org Cancer Care -- www.cancercare.org Cancer.Net -- www.cancer.net/coping- ...
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NASA Astrophysics Data System (ADS)
Hoerger, C. C.; Werner, A.; Plass-Duelmer, C.; Reimann, S.; Eckart, E.; Steinbrecher, R.; Aalto, J.; Arduini, J.; Bonnaire, N.; Cape, J. N.; Colomb, A.; Connolly, R.; Diskova, J.; Dumitrean, P.; Ehlers, C.; Gros, V.; Hakola, H.; Hill, M.; Hopkins, J. R.; Jäger, J.; Junek, R.; Kajos, M. K.; Klemp, D.; Leuchner, M.; Lewis, A. C.; Locoge, N.; Maione, M.; Martin, D.; Michl, K.; Nemitz, E.; O'Doherty, S.; Pérez Ballesta, P.; Ruuskanen, T. M.; Sauvage, S.; Schmidbauer, N.; Spain, T. G.; Straube, E.; Vana, M.; Vollmer, M. K.; Wegener, R.; Wenger, A.
2014-10-01
The performance of 20 European laboratories involved in long-term non-methane hydrocarbon (NMHC) measurements within the framework of Global Atmosphere Watch (GAW) and European Monitoring and Evaluation Programme (EMEP) was assessed with respect to the ACTRIS (Aerosols, Clouds, and Trace gases Research InfraStructure Network) and GAW data quality objectives (DQOs). Compared to previous intercomparisons the DQOs of ACTRIS are much more demanding with deviations to a reference value of less than 5% and repeatability of better than 2% for mole fractions above 0.1 nmol mol-1. The participants were asked to measure both a 30 component NMHC mixture in nitrogen (NMHC_N2) at approximately 1 nmol mol-1 and whole air (NMHC_air), following a standardised operation procedure including zero- and calibration gas measurements. Furthermore, they had to report details on their instruments and they were asked to assess measurement uncertainties. The NMHCs were analysed either by gas chromatography-flame ionisation detection or gas chromatography-mass spectrometer methods. Most systems performed well for the NMHC_N2 measurements (88% of the reported values were within the GAW DQOs and even 58% within the ACTRIS DQOs). For NMHC_air generally more frequent and larger deviations to the assigned values were observed compared to NMHC_N2 (77% of the reported values were within the GAW DQOs, but only 48% within the ACTRIS DQOs). Important contributors to the poorer performance in NMHC_air compared to NMHC_N2 were a more complex matrix and a larger span of NMHC mole fractions (0.03-2.5 nmol mol-1). Issues, which affected both NMHC mixtures, are the usage of direct vs. two-step calibration, breakthrough of C2-C3 hydrocarbons, blank values in zero-gas measurements (especially for those systems using a Nafion® Dryer), adsorptive losses of aromatic compounds, and insufficient chromatographic resolution. Essential for high-quality results are experienced operators, a comprehensive quality assurance and quality control, well characterised systems, and sufficient man-power to operate the systems and evaluate the data.
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Global synthesis of long-term cloud condensation nuclei observations
NASA Astrophysics Data System (ADS)
Schmale, Julia; Henning, Silvia; Stratmann, Frank; Henzing, Bas; Schlag, Patrick; Aalto, Pasi; Keskinen, Helmi; Sellegri, Karine; Ovadnevaite, Jurgita; Krüger, Mira; Jefferson, Anne; Whitehead, James; Carslaw, Ken; Yum, Seong Soo; Kristensson, Adam; Baltensperger, Urs; Gysel, Martin
2016-04-01
Cloud condensation nuclei (CCN) are aerosol particles with the ability to activate into droplets at a given super saturation and therefore influence the microphysical and optical properties of clouds. To predict cloud radiative properties understanding the spatial and temporal variability of CCN concentrations in different environments is important. However, currently, the effects of atmospheric particles on changes in cloud radiative forcing are still the largest contribution of uncertainty in climate forcing prediction (IPCC, 2013). Numerous intensive field campaigns have already explored detailed characteristics of CCN in many locations around the world. However, these rather short-term observations can generally not address seasonal or inter-annual variations and a comparison between campaign sites is difficult due to the higher influence of specific environmental circumstances on short-term measurements results. Here, we present results of more long-term CCN and aerosol number concentrations as well as size distribution data covering at least one full year between 2006 and 2014. The 12 locations include ACTRIS stations (http://www.actris.net/) in Europe, and further sites in North America, Brazil and Korea. The sites are located in different environments allowing for temporal and spatial characterization of CCN variability in different atmospheric regimes. Those include marine, remote-continental, boreal forest, rain forest, Arctic and monsoon-influenced environments, as well as boundary layer and free tropospheric conditions. The aerosol populations and their activation behavior show significant differences across the stations. While peak concentrations of CCN are observed in summer at the high altitude sites, in the Arctic the highest concentrations occur during the Haze period in spring. The rural-marine and rural-continental sites exhibit similar CCN concentration characteristics with a relatively flat annual cycle. At some stations, e.g. in the boreal environment, the annual cycle is more pronounced for higher SS. Geometric mean diameters of aerosol populations as well as the activation ratios on the basis of particles > 50 nm vary strongly among sites and throughout the seasons. Additionally, autocorrelation analysis is performed to investigate the persistence of variables over different timescales and to explore meaningful averaging periods for global modelling of CCN. In terms of CCN persistence, we find three different regimes: (1) CCN concentrations persist for a week or longer showing also seasonal patterns. (2) CCN concentrations persist for less than one week and there is little seasonal pattern. And (3) CCN concentrations are highly variable and do not persist longer than 2 days but show seasonal cycles. Several but not all sites show diurnal cycles. These different behaviors are influenced by environmental factors such as rainy seasons in the Amazon or Korea (monsoon) but also by anthropogenic pollution episodes such as during the Arctic Haze period.
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Federal Register 2010, 2011, 2012, 2013, 2014
2012-11-21
....onetcenter.org/ombclearance.html . DATES: Written comments must be submitted to the office listed in the... information in the O*NET Web sites including O*NET OnLine ( http://online.onetcenter.org ), My Next Move ( www.MyNextMove.gov ) and My Next Move for Veterans ( www.MyNextMove.org/vets ) O*NET Code Connector ( www...
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SPEED IS LIFE: WHY MACH and MANEUVERABILITY DOMINATE IN 2030
2016-06-01
www.ausairpower.net/ APA -S-400-Triumf.html. 6 Ibid. 7 Guy Plopsky & Fabrizio Bozzato, “The F-35 vs. The VHF Threat” The Diplomat, 21 Aug 2014, http...Carlo Kopp, “Sukhoi Flankers, The Shifting Balance of Regional Air Power,” Air Power Australia, 27 Jan 2014, http://www.ausairpower.net/ APA ...Australia, May 2008, http://www.ausairpower.net/ APA -DEW-HEL-Analysis.html#mozTocId345541. 82 Robin Hughes, “Raytheon Selected to Deliver Next
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The Strategic Importance of Defeating Underground Facilities
2012-03-20
German Submarine Pens: October 1942-April 1945,‖ December 7, 2010. http://www.usaaf.net/ ww2 /uboats/uboatspg6.htm (accessed 10 December 2011) 48...1945,‖ December 7, 2010. http://www.usaaf.net/ ww2 /uboats/uboatspg6.htm (accessed 10 December 2011). 51 Bradham, Hitler’s U-Boat Fortresses, 55. 52...The U.S. Army Air Forces in World War II, ―Bombing German Submarine Pens: October 1942-April 1945,‖ December 7, 2010. http://www.usaaf.net/ ww2
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2008-05-01
www.fbi.gov/congress/congress03/farnan051503.htm 63 Federal Bureau of Investigations. “Netting Cyber Criminals : Inside the Connecticut Computer Crimes Task...http://www.fbi.gov/cyberinvest/cyberhome.htm Federal Bureau of Investigations. “Netting Cyber Criminals : Inside the Connecticut Computer Crimes
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Validating Network Security Policies via Static Analysis of Router ACL Configuration
2006-12-01
this research effort. A. SOFTWARE IMPLEMENTATION The system software was created with Java, using NetBeans IDE 5.0 [12]. NetBeans is a free, open...11. P. Gupta, and N. McKeown (2001), Algorithms for Packet Classification, IEEE Network, vol. 15, issue 2, pp. 24-32. 12, NetBeans (2006), Welcome to... NetBeans , http://www.netbeans.org, last accessed on 25 November 2006. 13. IANA.org (2006), Port Numbers, http://www.iana.org/assignments/port
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Nonsurgical Strategies in Patients With NET Liver Metastases: A Protocol of Four Systematic Reviews.
Limani, Perparim; Tschuor, Christoph; Gort, Laura; Balmer, Bettina; Gu, Alexander; Ceresa, Christos; Raptis, Dimitri Aristotle; Lesurtel, Mickael; Puhan, Milo; Breitenstein, Stefan
2014-03-07
Patients diagnosed with neuroendocrine tumors (NETs) with hepatic metastases generally have a worse prognosis as compared with patients with nonmetastasized NETs. Due to tumor location and distant metastases, a surgical approach is often not possible and nonsurgical therapeutic strategies may apply. The aim of these systematic reviews is to evaluate the role of nonsurgical therapy options for patients with nonresectable liver metastases of NETs. An objective group of librarians will provide an electronic search strategy to examine the MEDLINE, EMBASE, and The Cochrane Library (Cochrane Database of Systematic Reviews, Database of Abstracts of Reviews of Effects, Cochrane Central Register of Controlled Trials [CENTRAL]) databases. There will be no restriction concerning language and publication date. The qualitative and quantitative synthesis of the systematic review will be conducted with randomized controlled trials (RCT), prospective, and retrospective comparative cohort, and case-control studies. Case series will be collected in a separate database and only used for descriptive purposes. This study is ongoing and presents a protocol of four systematic reviews to assess the role of nonsurgical treatment options in patients with neuroendocrine liver metastases. These systematic reviews, performed according to this protocol, will assess the value of noninvasive therapy options for patients with nonresectable liver metastases of NETs in combination with invasive techniques, such as percutaneous liver-directed techniques and local ablation techniques. International Prospective Register of Systematic Reviews (PROSPERO): CRD42012002657; http://www.metaxis.com/PROSPERO/full_doc.asp?RecordID=2657 (Archived by WebCite at http://www.webcitation.org/6NDlYi37O); CRD42012002658; http://www.metaxis.com/PROSPERO/full_doc.asp?RecordID=2658 (Archived by WebCite at http://www.webcitation.org/6NDlfWSuD); CRD42012002659; www.metaxis.com/PROSPERO/full_doc.asp?RecordID=2659 (Arichived by Webcite at http://www.webcitation.org/6NDlmWAFM); and CRD42012002660; http://www.metaxis.com/PROSPERO/full_doc.asp?RecordID=2660 (Archived by WebCite at http://www.webcitation.org/6NDmnylzp).
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76 FR 31884 - Reducing Regulatory Burden; Retrospective Review Plans Under E.O. 13563
Federal Register 2010, 2011, 2012, 2013, 2014
2011-06-02
... agencies have been posted on the White House Web site at: http://www.slideshare.net/whitehouse/hud-combined... effective and less burdensome in achieving HUD's mission to create strong, sustainable, inclusive... House Web site at: http://www.slideshare.net/whitehouse/hud-combined . The appendix to HUD's plan...
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The Intercontinental Ballistic Missile and Post Cold War Deterrence
2010-02-17
Bonnetain, Hugues and Philippe Mazzoni. " Histoire De Missiles...Le 1er GMS Du Plateau D’Albion." http://www.capcomespace.net/dossiers/espace_europeen...Mazzoni, " Histoire De Missiles...Le 1er GMS Du Plateau D’Albion," http://www.capcomespace.net/dossiers/espace_europeen/albion/; Ministère de la Défense
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Federal Register 2010, 2011, 2012, 2013, 2014
2012-08-30
...) proposed partnership structure and governance; (3) MDEpiNet as a framework for medical device postmarket.... 1061, Rockville, MD 20852 or electronic comments to http://www.regulations.gov . It is only necessary... transcript is available, it will be accessible at http://www.regulations.gov . It may be viewed at the...
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Tomopy is a Python toolbox to perform x-ray data processing, image reconstruction and data exchange tasks at synchrotron facilities. The dependencies of the software are currently as follows: -Python related python standard library (http://docs.python.org/2/library/) numpy (http://www.numpy.org/) scipy (http://scipy.org/) matplotlib (http://matplotlip.org/) sphinx (http://sphinx-doc.org) pil (http://www.pythonware.com/products/pil/) pyhdf (http://pysclint.sourceforge.net/pyhdf/) h5py (http://www.h5py.org) pywt (http://www.pybytes.com/pywavelets/) file.py (https://pyspec.svn.sourceforge.net/svnroot/pyspec/trunk/pyspec/ccd/files.py) -C/C++ related: gridec (anonymous?? C-code written back in 1997 that uses standard C library) fftw (http://www.fftw.org/) tomoRecon (multi-threaded C++ verion of gridrec. Author: Mark Rivers from APS. http://cars9.uchicago.edu/software/epics/tomoRecon.html) epics (http://www.aps.anl.gov/epics/)
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Federal Register 2010, 2011, 2012, 2013, 2014
2010-04-14
... Corridor. LACMTA operates the Metro transit system in Los Angeles County. The proposed project would..., 2009 and available on the LACMTA Web site ( http://www.metro.net/southbayextension ). Pursuant to 23... Analysis will be available at the meetings and are available on the LACMTA Web site ( http://www.metro.net...
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Measurement of stellar occultations
NASA Astrophysics Data System (ADS)
Eberle, Andreas
2008-09-01
Whenever an asteroid occults a star, we have the opportunity to study that asteroid in great detail. As frequently shown in the past, amateur astronomers1 have the necessary equipment to measure such events successfully2. Combined with the dense net of amateur observatories and online coordination tools3 for movable stations, they can create fine grids to detect even small bodies. The analysis of these events gives us the possibility to receive high precision astrometry data, to determine the asteroids size and shape (and therefore its albedo), and even to collect information on the star itself.4 While usually a set of several light curves is required to do so, a single recording5 of (10734) Wieck's occultation of HIP 22157 on 2008 Feb 08 was sufficient to retrieve the necessary data6. 1 Observation campaigns are organized by the International Occultation Timing Association (IOTA), http://www.iota-es.de/ 2 for results see e.g. euraster.net by E. Frappa, http://www.euraster.net/ 3 Occult Watcher by H. Pavlov, http://www.hristopavlov.net/OccultWatcher/OccultWatcher.html 4 see K. Miyashita's analysis of the observation of the occultation of TYC 1886-01206-1 by Kalliope and Linus, http://www005.upp.so-net.ne.jp/k miyash/occ02/kalliope/doublestar en.html 5 recording obtained by H. Michels, MPC Station Code 240 6 using Limovie by K. Miyashita
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Protecting the United States Against Information Warfare
2000-04-01
Information Systems Protection, An Invitation to a Dialogue, 2. ECommerce , "Business to Business to Consumer, Transaction Enabled Internet Solutions," n.d...available from <http://www.cplus.net/ ecommerce /estats.html>; Internet; accessed 7 February 2000. 7 Clinton, Defending America’s Cyberspace... ECommerce . "Business to Business to Consumer, Transaction Enabled Internet Solutions." n.d. Available from < http://www.cplus.net/ ecommerce
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VizieR Online Data Catalog: Orbital parameters of Kuiper Belt objects (Volk+, 2017)
NASA Astrophysics Data System (ADS)
Volk, K.; Malhotra, R.
2017-11-01
Our starting point is the list of minor planets in the outer solar system cataloged in the database of the Minor Planet Center (http://www.minorplanetcenter.net/iau/lists/t_centaurs.html and http://www.minorplanetcenter.net/iau/lists/t_tnos.html) as of 2016 October 20. The complete listing of our sample, including best-fit orbital parameters and sky locations, is provided in Table1. (1 data file).
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... for acetone. www.atsdr.cdc.gov/toxprofiles/TP.asp?id=5&tid=1 . Updated January 21, 2015. ... to the principles of the Health on the Net Foundation (www.hon.ch). The information provided herein ...
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A Business Case Study of Open Source Software
2001-07-01
LinuxPPC LinuxPPC www.linuxppc.com MandrakeSoft Linux -Mandrake www.linux-mandrake.com/ en / CLE Project CLE cle.linux.org.tw/CLE/e_index.shtml Red Hat... en Coyote Linux www2.vortech.net/coyte/coyte.htm MNIS www.mnis.fr Data-Portal www.data-portal.com Mr O’s Linux Emporium www.ouin.com DLX Linux www.wu...1998 1999 Year S h ip m en ts ( in m ill io n s) Source: IDC, 2000. Figure 11. Worldwide New Linux Shipments (Client and Server) 3.2.2 Market
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Popularity of Russian information sources of medical education.
Vasilyeva, Irina V; Arseniev, Sergey B
2014-01-01
The aim of the present study is to analyze the popularity of information sources of medical educational sites <webmedinfo.ru>, medical information portal <meduniver.com>, medical portal for students <6years.net>, electronic library of medical literature <booksmed.com>, <medliter.ru> and <medbook.net.ru>. Three sites (<www.webmedinfo.ru>, <meduniver.com> and <6years.net>) provide sources of medical literature, educational videos, medical histories, medical papers and medical popular literature. And three other sites (<www.booksmed.com>, <www.medliter.ru> and <www.medbook.net.ru>) provide sources for electronic medical books on various subjects. Using on-line programs Alexa and Cy-pr we have analyzed the website's rating and identified the main data and time-varying data of the sites. Calculated Alexa Rank rating was determined for each site. Our study has shown that the most popular information sources of medical education among the six studied sites for Russian users is <meduniver.com>; the site <booksmed.com> is at the second place referring to the Alexa Rank rating and the site <webmedinfo.ru> is at the second place referring to the citation index in Yandex. The most popular medical site of electronic medical books is <booksmed.com>.
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Aerosol classification using EARLINET measurements for an intensive observational period
NASA Astrophysics Data System (ADS)
Papagiannopoulos, Nikolaos; Mona, Lucia; Pappalardo, Gelsomina
2016-04-01
ACTRIS (Aerosols, Clouds and Trace gases Research Infrastructure Network) organized an intensive observation period during summer 2012. This campaign aimed at the provision of advanced observations of physical and chemical aerosol properties, at the delivery of information about the 3D distribution of European atmospheric aerosols, and at the monitoring of Saharan dust intrusions events. EARLINET (European Aerosol Research Lidar Network) participated in the ACTRIS campaign through the addition of measurements according to the EARLINET schedule as well as daily lidar-profiling measurements around sunset by 11 selected lidar stations for the period from 8 June - 17 July. EARLINET observations during this almost two-month period are used to characterize the optical properties and vertical distribution of long-range transported aerosol over the broader area of Mediterranean basin. The lidar measurements of aerosol intensive parameters (lidar ratio, depolarization, Angstrom exponents) are shown to vary with location and aerosol type. A methodology based on EARLINET observations of frequently observed aerosol types is used to classify aerosols into seven separate types. The summertime Mediterranean basin is prone to African dust aerosols. Two major dust events were studied. The first episode occurred from the 18 to 21 of the June and the second one lasted from 28 June to 6 July. The lidar ratio within the dust layer was found to be wavelength independent with mean values of 58±14 sr at 355 nm and 57±11 sr at 532 nm. For the particle linear depolarization ratio, mean values of 0.27±0.04 at 532 nm have been found. Acknowledgements. The financial support for EARLINET in the ACTRIS Research Infrastructure Project by the European Union's Horizon 2020 research and innovation programme under grant agreement no. 654169 and previously under grant agreement no. 262254 in the Seventh Framework Programme (FP7/2007-2013) is gratefully acknowledged.
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Constraining lidar stand-alone retrievals with lunar photometry measurements
NASA Astrophysics Data System (ADS)
Ortiz-Amezcua, Pablo; Luis Guerrero-Rascado, Juan; Antonio Benavent-Oltra, Jose; Román, Roberto; Böckmann, Christine; Alados-Arboledas, Lucas
2018-04-01
This study combines atmospheric optical information measured with lidar and nocturnal photometers in order to find configurations that allow for the retrieval of particle microphysical properties without "3+2" lidar setups. It has been carried out using data measured at the EARLINET Granada station during the experimental campaign SLOPE in the framework of ACTRIS-2 project.
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Stump, Reto; Haueis, Silvia; Kalt, Nicola; Tschuor, Christoph; Limani, Përparim; Raptis, Dimitri A; Puhan, Milo A; Breitenstein, Stefan
2013-12-23
Hepatic metastases of neuroendocrine tumors (NETs) are considered a major prognostic factor associated with significantly reduced survival compared to patients without liver metastases. Several surgical and nonsurgical strategies are present to treat resectable and nonresectable liver metastases, some of which have the potential to cure liver mestatases. The aims of the four systematic reviews presented in the paper are to determine the effectiveness of liver resection versus nonsurgical treatment of patients with NET liver metastases, to investigate the impact of neoadjuvant and adjuvant treatment options on the tumor-free survival, to assess the role of liver transplantation in patients presenting with unresectable bilateral hepatic metastases, and to evaluate the role of primary tumor resection in presence of unresectable liver metastases. Literature search was performed on Medical Literature Analysis and Retrieval System Online, Excerpta Medica Database, and the Cochrane Library (Cochrane Database of Systematic Reviews, Database of Abstracts of Reviews of Effects, and Cochrane Central Register of Controlled Trials). No language restrictions were applied. Randomized controlled trials, prospective and retrospective comparative cohort studies, and case-control studies will be used for the qualitative and quantitative synthesis of the systematic reviews. Case series will be only included in a separate database for descriptive purposes. This study is ongoing and presents a protocol system of four systematic reviews that will assist in determining the effectiveness of liver resection versus nonsurgical treatment of patients with NET liver metastases. This study is also assumed to investigate the impact of neoadjuvant and adjuvant treatment options on the tumor-free survival, the role of liver transplantation, and the relevance of primary tumor resection in presence of unresectable liver metastasis. The systematic reviews will show the current evidence based on the effectiveness of surgical strategies in patients with NET liver metastases and serve as basis for clinical practice guidelines. The systematic reviews have been prospectively registered with the International Prospective Register of Systematic Reviews: liver resection (CRD42012002652); http://www.crd.york.ac.uk/prospero/display_record.asp?ID=CRD42012002652 (Archived by WebCite at http://www.webcitation.org/6LQUqMnqL,). neoadjuvant and adjuvant treatment strategies (CRD42012002656); http://www.crd.york.ac.uk/prospero/display_record.asp?ID=CRD42012002656 (Archived by WebCite at http://www.webcitation.org/6LQVvEHuf). liver transplantation (CRD42012002655); http://www.crd.york.ac.uk/prospero/display_record.asp?ID=CRD42012002655 (Archived by WebCite at http://www.webcitation.org/6LQW7WFo3,). resection of the locoregional primary NET (CRD42012002654); http://www.crd.york.ac.uk/prospero/display_record.asp?ID=CRD42012002654 (Archived by WebCite at http://www.webcitation.org/6LQWEIuGe).
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Cancer Causes: Popular Myths about the Causes of Cancer
... myths/antiperspirants-fact-sheet. Accessed Nov. 1, 2016. Science fact or science fiction? – 9 common cancer myths. Cancer.Net. http://www.cancer.net/blog/2015-03/science-fact-or-science-fiction-%E2%80%93-9-common- ...
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SGDB: a database of synthetic genes re-designed for optimizing protein over-expression.
Wu, Gang; Zheng, Yuanpu; Qureshi, Imran; Zin, Htar Thant; Beck, Tyler; Bulka, Blazej; Freeland, Stephen J
2007-01-01
Here we present the Synthetic Gene Database (SGDB): a relational database that houses sequences and associated experimental information on synthetic (artificially engineered) genes from all peer-reviewed studies published to date. At present, the database comprises information from more than 200 published experiments. This resource not only provides reference material to guide experimentalists in designing new genes that improve protein expression, but also offers a dataset for analysis by bioinformaticians who seek to test ideas regarding the underlying factors that influence gene expression. The SGDB was built under MySQL database management system. We also offer an XML schema for standardized data description of synthetic genes. Users can access the database at http://www.evolvingcode.net/codon/sgdb/index.php, or batch downloads all information through XML files. Moreover, users may visually compare the coding sequences of a synthetic gene and its natural counterpart with an integrated web tool at http://www.evolvingcode.net/codon/sgdb/aligner.php, and discuss questions, findings and related information on an associated e-forum at http://www.evolvingcode.net/forum/viewforum.php?f=27.
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CancerNet redistribution via WWW.
Quade, G; Püschel, N; Far, F
1996-01-01
CancerNet from the National Cancer Institute contains nearly 500 ASCII-files, updated monthly, with up-to-date information about cancer and the "Golden Standard" in tumor therapy. Perl scripts are used to convert these files to HTML-documents. A complex algorithm, using regular expression matching and extensive exception handling, detects headlines, listings and other constructs of the original ASCII-text and converts them into their HTML-counterparts. A table of contents is also created during the process. The resulting files are indexed for full-text search via WAIS. Building the complete CancerNet WWW redistribution takes less than two hours with a minimum of manual work. For 26,000 requests of information from our service per month the average costs for the worldwide delivery of one document is about 19 cents.
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Federal Register 2010, 2011, 2012, 2013, 2014
2011-01-10
... site at http://www.factorshares.net or a Fund's periodic reports on Form 10-Q and/ or Form 10-K as... leveraged basis, each Fund will seek to rebalance daily both its long and short positions around the net asset value (``NAV'') Calculation Time (as described below under ``Net Asset Value''). The purpose of...
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GeosciNET: Building a Global Geoinformatics Partnership
NASA Astrophysics Data System (ADS)
Snyder, W. S.; Lehnert, K. A.; Ito, E.; Harms, U.; Klump, J.
2008-12-01
GeosciNET is a collaboration of several existing geoinformatics efforts organized to provide a more effective data system for geoscience projects. Current members are: CoreWall (www.corewall.org), Geoinformatics for Geochemistry (GfG; www.geoinfogeochem.org), System for Earth Sample Registration (SESAR; www.geosamples.org ), GeoStrat SYS (www.geostratsys.org (formerly: PaleoStrat, www.paleostrat.org)), and the International Continental Drilling Program (ICDP; www.icdp-online.org). GeosciNET's basic goal is to advance coordination, complementarity, and interoperability, and minimize duplication of efforts among the involved partner systems in order to streamline the development and operation of geoinformatics efforts. We believe that by advancing the development and data holdings of its member groups, the overall value of each site will be significantly enhanced and better meet the needs of the users. With the existing membership, GeosciNET can offer a comprehensive, integrated system for data acquisition, dissemination, archiving, visualization, integration, and analysis. The system will enable a single researcher or a group of collaborators to keep track of, visualize, and digitally archive any type of sample- or stratigraphic-based data produced from drill holes, dredges, measured stratigraphic sections, the field, or the laboratory. The challenge is to build a linked system that provides users a library of research data as well as tools to input, discover, access, integrate, manipulate, analyze, and model interdisciplinary data - all without corrupting the original data and insuring that the data are attributed to the originator at all times. Science runs on data, but despite the importance of data (legacy or otherwise), there are currently few convenient mechanisms that enable users to easily input their data into databases. While some efforts such as GfG databases, PetDB and SedDB have worked hard to compile such data, only users' active participation can capture the major part of critical legacy data, and insure that new data enter the digital stream as they are generated. GeosciNET wants to lower the barriers so users can take advantage of geoinformatics resources and embrace its promise as the platform for doing the science of the future. Once these benefits are understood by the user community, the obstacles that currently exist in building a larger geoinformatics system will start to erode. User participation requires the proper tools such as translators that can recognize tags and parse the data accordingly, and incentives such as tools for visualization, synthesis and analysis, and digital collaboration space. A major focus for GeosciNET is to support individual researchers and projects that do not have their own dedicated data management and education and outreach programs. One of the greatest challenges for geoinformatics lies in being perceived as a friendly resource by its users where they can easily link their observations and analyses and integrate them with other data. GeosciNET will be experimenting with mechanisms to accomplish these goals.
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American Jihadist Terrorism: Combating a Complex Threat
2010-09-20
www.nytimes.com/2010/07/30/us/30fbi.html. 177 Richard Esposito, “Terror Raids at JFK Airport Net American Alleged Terror Plotters Headed for Somalia...abcnews.com, June 6, 2010, http://abcnews.go.com/Blotter/terror-raids- jfk - airport -net-alleged-terror-plotters/story?id= 10839045. 178 U.S. v. Mohamed... Airport Net American Alleged Terror Plotters Headed for Somalia,” ABC News, June 6, 2010, http://abcnews.go.com/Blotter/terror-raids- jfk - airport -net
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Antipodean Theory for Educational Research
ERIC Educational Resources Information Center
Stewart, Georgina; Arndt, Sonja; Besley, Tina; Devine, Nesta; Forster, Daniella J.; Gibbons, Andrew; Grierson, Elizabeth; Jackson, Liz; Jandric, Petar; Locke, Kirsten; Peters, Michael A.; Tesar, Marek
2017-01-01
This article results from a collaborative investigation into Antipodean theory in education by members of the Editors' Collective (www.editorscollective.org.nz). The Prologue contains a brief personal account of the South Project (www.southernperspectives.net), as an example of the contemporary projects and activities falling under the banner of…
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Improved methods for predicting peptide binding affinity to MHC class II molecules.
Jensen, Kamilla Kjaergaard; Andreatta, Massimo; Marcatili, Paolo; Buus, Søren; Greenbaum, Jason A; Yan, Zhen; Sette, Alessandro; Peters, Bjoern; Nielsen, Morten
2018-07-01
Major histocompatibility complex class II (MHC-II) molecules are expressed on the surface of professional antigen-presenting cells where they display peptides to T helper cells, which orchestrate the onset and outcome of many host immune responses. Understanding which peptides will be presented by the MHC-II molecule is therefore important for understanding the activation of T helper cells and can be used to identify T-cell epitopes. We here present updated versions of two MHC-II-peptide binding affinity prediction methods, NetMHCII and NetMHCIIpan. These were constructed using an extended data set of quantitative MHC-peptide binding affinity data obtained from the Immune Epitope Database covering HLA-DR, HLA-DQ, HLA-DP and H-2 mouse molecules. We show that training with this extended data set improved the performance for peptide binding predictions for both methods. Both methods are publicly available at www.cbs.dtu.dk/services/NetMHCII-2.3 and www.cbs.dtu.dk/services/NetMHCIIpan-3.2. © 2018 John Wiley & Sons Ltd.
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ERIC Educational Resources Information Center
Lobodzinski, Suave, Ed.; Tomek, Ivan, Ed.
The 1997 WebNet conference addressed research, new developments, and experiences related to the Internet and intranets. The 257 contributions of WebNet 97 contained in this proceedings comprise the full and short papers accepted for presentation at the conference. Included are positions papers by leading experts in the field; descriptions of ideas…
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Aerosol variation over Continental Europe from 1980 to 2015 Using ALAD Aerosol Retrievals
NASA Astrophysics Data System (ADS)
Che, Yahui; Xue, Yong; Mei, Linlu; Guang, Jie; She, Lu
2017-04-01
The Advanced Very High Resolution Radiometer (AVHRR) on-board National Oceanic and Atmospheric Administration (NOAA) series satellites has been used to observe the Earth and is the only spaceborne instrument which can provide users continuous long time series global coverage for more than 35 years since 1979. The initial purpose of AVHRR is for cloud detection and monitoring thermal emission of the Earth so that it lacks visible channels (only 0.64μm) and spaceborne which is unignorably unfavourable to its applications in aerosol retrieving over bright and inhomogeneous surface. Using AVHRR data, an Algorithm for the retrieval over Land of the Aerosol optical Depth (ALAD) was developed data which has great potential to be used to retrieve long time series aerosol globally from 1979 to now. The core of ALAD is to assume that the contribution of aerosol at 3.75μm wavelength to reflectance at top of the atmosphere (TOA) is negligible. At this basis, one stable and firm relationship between surface reflectance at 0.64μm and 3.75μm will be found by regression analysis at different land types after separating reflectance from radiance at 3.75μm. Then, an atmospheric transfer model is applied to calculate AOD at 0.64μm. In this study, we recalibrate AVHRR Global Area Coverage (GAC) data and then apply ALAD to calculate AOD over continental Europe (30°N to 80°N, 170°W to 40°E) to investigate aerosol changes and possible reason in past 35 years from 1981 to 2015. The retrieved AOD has been validated with ground-based data from Aerosols, Clouds, and Trace gases Research InfraStructure (ACTRIS) and AErosol RObotic NETwork (AERONET). The correlation of ALAD AOD with AERONET and ACTRIS is 0.77 and 0.66, respectively. Further, we also make long time series comparison of monthly averaged ALAD AOD with AERONET, ACTRIS and MODIS, showing that ALAD underestimate AOD a little. Finally, we find that the AOD over most areas in Continental Europe are less than 0.3, even less than 0.1, changing little without any obvious increase.
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Danek, T; Protasiuk, R; Mańkowski, M; Brutkiewicz, A; Trześniewski, R; Podlińska, I; Milecka, A; Jonas, M; Danielewicz, R; Czerwiński, J
2016-06-01
In 2010 the formation of the Polish Hospitals Network of Organ Donation Coordinators, originated by Poltransplant, began. One of the goals of this project is to report all deaths in hospital ICUs in which a coordinator is posted. The aim of this strategy is to monitor donation potential, following the recruitment process of potential donors and indicating stages of that process that may be improved to increase effective recruitment. Until the end of 2014 all data were forwarded to Poltransplant as Excel files, but since January 1, 2015, reporting and data collection have been are performed using web tool www.koordynator.net. The aim of the paper is to present the essentials in functioning principles, structure, and usage of the www.koordynator.net system, its technical construction, and to display good practices (know-how) tested by 1 country, for countries such as Poland, that contend with organ insufficiency. The application www.koordynator.net allows for remote addition of individual records with information about deceased patients in hospital ICUs, the forwarding of data about potential and actual organ donors, the generation of complete reports about deceased patients in each hospital monthly, and the introduction of historical data. Introduction of a potential donation monitoring system in 209 hospitals with transplant coordinators increases the number of identified potential and effective actual donors due to self-assessment analysis. Eventually, the www.koordynator.net reporting system allowed for external evaluation by coordinators from other hospitals, regional coordinators, and Poltransplant. The system is a modern tool that improves and increases the quality system in the organ donation field (quality assurance program). Copyright © 2016 Elsevier Inc. All rights reserved.
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Automated Structure Annotation and Curation for MassBank: Potential and Pitfalls
The European MassBank server (www.massbank.eu) was founded in 2012 by the NORMAN Network (www.norman-network.net) to provide open access to mass spectra of substances of environmental interest contributed by NORMAN members. The automated workflow RMassBank was developed as a part...
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Perspectives or Telemedicine Development in Ukraine
2001-05-01
National Register of the individuals who are suffering from consequences of the Chernobyl disaster. This Register monitors the health of more than 700,000...integrate the Chernobyl Register net into ’UkrMedNet’ and to create a WWW server containing the Chernobyl Register information. To provide access to the
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X3D-Earth: Full Globe Coverage Utilizing Multiple Dataset
2010-09-01
DtedNvtProcessor Class ..................................................128 Figure 63. Subversion Checkout in Netbeans ...to the Ant build.xml file within a NetBeans Project: <target name=“moveToHamming” depends=““> <scp todir=“user@hamming.uc.nps.edu:/work/user/DTED...This task was generated using the NetBeans IDE (can be downloaded at www.netbeans.org). The task was then executed within NetBeans . This type of
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Gender and Power Issues in On-Line Learning Environments.
ERIC Educational Resources Information Center
Machanic, Mindy
The Internet (Net) and World Wide Web (WWW) have developed a variety of cultures and communities. Although most early users of the Net (mostly males) were well-intentioned and well-mannered, their social conventions (some blatantly sexist, others in the nature of macho posturing) have continued in many online chat rooms and virtual gaming…
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Raising the Degree of Service-Orientation of a SOA-based Software System: A Case Study
2009-12-01
protocols, as well as executable processes that can be compiled into runtime scripts” [2] The Business Process Modeling Notation ( BPMN ) provides a...Notation ( BPMN ) 1.2. Jan. 2009. URL: http://www.omg.org/spec/ BPMN /1.2/ [25] .NET Framework Developer Center. .NET Remoting Overview. 2003. URL: http
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Lundegaard, Claus; Lund, Ole; Nielsen, Morten
2008-06-01
Several accurate prediction systems have been developed for prediction of class I major histocompatibility complex (MHC):peptide binding. Most of these are trained on binding affinity data of primarily 9mer peptides. Here, we show how prediction methods trained on 9mer data can be used for accurate binding affinity prediction of peptides of length 8, 10 and 11. The method gives the opportunity to predict peptides with a different length than nine for MHC alleles where no such peptides have been measured. As validation, the performance of this approach is compared to predictors trained on peptides of the peptide length in question. In this validation, the approximation method has an accuracy that is comparable to or better than methods trained on a peptide length identical to the predicted peptides. The algorithm has been implemented in the web-accessible servers NetMHC-3.0: http://www.cbs.dtu.dk/services/NetMHC-3.0, and NetMHCpan-1.1: http://www.cbs.dtu.dk/services/NetMHCpan-1.1
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Federal Register 2010, 2011, 2012, 2013, 2014
2010-02-04
...: //[email protected]net . i. FERC Contact: Any questions on this notice should be addressed to... filings, please go to the Commission's Web site located at http://www.ferc.gov .filing-comments.asp... access the document. You may also register online at http://www.ferc.gov/docs-filing/esubscription.asp to...
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Genetic and Environmental Pathways in Type 1 Diabetes Complications
2010-09-26
setting? In the event that the project identifies a set of strongly predictive biomarkers an appropriate next step would be to approach TrialNet (see...http://www.diabetestrialnet.org). The TrialNet organization is a multi center study with the goal of identifying subjects for T1D prevention and...intervention trials. Children’s Hospital of Pittsburgh (CHP) is already acting as a clinical center for the TrialNet natural history study (Mahon et al
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Does Home Internet Use Influence the Academic Performance of Low-Income Children?
ERIC Educational Resources Information Center
Jackson, Linda A.; von Eye, Alexander; Biocca, Frank A.; Barbatsis, Gretchen; Zhao, Yong; Fitzgerald, Hiram E.
2006-01-01
HomeNetToo is a longitudinal field study designed to examine the antecedents and consequences of home Internet use in low-income families http://www.HomeNetToo.org). The study was done between December 2000 and June 2002. Among the consequences considered was children's academic performance. Participants were 140 children, mostly African…
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2014-09-01
The free, open-source Integrated Development Environment (IDE) NetBeans [11] was used in the creation of the Graphical User Interface (GUI) for the tool...Oracle Corporation (2013) NetBeans IDE 7.4, http://www.netbeans.org. 12. O’Shea, K., Pong, P. & Bulluss, G. (2012) Fit-for-Purpose Visualisation of
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Federal Register 2010, 2011, 2012, 2013, 2014
2010-03-05
..., ME 04930; telephone: (207) 924-0180; e-mail: http: //[email protected]net . i. FERC Contact... site at http://www.ferc.gov .filing- comments.asp. Please include the docket number (DI10-7-000) on any... document. You may also register online at http://www.ferc.gov/docs-filing/esubscription.asp to be notified...
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Federal Register 2010, 2011, 2012, 2013, 2014
2012-12-26
... megawatt and 780 feet of net head; (6) a 50-foot-long tailrace connecting the powerhouse with the Little... on the Commission's Web site http://www.ferc.gov/docs-filing/efiling.asp . Commenters can submit...://www.ferc.gov/docs-filing/ecomment.asp . You must include your name and contact information at the end...
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Federal Register 2010, 2011, 2012, 2013, 2014
2012-05-11
... unit rated at 5 megawatts or less at 150 feet of net head; (3) a tailrace channel discharging from the... instructions on the Commission's Web site http://www.ferc.gov/docs-filing/efiling.asp . Commenters can submit...://www.ferc.gov/docs-filing/ecomment.asp . You must include your name and contact information at the end...
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Federal Register 2010, 2011, 2012, 2013, 2014
2010-11-04
....5 Goose Creek Road, South Fork, CO 81154; (970) 925-6071; [email protected]net . j. FERC Contact...). Register online at http://www.ferc.gov/docs-filing/esubscription.asp to be notified via e-mail of new... on the Commission's Web site ( http://www.ferc.gov/docs-filing/ferconline.asp ) under the ``e- Filing...
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Federal Register 2010, 2011, 2012, 2013, 2014
2010-11-22
... on the Commission's Web site http://www.ferc.gov/docs-filing/efiling.asp . Commenters can submit...://www.ferc.gov/docs-filing/ecomment.asp . You must include your name and contact information at the end... cubic feet per second and a net head of 32 feet, directly connected to a horizontal generator unit with...
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Federal Register 2010, 2011, 2012, 2013, 2014
2011-11-02
... on the Commission's web site at http://www.ferc.gov/docs-filing/efiling.asp . If unable to be filed... http://www.ferc.gov/docs-filing/ecomment.asp . You must include your name and contact information at... account for differences in net head resulting from operations under the new license for the project. l...
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Privacy-Enhancing Technologies for the Internet
1997-01-01
http://www.communities.com/paper/swamp.html 7 David Chaum , ``Untraceable Electronic Mail, Return addresses, and Digital Pseudonyms,’’ Communications of...the ACM, February 1981, vol. 24 no. 2. http://www.eskimo.com/~weidai/mix-net.txt 8 David Chaum , ``Blind Signatures for Untraceable Payments...Privacy-enhancing technologies for the Internet Ian Goldberg David Wagner Eric Brewer University of California, Berkeley {iang,daw,brewer
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CHINA.COM The Effect of Globalization on Chinese Decision- Making
2004-05-18
for Democracy,” (New York: Routledge, 1999), 12. 42 Ibid., 18. 43 Ibid., 19. 44 Leslie David Simon , “The Net: Power and Policy in the 21st Century...2003, <http://www.ojr.org/ojr/world_reports/1068766903.php> [10 May 2004]. 52 Leslie David Simon , “The Net: Power and Policy in the 21st Century
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Deterring Malicious Behavior in Cyberspace
2015-01-01
Malicious Behavior in Cyberspace Strategic Studies Quarterly ♦ Spring 2015 [ 79 ] 8. Chris Pepper, ed., Defending against Denial of Service Attacks...Jackson Higgins , “Chinese Cyberespionage Tool Updated for Traditional Cyber- crime,” Dark Reading, 27 November 2012, http://www.darkreading.com/attacks...content /uploads/sites/43/vlpdfs/kaspersky-the-net-traveler-part1-final.pdf. 13. Kelly Jackson Higgins , “ ‘NetTraveler’ Cyberespionage Campaign
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... or abdominal pain. Your hernia becomes red, purple, dark, or discolored. Call your provider if you ... to the principles of the Health on the Net Foundation (www.hon.ch). The information provided herein ...
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ATHLI16: the ATHens Lidar Intercomparison campaign
NASA Astrophysics Data System (ADS)
Amodeo, Aldo; D'Amico, Giuseppe; Giunta, Aldo; Papagiannopoulos, Nikolaos; Papayannis, Alex; Argyrouli, Athina; Mylonaki, Maria; Tsaknakis, Georgios; Kokkalis, Panos; Soupiona, Ourania; Tzanis, Chris
2018-04-01
The results of the ATHLI16 (ATHens Lidar Intercomparison) campaign, held in Athens from 26/09 to 07/10 2016 are presented. The campaign was performed within the Lidar Calibration Centre activities (EU H2020 ACTRIS-2 project) to assess the performance of the EOLE lidar system (NTUA, Athens, Greece), operating within EARLINET, by comparing against the EARLINET reference lidar system MUSA (CNR-IMAA, Potenza, Italy). For both lidars only products retrieved by the EARLINET Single Calculus Chain have been compared.
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Regional Disease Vector Ecology Profile: The Koreas
2015-01-01
Lymantriidae): The larvae, pupae and adults of E. flava are covered with hairs that cause dermatitis (papulourticarial reaction) when they contact ...Information Services Division at (301) 295-8310/7476, DSN 295- 8310/7476 or the AFPMB Webmaster, http://www.afpmb.org/ contact . Current Information: Current...timely manner. For insect repellents, pesticides, pesticide application equipment, PPMs (bed nets, head nets, etc.) and respirators contact the DLA
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... dystrophies. In: Tasman W, Jaeger EA, eds. Duane's Foundations of Clinical Ophthalmology . 2013 ed. Philadelphia, PA: Lippincott ... the principles of the Health on the Net Foundation (www.hon.ch). The information provided herein should ...
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... MO: Elsevier Saunders; 2016:chap 10. Hupp JR. Principles of management of impacted teeth. In: Hupp JR, ... member of Hi-Ethics and subscribes to the principles of the Health on the Net Foundation (www. ...
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Text mining and expert curation to develop a database on psychiatric diseases and their genes
Gutiérrez-Sacristán, Alba; Bravo, Àlex; Portero-Tresserra, Marta; Valverde, Olga; Armario, Antonio; Blanco-Gandía, M.C.; Farré, Adriana; Fernández-Ibarrondo, Lierni; Fonseca, Francina; Giraldo, Jesús; Leis, Angela; Mané, Anna; Mayer, M.A.; Montagud-Romero, Sandra; Nadal, Roser; Ortiz, Jordi; Pavon, Francisco Javier; Perez, Ezequiel Jesús; Rodríguez-Arias, Marta; Serrano, Antonia; Torrens, Marta; Warnault, Vincent; Sanz, Ferran
2017-01-01
Abstract Psychiatric disorders constitute one of the main causes of disability worldwide. During the past years, considerable research has been conducted on the genetic architecture of such diseases, although little understanding of their etiology has been achieved. The difficulty to access up-to-date, relevant genotype-phenotype information has hampered the application of this wealth of knowledge to translational research and clinical practice in order to improve diagnosis and treatment of psychiatric patients. PsyGeNET (http://www.psygenet.org/) has been developed with the aim of supporting research on the genetic architecture of psychiatric diseases, by providing integrated and structured accessibility to their genotype–phenotype association data, together with analysis and visualization tools. In this article, we describe the protocol developed for the sustainable update of this knowledge resource. It includes the recruitment of a team of domain experts in order to perform the curation of the data extracted by text mining. Annotation guidelines and a web-based annotation tool were developed to support the curators’ tasks. A curation workflow was designed including a pilot phase and two rounds of curation and analysis phases. Negative evidence from the literature on gene–disease associations (GDAs) was taken into account in the curation process. We report the results of the application of this workflow to the curation of GDAs for PsyGeNET, including the analysis of the inter-annotator agreement and suggest this model as a suitable approach for the sustainable development and update of knowledge resources. Database URL: http://www.psygenet.org PsyGeNET corpus: http://www.psygenet.org/ds/PsyGeNET/results/psygenetCorpus.tar PMID:29220439
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NASA Astrophysics Data System (ADS)
Ozorovich, Yuri; Linkin, Vacheslav; Kosov, Alexandr; Fournier-Sicre, Alain; Klimov, Stanislav; Novikov, Denis; Ivanov, Anton; Skulachev, Dmitriy; Menshenin, Yaroslav
2016-04-01
This paper presents a new conceptual and methodological approach for geophysical survey of the planetary geoelectrical markers and oreols of the subsurface liquid ocean on the surface ice moons on the base "conceptual design phase" of the future space missions on the ice moons. At the design stage of such projects is considered the use of various space instruments and tools for the full the complex geophysical studies of the manifestations and planetary processes of the subsurface liquid ocean on the surface ice moons. The existence of various forms of the cryolithozone on terrestrial planets and their moons: advanced Martian permafrost zone in the form of existing of the frozen polar caps, subsurface frozen horizons, geological markers and oreols of the martian ancient (relict) ocean, subsurface oceans of Jupiter's and Saturn's moons-Europe and Enceladus, with the advanced form of permafrost freezes planetary caps, it allows to develop a common methodological basis and operational geophysical instruments (tools) for the future space program and planning space missions on these unique objects of the solar system, specialized for specific scientific problems of planetary missions. Geophysical practices and methodological principles, used in 1985-2015 by aurthors [ 1-5 ], respectively, as an example of the comprehensive geophysical experiment MARSES to study of the Martian permafrost zone and the martian ancient (relict) ocean, creating the preconditions for complex experimental setting and geo-physical monitoring of operational satellites of Jupiter and Saturn- Europe and Enceladus. This range of different planetary (like) planets with its geological history and prehistory of the common planetology formation processes of the planets formation and to define the role of a liquid ocean under the ice as a climate indicator of such planets, which is extremely important for the future construction of the geological and climatic history of the Earth. Main publications: [1]https://www.researchgate.net/publication/282151921_JUPITER%27S_MOON_EUROPA_PLANETARY_GEOELECTRICAL_MARKER_AND_OREOLS_UNDER_ICE_SUBSUEFACE_OCEAN_ON_THE_SURFACE_OF_THE_JUPITER%27S_MOON_EUROPA?ev=prf_pub [2]https://www.researchgate.net/publication/281270655_YUPITERS_MOON_EUROPA_PLANETARY_GEOELECTRICAL_MARKERS_AND_OREOPLS_OF_THE_LIQUID_OCEAN_UNDER_THE_ICE_ON_THE_SURFACE_OF_THE_YUPITERS_MOON_EUROPE [3] https://www.researchgate.net/publication/276005128_Science-technology_aspects_and_opportunities_of_em_sounding_frozen_%28_permafrost%29_soil [4]https://www.researchgate.net/publication/275638508_Cryolitozone_of_Mars_-_as_the_climatic_indicator_of_the_Martian_relict_ocean [5]https://www.researchgate.net/publication/275266762_Microwave_remote_sensing_of_Martian_cryolitozone
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... to a child of any race, religion, or economic status. Other types of child abuse are: Neglect ... member of Hi-Ethics and subscribes to the principles of the Health on the Net Foundation (www. ...
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... In: Kryger M, Roth T, Dement WC, eds. Principles and Practice of Sleep Medicine . 6th ed. Philadelphia, ... member of Hi-Ethics and subscribes to the principles of the Health on the Net Foundation (www. ...
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... wound References Simon BC, Hern HG. Wound management principles. In: Marx JA, Hockberger RS, Walls RM, et ... member of Hi-Ethics and subscribes to the principles of the Health on the Net Foundation (www. ...
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... coldness in your foot, or your toes look dark. You cannot move your toes. You have increased ... to the principles of the Health on the Net Foundation (www.hon.ch). The information provided herein ...
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... symptoms are often easy to manage and include: Dark urine Tiredness Loss of appetite Fever Nausea and ... to the principles of the Health on the Net Foundation (www.hon.ch). The information provided herein ...
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... right upper abdomen Clay-colored or pale stools Dark urine Tiredness Fever Yellow skin and eyes ( jaundice ) ... to the principles of the Health on the Net Foundation (www.hon.ch). The information provided herein ...
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[Quality of health information about epilepsy on the Internet: Evaluation of French websites].
Auvin, S; Dupont, S
2013-03-01
The Internet is now the single largest source of health information and is used by many patients who are affected by epilepsy and their families. To assess the quality of information provided by French website on the different forms of epilepsy and their treatment, we used search engines (French pages from Bing, Google and Yahoo) to look for information using the French equivalent of three keywords epilepsy (Épilepsie); epilepsy treatment (Épilepsie traitement) and seizure (Convulsions). The websites were evaluated for content quality by using an adaptation of the validated DISCERN rating instrument. Each website was evaluated by three investigators (a naive observer, a pediatric neurologist and a neurologist). Most of the information on epilepsy and its treatment were from community websites. We found six French websites which were scored higher than half of the maximal value of our scoring system (≥27.5/55): www.passeportsante.net; fr.wikipedia.org; www.fondation-epilepsie.fr; www.epilepsie-france.fr; www.doctissimo.fr; www.caducee.net. This study provides a list of French websites that have been evaluated for the quality of their information. We did not observe any correlation between the quality of the information and priority on search engine listings. Websites sponsored by patients associations and by institutions should update their content more frequently or work on their search engine indexation to appear higher on search engine listings. Copyright © 2012. Published by Elsevier Masson SAS.
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MedlinePlus Videos and Cool Tools
... to achieve this important distinction for online health information and services. Learn more about A.D.A. ... on the Net Foundation (www.hon.ch). The information provided herein should not be used during any ...
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... MF, eds. Creasy and Resnik's Maternal-Fetal Medicine: Principles and Practice . 7th ed. Philadelphia, PA: Elsevier Saunders; ... member of Hi-Ethics and subscribes to the principles of the Health on the Net Foundation (www. ...
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... thinning medicine does not work. Normal Results Normal value ranges may vary slightly among different laboratories. Talk ... to the principles of the Health on the Net Foundation (www.hon.ch). The information provided herein ...
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Understanding your cancer prognosis
... about: Treatment Palliative care Personal matters such as finances Knowing what to expect may make it easier ... treatment. www.cancer.net/navigating-cancer-care/cancer-basics/understanding-statistics-used-guide-prognosis-and-evaluate-treatment . ...
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Hwang, Sohyun; Rhee, Seung Y; Marcotte, Edward M; Lee, Insuk
2012-01-01
AraNet is a functional gene network for the reference plant Arabidopsis and has been constructed in order to identify new genes associated with plant traits. It is highly predictive for diverse biological pathways and can be used to prioritize genes for functional screens. Moreover, AraNet provides a web-based tool with which plant biologists can efficiently discover novel functions of Arabidopsis genes (http://www.functionalnet.org/aranet/). This protocol explains how to conduct network-based prediction of gene functions using AraNet and how to interpret the prediction results. Functional discovery in plant biology is facilitated by combining candidate prioritization by AraNet with focused experimental tests. PMID:21886106
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A Pattern for Increased Monitoring for Intellectual Property Theft by Departing Insiders
2012-04-01
2012 TECHNICAL REPORT CMU/SEI-2012-TR-008 ESC-TR-2012-008 CERT® Program http://www.sei.cmu.edu SEI markings v3.2 / 30 August 2011... Programs Conference (PLoP) 2011 (http://www.hillside.net/plop/2011/). This material is based upon work funded and supported by the United States...research project at the CERT® Program is identifying enterprise architectural patterns to protect against the insider threat to organizations. This
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Entering the Matrix: The Challenge of Regulating Radical Leveling Technologies
2015-12-01
Source Horizon: 3D Printing,” LinuxInsider, May 28, 2014, http://www.linuxinsider.com/story/ 80519.html; Nozomi Hayase, “ Blockchain Revolution: Open...Source Democracy for the 99%,” openDemocracy UK, August 4, 2014, https://www.opendemocracy.net/ourkingdom/nozomi-hayase/ blockchain -revolution-open...8,000. The funds raised on Kickstarter: $500,000.75 A private technology watchdog, the ETC Group, notified the US Department of Agriculture about
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38 CFR 39.31 - Preapplication requirements.
Code of Federal Regulations, 2014 CFR
2014-07-01
..., Veterans Cemetery Grants Service, through http://www.cem.va.gov/cem/scg_grants.asp. (b) No detailed... cemetery buildings, based on VA guidance on the net and gross square footage standards for cemetery...
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Prostatitis-bacterial - self-care
... R, Blaser MJ, eds. Mandell, Douglas, and Bennett's Principles and Practice of Infectious Diseases, Updated Edition . 8th ... member of Hi-Ethics and subscribes to the principles of the Health on the Net Foundation (www. ...
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Getting yourself healthy before surgery
... care - getting healthy References Neumayer L, Ghalyaie N. Principles of preoperative and operative surgery. In: Townsend CM, ... member of Hi-Ethics and subscribes to the principles of the Health on the Net Foundation (www. ...
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How Do You Know When It's Time to Give up the Keys?
... older adults. http: / / www. eldercare. gov/ ELDERCARE. NET/ Public/ Resources/ Brochures/ docs/ Trans_ Options_ Panels. pdf National Center on Senior Transportation (NCST) Includes resources on transportation options for older ...
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... a white plate will stand out against a dark blue or dark green place mat. Handle Medicines Safely You should: ... to the principles of the Health on the Net Foundation (www.hon.ch). The information provided herein ...
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A guide to help children understand cancer
... approach will depend on your child's age and maturity. Here is a general guide. CHILDREN AGES 0 ... child understands cancer. www.cancer.net/coping-and-emotions/communicating-loved-ones/how-child-understands-cancer . Updated ...
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An electronic consumer health library: NetWellness.
Guard, R; Haag, D; Kaya, B; Marine, S; Morris, T; Schick, L; Shoemaker, S
1996-01-01
NetWellness is a community-based, consumer-defined grant program supporting the delivery of electronic health information to rural residents of southern Ohio and urban and suburban communities in the Greater Cincinnati tri-state region. NetWellness is a collaboratively developed and publicly and privately funded demonstration project. Information is delivered via ISDN, standard dial, dedicated network connections, and the Internet. TriState Online (Greater Cincinnati's Free-Net) and other southern Ohio Free-Nets are key access points in the larger project communities. The other access points are more than forty workstations distributed at public sites throughout the project's primary geographical area. Design strengths and limitations, training initiatives, technical issues, and the project's impact on medical librarianship are examined in this paper. Also discussed are ways of determining community needs and interest, building political alliances, finding and developing funding sources, and overcoming technical obstacles. NetWellness's Internet address is: http:@www.netwellness.org. PMID:8913548
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Biopathways representation and simulation on hybrid functional petri net.
Matsuno, Hiroshi; Tanaka, Yukiko; Aoshima, Hitoshi; Doi, Atsushi; Matsui, Mika; Miyano, Satoru
2011-01-01
The following two matters should be resolved in order for biosimulation tools to be accepted by users in biology/medicine: (1) remove issues which are irrelevant to biological importance, and (2) allow users to represent biopathways intuitively and understand/manage easily the details of representation and simulation mechanism. From these criteria, we firstly define a novel notion of Petri net called Hybrid Functional Petri Net (HFPN). Then, we introduce a software tool, Genomic Object Net, for representing and simulating biopathways, which we have developed by employing the architecture of HFPN. In order to show the usefulness of Genomic Object Net for representing and simulating biopathways, we show two HFPN representations of gene regulation mechanisms of Drosophila melanogaster (fruit fly) circadian rhythm and apoptosis induced by Fas ligand. The simulation results of these biopathways are also correlated with biological observations. The software is available to academic users from http://www.GenomicObject.Net/.
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Snoopy--a unifying Petri net framework to investigate biomolecular networks.
Rohr, Christian; Marwan, Wolfgang; Heiner, Monika
2010-04-01
To investigate biomolecular networks, Snoopy provides a unifying Petri net framework comprising a family of related Petri net classes. Models can be hierarchically structured, allowing for the mastering of larger networks. To move easily between the qualitative, stochastic and continuous modelling paradigms, models can be converted into each other. We get models sharing structure, but specialized by their kinetic information. The analysis and iterative reverse engineering of biomolecular networks is supported by the simultaneous use of several Petri net classes, while the graphical user interface adapts dynamically to the active one. Built-in animation and simulation are complemented by exports to various analysis tools. Snoopy facilitates the addition of new Petri net classes thanks to its generic design. Our tool with Petri net samples is available free of charge for non-commercial use at http://www-dssz.informatik.tu-cottbus.de/snoopy.html; supported operating systems: Mac OS X, Windows and Linux (selected distributions).
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Helminth.net: expansions to Nematode.net and an introduction to Trematode.net
Martin, John; Rosa, Bruce A.; Ozersky, Philip; Hallsworth-Pepin, Kymberlie; Zhang, Xu; Bhonagiri-Palsikar, Veena; Tyagi, Rahul; Wang, Qi; Choi, Young-Jun; Gao, Xin; McNulty, Samantha N.; Brindley, Paul J.; Mitreva, Makedonka
2015-01-01
Helminth.net (http://www.helminth.net) is the new moniker for a collection of databases: Nematode.net and Trematode.net. Within this collection we provide services and resources for parasitic roundworms (nematodes) and flatworms (trematodes), collectively known as helminths. For over a decade we have provided resources for studying nematodes via our veteran site Nematode.net (http://nematode.net). In this article, (i) we provide an update on the expansions of Nematode.net that hosts omics data from 84 species and provides advanced search tools to the broad scientific community so that data can be mined in a useful and user-friendly manner and (ii) we introduce Trematode.net, a site dedicated to the dissemination of data from flukes, flatworm parasites of the class Trematoda, phylum Platyhelminthes. Trematode.net is an independent component of Helminth.net and currently hosts data from 16 species, with information ranging from genomic, functional genomic data, enzymatic pathway utilization to microbiome changes associated with helminth infections. The databases’ interface, with a sophisticated query engine as a backbone, is intended to allow users to search for multi-factorial combinations of species’ omics properties. This report describes updates to Nematode.net since its last description in NAR, 2012, and also introduces and presents its new sibling site, Trematode.net. PMID:25392426
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Lidar Ice nuclei estimates and how they relate with airborne in-situ measurements
NASA Astrophysics Data System (ADS)
Marinou, Eleni; Amiridis, Vassilis; Ansmann, Albert; Nenes, Athanasios; Balis, Dimitris; Schrod, Jann; Binietoglou, Ioannis; Solomos, Stavros; Mamali, Dimitra; Engelmann, Ronny; Baars, Holger; Kottas, Michael; Tsekeri, Alexandra; Proestakis, Emmanouil; Kokkalis, Panagiotis; Goloub, Philippe; Cvetkovic, Bojan; Nichovic, Slobodan; Mamouri, Rodanthi; Pikridas, Michael; Stavroulas, Iasonas; Keleshis, Christos; Sciare, Jean
2018-04-01
By means of available ice nucleating particle (INP) parameterization schemes we compute profiles of dust INP number concentration utilizing Polly-XT and CALIPSO lidar observations during the INUIT-BACCHUS-ACTRIS 2016 campaign. The polarization-lidar photometer networking (POLIPHON) method is used to separate dust and non-dust aerosol backscatter, extinction, mass concentration, particle number concentration (for particles with radius > 250 nm) and surface area concentration. The INP final products are compared with aerosol samples collected from unmanned aircraft systems (UAS) and analyzed using the ice nucleus counter FRIDGE.
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PsyGeNET: a knowledge platform on psychiatric disorders and their genes.
Gutiérrez-Sacristán, Alba; Grosdidier, Solène; Valverde, Olga; Torrens, Marta; Bravo, Àlex; Piñero, Janet; Sanz, Ferran; Furlong, Laura I
2015-09-15
PsyGeNET (Psychiatric disorders and Genes association NETwork) is a knowledge platform for the exploratory analysis of psychiatric diseases and their associated genes. PsyGeNET is composed of a database and a web interface supporting data search, visualization, filtering and sharing. PsyGeNET integrates information from DisGeNET and data extracted from the literature by text mining, which has been curated by domain experts. It currently contains 2642 associations between 1271 genes and 37 psychiatric disease concepts. In its first release, PsyGeNET is focused on three psychiatric disorders: major depression, alcohol and cocaine use disorders. PsyGeNET represents a comprehensive, open access resource for the analysis of the molecular mechanisms underpinning psychiatric disorders and their comorbidities. The PysGeNET platform is freely available at http://www.psygenet.org/. The PsyGeNET database is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/). lfurlong@imim.es Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.
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Petri net modelling of gene regulation of the Duchenne muscular dystrophy.
Grunwald, Stefanie; Speer, Astrid; Ackermann, Jörg; Koch, Ina
2008-05-01
Searching for therapeutic strategies for Duchenne muscular dystrophy, it is of great interest to understand the responsible molecular pathways down-stream of dystrophin completely. For this reason we have performed real-time PCR experiments to compare mRNA expression levels of relevant genes in tissues of affected patients and controls. To bring experimental data in context with the underlying pathway theoretical models are needed. Modelling of biological processes in the cell at higher description levels is still an open problem in the field of systems biology. In this paper, a new application of Petri net theory is presented to model gene regulatory processes of Duchenne muscular dystrophy. We have developed a Petri net model, which is based mainly on own experimental and literature data. We distinguish between up- and down-regulated states of gene expression. The analysis of the model comprises the computation of structural and dynamic properties with focus on a thorough T-invariant analysis, including clustering techniques and the decomposition of the network into maximal common transition sets (MCT-sets), which can be interpreted as functionally related building blocks. All possible pathways, which reflect the complex net behaviour in dependence of different gene expression patterns, are discussed. We introduce Mauritius maps of T-invariants, which enable, for example, theoretical knockout analysis. The resulted model serves as basis for a better understanding of pathological processes, and thereby for planning next experimental steps in searching for new therapeutic possibilities. Free availability of the Petri net editor and animator Snoopy and the clustering tool PInA via http://www-dssz.informatik.tu-cottbus.de/~ wwwdssz/. The Petri net models used can be accessed via http://www.tfh-berlin.de/bi/duchenne/.
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Virtual planets atlas 1.0 freeware
NASA Astrophysics Data System (ADS)
Legrand, C.; Chevalley, P.
2015-10-01
Since 2002, we develop the "Virtual Moon Atlas -http://www.ap-i.net/avl/en/start" a freeware to help Moon observing and to improve interest for Moon in general public. VMA freeware has been downloaded near 900000 times all over the world and is or has been used by several professional organizations such as Kitt Peak Observatory, National Japan Observatory, Birkbeck College / University College London (K. Joy), BBC Sky at night, several French astronomy magazines and astronomy writers (P. Harrington, S. French...) . Recommended by ESA, registered as educational software by French ministry for education, it has also yet been presented at 2006 & 2007 LPSC and PCC2 in 2011 We have declined this freeware in a new tool with the same goals, but for the telluric planets and satellites, the "Virtual Planets Atlas (VPA / http://www.ap-i.net/avp/en/start") now in version 1.0.
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2004-09-01
Rosetti USN U.S. Navy Chesterton, IN 6. Erik Chaum NUWC Newport, RI 7. David Bellino NPRI Newport, RI 8. Dick Nadolink NUWC Newport, RI...found at (http://www.parallelgraphics.com/products/cortona). G. JFREECHART JFreeChart is an open source Java API created by David Gilbert and...www.xj3d.org/. Accessed 3 September 2004. Hunter, David , Kurt Cagle, and Chris Dix, eds. Beginning XML, Second Edition. Indianapolis, IN
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Methods for Intelligent Mapping of the IPV6 Address Space
2015-03-01
the " Internet of Things " ( IoT ). (2013, Jan. 7). Forbes. [Online]. Available: http://www.forbes.com/sites/quora/2013/01/07/ how-many- things -are...currently-connected-to-the- internet -of- things - iot / 57 [13] G. Huston, “IPv4 address report,” Mar 2015. [Online]. Available: http://www.potaroo.net/tools/ipv4...distribution is unlimited 12b. DISTRIBUTION CODE 13. ABSTRACT (maximum 200 words) Due to the rapid growth of the Internet , the available pool of unique
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Enabling BOINC in infrastructure as a service cloud system
NASA Astrophysics Data System (ADS)
Montes, Diego; Añel, Juan A.; Pena, Tomás F.; Uhe, Peter; Wallom, David C. H.
2017-02-01
Volunteer or crowd computing is becoming increasingly popular for solving complex research problems from an increasingly diverse range of areas. The majority of these have been built using the Berkeley Open Infrastructure for Network Computing (BOINC) platform, which provides a range of different services to manage all computation aspects of a project. The BOINC system is ideal in those cases where not only does the research community involved need low-cost access to massive computing resources but also where there is a significant public interest in the research being done.We discuss the way in which cloud services can help BOINC-based projects to deliver results in a fast, on demand manner. This is difficult to achieve using volunteers, and at the same time, using scalable cloud resources for short on demand projects can optimize the use of the available resources. We show how this design can be used as an efficient distributed computing platform within the cloud, and outline new approaches that could open up new possibilities in this field, using Climateprediction.net (http://www.climateprediction.net/) as a case study.
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Communicating with the Net Generation
2011-03-11
rich , digitally constructed communication and information world.2 Although this generation is often referred to as Generation Y or Millennial...Generations at Work, Millenials at Work, http://www.generationsatwork. com /articles_millennials_at_work.php (accessed November 21, 2010). 31 Thomas
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Sakyo, Yumi; Nakayama, Kazuhiro; Komatsu, Hiroko; Setoyama, Yoko
2009-01-01
People are required to take in and comprehend a massive amount of health information and in turn make some serious decisions based on that information. We, at St. Luke's College of Nursing, provide a rich selection of high-quality health information, and have set up Nursing Net (The Kango Net:Kango is Nursing in Japanese). This website provides information for consumers as well as people interested in the nursing profession. In an attempt to identify the needs of users, this study conducted an analysis of the contents on the total consultation page. Many readers voted that responses to nursing techniques and symptoms questions proved instrumental in their queries. Based on the results of this study, we can conclude that this is an easy-to-access, convenient site for getting health information about physical symptoms and nursing techniques.
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Johansen, Morten Bo; Izarzugaza, Jose M. G.; Brunak, Søren; Petersen, Thomas Nordahl; Gupta, Ramneek
2013-01-01
We have developed a sequence conservation-based artificial neural network predictor called NetDiseaseSNP which classifies nsSNPs as disease-causing or neutral. Our method uses the excellent alignment generation algorithm of SIFT to identify related sequences and a combination of 31 features assessing sequence conservation and the predicted surface accessibility to produce a single score which can be used to rank nsSNPs based on their potential to cause disease. NetDiseaseSNP classifies successfully disease-causing and neutral mutations. In addition, we show that NetDiseaseSNP discriminates cancer driver and passenger mutations satisfactorily. Our method outperforms other state-of-the-art methods on several disease/neutral datasets as well as on cancer driver/passenger mutation datasets and can thus be used to pinpoint and prioritize plausible disease candidates among nsSNPs for further investigation. NetDiseaseSNP is publicly available as an online tool as well as a web service: http://www.cbs.dtu.dk/services/NetDiseaseSNP PMID:23935863
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Mentornet - E-Mentoring for Women Students in Engineering and Science
NASA Astrophysics Data System (ADS)
Single, Peg Boyle; Muller, Carol B.; Cunningham, Christine M.; Single, Richard M.; Carlsen, William S.
MentorNet www.MentorNet.net;, the E-Mentoring Network for Diversity in Engineering and Science, addresses the underrepresentation of women in science, technology, engineering, and mathematics "STEM". MentorNet offers a multiinstitutional, structured, electronic mentoring "e-mentoring" program that pairs undergraduate and graduate students, primarily women, with professionals and supports them through e-mentoring relationships of specified lengths. The program evaluations established that over 90% of the participants would recommend MentorNet to a friend or colleague. The e-mentoring program allowed participants to establish satisfactory and beneficial e-mentoring relationships based on investments of approximately 20 minutes per week - in between more serious exchanges, email exchanges that included light-hearted social interactions and jokes were an important aspect of sustaining e-mentoring relationships. Participation in MentorNet increased the students' self-confidence in their f elds - desire to obtain work in industry, national laboratories, or national agencies; and intent to pursue careers in their fields. Three years of evaluation results support the need for and efficacy of the program.
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... first to achieve this important distinction for online health information and services. Learn more about A.D.A. ... Ethics and subscribes to the principles of the Health on the Net Foundation (www.hon.ch). The information provided herein should not be used during any ...
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The Emerging Infrastructure of Autonomous Astronomy
NASA Astrophysics Data System (ADS)
Seaman, R.; Allan, A.; Axelrod, T.; Cook, K.; White, R.; Williams, R.
2007-10-01
Advances in the understanding of cosmic processes demand that sky transient events be confronted with statistical techniques honed on static phenomena. Time domain data sets require vast surveys such as LSST {http://www.lsst.org/lsst_home.shtml} and Pan-STARRS {http://www.pan-starrs.ifa.hawaii.edu}. A new autonomous infrastructure must close the loop from the scheduling of survey observations, through data archiving and pipeline processing, to the publication of transient event alerts and automated follow-up, and to the easy analysis of resulting data. The IVOA VOEvent {http://voevent.org} working group leads efforts to characterize sky transient alerts published through VOEventNet {http://voeventnet.org}. The Heterogeneous Telescope Networks (HTN {http://www.telescope-networks.org}) consortium are observatories and robotic telescope projects seeking interoperability with a long-term goal of creating an e-market for telescope time. Two projects relying on VOEvent and HTN are eSTAR {http://www.estar.org.uk} and the Thinking Telescope {http://www.thinkingtelescopes.lanl.gov} Project.
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Diagnosis and prediction of neuroendocrine liver metastases: a protocol of six systematic reviews.
Arigoni, Stephan; Ignjatovic, Stefan; Sager, Patrizia; Betschart, Jonas; Buerge, Tobias; Wachtl, Josephine; Tschuor, Christoph; Limani, Perparim; Puhan, Milo A; Lesurtel, Mickael; Raptis, Dimitri A; Breitenstein, Stefan
2013-12-23
Patients with hepatic metastases from neuroendocrine tumors (NETs) benefit from an early diagnosis, which is crucial for the optimal therapy and management. Diagnostic procedures include morphological and functional imaging, identification of biomarkers, and biopsy. The aim of six systematic reviews discussed in this study is to assess the predictive value of Ki67 index and other biomarkers, to compare the diagnostic accuracy of morphological and functional imaging, and to define the role of biopsy in the diagnosis and prediction of neuroendocrine tumor liver metastases. An objective group of librarians will provide an electronic search strategy to examine the following databases: MEDLINE, EMBASE and The Cochrane Library (Cochrane Database of Systematic Reviews, Cochrane Central Register of Controlled Trials (CENTRAL), Database of Abstracts of Reviews of Effects). There will be no restriction concerning language and publication date. The qualitative and quantitative synthesis of the systematic review will be conducted with randomized controlled trials (RCT), prospective and retrospective comparative cohort studies, and case-control studies. Case series will be collected in a separate database and only used for descriptive purposes. This study is ongoing and presents a protocol of six systematic reviews to elucidate the role of histopathological and biochemical markers, biopsies of the primary tumor and the metastases as well as morphological and functional imaging modalities for the diagnosis and prediction of neuroendocrine liver metastases. These systematic reviews will assess the value and accuracy of several diagnostic modalities in patients with NET liver metastases, and will provide a basis for the development of clinical practice guidelines. The systematic reviews have been prospectively registered with the International Prospective Register of Systematic Reviews (PROSPERO): CRD42012002644; http://www.metaxis.com/prospero/full_doc.asp?RecordID=2644 (Archived by WebCite at http://www.webcitation.org/6LzCLd5sF), CRD42012002647; http://www.metaxis.com/prospero/full_doc.asp?RecordID=2647 (Archived by WebCite at http://www.webcitation.org/6LzCRnZnO), CRD42012002648; http://www.metaxis.com/prospero/full_doc.asp?RecordID=2648 (Archived by WebCite at http://www.webcitation.org/6LzCVeuVR), CRD42012002649; http://www.metaxis.com/prospero/full_doc.asp?RecordID=2649 (Archived by WebCite at http://www.webcitation.org/6LzCZzZWU), CRD42012002650; http://www.metaxis.com/prospero/full_doc.asp?RecordID=2650 (Archived by WebCite at http://www.webcitation.org/6LzDPhGb8), CRD42012002651; http://www.crd.york.ac.uk/PROSPERO/display_record.asp?ID=CRD42012002651#.UrMglPRDuVo (Archived by WebCite at http://www.webcitation.org/6LzClCNff).
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2009-12-01
44 Figure 17. Average Retail Price of Electricity Sold by Sector, 1960–2007 (From: http://www.eia.doe.gov/ bookshelf /brochures/epa...Sold by Sector, 1960–2007 (From: http://www.eia.doe.gov/ bookshelf /brochures/epa/epa.html) All three illustrations, with the exception of the sharp... bookshelf /brochures/epa/epa.html 72 Fawls, C. (2006). Issues and unexplored opportunities within the navy working capital fund. Defense AT&L, 35(3), 38
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2008-12-01
University of Michigan Press. 116 Ba’aysir, A. B. ( 2008 ). Abu Bakar Bas’yir sermon. Retrieved April 25, 2008 , from http://www.abc.net.au/4corners...Behrend, T. (2003). Reading past the myth: public teachings of Abu Bakar Ba’asyir. Retrieved June 1, 2008 , from www.arts.auckland.ac.nz Berger, M. T...ideology as it developed during founders Abdullah Sungkar and Abu Bakar Ba’asyir’s own radicalization, and the dynamics of group identity, trust, and
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ERIC Educational Resources Information Center
Mooney, Paul; Gansle, Kristin A.; Denny, R. Kenton
2013-01-01
The stated mission of the Council for Children with Behavioral Disorders (CCBD) includes ''supporting the professional development and enhancing the expertise of those who work on behalf of children with challenging behavior and their families'' (http:// www.ccbd.net/About/OurMission). The stated goal of CCBD's journal "Behavioral…
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Structural Fingerprinting of Nanocrystals in the Transmission Electron Microscope
NASA Astrophysics Data System (ADS)
Rouvimov, Sergei; Plachinda, Pavel; Moeck, Peter
2010-03-01
Three novel strategies for the structurally identification of nanocrystals in a transmission electron microscope are presented. Either a single high-resolution transmission electron microscopy image [1] or a single precession electron diffractogram (PED) [2] may be employed. PEDs from fine-grained crystal powders may also be utilized. Automation of the former two strategies is in progress and shall lead to statistically significant results on ensembles of nanocrystals. Open-access databases such as the Crystallography Open Database which provides more than 81,500 crystal structure data sets [3] or its mainly inorganic and educational subsets [4] may be utilized. [1] http://www.scientificjournals.org/journals 2007/j/of/dissertation.htm [2] P. Moeck and S. Rouvimov, in: {Drugs and the Pharmaceutical Sciences}, Vol. 191, 2009, 270-313 [3] http://cod.ibt.lt, http://www.crystallography.net, http://cod.ensicaen.fr, http://nanocrystallography.org, http://nanocrystallography.net, http://journals.iucr.org/j/issues/2009/04/00/kk5039/kk5039.pdf [4] http://nanocrystallography.research.pdx.edu/CIF-searchable
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2017-08-01
This large repository of climate model results for North America (Wang and Kotamarthi 2013, 2014, 2015) is stored in Network Common Data Form (NetCDF...Network Common Data Form (NetCDF). UCAR/Unidata Program Center, Boulder, CO. Available at: http://www.unidata.ucar.edu/software/netcdf. Accessed on 6/20...emissions diverge from each other regarding fossil fuel use, technology, and other socioeconomic factors. As a result, the estimated emissions for each of
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Federal Register 2010, 2011, 2012, 2013, 2014
2012-04-18
... Plan for the Water Resources of the Susquehanna River Basin. The public should take note that this... available at the SRBC Water Resource Portal at www.srbc.net/wrp . Materials and supporting documents are... Processing Fee Schedule; and (3) amendment to the Comprehensive Plan for the Water Resources of the...
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Donation FAQs (Bone and Tissue Allografts)
... about organ, tissue and eye donation in your state, visit www.donatelife.net . Is there a difference between tissue and organ donation? In order for a person to become an organ donor (kidney, heart, liver, lung), blood and oxygen must flow through the organs until the time of recovery ...
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PA.NET International Quality Certification Protocol for blood pressure monitors.
Omboni, Stefano; Costantini, Carlo; Pini, Claudio; Bulegato, Roberto; Manfellotto, Dario; Rizzoni, Damiano; Palatini, Paolo; O'brien, Eoin; Parati, Gianfranco
2008-10-01
Although standard validation protocols provide assurance of the accuracy of blood pressure monitors (BPMs), there is no guidance for the consumer as to the overall quality of a device. The PA.NET International Quality Certification Protocol, developed by the Association for Research and Development of Biomedical Technologies and for Continuing Medical Education (ARSMED), a nonprofit organization, with the support of the Italian Society of Hypertension-Italian Hypertension League, and the dabl Educational Trust denotes additional criteria of quality for BPMs that fulfilled basic validation criteria, published in full in peer-reviewed medical journals. The certification is characterized by three phases: (i) to determine that the device fulfilled standard validation criteria; (ii) to determine the technical and functional characteristics of the device (e.g. operativity, display dimension, accessory functions, memory availability, etc.) and (iii) to determine the commercial characteristics (e.g. price-quality ratio, after-sale service, guarantee, etc.). At the end of the certification process, ARSMED attributes a quality index to the device, based on a scale ranging from 1 to 100, and a quality seal with four different grades (bronze, silver, gold and diamond) according to the achieved score. The seal is identified by a unique alphanumeric code. The quality seal may be used on the packaging of the appliance or in advertising. A quality certification is released to the manufacturer and published on www.pressionearteriosa.net and www.dableducational.org. The PA.NET International Quality Certification Protocol represents the first attempt to provide health care personnel and consumers with an independent and objective assessment of BPMs based on their quality.
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1999-12-01
9 . http://home.earthlink.net/-fradella/homepage.htm 10. http ://web.mit.edu/aeroastro/www/labs/GTL/research/micro/micro.html 11 . http://www.ecr.co.il...Meijer 7 LAS/DB&P/BO/OB&T taxv. aooi Jansen 8 LAS/DB&PIBO/OB 9 LAS/DB&P/BO/CIV 10 OGMAN/Externe plannen Infanterie 11 DM/C31 12 DM/COM 13 KPU-bedrijf 14...detailed specifications mentioned before. TNO-rapport TNO-MEP - R 99/490 9 van 51 Samenvatting In dit rapport wordt een eerste globale selectie gemaakt: van
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Road sign recognition using Viapix module and correlation
NASA Astrophysics Data System (ADS)
Ouerhani, Y.; Desthieux, M.; Alfalou, A.
2015-03-01
In this paper, we propose and validate a new system used to explore road assets. In this work we are interested on the vertical road signs. To do this, we are based on the combination of road signs detection, recognition and identification using data provides by sensors. The proposed approach consists on using panoramic views provided by the innovative device, VIAPIX®1, developed by our company ACTRIS2. We are based also on the optimized correlation technique for road signs recognition and identification on pictures. Obtained results shows the interest on using panoramic views compared to results obtained using images provided using only one camera.
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Research Operations for Advanced Warfighter Interface Technologies
2009-06-01
tk.sourceforge.net 11 Available at http://www.speech.kth.se/ snack 17 Cross-word triphone Multi-Space probability Distribution (MSD)-HMMs [23...prepared and delivered for shipment as part of on-going coating evaluations. 6) The IR terrain board was mounted to an extruded aluminum frame for ease of
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76 FR 12094 - Whitman River Dam, Inc.
Federal Register 2010, 2011, 2012, 2013, 2014
2011-03-04
[email protected]net . i. FERC Contact: Jeff Browning, (202) 502-8677 or [email protected] . j. Cooperating....ferc.gov/docs-filing/ferconline.asp ). Commenters can submit brief comments up to 6,000 characters, without prior registration, using the eComment system at http://www.ferc.gov/docs-filing/ecomment.asp...
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Small-unit Training for Adaptability and Resilience in Decision Making (STAR-DM)
2017-01-23
based training compared with theoretically less stressful (e.g. classroom lecture) and more Design Interactive, Inc... Design Interactive, Inc. Contract #: N00014-12-G-0427 1... Design Interactive, Inc. 3504 Lake Lynda Drive Suite 400 Orlando, FL 32825 407-706-0977, www.designinteractive.net Corporate Official: John
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Finite Element Analysis and Experimentation of an Icosahedron Frame under Compression
2015-09-17
Century of Flight. Jules Henri Gi_ard (1825 - 1882), January 2014. URL [Online]. Available: http://www.century-of-flight.net/Aviation%20history/to...20reality/ Jules % 20Henri%20Gi_ard.htm. [4] Compression test. [Online]. Available: http://en.wikipedia.org/wiki/Compressive_strength [5
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SafeSlinger: An Easy-to-use and Secure Approach for Human Trust Establishment
2012-03-12
communication modalities (Bluetooth, WiFi , 4G), camera, and sensors. Unfortunately, smartphone platforms suffer from many risks. Vulnerabilities exist in...December 2010. [31] Dave Neal. Defcon hackers get hacked over 4G. http://www.theinquirer.net/inquirer/news/ 16 2100989/defcon-hackers- hacked -4g
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My Two Boots ... A Walk through the Wetlands. An Annual Outing for 700 Middle School Students
ERIC Educational Resources Information Center
Cwikla, Julie; Lasalle, Mark; Wilner, Sybil
2009-01-01
Project WetKids (www.projectwetkids.net) provides wetland, environmental, estuary, and watershed experiences with local scientists, engineers, and naturalists to Pascagoula, Mississippi students and their families. Extensive activities provide participants: (1) real world, locally relevant science-based events; (2) meaningful scientific…
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Optimizing Secure Communication Standards for Disadvantaged Networks
2009-09-01
created using LATEX with the editor Kile [5]. 5.1.2 Libraries and APIs Several libraries were important to the successful completion of this study. The...Explorer. http://www.microsoft.com/windows/ internet-explorer/default.aspx. [5] Kile - An Integrated LaTeX Environment. http://kile.sourceforge.net/. [6
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Making Biology Relevant to Undergraduates
ERIC Educational Resources Information Center
Musante, Susan
2012-01-01
This article features Science Education for New Civic Engagements and Responsibilities (SENCER; www.sencer.net) Summer Institute. The SENCER program, which began formally in 2001, was the vision of David Burns; Karen Oates, currently Peterson Family Dean of Arts and Sciences at Worcester Polytechnic Institute; and Ric Wiebl, currently director of…
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TigerShark UAS noise flight test at Griffiss Airport : letter report to Dr. Mehmet Marsan
DOT National Transportation Integrated Search
2016-05-27
"This memorandum documents preliminary results of the noise flight test conducted on the Navmar TigerShark UAS at Griffiss International Airport (KRME, http://www.ocgov.net/airport) in Rome, New York on May 17, 2016. This memorandum is intended to pr...
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78 FR 69853 - Meeting of the Chronic Fatigue Syndrome Advisory Committee
Federal Register 2010, 2011, 2012, 2013, 2014
2013-11-21
..., pre-recorded video, or written comments. Registration is required in advance in order to submit public... scheduled public comment periods. Each speaker via telephone or pre-recorded video will be limited to five... prerecorded video testimony from international locations. Further details are available at www.blsmeetings.net...
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In-situ measurements of ice nucleating particles with FINCH (Fast Ice Nucleus Chamber)
NASA Astrophysics Data System (ADS)
Kohl, Rebecca; Frank, Fabian; Curtius, Joachim; Rose, Diana
2017-04-01
Ice nucleating particles (INPs), which are a small fraction of the total aerosol population, are capable of triggering ice formation under atmospheric conditions. Since INPs play an important role for the radiative properties of clouds as well as for the formation of precipitation it is important to get quantitative information on the ice activity of various atmospheric aerosol species. With the Fast Ice Nucleus Chamber (FINCH; Bundke et al., 2008) the number concentration of INP is determined at different freezing temperatures and supersaturations. In contrast to other commonly used INP counters, i.e., continuous flow diffusion chambers (CFDCs, DeMott et al., 2011), in FINCH the supersaturation is reached by mixing the sample flow of ambient aerosol with a warm moist as well as a cold dry airflow. By changing the flow rates and temperatures of the individual airflows the freezing temperature (down to -50°C) and supersaturation (up to above water saturation) can be varied relatively quickly. Particles that are ice active at the prescribed freezing temperature and supersaturation grow to crystals and are counted by a home-built optical particle counter (OPC) mounted below the chamber (Bundke et al., 2010). FINCH was operated during the four-week INUIT-BACCHUS-ACTRIS field campaign in Cyprus in April 2016. The measuring site was the location of the Cyprus Atmospheric Observatory (CAO) at Agia Marina Xyliatou, which is typically influenced by dust from the Sahara and the Middle East, an aerosol that is known to have relatively good ice nucleating ability. First results from this campaign will be presented. Acknowledgements: The authors thank the entire INUIT-BACCHUS-ACTRIS campaign team for their cooperation and support. The INUIT-2 project is financed by the German Research Foundation DFG (FOR 1525). The INUIT-Cyprus campaign is a cooperation with the EU-funded project BACCHUS and is also funded by ACTRIS-TNA. References: Bundke, U., Nillius, B., Jaenicke, R., Wetter, T., Klein, H., and Bingemer, H.: The fast Ice Nucleus chamber FINCH, Atmos. Res., 90, 180-186, 10.1016/j.atmosres.2008.02.008, 2008. Bundke, U., Reimann, B., Nillius, B., Jaenicke, R., and Bingemer, H.: Development of a Bioaerosol single particle detector (BIO IN) for the Fast Ice Nucleus CHamber FINCH, Atmos. Meas. Tech., 3, 263-271, doi:10.5194/amt-3-263-2010, 2010. DeMott, P. J., Moehler, O., Stetzer, O., Vali, G., Levin, Z., Petters, M. D., Murakami, M., Leisner, T., Bundke, U., Klein, H., Kanji, Z. A., Cotton, R., Jones, H., Benz, S., Brinkmann, M., Rzesanke, D., Saathoff, H., Nicolet, M., Saito, A., Nillius, B., Bingemer, H., Abbatt, J., Ardon, K., Ganor, E., Georgakopoulos, D. G., and Saunders, C.: Resurgence in ice nuclei measurement research, Bulletin of the American Meteorological Society, 92, 1623-1635, 10.1175/bams-d-10-3119.1, 2011.
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30 CFR 210.54 - Must I submit this royalty report electronically?
Code of Federal Regulations, 2010 CFR
2010-07-01
... with which either party may contract. (2) Web-based reporting—Reporters/payors may enter report data directly or upload files using the MMS electronic web form located at http://www.mrmreports.net. The... generated from a reporter's system application. (c) Refer to our electronic reporting guidelines in the MMS...
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Which Academic Papers Do Researchers Tend to Feature on ResearchGate?
ERIC Educational Resources Information Center
Liu, Xuan Zhen; Fang, Hui
2018-01-01
Introduction: The academic social network site ResearchGate (www.researchgate.net) enables researchers to feature up to five of their research products (including papers, datasets and chapters) in a 'Featured research' section on their ResearchGate home page. This provides an opportunity to discover how researchers view their own publications.…
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Investment Strategies for Improving Fifth-Generation Fighter Training
2011-01-01
The pod is part of the fifth-generation P5 Combat Training System/Tactical Combat Training System designed by Cubic Corporation. (See Shamim , 2007...http://www.rand.org/pubs/monograph_reports/MR1286/ Shamim , Asif, “F-35 Lightning II News: Cubic Lands Contract for F-35 ACMI Training System,” F-16.net
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Federal Register 2010, 2011, 2012, 2013, 2014
2010-01-12
... NYSE Amex Equities Rule 18 (``Compensation in Relation to Exchange System Failure'') to eliminate the..., the Commission's Public Reference Room, the Commission's Web site at http://www.sec.gov , and the... (``Compensation in Relation to Exchange System Failure'') to eliminate the $500 minimum net loss requirement for a...
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A Framework for Event Prioritization in Cyber Network Defense
2014-07-15
U.S.," Reuters (US online Edition), pp. http://www.reuters.com/article/2013/11/06/net-us-usa-china- hacking - idUSBRE9A51AN20131106, 6 Nov 2013. [2...expressed individually, or as a single vector by using the magnitude of these three factors (cell J5 in Table 5
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BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks
Rialle, Stéphanie; Felicori, Liza; Dias-Lopes, Camila; Pérès, Sabine; El Atia, Sanaâ; Thierry, Alain R.; Amar, Patrick; Molina, Franck
2010-01-01
Motivation: Synthetic biology studies how to design and construct biological systems with functions that do not exist in nature. Biochemical networks, although easier to control, have been used less frequently than genetic networks as a base to build a synthetic system. To date, no clear engineering principles exist to design such cell-free biochemical networks. Results: We describe a methodology for the construction of synthetic biochemical networks based on three main steps: design, simulation and experimental validation. We developed BioNetCAD to help users to go through these steps. BioNetCAD allows designing abstract networks that can be implemented thanks to CompuBioTicDB, a database of parts for synthetic biology. BioNetCAD enables also simulations with the HSim software and the classical Ordinary Differential Equations (ODE). We demonstrate with a case study that BioNetCAD can rationalize and reduce further experimental validation during the construction of a biochemical network. Availability and implementation: BioNetCAD is freely available at http://www.sysdiag.cnrs.fr/BioNetCAD. It is implemented in Java and supported on MS Windows. CompuBioTicDB is freely accessible at http://compubiotic.sysdiag.cnrs.fr/ Contact: stephanie.rialle@sysdiag.cnrs.fr; franck.molina@sysdiag.cnrs.fr Supplementary information: Supplementary data are available at Bioinformatics online. PMID:20628073
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20 CFR 656.3 - Definitions, for purposes of this part, of terms used in this part.
Code of Federal Regulations, 2010 CFR
2010-04-01
... for an employer and/or alien under this part. Barter, for purposes of an Application for Permanent... the system developed by the Department of Labor, Employment and Training Administration, to provide to... Occupational Classification system. Further information about O*NET can be found at http://www.onetcenter.org...
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Federal Register 2010, 2011, 2012, 2013, 2014
2013-06-07
.../enviro/guidelines.asp . \\1\\ The attachments referenced in this notice will not appear in the Federal... at Commission's Web site: http://www.ferc.gov/docs-filing/efiling.asp . With eFiling you can provide... the wider net of project types subject to the Plan and Procedure requirements. The revisions clarify...
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Federal Register 2010, 2011, 2012, 2013, 2014
2013-09-16
... In-Conduit Hydroelectric Net-Metered Project would be located on the City of Barre, Washington County....gov/docs-filing/efiling.asp . Commenters can submit brief comments up to 6,000 characters, without prior registration, using the eComment system at http://www.ferc.gov/docs-filing/ecomment.asp . You must...
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Connecting Students across Universities in Saudi Arabia
ERIC Educational Resources Information Center
Al-Jarf, Reima Sado
2005-01-01
The present study reports results of an experiment in which the author and her students at King Saud University (KSU) in Riyadh, Saudi Arabia shared an online grammar course with a professor and his students at Umm Al-Qura University (UQU) in Makkah, Saudi Arabia using www.makkahelearning.net. The experiment proved to be a total failure. Factors…
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Genome-wide analysis of tandem repeats in plants and green algae
Zhixin Zhao; Cheng Guo; Sreeskandarajan Sutharzan; Pei Li; Craig Echt; Jie Zhang; Chun Liang
2014-01-01
Tandem repeats (TRs) extensively exist in the genomes of prokaryotes and eukaryotes. Based on the sequenced genomes and gene annotations of 31 plant and algal species in Phytozome version 8.0 (http://www.phytozome.net/), we examined TRs in a genome-wide scale, characterized their distributions and motif features, and explored their putative biological functions. Among...
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ERIC Educational Resources Information Center
Kilburn, M. Rebecca, Ed.
2014-01-01
The Promising Practices Network (PPN) on Children, Families and Communities (www.promisingpractices.net) began as a partnership between four state-level organizations that help public and private organizations improve the well-being of children and families. The PPN website, archived in June 2014, featured summaries of programs and practices that…
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NRMRL-CIN-1351 Hofstetter**, P., and Hammitt, J. K. Human Health Metrics for Environmental Decision Support Tools: Lessons from Health Economics and Decision Analysis. Risk Analysis 600/R/01/104, Available: on internet, www.epa.gov/ORD/NRMRL/Pubs/600R01104, [NET]. 03/07/2001 D...
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Agile and Adaptive IT Ecosystem, Results, Outlook, and Recommendations
2014-06-01
http://netbeans.dzone.com/news/war-fighter- netbeans -platform 5 http://www.afei.org/events/4A07/Documents/1-DI2E%20Brochure%20ISA_10APR13.pdf 6...Client ( NetBeans ), and OSGI bundles (Karafe). DoD systems also use both the Android and iOS mobile operating systems. Each technology has a specific
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www.teld.net: Online Courseware Engine for Teaching by Examples and Learning by Doing.
ERIC Educational Resources Information Center
Huang, G. Q.; Shen, B.; Mak, K. L.
2001-01-01
Describes TELD (Teaching by Examples and Learning by Doing), a Web-based online courseware engine for higher education. Topics include problem-based learning; project-based learning; case methods; TELD as a Web server; course materials; TELD as a search engine; and TELD as an online virtual classroom for electronic delivery of electronic…
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Mathematics and Astronomy: Inquire Based Scientific Education at School
NASA Astrophysics Data System (ADS)
de Castro, Ana I. Gómez
2010-10-01
Mathematics is the language of science however, in secondary and high school education students are not made aware of the strong implications behind this statement. This is partially caused because mathematical training and the modelling of nature are not taught together. Astronomy provides firm scientific grounds for this joint training; the mathematics needed is simple, the data can be acquired with simple instrumentation in any place on the planet and the physics is rich with a broad range of levels. In addition, astronomy and space exploration are extremely appealing to young (14-17 years old) students helping to motivate them to study science doing science, i.e. to introduce Inquiry Based Scientific Education (IBSE). Since 1997 a global consortium is being developed to introduce IBSE techniques in secondary/high school education on a global scale: the Global Hands-On Universe association (www.globalhou.org) making use of the astronomical universe as a training lab. This contribution is a brief update on the current activities of the HOU consortium. Relevant URLS: www.globalhou.org, www.euhou.net, www.houspain.com.
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EARLINET Single Calculus Chain - overview on methodology and strategy
NASA Astrophysics Data System (ADS)
D'Amico, G.; Amodeo, A.; Baars, H.; Binietoglou, I.; Freudenthaler, V.; Mattis, I.; Wandinger, U.; Pappalardo, G.
2015-11-01
In this paper we describe the EARLINET Single Calculus Chain (SCC), a tool for the automatic analysis of lidar measurements. The development of this tool started in the framework of EARLINET-ASOS (European Aerosol Research Lidar Network - Advanced Sustainable Observation System); it was extended within ACTRIS (Aerosol, Clouds and Trace gases Research InfraStructure Network), and it is continuing within ACTRIS-2. The main idea was to develop a data processing chain that allows all EARLINET stations to retrieve, in a fully automatic way, the aerosol backscatter and extinction profiles starting from the raw lidar data of the lidar systems they operate. The calculus subsystem of the SCC is composed of two modules: a pre-processor module which handles the raw lidar data and corrects them for instrumental effects and an optical processing module for the retrieval of aerosol optical products from the pre-processed data. All input parameters needed to perform the lidar analysis are stored in a database to keep track of all changes which may occur for any EARLINET lidar system over the time. The two calculus modules are coordinated and synchronized by an additional module (daemon) which makes the whole analysis process fully automatic. The end user can interact with the SCC via a user-friendly web interface. All SCC modules are developed using open-source and freely available software packages. The final products retrieved by the SCC fulfill all requirements of the EARLINET quality assurance programs on both instrumental and algorithm levels. Moreover, the manpower needed to provide aerosol optical products is greatly reduced and thus the near-real-time availability of lidar data is improved. The high-quality of the SCC products is proven by the good agreement between the SCC analysis, and the corresponding independent manual retrievals. Finally, the ability of the SCC to provide high-quality aerosol optical products is demonstrated for an EARLINET intense observation period.
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NASA Astrophysics Data System (ADS)
Stavroulas, Iasonas; Pikridas, Michael; Oikonomou, Kostantina; Vasiliadou, Emily; Savvides, Chrysanthos; Vrekoussis, Mihalis; Mihalopoulos, Nikolaos; Gros, Valerie; Sciare, Jean
2017-04-01
Particulate matter with diameter smaller than 1{μ}m (PM1) induces direct and indirect effects on local and regional pollution, global climate and health. As of the beginning of 2015, the chemical composition of submicron aerosols, is continuously being monitored at the newly established Cyprus Atmospheric Observatory (CAO, http://www.cyi.ac.cy/index.php/cao.html), a national facility of the ACTRIS Research Infrastructure operated by The Cyprus Institute. Cyprus, an island located in the Eastern Mediterranean Middle East region and influenced by diverse air masses throughout the year, is ideal for monitoring photochemically aged aerosols and gaseous pollutants of both natural and anthropogenic origin. Furthermore this is a unique dataset for this area in such proximity to the Middle East, a poorly documented area in terms of atmospheric aerosol observations. An Aerodyne Quadrupole Aerosol Chemical Speciation Monitor (Q-ACSM) is currently deployed at the CAO premises (35.04N - 33.06E) situated at the rural area of Agia Marina Xyliatou on the foothill of mount Troodos at an elevation of 532m above sea level (asl). The ACSM delivers chemical composition of the major non-refractory aerosol (PM1) chemical constituents (organics, sulfate, nitrate, ammonium, chloride) with an effective (close to 100{%}) collection efficiency for particles in the diameter range of 65-700 nm at a 30 minute temporal resolution. Black Carbon (BC) was also monitored using both Magee Scientific AE-31 and AE-33 aethalometers. Quality control of the PM chemical dataset was conducted by comparison with chemical analysis performed on collocated 24-h filter samples (PM1) and comparison with 1-h PM2.5 derived from a Thermo Scientific TEOM (1400a) Monitor. Positive Matrix Factorization (PMF) was conducted and different organic aerosol factors were distinguished using the Igor based SoFi toolkit utilizing the ME-2 multilinear engine. Air mass origin was investigated for each measurement day using the Lagrangian dispersion model FLEXPART in backward mode. Analysis of the PMF on the organic mass spectra, based on good agreement with external standard mass spectra, led to the selection of a solution with three factors, an HOA (Hydrocarbon-like Organic Aerosol) factor with relatively low overall contribution (9{%}), a typical Low Volatility (LV-OOA) factor contributing 54{%}, and a factor attributed to Semi-Volatile organics (SV-OOA), contributing 37{%}. The FLEXPART model analysis, led to eight main regions of influence, namely Europe, West Turkey, Anatolia, Middle East, North Africa, Marine, Local and Mixed. Organic content exhibits maximum values when air masses originate from the wider northern sector (West Turkey and Anatolia) and the Middle East. Less aged organic content was identified for air masses originating from the immediate neighboring regions (West Turkey, Anatolia, Middle East and North Africa) while fresh organics peaked when air masses originated from the Middle East, coinciding with elevated BC concentrations, suggesting strong anthropogenic sources for this sector. This project received funding from the ChArMEx (Chemistry Aerosol Mediterranean Experiment) program, the ENVI-MED CyAr project, the European Union's Seventh Framework Programme (FP7) project BACCHUS under grant agreement no. 603445, and the European Union's Horizon 2020 research and innovation programme ACTRIS-2 under grant agreement No 654109.
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The Da Vinci European BioBank: A Metabolomics-Driven Infrastructure
Carotenuto, Dario; Luchinat, Claudio; Marcon, Giordana; Rosato, Antonio; Turano, Paola
2015-01-01
We present here the organization of the recently-constituted da Vinci European BioBank (daVEB, https://www.davincieuropeanbiobank.org/it). The biobank was created as an infrastructure to support the activities of the Fiorgen Foundation (http://www.fiorgen.net/), a nonprofit organization that promotes research in the field of pharmacogenomics and personalized medicine. The way operating procedures concerning samples and data have been developed at daVEB largely stems from the strong metabolomics connotation of Fiorgen and from the involvement of the scientific collaborators of the foundation in international/European projects aimed to tackle the standardization of pre-analytical procedures and the promotion of data standards in metabolomics. PMID:25913579
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DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes.
Piñero, Janet; Queralt-Rosinach, Núria; Bravo, Àlex; Deu-Pons, Jordi; Bauer-Mehren, Anna; Baron, Martin; Sanz, Ferran; Furlong, Laura I
2015-01-01
DisGeNET is a comprehensive discovery platform designed to address a variety of questions concerning the genetic underpinning of human diseases. DisGeNET contains over 380,000 associations between >16,000 genes and 13,000 diseases, which makes it one of the largest repositories currently available of its kind. DisGeNET integrates expert-curated databases with text-mined data, covers information on Mendelian and complex diseases, and includes data from animal disease models. It features a score based on the supporting evidence to prioritize gene-disease associations. It is an open access resource available through a web interface, a Cytoscape plugin and as a Semantic Web resource. The web interface supports user-friendly data exploration and navigation. DisGeNET data can also be analysed via the DisGeNET Cytoscape plugin, and enriched with the annotations of other plugins of this popular network analysis software suite. Finally, the information contained in DisGeNET can be expanded and complemented using Semantic Web technologies and linked to a variety of resources already present in the Linked Data cloud. Hence, DisGeNET offers one of the most comprehensive collections of human gene-disease associations and a valuable set of tools for investigating the molecular mechanisms underlying diseases of genetic origin, designed to fulfill the needs of different user profiles, including bioinformaticians, biologists and health-care practitioners. Database URL: http://www.disgenet.org/ © The Author(s) 2015. Published by Oxford University Press.
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Baumbach, Jan; Wittkop, Tobias; Rademacher, Katrin; Rahmann, Sven; Brinkrolf, Karina; Tauch, Andreas
2007-04-30
CoryneRegNet is an ontology-based data warehouse for the reconstruction and visualization of transcriptional regulatory interactions in prokaryotes. To extend the biological content of CoryneRegNet, we added comprehensive data on transcriptional regulations in the model organism Escherichia coli K-12, originally deposited in the international reference database RegulonDB. The enhanced web interface of CoryneRegNet offers several types of search options. The results of a search are displayed in a table-based style and include a visualization of the genetic organization of the respective gene region. Information on DNA binding sites of transcriptional regulators is depicted by sequence logos. The results can also be displayed by several layouters implemented in the graphical user interface GraphVis, allowing, for instance, the visualization of genome-wide network reconstructions and the homology-based inter-species comparison of reconstructed gene regulatory networks. In an application example, we compare the composition of the gene regulatory networks involved in the SOS response of E. coli and Corynebacterium glutamicum. CoryneRegNet is available at the following URL: http://www.cebitec.uni-bielefeld.de/groups/gi/software/coryneregnet/.
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NASA Astrophysics Data System (ADS)
Velasco, Almudena; Gutiérrez, Raúl; Solano, Enrique; García-Torres, Miguel; López, Mauro; Sarro, Luis Manuel
We describe here the main capabilities of the COROT archive. The archive (http://sdc.laeff.inta.es/corotfa/jsp/searchform.jsp), managed at LAEFF in the framework of the Spanish Virtual Observatory (http://svo.laeff.inta.es), has been developed following the standards and requirements defined by IVOA (http://www.ivoa.net). The COROT archive at LAEFF will be publicly available by the end of 2008.
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Second International Electronic Conference on Medicinal Chemistry (ECMC-2)
Mayence, Annie; Vanden Eynde, Jean Jacques
2017-01-01
The second International Electronic Conference on Medicinal Chemistry, organized and sponsored by the publisher MDPI AG and the Journal Pharmaceuticals, took place in November 2016 on the SciForum website (www.sciforum.net/conference/ecmc-12). More than 150 authors from 22 countries participated in the event. Selected works presented during the scientific meeting are disclosed in this report. PMID:28146112
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2010-04-19
... deficiency from Nasdaq is required to make a public announcement by filing a Form 8-K, where required by SEC... the deficiency is based. However, note that in the case of a deficiency related to the requirement to... electronic disclosure submission system available at www.nasdaq.net , except in emergency situations when...
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Integrating Research, Teaching and Learning: Preparing the Future National STEM Faculty
NASA Astrophysics Data System (ADS)
Hooper, E. J.; Pfund, C.; Mathieu, R.
2010-08-01
A network of universities (Howard, Michigan State, Texas A&M, University of Colorado at Boulder, University of Wisconsin-Madison, Vanderbilt) have created a National Science Foundation-funded network to prepare a future national STEM (science, technology, engineering, mathematics) faculty committed to learning, implementing, and advancing teaching techniques that are effective for the wide range of students enrolled in higher education. The Center for the Integration of Research, Teaching and Learning (CIRTL; http://www.cirtl.net) develops, implements and evaluates professional development programs for future and current faculty. The programs comprise graduate courses, internships, and workshops, all integrated within campus learning communities. These elements are unified and guided by adherence to three core principles, or pillars: "Teaching as Research," whereby research skills are applied to evaluating and advancing undergraduate learning; "Learning through Diversity," in which the diversity of students' backgrounds and experiences are used as a rich resource to enhance teaching and learning; and "Learning Communities" that foster shared learning and discovery among students, and between future and current faculty within a department or institution. CIRTL established a laboratory for testing its ideas and practices at the University of Wisconsin-Madison, known as the Delta Program in Research, Teaching and Learning (http://www.delta.wisc.edu). The program offers project-based graduate courses, research mentor training, and workshops for post-docs, staff, and faculty. In addition, graduate students and post-docs can partner with a faculty member in a teaching-as-research internship to define and tackle a specific teaching and learning problem. Finally, students can obtain a Delta Certificate as testimony to their engagement in and commitment to teaching and learning. Delta has proved very successful, having served over 1500 UW-Madison instructors from graduate students to full professors. UW-Madison values the program to the point of now funding it internally.
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NetMHCcons: a consensus method for the major histocompatibility complex class I predictions.
Karosiene, Edita; Lundegaard, Claus; Lund, Ole; Nielsen, Morten
2012-03-01
A key role in cell-mediated immunity is dedicated to the major histocompatibility complex (MHC) molecules that bind peptides for presentation on the cell surface. Several in silico methods capable of predicting peptide binding to MHC class I have been developed. The accuracy of these methods depends on the data available characterizing the binding specificity of the MHC molecules. It has, moreover, been demonstrated that consensus methods defined as combinations of two or more different methods led to improved prediction accuracy. This plethora of methods makes it very difficult for the non-expert user to choose the most suitable method for predicting binding to a given MHC molecule. In this study, we have therefore made an in-depth analysis of combinations of three state-of-the-art MHC-peptide binding prediction methods (NetMHC, NetMHCpan and PickPocket). We demonstrate that a simple combination of NetMHC and NetMHCpan gives the highest performance when the allele in question is included in the training and is characterized by at least 50 data points with at least ten binders. Otherwise, NetMHCpan is the best predictor. When an allele has not been characterized, the performance depends on the distance to the training data. NetMHCpan has the highest performance when close neighbours are present in the training set, while the combination of NetMHCpan and PickPocket outperforms either of the two methods for alleles with more remote neighbours. The final method, NetMHCcons, is publicly available at www.cbs.dtu.dk/services/NetMHCcons , and allows the user in an automatic manner to obtain the most accurate predictions for any given MHC molecule.
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NASA Astrophysics Data System (ADS)
Fuchsberger, Jürgen; Kirchengast, Gottfried; Bichler, Christoph; Kabas, Thomas; Lenz, Gunther; Leuprecht, Armin
2017-04-01
The Feldbach region in southeast Austria, characteristic for experiencing a rich variety of weather and climate patterns, has been selected as the focus area for a pioneering weather and climate observation network at very high resolution: The WegenerNet comprises 153 meteorological stations measuring temperature, humidity, precipitation, and other parameters, in a tightly spaced grid within an area of about 20 km × 15 km centered near the city of Feldbach (46.93°N, 15.90°E). With its stations about every 2 km2, each with 5-min time sampling, the network provides regular measurements since January 2007. Detailed information is available in the recent description by Kirchengast et al. (2014) and via www.wegcenter.at/wegenernet. As a smaller "sister network" of the WegenerNet Feldbach region, the WegenerNet Johnsbachtal consists of eleven meteorological stations (complemented by one hydrographic station at the Johnsbach creek), measuring temperature, humidity, precipitation, radiation, wind, and other parameters in an alpine setting at altitudes ranging from below 700 m to over 2100 m. Data are available partly since 2007, partly since more recent dates and have a temporal resolution of 10 minutes. The networks are set to serve as a long-term monitoring and validation facility for weather and climate research and applications. Uses include validation of nonhydrostatic models operated at 1-km-scale resolution and of statistical downscaling techniques (in particular for precipitation), validation of radar and satellite data, study of orography-climate relationships, and many others. Quality-controlled station time series and gridded field data (spacing 200 m × 200 m) are available in near-real time (data latency less than 1-2 h) for visualization and download via a data portal (www.wegenernet.org). This data portal has been undergoing a complete renewal over the last year, and now serves as a modern gateway to the WegenerNet's more than 10 years of high-resolution data. The poster gives a brief introduction to the WegenerNet design and setup and shows a detailed overview of the new data portal. It also focuses on showing examples for high-resolution precipitation measurements, especially heavy-precipitation and convective events. Reference: Kirchengast, G., T. Kabas, A. Leuprecht, C. Bichler, and H. Truhetz (2014): WegenerNet: A pioneering high-resolution network for monitoring weather and climate. Bull. Amer. Meteor. Soc., 95, 227-242, doi:10.1175/BAMS-D-11-00161.1.
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....asp . Commenters can submit brief comments up to 6,000 characters, without prior registration, using the eComment system at http://www.ferc.gov/docs-filing/ecomment.asp . You must include your name and... cubic feet per second (cfs) at a net head of 33 to 77 feet; (6) an approximately 24.5-foot-wide, 30-foot...
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Two-Bin Kanban: Ordering Impact at Navy Medical Center San Diego
2016-06-17
pretest (2013 data set) and posttest (2015 data set) analysis to avoid having the findings influenced by price changes. DMLSS does not track shipping...statistics based on those observations (Kabacoff, 2011, p. 112). Replacing the groups of observations with summary statistics allows the analyst...listed on the Acquisition Research Program website (www.acquisitionresearch.net). Acquisition Research Program Graduate School of Business & Public
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Setting the Scene--Introduction to Quality in Peer Production of eLearning
ERIC Educational Resources Information Center
Auvinen, Ari-Matti
2008-01-01
The "Setting the scene" deliverable of the QMPP project (www.qmpp.net) has been authored by Mr. Ari-Matti Auvinen (HCI Productions Oy) and many QMPP project partners. In addition to the definition of the scope of the project, it includes also a good list of references to the literature of user-generated content as well as good web links…
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2017-03-23
Dynamical Astronomy , vol. 90, no. January 2004, pp. 165–178, 2004. [Online]. Available: https://www.researchgate.net/publication/ 225231299 On The...Celestial Mechanics and Dynamical Astronomy , vol. 32, no. 1, pp. 53–71, 1984. [Online]. Available: https://engineering.purdue.edu/people/kathleen.howell
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Net-centric Information Sharing: Supporting the 21st Century Maritime Strategy
2008-09-01
and Budget, Paperwork Reduction Project (0704-0188) Washington DC 20503. 1. AGENCY USE ONLY (Leave blank) 2. REPORT DATE September 2008 3...FEMA Federal Emergency Management Agency FOUO For Official Use Only GIS Geospacial Information System IC Intelligence Community IC ISM Intelligence...TPPU Task, Post, Process, Use UCORE Universal Core UCore Universal Core ULEX Universal Lexical Exchange USAF United States Air Force WWW World
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Pathogen profile update: Fusarium oxysporum.
Michielse, Caroline B; Rep, Martijn
2009-05-01
Kingdom Fungi; Phylum Ascomycota; Class Sordariomycetes; Order Hypocreales; Family Nectriaceae; genus Fusarium. Very broad at the species level. More than 120 different formae speciales have been identified based on specificity to host species belonging to a wide range of plant families. Initial symptoms of vascular wilt include vein clearing and leaf epinasty, followed by stunting, yellowing of the lower leaves, progressive wilting, defoliation and, finally, death of the plant. On fungal colonization, the vascular tissue turns brown, which is clearly visible in cross-sections of the stem. Some formae speciales are not primarily vascular pathogens, but cause foot and root rot or bulb rot. Can cause severe losses in many vegetables and flowers, field crops, such as cotton, and plantation crops, such as banana, date palm and oil palm. Use of resistant varieties is the only practical measure for controlling the disease in the field. In glasshouses, soil sterilization can be performed. http://www.broad.mit.edu/annotation/genome/fusarium_group/MultiHome.html; http://www.fgsc.net/Fusarium/fushome.htm; http://www.phi-base.org/query.php
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The Faulkes Telescope Project at school
NASA Astrophysics Data System (ADS)
Neta, Miguel
2014-05-01
The Faulkes Telescope Project [1] was started in 2000 and is currently managed by the Las Cumbres Observatory Global Telescope Network (LCOGT) [2]. Allows student access to two remote telescopes (in Hawaii and in Australia), allowing you to capture images of the sky. Since January 2012 I conduct monthly observations with students: first with students from Escola Secundária de Loulé (ESL) [3] and starting from September 2013 with students from Agrupamento de Escolas Dra Laura Ayres [4], in Quarteira. Each session is previously prepared in order to make the best of the time available. For that we use a virtual planetarium that allows us to see the sky in place and time of the scheduled session. After the start of each session a student takes control in real time of one of the telescopes from a computer connected to the internet. This project is a tool that gives the students the feeling of doing science and meet the sky step by step. The observations made by my students can be found at www.miguelneta.pt/faulkestelescope. [1] http://www.faulkes-telescope.com [2] http://lcogt.net [3] https://www.es-loule.edu.pt [4] http://www.esla.edu.pt
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NASA Astrophysics Data System (ADS)
Petzold, A.; Perim de Faria, J.; Berg, M.; Bundke, U.; Freedman, A.
2015-12-01
Monitoring the direct impact of aerosol particles on climate requires the continuous measurement of aerosol optical parameters like the aerosol extinction coefficient on a regular basis. Remote sensing and ground-based networks are well in place (e.g., AERONET, ACTRIS), whereas the regular in situ measurement of vertical profiles of atmospheric aerosol optical properties remains still an important challenge in quantifying climate change. The European Research Infrastructure IAGOS (In-service Aircraft for a Global Observing System; www.iagos.org) responds to the increasing requests for long-term, routine in situ observational data by using commercial passenger aircraft as measurement platform. However, scientific instrumentation for the measurement of atmospheric constituents requires major modifications before being deployable aboard in-service passenger aircraft. Recently, a compact and robust family of optical instruments based on the cavity attenuated phase shift (CAPS) technique has become available for measuring aerosol light extinction. While this technique was successfully deployed for ground-based atmospheric measurements under various conditions, its suitability for operation aboard aircraft in the free and upper free troposphere still has to be demonstrated. In this work, the modifications of a CAPS PMex instrument for measuring aerosol light extinction on aircraft, the results from subsequent laboratory tests for evaluating the modified instrument prototype, and first results from a field deployment aboard a research aircraft will be covered. In laboratory studies, the instrument showed excellent agreement (deviation < 5%) with theoretical values calculated from Rayleigh scattering cross-sections, when operated on pressurized air and CO2 at ambient and low pressure (~200 hPa). For monodisperse and polydisperse aerosols, reference aerosol extinction coefficients were calculated from measured size distributions and agreed with the CAPS PMex instrument response within 10% deviation. During the field deployment, aerosol extinction coefficients and associated aerosol size distributions have been measured and will be presented as comparison studies between measured and calculated data.
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Weiss, Scott T.
2014-01-01
Bayesian Networks (BN) have been a popular predictive modeling formalism in bioinformatics, but their application in modern genomics has been slowed by an inability to cleanly handle domains with mixed discrete and continuous variables. Existing free BN software packages either discretize continuous variables, which can lead to information loss, or do not include inference routines, which makes prediction with the BN impossible. We present CGBayesNets, a BN package focused around prediction of a clinical phenotype from mixed discrete and continuous variables, which fills these gaps. CGBayesNets implements Bayesian likelihood and inference algorithms for the conditional Gaussian Bayesian network (CGBNs) formalism, one appropriate for predicting an outcome of interest from, e.g., multimodal genomic data. We provide four different network learning algorithms, each making a different tradeoff between computational cost and network likelihood. CGBayesNets provides a full suite of functions for model exploration and verification, including cross validation, bootstrapping, and AUC manipulation. We highlight several results obtained previously with CGBayesNets, including predictive models of wood properties from tree genomics, leukemia subtype classification from mixed genomic data, and robust prediction of intensive care unit mortality outcomes from metabolomic profiles. We also provide detailed example analysis on public metabolomic and gene expression datasets. CGBayesNets is implemented in MATLAB and available as MATLAB source code, under an Open Source license and anonymous download at http://www.cgbayesnets.com. PMID:24922310
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Radom, Marcin; Rybarczyk, Agnieszka; Szawulak, Bartlomiej; Andrzejewski, Hubert; Chabelski, Piotr; Kozak, Adam; Formanowicz, Piotr
2017-12-01
Model development and its analysis is a fundamental step in systems biology. The theory of Petri nets offers a tool for such a task. Since the rapid development of computer science, a variety of tools for Petri nets emerged, offering various analytical algorithms. From this follows a problem of using different programs to analyse a single model. Many file formats and different representations of results make the analysis much harder. Especially for larger nets the ability to visualize the results in a proper form provides a huge help in the understanding of their significance. We present a new tool for Petri nets development and analysis called Holmes. Our program contains algorithms for model analysis based on different types of Petri nets, e.g. invariant generator, Maximum Common Transitions (MCT) sets and cluster modules, simulation algorithms or knockout analysis tools. A very important feature is the ability to visualize the results of almost all analytical modules. The integration of such modules into one graphical environment allows a researcher to fully devote his or her time to the model building and analysis. Available at http://www.cs.put.poznan.pl/mradom/Holmes/holmes.html. piotr@cs.put.poznan.pl. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com
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McGeachie, Michael J; Chang, Hsun-Hsien; Weiss, Scott T
2014-06-01
Bayesian Networks (BN) have been a popular predictive modeling formalism in bioinformatics, but their application in modern genomics has been slowed by an inability to cleanly handle domains with mixed discrete and continuous variables. Existing free BN software packages either discretize continuous variables, which can lead to information loss, or do not include inference routines, which makes prediction with the BN impossible. We present CGBayesNets, a BN package focused around prediction of a clinical phenotype from mixed discrete and continuous variables, which fills these gaps. CGBayesNets implements Bayesian likelihood and inference algorithms for the conditional Gaussian Bayesian network (CGBNs) formalism, one appropriate for predicting an outcome of interest from, e.g., multimodal genomic data. We provide four different network learning algorithms, each making a different tradeoff between computational cost and network likelihood. CGBayesNets provides a full suite of functions for model exploration and verification, including cross validation, bootstrapping, and AUC manipulation. We highlight several results obtained previously with CGBayesNets, including predictive models of wood properties from tree genomics, leukemia subtype classification from mixed genomic data, and robust prediction of intensive care unit mortality outcomes from metabolomic profiles. We also provide detailed example analysis on public metabolomic and gene expression datasets. CGBayesNets is implemented in MATLAB and available as MATLAB source code, under an Open Source license and anonymous download at http://www.cgbayesnets.com.
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Adalsteinsson, David; McMillen, David; Elston, Timothy C
2004-03-08
Intrinsic fluctuations due to the stochastic nature of biochemical reactions can have large effects on the response of biochemical networks. This is particularly true for pathways that involve transcriptional regulation, where generally there are two copies of each gene and the number of messenger RNA (mRNA) molecules can be small. Therefore, there is a need for computational tools for developing and investigating stochastic models of biochemical networks. We have developed the software package Biochemical Network Stochastic Simulator (BioNetS) for efficiently and accurately simulating stochastic models of biochemical networks. BioNetS has a graphical user interface that allows models to be entered in a straightforward manner, and allows the user to specify the type of random variable (discrete or continuous) for each chemical species in the network. The discrete variables are simulated using an efficient implementation of the Gillespie algorithm. For the continuous random variables, BioNetS constructs and numerically solves the appropriate chemical Langevin equations. The software package has been developed to scale efficiently with network size, thereby allowing large systems to be studied. BioNetS runs as a BioSpice agent and can be downloaded from http://www.biospice.org. BioNetS also can be run as a stand alone package. All the required files are accessible from http://x.amath.unc.edu/BioNetS. We have developed BioNetS to be a reliable tool for studying the stochastic dynamics of large biochemical networks. Important features of BioNetS are its ability to handle hybrid models that consist of both continuous and discrete random variables and its ability to model cell growth and division. We have verified the accuracy and efficiency of the numerical methods by considering several test systems.
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NASA Astrophysics Data System (ADS)
O, Sungmin; Foelsche, U.; Kirchengast, G.; Fuchsberger, J.
2018-01-01
Eight years of daily rainfall data from WegenerNet were analyzed by comparison with data from Austrian national weather stations. WegenerNet includes 153 ground level weather stations in an area of about 15 km × 20 km in the Feldbach region in southeast Austria. Rainfall has been measured by tipping bucket gauges at 150 stations of the network since the beginning of 2007. Since rain gauge measurements are considered close to true rainfall, there are increasing needs for WegenerNet data for the validation of rainfall data products such as remote sensing based estimates or model outputs. Serving these needs, this paper aims at providing a clearer interpretation on WegenerNet rainfall data for users in hydro-meteorological communities. Five clusters - a cluster consists of one national weather station and its four closest WegenerNet stations - allowed us close comparison of datasets between the stations. Linear regression analysis and error estimation with statistical indices were conducted to quantitatively evaluate the WegenerNet daily rainfall data. It was found that rainfall data between the stations show good linear relationships with an average correlation coefficient (r) of 0.97 , while WegenerNet sensors tend to underestimate rainfall according to the regression slope (0.87). For the five clusters investigated, the bias and relative bias were - 0.97 mm d-1 and - 11.5 % on average (except data from new sensors). The average of bias and relative bias, however, could be reduced by about 80 % through a simple linear regression-slope correction, with the assumption that the underestimation in WegenerNet data was caused by systematic errors. The results from the study have been employed to improve WegenerNet data for user applications so that a new version of the data (v5) is now available at the WegenerNet data portal (www.wegenernet.org).
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Increasing the Mobility of Dismounted Marines
2009-10-01
actually been the inspiration for military UGV development programs, including the Defense Advanced Research Projects Agency’s (DARPA) Legged Squad Support...or wheel-based; only the BigDog is a leg -based system. This presented BigDog with certain advantages (particularly involving its ability to traverse...1,000 pounds) Website: http://www.dtiweb.net/index.html 50 General Discussion: Ranlo The Ranlo – named after Defense Technologies, Inc.’s ( DTI
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2015-01-01
argues that pay appears to be an ambivalent fac- tor in job satisfaction or dissatisfaction.20 Additionally, a 2012 survey by the Center for Strategic and...Cohn, “Who Will Serve? Labour Markets and Military Personnel Policy,” Res Militaris 3, no. 2 (Winter–Spring 2013): http://www.resmilitaris.net...ence to Education (New York: Columbia University Press, 1975). 11. Bruce C. Greenwald, “Adverse Selection in the Labour Market,” Review of Economic
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Motion Simulation in the Environment for Auditory Research
2011-08-01
Toolbox, Centre for Digital Music , Queen Mary University of London, 2009. http://www.isophonics.net/content/spatial-audio- matlab-toolbox (accessed July 27...this work. 46 Student Bio I studied Music Technology at Northwestern University, graduating as valedictorian of the School of... Music in 2008. In 2009, I was awarded the Gates Cambridge Scholarship to fund a postgraduate degree at the University of Cambridge. I read for a
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2007-04-01
some of their data, others employ different techniques. United States defense contractor Lockheed Martin developed an anti-jam GPS receiver in 2000 for...Europe in a New Generation of Satellite Navigation Services,” European Commission (9 Feb 1999): 16. 25. Ibid. 26. Anne Jolis , “Problems Run Rampant...European Outer Space,” Euro Topics (19 March 2007), found at http://www.eurotopics.net/en/presseschau/archiv/archiv_dossier/DOSSIER15435. 40. Jolis
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Bringing Intelligence About: Practitioners Reflect on Best Practices
2003-05-01
commercial news Le Quotidien du Maroc www.casanet.net.ma/quotidien Casablanca; Independent daily 48389Turner.fm5 Page 22 Thursday, June 12...2003 6:22 AM 23 cation, joined only by the independent L’Economiste and Le Quotidien du Maroc . Morocco’s news dailies are still largely...Economique , and Maroc Hebdo , are prominent exceptions. But with most other electronic publications from the region, the researcher’s quest is
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Federal Research and Development Agenda for Net-Zero Energy, High-Performance Green Buildings
2008-10-21
transportation combined by 2050 (DOE 2007a). Figure 1. Energy Consumption in the United States Source: 2007 DOE Buildings Energy Data Book , Tables...poor indoor air quality (IAQ) include Legionnaires’ disease, heart disease and lung cancer from secondhand smoke, and carbon monoxide poisoning. More...www.eere.energy.gov/buildings/publications/pdfs/highperformance/commercialbuildin gsroadmap.pdf DOE. 2007a. Buildings energy data book . http
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Characterization of the Radiological Environment at J-Village during Operation Tomodachi
2013-02-01
individual as compared to those for the helicopter crew members (Appendix A). 3.2.2. Other Relevant Dosimetry Results Thermoluminescent dosimeter ( TLD ...internal monitoring results are available for 14 of these individuals. External dosimetry data (EPD and TLD ) showed that the maximum recorded dose for an...Washington, DC. http://www.NNSAResponseData.net. Accessed December 7. USAFCRD (U. S. Air Force Center for Radiation Dosimetry ), 2011. Electronic Pocket
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Re-Casting the FAC Net: People, Platforms, and Policy in Forward Air Control
2015-06-01
100 Super Sabre “Misty FAC”. . . . . . . . . . . . . . . . . . . . . . . . . 58 1 i Introduction Through the first six months of Operation...threat was greatly increased, FACs used F-100 Super Sabres and F-4 Phantom IIs to improve chances of survival. Finally, the enemy continued to...visibility. Source: http://www.pacificaviationmuseum.org/pearl-harbor-blog/north- american-f-100f-super- sabre -s-n-58-1232 Other innovations
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Re-casting the FAC Net: People, Platforms, and Policy in Forward Air Control
2015-06-01
100 Super Sabre “Misty FAC”. . . . . . . . . . . . . . . . . . . . . . . . . 58 1 i Introduction Through the first six months of Operation...threat was greatly increased, FACs used F-100 Super Sabres and F-4 Phantom IIs to improve chances of survival. Finally, the enemy continued to...visibility. Source: http://www.pacificaviationmuseum.org/pearl-harbor-blog/north- american-f-100f-super- sabre -s-n-58-1232 Other innovations
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Paul Sopko; Larry Bradshaw; Matt Jolly
2016-01-01
The Wildland Fire Assessment System (WFAS, www.wfas.net) is a one-stop-shop giving wildland fire managers the ability to assess fire potential ranging in scale from national to regional and temporally from 1 to 5 days. Each day, broad-area maps are produced from fire weather station and lightning location networks. Three products are created using 24 hour...
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2008-09-01
Research Methods: Qualitative and Quantitative Approaches (Boston: Pearson, 2006), 1-592. 48 This project demanded the use of a primarily...enforcement practices. 200 Neuman, Social Research Methods: Qualitative and Quantitative Approaches, 152...www.socialresearchmethods.net/kb/strucres.php (accessed July 12, 2008). 203 Neuman, Social Research Methods: Qualitative and Quantitative Approaches, 149. 204 Paul
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Caught in the Middle at the U.S.-Canadian Border
2013-03-01
Ibid., 486–88. 85 World Trade Law , “Canada―United States Free Trade Agreement: Preamble,” (n.d.), http://www.worldtradelaw.net/ nafta /cusfta.pdf...Maritime Domain Awareness MDOT Michigan Department of Transportation MiSN Michigan Security Network MSOC Marine Security Operation Center NAFTA ...brother, Kevin, and in- laws , Bill and Susie Leining, have given throughout the years. I am especially grateful to my parents, Craig and Phyllis
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Kleinsorge, F; Smetanay, K; Rom, J; Hörmansdörfer, C; Hörmannsdörfer, C; Scharf, A; Schmidt, P
2010-12-01
In 2008, 2 351 first trimester screenings were calculated by a newly developed internet database ( http:// www.firsttrimester.net ) to evaluate the risk for the presence of Down's syndrome. All data were evaluated by the conventional first trimester screening according to Nicolaides (FTS), based on the previous JOY Software, and by the advanced first trimester screening (AFS). After receiving the feedback of the karyotype as well as the rates of the correct positives, correct negatives, false positives, false negatives, the sensitivity and specificity were calculated and compared. Overall 255 cases were investigated which were analysed by both methods. These included 2 cases of Down's syndrome and one case of trisomy 18. The FTS and the AFS had a sensitivity of 100%. The specificity was 88.5% for the FTS and 93.0% for the AFS. As already shown in former studies, the higher specificity of the AFS is a result of a reduction of the false positive rate (28 to 17 cases). As a consequence of the AFS with a detection rate of 100% the rate of further invasive diagnostics in pregnant women is decreased by having 39% fewer positive tested women. © Georg Thieme Verlag KG Stuttgart · New York.
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NASA Astrophysics Data System (ADS)
Cao, Dayong
2014-03-01
New observations show that some asteroids are looked like comets. http://www.astrowatch.net/2013/11/freakish-asteroid-discovered-resembles.html, http://www.astrowatch.net/2013/11/astronomers-puzzle-over-newfound.html. It supports my idea that ``many dark comets with very special tilted orbits were arrested and lurked in the solar system'' - ``Sun's companion-dark hole seasonal took its dark comets belt and much dark matter to impact near our earth. And some of them probability hit on our earth. So this model kept and triggered periodic mass extinctions on our earth every 25 to 27 million years. After every impaction, many dark comets with very special tilted orbits were arrested and lurked in the solar system. Because some of them picked up many solar matter, so it looked like the asteroids. When the dark hole-Tyche goes near the solar system again, they will impact near planets.'' The idea maybe explains why do the asteroid looks like the comet? Where are the asteroids come from? What relationship do they have with the impactions and extinctions? http://meetings.aps.org/link/BAPS.2011.CAL.C1.7, http://meetings.aps.org/Meeting/CAL12/Event/181168, http://meetings.aps.org/link/BAPS.2013.MAR.H1.267. During 2009 to 2010, I had presented there are many dark comets like dark Asteroids near the orbit of Jupiter in ASP Meetings. In 2010, NASA's WISE found them. http://meetings.aps.org/link/BAPS.2011.APR.K1.17, http://www.nasa.gov/mission_pages/WISE/news/wise20100122.html Avoid Earth Extinction Associ.
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An audit of best evidence topic reviews in the International Journal of Surgery.
Mabvuure, Nigel Tapiwa; Klimach, Stefan; Eisner, Mark; Rodrigues, Jeremy Neil
2015-05-01
IJS launched best evidence topic reviews (BETs) in 2011, when the guidelines for conducting and reporting these reviews were published in the journal. (1) Audit the adherence of all published BETs in IJS to these guidelines. (2) Assess the reach and impact of BETs published in IJS. BETs published between 2011 and February 2014 were identified from http://www.journal-surgery.net/. Standards audited included: completeness of description of study attrition, and independent verification of searches. Other extracted data included: relevant subspecialty, duration between searches and publication, and between acceptance and publication. Each BET's number of citations (http://scholar.google.co.uk/), number of tweets (http://www.altmetric.com/) and number of Researchgate views (https://www.researchgate.net/) were recorded. Thirty-four BETs were identified: the majority, 19 (56%), relating to upper gastrointestinal surgery and none to cardiothoracic, orthopaedic or paediatric surgery. Twenty-nine BETs (82%) fully described study attrition. Twenty-one (62%) had independently verified search results. The mean times from literature searching to publication and acceptance to publication were 38.5 weeks and 13 days respectively. There were a mean 40 (range 0-89) Researchgate views/article, mean 2 (range 0-7) citations/article and mean 0.36 (range 0-2) tweets/article. Adherence to BET guidelines has been variable. Authors are encouraged to adhere to journal guidelines and reviewers and editors to enforce them. BETs have received similar citation levels to other IJS articles. Means of increasing the visibility of published BETs such as social media sharing, conference presentation and deposition of abstracts in public repositories should be explored. More work is required to encourage more submissions from other surgical subspecialties other than gastrointestinal specialties. Copyright © 2015 IJS Publishing Group Limited. Published by Elsevier Ltd. All rights reserved.
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NASA Astrophysics Data System (ADS)
Burton, Paul
1998-05-01
Thirty useful physics-related sites are listed to help get you started. I hope you will find some of the following sites of use in your teaching or good for pointing your pupils in the right direction when doing research. I have not attempted to rank or sort them in any order. However, by the time you read this issue of Physics Education some of the sites may not be available; this is the nature of the net. Those not wishing to retype each address can access them from my school's physics page (http://www.bootham.demon.co.uk/physics/links.html) or e-mail me at pkb@bootham.demon.co.uk and I can send you a document with the hypertext live links in. The new IOP sponsored 16-19 Physics project is promising great things with its own Internet site. You will be able to download information, updates, worksheets etc. Any queries about the development of this project at present can be sent to Evelyn van Dyk at: 16-19project@iop.org Engineering and Physical Sciences Research Councilhttp://www.epsrc.ac.uk Particle Physics and Astronomy Research Councilhttp://www.pparc.ac.uk American Institute of Physicshttp://www.aip.org Usenet Physics FAQ (frequently asked questions)http://www.weburbia.demon.co.uk/physics/faq.html CERNhttp://www.cern.ch/ BBC Educationhttp://www.bbc.co.uk/education/ Useful data on the Periodic Tablehttp://www.shef.ac.uk/chemistry/web-elements/ JET WWW index page:http://www.jet.uk NERC satellite station, Dundee Universityhttp://www.sat.dundee.ac.uk/ The Meteorological Officehttp://www.meto.govt.uk/ The Smithsonian Institute, Washington, DChttp://www.si.edu/newstart.htm Frequently asked questions on time and frequencyhttp://www.boulder.nist.gov/timefreq/faq/faq.htm Physics newshttp://www.het.brown.edu/news/index.html TIPTOP: The Internet Pilot to Physicshttp://www.tp.umu.se/TIPTOP/ A Dictionary of Scientific Quotationshttp://naturalscience.com/dsqhome.html ScI-Journal: an on-line publication for science studentshttp://www.soton.ac.uk/~plf/ScI-Journal/ Science On-linehttp://www.shu.ac.uk/schools/sci/sol/contents.htm Physics humourhttp://quark.physics.uwo.ca/~harwood/humor12.htm Searching for someone's e-mail address?http://www.four11.com SKY publicationshttp://www.skypub.com Planet Sciencehttp://www.keysites.com New Scientisthttp://www.newscientist.com NASA links to the American space programhttp://www.nasa.gov NASA Jet Propulsion Laboratoryhttp://www.jpl.nasa.gov Hewlett-Packardhttp://www.hp.com The Bradford Schools Telescope Projecthttp://www.telescope.org/rti/nuffield/ To contact a professional societyhttp://www.lib.uwaterloo.ca/society/overview.html The Schools' Physics Group: post-16 issueshttp://diana.ecs.soton.ac.uk/~pm/Physics/post16.html Sleuth search for physics and chemistryhttp://www.isleuth.com/index.shtml The Particle Adventurehttp://pdg.lbl.gov/cpep/adventure_home.html Acknowledgments I thank colleagues David Robinson and Robin Peach for their help in selecting and validating these sites and William Try, pupil at Bootham School, for preparing and maintaining the department's homepage with hypertext links. Received 21 January 1998
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The Virtual Earth-Solar Observatory of the SCiESMEX
NASA Astrophysics Data System (ADS)
De la Luz, V.; Gonzalez-Esparza, A.; Cifuentes-Nava, G.
2015-12-01
The Mexican Space Weather Service (SCiESMEX, http://www.sciesmex.unam.mx) started operations in October 2014. The project includes the Virtual Earth-Solar Observatory (VESO, http://www.veso.unam.mx). The VESO is a improved project wich objetive is integrate the space weather instrumentation network from the National Autonomous University of Mexico (UNAM). The network includes the Mexican Array Radiotelescope (MEXART), the Callisto receptor (MEXART), a Neutron Telescope, a Cosmic Ray Telescope. the Schumann Antenna, the National Magnetic Service, and the mexican GPS network (TlalocNet). The VESO facility is located at the Geophysics Institute campus Michoacan (UNAM). We offer the service of data store, real-time data, and quasi real-time data. The hardware of VESO includes a High Performance Computer (HPC) dedicated specially to big data storage.
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Integration of gel-based proteome data with pProRep.
Laukens, Kris; Matthiesen, Rune; Lemière, Filip; Esmans, Eddy; Onckelen, Harry Van; Jensen, Ole Nørregaard; Witters, Erwin
2006-11-15
pProRep is a web application integrating electrophoretic and mass spectral data from proteome analyses into a relational database. The graphical web-interface allows users to upload, analyse and share experimental proteome data. It offers researchers the possibility to query all previously analysed datasets and can visualize selected features, such as the presence of a certain set of ions in a peptide mass spectrum, on the level of the two-dimensional gel. The pProRep package and instructions for its use can be downloaded from http://www.ptools.ua.ac.be/pProRep. The application requires a web server that runs PHP 5 (http://www.php.net) and MySQL. Some (non-essential) extensions need additional freely available libraries: details are described in the installation instructions.
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NASA Astrophysics Data System (ADS)
Mysiak, J.; Testella, F.; Bonaiuto, M.; Carrus, G.; De Dominicis, S.; Ganucci Cancellieri, U.; Firus, K.; Grifoni, P.
2013-11-01
Italy's recent history is punctuated with devastating flood disasters claiming high death toll and causing vast but underestimated economic, social and environmental damage. The responses to major flood and landslide disasters such as the Polesine (1951), Vajont (1963), Firenze (1966), Valtelina (1987), Piedmont (1994), Crotone (1996), Sarno (1998), Soverato (2000), and Piedmont (2000) events have contributed to shaping the country's flood risk governance. Insufficient resources and capacity, slow implementation of the (at that time) novel risk prevention and protection framework, embodied in the law 183/89 of 18 May 1989, increased the reliance on the response and recovery operations of the civil protection. As a result, the importance of the Civil Protection Mechanism and the relative body of norms and regulation developed rapidly in the 1990s. In the aftermath of the Sarno (1998) and Soverato (2000) disasters, the Department for Civil Protection (DCP) installed a network of advanced early warning and alerting centres, the cornerstones of Italy's preparedness for natural hazards and a best practice worth following. However, deep convective clouds, not uncommon in Italy, producing intense rainfall and rapidly developing localised floods still lead to considerable damage and loss of life that can only be reduced by stepping up the risk prevention efforts. The implementation of the EU Floods Directive (2007/60/EC) provides an opportunity to revise the model of flood risk governance and confront the shortcomings encountered during more than 20 yr of organised flood risk management. This brief communication offers joint recommendations towards this end from three projects funded by the 2nd CRUE ERA-NET (http://www.crue-eranet.net/) Funding Initiative: FREEMAN, IMRA and URFlood.
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The integrated water balance and soil data set of the Rollesbroich hydrological observatory
NASA Astrophysics Data System (ADS)
Qu, Wei; Bogena, Heye R.; Huisman, Johan A.; Schmidt, Marius; Kunkel, Ralf; Weuthen, Ansgar; Schiedung, Henning; Schilling, Bernd; Sorg, Jürgen; Vereecken, Harry
2016-10-01
The Rollesbroich headwater catchment located in western Germany is a densely instrumented hydrological observatory and part of the TERENO (Terrestrial Environmental Observatories) initiative. The measurements acquired in this observatory present a comprehensive data set that contains key hydrological fluxes in addition to important hydrological states and properties. Meteorological data (i.e., precipitation, air temperature, air humidity, radiation components, and wind speed) are continuously recorded and actual evapotranspiration is measured using the eddy covariance technique. Runoff is measured at the catchment outlet with a gauging station. In addition, spatiotemporal variations in soil water content and temperature are measured at high resolution with a wireless sensor network (SoilNet). Soil physical properties were determined using standard laboratory procedures from samples taken at a large number of locations in the catchment. This comprehensive data set can be used to validate remote sensing retrievals and hydrological models, to improve the understanding of spatial temporal dynamics of soil water content, to optimize data assimilation and inverse techniques for hydrological models, and to develop upscaling and downscaling procedures of soil water content information. The complete data set is freely available online (http://www.tereno.net, doi:10.5880/TERENO.2016.001, doi:10.5880/TERENO.2016.004, doi:10.5880/TERENO.2016.003) and additionally referenced by three persistent identifiers securing the long-term data and metadata availability.
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SoyNet: a database of co-functional networks for soybean Glycine max.
Kim, Eiru; Hwang, Sohyun; Lee, Insuk
2017-01-04
Soybean (Glycine max) is a legume crop with substantial economic value, providing a source of oil and protein for humans and livestock. More than 50% of edible oils consumed globally are derived from this crop. Soybean plants are also important for soil fertility, as they fix atmospheric nitrogen by symbiosis with microorganisms. The latest soybean genome annotation (version 2.0) lists 56 044 coding genes, yet their functional contributions to crop traits remain mostly unknown. Co-functional networks have proven useful for identifying genes that are involved in a particular pathway or phenotype with various network algorithms. Here, we present SoyNet (available at www.inetbio.org/soynet), a database of co-functional networks for G. max and a companion web server for network-based functional predictions. SoyNet maps 1 940 284 co-functional links between 40 812 soybean genes (72.8% of the coding genome), which were inferred from 21 distinct types of genomics data including 734 microarrays and 290 RNA-seq samples from soybean. SoyNet provides a new route to functional investigation of the soybean genome, elucidating genes and pathways of agricultural importance. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.
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Deciphering kinase-substrate relationships by analysis of domain-specific phosphorylation network.
Damle, Nikhil Prakash; Mohanty, Debasisa
2014-06-15
In silico prediction of site-specific kinase-substrate relationships (ssKSRs) is crucial for deciphering phosphorylation networks by linking kinomes to phosphoproteomes. However, currently available predictors for ssKSRs give rise to a large number of false-positive results because they use only a short sequence stretch around phosphosite as determinants of kinase specificity and do not consider the biological context of kinase-substrate recognition. Based on the analysis of domain-specific kinase-substrate relationships, we have constructed a domain-level phosphorylation network that implicitly incorporates various contextual factors. It reveals preferential phosphorylation of specific domains by certain kinases. These novel correlations have been implemented in PhosNetConstruct, an automated program for predicting target kinases for a substrate protein. PhosNetConstruct distinguishes cognate kinase-substrate pairs from a large number of non-cognate combinations. Benchmarking on independent datasets using various statistical measures demonstrates the superior performance of PhosNetConstruct over ssKSR-based predictors. PhosNetConstruct is freely available at http://www.nii.ac.in/phosnetconstruct.html. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
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Hoefsloot, Wouter; van Ingen, Jakko; Andrejak, Claire; Angeby, Kristian; Bauriaud, Rosine; Bemer, Pascale; Beylis, Natalie; Boeree, Martin J; Cacho, Juana; Chihota, Violet; Chimara, Erica; Churchyard, Gavin; Cias, Raquel; Daza, Rosa; Daley, Charles L; Dekhuijzen, P N Richard; Domingo, Diego; Drobniewski, Francis; Esteban, Jaime; Fauville-Dufaux, Maryse; Folkvardsen, Dorte Bek; Gibbons, Noel; Gómez-Mampaso, Enrique; Gonzalez, Rosa; Hoffmann, Harald; Hsueh, Po-Ren; Indra, Alexander; Jagielski, Tomasz; Jamieson, Frances; Jankovic, Mateja; Jong, Eefje; Keane, Joseph; Koh, Wo-Jung; Lange, Berit; Leao, Sylvia; Macedo, Rita; Mannsåker, Turid; Marras, Theodore K; Maugein, Jeannette; Milburn, Heather J; Mlinkó, Tamas; Morcillo, Nora; Morimoto, Kozo; Papaventsis, Dimitrios; Palenque, Elia; Paez-Peña, Mar; Piersimoni, Claudio; Polanová, Monika; Rastogi, Nalin; Richter, Elvira; Ruiz-Serrano, Maria Jesus; Silva, Anabela; da Silva, M Pedro; Simsek, Hulya; van Soolingen, Dick; Szabó, Nora; Thomson, Rachel; Tórtola Fernandez, Teresa; Tortoli, Enrico; Totten, Sarah E; Tyrrell, Greg; Vasankari, Tuula; Villar, Miguel; Walkiewicz, Renata; Winthrop, Kevin L; Wagner, Dirk
2013-12-01
A significant knowledge gap exists concerning the geographical distribution of nontuberculous mycobacteria (NTM) isolation worldwide. To provide a snapshot of NTM species distribution, global partners in the NTM-Network European Trials Group (NET) framework (www.ntm-net.org), a branch of the Tuberculosis Network European Trials Group (TB-NET), provided identification results of the total number of patients in 2008 in whom NTM were isolated from pulmonary samples. From these data, we visualised the relative distribution of the different NTM found per continent and per country. We received species identification data for 20 182 patients, from 62 laboratories in 30 countries across six continents. 91 different NTM species were isolated. Mycobacterium avium complex (MAC) bacteria predominated in most countries, followed by M. gordonae and M. xenopi. Important differences in geographical distribution of MAC species as well as M. xenopi, M. kansasii and rapid-growing mycobacteria were observed. This snapshot demonstrates that the species distribution among NTM isolates from pulmonary specimens in the year 2008 differed by continent and differed by country within these continents. These differences in species distribution may partly determine the frequency and manifestations of pulmonary NTM disease in each geographical location.
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IntNetLncSim: an integrative network analysis method to infer human lncRNA functional similarity
Hu, Yang; Yang, Haixiu; Zhou, Chen; Sun, Jie; Zhou, Meng
2016-01-01
Increasing evidence indicated that long non-coding RNAs (lncRNAs) were involved in various biological processes and complex diseases by communicating with mRNAs/miRNAs each other. Exploiting interactions between lncRNAs and mRNA/miRNAs to lncRNA functional similarity (LFS) is an effective method to explore function of lncRNAs and predict novel lncRNA-disease associations. In this article, we proposed an integrative framework, IntNetLncSim, to infer LFS by modeling the information flow in an integrated network that comprises both lncRNA-related transcriptional and post-transcriptional information. The performance of IntNetLncSim was evaluated by investigating the relationship of LFS with the similarity of lncRNA-related mRNA sets (LmRSets) and miRNA sets (LmiRSets). As a result, LFS by IntNetLncSim was significant positively correlated with the LmRSet (Pearson correlation γ2=0.8424) and LmiRSet (Pearson correlation γ2=0.2601). Particularly, the performance of IntNetLncSim is superior to several previous methods. In the case of applying the LFS to identify novel lncRNA-disease relationships, we achieved an area under the ROC curve (0.7300) in experimentally verified lncRNA-disease associations based on leave-one-out cross-validation. Furthermore, highly-ranked lncRNA-disease associations confirmed by literature mining demonstrated the excellent performance of IntNetLncSim. Finally, a web-accessible system was provided for querying LFS and potential lncRNA-disease relationships: http://www.bio-bigdata.com/IntNetLncSim. PMID:27323856
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IntNetLncSim: an integrative network analysis method to infer human lncRNA functional similarity.
Cheng, Liang; Shi, Hongbo; Wang, Zhenzhen; Hu, Yang; Yang, Haixiu; Zhou, Chen; Sun, Jie; Zhou, Meng
2016-07-26
Increasing evidence indicated that long non-coding RNAs (lncRNAs) were involved in various biological processes and complex diseases by communicating with mRNAs/miRNAs each other. Exploiting interactions between lncRNAs and mRNA/miRNAs to lncRNA functional similarity (LFS) is an effective method to explore function of lncRNAs and predict novel lncRNA-disease associations. In this article, we proposed an integrative framework, IntNetLncSim, to infer LFS by modeling the information flow in an integrated network that comprises both lncRNA-related transcriptional and post-transcriptional information. The performance of IntNetLncSim was evaluated by investigating the relationship of LFS with the similarity of lncRNA-related mRNA sets (LmRSets) and miRNA sets (LmiRSets). As a result, LFS by IntNetLncSim was significant positively correlated with the LmRSet (Pearson correlation γ2=0.8424) and LmiRSet (Pearson correlation γ2=0.2601). Particularly, the performance of IntNetLncSim is superior to several previous methods. In the case of applying the LFS to identify novel lncRNA-disease relationships, we achieved an area under the ROC curve (0.7300) in experimentally verified lncRNA-disease associations based on leave-one-out cross-validation. Furthermore, highly-ranked lncRNA-disease associations confirmed by literature mining demonstrated the excellent performance of IntNetLncSim. Finally, a web-accessible system was provided for querying LFS and potential lncRNA-disease relationships: http://www.bio-bigdata.com/IntNetLncSim.
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Mentoring, Women in Engineering and Related Sciences, and MentorNet
NASA Astrophysics Data System (ADS)
Dockter, J.; Muller, C.
2003-12-01
Mentoring is a frequently employed strategy for retention of women in engineering and science. The power of mentoring is sometimes poorly understood, and mentoring is not always effectively practiced, however. At its strongest, mentoring is understood as a powerful learning process, which assures the intergenerational transfer of knowledge and "know-how" on an ongoing basis throughout one's life. Mentoring helps make explicit the tacit knowledge of a discipline and its professional culture, which is especially important for underrepresented groups. MentorNet (www.MentorNet.net), the E-Mentoring Network for Women in Engineering and Science, is a nonprofit organization focused on furthering women's progress in scientific and technical fields through the use of a dynamic, technology-supported mentoring program. Since 1998, nearly 10,000 undergraduate and graduate women studying engineering and related sciences at more than 100 colleges and universities across the U.S., and in several other nations, have been matched in structured, one-on-one, email-based mentoring relationships with male and female scientific and technical professionals working in industry and government. This poster will describe the MentorNet program, and provide findings of annual program evaluations related to outcomes for participants with particular focus on women in the planetary and earth sciences. We also address the development of the partnership of approximately 100 organizations currently involved in MentorNet and the value each gains from its affiliation. MentorNet is an ongoing effort which supports the interests of all organizations and individuals working to advance women in engineering and related sciences.
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NetCTLpan: pan-specific MHC class I pathway epitope predictions
Larsen, Mette Voldby; Lundegaard, Claus; Nielsen, Morten
2010-01-01
Reliable predictions of immunogenic peptides are essential in rational vaccine design and can minimize the experimental effort needed to identify epitopes. In this work, we describe a pan-specific major histocompatibility complex (MHC) class I epitope predictor, NetCTLpan. The method integrates predictions of proteasomal cleavage, transporter associated with antigen processing (TAP) transport efficiency, and MHC class I binding affinity into a MHC class I pathway likelihood score and is an improved and extended version of NetCTL. The NetCTLpan method performs predictions for all MHC class I molecules with known protein sequence and allows predictions for 8-, 9-, 10-, and 11-mer peptides. In order to meet the need for a low false positive rate, the method is optimized to achieve high specificity. The method was trained and validated on large datasets of experimentally identified MHC class I ligands and cytotoxic T lymphocyte (CTL) epitopes. It has been reported that MHC molecules are differentially dependent on TAP transport and proteasomal cleavage. Here, we did not find any consistent signs of such MHC dependencies, and the NetCTLpan method is implemented with fixed weights for proteasomal cleavage and TAP transport for all MHC molecules. The predictive performance of the NetCTLpan method was shown to outperform other state-of-the-art CTL epitope prediction methods. Our results further confirm the importance of using full-type human leukocyte antigen restriction information when identifying MHC class I epitopes. Using the NetCTLpan method, the experimental effort to identify 90% of new epitopes can be reduced by 15% and 40%, respectively, when compared to the NetMHCpan and NetCTL methods. The method and benchmark datasets are available at http://www.cbs.dtu.dk/services/NetCTLpan/. Electronic supplementary material The online version of this article (doi:10.1007/s00251-010-0441-4) contains supplementary material, which is available to authorized users. PMID:20379710
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NASA Astrophysics Data System (ADS)
Mamali, Dimitra; Marinou, Eleni; Pikridas, Michael; Kottas, Michael; Binietoglou, Ioannis; Kokkalis, Panagiotis; Tsekeri, Aleksandra; Amiridis, Vasilis; Sciare, Jean; Keleshis, Christos; Engelmann, Ronny; Ansmann, Albert; Russchenberg, Herman W. J.; Biskos, George
2017-04-01
Vertical profiles of the aerosol mass concentration derived from light detection and ranging (lidar) measurements were compared to airborne dried optical particle counter (OPC MetOne; Model 212) measurements during the INUIT-BACCHUS-ACTRIS campaign. The campaign took place in April 2016 and its main focus was the study of aerosol dust particles. During the campaign the NOA Polly-XT Raman lidar located at Nicosia (35.08° N, 33.22° E) was providing round-the-clock vertical profiles of aerosol optical properties. In addition, an unmanned aerial vehicle (UAV) carrying an OPC flew on 7 days during the first morning hours. The flights were performed at Orounda (35.1018° N, 33.0944° E) reaching altitudes of 2.5 km a.s.l, which allows comparison with a good fraction of the recorded lidar data. The polarization lidar photometer networking method (POLIPHON) was used for the estimation of the fine (non-dust) and coarse (dust) mode aerosol mass concentration profiles. This method uses as input the particle backscatter coefficient and the particle depolarization profiles of the lidar at 532 nm wavelength and derives the aerosol mass concentration. The first step in this approach makes use of the lidar observations to separate the backscatter and extinction contributions of the weakly depolarizing non-dust aerosol components from the contributions of the strongly depolarizing dust particles, under the assumption of an externally mixed two-component aerosol. In the second step, sun photometer retrievals of the fine and the coarse modes aerosol optical thickness (AOT) and volume concentration are used to calculate the associated concentrations from the extinction coefficients retrieved from the lidar. The estimated aerosol volume concentrations were converted into mass concentration with an assumption for the bulk aerosol density, and compared with the OPC measurements. The first results show agreement within the experimental uncertainty. This project received funding from the European Union's Seventh Framework Programme (FP7) project BACCHUS under grant agreement no. 603445, and the European Union's Horizon 2020 research and innovation programme ACTRIS-2 under grant agreement No 654109.
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The Impacts of Social Media on Citizen Security Behavior in Mexico
2012-03-01
consumo -de-medios- digitales -2010. 72 Guillermo Perezbolde V, “Twitter en México 2011, slide 9 of 16,” Mente Digital Presentation, June 9, 2011, http...recent times.68 67 Millward Brown, “Estudio de Consumo de Medios Digitales en México 2010,” IAB...México, http://www.slideshare.net/iabmexico/estudio-de- consumo -de-medios- digitales -2010. 68 Ibid. 28 Figure 2.3. Devices Used to Connect to the
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Recommendations for recognizing video events by concept vocabularies
2014-06-01
authorized to reproduce and distribute reprints for Governmental purposes notwithstanding any copyright anno - tation thereon. Disclaimer: The views and...detection and recognition for semantic annotation of video, Multimedia Tools Appl. 51 (1) (2011) 279–302. [6] A. Berg, J . Deng, S. Satheesh, H. Su, F.-F...Li, Imagenet Large Scale Visual Recognition Challenge 2011. <http://www.image-net.org/challenges/LSVRC/ 2011/>. [7] J . Deng, W. Dong, R. Socher, L
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Annual Report to the President and the Congress
2004-01-01
planning process has determined is needed to meet the military tasks as- signed to the Department by the President in his national security strategy...Commands" document, which formally as- signs forces to combatant commanders. The Global Force Management Process subsumes two developmen- tal measures...www.t2net.org), which was signed by Deputy Secretary of Defense Paul Wolfowitz on June 10, 2003, is a road map to developing and fielding dynamic
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Third International Electronic Conference on Medicinal Chemistry (ECMC-3)
Mayence, Annie
2018-01-01
The third International Electronic Conference on Medicinal Chemistry, organized and sponsored by MDPI AG, publisher, and the journal Pharmaceuticals, took place in November 2017 on the SciForum website (www.sciforum.net/conference/ecmc-3). Around 300 authors from 34 different countries participated at the event, which hosted more than 70 presentations, keynotes, videos, and posters. A short description of some works presented during that scientific meeting is disclosed in this report. PMID:29425181
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Journal of Special Operations Medicine, Volume 7, Edition 1
2007-01-01
SOMA through www.somaonline.org or contact MSG Russell Justice at justicer@earthlink.net. SOMA pro - vides a very valuable means of obtaining SOF...battlefield. The committee now has representation from all the Serv- ices and is busy deciding which way it needs to pro - ceed. There should be a...medical lessons learned and unit after actions reports (AARs) that con - tain combat mission needs has been a discussed item; this has been
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Applying Insights from Transaction Cost Economics (TCE) to Improve DoD Cost Estimation
2007-04-30
from July 2002 to September 2004, teaching a variety of economics courses , and serving on a number of committees to revise curricula for both the ...appeared in the International Public Management Review. The article (available at www.ipmr.net) is entitled “A New Management Model for Government...professor for the University of California at Santa Cruz, he teaches courses in project management and leadership to Silicon Valley public- and
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Saudi Arabia: Background and U.S. Relations
2015-04-29
23, 2013. 6 Background information on Saudi cabinet members is available at http://www.saudiembassy.net/about/ Biographies - of-Ministers.aspx. Saudi...territories it occupied in 1967, (2) agree to the establishment of a Palestinian state with a capital in East Jerusalem , and provide for the (3) “[a...compromise on Palestinian sovereignty in Jerusalem .” Elhanan Miller, “Arab ministers back Abbas in rejecting ‘Jewish’ Israel,” Times of Israel, January
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The Management of Ethnic-Cultural Diversity in Western Armed Forces
2012-03-20
192-201. 12 Bruce A. Brant, ―Vanguard of Social Change?‖ Military Review, no. 73 (February 1993): 12-19. 13 Histoire du monde Home Page, http...11, 2008. http://inde.aujourdhuilemonde.com/les-separatistes-gorkhas-entament-un-blocus- general?page=7 (accessed January 25, 2012). 15 ― Histoire ...du monde Home Page, http://www.histoiredumonde.net/Gurkhas.html (accessed January 25, 2012). 16 Histoire du monde Home Page, http
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Cyber Mobilization: The Neglected Aspect of Information Operations and Counterinsurgency Doctrine
2007-01-01
because of their contribution to what Stanford psychologist Albert Bandura refers to as “moral disengagement.” In order for individuals to become lethal...15. The game is offered via its own Web site http://www.specialforce.net/ english/indexeng.htm. 16. Ibid., 92. 17. Ibid., 91. 18. Albert Bandura ...Tactical Considerations vol. 2, ed. James J. F. Forest (Westport, CT: Praeger Security International, 2005) 34–50; Also, see Albert Bandura
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da Rocha, Edroaldo Lummertz; Ung, Choong Yong; McGehee, Cordelia D; Correia, Cristina; Li, Hu
2016-06-02
The sequential chain of interactions altering the binary state of a biomolecule represents the 'information flow' within a cellular network that determines phenotypic properties. Given the lack of computational tools to dissect context-dependent networks and gene activities, we developed NetDecoder, a network biology platform that models context-dependent information flows using pairwise phenotypic comparative analyses of protein-protein interactions. Using breast cancer, dyslipidemia and Alzheimer's disease as case studies, we demonstrate NetDecoder dissects subnetworks to identify key players significantly impacting cell behaviour specific to a given disease context. We further show genes residing in disease-specific subnetworks are enriched in disease-related signalling pathways and information flow profiles, which drive the resulting disease phenotypes. We also devise a novel scoring scheme to quantify key genes-network routers, which influence many genes, key targets, which are influenced by many genes, and high impact genes, which experience a significant change in regulation. We show the robustness of our results against parameter changes. Our network biology platform includes freely available source code (http://www.NetDecoder.org) for researchers to explore genome-wide context-dependent information flow profiles and key genes, given a set of genes of particular interest and transcriptome data. More importantly, NetDecoder will enable researchers to uncover context-dependent drug targets. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.
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MetNet: Software to Build and Model the Biogenetic Lattice of Arabidopsis
Wurtele, Eve Syrkin; Li, Jie; Diao, Lixia; ...
2003-01-01
MetNet (http://www.botany.iastate.edu/∼mash/metnetex/metabolicnetex.html) is publicly available software in development for analysis of genome-wide RNA, protein and metabolite profiling data. The software is designed to enable the biologist to visualize, statistically analyse and model a metabolic and regulatory network map of Arabidopsis , combined with gene expression profiling data. It contains a JAVA interface to an interactions database (MetNetDB) containing information on regulatory and metabolic interactions derived from a combination of web databases (TAIR, KEGG, BRENDA) and input from biologists in their area of expertise. FCModeler captures input from MetNetDB in a graphical form. Sub-networks can be identified and interpreted using simplemore » fuzzy cognitive maps. FCModeler is intended to develop and evaluate hypotheses, and provide a modelling framework for assessing the large amounts of data captured by high-throughput gene expression experiments. FCModeler and MetNetDB are currently being extended to three-dimensional virtual reality display. The MetNet map, together with gene expression data, can be viewed using multivariate graphics tools in GGobi linked with the data analytic tools in R. Users can highlight different parts of the metabolic network and see the relevant expression data highlighted in other data plots. Multi-dimensional expression data can be rotated through different dimensions. Statistical analysis can be computed alongside the visual. MetNet is designed to provide a framework for the formulation of testable hypotheses regarding the function of specific genes, and in the long term provide the basis for identification of metabolic and regulatory networks that control plant composition and development.« less
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2002-08-01
Insurance DOT Dictionary of Occupational Titles O*NET Occupational Information Network SGA substantial gainful activity SSA Social Security Administration...Examining Disability Criteria broader social changes that focus on building and supporting the work capacities of people with disabilities. To this...available at no charge on the GAO Web site at http://www.gao.gov. If you have any Page 35 GAO-02-597 Re-Examining Disability Criteria questions about
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2011-02-01
run a Microsoft OS. Apple iTunes Online sales and distribution of streaming and stored entertain- ment content www.itunes.com Apple provides the...Apple iTunes Online sales and distribu- tion of streaming and stored entertainment con- tent PodCast Creator Podcast Creator provides integrated...Commercial examples of software system COEs include Cisco WebEx, Microsoft NetMeet- CMU/SEI-2010-SR-025 | 16 ing, and Apple iTunes . Example Problem Space
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2015-07-27
R. (2013). Municipalities’ contracting out decisions: An empirical study on motives. Local Government Studies , 39(3), 414-434. Williamson, O...please contact any of the staff listed on the Acquisition Research Program website (www.acquisitionresearch.net). i Acquisition Research Program...market conditions on the use of fixed-price and cost reimbursement contracts by the Department of Defense. When the product is easy to specify
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Instability in the Horn of Africa: An Assessment of Ethiopian-Eritrean Conflict
2010-09-01
2000. 169 Zenebeworke Tadesse , “The Ethiopia-Eritrea Conflict,” 113, at: http://www.conflicttransform.net/Eritrea%20&%20Ethiopia.pdf (accessed July 20...dispute. The United States’ rapid diplomatic response team led by Susan Rice, U.S. Assistant Secretary of State, worked closely with Paul Kagame...actors to advance implementation have failed, resulting in continuing deadlock. B. THE U.S-RWANDA PEACE PLAN The U.S-Rwanda team was the first to
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Reference publication year spectroscopy (RPYS) of Eugene Garfield's publications.
Bornmann, Lutz; Haunschild, Robin; Leydesdorff, Loet
2018-01-01
Which studies, theories, and ideas have influenced Eugene Garfield's scientific work? Recently, the method reference publication year spectroscopy (RPYS) has been introduced, which can be used to answer this and related questions. Since then, several studies have been published dealing with the historical roots of research fields and scientists. The program CRExplorer (http://www.crexplorer.net) was specifically developed for RPYS. In this study, we use this program to investigate the historical roots of Eugene Garfield's oeuvre.
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Communications Channels in the Sahel Using Mauritania, Mali, Niger, and Chad as a Case Study
2007-05-01
issues, family, AIDS, etc. Malians listen to rap, but the lyrics are more positive than Western rap music. Dr. Arnoldi said the beat is similar to...Hassan, eds. The Muse of Modernity: Essays on Culture as Development in Africa. (Trenton: Africa World Press, Inc., 1996). Page 10 of 107 cultural...http://www.nollywood.net/ Essays /p2_articleid/126/p2_page/3>. Theatre for Development encourages community participation, increasing the
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Property Investigation of Laser Cladded, Laser Melted and Electron Beam Melted Ti-Al6-V4
2006-05-01
UNCLASSIFIED/UNLIMITED UNCLASSIFIED/UNLIMITED Figure 3: Examples of electron beam melted net shape parts; powder bed [3]. 1.4 Laser Cladding ...description, www.arcam.com. [4] K.-H. Hermann, S. Orban, S. Nowotny, Laser Cladding of Titanium Alloy Ti6242 to Restore Damaged Blades, Proceedings...Property Investigation of Laser Cladded , Laser Melted and Electron Beam Melted Ti-Al6-V4 Johannes Vlcek EADS Deutschland GmbH Corporate Research
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Measuring Perceptions About the Pashtun People
2011-03-01
PakTribune.com, November 22, 2010. BaNo, Sher. “Report from a Pashtun Teen .” New York Times, February 18, 2010. Barnes, Julian E. “Effort to Recruit More...Afghanistan.” http://www.joshuaproject.net/. Kamrany, Nake M. Review of After the Taliban: Nation Building in Afghanistan, by James F. Dobbins. Middle East...Journal 63, no. 5 (Fall 2010). Kamrany, Nake M., and Michael D. Intriligator. “Time to Quit Afghanistan Now.” Huffington Post, November 23, 2010
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Needle Decompression of Tension Pneumothorax Tactical Combat Casualty Care Guideline Recommendations
2012-07-06
Oxford Centre for Evidence - Based Medicine (OCEBM) method. 11. FINDINGS Thoracic injuries are one of the leading causes of death in trauma...for Evidence - Based Medicine . http://www.cebm.net/index.aspx?o=5653. Accessed on May 24, 2012 12. Davis DP, Pettit K, Rom CD, et al: The safety...TABLE Oxford Centre for Evidence - Based Medicine 2011 Levels of Evidence * Level may be graded down on the basis of study quality, imprecision
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OmicsNet: a web-based tool for creation and visual analysis of biological networks in 3D space.
Zhou, Guangyan; Xia, Jianguo
2018-06-07
Biological networks play increasingly important roles in omics data integration and systems biology. Over the past decade, many excellent tools have been developed to support creation, analysis and visualization of biological networks. However, important limitations remain: most tools are standalone programs, the majority of them focus on protein-protein interaction (PPI) or metabolic networks, and visualizations often suffer from 'hairball' effects when networks become large. To help address these limitations, we developed OmicsNet - a novel web-based tool that allows users to easily create different types of molecular interaction networks and visually explore them in a three-dimensional (3D) space. Users can upload one or multiple lists of molecules of interest (genes/proteins, microRNAs, transcription factors or metabolites) to create and merge different types of biological networks. The 3D network visualization system was implemented using the powerful Web Graphics Library (WebGL) technology that works natively in most major browsers. OmicsNet supports force-directed layout, multi-layered perspective layout, as well as spherical layout to help visualize and navigate complex networks. A rich set of functions have been implemented to allow users to perform coloring, shading, topology analysis, and enrichment analysis. OmicsNet is freely available at http://www.omicsnet.ca.
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EviNet: a web platform for network enrichment analysis with flexible definition of gene sets.
Jeggari, Ashwini; Alekseenko, Zhanna; Petrov, Iurii; Dias, José M; Ericson, Johan; Alexeyenko, Andrey
2018-06-09
The new web resource EviNet provides an easily run interface to network enrichment analysis for exploration of novel, experimentally defined gene sets. The major advantages of this analysis are (i) applicability to any genes found in the global network rather than only to those with pathway/ontology term annotations, (ii) ability to connect genes via different molecular mechanisms rather than within one high-throughput platform, and (iii) statistical power sufficient to detect enrichment of very small sets, down to individual genes. The users' gene sets are either defined prior to upload or derived interactively from an uploaded file by differential expression criteria. The pathways and networks used in the analysis can be chosen from the collection menu. The calculation is typically done within seconds or minutes and the stable URL is provided immediately. The results are presented in both visual (network graphs) and tabular formats using jQuery libraries. Uploaded data and analysis results are kept in separated project directories not accessible by other users. EviNet is available at https://www.evinet.org/.
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BoolNet--an R package for generation, reconstruction and analysis of Boolean networks.
Müssel, Christoph; Hopfensitz, Martin; Kestler, Hans A
2010-05-15
As the study of information processing in living cells moves from individual pathways to complex regulatory networks, mathematical models and simulation become indispensable tools for analyzing the complex behavior of such networks and can provide deep insights into the functioning of cells. The dynamics of gene expression, for example, can be modeled with Boolean networks (BNs). These are mathematical models of low complexity, but have the advantage of being able to capture essential properties of gene-regulatory networks. However, current implementations of BNs only focus on different sub-aspects of this model and do not allow for a seamless integration into existing preprocessing pipelines. BoolNet efficiently integrates methods for synchronous, asynchronous and probabilistic BNs. This includes reconstructing networks from time series, generating random networks, robustness analysis via perturbation, Markov chain simulations, and identification and visualization of attractors. The package BoolNet is freely available from the R project at http://cran.r-project.org/ or http://www.informatik.uni-ulm.de/ni/mitarbeiter/HKestler/boolnet/ under Artistic License 2.0. hans.kestler@uni-ulm.de Supplementary data are available at Bioinformatics online.
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König, Claudia; Mittelmark, Maurice B
2008-01-01
This report summarises opportunities in Europe for master's degree level training in health promotion. Using data available at www.HP-Source.net, 105 study programmes at 71 institutions, spread over 20 European countries, were identified that include health promotion as a main subject. The programmes were analysed along a number of dimensions, including title, learning objectives, curricula, learning and teaching methods, entry requirements, duration, accreditation, language(s) of instruction and participation in European educational structures. The present analysis reveals great diversity along all these dimensions, but also several clusters of programmes that offer quite similar education in health promotion. Of special interest is the range of options available in Europe for length of study, ranging from one to two years, with part-time as well as full-time options.
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NASA Astrophysics Data System (ADS)
Hobson, Michael; Graff, Philip; Feroz, Farhan; Lasenby, Anthony
2014-05-01
Machine-learning methods may be used to perform many tasks required in the analysis of astronomical data, including: data description and interpretation, pattern recognition, prediction, classification, compression, inference and many more. An intuitive and well-established approach to machine learning is the use of artificial neural networks (NNs), which consist of a group of interconnected nodes, each of which processes information that it receives and then passes this product on to other nodes via weighted connections. In particular, I discuss the first public release of the generic neural network training algorithm, called SkyNet, and demonstrate its application to astronomical problems focusing on its use in the BAMBI package for accelerated Bayesian inference in cosmology, and the identification of gamma-ray bursters. The SkyNet and BAMBI packages, which are fully parallelised using MPI, are available at http://www.mrao.cam.ac.uk/software/.
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The geospatial data quality REST API for primary biodiversity data
Otegui, Javier; Guralnick, Robert P.
2016-01-01
Summary: We present a REST web service to assess the geospatial quality of primary biodiversity data. It enables access to basic and advanced functions to detect completeness and consistency issues as well as general errors in the provided record or set of records. The API uses JSON for data interchange and efficient parallelization techniques for fast assessments of large datasets. Availability and implementation: The Geospatial Data Quality API is part of the VertNet set of APIs. It can be accessed at http://api-geospatial.vertnet-portal.appspot.com/geospatial and is already implemented in the VertNet data portal for quality reporting. Source code is freely available under GPL license from http://www.github.com/vertnet/api-geospatial. Contact: javier.otegui@gmail.com or rguralnick@flmnh.ufl.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26833340
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The geospatial data quality REST API for primary biodiversity data.
Otegui, Javier; Guralnick, Robert P
2016-06-01
We present a REST web service to assess the geospatial quality of primary biodiversity data. It enables access to basic and advanced functions to detect completeness and consistency issues as well as general errors in the provided record or set of records. The API uses JSON for data interchange and efficient parallelization techniques for fast assessments of large datasets. The Geospatial Data Quality API is part of the VertNet set of APIs. It can be accessed at http://api-geospatial.vertnet-portal.appspot.com/geospatial and is already implemented in the VertNet data portal for quality reporting. Source code is freely available under GPL license from http://www.github.com/vertnet/api-geospatial javier.otegui@gmail.com or rguralnick@flmnh.ufl.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.
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A Semantic Lexicon-Based Approach for Sense Disambiguation and Its WWW Application
NASA Astrophysics Data System (ADS)
di Lecce, Vincenzo; Calabrese, Marco; Soldo, Domenico
This work proposes a basic framework for resolving sense disambiguation through the use of Semantic Lexicon, a machine readable dictionary managing both word senses and lexico-semantic relations. More specifically, polysemous ambiguity characterizing Web documents is discussed. The adopted Semantic Lexicon is WordNet, a lexical knowledge-base of English words widely adopted in many research studies referring to knowledge discovery. The proposed approach extends recent works on knowledge discovery by focusing on the sense disambiguation aspect. By exploiting the structure of WordNet database, lexico-semantic features are used to resolve the inherent sense ambiguity of written text with particular reference to HTML resources. The obtained results may be extended to generic hypertextual repositories as well. Experiments show that polysemy reduction can be used to hint about the meaning of specific senses in given contexts.
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LPSN—list of prokaryotic names with standing in nomenclature
Parte, Aidan C.
2014-01-01
The List of Prokaryotic Names with Standing in Nomenclature (LPSN; http://www.bacterio.net) is a database that lists the names of prokaryotes (Bacteria and Archaea) that have been validly published in the International Journal of Systematic and Evolutionary Microbiology directly or by inclusion in a Validation List, under the Rules of International Code of Nomenclature of Bacteria. Currently there are 15 974 taxa listed. In addition, LPSN has an up-to-date classification of prokaryotes and information on prokaryotic nomenclature and culture collections. PMID:24243842
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Water Sustainability Assessments for Four Net Zero Water Installations
2013-12-01
es ea rc h La bo ra to ry Elisabeth M. Jenicek, Laura Curvey, Yuki Cruz, and Rachel Phillips December 2013 Approved for public release...for the Army, the Department of Defense, civilian agencies, and our nation’s public good. Find out more at www.erdc.usace.army.mil. To search for... public release; distribution is unlimited. Prepared for DASA(IEE) Arlington, VA 22202 Under Work Unit H83G56 ERDC/CERL TR-13-25 ii Abstract The
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Human Rights and United States Military Humanitarian and Civic Assistance in Latin America
2004-06-01
hearts and minds of local populations by seeing to the provision of their basic needs, such as potable water and healthcare. These projects, many...Socialist Deputy Questions U.S. Troop Presence,” G1. 102 Ibid.; “Deputy Aguas Rejects U.S. Military Presence,” [text] Quito, Quito Radio [Spanish], 2300 GMT...online: www.humanrights- usa.net/statements/0425RtoD.htm Accessed 3 September 2003. “Deputy Aguas Rejects U.S. Military Presence,” [text] Quito, Quito
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Net-Centric Warfare 2.0: Cloud Computing and the New Age of War
2009-02-01
Ellyssa Kroski, author of The Hive Mind: Folksonomies and User-based Tagging, writes: “With the advent of social software and Web 2.0, we usher in a new... Folksonomies and User-Based Tagging, (2007), http://infotangle.blogsome. com/2005/12/07/the-hive-mind- folksonomies -and-user-based-tagging/. 45 Office...www.govexec.com/dailyfed/1007/101007cdam1.htm (accessed February 4, 2009). Kroski, Ellyssa. "The Hive Mind: Folksonomies and User-Based Tagging
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Freeware for reporting radiation dosimetry following the administration of radiopharmaceuticals.
Gómez Perales, Jesús Luis; García Mendoza, Antonio
2015-09-01
This work describes the development of a software application for reporting patient radiation dosimetry following radiopharmaceutical administration. The resulting report may be included within the patient's medical records. The application was developed in the Visual Basic programming language. The dosimetric calculations are based on the values given by the International Commission on Radiological Protection (ICRP). The software is available in both Spanish and English and can be downloaded at no cost from www.radiopharmacy.net. Copyright © 2015 Elsevier Ltd. All rights reserved.
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How can the West Better Assist Partner Nations in Establishing Internal Security
2017-03-31
Force: The Art of War in the Modern World (London: Penguin Books, 2005), 5-6; Herfried Münkler, The New Wars, trans. Patrick Camiller (Cambridge...role. The organizations will not be special forces as understood as elite units, the 48 distillation of martial spirit, but forces which are...keeping,” (June 27, 1992) http://www.un- documents.net/a47-277.htm Smith, Rupert. The Utility of Force: The Art of War in the Modern World. London
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Crony Attack: Strategic Attack’s Silver Bullet
2006-11-01
Politics. 1. Bueno de Mesquita et al ., “Policy Failure and Political Survival,” 14–1. 1. Ibid., 149. 19. Ibid., 0. 20. Kirschner, “Microfoundations of...fighting. Notes 1. See Bueno de Mesquita et al ., “Policy Failure and Political Survival,” 147–61. 2. For more discussion of leadership’s manipulation...accessed 2 April 2003). http://www.d-i.net/fcs/;ppt/ellis_ kosovo_aar.ppt#315,7,Short War Syndrome (accessed 14 July 2006). Bueno de Mesquita, Bruce, et al
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Perl Extension to the Bproc Library
DOE Office of Scientific and Technical Information (OSTI.GOV)
Grunau, Daryl W.
2004-06-07
The Beowulf Distributed process Space (Bproc) software stack is comprised of UNIX/Linux kernel modifications and a support library by which a cluster of machines, each running their own private kernel, can present itself as a unified process space to the user. A Bproc cluster contains a single front-end machine and many back-end nodes which receive and run processes given to them by the front-end. Any process which is migrated to a back-end node is also visible as a ghost process on the fron-end, and may be controlled there using traditional UNIX semantics (e.g. ps(1), kill(1), etc). This software is amore » Perl extension to the Bproc library which enables the Perl programmer to make direct calls to functions within the Bproc library. See http://www.clustermatic.org, http://bproc.sourceforge.net, and http://www.perl.org« less
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Renewal of K-NET (National Strong-motion Observation Network of Japan)
NASA Astrophysics Data System (ADS)
Kunugi, T.; Fujiwara, H.; Aoi, S.; Adachi, S.
2004-12-01
The National Research Institute for Earth Science and Disaster Prevention (NIED) operates K-NET (Kyoshin Network), the national strong-motion observation network, which evenly covers the whole of Japan at intervals of 25 km on average. K-NET was constructed after the Hyogoken-Nambu (Kobe) earthquake in January 1995, and began operation in June 1996. Thus, eight years have passed since K-NET started, and large amounts of strong-motion records have been obtained. As technology has progressed and new technologies have become available, NIED has developed a new K-NET with improved functionality. New seismographs have been installed at 443 observatories mainly in southwestern Japan where there is a risk of strong-motion due to the Nankai and Tonankai earthquakes. The new system went into operation in June 2004, although seismographs have still to be replaced in other areas. The new seismograph (K-NET02) consists of a sensor module, a measurement module and a communication module. A UPS, a GPS antenna and a dial-up router are also installed together with a K-NET02. A triaxial accelerometer, FBA-ES-DECK (Kinemetrics Inc.) is built into the sensor module. The measurement module functions as a conventional strong-motion seismograph for high-precision observation. The communication module can perform sophisticated processes, such as calculation of the Japan Meteorological Agency (JMA) seismic intensity, continuous recording of data and near real-time data transmission. It connects to the Data Management Center (DMC) using an ISDN line. In case of a power failure, the measurement module can control the power supply to the router and the communication module to conserve battery power. One of the main features of K-NET02 is a function for processing JMA seismic intensity. K-NET02 functions as a proper seismic intensity meter that complies with the official requirements of JMA, although the old strong-motion seismograph (K-NET95) does not calculate seismic intensity. Another feature is near real-time data transmission. When a K-NET02 detects a strong-motion, it can automatically connect to the DMC in 2 to 5 seconds and then transmits seismic data. Furthermore, the full-scale is improved from 2000 gals to 4000 gals and the dynamic range of AD conversion is more than 132 dB. Strong-motion records of the new K-NET are available at: http://www.kyoshin.bosai.go.jp/
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Confidence limits for data mining models of options prices
NASA Astrophysics Data System (ADS)
Healy, J. V.; Dixon, M.; Read, B. J.; Cai, F. F.
2004-12-01
Non-parametric methods such as artificial neural nets can successfully model prices of financial options, out-performing the Black-Scholes analytic model (Eur. Phys. J. B 27 (2002) 219). However, the accuracy of such approaches is usually expressed only by a global fitting/error measure. This paper describes a robust method for determining prediction intervals for models derived by non-linear regression. We have demonstrated it by application to a standard synthetic example (29th Annual Conference of the IEEE Industrial Electronics Society, Special Session on Intelligent Systems, pp. 1926-1931). The method is used here to obtain prediction intervals for option prices using market data for LIFFE “ESX” FTSE 100 index options ( http://www.liffe.com/liffedata/contracts/month_onmonth.xls). We avoid special neural net architectures and use standard regression procedures to determine local error bars. The method is appropriate for target data with non constant variance (or volatility).
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Hazan, Lynn; Zugaro, Michaël; Buzsáki, György
2006-09-15
Recent technological advances now allow for simultaneous recording of large populations of anatomically distributed neurons in behaving animals. The free software package described here was designed to help neurophysiologists process and view recorded data in an efficient and user-friendly manner. This package consists of several well-integrated applications, including NeuroScope (http://neuroscope.sourceforce.net), an advanced viewer for electrophysiological and behavioral data with limited editing capabilities, Klusters (http://klusters.sourceforge.net), a graphical cluster cutting application for manual and semi-automatic spike sorting, NDManager (GPL,see http://www.gnu.org/licenses/gpl.html), an experimental parameter and data processing manager. All of these programs are distributed under the GNU General Public License (GPL, see ), which gives its users legal permission to copy, distribute and/or modify the software. Also included are extensive user manuals and sample data, as well as source code and documentation.
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Larsen, Pernille Stemann; Kamper-Jørgensen, Mads; Adamson, Ashley; Barros, Henrique; Bonde, Jens Peter; Brescianini, Sonia; Brophy, Sinead; Casas, Maribel; Charles, Marie-Aline; Devereux, Graham; Eggesbø, Merete; Fantini, Maria Pia; Frey, Urs; Gehring, Ulrike; Grazuleviciene, Regina; Henriksen, Tine Brink; Hertz-Picciotto, Irva; Heude, Barbara; Hryhorczuk, Daniel O; Inskip, Hazel; Jaddoe, Vincent W V; Lawlor, Debbie A; Ludvigsson, Johnny; Kelleher, Cecily; Kiess, Wieland; Koletzko, Berthold; Kuehni, Claudia Elisabeth; Kull, Inger; Kyhl, Henriette Boye; Magnus, Per; Momas, Isabelle; Murray, Dierdre; Pekkanen, Juha; Polanska, Kinga; Porta, Daniela; Poulsen, Gry; Richiardi, Lorenzo; Roeleveld, Nel; Skovgaard, Anne Mette; Sram, Radim J; Strandberg-Larsen, Katrine; Thijs, Carel; Van Eijsden, Manon; Wright, John; Vrijheid, Martine; Andersen, Anne-Marie Nybo
2013-07-01
During the past 25 years, many pregnancy and birth cohorts have been established. Each cohort provides unique opportunities for examining associations of early-life exposures with child development and health. However, to fully exploit the large amount of available resources and to facilitate cross-cohort collaboration, it is necessary to have accessible information on each cohort and its individual characteristics. The aim of this work was to provide an overview of European pregnancy and birth cohorts registered in a freely accessible database located at http://www.birthcohorts.net. European pregnancy and birth cohorts initiated in 1980 or later with at least 300 mother-child pairs enrolled during pregnancy or at birth, and with postnatal data, were eligible for inclusion. Eligible cohorts were invited to provide information on the data and biological samples collected, as well as the timing of data collection. In total, 70 cohorts were identified. Of these, 56 fulfilled the inclusion criteria encompassing a total of more than 500,000 live-born European children. The cohorts represented 19 countries with the majority of cohorts located in Northern and Western Europe. Some cohorts were general with multiple aims, whilst others focused on specific health or exposure-related research questions. This work demonstrates a great potential for cross-cohort collaboration addressing important aspects of child health. The web site, http://www.birthcohorts.net, proved to be a useful tool for accessing information on European pregnancy and birth cohorts and their characteristics. © 2013 John Wiley & Sons Ltd.
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NASA Astrophysics Data System (ADS)
Knouft, J.; Ficklin, D. L.; Bart, H. L.; Rios, N. E.
2017-12-01
Streamflow and water temperature are primary factors influencing the traits, distribution, and diversity of freshwater species. Ongoing changes in climate are causing directional alteration of these environmental conditions, which can impact local ecological processes. Accurate estimation of these variables is critical for predicting the responses of species to ongoing changes in freshwater habitat, yet ecologically relevant high-resolution data describing variation in streamflow and water temperature across North America are not available. Considering the vast amount of web-accessible freshwater biodiversity data, development and application of appropriate hydrologic data are critical to the advancement of our understanding of freshwater systems. To address this issue, we are developing the "HydroClim" database, which will provide web-accessible (www.hydroclim.org) historical and projected monthly streamflow and water temperature data for stream sections in all major watersheds across the United States and Canada from 1950-2099. These data will also be integrated with FishNet 2 (www.fishnet2.net), an online biodiversity database that provides open access to over 2 million localities of freshwater fish species in the United States and Canada, thus allowing for the characterization of the habitat requirements of freshwater species across this region. HydroClim should provide a vast array of opportunities for a greater understanding of water resources as well as information for the conservation of freshwater biodiversity in the United States and Canada in the coming century.
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Andreatta, Massimo; Karosiene, Edita; Rasmussen, Michael; Stryhn, Anette; Buus, Søren; Nielsen, Morten
2015-11-01
A key event in the generation of a cellular response against malicious organisms through the endocytic pathway is binding of peptidic antigens by major histocompatibility complex class II (MHC class II) molecules. The bound peptide is then presented on the cell surface where it can be recognized by T helper lymphocytes. NetMHCIIpan is a state-of-the-art method for the quantitative prediction of peptide binding to any human or mouse MHC class II molecule of known sequence. In this paper, we describe an updated version of the method with improved peptide binding register identification. Binding register prediction is concerned with determining the minimal core region of nine residues directly in contact with the MHC binding cleft, a crucial piece of information both for the identification and design of CD4(+) T cell antigens. When applied to a set of 51 crystal structures of peptide-MHC complexes with known binding registers, the new method NetMHCIIpan-3.1 significantly outperformed the earlier 3.0 version. We illustrate the impact of accurate binding core identification for the interpretation of T cell cross-reactivity using tetramer double staining with a CMV epitope and its variants mapped to the epitope binding core. NetMHCIIpan is publicly available at http://www.cbs.dtu.dk/services/NetMHCIIpan-3.1 .
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NASA Astrophysics Data System (ADS)
Fröhlich, R.; Crenn, V.; Setyan, A.; Belis, C. A.; Canonaco, F.; Favez, O.; Riffault, V.; Slowik, J. G.; Aas, W.; Aijälä, M.; Alastuey, A.; Artiñano, B.; Bonnaire, N.; Bozzetti, C.; Bressi, M.; Carbone, C.; Coz, E.; Croteau, P. L.; Cubison, M. J.; Esser-Gietl, J. K.; Green, D. C.; Gros, V.; Heikkinen, L.; Herrmann, H.; Jayne, J. T.; Lunder, C. R.; Minguillón, M. C.; Močnik, G.; O'Dowd, C. D.; Ovadnevaite, J.; Petralia, E.; Poulain, L.; Priestman, M.; Ripoll, A.; Sarda-Estève, R.; Wiedensohler, A.; Baltensperger, U.; Sciare, J.; Prévôt, A. S. H.
2015-02-01
Chemically resolved atmospheric aerosol data sets from the largest intercomparison of the Aerodyne aerosol chemical speciation monitors (ACSM) performed to date were collected at the French atmospheric supersite SIRTA. In total 13 quadrupole ACSMs (Q-ACSM) from the European ACTRIS ACSM network, one time-of-flight ACSM (ToF-ACSM), and one high-resolution ToF aerosol mass spectrometer (AMS) were operated in parallel for about three weeks in November and December 2013. Part 1 of this study reports on the accuracy and precision of the instruments for all the measured species. In this work we report on the intercomparison of organic components and the results from factor analysis source apportionment by positive matrix factorisation (PMF) utilising the multilinear engine 2 (ME-2). Except for the organic contribution of m/z 44 to the total organics (f44), which varied by factors between 0.6 and 1.3 compared to the mean, the peaks in the organic mass spectra were similar among instruments. The m/z 44 differences in the spectra resulted in a variable f44 in the source profiles extracted by ME-2, but had only a minor influence on the extracted mass contributions of the sources. The presented source apportionment yielded four factors for all 15 instruments: hydrocarbon-like organic aerosol (HOA), cooking-related organic aerosol (COA), biomass burning-related organic aerosol (BBOA) and secondary oxygenated organic aerosol (OOA). Individual application and optimisation of the ME-2 boundary conditions (profile constraints) are discussed together with the investigation of the influence of alternative anchors (reference profiles). A comparison of the ME-2 source apportionment output of all 15 instruments resulted in relative SD from the mean between 13.7 and 22.7% of the source's average mass contribution depending on the factors (HOA: 14.3 ± 2.2%, COA: 15.0 ± 3.4%, OOA: 41.5 ± 5.7%, BBOA: 29.3 ± 5.0%). Factors which tend to be subject to minor factor mixing (in this case COA) have higher relative uncertainties than factors which are recognised more readily like the OOA. Averaged over all factors and instruments the relative first SD from the mean of a source extracted with ME-2 was 17.2%.
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ESO Reflex: A Graphical Workflow Engine for Data Reduction
NASA Astrophysics Data System (ADS)
Hook, R.; Romaniello, M.; Péron, M.; Ballester, P.; Gabasch, A.; Izzo, C.; Ullgrén, M.; Maisala, S.; Oittinen, T.; Solin, O.; Savolainen, V.; Järveläinen, P.; Tyynelä, J.
2008-08-01
Sampo {http://www.eso.org/sampo} (Hook et al. 2005) is a project led by ESO and conducted by a software development team from Finland as an in-kind contribution to joining ESO. The goal is to assess the needs of the ESO community in the area of data reduction environments and to create pilot software products that illustrate critical steps along the road to a new system. Those prototypes will not only be used to validate concepts and understand requirements but will also be tools of immediate value for the community. Most of the raw data produced by ESO instruments can be reduced using CPL {http://www.eso.org/cpl} recipes: compiled C programs following an ESO standard and utilizing routines provided by the Common Pipeline Library. Currently reduction recipes are run in batch mode as part of the data flow system to generate the input to the ESO VLT/VLTI quality control process and are also made public for external users. Sampo has developed a prototype application called ESO Reflex {http://www.eso.org/sampo/reflex/} that integrates a graphical user interface and existing data reduction algorithms. ESO Reflex can invoke CPL-based recipes in a flexible way through a dedicated interface. ESO Reflex is based on the graphical workflow engine Taverna {http://taverna.sourceforge.net} that was originally developed by the UK eScience community, mostly for work in the life sciences. Workflows have been created so far for three VLT/VLTI instrument modes ( VIMOS/IFU {http://www.eso.org/instruments/vimos/}, FORS spectroscopy {http://www.eso.org/instruments/fors/} and AMBER {http://www.eso.org/instruments/amber/}), and the easy-to-use GUI allows the user to make changes to these or create workflows of their own. Python scripts and IDL procedures can be easily brought into workflows and a variety of visualisation and display options, including custom product inspection and validation steps, are available.
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Electronic patient record and archive of records in Cardio.net system for telecardiology.
Sierdziński, Janusz; Karpiński, Grzegorz
2003-01-01
In modern medicine the well structured patient data set, fast access to it and reporting capability become an important question. With the dynamic development of information technology (IT) such question is solved via building electronic patient record (EPR) archives. We then obtain fast access to patient data, diagnostic and treatment protocols etc. It results in more efficient, better and cheaper treatment. The aim of the work was to design a uniform Electronic Patient Record, implemented in cardio.net system for telecardiology allowing the co-operation among regional hospitals and reference centers. It includes questionnaires for demographic data and questionnaires supporting doctor's work (initial diagnosis, final diagnosis, history and physical, ECG at the discharge, applied treatment, additional tests, drugs, daily and periodical reports). The browser is implemented in EPR archive to facilitate data retrieval. Several tools for creating EPR and EPR archive were used such as: XML, PHP, Java Script and MySQL. The separate question is the security of data on WWW server. The security is ensured via Security Socket Layer (SSL) protocols and other tools. EPR in Cardio.net system is a module enabling the co-work of many physicians and the communication among different medical centers.
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Yan, Xianghe; Peng, Yun; Meng, Jianghong; Ruzante, Juliana; Fratamico, Pina M; Huang, Lihan; Juneja, Vijay; Needleman, David S
2011-01-01
Several factors have hindered effective use of information and resources related to food safety due to inconsistency among semantically heterogeneous data resources, lack of knowledge on profiling of food-borne pathogens, and knowledge gaps among research communities, government risk assessors/managers, and end-users of the information. This paper discusses technical aspects in the establishment of a comprehensive food safety information system consisting of the following steps: (a) computational collection and compiling publicly available information, including published pathogen genomic, proteomic, and metabolomic data; (b) development of ontology libraries on food-borne pathogens and design automatic algorithms with formal inference and fuzzy and probabilistic reasoning to address the consistency and accuracy of distributed information resources (e.g., PulseNet, FoodNet, OutbreakNet, PubMed, NCBI, EMBL, and other online genetic databases and information); (c) integration of collected pathogen profiling data, Foodrisk.org ( http://www.foodrisk.org ), PMP, Combase, and other relevant information into a user-friendly, searchable, "homogeneous" information system available to scientists in academia, the food industry, and government agencies; and (d) development of a computational model in semantic web for greater adaptability and robustness.
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NASA Astrophysics Data System (ADS)
Haidl, F. M.; Vodden, C.; Bates, J. L.; Morgan, A. V.
2009-05-01
CGEN, the outreach arm of the Canadian Federation of Earth Sciences, is a network of more than 270 individuals from all over Canada who work to promote geoscience education and public awareness of science. CGEN's priorities are threefold: to improve the quality of Earth science education delivered in our primary and secondary schools; to raise public awareness about the Earth sciences and their impact on everyday life; and to encourage student interest in the Earth sciences as a career option. These priorities are supported by CGEN's six core programs: 1) The national EdGEO program (www.edgeo.org), initiated in the 1970s, supports Earth science workshops for teachers. These workshops, organized by teams of local educators and geoscientists, provide teachers with "enhanced knowledge, classroom resources and increased confidence" to more effectively teach Earth science. In 2008, a record 521 teachers attended 14 EdGEO workshops. 2) EarthNet (www.earthnet-geonet.ca) is a virtual resource centre that provides support for teachers and for geoscientists involved in education and outreach. In 2008, EarthNet received a $11,500 grant from Encana Corporation to develop energy-related content. 3) The new Careers in Earth Science website (www.earthsciencescanada.com/careers), launched in October 2008, enhances CGEN's capacity to encourage students to pursue a career in the Earth sciences. This project exemplifies the value of collaboration with other organizations. Seven groups provided financial support for the project and many other organizations and individuals contributed in-kind support. 4) Geoscape Canada and Waterscape Canada, programs led by the Geological Survey of Canada, communicate practical Earth science information to teachers, students, and other members of communities across Canada through a series of electronic and hard-copy posters and other resources. Many of the resources created from 1998 to 2007 are available online (www.geoscape.nrcan.gc.ca). A northern British Columbia geological highway map was published in 2008. In the works are a geological map for southern British Columbia and three community and regional geoscience guides. 5) What on Earth (www.whatonearth.org), a biannual national newsletter established at the University of Waterloo in 1987, provides a range of Earth science information for teachers in Canada and elsewhere. It was originally published as a colourful printed newsletter, which in recent years was also available online; new issues will be available only online. 6) Friends of Canadian Geoheritage is a new national program currently being piloted in the Ottawa-Gatineau area, where it is working with municipal and other government agencies, schools, universities, and community groups to help preserve, protect and promote Canada's rich geoheritage. A new Geo-Park, a book on building materials in Ottawa, a Geoheritage day, field trips and public talks are just some of the initiatives underway.
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MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.
Kumar, Sudhir; Stecher, Glen; Li, Michael; Knyaz, Christina; Tamura, Koichiro
2018-06-01
The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.
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The Groningen Protocol: what is it, how do the Dutch use it, and do we use it here?
Catlin, Anita; Novakovich, Renee
2008-01-01
In this article, a sensitive, complex and provocative issue is discussed. It will undoubtedly stimulate a variety of opinions. What do you think? Post your comments about this topic on the Pediatric Nursing Web site and read what others have to say as well. Visit our homepage at www.pediatricnursing.net and click on "Discussions." The opinions and assertions contained herein are the private views of the contributors and do not necessarily reflect the views of Pediatric Nursing or the publisher.
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NASA Technical Reports Server (NTRS)
Anderson, Eric
2016-01-01
SERVIR is a joint NASA - US Agency for International Development (USAID) project to improve environmental decision-making using Earth observations and geospatial technologies. A common need identified among SERVIR regions has been improved information for disaster risk reduction and in specific surface water and flood extent mapping, monitoring and forecasting. Of the 70 SERVIR products (active, complete, and in development), 4 are related to surface water and flood extent mapping, monitoring or forecasting. Visit http://www.servircatalog.net for more product details.
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Protection of Northern Chile as an ICOMOS/IAU ``Window to the Universe''
NASA Astrophysics Data System (ADS)
Smith, Malcolm G.
2015-03-01
Over the last two decades, La Serena's population has increased by about 70 percent. A site description of the AURA Observatory in Chile as a ``Window to the Universe`` is now available on the recently-launched UNESCO-IAU Astronomical Heritage Web Portal, www.astronomicalheritage.net This can serve as an example of possible material for the Chilean authorities, should they wish to propose the dark skies over much of northern Chile for protection as a World Scientific Heritage site. Some of the steps involved are discussed briefly here.
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IRONSIDES: DNS With No Single Packet Denial of Service or Remote Code Execution Vulnerabilities
2012-02-27
Caching DNSSEC TSIG 1Pv6 Wildcard S fi.. In terface y y Y * N __ mo e ---- o •• vare y y y N NN y m progress y y y NY N Web, Y command...Proceedings of the 2007 IEEE Aerospace Conference. [6) C. Heitmeyer, M . Archer, E. Leonard and J. Mclean, "Applying formal methods to a certifiably secure...2003). [1 5] DNSSEC-The DNS Security Extensions, http:// http://www.dnssec.net/ (16] S . Conchon, E. Contcjean and J. Kanig, "Ergo : A theorem prover
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CNOP testimony on their understanding of training programs in optics
NASA Astrophysics Data System (ADS)
Lasagesse, Laétitia
2005-10-01
Within the National Commission for Training in Optics & Photonics (CNOP), the state of play in education for optics has been compiled at national level from primary & secondary level to University and technological training levels. Partners from CNOP propose to: - Present the www.optra.net Website webmastered by Opticsvalley, on which a list of optics training in Europe is available- Zoom in on Professional diplomas such as CQPM "optician de précision", CQPM "monteur de précision"- Present the existing baccalaureat (French A Level) concerning Optics - ...
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2008-05-09
using better technology as a means might be an effective strategy to achieve desired effects and to reduce risk. Tim Berners - Lee , founder of the World...of information disclosure persecution. Tim Berners - Lee advises, “human communication scales up only if we can be tolerant of the differences while we...the government to define intended use Figure 1: Slide by Tim Berners - Lee at http://www.w3.org/2000/Talks/1206-xml2k- tbl.27 The Author added the
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Fusing literature and full network data improves disease similarity computation.
Li, Ping; Nie, Yaling; Yu, Jingkai
2016-08-30
Identifying relatedness among diseases could help deepen understanding for the underlying pathogenic mechanisms of diseases, and facilitate drug repositioning projects. A number of methods for computing disease similarity had been developed; however, none of them were designed to utilize information of the entire protein interaction network, using instead only those interactions involving disease causing genes. Most of previously published methods required gene-disease association data, unfortunately, many diseases still have very few or no associated genes, which impeded broad adoption of those methods. In this study, we propose a new method (MedNetSim) for computing disease similarity by integrating medical literature and protein interaction network. MedNetSim consists of a network-based method (NetSim), which employs the entire protein interaction network, and a MEDLINE-based method (MedSim), which computes disease similarity by mining the biomedical literature. Among function-based methods, NetSim achieved the best performance. Its average AUC (area under the receiver operating characteristic curve) reached 95.2 %. MedSim, whose performance was even comparable to some function-based methods, acquired the highest average AUC in all semantic-based methods. Integration of MedSim and NetSim (MedNetSim) further improved the average AUC to 96.4 %. We further studied the effectiveness of different data sources. It was found that quality of protein interaction data was more important than its volume. On the contrary, higher volume of gene-disease association data was more beneficial, even with a lower reliability. Utilizing higher volume of disease-related gene data further improved the average AUC of MedNetSim and NetSim to 97.5 % and 96.7 %, respectively. Integrating biomedical literature and protein interaction network can be an effective way to compute disease similarity. Lacking sufficient disease-related gene data, literature-based methods such as MedSim can be a great addition to function-based algorithms. It may be beneficial to steer more resources torward studying gene-disease associations and improving the quality of protein interaction data. Disease similarities can be computed using the proposed methods at http:// www.digintelli.com:8000/ .
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The UMIST database for astrochemistry 2006
NASA Astrophysics Data System (ADS)
Woodall, J.; Agúndez, M.; Markwick-Kemper, A. J.; Millar, T. J.
2007-05-01
Aims:We present a new version of the UMIST Database for Astrochemistry, the fourth such version to be released to the public. The current version contains some 4573 binary gas-phase reactions, an increase of 10% from the previous (1999) version, among 420 species, of which 23 are new to the database. Methods: Major updates have been made to ion-neutral reactions, neutral-neutral reactions, particularly at low temperature, and dissociative recombination reactions. We have included for the first time the interstellar chemistry of fluorine. In addition to the usual database, we have also released a reaction set in which the effects of dipole-enhanced ion-neutral rate coefficients are included. Results: These two reactions sets have been used in a dark cloud model and the results of these models are presented and discussed briefly. The database and associated software are available on the World Wide Web at www.udfa.net. Tables 1, 2, 4 and 9 are only available in electronic form at http://www.aanda.org
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Vorwerk, D
2002-02-01
Eurorad (www.eurorad.org) is a joint project of EAR and has support of 27 national and 8 subspeciality radiology societies. Eurorad is the first noncommercial radiological publication that is exclusively based on the internet as a communication line with all steps of submission, reviewing and publication being performed online. Eurorad wants to build up a huge and exhaustive case file of diagnostic and interventional radiology. Like all scientific publications, Eurorad bases on an editor in chief and 13 section editors who are responsible for organizing each section of Eurorad. Each section has a number of peer reviewer with an overall total of more than 100. For submission and publication, all cases are structured in the same manner with case report, method and discussion. For the time being, Eurorad hosts 779 cases, of whom 346 are free available on the net. The actual rejection rate is 4.5%, other cases are under review.
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Rotation-Infall Motion around the Protostar IRAS 16293-2422 Traced by Water Maser Emission
NASA Astrophysics Data System (ADS)
Imai, Hiroshi; Iwata, Takahiro; Miyoshi, Makoto
1999-08-01
We made VLBI observations of the water maser emission associated with a protostar, IRAS 16293-2422, using the Kashima-Nobeyama Interferometer (KNIFE) and the Japanese domestic VLBI network (J-Net).\\footnote[2]. These distributions of water maser features showed the blue-shifted and red-shifted components separated in the north-south direction among three epochs spanning three years. The direction of the separation was perpendicular to the molecular outflow and parallel to the elongation of the molecular disk. These steady distributions were successfully modeled by a rotating-infalling disk with an outer radius of 100 AU around a central object with a mass of 0.3 MO . The local specific angular momentum of the disk was calculated to be 0.2-1.0times 10-3 km s-1 pc at a radius of 20-100 AU. This value is roughly equal to that of the disk of IRAS 00338+6312 in L1287 and those of the molecular disks around the protostars in the Taurus molecular cloud. The relatively large disk radius of about 100 AU traced by water maser emission suggests that impinging clumps onto the disk should be hotter than 200 K to excite the water maser emission. Mizusawa, Nobeyama, and Kagoshima stations are operated by staff members of National Astronomical Observatory of the Ministry of Education, Science, Sports and Culture. Kashima station is operated by staff members of Communications Research Laboratory of the Ministry of Posts and Telecomunications. The recent status of J-Net is seen in the WWW home page: http://www.nro.nao.ac.jp/\\ \\ miyaji/Jnet.
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Petersson, Ingemar F; Strömbeck, Britta; Andersen, Lene; Cimmino, Marco; Greiff, Rolf; Loza, Estibaliz; Sciré, Carlo; Stamm, Tanja; Stoffer, Michaela; Uhlig, Till; Woolf, Anthony D; Vliet Vlieland, Theodora P M
2014-05-01
Eumusc.net (http://www.eumusc.net) is a European project supported by the EU and European League Against Rheumatism to improve musculoskeletal care in Europe. To develop patient-centred healthcare quality indicators (HCQIs) for healthcare provision for rheumatoid arthritis (RA) patients. Based on a systematic literature search, existing HCQIs for RA were identified and their contents analysed and categorised referring to a list of 16 standards of care developed within the eumusc.net. An international expert panel comprising 14 healthcare providers and two patient representatives added topics and during repeated Delphi processes by email ranked the topics and rephrased suggested HCQIs with the preliminary set being established during a second expert group meeting. After an audit process by rheumatology units (including academic centres) in six countries (The Netherlands, Norway, Romania, Italy, Austria and Sweden), a final version of the HCQIs was established. 56 possible topics for HCQIs were processed resulting in a final set of HCQIs for RA (n=14) including two for structure (patient information and calculation of composite scores), 11 for process (eg, access to care, assessments, and pharmacological and non-pharmacological treatments) and one for outcome (effect of treatment on disease activity). They included definitions to be used in clinical practice and also by patients. Further, the numerators and the denominators for each HCQI were defined. A set of 14 patient-centred HCQIs for RA was developed to be used in quality improvement and bench marking in countries across Europe.
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Israel Marine Bio-geographic Database (ISRAMAR-BIO)
NASA Astrophysics Data System (ADS)
Greengrass, Eyal; Krivenko, Yevgeniya; Ozer, Tal; Ben Yosef, Dafna; Tom, Moshe; Gertman, Isaac
2015-04-01
The knowledge of the space/time variations of species is the basis for any ecological investigations. While historical observations containing integral concentrations of biological parameters (chlorophyll, abundance, biomass…) are organized partly in ISRAMAR Cast Database, the taxon-specific data collected in Israel has not been sufficiently organized. This has been hindered by the lack of standards, variability of methods and complexity of biological data formalization. The ISRAMAR-BIO DB was developed to store various types of historical and future available information related to marine species observations and related metadata. Currently the DB allows to store biological data acquired by the following sampling devices such as: van veer grab, box corer, sampling bottles, nets (plankton, trawls and fish), quadrates, and cameras. The DB's logical unit is information regarding a specimen (taxa name, barcode, image), related attributes (abundance, size, age, contaminants…), habitat description, sampling device and method, time and space of sampling, responsible organization and scientist, source of information (cruise, project and publication). The following standardization of specimen and attributes naming were implemented: Taxonomy according to World Register of Marine Species (WoRMS: http://www.marinespecies.org). Habitat description according to Coastal and Marine Ecological Classification Standards (CMECS: http://www.cmecscatalog.org) Parameter name; Unit; Device name; Developmental stage; Institution name; Country name; Marine region according to SeaDataNet Vocabularies (http://www.seadatanet.org/Standards-Software/Common-Vocabularies). This system supports two types of data submission procedures, which support the above stated data structure. The first is a downloadable excel file with drop-down fields based on the ISRAMAR-BIO vocabularies. The file is filled and uploaded online by the data contributor. Alternatively, the same dataset can be assembled by filling online forms and then submitted to the DB. Online access to the ISRAMAR-BIO is available through taxon search page, where one can get both biological and geographical data regarding a certain taxon. Further development of the online data access is ongoing. It will include interactive geographical map interface where data may be queried, analyzed and downloaded.
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Passing messages between biological networks to refine predicted interactions.
Glass, Kimberly; Huttenhower, Curtis; Quackenbush, John; Yuan, Guo-Cheng
2013-01-01
Regulatory network reconstruction is a fundamental problem in computational biology. There are significant limitations to such reconstruction using individual datasets, and increasingly people attempt to construct networks using multiple, independent datasets obtained from complementary sources, but methods for this integration are lacking. We developed PANDA (Passing Attributes between Networks for Data Assimilation), a message-passing model using multiple sources of information to predict regulatory relationships, and used it to integrate protein-protein interaction, gene expression, and sequence motif data to reconstruct genome-wide, condition-specific regulatory networks in yeast as a model. The resulting networks were not only more accurate than those produced using individual data sets and other existing methods, but they also captured information regarding specific biological mechanisms and pathways that were missed using other methodologies. PANDA is scalable to higher eukaryotes, applicable to specific tissue or cell type data and conceptually generalizable to include a variety of regulatory, interaction, expression, and other genome-scale data. An implementation of the PANDA algorithm is available at www.sourceforge.net/projects/panda-net.
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Schmale, Julia; Henning, Silvia; Henzing, Bas; Keskinen, Helmi; Sellegri, Karine; Ovadnevaite, Jurgita; Bougiatioti, Aikaterini; Kalivitis, Nikos; Stavroulas, Iasonas; Jefferson, Anne; Park, Minsu; Schlag, Patrick; Kristensson, Adam; Iwamoto, Yoko; Pringle, Kirsty; Reddington, Carly; Aalto, Pasi; Äijälä, Mikko; Baltensperger, Urs; Bialek, Jakub; Birmili, Wolfram; Bukowiecki, Nicolas; Ehn, Mikael; Fjæraa, Ann Mari; Fiebig, Markus; Frank, Göran; Fröhlich, Roman; Frumau, Arnoud; Furuya, Masaki; Hammer, Emanuel; Heikkinen, Liine; Herrmann, Erik; Holzinger, Rupert; Hyono, Hiroyuki; Kanakidou, Maria; Kiendler-Scharr, Astrid; Kinouchi, Kento; Kos, Gerard; Kulmala, Markku; Mihalopoulos, Nikolaos; Motos, Ghislain; Nenes, Athanasios; O’Dowd, Colin; Paramonov, Mikhail; Petäjä, Tuukka; Picard, David; Poulain, Laurent; Prévôt, André Stephan Henry; Slowik, Jay; Sonntag, Andre; Swietlicki, Erik; Svenningsson, Birgitta; Tsurumaru, Hiroshi; Wiedensohler, Alfred; Wittbom, Cerina; Ogren, John A.; Matsuki, Atsushi; Yum, Seong Soo; Myhre, Cathrine Lund; Carslaw, Ken; Stratmann, Frank; Gysel, Martin
2017-01-01
Cloud condensation nuclei (CCN) number concentrations alongside with submicrometer particle number size distributions and particle chemical composition have been measured at atmospheric observatories of the Aerosols, Clouds, and Trace gases Research InfraStructure (ACTRIS) as well as other international sites over multiple years. Here, harmonized data records from 11 observatories are summarized, spanning 98,677 instrument hours for CCN data, 157,880 for particle number size distributions, and 70,817 for chemical composition data. The observatories represent nine different environments, e.g., Arctic, Atlantic, Pacific and Mediterranean maritime, boreal forest, or high alpine atmospheric conditions. This is a unique collection of aerosol particle properties most relevant for studying aerosol-cloud interactions which constitute the largest uncertainty in anthropogenic radiative forcing of the climate. The dataset is appropriate for comprehensive aerosol characterization (e.g., closure studies of CCN), model-measurement intercomparison and satellite retrieval method evaluation, among others. Data have been acquired and processed following international recommendations for quality assurance and have undergone multiple stages of quality assessment. PMID:28291234
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NASA Astrophysics Data System (ADS)
Schmale, Julia; Henning, Silvia; Henzing, Bas; Keskinen, Helmi; Sellegri, Karine; Ovadnevaite, Jurgita; Bougiatioti, Aikaterini; Kalivitis, Nikos; Stavroulas, Iasonas; Jefferson, Anne; Park, Minsu; Schlag, Patrick; Kristensson, Adam; Iwamoto, Yoko; Pringle, Kirsty; Reddington, Carly; Aalto, Pasi; Äijälä, Mikko; Baltensperger, Urs; Bialek, Jakub; Birmili, Wolfram; Bukowiecki, Nicolas; Ehn, Mikael; Fjæraa, Ann Mari; Fiebig, Markus; Frank, Göran; Fröhlich, Roman; Frumau, Arnoud; Furuya, Masaki; Hammer, Emanuel; Heikkinen, Liine; Herrmann, Erik; Holzinger, Rupert; Hyono, Hiroyuki; Kanakidou, Maria; Kiendler-Scharr, Astrid; Kinouchi, Kento; Kos, Gerard; Kulmala, Markku; Mihalopoulos, Nikolaos; Motos, Ghislain; Nenes, Athanasios; O'Dowd, Colin; Paramonov, Mikhail; Petäjä, Tuukka; Picard, David; Poulain, Laurent; Prévôt, André Stephan Henry; Slowik, Jay; Sonntag, Andre; Swietlicki, Erik; Svenningsson, Birgitta; Tsurumaru, Hiroshi; Wiedensohler, Alfred; Wittbom, Cerina; Ogren, John A.; Matsuki, Atsushi; Yum, Seong Soo; Myhre, Cathrine Lund; Carslaw, Ken; Stratmann, Frank; Gysel, Martin
2017-03-01
Cloud condensation nuclei (CCN) number concentrations alongside with submicrometer particle number size distributions and particle chemical composition have been measured at atmospheric observatories of the Aerosols, Clouds, and Trace gases Research InfraStructure (ACTRIS) as well as other international sites over multiple years. Here, harmonized data records from 11 observatories are summarized, spanning 98,677 instrument hours for CCN data, 157,880 for particle number size distributions, and 70,817 for chemical composition data. The observatories represent nine different environments, e.g., Arctic, Atlantic, Pacific and Mediterranean maritime, boreal forest, or high alpine atmospheric conditions. This is a unique collection of aerosol particle properties most relevant for studying aerosol-cloud interactions which constitute the largest uncertainty in anthropogenic radiative forcing of the climate. The dataset is appropriate for comprehensive aerosol characterization (e.g., closure studies of CCN), model-measurement intercomparison and satellite retrieval method evaluation, among others. Data have been acquired and processed following international recommendations for quality assurance and have undergone multiple stages of quality assessment.
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Electronics Environmental Benefits Calculator
The Electronics Environmental Benefits Calculator (EEBC) was developed to assist organizations in estimating the environmental benefits of greening their purchase, use and disposal of electronics.The EEBC estimates the environmental and economic benefits of: Purchasing Electronic Product Environmental Assessment Tool (EPEAT)-registered products; Enabling power management features on computers and monitors above default percentages; Extending the life of equipment beyond baseline values; Reusing computers, monitors and cell phones; and Recycling computers, monitors, cell phones and loads of mixed electronic products.The EEBC may be downloaded as a Microsoft Excel spreadsheet.See https://www.federalelectronicschallenge.net/resources/bencalc.htm for more details.
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Gene-chromosome locations of neuropsychiatric diseases.
Shapshak, Paul; Somboonwit, Charurut; Sinnott, John; Commins, Deborah; Singer, Elyse; Levine, Andrew
2011-01-01
A number of genes are involved in various neuropsychiatric disorders. A comprehensive compilation of these genes is important for a better understanding of these diseases. We report an online file that lists genes by chromosome number and location. This is useful for the rapid examination of chromosome bands for genes involved in these diseases. This is not an exhaustive list and does not include single nucleotide polymorphism (SNP) results for genes that are currently being examined by genome wide association studies (GWAS) and other molecular methodologies. The database is available for free at http://www.bioinformation.net/007/paul.xls.
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MASTER-SAAO: contradictory SN and flaring OT
NASA Astrophysics Data System (ADS)
Balanutsa, P.; Lipunov, V.; Buckley, D.; Gorbovskoy, E.; Tiurina, N.; Kuznetsov, A.; Kornilov, V.; Gress, O.; Pogrosheva, T.; Shumkov, V.; Vladimirov, V.; Vlasenko, D.; Kuvshinov, D.; Gabovich, A.
2017-07-01
MASTER-SAAO auto-detection system ( Lipunov et al., "MASTER Global Robotic Net", Advances in Astronomy, 2010, 30L ) discovered OT source at (RA, Dec) = 03h 42m 50.70s , -01d 52m 28s.7 on 2017-07-01.1753UT with unfiltered (6 images), that contradicts to Ia type detected in ATEL #10240 , ATEL #10225 for ATLAS17dcl ( http://www.supernova.thistlethwaites.com/sn2017/sndate.html ). It is in 8.4"W,20"S of PGC135685 with Btc=15.13, Vgsr=2773 http://leda.univ-lyon1.fr/ledacat.cgi?PGC135685 Spectral observations are required.
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Elementary particles, dark matter candidate and new extended standard model
NASA Astrophysics Data System (ADS)
Hwang, Jaekwang
2017-01-01
Elementary particle decays and reactions are discussed in terms of the three-dimensional quantized space model beyond the standard model. Three generations of the leptons and quarks correspond to the lepton charges. Three heavy leptons and three heavy quarks are introduced. And the bastons (new particles) are proposed as the possible candidate of the dark matters. Dark matter force, weak force and strong force are explained consistently. Possible rest masses of the new particles are, tentatively, proposed for the experimental searches. For more details, see the conference paper at https://www.researchgate.net/publication/308723916.
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BOREAS TE-17 Production Efficiency Model Images
NASA Technical Reports Server (NTRS)
Hall, Forrest G.; Papagno, Andrea (Editor); Goetz, Scott J.; Goward, Samual N.; Prince, Stephen D.; Czajkowski, Kevin; Dubayah, Ralph O.
2000-01-01
A Boreal Ecosystem-Atmospheric Study (BOREAS) version of the Global Production Efficiency Model (http://www.inform.umd.edu/glopem/) was developed by TE-17 (Terrestrial Ecology) to generate maps of gross and net primary production, autotrophic respiration, and light use efficiency for the BOREAS region. This document provides basic information on the model and how the maps were generated. The data generated by the model are stored in binary image-format files. The data files are available on a CD-ROM (see document number 20010000884), or from the Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC).
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Emergence, Agency, and Interaction-Notes from the Field.
Penny, Simon
2015-01-01
This article describes the development of several interactive installations and robotic artworks developed through the 1990s and the technological, theoretical, and discursive context in which those works arose. The main works discussed are Petit Mal (1989-1995), Sympathetic Sentience (1996-1997), Fugitive I (1996-1997), Traces (1998-1999), and Fugitive II (2001-2004)-full documentation at ( www.simonpenny.net/works ). These works were motivated by a critical analysis of cognitivist computer science, which contrasted with notions of embodied experience arising from the arts. The works address questions of agency and interaction, informed by cybernetics and artificial life.
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NASA Astrophysics Data System (ADS)
Weber, Daniel; Schrod, Jann; Drücke, Jaqueline; Keleshis, Christos; Pikridas, Michael; Ebert, Martin; Cvetkovic, Bojan; Nickovic, Slobodan; Baars, Holger; Marinou, Eleni; Vrekoussis, Mihalis; Sciare, Jean; Mihalopoulos, Nikos; Curtius, Joachim; Bingemer, Heinz G.
2017-04-01
During the intensive INUIT-BACCHUS-ACTRIS field campaign focusing on aerosols, clouds and ice nucleation in the Eastern Mediterranean in April 2016, we have measured the abundance of ice nucleating particles (INP) in the lower troposphere both with unmanned aircraft systems (UAS) as well as from the ground. Aerosol samples were collected by miniaturized electrostatic precipitators onboard the UAS and were analyzed immediately after collection on site in the ice nucleus counter FRIDGE for INP active at -20˚ C to -30˚ C in the deposition/condensation mode (INPD). Immersion freezing INP (INPI) were sampled on membrane filters and were analysed in aqueous extracts by the drop freezing method on the cold stage of FRIDGE. Ground samples were collected at the Cyprus Atmospheric Observatory (CAO) in Agia Marina Xyliatou (Latitude; 35˚ 2' 8" N; Longitude: 33˚ 3' 26" E; Altitude: 532 m a.s.l.). During the one-month campaign, we encountered a series of Saharan dust plumes that traveled at several kilometers altitude. Here we present INP data from 42 individual flights, together with OPC aerosol number concentrations, backscatter and depolarization retrievals from the Polly-XT Raman Lidar, dust concentrations derived by the dust transport model DREAM (Dust Regional Atmospheric Model), and results from scanning electron microscopy. The effect of the dust plumes is reflected by the coincidence of INP with the particulate mass (PM), the Lidar retrievals and the predicted dust mass of the model. This suggests that mineral dust or a constituent related to dust was a major contributor to the ice nucleating properties of the aerosol. Peak concentrations of above 100 INP std.l-1 were measured at -30˚ C. The INPD concentration in elevated plumes was on average a factor of 10 higher than at ground level. The INPI concentration at ground also agreed with PM levels and exceeded the ground-based INPD concentration by more than one order of magnitude. Since desert dust is transported for long distances over wide areas of the globe predominantly at several km altitude, we conclude that INP measurements at ground level may be of limited significance for the situation at the level of cloud formation. This project received funding from the European Union's Seventh Framework Programme (FP7) project BACCHUS under grant agreement no. 603445, and the European Union's Horizon 2020 research and innovation programme ACTRIS-2 under grant agreement No 654109, and the Deutsche Forschungsgemeinschaft (DFG) under the Research Unit FOR 1525 (INUIT).
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NASA Astrophysics Data System (ADS)
Fröhlich, R.; Crenn, V.; Setyan, A.; Belis, C. A.; Canonaco, F.; Favez, O.; Riffault, V.; Slowik, J. G.; Aas, W.; Aijälä, M.; Alastuey, A.; Artiñano, B.; Bonnaire, N.; Bozzetti, C.; Bressi, M.; Carbone, C.; Coz, E.; Croteau, P. L.; Cubison, M. J.; Esser-Gietl, J. K.; Green, D. C.; Gros, V.; Heikkinen, L.; Herrmann, H.; Jayne, J. T.; Lunder, C. R.; Minguillón, M. C.; Močnik, G.; O'Dowd, C. D.; Ovadnevaite, J.; Petralia, E.; Poulain, L.; Priestman, M.; Ripoll, A.; Sarda-Estève, R.; Wiedensohler, A.; Baltensperger, U.; Sciare, J.; Prévôt, A. S. H.
2015-06-01
Chemically resolved atmospheric aerosol data sets from the largest intercomparison of the Aerodyne aerosol chemical speciation monitors (ACSMs) performed to date were collected at the French atmospheric supersite SIRTA. In total 13 quadrupole ACSMs (Q-ACSM) from the European ACTRIS ACSM network, one time-of-flight ACSM (ToF-ACSM), and one high-resolution ToF aerosol mass spectrometer (AMS) were operated in parallel for about 3 weeks in November and December~2013. Part 1 of this study reports on the accuracy and precision of the instruments for all the measured species. In this work we report on the intercomparison of organic components and the results from factor analysis source apportionment by positive matrix factorisation (PMF) utilising the multilinear engine 2 (ME-2). Except for the organic contribution of mass-to-charge ratio m/z 44 to the total organics (f44), which varied by factors between 0.6 and 1.3 compared to the mean, the peaks in the organic mass spectra were similar among instruments. The m/z 44 differences in the spectra resulted in a variable f44 in the source profiles extracted by ME-2, but had only a minor influence on the extracted mass contributions of the sources. The presented source apportionment yielded four factors for all 15 instruments: hydrocarbon-like organic aerosol (HOA), cooking-related organic aerosol (COA), biomass burning-related organic aerosol (BBOA) and secondary oxygenated organic aerosol (OOA). ME-2 boundary conditions (profile constraints) were optimised individually by means of correlation to external data in order to achieve equivalent / comparable solutions for all ACSM instruments and the results are discussed together with the investigation of the influence of alternative anchors (reference profiles). A comparison of the ME-2 source apportionment output of all 15 instruments resulted in relative standard deviations (SD) from the mean between 13.7 and 22.7 % of the source's average mass contribution depending on the factors (HOA: 14.3 ± 2.2 %, COA: 15.0 ± 3.4 %, OOA: 41.5 ± 5.7 %, BBOA: 29.3 ± 5.0 %). Factors which tend to be subject to minor factor mixing (in this case COA) have higher relative uncertainties than factors which are recognised more readily like the OOA. Averaged over all factors and instruments the relative first SD from the mean of a source extracted with ME-2 was 17.2 %.
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DISTANT EARLY WARNING SYSTEM for Tsunamis - A wide-area and multi-hazard approach
NASA Astrophysics Data System (ADS)
Hammitzsch, Martin; Lendholt, Matthias; Wächter, Joachim
2010-05-01
The DEWS (Distant Early Warning System) [1] project, funded under the 6th Framework Programme of the European Union, has the objective to create a new generation of interoperable early warning systems based on an open sensor platform. This platform integrates OGC [2] SWE [3] compliant sensor systems for the rapid detection of hazardous events, like earthquakes, sea level anomalies, ocean floor occurrences, and ground displacements in the case of tsunami early warning. Based on the upstream information flow DEWS focuses on the improvement of downstream capacities of warning centres especially by improving information logistics for effective and targeted warning message aggregation for a multilingual environment. Multiple telecommunication channels will be used for the dissemination of warning messages. Wherever possible, existing standards have been integrated. The Command and Control User Interface (CCUI), a rich client application based on Eclipse RCP (Rich Client Platform) [4] and the open source GIS uDig [5], integrates various OGC services. Using WMS (Web Map Service) [6] and WFS (Web Feature Service) [7] spatial data are utilized to depict the situation picture and to integrate a simulation system via WPS (Web Processing Service) [8] to identify affected areas. Warning messages are compiled and transmitted in the OASIS [9] CAP (Common Alerting Protocol) [10] standard together with addressing information defined via EDXL-DE (Emergency Data Exchange Language - Distribution Element) [11]. Internal interfaces are realized with SOAP [12] web services. Based on results of GITEWS [13] - in particular the GITEWS Tsunami Service Bus [14] - the DEWS approach provides an implementation for tsunami early warning systems but other geological paradigms are going to follow, e.g. volcanic eruptions or landslides. Therefore in future also multi-hazard functionality is conceivable. The specific software architecture of DEWS makes it possible to dock varying sensors to the system and to extend the CCUI with hazard specific functionality. The presentation covers the DEWS project, the system architecture and the CCUI in conjunction with details of information logistics. The DEWS Wide Area Centre connecting national centres to allow the international communication and warning exchange is presented also. REFERENCES: [1] DEWS, www.dews-online.org [2] OGC, www.opengeospatial.org [3] SWE, www.opengeospatial.org/projects/groups/sensorweb [4] Eclipse RCP, www.eclipse.org/home/categories/rcp.php [5] uDig, udig.refractions.net [6] WMS, www.opengeospatial.org/standards/wms [7] WFS, www.opengeospatial.org/standards/wfs [8] WPS, www.opengeospatial.org/standards/wps [9] OASIS, www.oasis-open.org [10] CAP, www.oasis-open.org/specs/#capv1.1 [11] EDXL-DE, www.oasis-open.org/specs/#edxlde-v1.0 [12] SOAP, www.w3.org/TR/soap [13] GITEWS (German Indonesian Tsunami Early Warning System) is a project of the German Federal Government to aid the recon¬struction of the tsunami-prone Indian Ocean region, www.gitews.org [14] The Tsunami Service Bus is the GITEWS sensor system integration platform offering standardised services for the detection and monitoring of tsunamis
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NASA Astrophysics Data System (ADS)
Cimino, C.
2013-07-01
In times of economic hardship, the support given by specialized civil society organisations to public institutions in the protection of cultural heritage has often proved very useful, and there is evidence that their contribution is essential in times of conflicts and natural disasters, if well-designed plans and measures are organized efficiently, thoroughly tested and properly implemented. The 1954 Hague Convention for the Protection of Cultural Property in the Event of Armed Conflict (HC), its two Protocols and other international juridical instruments address these situations since decades, however, they remained widely not-applied in absence of proper regulatory instruments. In 2004, the Second Protocol of the Hague Convention (1999HP) entered into force and the Committee of the State Parties was formed. It became clear that a new trend started when, in 2009, draft Guidelines for the implementation of the 1999HP were issued. Meanwhile, WATCH, in partnership with the Council of the United Municipalitities of Jbail (Lebanon) and the Head of the Municipality of Mtskheta (Georgia) prepared a project proposal aimed to set a precedent in the governance of urban sites that are registered in the World Heritage List which are at risk of armed conflict. The project War Free World Heritage Listed Cities http://www.warfreeheritage.net/ was co-financed in 2010 with a grant within the framework of the EC CIUDAD programme and it is currently at an advanced level of implementation. This presentation will focus on achievements and contingencies faced during implementation as well as lessons learned that could be surely useful for pers pective applicants.
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Using Galaxy to Perform Large-Scale Interactive Data Analyses
Hillman-Jackson, Jennifer; Clements, Dave; Blankenberg, Daniel; Taylor, James; Nekrutenko, Anton
2012-01-01
Innovations in biomedical research technologies continue to provide experimental biologists with novel and increasingly large genomic and high-throughput data resources to be analyzed. As creating and obtaining data has become easier, the key decision faced by many researchers is a practical one: where and how should an analysis be performed? Datasets are large and analysis tool set-up and use is riddled with complexities outside of the scope of core research activities. The authors believe that Galaxy (galaxyproject.org) provides a powerful solution that simplifies data acquisition and analysis in an intuitive web-application, granting all researchers access to key informatics tools previously only available to computational specialists working in Unix-based environments. We will demonstrate through a series of biomedically relevant protocols how Galaxy specifically brings together 1) data retrieval from public and private sources, for example, UCSC’s Eukaryote and Microbial Genome Browsers (genome.ucsc.edu), 2) custom tools (wrapped Unix functions, format standardization/conversions, interval operations) and 3rd party analysis tools, for example, Bowtie/Tuxedo Suite (bowtie-bio.sourceforge.net), Lastz (www.bx.psu.edu/~rsharris/lastz/), SAMTools (samtools.sourceforge.net), FASTX-toolkit (hannonlab.cshl.edu/fastx_toolkit), and MACS (liulab.dfci.harvard.edu/MACS), and creates results formatted for visualization in tools such as the Galaxy Track Browser (GTB, galaxyproject.org/wiki/Learn/Visualization), UCSC Genome Browser (genome.ucsc.edu), Ensembl (www.ensembl.org), and GeneTrack (genetrack.bx.psu.edu). Galaxy rapidly has become the most popular choice for integrated next generation sequencing (NGS) analytics and collaboration, where users can perform, document, and share complex analysis within a single interface in an unprecedented number of ways. PMID:18428782
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NASA Astrophysics Data System (ADS)
Lengert, W.; Mondon, E.; Bégin, M. E.; Ferrer, M.; Vallois, F.; DelaMar, J.
2015-12-01
Helix Nebula, a European science cross-domain initiative building on an active PPP, is aiming to implement the concept of an open science commons[1] while using a cloud hybrid model[2] as the proposed implementation solution. This approach allows leveraging and merging of complementary data intensive Earth Science disciplines (e.g. instrumentation[3] and modeling), without introducing significant changes in the contributors' operational set-up. Considering the seamless integration with life-science (e.g. EMBL), scientific exploitation of meteorological, climate, and Earth Observation data and models open an enormous potential for new big data science. The work of Helix Nebula has shown that is it feasible to interoperate publicly funded infrastructures, such as EGI [5] and GEANT [6], with commercial cloud services. Such hybrid systems are in the interest of the existing users of publicly funded infrastructures and funding agencies because they will provide "freedom and choice" over the type of computing resources to be consumed and the manner in which they can be obtained. But to offer such freedom and choice across a spectrum of suppliers, various issues such as intellectual property, legal responsibility, service quality agreements and related issues need to be addressed. Finding solutions to these issues is one of the goals of the Helix Nebula initiative. [1] http://www.egi.eu/news-and-media/publications/OpenScienceCommons_v3.pdf [2] http://www.helix-nebula.eu/events/towards-the-european-open-science-cloud [3] e.g. https://sentinel.esa.int/web/sentinel/sentinel-data-access [5] http://www.egi.eu/ [6] http://www.geant.net/
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BrainNet Viewer: a network visualization tool for human brain connectomics.
Xia, Mingrui; Wang, Jinhui; He, Yong
2013-01-01
The human brain is a complex system whose topological organization can be represented using connectomics. Recent studies have shown that human connectomes can be constructed using various neuroimaging technologies and further characterized using sophisticated analytic strategies, such as graph theory. These methods reveal the intriguing topological architectures of human brain networks in healthy populations and explore the changes throughout normal development and aging and under various pathological conditions. However, given the huge complexity of this methodology, toolboxes for graph-based network visualization are still lacking. Here, using MATLAB with a graphical user interface (GUI), we developed a graph-theoretical network visualization toolbox, called BrainNet Viewer, to illustrate human connectomes as ball-and-stick models. Within this toolbox, several combinations of defined files with connectome information can be loaded to display different combinations of brain surface, nodes and edges. In addition, display properties, such as the color and size of network elements or the layout of the figure, can be adjusted within a comprehensive but easy-to-use settings panel. Moreover, BrainNet Viewer draws the brain surface, nodes and edges in sequence and displays brain networks in multiple views, as required by the user. The figure can be manipulated with certain interaction functions to display more detailed information. Furthermore, the figures can be exported as commonly used image file formats or demonstration video for further use. BrainNet Viewer helps researchers to visualize brain networks in an easy, flexible and quick manner, and this software is freely available on the NITRC website (www.nitrc.org/projects/bnv/).
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Europlanet/IDIS: Combining Diverse Planetary Observations and Models
NASA Astrophysics Data System (ADS)
Schmidt, Walter; Capria, Maria Teresa; Chanteur, Gerard
2013-04-01
Planetary research involves a diversity of research fields from astrophysics and plasma physics to atmospheric physics, climatology, spectroscopy and surface imaging. Data from all these disciplines are collected from various space-borne platforms or telescopes, supported by modelling teams and laboratory work. In order to interpret one set of data often supporting data from different disciplines and other missions are needed while the scientist does not always have the detailed expertise to access and utilize these observations. The Integrated and Distributed Information System (IDIS) [1], developed in the framework of the Europlanet-RI project, implements a Virtual Observatory approach ([2] and [3]), where different data sets, stored in archives around the world and in different formats, are accessed, re-formatted and combined to meet the user's requirements without the need of familiarizing oneself with the different technical details. While observational astrophysical data from different observatories could already earlier be accessed via Virtual Observatories, this concept is now extended to diverse planetary data and related model data sets, spectral data bases etc. A dedicated XML-based Europlanet Data Model (EPN-DM) [4] was developed based on data models from the planetary science community and the Virtual Observatory approach. A dedicated editor simplifies the registration of new resources. As the EPN-DM is a super-set of existing data models existing archives as well as new spectroscopic or chemical data bases for the interpretation of atmospheric or surface observations, or even modeling facilities at research institutes in Europe or Russia can be easily integrated and accessed via a Table Access Protocol (EPN-TAP) [5] adapted from the corresponding protocol of the International Virtual Observatory Alliance [6] (IVOA-TAP). EPN-TAP allows to search catalogues, retrieve data and make them available through standard IVOA tools if the access to the archive is compatible with IVOA standards. For some major data archives with different standards adaptation tools are available to make the access transparent to the user. EuroPlaNet-IDIS has contributed to the definition of PDAP, the Planetary Data Access Protocol of the International Planetary Data Alliance (IPDA) [7] to access the major planetary data archives of NASA in the USA [8], ESA in Europe [9] and JAXA in Japan [10]. Acknowledgement: Europlanet-RI was funded by the European Commission under the 7th Framework Program, grant 228319 "Capacities Specific Programme" - Research Infrastructures Action. Reference: [1] Details to IDIS and the Europlanet-RI via Web-site: http://www.idis.europlanet-ri.eu/ [2] Demonstrator implementation for Plasma-VO AMDA: http://cdpp-amda.cesr.fr/DDHTML/index.html [3] Demonstrator implementation for the IDIS-VO: http://www.idis-dyn.europlanet-ri.eu/vodev.shtml [4] Europlanet Data Model EPN-DM: http://www.europlanet-idis.fi/documents/public_documents/EPN-DM-v2.0.pdf [5] Europlanet Table Access Protocol EPN-TAP: http://www.europlanet-idis.fi/documents/public_documents/EPN-TAPV_0.26.pdf [6] International Virtual Observatory Alliance IVOA: http://www.ivoa.net [7] International Planetary Data Alliance IPDA: http://planetarydata.org/ [8] NASA's Planetary Data System: http://pds.jpl.nasa.gov/ [9] ESA's Planetary Science Archive PSA: http://www.sciops.esa.int/index.php?project=PSA [10] JAXAs Data Archive and Transmission System DARTS: http://darts.isas.jaxa.jp/
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Del Carratore, Francesco; Jankevics, Andris; Eisinga, Rob; Heskes, Tom; Hong, Fangxin; Breitling, Rainer
2017-09-01
The Rank Product (RP) is a statistical technique widely used to detect differentially expressed features in molecular profiling experiments such as transcriptomics, metabolomics and proteomics studies. An implementation of the RP and the closely related Rank Sum (RS) statistics has been available in the RankProd Bioconductor package for several years. However, several recent advances in the understanding of the statistical foundations of the method have made a complete refactoring of the existing package desirable. We implemented a completely refactored version of the RankProd package, which provides a more principled implementation of the statistics for unpaired datasets. Moreover, the permutation-based P -value estimation methods have been replaced by exact methods, providing faster and more accurate results. RankProd 2.0 is available at Bioconductor ( https://www.bioconductor.org/packages/devel/bioc/html/RankProd.html ) and as part of the mzMatch pipeline ( http://www.mzmatch.sourceforge.net ). rainer.breitling@manchester.ac.uk. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.
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Shock competition and circulation deposition in shock interactions with heavy prolate cylinders
NASA Astrophysics Data System (ADS)
Ray, Jaideep; Samtaney, R.; Zabusky, Norman J.
1998-11-01
We investigate the interaction of a shock wave with elliptical heavier-than-ambient gaseous cylinders. We identify two different modes of interaction between the incident and transmitted shocks on the leeward side of the cylinder which yeild different mechanisms for the baroclinic vorticity generation. We model the net baroclinic circulation generated on the interface by both the shocks and validate the model via numerical simulations of the Euler equations. The principal parameters governing the interaction are the Mach number of the shock (M), the density ratio of the two gases (η, η > 1), λ (the aspect ratio) and the ratio of specific heats of the two gases. We derive a time ratio which uniquely characterizes the mode of interaction. In the range 1.2 <= M <= 3.5, 1.54 <= η <= 5.04 and λ = 1.5 and 3.0, our model predicts circulation within 10 % of the simulation results. Further developments on this topic will be posted on the Web at http://www.caip.rutgers.edu/ ~jaray/ellipse/RM_ellipse.html.
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Reproducible Computing: a new Technology for Statistics Education and Educational Research
NASA Astrophysics Data System (ADS)
Wessa, Patrick
2009-05-01
This paper explains how the R Framework (http://www.wessa.net) and a newly developed Compendium Platform (http://www.freestatistics.org) allow us to create, use, and maintain documents that contain empirical research results which can be recomputed and reused in derived work. It is illustrated that this technological innovation can be used to create educational applications that can be shown to support effective learning of statistics and associated analytical skills. It is explained how a Compendium can be created by anyone, without the need to understand the technicalities of scientific word processing (L style="font-variant: small-caps">ATEX) or statistical computing (R code). The proposed Reproducible Computing system allows educational researchers to objectively measure key aspects of the actual learning process based on individual and constructivist activities such as: peer review, collaboration in research, computational experimentation, etc. The system was implemented and tested in three statistics courses in which the use of Compendia was used to create an interactive e-learning environment that simulated the real-world process of empirical scientific research.
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hi-class: Horndeski in the Cosmic Linear Anisotropy Solving System
DOE Office of Scientific and Technical Information (OSTI.GOV)
Zumalacárregui, Miguel; Bellini, Emilio; Sawicki, Ignacy
We present the public version of hi-class (www.hiclass-code.net), an extension of the Boltzmann code CLASS to a broad ensemble of modifications to general relativity. In particular, hi-class can calculate predictions for models based on Horndeski's theory, which is the most general scalar-tensor theory described by second-order equations of motion and encompasses any perfect-fluid dark energy, quintessence, Brans-Dicke, f ( R ) and covariant Galileon models. hi-class has been thoroughly tested and can be readily used to understand the impact of alternative theories of gravity on linear structure formation as well as for cosmological parameter extraction.
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Saint: a lightweight integration environment for model annotation.
Lister, Allyson L; Pocock, Matthew; Taschuk, Morgan; Wipat, Anil
2009-11-15
Saint is a web application which provides a lightweight annotation integration environment for quantitative biological models. The system enables modellers to rapidly mark up models with biological information derived from a range of data sources. Saint is freely available for use on the web at http://www.cisban.ac.uk/saint. The web application is implemented in Google Web Toolkit and Tomcat, with all major browsers supported. The Java source code is freely available for download at http://saint-annotate.sourceforge.net. The Saint web server requires an installation of libSBML and has been tested on Linux (32-bit Ubuntu 8.10 and 9.04).
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Lundegaard, Claus; Lamberth, Kasper; Harndahl, Mikkel; Buus, Søren; Lund, Ole; Nielsen, Morten
2008-07-01
NetMHC-3.0 is trained on a large number of quantitative peptide data using both affinity data from the Immune Epitope Database and Analysis Resource (IEDB) and elution data from SYFPEITHI. The method generates high-accuracy predictions of major histocompatibility complex (MHC): peptide binding. The predictions are based on artificial neural networks trained on data from 55 MHC alleles (43 Human and 12 non-human), and position-specific scoring matrices (PSSMs) for additional 67 HLA alleles. As only the MHC class I prediction server is available, predictions are possible for peptides of length 8-11 for all 122 alleles. artificial neural network predictions are given as actual IC(50) values whereas PSSM predictions are given as a log-odds likelihood scores. The output is optionally available as download for easy post-processing. The training method underlying the server is the best available, and has been used to predict possible MHC-binding peptides in a series of pathogen viral proteomes including SARS, Influenza and HIV, resulting in an average of 75-80% confirmed MHC binders. Here, the performance is further validated and benchmarked using a large set of newly published affinity data, non-redundant to the training set. The server is free of use and available at: http://www.cbs.dtu.dk/services/NetMHC.
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Seafood Safety and Quality: The Consumer’s Role
Hicks, Doris T.
2016-01-01
All the good news about seafood—the health and nutritional benefits, the wide varieties and flavors—has had a positive effect on consumption: people are eating more seafood (http://www.seagrant.sunysb.edu/seafood/pdfs/SeafoodSavvy.pdf). Yet consumers want to be assured that seafood is as safe as, or safer to eat than, other foods. When you hear “seafood safety”, think of a safety net designed to protect you, the consumer, from food-borne illness. Every facet of the seafood industry, from harvester to consumer, plays a role in holding up the safety net. The role of state and federal agencies, fishermen, aquaculturists, retailers, processors, restaurants, and scientists is to provide, update, and carry out the necessary handling, processing, and inspection procedures to give consumers the safest seafood possible. The consumer’s responsibility is to follow through with proper handling techniques, from purchase to preparation. It doesn’t matter how many regulations and inspection procedures are set up; the final edge of the safety net is held by the consumer. This article will give you the information you need to educate yourself and be assured that the fish and shellfish you consume are safe. The most common food-borne illnesses are caused by a combination of bacteria naturally present in our environment and food handling errors made in commercial settings, food service institutions, or at home. PMID:28231165
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Shim, Hongseok; Kim, Ji Hyun; Kim, Chan Yeong; Hwang, Sohyun; Kim, Hyojin; Yang, Sunmo; Lee, Ji Eun; Lee, Insuk
2016-11-16
Whole exome sequencing (WES) accelerates disease gene discovery using rare genetic variants, but further statistical and functional evidence is required to avoid false-discovery. To complement variant-driven disease gene discovery, here we present function-driven disease gene discovery in zebrafish (Danio rerio), a promising human disease model owing to its high anatomical and genomic similarity to humans. To facilitate zebrafish-based function-driven disease gene discovery, we developed a genome-scale co-functional network of zebrafish genes, DanioNet (www.inetbio.org/danionet), which was constructed by Bayesian integration of genomics big data. Rigorous statistical assessment confirmed the high prediction capacity of DanioNet for a wide variety of human diseases. To demonstrate the feasibility of the function-driven disease gene discovery using DanioNet, we predicted genes for ciliopathies and performed experimental validation for eight candidate genes. We also validated the existence of heterozygous rare variants in the candidate genes of individuals with ciliopathies yet not in controls derived from the UK10K consortium, suggesting that these variants are potentially involved in enhancing the risk of ciliopathies. These results showed that an integrated genomics big data for a model animal of diseases can expand our opportunity for harnessing WES data in disease gene discovery. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.
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Nielsen, Morten; Andreatta, Massimo
2016-03-30
Binding of peptides to MHC class I molecules (MHC-I) is essential for antigen presentation to cytotoxic T-cells. Here, we demonstrate how a simple alignment step allowing insertions and deletions in a pan-specific MHC-I binding machine-learning model enables combining information across both multiple MHC molecules and peptide lengths. This pan-allele/pan-length algorithm significantly outperforms state-of-the-art methods, and captures differences in the length profile of binders to different MHC molecules leading to increased accuracy for ligand identification. Using this model, we demonstrate that percentile ranks in contrast to affinity-based thresholds are optimal for ligand identification due to uniform sampling of the MHC space. We have developed a neural network-based machine-learning algorithm leveraging information across multiple receptor specificities and ligand length scales, and demonstrated how this approach significantly improves the accuracy for prediction of peptide binding and identification of MHC ligands. The method is available at www.cbs.dtu.dk/services/NetMHCpan-3.0 .
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Passing Messages between Biological Networks to Refine Predicted Interactions
Glass, Kimberly; Huttenhower, Curtis; Quackenbush, John; Yuan, Guo-Cheng
2013-01-01
Regulatory network reconstruction is a fundamental problem in computational biology. There are significant limitations to such reconstruction using individual datasets, and increasingly people attempt to construct networks using multiple, independent datasets obtained from complementary sources, but methods for this integration are lacking. We developed PANDA (Passing Attributes between Networks for Data Assimilation), a message-passing model using multiple sources of information to predict regulatory relationships, and used it to integrate protein-protein interaction, gene expression, and sequence motif data to reconstruct genome-wide, condition-specific regulatory networks in yeast as a model. The resulting networks were not only more accurate than those produced using individual data sets and other existing methods, but they also captured information regarding specific biological mechanisms and pathways that were missed using other methodologies. PANDA is scalable to higher eukaryotes, applicable to specific tissue or cell type data and conceptually generalizable to include a variety of regulatory, interaction, expression, and other genome-scale data. An implementation of the PANDA algorithm is available at www.sourceforge.net/projects/panda-net. PMID:23741402
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Analysis and recognition of 5′ UTR intron splice sites in human pre-mRNA
Eden, E.; Brunak, S.
2004-01-01
Prediction of splice sites in non-coding regions of genes is one of the most challenging aspects of gene structure recognition. We perform a rigorous analysis of such splice sites embedded in human 5′ untranslated regions (UTRs), and investigate correlations between this class of splice sites and other features found in the adjacent exons and introns. By restricting the training of neural network algorithms to ‘pure’ UTRs (not extending partially into protein coding regions), we for the first time investigate the predictive power of the splicing signal proper, in contrast to conventional splice site prediction, which typically relies on the change in sequence at the transition from protein coding to non-coding. By doing so, the algorithms were able to pick up subtler splicing signals that were otherwise masked by ‘coding’ noise, thus enhancing significantly the prediction of 5′ UTR splice sites. For example, the non-coding splice site predicting networks pick up compositional and positional bias in the 3′ ends of non-coding exons and 5′ non-coding intron ends, where cytosine and guanine are over-represented. This compositional bias at the true UTR donor sites is also visible in the synaptic weights of the neural networks trained to identify UTR donor sites. Conventional splice site prediction methods perform poorly in UTRs because the reading frame pattern is absent. The NetUTR method presented here performs 2–3-fold better compared with NetGene2 and GenScan in 5′ UTRs. We also tested the 5′ UTR trained method on protein coding regions, and discovered, surprisingly, that it works quite well (although it cannot compete with NetGene2). This indicates that the local splicing pattern in UTRs and coding regions is largely the same. The NetUTR method is made publicly available at www.cbs.dtu.dk/services/NetUTR. PMID:14960723
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Petersen, Bent; Lundegaard, Claus; Petersen, Thomas Nordahl
2010-01-01
β-turns are the most common type of non-repetitive structures, and constitute on average 25% of the amino acids in proteins. The formation of β-turns plays an important role in protein folding, protein stability and molecular recognition processes. In this work we present the neural network method NetTurnP, for prediction of two-class β-turns and prediction of the individual β-turn types, by use of evolutionary information and predicted protein sequence features. It has been evaluated against a commonly used dataset BT426, and achieves a Matthews correlation coefficient of 0.50, which is the highest reported performance on a two-class prediction of β-turn and not-β-turn. Furthermore NetTurnP shows improved performance on some of the specific β-turn types. In the present work, neural network methods have been trained to predict β-turn or not and individual β-turn types from the primary amino acid sequence. The individual β-turn types I, I', II, II', VIII, VIa1, VIa2, VIba and IV have been predicted based on classifications by PROMOTIF, and the two-class prediction of β-turn or not is a superset comprised of all β-turn types. The performance is evaluated using a golden set of non-homologous sequences known as BT426. Our two-class prediction method achieves a performance of: MCC = 0.50, Qtotal = 82.1%, sensitivity = 75.6%, PPV = 68.8% and AUC = 0.864. We have compared our performance to eleven other prediction methods that obtain Matthews correlation coefficients in the range of 0.17 – 0.47. For the type specific β-turn predictions, only type I and II can be predicted with reasonable Matthews correlation coefficients, where we obtain performance values of 0.36 and 0.31, respectively. Conclusion The NetTurnP method has been implemented as a webserver, which is freely available at http://www.cbs.dtu.dk/services/NetTurnP/. NetTurnP is the only available webserver that allows submission of multiple sequences. PMID:21152409
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MetNetAPI: A flexible method to access and manipulate biological network data from MetNet
2010-01-01
Background Convenient programmatic access to different biological databases allows automated integration of scientific knowledge. Many databases support a function to download files or data snapshots, or a webservice that offers "live" data. However, the functionality that a database offers cannot be represented in a static data download file, and webservices may consume considerable computational resources from the host server. Results MetNetAPI is a versatile Application Programming Interface (API) to the MetNetDB database. It abstracts, captures and retains operations away from a biological network repository and website. A range of database functions, previously only available online, can be immediately (and independently from the website) applied to a dataset of interest. Data is available in four layers: molecular entities, localized entities (linked to a specific organelle), interactions, and pathways. Navigation between these layers is intuitive (e.g. one can request the molecular entities in a pathway, as well as request in what pathways a specific entity participates). Data retrieval can be customized: Network objects allow the construction of new and integration of existing pathways and interactions, which can be uploaded back to our server. In contrast to webservices, the computational demand on the host server is limited to processing data-related queries only. Conclusions An API provides several advantages to a systems biology software platform. MetNetAPI illustrates an interface with a central repository of data that represents the complex interrelationships of a metabolic and regulatory network. As an alternative to data-dumps and webservices, it allows access to a current and "live" database and exposes analytical functions to application developers. Yet it only requires limited resources on the server-side (thin server/fat client setup). The API is available for Java, Microsoft.NET and R programming environments and offers flexible query and broad data- retrieval methods. Data retrieval can be customized to client needs and the API offers a framework to construct and manipulate user-defined networks. The design principles can be used as a template to build programmable interfaces for other biological databases. The API software and tutorials are available at http://www.metnetonline.org/api. PMID:21083943
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Petersen, Bent; Lundegaard, Claus; Petersen, Thomas Nordahl
2010-11-30
β-turns are the most common type of non-repetitive structures, and constitute on average 25% of the amino acids in proteins. The formation of β-turns plays an important role in protein folding, protein stability and molecular recognition processes. In this work we present the neural network method NetTurnP, for prediction of two-class β-turns and prediction of the individual β-turn types, by use of evolutionary information and predicted protein sequence features. It has been evaluated against a commonly used dataset BT426, and achieves a Matthews correlation coefficient of 0.50, which is the highest reported performance on a two-class prediction of β-turn and not-β-turn. Furthermore NetTurnP shows improved performance on some of the specific β-turn types. In the present work, neural network methods have been trained to predict β-turn or not and individual β-turn types from the primary amino acid sequence. The individual β-turn types I, I', II, II', VIII, VIa1, VIa2, VIba and IV have been predicted based on classifications by PROMOTIF, and the two-class prediction of β-turn or not is a superset comprised of all β-turn types. The performance is evaluated using a golden set of non-homologous sequences known as BT426. Our two-class prediction method achieves a performance of: MCC=0.50, Qtotal=82.1%, sensitivity=75.6%, PPV=68.8% and AUC=0.864. We have compared our performance to eleven other prediction methods that obtain Matthews correlation coefficients in the range of 0.17-0.47. For the type specific β-turn predictions, only type I and II can be predicted with reasonable Matthews correlation coefficients, where we obtain performance values of 0.36 and 0.31, respectively. The NetTurnP method has been implemented as a webserver, which is freely available at http://www.cbs.dtu.dk/services/NetTurnP/. NetTurnP is the only available webserver that allows submission of multiple sequences.
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Latest developments for the IAGOS database: Interoperability and metadata
NASA Astrophysics Data System (ADS)
Boulanger, Damien; Gautron, Benoit; Thouret, Valérie; Schultz, Martin; van Velthoven, Peter; Broetz, Bjoern; Rauthe-Schöch, Armin; Brissebrat, Guillaume
2014-05-01
In-service Aircraft for a Global Observing System (IAGOS, http://www.iagos.org) aims at the provision of long-term, frequent, regular, accurate, and spatially resolved in situ observations of the atmospheric composition. IAGOS observation systems are deployed on a fleet of commercial aircraft. The IAGOS database is an essential part of the global atmospheric monitoring network. Data access is handled by open access policy based on the submission of research requests which are reviewed by the PIs. Users can access the data through the following web sites: http://www.iagos.fr or http://www.pole-ether.fr as the IAGOS database is part of the French atmospheric chemistry data centre ETHER (CNES and CNRS). The database is in continuous development and improvement. In the framework of the IGAS project (IAGOS for GMES/COPERNICUS Atmospheric Service), major achievements will be reached, such as metadata and format standardisation in order to interoperate with international portals and other databases, QA/QC procedures and traceability, CARIBIC (Civil Aircraft for the Regular Investigation of the Atmosphere Based on an Instrument Container) data integration within the central database, and the real-time data transmission. IGAS work package 2 aims at providing the IAGOS data to users in a standardized format including the necessary metadata and information on data processing, data quality and uncertainties. We are currently redefining and standardizing the IAGOS metadata for interoperable use within GMES/Copernicus. The metadata are compliant with the ISO 19115, INSPIRE and NetCDF-CF conventions. IAGOS data will be provided to users in NetCDF or NASA Ames format. We also are implementing interoperability between all the involved IAGOS data services, including the central IAGOS database, the former MOZAIC and CARIBIC databases, Aircraft Research DLR database and the Jülich WCS web application JOIN (Jülich OWS Interface) which combines model outputs with in situ data for intercomparison. The optimal data transfer protocol is being investigated to insure the interoperability. To facilitate satellite and model validation, tools will be made available for co-location and comparison with IAGOS. We will enhance the JOIN application in order to properly display aircraft data as vertical profiles and along individual flight tracks and to allow for graphical comparison to model results that are accessible through interoperable web services, such as the daily products from the GMES/Copernicus atmospheric service.
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GMES: A Python package for solving Maxwell’s equations using the FDTD method
NASA Astrophysics Data System (ADS)
Chun, Kyungwon; Kim, Huioon; Kim, Hyounggyu; Jung, Kil Su; Chung, Youngjoo
2013-04-01
This paper describes GMES, a free Python package for solving Maxwell’s equations using the finite-difference time-domain (FDTD) method. The design of GMES follows the object-oriented programming (OOP) approach and adopts a unique design strategy where the voxels in the computational domain are grouped and then updated according to its material type. This piecewise updating scheme ensures that GMES can adopt OOP without losing its simple structure and time-stepping speed. The users can easily add various material types, sources, and boundary conditions into their code using the Python programming language. The key design features, along with the supported material types, excitation sources, boundary conditions and parallel calculations employed in GMES are also described in detail. Catalog identifier: AEOK_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEOK_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License v3.0 No. of lines in distributed program, including test data, etc.: 17700 No. of bytes in distributed program, including test data, etc.: 89878 Distribution format: tar.gz Programming language: C++, Python. Computer: Any computer with a Unix-like system with a C++ compiler, and a Python interpreter; developed on 2.53 GHz Intel CoreTM i3. Operating system: Any Unix-like system; developed under Ubuntu 12.04 LTS 64 bit. Has the code been vectorized or parallelized?: Yes. Parallelized with MPI directives (optional). RAM: Problem dependent (a simulation with real valued electromagnetic field uses roughly 0.18 KB per Yee cell.) Classification: 10. External routines: SWIG [1], Cython [2], NumPy [3], SciPy [4], matplotlib [5], MPI for Python [6] Nature of problem: Classical electrodynamics Solution method: Finite-difference time-domain (FDTD) method Additional comments: This article describes version 0.9.5. The most recent version can be downloaded at the GMES project homepage [7]. Running time: Problem dependent (a simulation with real valued electromagnetic field takes typically about 0.16 μs per Yee cell per time-step.) SWIG, http://www.swig.org. Cython, http://www.cython.org. NumPy, http://numpy.scipy.org. SciPy, http://www.scipy.org. matplotlib, http://matplotlib.sourceforge.net. MPI for Python, http://mpi4py.scipy.org. GMES, http://sourceforge.net/projects/gmes.
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Representing Simple Geometry Types in NetCDF-CF
NASA Astrophysics Data System (ADS)
Blodgett, D. L.; Koziol, B. W.; Whiteaker, T. L.; Simons, R.
2016-12-01
The Climate and Forecast (CF) metadata convention is well-suited for representing gridded and point-based observational datasets. However, CF currently has no accepted mechanism for representing simple geometry types such as lines and polygons. Lack of support for simple geometries within CF has unintentionally excluded a broad set of geoscientific data types from NetCDF-CF data encodings. For example, hydrologic datasets often contain polygon watershed catchments and polyline stream reaches in addition to point sampling stations and water management infrastructure. The latter has an associated CF specification. In the interest of supporting all simple geometry types within CF, a working group was formed following an EarthCube workshop on Advancing NetCDF-CF [1] to draft a CF specification for simple geometries: points, lines, polygons, and their associated multi-geometry representations [2]. The draft also includes parametric geometry types such as circles and ellipses. This presentation will provide an overview of the scope and content of the proposed specification focusing on mechanisms for representing coordinate arrays using variable length or continuous ragged arrays, capturing multi-geometries, and accounting for type-specific geometry artifacts such as polygon holes/interiors, node ordering, etc. The concepts contained in the specification proposal will be described with a use case representing streamflow in rivers and evapotranspiration from HUC12 watersheds. We will also introduce Python and R reference implementations developed alongside the technical specification. These in-development, open source Python and R libraries convert between commonly used GIS software objects (i.e. GEOS-based primitives) and their associated simple geometry CF representation. [1] http://www.unidata.ucar.edu/events/2016CFWorkshop/[2] https://github.com/bekozi/netCDF-CF-simple-geometry
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Zapata, Carly; Lum, Hillary D; Wistar, Emily; Horton, Claire; Sudore, Rebecca L
2018-02-20
Primary care providers in safety-net settings often do not have time to discuss advance care planning (ACP). Group visits (GV) may be an efficient means to provide ACP education. To assess the feasibility and impact of a video-based website to facilitate GVs to engage diverse adults in ACP. Feasibility pilot among patients who were ≥55 years of age from two primary care clinics in a Northern California safety-net setting. Participants attended two 90-minute GVs and viewed the five steps of the movie version of the PREPARE website ( www.prepareforyourcare.org ) concerning surrogates, values, and discussing wishes in video format. Two clinician facilitators were available to encourage participation. We assessed pre-to-post ACP knowledge, whether participants designated a surrogate or completed an advance directive (AD), and acceptability of GVs and PREPARE materials. We conducted two GVs with 22 participants. Mean age was 64 years (±7), 55% were women, 73% nonwhite, and 55% had limited literacy. Knowledge improved about surrogate designation (46% correct pre vs. 85% post, p = 0.01) and discussing decisions with others (59% vs. 90%, p = 0.01). Surrogate designation increased (48% vs. 85%, p = 0.01) and there was a trend toward AD completion (9% vs. 24%, p = 0.21). Participants rated the GVs and PREPARE materials a mean of 8 (±3.1) on a 10-point acceptability scale. Using the PREPARE movie to facilitate ACP GVs for diverse adults in safety net, primary care settings is feasible and shows potential for increasing ACP engagement.
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atBioNet--an integrated network analysis tool for genomics and biomarker discovery.
Ding, Yijun; Chen, Minjun; Liu, Zhichao; Ding, Don; Ye, Yanbin; Zhang, Min; Kelly, Reagan; Guo, Li; Su, Zhenqiang; Harris, Stephen C; Qian, Feng; Ge, Weigong; Fang, Hong; Xu, Xiaowei; Tong, Weida
2012-07-20
Large amounts of mammalian protein-protein interaction (PPI) data have been generated and are available for public use. From a systems biology perspective, Proteins/genes interactions encode the key mechanisms distinguishing disease and health, and such mechanisms can be uncovered through network analysis. An effective network analysis tool should integrate different content-specific PPI databases into a comprehensive network format with a user-friendly platform to identify key functional modules/pathways and the underlying mechanisms of disease and toxicity. atBioNet integrates seven publicly available PPI databases into a network-specific knowledge base. Knowledge expansion is achieved by expanding a user supplied proteins/genes list with interactions from its integrated PPI network. The statistically significant functional modules are determined by applying a fast network-clustering algorithm (SCAN: a Structural Clustering Algorithm for Networks). The functional modules can be visualized either separately or together in the context of the whole network. Integration of pathway information enables enrichment analysis and assessment of the biological function of modules. Three case studies are presented using publicly available disease gene signatures as a basis to discover new biomarkers for acute leukemia, systemic lupus erythematosus, and breast cancer. The results demonstrated that atBioNet can not only identify functional modules and pathways related to the studied diseases, but this information can also be used to hypothesize novel biomarkers for future analysis. atBioNet is a free web-based network analysis tool that provides a systematic insight into proteins/genes interactions through examining significant functional modules. The identified functional modules are useful for determining underlying mechanisms of disease and biomarker discovery. It can be accessed at: http://www.fda.gov/ScienceResearch/BioinformaticsTools/ucm285284.htm.
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Lee, Simon Craddock; Marks, Emily G; Persaud, Donna; Skinner, Celette Sugg; Street, Richard L; Wiebe, Deborah J; Farrell, David; Bishop, Wendy Pechero; Fuller, Sobha; Baldwin, Austin S
2016-01-01
Background Human papillomavirus (HPV)-related cancers are a significant burden on the US health care system that can be prevented through adolescent HPV vaccination. Despite guidelines recommending vaccination, coverage among US adolescents is suboptimal particularly among underserved patients (uninsured, low income, racial, and ethnic minorities) seen in safety-net health care settings. Many parents are ambivalent about the vaccine and delay making a decision or talking with a provider about it. Self-persuasion—generating one’s own arguments for a health behavior—may be particularly effective for parents who are undecided or not motivated to make a vaccine decision. Objective Through a 3-stage mixed-methods protocol, we will identify an optimal and feasible self-persuasion intervention strategy to promote adolescent HPV vaccination in safety-net clinics. Methods In Stage 1, we will define content for a tablet-based self-persuasion app by characterizing (1) parents’ self-generated arguments through cognitive interviews conducted with parents (n=50) of patients and (2) parent-provider HPV vaccine discussions through audio recordings of clinic visits (n=50). In Stage 2, we will compare the effects of the four self-persuasion intervention conditions that vary by cognitive processing level (parents verbalize vs listen to arguments) and choice of argument topics (parents choose vs are assigned topics) on parental vaccine intentions in a 2 × 2 factorial design randomized controlled trial (n=160). This proof-of-concept trial design will identify which intervention condition is optimal by quantitatively examining basic self-persuasion mechanisms (cognitive processing and choice) and qualitatively exploring parent experiences with intervention tasks. In Stage 3, we will conduct a pilot trial (n=90) in the safety-net clinics to assess feasibility of the optimal intervention condition identified in Stage 2. We will also assess its impact on parent-provider discussions. Results This paper describes the study protocol and activities to date. Currently, we have developed the initial prototype of the tablet app for English- and Spanish-speaking populations, and completed Stage 1 data collection. Conclusions Our systematic collaboration between basic and applied behavioral scientists accelerates translation of promising basic psychological research into innovative interventions suitable for underserved, safety-net populations. At project’s end, we plan to have a feasible and acceptable self-persuasion intervention that can affect key cancer disparities in the United States through prevention of HPV-related cancers. Trial Registration ClinicalTrials.gov http://clinicaltrials.gov/ct2/show/NCT02537756 and http://clinicaltrials.gov/ct2/show/NCT02535845 (Archived by WebCite at http://www.webcitation.org/6e5XcOGXz and http://www.webcitation.org/6e5XfHoic, respectively). PMID:26825137
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Tiro, Jasmin A; Lee, Simon Craddock; Marks, Emily G; Persaud, Donna; Skinner, Celette Sugg; Street, Richard L; Wiebe, Deborah J; Farrell, David; Bishop, Wendy Pechero; Fuller, Sobha; Baldwin, Austin S
2016-01-29
Human papillomavirus (HPV)-related cancers are a significant burden on the US health care system that can be prevented through adolescent HPV vaccination. Despite guidelines recommending vaccination, coverage among US adolescents is suboptimal particularly among underserved patients (uninsured, low income, racial, and ethnic minorities) seen in safety-net health care settings. Many parents are ambivalent about the vaccine and delay making a decision or talking with a provider about it. Self-persuasion-generating one's own arguments for a health behavior-may be particularly effective for parents who are undecided or not motivated to make a vaccine decision. Through a 3-stage mixed-methods protocol, we will identify an optimal and feasible self-persuasion intervention strategy to promote adolescent HPV vaccination in safety-net clinics. In Stage 1, we will define content for a tablet-based self-persuasion app by characterizing (1) parents' self-generated arguments through cognitive interviews conducted with parents (n=50) of patients and (2) parent-provider HPV vaccine discussions through audio recordings of clinic visits (n=50). In Stage 2, we will compare the effects of the four self-persuasion intervention conditions that vary by cognitive processing level (parents verbalize vs listen to arguments) and choice of argument topics (parents choose vs are assigned topics) on parental vaccine intentions in a 2 × 2 factorial design randomized controlled trial (n=160). This proof-of-concept trial design will identify which intervention condition is optimal by quantitatively examining basic self-persuasion mechanisms (cognitive processing and choice) and qualitatively exploring parent experiences with intervention tasks. In Stage 3, we will conduct a pilot trial (n=90) in the safety-net clinics to assess feasibility of the optimal intervention condition identified in Stage 2. We will also assess its impact on parent-provider discussions. This paper describes the study protocol and activities to date. Currently, we have developed the initial prototype of the tablet app for English- and Spanish-speaking populations, and completed Stage 1 data collection. Our systematic collaboration between basic and applied behavioral scientists accelerates translation of promising basic psychological research into innovative interventions suitable for underserved, safety-net populations. At project's end, we plan to have a feasible and acceptable self-persuasion intervention that can affect key cancer disparities in the United States through prevention of HPV-related cancers. ClinicalTrials.gov http://clinicaltrials.gov/ct2/show/NCT02537756 and http://clinicaltrials.gov/ct2/show/NCT02535845 (Archived by WebCite at http://www.webcitation.org/6e5XcOGXz and http://www.webcitation.org/6e5XfHoic, respectively).
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Generation of a mouse with conditionally activated signaling through the BMP receptor, ALK2.
Fukuda, Tomokazu; Scott, Gregory; Komatsu, Yoshihiro; Araya, Runa; Kawano, Masako; Ray, Manas K; Yamada, Masahisa; Mishina, Yuji
2006-04-01
BMP signaling plays pleiotropic roles in various tissues. Transgenic mouse lines that overexpress BMP signaling in a tissue-specific manner would be beneficial; however, production of each tissue-specific transgenic mouse line is labor-intensive. Here, using a Cre-loxP system, we generated a conditionally overexpressing mouse line for BMP signaling through the type I receptor ALK2 (alternatively known as AVCRI, ActRI, or ActRIA). By mating this line with Cre-expression mouse lines, Cre-mediated recombination removes an intervening floxed lacZ expression cassette and thereby permits the expression of a constitutively active form of Alk2 (caAlk2) driven by a ubiquitous promoter, CAG. Tissue specificity of Cre recombination was monitored by a bicistronically expressed EGFP following Alk2 cDNA. Increased BMP signaling was confirmed by ectopic phosphorylation of SMAD1/5/8 in the areas where Cre recombination had occurred. The conditional overexpression system described here provides versatility in investigating gene functions in a tissue-specific manner without having to generate independent tissue-specific transgenic lines. Published 2006 Wiley-Liss, Inc.
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Telemedicine in the context of different medical specialities. The Polish perspective.
Rudowski, Robert
2003-01-01
Two types of telemedicine are considered in the paper: pre-recorded and real-time. The advantages and disadvantages of each type are described.The choice of telemedicine type depends on medical speciality. The separate branch of telemedicine--teleprevention of civilization diseases is discussed and examples of relevant WWW services in Poland are given. The own work examples of the Dept. of Medical Informatics, MUW, namely Onco-service of 200 protocols used in hematology and oncology and Cardio.net--a distributed teleinformation system for cardiology, are presented. the barriers of the development of telemedicine in Poland are caused by the organization of health service--Patients Funds using different software, no messaging standards and different reimbursement systems.
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TNAURice: Database on rice varieties released from Tamil Nadu Agricultural University
Ramalingam, Jegadeesan; Arul, Loganathan; Sathishkumar, Natarajan; Vignesh, Dhandapani; Thiyagarajan, Katiannan; Samiyappan, Ramasamy
2010-01-01
We developed, TNAURice: a database comprising of the rice varieties released from a public institution, Tamil Nadu Agricultural University (TNAU), Coimbatore, India. Backed by MS-SQL, and ASP-Net at the front end, this database provide information on both quantitative and qualitative descriptors of the rice varities inclusive of their parental details. Enabled by an user friendly search utility, the database can be effectively searched by the varietal descriptors, and the entire contents are navigable as well. The database comes handy to the plant breeders involved in the varietal improvement programs to decide on the choice of parental lines. TNAURice is available for public access at http://www.btistnau.org/germdefault.aspx. PMID:21364829
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TNAURice: Database on rice varieties released from Tamil Nadu Agricultural University.
Ramalingam, Jegadeesan; Arul, Loganathan; Sathishkumar, Natarajan; Vignesh, Dhandapani; Thiyagarajan, Katiannan; Samiyappan, Ramasamy
2010-11-27
WE DEVELOPED, TNAURICE: a database comprising of the rice varieties released from a public institution, Tamil Nadu Agricultural University (TNAU), Coimbatore, India. Backed by MS-SQL, and ASP-Net at the front end, this database provide information on both quantitative and qualitative descriptors of the rice varities inclusive of their parental details. Enabled by an user friendly search utility, the database can be effectively searched by the varietal descriptors, and the entire contents are navigable as well. The database comes handy to the plant breeders involved in the varietal improvement programs to decide on the choice of parental lines. TNAURice is available for public access at http://www.btistnau.org/germdefault.aspx.
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GAPIT: genome association and prediction integrated tool.
Lipka, Alexander E; Tian, Feng; Wang, Qishan; Peiffer, Jason; Li, Meng; Bradbury, Peter J; Gore, Michael A; Buckler, Edward S; Zhang, Zhiwu
2012-09-15
Software programs that conduct genome-wide association studies and genomic prediction and selection need to use methodologies that maximize statistical power, provide high prediction accuracy and run in a computationally efficient manner. We developed an R package called Genome Association and Prediction Integrated Tool (GAPIT) that implements advanced statistical methods including the compressed mixed linear model (CMLM) and CMLM-based genomic prediction and selection. The GAPIT package can handle large datasets in excess of 10 000 individuals and 1 million single-nucleotide polymorphisms with minimal computational time, while providing user-friendly access and concise tables and graphs to interpret results. http://www.maizegenetics.net/GAPIT. zhiwu.zhang@cornell.edu Supplementary data are available at Bioinformatics online.
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Worldwide Emerging Environmental Issues Affecting the U.S. Military. October 2005 Report
2005-10-01
Reports to Review………………………………………………………….…….…….12 7.1 Nordic Countries Suggest Actions to Cope with Global Warming ……………….…12 7.2 Energy and Security...www.kurzweilai.net/news/frame.html?main=news_single.html?id%3D4934 Item 7. Reports to Review 7.1 Nordic Countries Suggest Actions to Cope with Global Warming Conservation...of Nordic Nature in a Changing Climate is a report commissioned by the Nordic Council of Ministers to analyze global warming causes and to
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Controlling Costs: The 6-3-5 Method - Case Studies at NAVSEA and NATO
2016-04-30
Catalyst Technologies Costing for the Future: Exploring Cost Estimation With Unmanned Autonomous Systems Ricardo Valerdi, Professor, University of... systems was a Hughes Aircraft spinoff company. The ATCSs being developed required the use of touchscreens (a new technology at the time) and had the...www.acquisitionresearch.net). ^Åèìáëáíáçå=oÉëÉ~êÅÜ=mêçÖê~ãW= `êÉ~íáåÖ=póåÉêÖó=Ñçê=fåÑçêãÉÇ=`Ü~åÖÉ= - 282 - Panel 18. Forecasting and Controlling Costs in Weapons Systems
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NASA Astrophysics Data System (ADS)
Clemen, Hans-Christian; Schneider, Johannes; Köllner, Franziska; Klimach, Thomas; Pikridas, Michael; Stavroulas, Iasonas; Sciare, Jean; Borrmann, Stephan
2017-04-01
The Mediterranean region is one of the most climatically sensitive areas and is influenced by air masses of different origin. Aerosol particles are one important factor contributing to the Earth's radiative forcing, but knowledge about their composition and sources is still limited. Here, we report on results from the INUIT-BACCHUS-ACTRIS campaign, which was conducted at the Cyprus Atmospheric Observatory (CAO, Agia Marina Xyliatou) in Cyprus in April 2016. Our results show that the chemical composition of the aerosol particles in the eastern Mediterranean is strongly dependent on their source region. The composition of particles in a size range between 150 nm and 3 μm was measured using the Aircraft-based Laser ABlation Aerosol MAss spectrometer (ALABAMA), which is a single particle laser ablation instrument using a bipolar time-of-flight mass spectrometer. The mass spectral information on cations and anions allow for the analysis of different molecular fragments. The information about the source regions results from backward trajectories using HYSPLIT Trajectory Model (Trajectory Ensemble) on hourly basis. To assess the influence of certain source regions on the air masses arriving at CAO, we consider the number of trajectories that crossed the respective source region within defined time steps. For a more detailed picture also the height and the velocity of the air masses during their overpass above the source regions will be considered. During the campaign at CAO in April 2016 three main air mass source regions were observed: 1) Northern Central Europe, likely with an enhanced anthropogenic influence (e.g. sulfate and black carbon from combustion processes, fly ash particles from power plants, characterized by Sr and Ba), 2) Southwest Europe, with a higher influence of the Mediterranean Sea including sea salt particles (characterized by, e.g., NaxCly, NaClxNOy), 3) Northern Africa/Sahara, with air masses that are expected to have a higher load of mineral dust particles (characterized by typical elements like Al, Si, Ca, Fe). To estimate the influence of the selected regions, we compare the time series of the dominating elements or molecular fragments to the times with trajectories from specific source regions. For differentiation between short and long-range transported particles, molecules that are typical for aging processes in the atmosphere, e.g., products from reaction with ozone, nitric and sulfuric acid will be considered. Additionally, modifications of the internal mixing state of the particles during the measurement period will be studied. This project was supported by DFG (FOR 1525 "INUIT) and has received funding from the European Union's Seventh Framework Programme (FP7) project BACCHUS under grant agreement no. 603445 and from the European Union's Horizon 2020 research and innovation programme ACTRIS-2 under grant agreement No 654109.
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Towards a global terrestrial species monitoring program
Schmeller, Dirk S.; Julliard, Romain; Bellingham, Peter J.; Böhm, Monika; Brummitt, Neil; Chiarucci, Alessandro; Couvet, Denis; Elmendorf, Sarah; Forsyth, David M.; Moreno, Jaime García; Gregory, Richard D.; Magnusson, William E.; Martin, Laura J.; McGeoch, Melodie A.; Mihoub, Jean-Baptiste; Pereira, Henrique M.; Proença, Vânia; van Swaay, Chris A.M.; Yahara, Tetsukazu; Belnap, Jayne
2015-01-01
Introduction: The Convention for Biological Diversity’s (CBD) Strategic Plan for Biodiversity 2011-2020 envisions that “By 2050, biodiversity is valued, conserved, restored and wisely used, maintaining ecosystem services, sustaining a healthy planet and delivering benefits essential for all people.” Although 193 parties have adopted these goals, there is little infrastructure in place to monitor global biodiversity trends. Recent international conservation policy requires such data to be up-to-date, reliable, comparable among sites, relevant, and understandable; as is becoming obvious from the work plan adopted by the Intergovernmental Panel for Biodiversity and Ecosystem Services (IPBES: www.ipbes.net/; http://tinyurl.com/ohdnknq). In order to meet the five strategic goals of the Strategic Plan for Biodiversity 2011-2020 and its 20 accompanying Aichi Targets for 2020 (www.cbd.int/sp/targets/), advances need to be made in coordinating large-scale biodiversity monitoring and linking these with environmental data to develop a comprehensive Global Observation Network, as is the main idea behind GEOSS the Global Earth Observation System of Systems (Christian 2005)...Here we identify ten requirements important for the successful implementation of a global biodiversity monitoring network under the flag of GEO BON and especially a global terrestrial species monitoring program.
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New Approaches to the Gulf Hypoxia Problem
NASA Astrophysics Data System (ADS)
Bianchi, Thomas S.; Allison, Mead A.; Chapman, Piers; Cowan, James H.; Dagg, Michael J.; Day, John W.; DiMarco, Steve F.; Hetland, Robert D.; Powell, Rodney
2010-05-01
Coastal water hypoxia, where dissolved oxygen is less than 2 milligrams per liter, is a global environmental problem [e.g., Diaz and Rosenberg, 2008]. It is largely associated with eutrophication, whereby nutrient inputs (nitrogen and phosphorous) to coastal waters lead to elevated primary production and accelerated rates of microbial respiration, which results in oxygen depletion. Despite more than 25 years of monitoring [Rabalais et al., 2007] (see also Figure S1 in the online supplement to this Eos issue (http://www.agu.org/eos_elec/)), the relative importance of the various processes that control hypoxia in bottom waters of the northern Gulf of Mexico (GOM)—in particular, those beyond the direct influence of river plumes [Dagg et al., 2007; Bianchi et al., 2008, 2010, and references therein]—remains uncertain. For example, a prediction last June pronounced that the 2009 hypoxic area would be the largest on record (˜23,000 square kilometers; see http://www.gulfhypoxia.net/Research/Shelfwide%20Cruises/2009/Files/2009_Hypoxia_Forecast.pdf). However, the most recent annual surveys estimated its size at 8000 square kilometers, only 35% of that predicted. This occurred in the absence of a significant hurricane impact on this margin in 2009—hurricanes tend to dissipate hypoxia.
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Quinoa - Adaptive Computational Fluid Dynamics, 0.2
DOE Office of Scientific and Technical Information (OSTI.GOV)
Bakosi, Jozsef; Gonzalez, Francisco; Rogers, Brandon
Quinoa is a set of computational tools that enables research and numerical analysis in fluid dynamics. At this time it remains a test-bed to experiment with various algorithms using fully asynchronous runtime systems. Currently, Quinoa consists of the following tools: (1) Walker, a numerical integrator for systems of stochastic differential equations in time. It is a mathematical tool to analyze and design the behavior of stochastic differential equations. It allows the estimation of arbitrary coupled statistics and probability density functions and is currently used for the design of statistical moment approximations for multiple mixing materials in variable-density turbulence. (2) Inciter,more » an overdecomposition-aware finite element field solver for partial differential equations using 3D unstructured grids. Inciter is used to research asynchronous mesh-based algorithms and to experiment with coupling asynchronous to bulk-synchronous parallel code. Two planned new features of Inciter, compared to the previous release (LA-CC-16-015), to be implemented in 2017, are (a) a simple Navier-Stokes solver for ideal single-material compressible gases, and (b) solution-adaptive mesh refinement (AMR), which enables dynamically concentrating compute resources to regions with interesting physics. Using the NS-AMR problem we plan to explore how to scale such high-load-imbalance simulations, representative of large production multiphysics codes, to very large problems on very large computers using an asynchronous runtime system. (3) RNGTest, a test harness to subject random number generators to stringent statistical tests enabling quantitative ranking with respect to their quality and computational cost. (4) UnitTest, a unit test harness, running hundreds of tests per second, capable of testing serial, synchronous, and asynchronous functions. (5) MeshConv, a mesh file converter that can be used to convert 3D tetrahedron meshes from and to either of the following formats: Gmsh, (http://www.geuz.org/gmsh), Netgen, (http://sourceforge.net/apps/mediawiki/netgen-mesher), ExodusII, (http://sourceforge.net/projects/exodusii), HyperMesh, (http://www.altairhyperworks.com/product/HyperMesh).« less
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Mapping habitat for multiple species in the Desert Southwest
Inman, Richard D.; Nussear, Kenneth E.; Esque, Todd C.; Vandergast, Amy G.; Hathaway, Stacie A.; Wood, Dustin A.; Barr, Kelly R.; Fisher, Robert N.
2014-01-01
Many utility scale renewable energy projects are currently proposed across the Mojave Ecoregion. Agencies that manage biological resources throughout this region need to understand the potential impacts of these renewable energy projects and their associated infrastructure (for example, transmission corridors, substations, access roads, etc.) on species movement, genetic exchange among populations, and species’ abilities to adapt to changing environmental conditions. Understanding these factors will help managers’ select appropriate project sites and possibly mitigate for anticipated effects of management activities. We used species distribution models to map habitat for 15 species across the Mojave Ecoregion to aid regional land-use management planning. Models were developed using a common 1 × 1 kilometer resolution with maximum entropy and generalized additive models. Occurrence data were compiled from multiple sources, including VertNet (http://vertnet.org/), HerpNET (http://www.herpnet.org), and MaNIS (http://manisnet.org), as well as from internal U.S. Geological Survey databases and other biologists. Background data included 20 environmental covariates representing terrain, vegetation, and climate covariates. This report summarizes these environmental covariates and species distribution models used to predict habitat for the 15 species across the Mojave Ecoregion.
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The multilocus sequence typing network: mlst.net.
Aanensen, David M; Spratt, Brian G
2005-07-01
The unambiguous characterization of strains of a pathogen is crucial for addressing questions relating to its epidemiology, population and evolutionary biology. Multilocus sequence typing (MLST), which defines strains from the sequences at seven house-keeping loci, has become the method of choice for molecular typing of many bacterial and fungal pathogens (and non-pathogens), and MLST schemes and strain databases are available for a growing number of prokaryotic and eukaryotic organisms. Sequence data are ideal for strain characterization as they are unambiguous, meaning strains can readily be compared between laboratories via the Internet. Laboratories undertaking MLST can quickly progress from sequencing the seven gene fragments to characterizing their strains and relating them to those submitted by others and to the population as a whole. We provide the gateway to a number of MLST schemes, each of which contain a set of tools for the initial characterization of strains, and methods for relating query strains to other strains of the species, including clustering based on differences in allelic profiles, phylogenetic trees based on concatenated sequences, and a recently developed method (eBURST) for identifying clonal complexes within a species and displaying the overall structure of the population. This network of MLST websites is available at http://www.mlst.net.
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DeJongh, Matthew; Bockstege, Benjamin; Frybarger, Paul; Hazekamp, Nicholas; Kammeraad, Joshua; McGeehan, Travis
2012-01-01
Summary: CytoSEED is a Cytoscape plugin for viewing, manipulating and analyzing metabolic models created using the Model SEED. The CytoSEED plugin enables users of the Model SEED to create informative visualizations of the reaction networks generated for their organisms of interest. These visualizations are useful for understanding organism-specific biochemistry and for highlighting the results of flux variability analysis experiments. Availability and Implementation: Freely available for download on the web at http://sourceforge.net/projects/cytoseed/. Implemented in Java SE 6 and supported on all platforms that support Cytoscape. Contact: dejongh@hope.edu Supplementary information: Installation instructions, a tutorial, and full-size figures are available at http://www.cs.hope.edu/cytoseed/. PMID:22210867
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GoIFISH: a system for the quantification of single cell heterogeneity from IFISH images.
Trinh, Anne; Rye, Inga H; Almendro, Vanessa; Helland, Aslaug; Russnes, Hege G; Markowetz, Florian
2014-08-26
Molecular analysis has revealed extensive intra-tumor heterogeneity in human cancer samples, but cannot identify cell-to-cell variations within the tissue microenvironment. In contrast, in situ analysis can identify genetic aberrations in phenotypically defined cell subpopulations while preserving tissue-context specificity. GoIFISHGoIFISH is a widely applicable, user-friendly system tailored for the objective and semi-automated visualization, detection and quantification of genomic alterations and protein expression obtained from fluorescence in situ analysis. In a sample set of HER2-positive breast cancers GoIFISHGoIFISH is highly robust in visual analysis and its accuracy compares favorably to other leading image analysis methods. GoIFISHGoIFISH is freely available at www.sourceforge.net/projects/goifish/.
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Lessons from the MicroObservatory Net
NASA Astrophysics Data System (ADS)
Brecher, K.; Sadler, P.; Gould, R.; Leiker, S.; Antonucci, P.; Deutsch, F.
1998-12-01
Over the past several years, we have developed a fully integrated automated astronomical telescope system which combines the imaging power of a cooled CCD, with a self-contained and weatherized 15 cm reflecting optical telescope and mount. Each telescope can be pointed and focused remotely, and filters, field of view and exposure times can be changed easily. The MicroObservatory Net consists of five of these telescopes. They are being deployed around the world at widely distributed longitudes for access to distant night skies during local daytime. Remote access to the MicroObservatories over the Internet has been available to select schools since 1995. The telescopes can be controlled in real time or in delay mode, from any computer using Web-based software. Individuals have access to all of the telescope control functions without the need for an `on-site' operator. After a MicroObservatory completes a job, the user is automatically notified by e-mail that the image is available for viewing and downloading from the Web site. Images are archived at the Web site, along with sample challenges and a user bulletin board, all of which encourage collaboration between schools. The Internet address of the telescopes is http://mo-www.harvard.edu/MicroObservatory/. The telescopes were designed for classroom instruction by teachers, as well as for use by students and amateur astronomers for original scientific research projects. In this talk, we will review some of the experiences we, students and teachers have had in using the telescopes. Support for the MicroObservatory Net has been provided by the NSF, Apple Computer, Inc. and Kodak, Inc.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Jones, T.
2000-07-01
The Write One, Run Many (WORM) site (worm.csirc.net) is the on-line home of the WORM language and is hosted by the Criticality Safety Information Resource Center (CSIRC) (www.csirc.net). The purpose of this web site is to create an on-line community for WORM users to gather, share, and archive WORM-related information. WORM is an embedded, functional, programming language designed to facilitate the creation of input decks for computer codes that take standard ASCII text files as input. A functional programming language is one that emphasizes the evaluation of expressions, rather than execution of commands. The simplest and perhaps most common examplemore » of a functional language is a spreadsheet such as Microsoft Excel. The spreadsheet user specifies expressions to be evaluated, while the spreadsheet itself determines the commands to execute, as well as the order of execution/evaluation. WORM functions in a similar fashion and, as a result, is very simple to use and easy to learn. WORM improves the efficiency of today's criticality safety analyst by allowing: (1) input decks for parameter studies to be created quickly and easily; (2) calculations and variables to be embedded into any input deck, thus allowing for meaningful parameter specifications; (3) problems to be specified using any combination of units; and (4) complex mathematically defined models to be created. WORM is completely written in Perl. Running on all variants of UNIX, Windows, MS-DOS, MacOS, and many other operating systems, Perl is one of the most portable programming languages available. As such, WORM works on practically any computer platform.« less
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HamSCI: The Ham Radio Science Citizen Investigation
NASA Astrophysics Data System (ADS)
Frissell, N. A.; Moses, M. L.; Earle, G. D.; McGwier, R. W.; Miller, E. S.; Kaeppler, S. R.; Silver, H. W.; Ceglia, F.; Pascoe, D.; Sinanis, N.; Smith, P.; Williams, R.; Shovkoplyas, A.; Gerrard, A. J.
2016-12-01
Amateur (or "ham") radio operators are individuals with a non-pecuniary interest in radio technology, engineering, communications, science, and public service. They are licensed by their national governments to transmit on amateur radio frequencies. In many jurisdictions, there is no age requirement for a ham radio license, and operators from diverse backgrounds participate. There are more than 740,000 hams in the US, and over 3 million (estimated) worldwide. Many amateur communications are conducted using transionospheric links and thus affected by space weather and ionospheric processes. Recent technological advances have enabled the development of automated ham radio observation networks (e.g. the Reverse Beacon Network, www.reversebeacon.net) and specialized operating modes for the study of weak-signal propagation. The data from these networks have been shown to be useful for the study of ionospheric processes. In order to connect professional researchers with the volunteer-based ham radio community, HamSCI (Ham Radio Science Citizen Investigation, www.hamsci.org) has been established. HamSCI is a platform for publicizing and promoting projects that are consistent with the following objectives: (1) Advance scientific research and understanding through amateur radio activities. (2) Encourage the development of new technologies to support this research. (3) Provide educational opportunities for the amateur community and the general public. HamSCI researchers are working with the American Radio Relay League (ARRL, www.arrl.org) to publicize these objectives and recruit interested hams. The ARRL is the US national organization for amateur radio with a membership of over 170,000 and a monthly magazine, QST. HamSCI is currently preparing to support ionospheric research connected to the 21 Aug 2017 Total Solar Eclipse by expanding coverage of the Reverse Beacon Network and organizing a large-scale ham radio operating event ("QSO Party") to generate data during the eclipse.
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NASA Astrophysics Data System (ADS)
Spokas, K.; Patrizio, P.; Leduc, S.; Mesfun, S.; Kraxner, F.
2017-12-01
Reducing electricity-sector emissions relies heavily on countries' abilities to either transition away from carbon-intensive energy generation or to sequester its resultant emissions with carbon capture and storage (CCS) technologies. The use of biomass energy technologies in conjunction with carbon capture and sequestration (BECCS) presents the opportunity for net reductions in atmospheric carbon dioxide. In this study, we investigate the limitations of several common policy mechanisms to incentivize the deployment of BECCS using the techno-economic spatial optimization model BeWhere (www.iiasa.ac.at/bewhere). We consider a set of coal and natural gas power plants in the United States (U.S.) selected using a screening process that considers capacity, boiler age, and capacity factor for electricity-generation units from the EPA 2014 eGRID database. The set makes up 470 GW of generation, and produces 8,400 PJ and 2.07 GtCO2 annually. Co-firing up to 15% for coal power plants is considered, using woody-biomass residues sourced from certified and managed U.S. forests obtained from the G4M (www.iiasa.ac.at/g4m) and GeoWiki (www.geo-wiki.org) database. Geologic storage is considered with injectivity and geomechanical limitations to ensure safe storage. Costs are minimized under two policy mechanisms: a carbon tax and geologic carbon sequestration credits, such as the Q45 credits. Results show that the carbon tax scenario incentivizes co-firing at low to medium carbon taxes, but is replaced by CCS at higher tax values. Carbon taxes do not strongly incentivize BECCS, as negative emissions associated with sequestering carbon content are not accounted as revenue. On the other hand, carbon credit scenarios result in significant CCS deployment, but lack any incentive for co-firing.
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Evolutionary and comparative analyses of the soybean genome
Cannon, Steven B.; Shoemaker, Randy C.
2012-01-01
The soybean genome assembly has been available since the end of 2008. Significant features of the genome include large, gene-poor, repeat-dense pericentromeric regions, spanning roughly 57% of the genome sequence; a relatively large genome size of ~1.15 billion bases; remnants of a genome duplication that occurred ~13 million years ago (Mya); and fainter remnants of older polyploidies that occurred ~58 Mya and >130 Mya. The genome sequence has been used to identify the genetic basis for numerous traits, including disease resistance, nutritional characteristics, and developmental features. The genome sequence has provided a scaffold for placement of many genomic feature elements, both from within soybean and from related species. These may be accessed at several websites, including http://www.phytozome.net, http://soybase.org, http://comparative-legumes.org, and http://www.legumebase.brc.miyazaki-u.ac.jp. The taxonomic position of soybean in the Phaseoleae tribe of the legumes means that there are approximately two dozen other beans and relatives that have undergone independent domestication, and which may have traits that will be useful for transfer to soybean. Methods of translating information between species in the Phaseoleae range from design of markers for marker assisted selection, to transformation with Agrobacterium or with other experimental transformation methods. PMID:23136483
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Science Hack Day: an opportunity for public engagement, art/science mash-ups, and inspiration
NASA Astrophysics Data System (ADS)
Bellis, Matthew
2013-04-01
The idea of a Science Hack Day (http://sciencehackday.com/) is to put non-scientists (designers, web developers, artists, interested enthusiasts) in a room with scientists and some good ideas, and see what science-themed project they can create in a weekend (about 24 hours of real hacking). The motto of the organizers is ``Get Excited and Make Things with Science!'' I have participated in several of these events including the first one held in the United State in Palo Alto in 2010 and as a remote advisor to participants in Nairobi, Kenya. To these events I have brought particle physics data from both the BaBar and the CMS (Compact Muon Solenoid) experiments, data from the CoGeNT dark matter direct-detection experiment, and my expertise and enthusiasm. The experience has been transformative for me as both a scientist and a science advocate. This talk will recount my experiences with Science Hack Day events in general and detail some projects that have come out of these days, including the Particle Physics Wind Chime (http://www.mattbellis.com/windchime/) and the Standard Model of Cocktail Physics (http://www.physicsdavid.net/2012/11/standard-model-of-cocktail-physics/). Opportunities for other scientists to take part in similar events will be discussed.
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One-dimensional statistical parametric mapping in Python.
Pataky, Todd C
2012-01-01
Statistical parametric mapping (SPM) is a topological methodology for detecting field changes in smooth n-dimensional continua. Many classes of biomechanical data are smooth and contained within discrete bounds and as such are well suited to SPM analyses. The current paper accompanies release of 'SPM1D', a free and open-source Python package for conducting SPM analyses on a set of registered 1D curves. Three example applications are presented: (i) kinematics, (ii) ground reaction forces and (iii) contact pressure distribution in probabilistic finite element modelling. In addition to offering a high-level interface to a variety of common statistical tests like t tests, regression and ANOVA, SPM1D also emphasises fundamental concepts of SPM theory through stand-alone example scripts. Source code and documentation are available at: www.tpataky.net/spm1d/.
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De Oliveira, T; Miller, R; Tarin, M; Cassol, S
2003-01-01
Sequence databases encode a wealth of information needed to develop improved vaccination and treatment strategies for the control of HIV and other important pathogens. To facilitate effective utilization of these datasets, we developed a user-friendly GDE-based LINUX interface that reduces input/output file formatting. GDE was adapted to the Linux operating system, bioinformatics tools were integrated with microbe-specific databases, and up-to-date GDE menus were developed for several clinically important viral, bacterial and parasitic genomes. Each microbial interface was designed for local access and contains Genbank, BLAST-formatted and phylogenetic databases. GDE-Linux is available for research purposes by direct application to the corresponding author. Application-specific menus and support files can be downloaded from (http://www.bioafrica.net).
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How to Manage Rejected Scientific Papers? UNAIS as Final Solution.
Diana, Alessandro
2012-01-01
Before publication, biomedical papers might undergo a very complex process, from journal selection, authors' motivations for submissions, modifications, and final publication or refusal. UNAIS (Unpublished Articles In Science) is an online repository in which authors can publish previously rejected scientific articles or articles that have never been submitted for publication. At UNAIS, authors can also publish the reasons behind the refusals to publication. UNAIS is more than an e-journal: it is a scientific drop box in which scientists can find indicative and negative results, as well as ideas that can inspire others. UNAIS's goal is also to help students and scientists who want to learn how to write scientific articles. UNAIS' aim is to exchange and promote knowledge. Have a look on www.unais.net.
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viRome: an R package for the visualization and analysis of viral small RNA sequence datasets.
Watson, Mick; Schnettler, Esther; Kohl, Alain
2013-08-01
RNA interference (RNAi) is known to play an important part in defence against viruses in a range of species. Second-generation sequencing technologies allow us to assay these systems and the small RNAs that play a key role with unprecedented depth. However, scientists need access to tools that can condense, analyse and display the resulting data. Here, we present viRome, a package for R that takes aligned sequence data and produces a range of essential plots and reports. viRome is released under the BSD license as a package for R available for both Windows and Linux http://virome.sf.net. Additional information and a tutorial is available on the ARK-Genomics website: http://www.ark-genomics.org/bioinformatics/virome. mick.watson@roslin.ed.ac.uk.
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Theme section for 36th International Symposium for Remote Sensing of the Environment in Berlin
NASA Astrophysics Data System (ADS)
Trinder, John; Waske, Björn
2016-09-01
The International Symposium for Remote Sensing of the Environment (ISRSE) is the longest series of international conferences held on the topic of Remote Sensing, commencing in Ann Arbor, Michigan USA in 1962. While the name of the conference has changed over the years, it is regularly held approximately every 2 years and continues to be one of the leading international conferences on remote sensing. The latest of these conferences, the 36th ISRSE, was held in Berlin, Germany from 11 to 15 May 2015. All complete papers from the conference are available in the ISPRS International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences at http://www.int-arch-photogramm-remote-sens-spatial-inf-sci.net/XL-7-W3/index.html.
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Kannisto, Kati Anneli; Korhonen, Joonas; Adams, Clive E; Koivunen, Marita Hannele; Vahlberg, Tero; Välimäki, Maritta Anneli
2017-02-21
Clinical trials are the gold standard of evidence-based practice. Still many papers inadequately report methodology in randomized controlled trials (RCTs), particularly for mHealth interventions for people with serious mental health problems. To ensure robust enough evidence, it is important to understand which study phases are the most vulnerable in the field of mental health care. We mapped the recruitment and the trial follow-up periods of participants to provide a picture of the dropout predictors from a mHealth-based trial. As an example, we used a mHealth-based multicenter RCT, titled "Mobile.Net," targeted at people with serious mental health problems. Recruitment and follow-up processes of the Mobile.Net trial were monitored and analyzed. Recruitment outcomes were recorded as screened, eligible, consent not asked, refused, and enrolled. Patient engagement was recorded as follow-up outcomes: (1) attrition during short message service (SMS) text message intervention and (2) attrition during the 12-month follow-up period. Multiple regression analysis was used to identify which demographic factors were related to recruitment and retention. We recruited 1139 patients during a 15-month period. Of 11,530 people screened, 36.31% (n=4186) were eligible. This eligible group tended to be significantly younger (mean 39.2, SD 13.2 years, P<.001) and more often women (2103/4181, 50.30%) than those who were not eligible (age: mean 43.7, SD 14.6 years; women: 3633/6514, 55.78%). At the point when potential participants were asked to give consent, a further 2278 refused. Those who refused were a little older (mean 40.2, SD 13.9 years) than those who agreed to participate (mean 38.3, SD 12.5 years; t1842=3.2, P<.001). We measured the outcomes after 12 months of the SMS text message intervention. Attrition from the SMS text message intervention was 4.8% (27/563). The patient dropout rate after 12 months was 0.36% (4/1123), as discovered from the register data. In all, 3.12% (35/1123) of the participants withdrew from the trial. However, dropout rates from the patient survey (either by paper or telephone interview) were 52.45% (589/1123) and 27.8% (155/558), respectively. Almost all participants (536/563, 95.2%) tolerated the intervention, but those who discontinued were more often women (21/27, 78%; P=.009). Finally, participants' age (P<.001), gender (P<.001), vocational education (P=.04), and employment status (P<.001) seemed to predict their risk of dropping out from the postal survey. Patient recruitment and engagement in the 12-month follow-up conducted with a postal survey were the most vulnerable phases in the SMS text message-based trial. People with serious mental health problems may need extra support during the recruitment process and in engaging them in SMS text message-based trials to ensure robust enough evidence for mental health care. International Standard Randomized Controlled Trial Number (ISRCTN): 27704027; http://www.isrctn.com/ISRCTN27704027 (Archived by WebCite at http://www.webcitation.org/6oHcU2SFp). ©Kati Anneli Kannisto, Joonas Korhonen, Clive E Adams, Marita Hannele Koivunen, Tero Vahlberg, Maritta Anneli Välimäki. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 21.02.2017.
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DIET@NET: Best Practice Guidelines for dietary assessment in health research.
Cade, Janet E; Warthon-Medina, Marisol; Albar, Salwa; Alwan, Nisreen A; Ness, Andrew; Roe, Mark; Wark, Petra A; Greathead, Katharine; Burley, Victoria J; Finglas, Paul; Johnson, Laura; Page, Polly; Roberts, Katharine; Steer, Toni; Hooson, Jozef; Greenwood, Darren C; Robinson, Sian
2017-11-15
Dietary assessment is complex, and strategies to select the most appropriate dietary assessment tool (DAT) in epidemiological research are needed. The DIETary Assessment Tool NETwork (DIET@NET) aimed to establish expert consensus on Best Practice Guidelines (BPGs) for dietary assessment using self-report. The BPGs were developed using the Delphi technique. Two Delphi rounds were conducted. A total of 131 experts were invited, and of these 65 accepted, with 48 completing Delphi round I and 51 completing Delphi round II. In all, a total of 57 experts from North America, Europe, Asia and Australia commented on the 47 suggested guidelines. Forty-three guidelines were generated, grouped into the following four stages: Stage I. Define what is to be measured in terms of dietary intake (what? who? and when?); Stage II. Investigate different types of DATs; Stage III. Evaluate existing tools to select the most appropriate DAT by evaluating published validation studies; Stage IV. Think through the implementation of the chosen DAT and consider sources of potential biases. The Delphi technique consolidated expert views on best practice in assessing dietary intake. The BPGs provide a valuable guide for health researchers to choose the most appropriate dietary assessment method for their studies. These guidelines will be accessible through the Nutritools website, www.nutritools.org .
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FamNet: A Framework to Identify Multiplied Modules Driving Pathway Expansion in Plants1
Tohge, Takayuki; Klie, Sebastian; Fernie, Alisdair R.
2016-01-01
Gene duplications generate new genes that can acquire similar but often diversified functions. Recent studies of gene coexpression networks have indicated that, not only genes, but also pathways can be multiplied and diversified to perform related functions in different parts of an organism. Identification of such diversified pathways, or modules, is needed to expand our knowledge of biological processes in plants and to understand how biological functions evolve. However, systematic explorations of modules remain scarce, and no user-friendly platform to identify them exists. We have established a statistical framework to identify modules and show that approximately one-third of the genes of a plant’s genome participate in hundreds of multiplied modules. Using this framework as a basis, we implemented a platform that can explore and visualize multiplied modules in coexpression networks of eight plant species. To validate the usefulness of the platform, we identified and functionally characterized pollen- and root-specific cell wall modules that multiplied to confer tip growth in pollen tubes and root hairs, respectively. Furthermore, we identified multiplied modules involved in secondary metabolite synthesis and corroborated them by metabolite profiling of tobacco (Nicotiana tabacum) tissues. The interactive platform, referred to as FamNet, is available at http://www.gene2function.de/famnet.html. PMID:26754669
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Jørgensen, Kasper W; Rasmussen, Michael; Buus, Søren; Nielsen, Morten
2014-01-01
Major histocompatibility complex class I (MHC-I) molecules play an essential role in the cellular immune response, presenting peptides to cytotoxic T lymphocytes (CTLs) allowing the immune system to scrutinize ongoing intracellular production of proteins. In the early 1990s, immunogenicity and stability of the peptide–MHC-I (pMHC-I) complex were shown to be correlated. At that time, measuring stability was cumbersome and time consuming and only small data sets were analysed. Here, we investigate this fairly unexplored area on a large scale compared with earlier studies. A recent small-scale study demonstrated that pMHC-I complex stability was a better correlate of CTL immunogenicity than peptide–MHC-I affinity. We here extended this study and analysed a total of 5509 distinct peptide stability measurements covering 10 different HLA class I molecules. Artificial neural networks were used to construct stability predictors capable of predicting the half-life of the pMHC-I complex. These predictors were shown to predict T-cell epitopes and MHC ligands from SYFPEITHI and IEDB to form significantly more stable MHC-I complexes compared with affinity-matched non-epitopes. Combining the stability predictions with a state-of-the-art affinity predictions NetMHCcons significantly improved the performance for identification of T-cell epitopes and ligands. For the HLA alleles included in the study, we could identify distinct sub-motifs that differentiate between stable and unstable peptide binders and demonstrate that anchor positions in the N-terminal of the binding motif (primarily P2 and P3) play a critical role for the formation of stable pMHC-I complexes. A webserver implementing the method is available at http://www.cbs.dtu.dk/services/NetMHCstab. PMID:23927693
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Sharing electronic structure and crystallographic data with ETSF_IO
NASA Astrophysics Data System (ADS)
Caliste, D.; Pouillon, Y.; Verstraete, M. J.; Olevano, V.; Gonze, X.
2008-11-01
We present a library of routines whose main goal is to read and write exchangeable files (NetCDF file format) storing electronic structure and crystallographic information. It is based on the specification agreed inside the European Theoretical Spectroscopy Facility (ETSF). Accordingly, this library is nicknamed ETSF_IO. The purpose of this article is to give both an overview of the ETSF_IO library and a closer look at its usage. ETSF_IO is designed to be robust and easy to use, close to Fortran read and write routines. To facilitate its adoption, a complete documentation of the input and output arguments of the routines is available in the package, as well as six tutorials explaining in detail various possible uses of the library routines. Catalogue identifier: AEBG_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBG_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Gnu Lesser General Public License No. of lines in distributed program, including test data, etc.: 63 156 No. of bytes in distributed program, including test data, etc.: 363 390 Distribution format: tar.gz Programming language: Fortran 95 Computer: All systems with a Fortran95 compiler Operating system: All systems with a Fortran95 compiler Classification: 7.3, 8 External routines: NetCDF, http://www.unidata.ucar.edu/software/netcdf Nature of problem: Store and exchange electronic structure data and crystallographic data independently of the computational platform, language and generating software Solution method: Implement a library based both on NetCDF file format and an open specification (http://etsf.eu/index.php?page=standardization)
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2012-01-01
Background The first draft assembly and gene prediction of the grapevine genome (8X base coverage) was made available to the scientific community in 2007, and functional annotation was developed on this gene prediction. Since then additional Sanger sequences were added to the 8X sequences pool and a new version of the genomic sequence with superior base coverage (12X) was produced. Results In order to more efficiently annotate the function of the genes predicted in the new assembly, it is important to build on as much of the previous work as possible, by transferring 8X annotation of the genome to the 12X version. The 8X and 12X assemblies and gene predictions of the grapevine genome were compared to answer the question, “Can we uniquely map 8X predicted genes to 12X predicted genes?” The results show that while the assemblies and gene structure predictions are too different to make a complete mapping between them, most genes (18,725) showed a one-to-one relationship between 8X predicted genes and the last version of 12X predicted genes. In addition, reshuffled genomic sequence structures appeared. These highlight regions of the genome where the gene predictions need to be taken with caution. Based on the new grapevine gene functional annotation and in-depth functional categorization, twenty eight new molecular networks have been created for VitisNet while the existing networks were updated. Conclusions The outcomes of this study provide a functional annotation of the 12X genes, an update of VitisNet, the system of the grapevine molecular networks, and a new functional categorization of genes. Data are available at the VitisNet website (http://www.sdstate.edu/ps/research/vitis/pathways.cfm). PMID:22554261
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A data delivery system for IMOS, the Australian Integrated Marine Observing System
NASA Astrophysics Data System (ADS)
Proctor, R.; Roberts, K.; Ward, B. J.
2010-09-01
The Integrated Marine Observing System (IMOS, www.imos.org.au), an AUD 150 m 7-year project (2007-2013), is a distributed set of equipment and data-information services which, among many applications, collectively contribute to meeting the needs of marine climate research in Australia. The observing system provides data in the open oceans around Australia out to a few thousand kilometres as well as the coastal oceans through 11 facilities which effectively observe and measure the 4-dimensional ocean variability, and the physical and biological response of coastal and shelf seas around Australia. Through a national science rationale IMOS is organized as five regional nodes (Western Australia - WAIMOS, South Australian - SAIMOS, Tasmania - TASIMOS, New SouthWales - NSWIMOS and Queensland - QIMOS) surrounded by an oceanic node (Blue Water and Climate). Operationally IMOS is organized as 11 facilities (Argo Australia, Ships of Opportunity, Southern Ocean Automated Time Series Observations, Australian National Facility for Ocean Gliders, Autonomous Underwater Vehicle Facility, Australian National Mooring Network, Australian Coastal Ocean Radar Network, Australian Acoustic Tagging and Monitoring System, Facility for Automated Intelligent Monitoring of Marine Systems, eMarine Information Infrastructure and Satellite Remote Sensing) delivering data. IMOS data is freely available to the public. The data, a combination of near real-time and delayed mode, are made available to researchers through the electronic Marine Information Infrastructure (eMII). eMII utilises the Australian Academic Research Network (AARNET) to support a distributed database on OPeNDAP/THREDDS servers hosted by regional computing centres. IMOS instruments are described through the OGC Specification SensorML and where-ever possible data is in CF compliant netCDF format. Metadata, conforming to standard ISO 19115, is automatically harvested from the netCDF files and the metadata records catalogued in the OGC GeoNetwork Metadata Entry and Search Tool (MEST). Data discovery, access and download occur via web services through the IMOS Ocean Portal (http://imos.aodn.org.au) and tools for the display and integration of near real-time data are in development.
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NASA Astrophysics Data System (ADS)
Pasachoff, Jay M.; Leich, Pierre
2015-01-01
Simon Mayr's (Marius's) Mundus Iovialis Anno M·DC·IX Detectus Ope Perspicilli Belgici (The World of Jupiter...) was published in Nuremberg in 1614; Marius was the Ansbach court mathematician. The frontispiece includes not only a portrait of Marius (1573-1624) himself but also, in the foreground, a long tube labelled "perspicillum," the first known image of a telescopic device used for astronomy; the name "telescope" came later. A schematic diagram of Jupiter with four moons orbiting appears at upper left; Marius, following a suggestion from Kepler, gave these Galilean satellites the names now still in use: Io, Europa. Ganymede, and Callisto. The title continues Hoc est, Quatuor Joviali cum Planetarum, cum Theoria, tum Tabulae, Propriis Observationibus Maxime Fundate.... A pair of conferences was held in Germany in 2014 to commemorate the 400th anniversary of Marius's book and to discuss Marius's work and its relation to Galileo's work (http://www.simon-marius.net; http://www.simon-marius.net/index.php?lang=en&menu=1 28 languages are available). Marius (Mayr) had independently discovered the four satellites of Jupiter, apparently one day after Galileo, on December 29 O.S., 1609; by the time he published his work four years later (a local-circulation publication had appeared in Nuremberg in 1611 in Prognosticon Astrologicum auf das Jahr 1612), Galileo had gained fame and priority, and Galileo accused Marius of plagiarism in Il Saggiatore (1623). With his Belgian telescope, Marius also noted the tilt of the orbital plane of Jupiter's moons, sunspots (1611), and the Andromeda Nebula (1612). He claimed to have worked out a system of cosmology similar to the Tychonic system in 1596, contemporaneously to Kepler's Mysterium Cosmographicum. A crater, the Marius Hills, and the Rima Marius on the Moon are named for him by the I.A.U., as well as, to celebrate the quadricentennial, a main-belt asteroid, now (7984) Marius. Acknowledgment: JMP thanks Seth Fagen, PRPH Books in New York, for introducing him to Marius's book 18 years ago.
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Manasa, Justen; Lessells, Richard; Rossouw, Theresa; Naidu, Kevindra; Van Vuuren, Cloete; Goedhals, Dominique; van Zyl, Gert; Bester, Armand; Skingsley, Andrew; Stott, Katharine; Danaviah, Siva; Chetty, Terusha; Singh, Lavanya; Moodley, Pravi; Iwuji, Collins; McGrath, Nuala; Seebregts, Christopher J.; de Oliveira, Tulio
2014-01-01
Abstract Substantial amounts of data have been generated from patient management and academic exercises designed to better understand the human immunodeficiency virus (HIV) epidemic and design interventions to control it. A number of specialized databases have been designed to manage huge data sets from HIV cohort, vaccine, host genomic and drug resistance studies. Besides databases from cohort studies, most of the online databases contain limited curated data and are thus sequence repositories. HIV drug resistance has been shown to have a great potential to derail the progress made thus far through antiretroviral therapy. Thus, a lot of resources have been invested in generating drug resistance data for patient management and surveillance purposes. Unfortunately, most of the data currently available relate to subtype B even though >60% of the epidemic is caused by HIV-1 subtype C. A consortium of clinicians, scientists, public health experts and policy markers working in southern Africa came together and formed a network, the Southern African Treatment and Resistance Network (SATuRN), with the aim of increasing curated HIV-1 subtype C and tuberculosis drug resistance data. This article describes the HIV-1 data curation process using the SATuRN Rega database. The data curation is a manual and time-consuming process done by clinical, laboratory and data curation specialists. Access to the highly curated data sets is through applications that are reviewed by the SATuRN executive committee. Examples of research outputs from the analysis of the curated data include trends in the level of transmitted drug resistance in South Africa, analysis of the levels of acquired resistance among patients failing therapy and factors associated with the absence of genotypic evidence of drug resistance among patients failing therapy. All these studies have been important for informing first- and second-line therapy. This database is a free password-protected open source database available on www.bioafrica.net. Database URL: http://www.bioafrica.net/regadb/ PMID:24504151
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CHEMICAL PRIORITIZATION FOR DEVELOPMENTAL ...
Defining a predictive model of developmental toxicity from in vitro and high-throughput screening (HTS) assays can be limited by the availability of developmental defects data. ToxRefDB (www.epa.gov/ncct/todrefdb) was built from animal studies on data-rich environmental chemicals, and has been used as an anchor for predictive modeling of ToxCast™ data. Scaling to thousands of untested chemicals requires another approach. ToxPlorer™ was developed as a tool to query and extract specific facts about defined biological entities from the open scientific literature and to coherently synthesize relevant knowledge about relationships, pathways and processes in toxicity. Here, we investigated the specific application of ToxPlorer to weighting HTS assay targets for relevance to developmental defects as defined in the literature. First, we systemically analyzed 88,193 Pubmed abstracts selected by bulk query using harmonized terminology for 862 developmental endpoints (www.devtox.net) and 364,334 dictionary term entities in our VT-KB (virtual tissues knowledgebase). We specifically focused on entities corresponding to genes/proteins mapped across of >500 ToxCast HTS assays. The 88,193 devtox abstracts mentioned 244 gene/protein entities in an aggregated total of ~8,000 occurrences. Each of the 244 assays was scored and weighted by the number of devtox articles and relevance to developmental processes. This score was used as a feature for chemical prioritization by Toxic
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NASA Astrophysics Data System (ADS)
Kaspar, F.; Helmschrot, J.; Mhanda, A.; Butale, M.; de Clercq, W.; Kanyanga, J. K.; Neto, F. O. S.; Kruger, S.; Castro Matsheka, M.; Muche, G.; Hillmann, T.; Josenhans, K.; Posada, R.; Riede, J.; Seely, M.; Ribeiro, C.; Kenabatho, P.; Vogt, R.; Jürgens, N.
2015-07-01
A major task of the newly established "Southern African Science Service Centre for Climate Change and Adaptive Land Management" (SASSCAL; www.sasscal.org) and its partners is to provide science-based environmental information and knowledge which includes the provision of consistent and reliable climate data for Southern Africa. Hence, SASSCAL, in close cooperation with the national weather authorities of Angola, Botswana, Germany and Zambia as well as partner institutions in Namibia and South Africa, supports the extension of the regional meteorological observation network and the improvement of the climate archives at national level. With the ongoing rehabilitation of existing weather stations and the new installation of fully automated weather stations (AWS), altogether 105 AWS currently provide a set of climate variables at 15, 30 and 60 min intervals respectively. These records are made available through the SASSCAL WeatherNet, an online platform providing near-real time data as well as various statistics and graphics, all in open access. This effort is complemented by the harmonization and improvement of climate data management concepts at the national weather authorities, capacity building activities and an extension of the data bases with historical climate data which are still available from different sources. These activities are performed through cooperation between regional and German institutions and will provide important information for climate service related activities.
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A database of new zeolite-like materials.
Pophale, Ramdas; Cheeseman, Phillip A; Deem, Michael W
2011-07-21
We here describe a database of computationally predicted zeolite-like materials. These crystals were discovered by a Monte Carlo search for zeolite-like materials. Positions of Si atoms as well as unit cell, space group, density, and number of crystallographically unique atoms were explored in the construction of this database. The database contains over 2.6 M unique structures. Roughly 15% of these are within +30 kJ mol(-1) Si of α-quartz, the band in which most of the known zeolites lie. These structures have topological, geometrical, and diffraction characteristics that are similar to those of known zeolites. The database is the result of refinement by two interatomic potentials that both satisfy the Pauli exclusion principle. The database has been deposited in the publicly available PCOD database and in www.hypotheticalzeolites.net/database/deem/. This journal is © the Owner Societies 2011
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Ren, Shenghan; Chen, Xueli; Wang, Hailong; Qu, Xiaochao; Wang, Ge; Liang, Jimin; Tian, Jie
2013-01-01
The study of light propagation in turbid media has attracted extensive attention in the field of biomedical optical molecular imaging. In this paper, we present a software platform for the simulation of light propagation in turbid media named the “Molecular Optical Simulation Environment (MOSE)”. Based on the gold standard of the Monte Carlo method, MOSE simulates light propagation both in tissues with complicated structures and through free-space. In particular, MOSE synthesizes realistic data for bioluminescence tomography (BLT), fluorescence molecular tomography (FMT), and diffuse optical tomography (DOT). The user-friendly interface and powerful visualization tools facilitate data analysis and system evaluation. As a major measure for resource sharing and reproducible research, MOSE aims to provide freeware for research and educational institutions, which can be downloaded at http://www.mosetm.net. PMID:23577215
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Göritz, Anja S; Birnbaum, Michael H
2005-11-01
The customizable PHP script Generic HTML Form Processor is intended to assist researchers and students in quickly setting up surveys and experiments that can be administered via the Web. This script relieves researchers from the burdens of writing new CGI scripts and building databases for each Web study. Generic HTML Form Processor processes any syntactically correct HTML forminput and saves it into a dynamically created open-source database. We describe five modes for usage of the script that allow increasing functionality but require increasing levels of knowledge of PHP and Web servers: The first two modes require no previous knowledge, and the fifth requires PHP programming expertise. Use of Generic HTML Form Processor is free for academic purposes, and its Web address is www.goeritz.net/brmic.
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VREPAR 2: VR in eating disorders.
Riva, G; Bacchetta, M; Baruffi, M; Defrance, C; Gatti, F; Galimberti, C; Nugues, P; Ferretti, G S; Tonci, A
1999-01-01
Virtual Reality Environments for Psychoneurophysiological Assessment and Rehabilitation (VREPAR) are two European Community funded projects (Telematics for health-HC 1053/HC 1055-http://www.psicologia.net) whose aim is (a) to develop a PC based virtual reality system (PC-VRS) for the medical market that can be marketed at a price that is accessible to its possible endusers (hospitals, universities, and research centres) and that would have the modular, connectability and interoperability characteristics that the existing systems lack; and (b) to develop three hardware/software modules for the application of the PC-VRS in psychoneurophysiological assessment and rehabilitation. The chosen development areas are eating disorders (bulimia, anorexia, and obesity), movement disorders (Parkinson's disease and torsion dystonia), and stroke disorders (unilateral neglect and hemiparesis). In particular, the VREPAR 2 project is now testing the eating disorders module on a clinical sample.
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NASA Astrophysics Data System (ADS)
Nagothu, U. S.
2016-12-01
Agricultural extension services, among others, contribute to improving rural livelihoods and enhancing economic development. Knowledge development and transfer from the cognitive science point of view, is about, how farmers use and apply their experiential knowledge as well as acquired new knowledge to solve new problems. This depends on the models adopted, the way knowledge is generated and delivered. New extension models based on ICT platforms and smart phones are promising. Results from a 5-year project (www.climaadapt.org) in India shows that farmer led-on farm validations of technologies and knowledge exchange through ICT based platforms outperformed state operated linear extension programs. Innovation here depends on the connectivity, net-working between stakeholders that are involved in generating, transferring and using the knowledge. Key words: Smallholders, Knowledge, Extension, Innovation, India
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The EMBRACE web service collection
Pettifer, Steve; Ison, Jon; Kalaš, Matúš; Thorne, Dave; McDermott, Philip; Jonassen, Inge; Liaquat, Ali; Fernández, José M.; Rodriguez, Jose M.; Partners, INB-; Pisano, David G.; Blanchet, Christophe; Uludag, Mahmut; Rice, Peter; Bartaseviciute, Edita; Rapacki, Kristoffer; Hekkelman, Maarten; Sand, Olivier; Stockinger, Heinz; Clegg, Andrew B.; Bongcam-Rudloff, Erik; Salzemann, Jean; Breton, Vincent; Attwood, Teresa K.; Cameron, Graham; Vriend, Gert
2010-01-01
The EMBRACE (European Model for Bioinformatics Research and Community Education) web service collection is the culmination of a 5-year project that set out to investigate issues involved in developing and deploying web services for use in the life sciences. The project concluded that in order for web services to achieve widespread adoption, standards must be defined for the choice of web service technology, for semantically annotating both service function and the data exchanged, and a mechanism for discovering services must be provided. Building on this, the project developed: EDAM, an ontology for describing life science web services; BioXSD, a schema for exchanging data between services; and a centralized registry (http://www.embraceregistry.net) that collects together around 1000 services developed by the consortium partners. This article presents the current status of the collection and its associated recommendations and standards definitions. PMID:20462862
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Model-based approach for cyber-physical attack detection in water distribution systems.
Housh, Mashor; Ohar, Ziv
2018-08-01
Modern Water Distribution Systems (WDSs) are often controlled by Supervisory Control and Data Acquisition (SCADA) systems and Programmable Logic Controllers (PLCs) which manage their operation and maintain a reliable water supply. As such, and with the cyber layer becoming a central component of WDS operations, these systems are at a greater risk of being subjected to cyberattacks. This paper offers a model-based methodology based on a detailed hydraulic understanding of WDSs combined with an anomaly detection algorithm for the identification of complex cyberattacks that cannot be fully identified by hydraulically based rules alone. The results show that the proposed algorithm is capable of achieving the best-known performance when tested on the data published in the BATtle of the Attack Detection ALgorithms (BATADAL) competition (http://www.batadal.net). Copyright © 2018. Published by Elsevier Ltd.
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NASA Astrophysics Data System (ADS)
Hirsikko, Anne; Brus, David; O'Connor, Ewan J.; Filioglou, Maria; Komppula, Mika; Romakkaniemi, Sami
2017-04-01
In the high and mid latitudes super-cooled liquid water layers are frequently observed on top of clouds. These layers are difficult to forecast with numerical weather prediction models, even though, they have strong influence on atmospheric radiative properties, cloud microphysical properties, and subsequently, precipitation. This work investigates properties of super-cooled liquid water layer topped sub-arctic clouds and precipitation observed with ground-based in-situ (cloud probes) and remote-sensing (a cloud radar, Doppler and multi-wavelength lidars) instrumentation during two-month long Pallas Cloud Experiment (PaCE 2015) in autumn 2015. Analysis is based on standard Cloudnet scheme supplemented with new retrieval products of the specific clouds and their properties. Combination of two scales of observation provides new information on properties of clouds and precipitation in the sub-arctic Pallas region. Current status of results will be presented during the conference. The authors acknowledge financial support by the Academy of Finland (Centre of Excellence Programme, grant no 272041; and ICINA project, grant no 285068), the ACTRIS2 - European Union's Horizon 2020 research and innovation programme under grant agreement No 654109, the KONE foundation, and the EU FP7 project BACCHUS (grant no 603445).
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NASA Astrophysics Data System (ADS)
Kabas, T.; Leuprecht, A.; Bichler, C.; Kirchengast, G.
2010-12-01
South-eastern Austria is characteristic for experiencing a rich variety of weather and climate patterns. For this reason, the county of Feldbach was selected by the Wegener Center as a focus area for a pioneering observation experiment at very high resolution: The WegenerNet climate station network (in brief WegenerNet) comprises 151 meteorological stations within an area of about 20 km × 15 km (~ 1.4 km × 1.4 km station grid). All stations measure the main parameters temperature, humidity and precipitation with 5 minute sampling. Selected further stations include measurements of wind speed and direction completed by soil parameters as well as air pressure and net radiation. The collected data is integrated in an automatic processing system including data transfer, quality control, product generation, and visualization. Each station is equipped with an internet-attached data logger and the measurements are transferred as binary files via GPRS to the WegenerNet server in 1 hour intervals. The incoming raw data files of measured parameters as well as several operating values of the data logger are stored in a relational database (PostgreSQL). Next, the raw data pass the Quality Control System (QCS) in which the data are checked for its technical and physical plausibility (e.g., sensor specifications, temporal and spatial variability). In consideration of the data quality (quality flag), the Data Product Generator (DPG) results in weather and climate data products on various temporal scales (from 5 min to annual) for single stations and regular grids. Gridded data are derived by vertical scaling and squared inverse distance interpolation (1 km × 1 km and 0.01° × 0.01° grids). Both subsystems (QCS and DPG) are realized by the programming language Python. For application purposes the resulting data products are available via the bi-lingual (dt, en) WegenerNet data portal (www.wegenernet.org). At this time, the main interface is still online in a system in which MapServer is used to import spatial data by its database interface and to generate images of static geographic formats. However, a Java applet is additionally needed to display these images on the users local host. Furthermore, station data are visualized as time series by the scripting language PHP. Since February 2010, the visualization of gridded data products is a first step to a new data portal based on OpenLayers. In this GIS framework, all geographic information (e.g., OpenStreetMap) is displayed with MapServer. Furthermore, the visualization of all meteorological parameters are generated on the fly by a Python CGI script and transparently overlayed on the maps. Hence, station data and gridded data are visualized and further prepared for download in common data formats (csv, NetCDF). In conclusion, measured data and generated data products are provided with a data latency less than 1-2 hours in standard operation (near real time). Following an introduction of the processing system along the lines above, resulting data products are presented online at the WegenerNet data portal.
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The German national registry for primary immunodeficiencies (PID)
Gathmann, B; Goldacker, S; Klima, M; Belohradsky, B H; Notheis, G; Ehl, S; Ritterbusch, H; Baumann, U; Meyer-Bahlburg, A; Witte, T; Schmidt, R; Borte, M; Borte, S; Linde, R; Schubert, R; Bienemann, K; Laws, H-J; Dueckers, G; Roesler, J; Rothoeft, T; Krüger, R; Scharbatke, E C; Masjosthusmann, K; Wasmuth, J-C; Moser, O; Kaiser, P; Groß-Wieltsch, U; Classen, C F; Horneff, G; Reiser, V; Binder, N; El-Helou, S M; Klein, C; Grimbacher, B; Kindle, G
2013-01-01
In 2009, a federally funded clinical and research consortium (PID–NET, http://www.pid-net.org) established the first national registry for primary immunodeficiencies (PID) in Germany. The registry contains clinical and genetic information on PID patients and is set up within the framework of the existing European Database for Primary Immunodeficiencies, run by the European Society for Primary Immunodeficiencies. Following the example of other national registries, a central data entry clerk has been employed to support data entry at the participating centres. Regulations for ethics approvals have presented a major challenge for participation of individual centres and have led to a delay in data entry in some cases. Data on 630 patients, entered into the European registry between 2004 and 2009, were incorporated into the national registry. From April 2009 to March 2012, the number of contributing centres increased from seven to 21 and 738 additional patients were reported, leading to a total number of 1368 patients, of whom 1232 were alive. The age distribution of living patients differs significantly by gender, with twice as many males than females among children, but 15% more women than men in the age group 30 years and older. The diagnostic delay between onset of symptoms and diagnosis has decreased for some PID over the past 20 years, but remains particularly high at a median of 4 years in common variable immunodeficiency (CVID), the most prevalent PID. PMID:23607573
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Lee, Insuk; Li, Zhihua; Marcotte, Edward M.
2007-01-01
Background Probabilistic functional gene networks are powerful theoretical frameworks for integrating heterogeneous functional genomics and proteomics data into objective models of cellular systems. Such networks provide syntheses of millions of discrete experimental observations, spanning DNA microarray experiments, physical protein interactions, genetic interactions, and comparative genomics; the resulting networks can then be easily applied to generate testable hypotheses regarding specific gene functions and associations. Methodology/Principal Findings We report a significantly improved version (v. 2) of a probabilistic functional gene network [1] of the baker's yeast, Saccharomyces cerevisiae. We describe our optimization methods and illustrate their effects in three major areas: the reduction of functional bias in network training reference sets, the application of a probabilistic model for calculating confidences in pair-wise protein physical or genetic interactions, and the introduction of simple thresholds that eliminate many false positive mRNA co-expression relationships. Using the network, we predict and experimentally verify the function of the yeast RNA binding protein Puf6 in 60S ribosomal subunit biogenesis. Conclusions/Significance YeastNet v. 2, constructed using these optimizations together with additional data, shows significant reduction in bias and improvements in precision and recall, in total covering 102,803 linkages among 5,483 yeast proteins (95% of the validated proteome). YeastNet is available from http://www.yeastnet.org. PMID:17912365
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Reading level of privacy policies on Internet health Web sites.
Graber, Mark A; D'Alessandro, Donna M; Johnson-West, Jill
2002-07-01
Most individuals would like to maintain the privacy of their medical information on the World Wide Web (WWW). In response, commercial interests and other sites post privacy policies that are designed to inform users of how their information will be used. However, it is not known if these statements are comprehensible to most WWW users. The purpose of this study was to determine the reading level of privacy statements on Internet health Web sites and to determine whether these statements can inform users of their rights. This was a descriptive study. Eighty Internet health sites were examined and the readability of their privacy policies was determined. The selected sample included the top 25 Internet health sites as well as other sites that a user might encounter while researching a common problem such as high blood pressure. Sixty percent of the sites were commercial (.com), 17.5% were organizations (.org), 8.8% were from the United Kingdom (.uk), 3.8% were United States governmental (.gov), and 2.5% were educational (.edu). The readability level of the privacy policies was calculated using the Flesch, the Fry, and the SMOG readability levels. Of the 80 Internet health Web sites studied, 30% (including 23% of the commercial Web sites) had no privacy policy posted. The average readability level of the remaining sites required 2 years of college level education to comprehend, and no Web site had a privacy policy that was comprehensible by most English-speaking individuals in the United States. The privacy policies of health Web sites are not easily understood by most individuals in the United States and do not serve to inform users of their rights. Possible remedies include rewriting policies to make them comprehensible and protecting online health information by using legal statutes or standardized insignias indicating compliance with a set of privacy standards (eg, "Health on the Net" [HON] http://www.hon.ch).
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NASA Astrophysics Data System (ADS)
Ryan, J. G.
2014-12-01
The 2012 PCAST report identified the improvement of "gateway" science courses as critical to increasing the number of STEM graduates to levels commensurate with national needs. The urgent need to recruit/ retain more STEM graduates is particularly acute in the geosciences, where growth in employment opportunities, an aging workforce and flat graduation rates are leading to substantial unmet demand for geoscience-trained STEM graduates. The need to increase the number of Bachelors-level geoscience graduates was an identified priority at the Summit on the Future of Undergraduate Geoscience Education (http://www.jsg.utexas.edu/events/future-of-geoscience-undergraduateeducation/), as was the necessity of focusing on 2-year colleges, where a growing number of students are being introduced to geosciences. Undergraduate research as an instructional tool can help engage and retain students, but has largely not been part of introductory geoscience courses because of the challenge of scaling such activities for large student numbers. However, burgeoning information technology resources, including publicly available earth and planetary data repositories and freely available, intuitive data visualization platforms makes structured, in-classroom investigations of geoscience questions tractable, and open-ended student inquiry possible. Examples include "MARGINS Mini-Lessons", instructional resources developed with the support of two NSF-DUE grant awards that involve investigations of marine geosciences data resources (overseen by the Integrated Earth Data Applications (IEDA) portal: www.iedadata.org) and data visualization using GeoMapApp (www.geomapapp.org); and the growing suite of Google-Earth based data visualization and exploration activities overseen by the Google Earth in Onsite and Distance Education project (geode.net). Sample-based investigations are also viable in introductory courses, thanks to remote instrument operations technologies that allow real student participation in instrument-based data collection and interpretation. It is thus possible to model for students nearly the entire scientific process in introductory geoscience courses, allowing them to experience the excitement of "doing" science and thereby enticing more of them into the field.
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Interval-level measurement with visual analogue scales in Internet-based research: VAS Generator.
Reips, Ulf-Dietrich; Funke, Frederik
2008-08-01
The present article describes VAS Generator (www.vasgenerator.net), a free Web service for creating a wide range of visual analogue scales that can be used as measurement devices in Web surveys and Web experimentation, as well as for local computerized assessment. A step-by-step example for creating and implementing a visual analogue scale with visual feedback is given. VAS Generator and the scales it generates work independently of platforms and use the underlying languages HTML and JavaScript. Results from a validation study with 355 participants are reported and show that the scales generated with VAS Generator approximate an interval-scale level. In light of previous research on visual analogue versus categorical (e.g., radio button) scales in Internet-based research, we conclude that categorical scales only reach ordinal-scale level, and thus visual analogue scales are to be preferred whenever possible.
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Laboratory Animal Management Assistant (LAMA): a LIMS for active research colonies.
Milisavljevic, Marko; Hearty, Taryn; Wong, Tony Y T; Portales-Casamar, Elodie; Simpson, Elizabeth M; Wasserman, Wyeth W
2010-06-01
Laboratory Animal Management Assistant (LAMA) is an internet-based system for tracking large laboratory mouse colonies. It has a user-friendly interface with powerful search capabilities that ease day-to-day tasks such as tracking breeding cages and weaning litters. LAMA was originally developed to manage hundreds of new mouse strains generated by a large functional genomics program, the Pleiades Promoter Project ( http://www.pleiades.org ). The software system has proven to be highly flexible, suitable for diverse management approaches to mouse colonies. It allows custom tagging and grouping of animals, simplifying project-specific handling and access to data. Finally, LAMA was developed in close collaboration with mouse technicians to ease the transition from paper- or Excel-based management systems to computerized tracking, allowing data export in a popular spreadsheet format and automatic printing of cage cards. LAMA is an open-access software tool, freely available to the research community at http://launchpad.net/mousedb .
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2015-01-28
VANDENBERG AIR FORCE BASE, Calif. – The launch gantry is rolled back to reveal the United Launch Alliance Delta II rocket with the Soil Moisture Active Passive, or SMAP, satellite aboard, at Space Launch Complex 2 on Vandenberg Air Force Base in California. SMAP is a remote sensing mission designed to measure and map the Earth's soil moisture distribution and freeze/thaw stat with unprecedented accuracy, resolution and coverage. SMAP will provide global measurements of soil moisture and its freeze/thaw state. These measurements will be used to enhance understanding of processes that link the water, energy and carbon cycles, and to extend the capabilities of weather and climate prediction models. SMAP data also will be used to quantify net carbon flux in boreal landscapes and to develop improved flood prediction and drought monitoring capabilities. Launch is scheduled for Jan. 29, 2015. To learn more about SMAP, visit http://www.nasa.gov/smap. Photo credit: NASA/Randy Beaudoin
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2015-01-28
VANDENBERG AIR FORCE BASE, Calif. – The launch gantry is rolled back to reveal the United Launch Alliance Delta II rocket with the Soil Moisture Active Passive, or SMAP, satellite aboard, at Space Launch Complex 2 on Vandenberg Air Force Base in California. SMAP is a remote sensing mission designed to measure and map the Earth's soil moisture distribution and freeze/thaw stat with unprecedented accuracy, resolution and coverage. SMAP will provide global measurements of soil moisture and its freeze/thaw state. These measurements will be used to enhance understanding of processes that link the water, energy and carbon cycles, and to extend the capabilities of weather and climate prediction models. SMAP data also will be used to quantify net carbon flux in boreal landscapes and to develop improved flood prediction and drought monitoring capabilities. Launch is scheduled for Jan. 29, 2015. To learn more about SMAP, visit http://www.nasa.gov/smap. Photo credit: NASA/Randy Beaudoin
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2015-01-28
VANDENBERG AIR FORCE BASE, Calif. – The launch gantry is rolled back to reveal the United Launch Alliance Delta II rocket with the Soil Moisture Active Passive, or SMAP, satellite aboard, at Space Launch Complex 2 on Vandenberg Air Force Base in California. SMAP is a remote sensing mission designed to measure and map the Earth's soil moisture distribution and freeze/thaw stat with unprecedented accuracy, resolution and coverage. SMAP will provide global measurements of soil moisture and its freeze/thaw state. These measurements will be used to enhance understanding of processes that link the water, energy and carbon cycles, and to extend the capabilities of weather and climate prediction models. SMAP data also will be used to quantify net carbon flux in boreal landscapes and to develop improved flood prediction and drought monitoring capabilities. Launch is scheduled for Jan. 29, 2015. To learn more about SMAP, visit http://www.nasa.gov/smap. Photo credit: NASA/Randy Beaudoin
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NASA Astrophysics Data System (ADS)
Lyons, M.; Siegel, Edward Carl-Ludwig
2011-03-01
Weiss-Page-Holthaus[Physica A,341,586(04); http://arxiv.org/abs/cond-mat/0403295] number-FACTORIZATION VIA BEQS BEC VS.(?) Shor-algorithm, strongly-supporting Watkins' [www.secamlocal.ex.ac.uk/people/staff/mrwatkin/] Intersection of number-theory "pure"-maths WITH (Statistical)-Physics, as Siegel[AMS Joint.Mtg.(02)-Abs.973-60-124] Benford logarithmic-law algebraic-INVERSION to ONLY BEQS with d=0 digit P (d = 0) > = oogapFULBEC ! ! ! SiegelRiemann - hypothesisproofviaRayleigh [ Phil . Trans . CLXI (1870) ] - Polya [ Math . Ann . (21) ] - [ Random - WalksElectric - Nets . , MAA (81) ] - nderson [ PRL (58) ] - localization - Siegel [ Symp . Fractals , MRSFallMtg . (89) - 5 - papers ! ! ! ] FUZZYICS = CATEGORYICS : [ LOCALITY ]- MORPHISM / CROSSOVER / AUTMATHCAT / DIM - CAT / ANTONYM- > (GLOBALITY) FUNCTOR / SYNONYM / concomitancetonoise = / Fluct . - Dissip . theorem / FUNCTOR / SYNONYM / equivalence / proportionalityto = > generalized - susceptibilitypower - spectrum [ FLAT / FUNCTIONLESS / WHITE ]- MORPHISM / CROSSOVER / AUTMATHCAT / DIM - CAT / ANTONYM- > HYPERBOLICITY/ZIPF-law INEVITABILITY) intersection with ONLY BEQS BEC).
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Prevention of suicidal behavior
Hegerl, Ulrich
2016-01-01
More than 800 000 people die every year from suicide, and about 20 times more attempt suicide. In most countries, suicide risk is highest in older males, and risk of attempted suicide is highest in younger females. The higher lethal level of suicidal acts in males is explained by the preference for more lethal methods, as well as other factors. In the vast majority of cases, suicidal behavior occurs in the context of psychiatric disorders, depression being the most important one. Improving the treatment of depression, restricting access to lethal means, and avoiding the Werther effect (imitation suicide) are central aspects of suicide prevention programs. In several European regions, the four-level intervention concept of the European Alliance Against Depression (www.EAAD.net), simultaneously targeting depression and suicidal behavior, has been found to have preventive effects on suicidal behavior. It has already been implemented in more than 100 regions in Europe. PMID:27489458
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2015-01-28
VANDENBERG AIR FORCE BASE, Calif. – The launch gantry is rolled back to reveal the United Launch Alliance Delta II rocket with the Soil Moisture Active Passive, or SMAP, satellite aboard, at Space Launch Complex 2 on Vandenberg Air Force Base in California. SMAP is a remote sensing mission designed to measure and map the Earth's soil moisture distribution and freeze/thaw stat with unprecedented accuracy, resolution and coverage. SMAP will provide global measurements of soil moisture and its freeze/thaw state. These measurements will be used to enhance understanding of processes that link the water, energy and carbon cycles, and to extend the capabilities of weather and climate prediction models. SMAP data also will be used to quantify net carbon flux in boreal landscapes and to develop improved flood prediction and drought monitoring capabilities. Launch is scheduled for Jan. 29, 2015. To learn more about SMAP, visit http://www.nasa.gov/smap. Photo credit: NASA/Randy Beaudoin
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The use of PC based VR in clinical medicine: the VREPAR projects.
Riva, G; Bacchetta, M; Baruffi, M; Borgomainerio, E; Defrance, C; Gatti, F; Galimberti, C; Fontaneto, S; Marchi, S; Molinari, E; Nugues, P; Rinaldi, S; Rovetta, A; Ferretti, G S; Tonci, A; Wann, J; Vincelli, F
1999-01-01
Virtual reality (VR) is an emerging technology that alters the way individuals interact with computers: a 3D computer-generated environment in which a person can move about and interact as if he actually was inside it. Given to the high computational power required to create virtual environments, these are usually developed on expensive high-end workstations. However, the significant advances in PC hardware that have been made over the last three years, are making PC-based VR a possible solution for clinical assessment and therapy. VREPAR - Virtual Reality Environments for Psychoneurophysiological Assessment and Rehabilitation - are two European Community funded projects (Telematics for health - HC 1053/HC 1055 - http://www.psicologia.net) that are trying to develop a modular PC-based virtual reality system for the medical market. The paper describes the rationale of the developed modules and the preliminary results obtained.
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CliniProteus: A flexible clinical trials information management system
Mathura, Venkatarajan S; Rangareddy, Mahendiranath; Gupta, Pankaj; Mullan, Michael
2007-01-01
Clinical trials involve multi-site heterogeneous data generation with complex data input-formats and forms. The data should be captured and queried in an integrated fashion to facilitate further analysis. Electronic case-report forms (eCRF) are gaining popularity since it allows capture of clinical information in a rapid manner. We have designed and developed an XML based flexible clinical trials data management framework in .NET environment that can be used for efficient design and deployment of eCRFs to efficiently collate data and analyze information from multi-site clinical trials. The main components of our system include an XML form designer, a Patient registration eForm, reusable eForms, multiple-visit data capture and consolidated reports. A unique id is used for tracking the trial, site of occurrence, the patient and the year of recruitment. Availability http://www.rfdn.org/bioinfo/CTMS/ctms.html. PMID:21670796
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Gražulis, Saulius; Daškevič, Adriana; Merkys, Andrius; Chateigner, Daniel; Lutterotti, Luca; Quirós, Miguel; Serebryanaya, Nadezhda R.; Moeck, Peter; Downs, Robert T.; Le Bail, Armel
2012-01-01
Using an open-access distribution model, the Crystallography Open Database (COD, http://www.crystallography.net) collects all known ‘small molecule / small to medium sized unit cell’ crystal structures and makes them available freely on the Internet. As of today, the COD has aggregated ∼150 000 structures, offering basic search capabilities and the possibility to download the whole database, or parts thereof using a variety of standard open communication protocols. A newly developed website provides capabilities for all registered users to deposit published and so far unpublished structures as personal communications or pre-publication depositions. Such a setup enables extension of the COD database by many users simultaneously. This increases the possibilities for growth of the COD database, and is the first step towards establishing a world wide Internet-based collaborative platform dedicated to the collection and curation of structural knowledge. PMID:22070882
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Astronomy4Kids: A new, online, STEM-focused, video education outreach program
NASA Astrophysics Data System (ADS)
Pearson, Richard L.; Pearson, Sarah R.
2017-06-01
Recent research indicates significant benefits of early childhood introductions to language, mathematics, and general science concepts. Specifically, a child that is introduced to a concept at a young age is more prepared to receive it in its entirety later. Astronomy4Kids was created to bring science, technology, engineering, and math (STEM) concepts to the youngest learners (those under the age of eight, or those from pre-school to about second-grade). The videos are presented in a succinct, one-on-one manner, and provide a creative learning environment for the viewers. Following the preschool education video principles established by Fred Rogers, we hope to give young children access to an expert astronomer who can explain things simply and sincerely. We believe presenting the material in this manner will make it engaging for even the youngest scholar and available to any interested party. The videos can be freely accessed at www.astronomy4kids.net.
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Dewa, Carolyn S
2011-01-01
In 2009, four institutes of the Canadian Institutes of Health Research (Gender and Health; Health Services and Policy Research; Neurosciences, Mental Health and Addiction; and Population and Public Health) sponsored the Fourth Annual Canadian Research Congress on Mental Health and Addictions in the Workplace, in Toronto, Ontario. Hosted by the Work and Well-Being Research and Evaluation Program at the Centre for Addiction and Mental Health, the theme of the congress was We Can Do It! Evidence and Interventions for Transforming Mental Health in the Workplace (see http://www.kewa.camh.net/researchers/areas/work_wellbeing/Pages/default.aspx for more details). Coincidentally, in the same year, an idealistic presidential hopeful named Barack Obama adopted a similar slogan for his White House run. Obama recognized that change that challenges established barriers can only come about through co-operation and a collective investment. Copyright © 2011 Longwoods Publishing.
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2015-01-28
VANDENBERG AIR FORCE BASE, Calif. – The launch gantry is rolled back to reveal the United Launch Alliance Delta II rocket with the Soil Moisture Active Passive, or SMAP, satellite aboard, at Space Launch Complex 2 on Vandenberg Air Force Base in California. SMAP is a remote sensing mission designed to measure and map the Earth's soil moisture distribution and freeze/thaw stat with unprecedented accuracy, resolution and coverage. SMAP will provide global measurements of soil moisture and its freeze/thaw state. These measurements will be used to enhance understanding of processes that link the water, energy and carbon cycles, and to extend the capabilities of weather and climate prediction models. SMAP data also will be used to quantify net carbon flux in boreal landscapes and to develop improved flood prediction and drought monitoring capabilities. Launch is scheduled for Jan. 29, 2015. To learn more about SMAP, visit http://www.nasa.gov/smap. Photo credit: NASA/Randy Beaudoin
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2015-01-28
VANDENBERG AIR FORCE BASE, Calif. – The launch gantry is rolled back to reveal the United Launch Alliance Delta II rocket with the Soil Moisture Active Passive, or SMAP, satellite aboard, at Space Launch Complex 2 on Vandenberg Air Force Base in California. SMAP is a remote sensing mission designed to measure and map the Earth's soil moisture distribution and freeze/thaw stat with unprecedented accuracy, resolution and coverage. SMAP will provide global measurements of soil moisture and its freeze/thaw state. These measurements will be used to enhance understanding of processes that link the water, energy and carbon cycles, and to extend the capabilities of weather and climate prediction models. SMAP data also will be used to quantify net carbon flux in boreal landscapes and to develop improved flood prediction and drought monitoring capabilities. Launch is scheduled for Jan. 29, 2015. To learn more about SMAP, visit http://www.nasa.gov/smap. Photo credit: NASA/Randy Beaudoin
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Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization.
Bauer, Markus; Klau, Gunnar W; Reinert, Knut
2007-07-27
The discovery of functional non-coding RNA sequences has led to an increasing interest in algorithms related to RNA analysis. Traditional sequence alignment algorithms, however, fail at computing reliable alignments of low-homology RNA sequences. The spatial conformation of RNA sequences largely determines their function, and therefore RNA alignment algorithms have to take structural information into account. We present a graph-based representation for sequence-structure alignments, which we model as an integer linear program (ILP). We sketch how we compute an optimal or near-optimal solution to the ILP using methods from combinatorial optimization, and present results on a recently published benchmark set for RNA alignments. The implementation of our algorithm yields better alignments in terms of two published scores than the other programs that we tested: This is especially the case with an increasing number of input sequences. Our program LARA is freely available for academic purposes from http://www.planet-lisa.net.
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TriageTools: tools for partitioning and prioritizing analysis of high-throughput sequencing data.
Fimereli, Danai; Detours, Vincent; Konopka, Tomasz
2013-04-01
High-throughput sequencing is becoming a popular research tool but carries with it considerable costs in terms of computation time, data storage and bandwidth. Meanwhile, some research applications focusing on individual genes or pathways do not necessitate processing of a full sequencing dataset. Thus, it is desirable to partition a large dataset into smaller, manageable, but relevant pieces. We present a toolkit for partitioning raw sequencing data that includes a method for extracting reads that are likely to map onto pre-defined regions of interest. We show the method can be used to extract information about genes of interest from DNA or RNA sequencing samples in a fraction of the time and disk space required to process and store a full dataset. We report speedup factors between 2.6 and 96, depending on settings and samples used. The software is available at http://www.sourceforge.net/projects/triagetools/.
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Grethe, Jeffrey S; Ross, Edward; Little, David; Sanders, Brian; Gupta, Amarnath; Astakhov, Vadim
2009-01-01
This paper presents current progress in the development of semantic data integration environment which is a part of the Biomedical Informatics Research Network (BIRN; http://www.nbirn.net) project. BIRN is sponsored by the National Center for Research Resources (NCRR), a component of the National Institutes of Health (NIH). A goal is the development of a cyberinfrastructure for biomedical research that supports advance data acquisition, data storage, data management, data integration, data mining, data visualization, and other computing and information processing services over the Internet. Each participating institution maintains storage of their experimental or computationally derived data. Mediator-based data integration system performs semantic integration over the databases to enable researchers to perform analyses based on larger and broader datasets than would be available from any single institution's data. This paper describes recent revision of the system architecture, implementation, and capabilities of the semantically based data integration environment for BIRN.
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How to keep high-risk studies ethical: classifying candidate solutions.
Eyal, Nir
2017-02-01
This article lays out a wide spectrum of candidate ethical solutions for the challenge on which this JME symposium focuses: the benefit:risk ratio challenge to some early-phase HIV cure and remission studies. These candidate solutions fall into four categories: ones that seek to reduce risks in early-phase HIV cure and remission studies, ones that enhance the benefits for these studies' participants (or show that those were adequate in the first place), ones that focus on participants' free and informed consent to participate and ones according to whom the large benefits to non-participants can defeat considerations about individual participant net risks. In so doing, this article also structures the rest of the symposium. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.
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BOLDMirror: a global mirror system of DNA barcode data.
Liu, D; Liu, L; Guo, G; Wang, W; Sun, Q; Parani, M; Ma, J
2013-11-01
DNA barcoding is a novel concept for taxonomic identification using short, specific genetic markers and has been applied to study a large number of eukaryotes. The huge amount of data output generated by DNA barcoding requires well-organized information systems. Besides the Barcode of Life Data system (BOLD) established in Canada, the mirror system is also important for the international barcode of life project (iBOL). For this purpose, we developed the BOLDMirror, a global mirror system of DNA barcode data. It is open-sourced and can run on the LAMP (Linux + Apache + MySQL + PHP) environment. BOLDMirror has data synchronization, data representation and statistics modules, and also provides spaces to store user operation history. BOLDMirror can be accessed at http://www.boldmirror.net and several countries have used it to setup their site of DNA barcoding. © 2012 John Wiley & Sons Ltd.
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Carlsson, Lars; Spjuth, Ola; Adams, Samuel; Glen, Robert C; Boyer, Scott
2010-07-01
Predicting metabolic sites is important in the drug discovery process to aid in rapid compound optimisation. No interactive tool exists and most of the useful tools are quite expensive. Here a fast and reliable method to analyse ligands and visualise potential metabolic sites is presented which is based on annotated metabolic data, described by circular fingerprints. The method is available via the graphical workbench Bioclipse, which is equipped with advanced features in cheminformatics. Due to the speed of predictions (less than 50 ms per molecule), scientists can get real time decision support when editing chemical structures. Bioclipse is a rich client, which means that all calculations are performed on the local computer and do not require network connection. Bioclipse and MetaPrint2D are free for all users, released under open source licenses, and available from http://www.bioclipse.net.
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T-Epitope Designer: A HLA-peptide binding prediction server.
Kangueane, Pandjassarame; Sakharkar, Meena Kishore
2005-05-15
The current challenge in synthetic vaccine design is the development of a methodology to identify and test short antigen peptides as potential T-cell epitopes. Recently, we described a HLA-peptide binding model (using structural properties) capable of predicting peptides binding to any HLA allele. Consequently, we have developed a web server named T-EPITOPE DESIGNER to facilitate HLA-peptide binding prediction. The prediction server is based on a model that defines peptide binding pockets using information gleaned from X-ray crystal structures of HLA-peptide complexes, followed by the estimation of peptide binding to binding pockets. Thus, the prediction server enables the calculation of peptide binding to HLA alleles. This model is superior to many existing methods because of its potential application to any given HLA allele whose sequence is clearly defined. The web server finds potential application in T cell epitope vaccine design. http://www.bioinformation.net/ted/
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SED-ED, a workflow editor for computational biology experiments written in SED-ML.
Adams, Richard R
2012-04-15
The simulation experiment description markup language (SED-ML) is a new community data standard to encode computational biology experiments in a computer-readable XML format. Its widespread adoption will require the development of software support to work with SED-ML files. Here, we describe a software tool, SED-ED, to view, edit, validate and annotate SED-ML documents while shielding end-users from the underlying XML representation. SED-ED supports modellers who wish to create, understand and further develop a simulation description provided in SED-ML format. SED-ED is available as a standalone Java application, as an Eclipse plug-in and as an SBSI (www.sbsi.ed.ac.uk) plug-in, all under an MIT open-source license. Source code is at https://sed-ed-sedmleditor.googlecode.com/svn. The application itself is available from https://sourceforge.net/projects/jlibsedml/files/SED-ED/.
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NASA Astrophysics Data System (ADS)
Brauer, Claudia; Torfs, Paul; Teuling, Ryan; Uijlenhoet, Remko
2015-04-01
Recently, we developed the Wageningen Lowland Runoff Simulator (WALRUS) to fill the gap between complex, spatially distributed models often used in lowland catchments and simple, parametric models which have mostly been developed for mountainous catchments (Brauer et al., 2014ab). This parametric rainfall-runoff model can be used all over the world in both freely draining lowland catchments and polders with controlled water levels. The open source model code is implemented in R and can be downloaded from www.github.com/ClaudiaBrauer/WALRUS. The structure and code of WALRUS are simple, which facilitates detailed investigation of the effect of parameters on all model variables. WALRUS contains only four parameters requiring calibration; they are intended to have a strong, qualitative relation with catchment characteristics. Parameter estimation remains a challenge, however. The model structure contains three main feedbacks: (1) between groundwater and surface water; (2) between saturated and unsaturated zone; (3) between catchment wetness and (quick/slow) flowroute division. These feedbacks represent essential rainfall-runoff processes in lowland catchments, but increase the risk of parameter dependence and equifinality. Therefore, model performance should not only be judged based on a comparison between modelled and observed discharges, but also based on the plausibility of the internal modelled variables. Here, we present a method to analyse the effect of parameter values on internal model states and fluxes in a qualitative and intuitive way using interactive parallel plotting. We applied WALRUS to ten Dutch catchments with different sizes, slopes and soil types and both freely draining and polder areas. The model was run with a large number of parameter sets, which were created using Latin Hypercube Sampling. The model output was characterised in terms of several signatures, both measures of goodness of fit and statistics of internal model variables (such as the percentage of rain water travelling through the quickflow reservoir). End users can then eliminate parameter combinations with unrealistic outcomes based on expert knowledge using interactive parallel plots. In these plots, for instance, ranges can be selected for each signature and only model runs which yield signature values in these ranges are highlighted. The resulting selection of realistic parameter sets can be used for ensemble simulations. C.C. Brauer, A.J. Teuling, P.J.J.F. Torfs, R. Uijlenhoet (2014a): The Wageningen Lowland Runoff Simulator (WALRUS): a lumped rainfall-runoff model for catchments with shallow groundwater, Geoscientific Model Development, 7, 2313-2332, www.geosci-model-dev.net/7/2313/2014/gmd-7-2313-2014.pdf C.C. Brauer, P.J.J.F. Torfs, A.J. Teuling, R. Uijlenhoet (2014b): The Wageningen Lowland Runoff Simulator (WALRUS): application to the Hupsel Brook catchment and Cabauw polder, Hydrology and Earth System Sciences, 18, 4007-4028, www.hydrol-earth-syst-sci.net/18/4007/2014/hess-18-4007-2014.pdf
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NASA Astrophysics Data System (ADS)
Vamvakeridou-Lyroudia, Lydia; Alexandri, Eva; Blanco, Maria; Chew, Chengzi; Conradt, Tobias; Daskalou, Olympia; Evans, Barry; Guitart, Francesc; Mereu, Simone; Sartori, Martina; Susnik, Janez; Savic, Dragan
2017-04-01
A four-year EU H2020 project "Sustainable Integrated Management FOR the NEXUS of water-land-food-energy-climate for a resource-efficient Europe (SIM4NEXUS)" started in June 2016, with an overall grant of € 7.9M (www.sim4nexus.eu). The project involves 25 partners from 15 European countries. SIM4NEXUS has four objectives: (i) to adopt existing knowledge and develop new expertise on the water-energy-food-climate-land use Nexus; (ii) to reduce uncertainties of how policies, governance and institutions affect complex environmental systems; (iii) to showcase the implementation via a network of three regional, five national, two transboundary case studies in Europe, as well as continental and global studies; (iv) to valorise the project outputs by suitable business models. SIM4NEXUS develops an innovative concept and methodologies to facilitate the design of policies and bridge knowledge and technology gaps in the field of the Nexus under global change. The project will develop a methodology of integration using a complexity science approach and a Serious Game (a decision-based platform that allows policy makers to play out scenarios to see what would bring the best outcome) as an integrating tool for testing and evaluating policy decisions. The Serious Game is based on Aqua Republica (http://www.dhigroup.com/upload/publications/scribd/172629015-Exploring-the-World-of-Aqua-Republica-DHI-Case-Story.pdf ) and will cover a vast array of scenarios for all the case studies, over short, medium and long terms. In this presentation we focus on all the stages of the development of the Serious Game for one of our Case Studies (Sardinia, Italy) which is being used as a pilot example prior to wider rollout. Specifically we detail the components and steps involved in Game development including: (i) linking thematic models (CAPRI- http://www.capri-model.org/dokuwiki/doku.php and E3ME- http://www.e3me.com/) and downscaling to regional level; (ii) climate change scenarios (using and downscaling HADGEM2 models - http://www.metoffice.gov.uk/research/modelling-systems/unified-model/climate-models/hadgem2); (iii) socio-economic inputs and projections (GTAP - http://en.openei.org/wiki/Global_Trade_and_Analysis_Project_(GTAP)_Model) with System Dynamic Modelling (SDM) using STELLA for the visual environment- http://www.iseesystems.com/store/products/stella-professional.aspx and STELLAR as an open source programming language - http://www.r-gis.net/stellar/); (iv) creating a Knowledge Elicitation Engine (KEE), providing nexus semantics to the outputs of the SDM and (v) generating knowledge from Serious Game user interaction. Local data from Sardinian experts and stakeholders are being used in the pilot, which has been developed with their participation. The presentation will show results from sample scenarios and the approach to simulating uncertainties using SDM, as well as the overall data transfer and management scheme. It should be pointed out that the process of linking thematic models to System Dynamics (Complexity Science Modelling) and creating a KEE out of this combination is, to the best of our knowledge, novel and does not exist in the literature.
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This EnviroAtlas dataset contains data on the mean livestock manure application to cultivated crop and hay/pasture lands by 12-digit Hydrologic Unit (HUC) in 2006. Livestock manure inputs to cultivated crop and hay/pasture lands were estimated using county-level estimates of recoverable animal manure from confined feeding operations compiled for 2007. Recoverable manure is defined as manure that is collected, stored, and available for land application from confined feeding operations. County-scale data on livestock populations -- needed to calculate manure inputs -- were only available for the year 2007 from the USDA Census of Agriculture (http://www.agcensus.usda.gov/index.php). We acquired county-level data describing total farm-level inputs (kg N/yr) of recoverable manure to individual counties in 2007 from the International Plant Nutrition Institute (IPNI) Nutrient Geographic Information System (NuGIS; http://www.ipni.net/nugis). These data were converted to per area rates (kg N/ha/yr) of manure N inputs by dividing the total N input by the land area (ha) of combined cultivated crop and hay/pasture (agricultural) lands within a county as determined from county-level summarization of the 2006 NLCD. We distributed county-specific, per area N inputs rates to cultivated crop and hay/pasture lands (30 x 30 m pixels) within the corresponding county. Manure data described here represent an average input to a typical agricultural land type within a county, i.e., the
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A systems biology approach toward understanding seed composition in soybean.
Li, Ling; Hur, Manhoi; Lee, Joon-Yong; Zhou, Wenxu; Song, Zhihong; Ransom, Nick; Demirkale, Cumhur Yusuf; Nettleton, Dan; Westgate, Mark; Arendsee, Zebulun; Iyer, Vidya; Shanks, Jackie; Nikolau, Basil; Wurtele, Eve Syrkin
2015-01-01
The molecular, biochemical, and genetic mechanisms that regulate the complex metabolic network of soybean seed development determine the ultimate balance of protein, lipid, and carbohydrate stored in the mature seed. Many of the genes and metabolites that participate in seed metabolism are unknown or poorly defined; even more remains to be understood about the regulation of their metabolic networks. A global omics analysis can provide insights into the regulation of seed metabolism, even without a priori assumptions about the structure of these networks. With the future goal of predictive biology in mind, we have combined metabolomics, transcriptomics, and metabolic flux technologies to reveal the global developmental and metabolic networks that determine the structure and composition of the mature soybean seed. We have coupled this global approach with interactive bioinformatics and statistical analyses to gain insights into the biochemical programs that determine soybean seed composition. For this purpose, we used Plant/Eukaryotic and Microbial Metabolomics Systems Resource (PMR, http://www.metnetdb.org/pmr, a platform that incorporates metabolomics data to develop hypotheses concerning the organization and regulation of metabolic networks, and MetNet systems biology tools http://www.metnetdb.org for plant omics data, a framework to enable interactive visualization of metabolic and regulatory networks. This combination of high-throughput experimental data and bioinformatics analyses has revealed sets of specific genes, genetic perturbations and mechanisms, and metabolic changes that are associated with the developmental variation in soybean seed composition. Researchers can explore these metabolomics and transcriptomics data interactively at PMR.
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Digital diagnosis of medical images
NASA Astrophysics Data System (ADS)
Heinonen, Tomi; Kuismin, Raimo; Jormalainen, Raimo; Dastidar, Prasun; Frey, Harry; Eskola, Hannu
2001-08-01
The popularity of digital imaging devices and PACS installations has increased during the last years. Still, images are analyzed and diagnosed using conventional techniques. Our research group begun to study the requirements for digital image diagnostic methods to be applied together with PACS systems. The research was focused on various image analysis procedures (e.g., segmentation, volumetry, 3D visualization, image fusion, anatomic atlas, etc.) that could be useful in medical diagnosis. We have developed Image Analysis software (www.medimag.net) to enable several image-processing applications in medical diagnosis, such as volumetry, multimodal visualization, and 3D visualizations. We have also developed a commercial scalable image archive system (ActaServer, supports DICOM) based on component technology (www.acta.fi), and several telemedicine applications. All the software and systems operate in NT environment and are in clinical use in several hospitals. The analysis software have been applied in clinical work and utilized in numerous patient cases (500 patients). This method has been used in the diagnosis, therapy and follow-up in various diseases of the central nervous system (CNS), respiratory system (RS) and human reproductive system (HRS). In many of these diseases e.g. Systemic Lupus Erythematosus (CNS), nasal airways diseases (RS) and ovarian tumors (HRS), these methods have been used for the first time in clinical work. According to our results, digital diagnosis improves diagnostic capabilities, and together with PACS installations it will become standard tool during the next decade by enabling more accurate diagnosis and patient follow-up.
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A cognitive network for oracle bone characters related to animals
NASA Astrophysics Data System (ADS)
Dress, Andreas; Grünewald, Stefan; Zeng, Zhenbing
2016-01-01
In this paper, we present an analysis of oracle bone characters for animals from a “cognitive” point of view. After some general remarks on oracle-bone characters presented in Sec. 1 and a short outline of the paper in Sec. 2, we collect various oracle-bone characters for animals from published resources in Sec. 3. In the next section, we begin analyzing a group of 60 ancient animal characters from www.zdic.net, a highly acclaimed internet dictionary of Chinese characters that is strictly based on historical sources, and introduce five categories of specific features regarding their (graphical) structure that will be used in Sec. 5 to associate corresponding feature vectors to these characters. In Sec. 6, these feature vectors will be used to investigate their dissimilarity in terms of a family of parameterized distance measures. And in the last section, we apply the SplitsTree method as encoded in the NeighborNet algorithms to construct a corresponding family of dissimilarity-based networks with the intention of elucidating how the ancient Chinese might have perceived the “animal world” in the late bronze age and to demonstrate that these pictographs reflect an intuitive understanding of this world and its inherent structure that predates its classification in the oldest surviving Chinese encyclopedia from approximately the third century BC, the Er Ya, as well as similar classification systems in the West by one to two millennia. We also present an English dictionary of 70 oracle bone characters for animals in Appendix A. In Appendix B, we list various variants of animal characters that were published in the Jia Gu Wen Bian (cf. 甲骨文编, A Complete Collection of Oracle Bone Characters, edited by the Institute of Archaeology of the Chinese Academy of Social Sciences, published by the Zhonghua Book Company in 1965). We recall the frequencies of the 521 most frequent oracle bone characters in Appendix C as reported in [T. Chen, Yin-Shang Jiaguwen Zixing Xitong Zai Yanjiu, (The Structural System of Oracle Inscriptions) (Shanghai Renmin Chubanshe, Shanghai, 2010); Jiaguwen Shiwen Yongzi Pinlü Biao (A Frequency List of Oracle Characters), Center for the Study and Application of Chinese Characters (East China Normal University, Shanghai, 2010), http://www.wenzi.cn/en/default.aspx. And in Appendix D, we list the animals registered in the last five chapters of the Er Ya.
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A cognitive network for oracle-bone characters related to animals
NASA Astrophysics Data System (ADS)
Dress. Andreas; Grünewald, Stefan; Zeng, Zhenbing
This paper is dedicated to HAO Bailin on the occasion of his eighties birthday, the great scholar and very good friend who never tired to introduce us to the wonderful and complex intricacies of Chinese culture and history.
In this paper, we present an analysis of oracle-bone characters for animals from a `cognitive' point of view. After some general remarks on oraclebone characters presented in Section 1 and a short outline of the paper in Section 2, we collect various oracle-bone characters for animals from published resources in Section 3. In the next section, we begin analysing a group of 60 ancient animal characters from www.zdic.net, a highly acclaimed internet dictionary of Chinese characters that is strictly based on historical sources, and introduce five categories of specific features regarding their (graphical) structure that will be used in Section 5 to associate corresponding feature vectors to these characters. In Section 6, these feature vectors will be used to investigate their dissimilarity in terms of a family of parameterised distance measures. And in the last section, we apply the SplitsTree method as encoded in the NeighbourNet algorithms to construct a corresponding family of dissimilarity-based networks with the intention of elucidating how the ancient Chinese might have perceived the `animal world' in the late bronze age and to demonstrate that these pictographs reflect an intuitive understanding of this world and its inherent structure that predates its classification in the oldest surviving Chinese encyclopedia from approximately the 3rd century BC, the ErYa, as well as similar classification systems in the West by one to two millennia. We also present an English dictionary of 70 oracle-bone characters for animals in Appendix 1. In Appendix 2, we list various variants of animal characters that were published in the Jia Gu Wen Bian (cf. , A Complete Collection of Oracle Bone Characters, edited by the Institute of Archaeology of the Chinese Academy of Social Sciences, published by the Zhonghua Book Company in 1965). We recall the frequencies of the 521 most frequent oracle-bone characters in Appendix 3 as reported in [7, 8]. And in Appendix 4, we list the animals registered in the last five chapters of the ErYa. -
Homma, Shunichi; Thompson, John L.P.; Qian, Min; Ye, Siqin; Di Tullio, Marco R.; Lip, Gregory Y.H.; Mann, Douglas L.; Sacco, Ralph L.; Levin, Bruce; Pullicino, Patrick M.; Freudenberger, Ronald S.; Teerlink, John R.; Graham, Susan; Mohr, J.P.; Labovitz, Arthur J.; Buchsbaum, Richard; Estol, Conrado J.; Lok, Dirk J.; Ponikowski, Piotr; Anker, Stefan D.
2015-01-01
Background The aim of this study is to examine the relationship between time in therapeutic range (TTR) and clinical outcomes in heart failure (HF) patients in sinus rhythm (SR) treated with warfarin. Methods and Results We used data from the Warfarin vs. Aspirin in Reduced Cardiac Ejection Fraction Trial (WARCEF) to assess the relationship of TTR with the WARCEF primary outcome (ischemic stroke, intracerebral hemorrhage, or death); with death alone; ischemic stroke alone; major hemorrhage alone; and net clinical benefit (primary outcome and major hemorrhage combined). Multivariable Cox models were used to examine how the event risk changed with TTR and to compare the high TTR, low TTR, and aspirin patients, with TTR being treated as a time-dependent covariate. 2,217 patients were included in the analyses, among whom 1,067 were randomized to warfarin and 1,150 were randomized to aspirin. The median (IQR) follow-up duration was 3.6 (2.0–5.0) years. Mean (±SD) age was 61±11.3 years, with 80% being men. The mean (±SD) TTR was 57% (±28.5%). Increasing TTR was significantly associated with reduction in primary outcome (adjusted p<0.001), death alone (adjusted p=0.001), and improved net clinical benefit (adjusted p<0.001). A similar trend was observed for the other two outcomes but significance was not reached (adjusted p=0.082 for ischemic stroke, adjusted p=0.109 for major hemorrhage). Conclusions In HF patients in SR, increasing TTR is associated with better outcome and improved net clinical benefit. Patients in whom good quality anticoagulation can be achieved may benefit from the use of anticoagulants. Clinical Trial Registration URL: http://www.clinicaltrials.gov. Unique identifier: NCT00041938. PMID:25850425
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Greber, Boris; Siatkowski, Marcin; Paudel, Yogesh; Warsow, Gregor; Cap, Clemens; Schöler, Hans; Fuellen, Georg
2010-01-01
Background Analysis of the mechanisms underlying pluripotency and reprogramming would benefit substantially from easy access to an electronic network of genes, proteins and mechanisms. Moreover, interpreting gene expression data needs to move beyond just the identification of the up-/downregulation of key genes and of overrepresented processes and pathways, towards clarifying the essential effects of the experiment in molecular terms. Methodology/Principal Findings We have assembled a network of 574 molecular interactions, stimulations and inhibitions, based on a collection of research data from 177 publications until June 2010, involving 274 mouse genes/proteins, all in a standard electronic format, enabling analyses by readily available software such as Cytoscape and its plugins. The network includes the core circuit of Oct4 (Pou5f1), Sox2 and Nanog, its periphery (such as Stat3, Klf4, Esrrb, and c-Myc), connections to upstream signaling pathways (such as Activin, WNT, FGF, BMP, Insulin, Notch and LIF), and epigenetic regulators as well as some other relevant genes/proteins, such as proteins involved in nuclear import/export. We describe the general properties of the network, as well as a Gene Ontology analysis of the genes included. We use several expression data sets to condense the network to a set of network links that are affected in the course of an experiment, yielding hypotheses about the underlying mechanisms. Conclusions/Significance We have initiated an electronic data repository that will be useful to understand pluripotency and to facilitate the interpretation of high-throughput data. To keep up with the growth of knowledge on the fundamental processes of pluripotency and reprogramming, we suggest to combine Wiki and social networking software towards a community curation system that is easy to use and flexible, and tailored to provide a benefit for the scientist, and to improve communication and exchange of research results. A PluriNetWork tutorial is available at http://www.ibima.med.uni-rostock.de/IBIMA/PluriNetWork/. PMID:21179244
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Min, Peiru; Zhang, Zheng; Grassetti, Luca; Perdanasari, Aurelia Trisliana; Torresetti, Matteo; Pu, Zheming; Zhang, Yan; Han, Sheng; Marsili, Riccardo; Zhang, Yi Xin; di Benedetto, Giovanni; Lazzeri, Davide
2016-06-01
Although application of botulinum toxin type A (BTX-A) for the treatment of forehead rhytides has become very popular, the effects of its intramuscular injections on the skin mechanical properties remain unclear. We prospectively investigated the alterations in the mechanical properties of the skin of patients who received intramuscular injections of botulinum toxin A (BTX-A) for forehead rhytides and compared two injection doses. Of the 42 enrolled patients, one randomly assigned half received intramuscular injections of two units (group I), and the other half received four units (group II) of BTX-A in each injection point. The baseline and post-treatment skin mechanical parameters, including gross elasticity (R2), net elasticity (R5), viscoelastic ratio (R6) and biological elasticity (R7), were measured using the Cutometer(®) and compared. Treatment with BTX-A resulted in significant overall alterations in the mechanical properties of skin at the injection sites of both treatment groups during the 16-week period, and no significant differences were observed between groups. Significant decreases in biological elasticity, net elasticity and viscoelasticity properties were observed at 2 weeks follow-up and began to recover at that time. All of the skin mechanical properties recovered to baseline levels by 16 weeks of follow-up in both dosage groups, which indicates that the higher dosage (4 units) did not delay relapse compared to the two-unit dosage. We concluded that intramuscular injections of BTX-A significantly regulated the gross elasticity, net elasticity, functional elasticity and viscoelastic elasticity at the injection point over a radius of 1.5 cm at 2, 4 and 8 weeks follow-up. The alteration in the skin measurements had completely diminished by the 16-week follow-up. This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .
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Astronomical Research with the MicroObservatory Net
NASA Astrophysics Data System (ADS)
Brecher, K.; Sadler, P.; Gould, R.; Leiker, S.; Antonucci, P.; Deutsch, F.
1997-05-01
We have developed a fully integrated automated astronomical telescope system which combines the imaging power of a cooled CCD, with a self-contained and weatherized 15 cm reflecting optical telescope and mount. The MicroObservatory Net consists of five of these telescopes. They are currently being deployed around the world at widely distributed longitudes. Remote access to the MicroObservatories over the Internet has now been implemented. Software for computer control, pointing, focusing, filter selection as well as pattern recognition have all been developed as part of the project. The telescopes can be controlled in real time or in delay mode, from a Macintosh, PC or other computer using Web-based software. The Internet address of the telescopes is http://cfa- www.harvard.edu/cfa/sed/MicroObservatory/MicroObservatory.html. In the real-time mode, individuals have access to all of the telescope control functions without the need for an `on-site' operator. Users can sign up for a specific period of ti me. In the batch mode, users can submit requests for delayed telescope observations. After a MicroObservatory completes a job, the user is automatically notified by e-mail that the image is available for viewing and downloading from the Web site. The telescopes were designed for classroom instruction, as well as for use by students and amateur astronomers for original scientific research projects. We are currently examining a variety of technical and educational questions about the use of the telescopes including: (1) What are the best approaches to scheduling real-time versus batch mode observations? (2) What criteria should be used for allocating telescope time? (3) With deployment of more than one telescope, is it advantageous for each telescope to be used for just one type of observation, i.e., some for photometric use, others for imaging? And (4) What are the most valuable applications of the MicroObservatories in astronomical research? Support for the MicroObservatory Net has been provided by the NSF, Apple Computer, Inc. and Kodak, Inc.
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Shah, Ravi; Heydari, Bobak; Coelho-Filho, Otavio; Murthy, Venkatesh L; Abbasi, Siddique; Feng, Jiazhuo H; Pencina, Michael; Neilan, Tomas G; Meadows, Judith L; Francis, Sanjeev; Blankstein, Ron; Steigner, Michael; di Carli, Marcelo; Jerosch-Herold, Michael; Kwong, Raymond Y
2013-08-06
A recent large-scale clinical trial found that an initial invasive strategy does not improve cardiac outcomes beyond optimized medical therapy in patients with stable coronary artery disease. Novel methods to stratify at-risk patients may refine therapeutic decisions to improve outcomes. In a cohort of 815 consecutive patients referred for evaluation of myocardial ischemia, we determined the net reclassification improvement of the risk of cardiac death or nonfatal myocardial infarction (major adverse cardiac events) incremental to clinical risk models, using guideline-based low (<1%), moderate (1% to 3%), and high (>3%) annual risk categories. In the whole cohort, inducible ischemia demonstrated a strong association with major adverse cardiac events (hazard ratio=14.66; P<0.0001) with low negative event rates of major adverse cardiac events and cardiac death (0.6% and 0.4%, respectively). This prognostic robustness was maintained in patients with previous coronary artery disease (hazard ratio=8.17; P<0.0001; 1.3% and 0.6%, respectively). Adding inducible ischemia to the multivariable clinical risk model (adjusted for age and previous coronary artery disease) improved discrimination of major adverse cardiac events (C statistic, 0.81-0.86; P=0.04; adjusted hazard ratio=7.37; P<0.0001) and reclassified 91.5% of patients at moderate pretest risk (65.7% to low risk; 25.8% to high risk) with corresponding changes in the observed event rates (0.3%/y and 4.9%/y for low and high risk posttest, respectively). Categorical net reclassification index was 0.229 (95% confidence interval, 0.063-0.391). Continuous net reclassification improvement was 1.11 (95% confidence interval, 0.81-1.39). Stress cardiac magnetic resonance imaging effectively reclassifies patient risk beyond standard clinical variables, specifically in patients at moderate to high pretest clinical risk and in patients with previous coronary artery disease. http://www.clinicaltrials.gov. Unique identifier: NCT01821924.
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2017-01-01
Peptide binding to MHC class I molecules is the single most selective step in antigen presentation and the strongest single correlate to peptide cellular immunogenicity. The cost of experimentally characterizing the rules of peptide presentation for a given MHC-I molecule is extensive, and predictors of peptide–MHC interactions constitute an attractive alternative. Recently, an increasing amount of MHC presented peptides identified by mass spectrometry (MS ligands) has been published. Handling and interpretation of MS ligand data is, in general, challenging due to the polyspecificity nature of the data. We here outline a general pipeline for dealing with this challenge and accurately annotate ligands to the relevant MHC-I molecule they were eluted from by use of GibbsClustering and binding motif information inferred from in silico models. We illustrate the approach here in the context of MHC-I molecules (BoLA) of cattle. Next, we demonstrate how such annotated BoLA MS ligand data can readily be integrated with in vitro binding affinity data in a prediction model with very high and unprecedented performance for identification of BoLA-I restricted T-cell epitopes. The prediction model is freely available at http://www.cbs.dtu.dk/services/NetMHCpan/NetBoLApan. The approach has here been applied to the BoLA-I system, but the pipeline is readily applicable to MHC systems in other species. PMID:29115832
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Nielsen, Morten; Connelley, Tim; Ternette, Nicola
2018-01-05
Peptide binding to MHC class I molecules is the single most selective step in antigen presentation and the strongest single correlate to peptide cellular immunogenicity. The cost of experimentally characterizing the rules of peptide presentation for a given MHC-I molecule is extensive, and predictors of peptide-MHC interactions constitute an attractive alternative. Recently, an increasing amount of MHC presented peptides identified by mass spectrometry (MS ligands) has been published. Handling and interpretation of MS ligand data is, in general, challenging due to the polyspecificity nature of the data. We here outline a general pipeline for dealing with this challenge and accurately annotate ligands to the relevant MHC-I molecule they were eluted from by use of GibbsClustering and binding motif information inferred from in silico models. We illustrate the approach here in the context of MHC-I molecules (BoLA) of cattle. Next, we demonstrate how such annotated BoLA MS ligand data can readily be integrated with in vitro binding affinity data in a prediction model with very high and unprecedented performance for identification of BoLA-I restricted T-cell epitopes. The prediction model is freely available at http://www.cbs.dtu.dk/services/NetMHCpan/NetBoLApan . The approach has here been applied to the BoLA-I system, but the pipeline is readily applicable to MHC systems in other species.
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Does Vesta Have Moons?: Dawn's Search for Satellites
NASA Technical Reports Server (NTRS)
McFadden, L. A.; Sykes, M. V.; Tricarico, P.; Carsenty, U.; Gutierrez-Marques, P.; Jacobson, R. A.; Joy, S.; Keller, H. U.; Li, J.-Y.; McLean, B.;
2011-01-01
Upon approach to asteroid 4 Vesta, the Dawn mission included a dedicated satellite search observation of the operational sphere of the spacecraft around Vesta. Discovery of moons of Vesta would constrain theories of satellite f()rmation. The sequence using the framing camera and clear filter includes three mosaics of six stations acquired on July 9-10. 2011. Each station consists of four sets with three different exposures, 1.5,20 and 270 s. We also processed and scanned the optical navigation sequences until Vesta filled the field of view. Analysis of images involves looking for moving objects in the mosaics and identifying catalogued stars, subtracting them from the image and examining residual objects for evidence of bodies in orbit around Vesta. Celestial coordinates were determined using Astrometry.net, an astrometry calibration service (http://astrometry.net/use.html). We processed the images by subtracting dark and bias fields and dividing by a Hatfield. Images were further filtered subtracting a box car filter (9x9 average) to remove effects of scattered light from Vesta itself. Images were scanned by eye for evidence of motion in directions different from the background stars. All objects were compared with Hubble Space Telescope's Guide Star Catalogue and US Naval Observatory's UCAC3 catalog. We report findings from these observations and analysis, including limits of magnitude, size and motion of objects in orbit around Vesta. We gratefully acknowledge modifications made to Astrometrica http://www.astrometrica.at/ for purposes of this effort.
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The long-term Global LAnd Surface Satellite (GLASS) product suite and applications
NASA Astrophysics Data System (ADS)
Liang, S.
2015-12-01
Our Earth's environment is experiencing rapid changes due to natural variability and human activities. To monitor, understand and predict environment changes to meet the economic, social and environmental needs, use of long-term high-quality satellite data products is critical. The Global LAnd Surface Satellite (GLASS) product suite, generated at Beijing Normal University, currently includes 12 products, including leaf area index (LAI), broadband shortwave albedo, broadband longwave emissivity, downwelling shortwave radiation and photosynthetically active radiation, land surface skin temperature, longwave net radiation, daytime all-wave net radiation, fraction of absorbed photosynetically active radiation absorbed by green vegetation (FAPAR), fraction of green vegetation coverage, gross primary productivity (GPP), and evapotranspiration (ET). Most products span from 1981-2014. The algorithms for producing these products have been published in the top remote sensing related journals and books. More and more applications have being reported in the scientific literature. The GLASS products are freely available at the Center for Global Change Data Processing and Analysis of Beijing Normal University (http://www.bnu-datacenter.com/), and the University of Maryland Global Land Cover Facility (http://glcf.umd.edu). After briefly introducing the basic characteristics of GLASS products, we will present some applications on the long-term environmental changes detected from GLASS products at both global and local scales. Detailed analysis of regional hotspots, such as Greenland, Tibetan plateau, and northern China, will be emphasized, where environmental changes have been mainly associated with climate warming, drought, land-atmosphere interactions, and human activities.
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Ethics in the driver, Mosaic is the vehicle, and network instruction is the precious cargo
DOE Office of Scientific and Technical Information (OSTI.GOV)
Woodbury, M.; Schmitz, J.
1994-12-31
The College of Agriculture at the University of Illinois had an ambitious goal: train 500 incoming freshman students how to take advantage of their computer network privileges without placing undue demands on their time. Because the College already had outstanding computer facilities and expertise, the Department of Academic Programs chose AIM lab to handle the task. AIM stands for Agriculture Instructional Media, and the staff, led by John Schmitz, searched for the most helpful message, meaning, and means to deliver the project. John and I created and developed the computer tutorial, and because both of us are enthused about {open_quotes}themore » Net{close_quotes} and being good citizens in the cyber community, we built ethics into our design from the earliest stages. You can examine our team`s product on the Web at/http://gopher.ag.uiuc.edu/WWW/AIM/Discovery/Net/intro.html. To give a brief overview of our message to the students, and the University community which will also share in our work, here is the wording from the opening Mosaic screen, a clear statement of the goals of our project: We believe that access to the Internet is a privilege. You need a basic knowledge of the {open_quotes}rules of the road{close_quotes} in order to be a good citizen of the Internet community. You should be required to earn a driver`s license to use the Information Superhighway.« less
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Panji, Sumir; Fernandes, Pedro L.; Judge, David P.; Ghouila, Amel; Salifu, Samson P.; Ahmed, Rehab; Kayondo, Jonathan; Ssemwanga, Deogratius
2017-01-01
Africa is not unique in its need for basic bioinformatics training for individuals from a diverse range of academic backgrounds. However, particular logistical challenges in Africa, most notably access to bioinformatics expertise and internet stability, must be addressed in order to meet this need on the continent. H3ABioNet (www.h3abionet.org), the Pan African Bioinformatics Network for H3Africa, has therefore developed an innovative, free-of-charge “Introduction to Bioinformatics” course, taking these challenges into account as part of its educational efforts to provide on-site training and develop local expertise inside its network. A multiple-delivery–mode learning model was selected for this 3-month course in order to increase access to (mostly) African, expert bioinformatics trainers. The content of the course was developed to include a range of fundamental bioinformatics topics at the introductory level. For the first iteration of the course (2016), classrooms with a total of 364 enrolled participants were hosted at 20 institutions across 10 African countries. To ensure that classroom success did not depend on stable internet, trainers pre-recorded their lectures, and classrooms downloaded and watched these locally during biweekly contact sessions. The trainers were available via video conferencing to take questions during contact sessions, as well as via online “question and discussion” forums outside of contact session time. This learning model, developed for a resource-limited setting, could easily be adapted to other settings. PMID:28981516
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Hoddinott, Pat; Thomson, Gill; Morgan, Heather; Crossland, Nicola; MacLennan, Graeme; Dykes, Fiona; Stewart, Fiona; Bauld, Linda; Campbell, Marion K
2015-11-13
To explore the acceptability, mechanisms and consequences of provider incentives for smoking cessation and breast feeding as part of the Benefits of Incentives for Breastfeeding and Smoking cessation in pregnancy (BIBS) study. Cross-sectional survey and qualitative interviews. Scotland and North West England. Early years professionals: 497 survey respondents included 156 doctors; 197 health visitors/maternity staff; 144 other health staff. Qualitative interviews or focus groups were conducted with 68 pregnant/postnatal women/family members; 32 service providers; 22 experts/decision-makers; 63 conference attendees. Early years professionals were surveyed via email about the acceptability of payments to local health services for reaching smoking cessation in pregnancy and breastfeeding targets. Agreement was measured on a 5-point scale using multivariable ordered logit models. A framework approach was used to analyse free-text survey responses and qualitative data. Health professional net agreement for provider incentives for smoking cessation targets was 52.9% (263/497); net disagreement was 28.6% (142/497). Health visitors/maternity staff were more likely than doctors to agree: OR 2.35 (95% CI 1.51 to 3.64; p<0.001). Net agreement for provider incentives for breastfeeding targets was 44.1% (219/497) and net disagreement was 38.6% (192/497). Agreement was more likely for women (compared with men): OR 1.81 (1.09 to 3.00; p=0.023) and health visitors/maternity staff (compared with doctors): OR 2.54 (95% CI 1.65 to 3.91; p<0.001). Key emergent themes were 'moral tensions around acceptability', 'need for incentives', 'goals', 'collective or divisive action' and 'monitoring and proof'. While provider incentives can focus action and resources, tensions around the impact on relationships raised concerns. Pressure, burden of proof, gaming, box-ticking bureaucracies and health inequalities were counterbalances to potential benefits. Provider incentives are favoured by non-medical staff. Solutions which increase trust and collaboration towards shared goals, without negatively impacting on relationships or increasing bureaucracy are required. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/
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ABINIT: First-principles approach to material and nanosystem properties
NASA Astrophysics Data System (ADS)
Gonze, X.; Amadon, B.; Anglade, P.-M.; Beuken, J.-M.; Bottin, F.; Boulanger, P.; Bruneval, F.; Caliste, D.; Caracas, R.; Côté, M.; Deutsch, T.; Genovese, L.; Ghosez, Ph.; Giantomassi, M.; Goedecker, S.; Hamann, D. R.; Hermet, P.; Jollet, F.; Jomard, G.; Leroux, S.; Mancini, M.; Mazevet, S.; Oliveira, M. J. T.; Onida, G.; Pouillon, Y.; Rangel, T.; Rignanese, G.-M.; Sangalli, D.; Shaltaf, R.; Torrent, M.; Verstraete, M. J.; Zerah, G.; Zwanziger, J. W.
2009-12-01
ABINIT [ http://www.abinit.org] allows one to study, from first-principles, systems made of electrons and nuclei (e.g. periodic solids, molecules, nanostructures, etc.), on the basis of Density-Functional Theory (DFT) and Many-Body Perturbation Theory. Beyond the computation of the total energy, charge density and electronic structure of such systems, ABINIT also implements many dynamical, dielectric, thermodynamical, mechanical, or electronic properties, at different levels of approximation. The present paper provides an exhaustive account of the capabilities of ABINIT. It should be helpful to scientists that are not familiarized with ABINIT, as well as to already regular users. First, we give a broad overview of ABINIT, including the list of the capabilities and how to access them. Then, we present in more details the recent, advanced, developments of ABINIT, with adequate references to the underlying theory, as well as the relevant input variables, tests and, if available, ABINIT tutorials. Program summaryProgram title: ABINIT Catalogue identifier: AEEU_v1_0 Distribution format: tar.gz Journal reference: Comput. Phys. Comm. Programming language: Fortran95, PERL scripts, Python scripts Computer: All systems with a Fortran95 compiler Operating system: All systems with a Fortran95 compiler Has the code been vectorized or parallelized?: Sequential, or parallel with proven speed-up up to one thousand processors. RAM: Ranges from a few Mbytes to several hundred Gbytes, depending on the input file. Classification: 7.3, 7.8 External routines: (all optional) BigDFT [1], ETSF IO [2], libxc [3], NetCDF [4], MPI [5], Wannier90 [6] Nature of problem: This package has the purpose of computing accurately material and nanostructure properties: electronic structure, bond lengths, bond angles, primitive cell size, cohesive energy, dielectric properties, vibrational properties, elastic properties, optical properties, magnetic properties, non-linear couplings, electronic and vibrational lifetimes, etc. Solution method: Software application based on Density-Functional Theory and Many-Body Perturbation Theory, pseudopotentials, with planewaves, Projector-Augmented Waves (PAW) or wavelets as basis functions. Running time: From less than one second for the simplest tests, to several weeks. The vast majority of the >600 provided tests run in less than 30 seconds. References:[1] http://inac.cea.fr/LSim/BigDFT. [2] http://etsf.eu/index.php?page=standardization. [3] http://www.tddft.org/programs/octopus/wiki/index.php/Libxc. [4] http://www.unidata.ucar.edu/software/netcdf. [5] http://en.wikipedia.org/wiki/MessagePassingInterface. [6] http://www.wannier.org.
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An Open Software Platform for Sharing Water Resource Models, Code and Data
NASA Astrophysics Data System (ADS)
Knox, Stephen; Meier, Philipp; Mohamed, Khaled; Korteling, Brett; Matrosov, Evgenii; Huskova, Ivana; Harou, Julien; Rosenberg, David; Tilmant, Amaury; Medellin-Azuara, Josue; Wicks, Jon
2016-04-01
The modelling of managed water resource systems requires new approaches in the face of increasing future uncertainty. Water resources management models, even if applied to diverse problem areas, use common approaches such as representing the problem as a network of nodes and links. We propose a data management software platform, called Hydra, that uses this commonality to allow multiple models using a node-link structure to be managed and run using a single software system. Hydra's user interface allows users to manage network topology and associated data. Hydra feeds this data directly into a model, importing from and exporting to different file formats using Apps. An App connects Hydra to a custom model, a modelling system such as GAMS or MATLAB or to different file formats such as MS Excel, CSV and ESRI Shapefiles. Hydra allows users to manage their data in a single, consistent place. Apps can be used to run domain-specific models and allow users to work with their own required file formats. The Hydra App Store offers a collaborative space where model developers can publish, review and comment on Apps, models and data. Example Apps and open-source libraries are available in a variety of languages (Python, Java and .NET). The App Store can act as a hub for water resource modellers to view and share Apps, models and data easily. This encourages an ecosystem of development using a shared platform, resulting in more model integration and potentially greater unity within resource modelling communities. www.hydraplatform.org www.hydraappstore.com
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Hardwick, J Christopher R; MacKenzie, Fiona M
2003-01-10
To identify websites providing information about early pregnancy loss and compare this information with published guidelines from the Royal College of Obstetricians and Gynaecologists (RCOG). The value of 'Silberg' and 'Health on the net (HON)' website scoring systems in predicting the information provided via websites identified was assessed. A cross-sectional survey. Nineteen websites identified via two search engines (http://www.lycos.co.uk and http://www.msn.co.uk). Websites were searched for specific information in a structured manner and then scored by two independent observers against the website scoring systems and against a scoring system derived from guidelines published by the RCOG. Website scores against the scoring systems and against RCOG guidelines. Information concerning miscarriage contained within these websites was poor and scored accordingly against the RCOG guidelines (median score, 4.5/8). The website scoring systems did not predict the RCOG scores for a website (HON score R(S)=0.193 (95% confidence interval from -0.286 to 0.595), Silberg score, R(S)=0.035 (95% confidence interval from -0.426 to 0.482)). Few relevant websites were identified despite searching a large number via two search engines. The websites found did not answer our specific questions and consequently scored poorly against the RCOG guidelines. RCOG scores did not correlate with either scoring system. Web-based information for women attending with early pregnancy complications needs to be easily accessed and comprehensive. Written information given to women when seen with early pregnancy complications should include details of available comprehensive websites. Professional organisations, colleges or Government agencies should provide this type of information.
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Observing Solar Eclipses in the Developing World
NASA Astrophysics Data System (ADS)
Pasachoff, J. M.
2006-08-01
The paths of totality of total solar eclipses cross the world, with each spot receiving such a view about every 300 years. The areas of the world from which partial eclipses are visible are much wider. For the few days prior to a total eclipse, the attention of a given country is often drawn toward the eclipse, providing a teachable moment that we can use to bring astronomy to the public's attention. Also, it is important to describe how to observe the partial phases of the eclipse safely. Further, it is important to describe to those people in the zone of totality that it is not only safe but also interesting to view totality. Those who are misled by false warnings that overstate the hazards of viewing the eclipse, or that fail to distinguish between safe and unsafe times for naked-eye viewing, may well be skeptical when other health warnings--perhaps about AIDS or malaria prevention or polio inoculations--come from the authorities, meaning that the penalties for misunderstanding the astronomical event can be severe. Through the International Astronomical Union's Working Group on Solar Eclipses and through the I.A.U.'s Program Group on Public Education at the Times of Eclipses, part of the Commission on Education and Development, we make available information to national authorities, to colleagues in the relevant countries, and to others, through our Websites at http://www.eclipses.info and http://www.totalsolareclipse.net and through personal communication. Among our successes at the 29 March 2006 total solar eclipse was the distribution through a colleague in Nigeria of 400,000 eye-protection filters.
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Wang, Li Yan; O'Brien, Mary Jane; Maughan, Erin D
2016-11-01
This paper describes a user-friendly, Excel spreadsheet model and two data collection instruments constructed by the authors to help states and districts perform cost-benefit analyses of school nursing services delivered by full-time school nurses. Prior to applying the model, states or districts need to collect data using two forms: "Daily Nurse Data Collection Form" and the "Teacher Survey." The former is used to record daily nursing activities, including number of student health encounters, number of medications administered, number of student early dismissals, and number of medical procedures performed. The latter is used to obtain estimates for the time teachers spend addressing student health issues. Once inputs are entered in the model, outputs are automatically calculated, including program costs, total benefits, net benefits, and benefit-cost ratio. The spreadsheet model, data collection tools, and instructions are available at the NASN website ( http://www.nasn.org/The/CostBenefitAnalysis ).
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Analysis and prediction of leucine-rich nuclear export signals.
la Cour, Tanja; Kiemer, Lars; Mølgaard, Anne; Gupta, Ramneek; Skriver, Karen; Brunak, Søren
2004-06-01
We present a thorough analysis of nuclear export signals and a prediction server, which we have made publicly available. The machine learning prediction method is a significant improvement over the generally used consensus patterns. Nuclear export signals (NESs) are extremely important regulators of the subcellular location of proteins. This regulation has an impact on transcription and other nuclear processes, which are fundamental to the viability of the cell. NESs are studied in relation to cancer, the cell cycle, cell differentiation and other important aspects of molecular biology. Our conclusion from this analysis is that the most important properties of NESs are accessibility and flexibility allowing relevant proteins to interact with the signal. Furthermore, we show that not only the known hydrophobic residues are important in defining a nuclear export signals. We employ both neural networks and hidden Markov models in the prediction algorithm and verify the method on the most recently discovered NESs. The NES predictor (NetNES) is made available for general use at http://www.cbs.dtu.dk/.
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Polarized Continuum Radiation from Stellar Atmospheres
NASA Astrophysics Data System (ADS)
Harrington, J. Patrick
2015-10-01
Continuum scattering by free electrons can be significant in early type stars, while in late type stars Rayleigh scattering by hydrogen atoms or molecules may be important. Computer programs used to construct models of stellar atmospheres generally treat the scattering of the continuum radiation as isotropic and unpolarized, but this scattering has a dipole angular dependence and will produce polarization. We review an accurate method for evaluating the polarization and limb darkening of the radiation from model stellar atmospheres. We use this method to obtain results for: (i) Late type stars, based on the MARCS code models (Gustafsson et al. 2008), and (ii) Early type stars, based on the NLTE code TLUSTY (Lanz and Hubeny 2003). These results are tabulated at http://www.astro.umd.edu/~jph/Stellar_Polarization.html. While the net polarization vanishes for an unresolved spherical star, this symmetry is broken by rapid rotation or by the masking of part of the star by a binary companion or during the transit of an exoplanet. We give some numerical results for these last cases.
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Manthorpe, Jill; Hussein, Shereen; Moriarty, Jo
2005-07-01
Social work education in England underwent significant change in its move to degree status in 2003. It is hoped that the result will be increased professional standing for social workers, an improvement in the current widespread problems with recruitment, and assurance that all newly qualified social workers meet the National Occupational Standards for Social Work (Available from: http://www.topssengland.net/files/cd/). This change has pre-occupied social work educators and debate within the profession has concentrated on the practicalities and expectations of reform. This paper suggests that those working in nurse education may observe a number of similarities with its own earlier reforms and with current debates on whether nursing should move to an all-graduate profession. It then highlights three aspects of the new requirements for social work training: service user involvement, the place of research-minded practice, and the primacy of practice--that may be of interest and relevance to nursing colleagues.
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MoZis: mobile zoo information system: a case study for the city of Osnabrueck
NASA Astrophysics Data System (ADS)
Michel, Ulrich
2007-10-01
This paper describes a new project of the Institute for Geoinformatics and Remote Sensing, funded by the German Federal Foundation for the Environment (DBU, Deutsche Bundesstiftung Umwelt www.dbu.de). The goal of this project is to develop a mobile zoo information system for Pocket PCs and Smart phones. Visitors of the zoo will be able to use their own mobile devices or use Pocket PCs, which could be borrowed from the zoo to navigate around the zoo's facilities. The system will also provide additional multimedia based information such as audio-based material, animal video clips, and maps of their natural habitat. People could have access to the project at the zoo via wireless local area network or by downloading the necessary files using a home internet connection. Our software environment consists of proprietary and non-proprietary software solutions in order to make it as flexible as possible. Our first prototype was developed with Visual Studio 2003 and Visual Basic.Net.
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CFS MATLAB toolbox: An experiment builder for continuous flash suppression (CFS) task.
Nuutinen, Mikko; Mustonen, Terhi; Häkkinen, Jukka
2017-09-15
CFS toolbox is an open-source collection of MATLAB functions that utilizes PsychToolbox-3 (PTB-3). It is designed to allow a researcher to create and run continuous flash suppression experiments using a variety of experimental parameters (i.e., stimulus types and locations, noise characteristics, and experiment window settings). In a CFS experiment, one of the eyes at a time is presented with a dynamically changing noise pattern, while the other eye is concurrently presented with a static target stimulus, such as a Gabor patch. Due to the strong interocular suppression created by the dominant noise pattern mask, the target stimulus is rendered invisible for an extended duration. Very little knowledge of MATLAB is required for using the toolbox; experiments are generated by modifying csv files with the required parameters, and result data are output to text files for further analysis. The open-source code is available on the project page under a Creative Commons License ( http://www.mikkonuutinen.arkku.net/CFS_toolbox/ and https://bitbucket.org/mikkonuutinen/cfs_toolbox ).
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Riva, G; Bacchetta, M; Baruffi, M; Borgomainerio, E; Defrance, C; Gatti, F; Galimberti, C; Fontaneto, S; Marchi, S; Molinari, E; Nugues, P; Rinaldi, S; Rovetta, A; Ferretti, G S; Tonci, A; Wann, J; Vincelli, F
1999-01-01
Due, in large part, to the significant advances in PC hardware that have been made over the last 3 years, PC-based virtual environments are approaching reality. Virtual Reality Environments for Psychoneurophysiological Assessment and Rehabilitation (VREPAR) are two European Community funded projects (Telematics for health-HC 1053/HC 1055, http:// www.psicologia.net) that are trying to develop a PC-based virtual reality system (PC-VRS) for the medical market that can be marketed at a price that is accessible to its possible endusers (hospitals, universities, and research centres) and that would have the modular, connectability, and interoperability characteristics that the existing systems lack. In particular, the projects are developing three hardware/software modules for the application of the PCVRS in psycho-neuro-physiological assessment and rehabilitation. The chosen development areas are eating disorders (bulimia, anorexia, and obesity), movement disorders (Parkinson's disease and torsion dystonia) and stroke disorders (unilateral neglect and hemiparesis). This article describes the rationale of the modules and the preliminary results obtained.
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STITCHER 2.0: primer design for overlapping PCR applications
O’Halloran, Damien M.; Uriagereka-Herburger, Isabel; Bode, Katrin
2017-01-01
Overlapping polymerase chain reaction (PCR) is a common technique used by researchers in very diverse fields that enables the user to ‘stitch’ individual pieces of DNA together. Previously, we have reported a web based tool called STITCHER that provides a platform for researchers to automate the design of primers for overlapping PCR applications. Here we present STITCHER 2.0, which represents a substantial update to STITCHER. STITCHER 2.0 is a newly designed web tool that automates the design of primers for overlapping PCR. Unlike STITCHER, STITCHER 2.0 considers diverse algorithmic parameters, and returns multiple result files that include a facility for the user to draw their own primers as well as comprehensive visual guides to the user’s input, output, and designed primers. These result files provide greater control and insight during experimental design and troubleshooting. STITCHER 2.0 is freely available to all users without signup or login requirements and can be accessed at the following webpage: www.ohalloranlab.net/STITCHER2.html. PMID:28358011
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STITCHER 2.0: primer design for overlapping PCR applications.
O'Halloran, Damien M; Uriagereka-Herburger, Isabel; Bode, Katrin
2017-03-30
Overlapping polymerase chain reaction (PCR) is a common technique used by researchers in very diverse fields that enables the user to 'stitch' individual pieces of DNA together. Previously, we have reported a web based tool called STITCHER that provides a platform for researchers to automate the design of primers for overlapping PCR applications. Here we present STITCHER 2.0, which represents a substantial update to STITCHER. STITCHER 2.0 is a newly designed web tool that automates the design of primers for overlapping PCR. Unlike STITCHER, STITCHER 2.0 considers diverse algorithmic parameters, and returns multiple result files that include a facility for the user to draw their own primers as well as comprehensive visual guides to the user's input, output, and designed primers. These result files provide greater control and insight during experimental design and troubleshooting. STITCHER 2.0 is freely available to all users without signup or login requirements and can be accessed at the following webpage: www.ohalloranlab.net/STITCHER2.html.
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Park, Jeongbin; Bae, Sangsu
2018-03-15
Following the type II CRISPR-Cas9 system, type V CRISPR-Cpf1 endonucleases have been found to be applicable for genome editing in various organisms in vivo. However, there are as yet no web-based tools capable of optimally selecting guide RNAs (gRNAs) among all possible genome-wide target sites. Here, we present Cpf1-Database, a genome-wide gRNA library design tool for LbCpf1 and AsCpf1, which have DNA recognition sequences of 5'-TTTN-3' at the 5' ends of target sites. Cpf1-Database provides a sophisticated but simple way to design gRNAs for AsCpf1 nucleases on the genome scale. One can easily access the data using a straightforward web interface, and using the powerful collections feature one can easily design gRNAs for thousands of genes in short time. Free access at http://www.rgenome.net/cpf1-database/. sangsubae@hanyang.ac.kr.
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A User-centered Model for Web Site Design
Kinzie, Mable B.; Cohn, Wendy F.; Julian, Marti F.; Knaus, William A.
2002-01-01
As the Internet continues to grow as a delivery medium for health information, the design of effective Web sites becomes increasingly important. In this paper, the authors provide an overview of one effective model for Web site design, a user-centered process that includes techniques for needs assessment, goal/task analysis, user interface design, and rapid prototyping. They detail how this approach was employed to design a family health history Web site, Health Heritage
. This Web site helps patients record and maintain their family health histories in a secure, confidential manner. It also supports primary care physicians through analysis of health histories, identification of potential risks, and provision of health care recommendations. Visual examples of the design process are provided to show how the use of this model resulted in an easy-to-use Web site that is likely to meet user needs. The model is effective across diverse content arenas and is appropriate for applications in varied media. PMID:12087113 -
[HyperPsych--resources for medicine and psychology on the World Wide Web].
Laszig, P
1997-07-01
Progress in the research of interactive communication technology and the acceleration of processing and transmitting information have promoted the development of computer networks allowing global access to scientific information and services. The recently most well-known net is the internet. Based on its integrative structure as a communication-directed as well as an information-directed medium, the internet helps researchers design scientific research. Especially medicine and psychology as information-dependent scientific disciplines may profit by using this technological offer. As a method to coordinate to the vast amount of medical and psychological data around the globe and to communicate with researchers world-wide, it enhances innovative possibilities for research, diagnosis and therapy. Currently, the World Wide Web is regarded as the most user-friendly and practical of all the internet resources. Based on a systematic introduction to the applications of the WWW, this article discusses relevant resources, points out possibilities and limits of network-supported scientific research and proposes many uses of this new medium.
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Antiretroviral treatment for HIV infection: Swedish recommendations 2016.
Eriksen, Jaran; Albert, Jan; Blaxhult, Anders; Carlander, Christina; Flamholc, Leo; Gisslén, Magnus; Josephson, Filip; Karlström, Olof; Navér, Lars; Svedhem, Veronica; Yilmaz, Aylin; Sönnerborg, Anders
2017-01-01
The Swedish Medical Products Agency and the Swedish Reference Group for Antiviral Therapy (RAV) have jointly published recommendations for the treatment of HIV infection on seven previous occasions (2002, 2003, 2005, 2007, 2009, 2011 and 2014). In February 2016, an expert group under the guidance of RAV once more revised the guidelines. The most important updates in the present guidelines are as follows: Tenofovir alafenamide (TAF) has recently been registered. TAF has several advantages over tenofovir disoproxilfumarate (TDF) and is recommended instead of TDF in most cases. First-line treatment for previously untreated individuals includes dolutegravir, boosted darunavir or efavirenz with either abacavir/lamivudine or tenofovir (TDF/TAF)/emtricitabine. Pre-exposure prophylaxis (PrEP) is recommended for high-risk individuals. As in the case of the previous publication, recommendations are evidence-graded in accordance with the Oxford Centre for Evidence Based Medicine ( http://www.cebm.net/oxford-centre-evidence-based-medicine-levels-evidence-march-2009/ ) ( Table 1 ). This document does not cover treatment of opportunistic infections and tumours. [Table: see text].
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Kumar, Sudhir; Stecher, Glen; Peterson, Daniel; Tamura, Koichiro
2012-10-15
There is a growing need in the research community to apply the molecular evolutionary genetics analysis (MEGA) software tool for batch processing a large number of datasets and to integrate it into analysis workflows. Therefore, we now make available the computing core of the MEGA software as a stand-alone executable (MEGA-CC), along with an analysis prototyper (MEGA-Proto). MEGA-CC provides users with access to all the computational analyses available through MEGA's graphical user interface version. This includes methods for multiple sequence alignment, substitution model selection, evolutionary distance estimation, phylogeny inference, substitution rate and pattern estimation, tests of natural selection and ancestral sequence inference. Additionally, we have upgraded the source code for phylogenetic analysis using the maximum likelihood methods for parallel execution on multiple processors and cores. Here, we describe MEGA-CC and outline the steps for using MEGA-CC in tandem with MEGA-Proto for iterative and automated data analysis. http://www.megasoftware.net/.
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Detrended Fluctuation Analysis: A Scale-Free View on Neuronal Oscillations
Hardstone, Richard; Poil, Simon-Shlomo; Schiavone, Giuseppina; Jansen, Rick; Nikulin, Vadim V.; Mansvelder, Huibert D.; Linkenkaer-Hansen, Klaus
2012-01-01
Recent years of research have shown that the complex temporal structure of ongoing oscillations is scale-free and characterized by long-range temporal correlations. Detrended fluctuation analysis (DFA) has proven particularly useful, revealing that genetic variation, normal development, or disease can lead to differences in the scale-free amplitude modulation of oscillations. Furthermore, amplitude dynamics is remarkably independent of the time-averaged oscillation power, indicating that the DFA provides unique insights into the functional organization of neuronal systems. To facilitate understanding and encourage wider use of scaling analysis of neuronal oscillations, we provide a pedagogical explanation of the DFA algorithm and its underlying theory. Practical advice on applying DFA to oscillations is supported by MATLAB scripts from the Neurophysiological Biomarker Toolbox (NBT) and links to the NBT tutorial website http://www.nbtwiki.net/. Finally, we provide a brief overview of insights derived from the application of DFA to ongoing oscillations in health and disease, and discuss the putative relevance of criticality for understanding the mechanism underlying scale-free modulation of oscillations. PMID:23226132
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Accessing wound-care information on the Internet: the implications for patients.
Bovill, E S; Hormbrey, E; Gillespie, P H; Banwell, P E
2001-02-01
The Internet and the World Wide Web have revolutionised communication and provide a unique forum for the exchange of information. It has been proposed that the Internet has given the public more access to medical information resources and improved patient education. This study assessed the impact of the Internet on the availability of information on wound care management. The search phrases 'wound care', 'wound healing' and 'wounds' were analysed using a powerful Metacrawler search engine (www.go2net.com). Web site access was classified according to the target audience (wound-care specialists, other health professionals, patients) and the author (societies, institutions or commercial companies). The largest proportion of web sites were commercially based (32%). Of the total number, 23% specifically targeted patients, mostly by advertising. Only 20% were aimed at wound specialists. Extensive surfing was required to obtain wound-care information, and objective information sites were under-represented. Regulated, easily accessible, objective information sites on wound-healing topics are needed for improved patient education and to balance the existing commercial bias.
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NASA Astrophysics Data System (ADS)
Jones, Bob; Casu, Francesco
2013-04-01
The feasibility of using commercial cloud services for scientific research is of great interest to research organisations such as CERN, ESA and EMBL, to the suppliers of cloud-based services and to the national and European funding agencies. Through the Helix Nebula - the Science Cloud [1] initiative and with the support of the European Commission, these stakeholders are driving a two year pilot-phase during which procurement processes and governance issues for a framework of public/private partnership will be appraised. Three initial flagship use cases from high energy physics, molecular biology and earth-observation are being used to validate the approach, enable a cost-benefit analysis to be undertaken and prepare the next stage of the Science Cloud Strategic Plan [2] to be developed and approved. The power of Helix Nebula lies in a shared set of services for initially 3 very different sciences each supporting a global community and thus building a common e-Science platform. Of particular relevance is the ESA sponsored flagship application SuperSites Exploitation Platform (SSEP [3]) that offers the global geo-hazard community a common platform for the correlation and processing of observation data for supersites monitoring. The US-NSF Earth Cube [4] and Ocean Observatory Initiative [5] (OOI) are taking a similar approach for data intensive science. The work of Helix Nebula and its recent architecture model [6] has shown that is it technically feasible to allow publicly funded infrastructures, such as EGI [7] and GEANT [8], to interoperate with commercial cloud services. Such hybrid systems are in the interest of the existing users of publicly funded infrastructures and funding agencies because they will provide "freedom of choice" over the type of computing resources to be consumed and the manner in which they can be obtained. But to offer such freedom-of choice across a spectrum of suppliers, various issues such as intellectual property, legal responsibility, service quality agreements and related issues need to be addressed. Investigating these issues is one of the goals of the Helix Nebula initiative. The next generation of researchers will put aside the historical categorisation of research as a neatly defined set of disciplines and integrate the data from different sources and instruments into complex models that are as applicable to earth observation or biomedicine as they are to high-energy physics. This aggregation of datasets and development of new models will accelerate scientific development but will only be possible if the issues of data intensive science described above are addressed. The culture of science has the possibility to develop with the availability of Helix Nebula as a "Science Cloud" because: • Large scale datasets from many disciplines will be accessible • Scientists and others will be able to develop and contribute open source tools to expand the set of services available • Collaboration of scientists will take place around the on-demand availability of data, tools and services • Cross-domain research will advance at a faster pace due to the availability of a common platform. References: 1 http://www.helix-nebula.eu/ 2 http://cdsweb.cern.ch/record/1374172/files/CERN-OPEN-2011-036.pdf 3 http://www.helix-nebula.eu/index.php/helix-nebula-use-cases/uc3.html 4 http://www.nsf.gov/geo/earthcube/ 5 http://www.oceanobservatories.org/ 6 http://cdsweb.cern.ch/record/1478364/files/HelixNebula-NOTE-2012-001.pdf 7 http://www.nsf.gov/geo/earthcube/ 8 http://www.geant.net/
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Fusarium culmorum: causal agent of foot and root rot and head blight on wheat.
Scherm, Barbara; Balmas, Virgilio; Spanu, Francesca; Pani, Giovanna; Delogu, Giovanna; Pasquali, Matias; Migheli, Quirico
2013-05-01
Fusarium culmorum is a ubiquitous soil-borne fungus able to cause foot and root rot and Fusarium head blight on different small-grain cereals, in particular wheat and barley. It causes significant yield and quality losses and results in contamination of the grain with mycotoxins. This review summarizes recent research activities related to F. culmorum, including studies into its population diversity, mycotoxin biosynthesis, mechanisms of pathogenesis and resistance, the development of diagnostic tools and preliminary genome sequence surveys. We also propose potential research areas that may expand our basic understanding of the wheat-F. culmorum interaction and assist in the management of the disease caused by this pathogen. Fusarium culmorum (W.G. Smith) Sacc. Kingdom Fungi; Phylum Ascomycota; Subphylum Pezizomycotina; Class Sordariomycetes; Subclass Hypocreomycetidae; Order Hypocreales; Family Nectriaceae; Genus Fusarium. Foot and root rot (also known as Fusarium crown rot): seedling blight with death of the plant before or after emergence; brown discoloration on roots and coleoptiles of the infected seedlings; brown discoloration on subcrown internodes and on the first two/three internodes of the main stem; tiller abortion; formation of whiteheads with shrivelled white grains; Fusarium head blight: prematurely bleached spikelets or blighting of the entire head, which remains empty or contains shrunken dark kernels. IDENTIFICATION AND DETECTION: Morphological identification is based on the shape of the macroconidia formed on sporodochia on carnation leaf agar. The conidiophores are branched monophialides, short and wide. The macroconidia are relatively short and stout with an apical cell blunt or slightly papillate; the basal cell is foot-shaped or just notched. Macroconidia are thick-walled and curved, usually 3-5 septate, and mostly measuring 30-50 × 5.0-7.5 μm. Microconidia are absent. Oval to globose chlamydospores are formed, intercalary in the hyphae, solitary, in chains or in clumps; they are also formed from macroconidia. The colony grows very rapidly (1.6-2.2 cm/day) on potato dextrose agar (PDA) at the optimum temperature of 25 °C. The mycelium on PDA is floccose, whitish, light yellow or red. The pigment on the reverse plate on PDA varies from greyish-rose, carmine red or burgundy. A wide array of polymerase chain reaction (PCR) and real-time PCR tools, as well as complementary methods, which are summarised in the first two tables, have been developed for the detection and/or quantification of F. culmorum in culture and in naturally infected plant tissue. Fusarium culmorum has a wide range of host plants, mainly cereals, such as wheat, barley, oats, rye, corn, sorghum and various grasses. In addition, it has been isolated from sugar beet, flax, carnation, bean, pea, asparagus, red clover, hop, leeks, Norway spruce, strawberry and potato tuber. Fusarium culmorum has also been associated with dermatitis on marram grass planters in the Netherlands, although its role as a causal agent of skin lesions appears questionable. It is also isolated as a symbiont able to confer resistance to abiotic stress, and has been proposed as a potential biocontrol agent to control the aquatic weed Hydrilla spp. http://isolate.fusariumdb.org/; http://sppadbase.ipp.cnr.it/; http://www.broad.mit.edu/annotation/genome/fusarium_group/MultiHome.html; http://www.fgsc.net/Fusarium/fushome.htm; http://plantpath.psu.edu/facilities/fusarium-research-center; http://www.phi-base.org/; http://www.uniprot.org/; http://www.cabi.org/; http://www.indexfungorum.org/ © 2012 BSPP AND BLACKWELL PUBLISHING LTD.
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Nielsen, Morten; Lundegaard, Claus; Blicher, Thomas; Lamberth, Kasper; Harndahl, Mikkel; Justesen, Sune; Røder, Gustav; Peters, Bjoern; Sette, Alessandro; Lund, Ole; Buus, Søren
2007-01-01
Background Binding of peptides to Major Histocompatibility Complex (MHC) molecules is the single most selective step in the recognition of pathogens by the cellular immune system. The human MHC class I system (HLA-I) is extremely polymorphic. The number of registered HLA-I molecules has now surpassed 1500. Characterizing the specificity of each separately would be a major undertaking. Principal Findings Here, we have drawn on a large database of known peptide-HLA-I interactions to develop a bioinformatics method, which takes both peptide and HLA sequence information into account, and generates quantitative predictions of the affinity of any peptide-HLA-I interaction. Prospective experimental validation of peptides predicted to bind to previously untested HLA-I molecules, cross-validation, and retrospective prediction of known HIV immune epitopes and endogenous presented peptides, all successfully validate this method. We further demonstrate that the method can be applied to perform a clustering analysis of MHC specificities and suggest using this clustering to select particularly informative novel MHC molecules for future biochemical and functional analysis. Conclusions Encompassing all HLA molecules, this high-throughput computational method lends itself to epitope searches that are not only genome- and pathogen-wide, but also HLA-wide. Thus, it offers a truly global analysis of immune responses supporting rational development of vaccines and immunotherapy. It also promises to provide new basic insights into HLA structure-function relationships. The method is available at http://www.cbs.dtu.dk/services/NetMHCpan. PMID:17726526
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Cravotta, Charles A.; Means, Brent P; Arthur, Willam; McKenzie, Robert M; Parkhurst, David L.
2015-01-01
Alkaline chemicals are commonly added to discharges from coal mines to increase pH and decrease concentrations of acidity and dissolved aluminum, iron, manganese, and associated metals. The annual cost of chemical treatment depends on the type and quantities of chemicals added and sludge produced. The AMDTreat computer program, initially developed in 2003, is widely used to compute such costs on the basis of the user-specified flow rate and water quality data for the untreated AMD. Although AMDTreat can use results of empirical titration of net-acidic or net-alkaline effluent with caustic chemicals to accurately estimate costs for treatment, such empirical data are rarely available. A titration simulation module using the geochemical program PHREEQC has been incorporated with AMDTreat 5.0+ to improve the capability of AMDTreat to estimate: (1) the quantity and cost of caustic chemicals to attain a target pH, (2) the chemical composition of the treated effluent, and (3) the volume of sludge produced by the treatment. The simulated titration results for selected caustic chemicals (NaOH, CaO, Ca(OH)2, Na2CO3, or NH3) without aeration or with pre-aeration can be compared with or used in place of empirical titration data to estimate chemical quantities, treated effluent composition, sludge volume (precipitated metals plus unreacted chemical), and associated treatment costs. This paper describes the development, evaluation, and potential utilization of the PHREEQC titration module with the new AMDTreat 5.0+ computer program available at http://www.amd.osmre.gov/.
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An application programming interface for CellNetAnalyzer.
Klamt, Steffen; von Kamp, Axel
2011-08-01
CellNetAnalyzer (CNA) is a MATLAB toolbox providing computational methods for studying structure and function of metabolic and cellular signaling networks. In order to allow non-experts to use these methods easily, CNA provides GUI-based interactive network maps as a means of parameter input and result visualization. However, with the availability of high-throughput data, there is a need to make CNA's functionality also accessible in batch mode for automatic data processing. Furthermore, as some algorithms of CNA are of general relevance for network analysis it would be desirable if they could be called as sub-routines by other applications. For this purpose, we developed an API (application programming interface) for CNA allowing users (i) to access the content of network models in CNA, (ii) to use CNA's network analysis capabilities independent of the GUI, and (iii) to interact with the GUI to facilitate the development of graphical plugins. Here we describe the organization of network projects in CNA and the application of the new API functions to these projects. This includes the creation of network projects from scratch, loading and saving of projects and scenarios, and the application of the actual analysis methods. Furthermore, API functions for the import/export of metabolic models in SBML format and for accessing the GUI are described. Lastly, two example applications demonstrate the use and versatile applicability of CNA's API. CNA is freely available for academic use and can be downloaded from http://www.mpi-magdeburg.mpg.de/projects/cna/cna.html. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.
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Water and CO2 Exchange for Different Land Use in Pampa Biome in Southern Brazil
NASA Astrophysics Data System (ADS)
Roberti, D. R.; de Moraes, O. L. L.; Diaz, M.; Tatsch, J. D.; Acevedo, O. C.; Zimermann, H. R.; Rubert, G. C.; Acosta, R.; Campos Velho, H. F.
2015-12-01
The Pampa is the newest and most unknown Brazilian Biome. It is located in the Southern portion of the country, as well as part of Argentina and the entire Uruguay, and is formed principally by natural grasslands that have been used for centuries for grazing livestock. In recent decades it has gone through a process of intense land use change and degradation, with the replacement of natural vegetation by rice paddy crops, soybean and exotic forests. Recent studies show that the Pampa has only 36% of its original vegetation in Brazil. Research on carbon and greenhouse gas emissions in Pampa Biome are recent. It is known that the Pampa natural areas contain high stocks of soil organic carbon, and therefore their conservation is relevant for climate change mitigation. However, the net exchange of carbon and water between the surface and the atmosphere are unknown. To fill this gap, a flux tower network, SULFLUX - www.ufsm.br/sulfux, was created. Currently, SULFLUX comprises three flux towers in the Pampa biome, two of them being over natural vegetation and the other one over a rice paddy. The flux towers are nearly 100 km apart from each other. We examine the effects of climate on carbon fluxes of through the year 2014. Analysis of temporal variability in water and CO2 fluxes are examined at daily to annual scales. Overall, regional variability in climatic drivers, land use and soil proprieties appears to have a greater effect on evapotranspiration than on net carbon exchange.
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The impact of tobacco taxes on mortality in the USA, 1970-2005.
Bowser, Diana; Canning, David; Okunogbe, Adeyemi
2016-01-01
This paper aimed to estimate the effect of tobacco taxes on total mortality and cause-specific mortality in the 50 States plus the District of Columbia, USA, over the period 1970-2005 as well as the net effect on deaths averted in 2010. We used a fixed effects panel regression to measure the impact of changes in total tobacco taxes on total and cause-specific mortality rates over the period 1970-2005, using a 5-year lag structure between changes in tobacco taxes and mortality rates. The estimates were used to determine the number of deaths averted in the year 2010 by tobacco tax increases over the period 1970-2005. Descriptive results showed that nominal total tobacco tax increased from US$0.18 in 1970 to US$1.24 in 2005, which after adjusting to 2005 US$, corresponds to an increase in real total tobacco tax from US$ 0.89 in 1970 to US$ 1.24 in 2005. We found that increases in total tobacco tax were beneficial, with a $1 increase in total tobacco tax decreasing overall mortality rate by 8.0%. Based on these results, we estimated a net saving of 53 300 lives in 2010 due to the tobacco tax changes over the period 1970-2005. Our results demonstrate that higher tobacco taxes lead to lower total mortality rates and avoided deaths. Strong tobacco tax policies are essential to improving overall population health. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/
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Global Ocean Currents Database
NASA Astrophysics Data System (ADS)
Boyer, T.; Sun, L.
2016-02-01
The NOAA's National Centers for Environmental Information has released an ocean currents database portal that aims 1) to integrate global ocean currents observations from a variety of instruments with different resolution, accuracy and response to spatial and temporal variability into a uniform network common data form (NetCDF) format and 2) to provide a dedicated online data discovery, access to NCEI-hosted and distributed data sources for ocean currents data. The portal provides a tailored web application that allows users to search for ocean currents data by platform types and spatial/temporal ranges of their interest. The dedicated web application is available at http://www.nodc.noaa.gov/gocd/index.html. The NetCDF format supports widely-used data access protocols and catalog services such as OPeNDAP (Open-source Project for a Network Data Access Protocol) and THREDDS (Thematic Real-time Environmental Distributed Data Services), which the GOCD users can use data files with their favorite analysis and visualization client software without downloading to their local machine. The potential users of the ocean currents database include, but are not limited to, 1) ocean modelers for their model skills assessments, 2) scientists and researchers for studying the impact of ocean circulations on the climate variability, 3) ocean shipping industry for safety navigation and finding optimal routes for ship fuel efficiency, 4) ocean resources managers while planning for the optimal sites for wastes and sewages dumping and for renewable hydro-kinematic energy, and 5) state and federal governments to provide historical (analyzed) ocean circulations as an aid for search and rescue
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Shital Kiran, D P; Bargale, Seema; Pandya, Parth; Bhatt, Kuntal; Barad, Nirav; Shah, Nilay; Venkataraghavan, Karthik; Ramesh, K
2015-08-01
The aim of this study was to evaluate the reliability of websites on the thumb sucking habit using DISCERN instrument and Health on the Net (HON) seal code at a single moment in time. An Internet search engine (www.google.com) was used to identify websites comprising information on "thumb sucking habit." Of over 204,000 links for thumb sucking habit, the first 100 were analyzed in detail. After excluding discussion groups, news and video feeds, and removing carbon copy sites, only 36 relevant websites remained, which were then assessed using the DISCERN instrument and HON seal code. Using the 16 questions of DISCERN for assessing the reliability and quality of the consumer information which were scored from 1 to 5, an appropriate index of the quality of the information was generated. All the assessed websites were also checked for presence or absence of HON seal code. The maximum score attainable for an outstanding website is 80. Of the 36 websites that were scored the highest score obtained by one of the websites according to the DISCERN tool was 55 of 80, and the lowest score achieved was 16 of 80. The websites achieving the maximum and minimum score were children.webmd.com and thebehaviorsolution.com, respectively. The HON seal was displayed only in three websites, which were medicinenet.com, righthealth.com, and children.webmd.com. By directing patients to validated websites on the thumb sucking habit, clinicians can ensure patients find appropriate information.
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Workflows for ingest of research data into digital archives - tests with Archivematica
NASA Astrophysics Data System (ADS)
Kirchner, I.; Bertelmann, R.; Gebauer, P.; Hasler, T.; Hirt, M.; Klump, J. F.; Peters-Kotting, W.; Rusch, B.; Ulbricht, D.
2013-12-01
Publication of research data and future re-use of measured data require the long-term preservation of digital objects. The ISO OAIS reference model defines responsibilities for long-term preservation of digital objects and although there is software available to support preservation of digital data, there are still problems remaining to be solved. A key task in preservation is to make the datasets ready for ingest into the archive, which is called the creation of Submission Information Packages (SIPs) in the OAIS model. This includes the creation of appropriate preservation metadata. Scientists need to be trained to deal with different types of data and to heighten their awareness for quality metadata. Other problems arise during the assembly of SIPs and during ingest into the archive because file format validators may produce conflicting output for identical data files and these conflicts are difficult to resolve automatically. Also, validation and identification tools are notorious for their poor performance. In the project EWIG Zuse-Institute Berlin acts as an infrastructure facility, while the Institute for Meteorology at FU Berlin and the German research Centre for Geosciences GFZ act as two different data producers. The aim of the project is to develop workflows for the transfer of research data into digital archives and the future re-use of data from long-term archives with emphasis on data from the geosciences. The technical work is supplemented by interviews with data practitioners at several institutions to identify problems in digital preservation workflows and by the development of university teaching materials to train students in the curation of research data and metadata. The free and open-source software Archivematica [1] is used as digital preservation system. The creation and ingest of SIPs has to meet several archival standards and be compatible to the Metadata Encoding and Transmission Standard (METS). The two data producers use different software in their workflows to test the assembly of SIPs and ingest of SIPs into the archive. GFZ Potsdam uses a combination of eSciDoc [2], panMetaDocs [3], and bagit [4] to collect research data and assemble SIPs for ingest into Archivematica, while the Institute for Meteorology at FU Berlin evaluates a variety of software solutions to describe data and publications and to generate SIPs. [1] http://www.archivematica.org [2] http://www.escidoc.org [3] http://panmetadocs.sf.net [4] http://sourceforge.net/projects/loc-xferutils/
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Partnerships University Partners Government Partners Industry Partners Ansys, Inc. www.ansys.com AVL North www.ncode.com Henkel North America www.henkel-northamerica.com Quantum Signal LLC www.quantumsignal.com RAMDO Solutions ramdosolutions.com Rolls-Royce North America www.rolls-royce.com Soar Technology www.soartech.com
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Oceanotron, Scalable Server for Marine Observations
NASA Astrophysics Data System (ADS)
Loubrieu, T.; Bregent, S.; Blower, J. D.; Griffiths, G.
2013-12-01
Ifremer, French marine institute, is deeply involved in data management for different ocean in-situ observation programs (ARGO, OceanSites, GOSUD, ...) or other European programs aiming at networking ocean in-situ observation data repositories (myOcean, seaDataNet, Emodnet). To capitalize the effort for implementing advance data dissemination services (visualization, download with subsetting) for these programs and generally speaking water-column observations repositories, Ifremer decided to develop the oceanotron server (2010). Knowing the diversity of data repository formats (RDBMS, netCDF, ODV, ...) and the temperamental nature of the standard interoperability interface profiles (OGC/WMS, OGC/WFS, OGC/SOS, OpeNDAP, ...), the server is designed to manage plugins: - StorageUnits : which enable to read specific data repository formats (netCDF/OceanSites, RDBMS schema, ODV binary format). - FrontDesks : which get external requests and send results for interoperable protocols (OGC/WMS, OGC/SOS, OpenDAP). In between a third type of plugin may be inserted: - TransformationUnits : which enable ocean business related transformation of the features (for example conversion of vertical coordinates from pressure in dB to meters under sea surface). The server is released under open-source license so that partners can develop their own plugins. Within MyOcean project, University of Reading has plugged a WMS implementation as an oceanotron frontdesk. The modules are connected together by sharing the same information model for marine observations (or sampling features: vertical profiles, point series and trajectories), dataset metadata and queries. The shared information model is based on OGC/Observation & Measurement and Unidata/Common Data Model initiatives. The model is implemented in java (http://www.ifremer.fr/isi/oceanotron/javadoc/). This inner-interoperability level enables to capitalize ocean business expertise in software development without being indentured to specific data formats or protocols. Oceanotron is deployed at seven European data centres for marine in-situ observations within myOcean. While additional extensions are still being developed, to promote new collaborative initiatives, a work is now done on continuous and distributed integration (jenkins, maven), shared reference documentation (on alfresco) and code and release dissemination (sourceforge, github).
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Warren-Gash, Charlotte; Bartley, Angela; Bayly, Jude; Dutey-Magni, Peter; Edwards, Sarah; Madge, Sara; Miller, Charlotte; Nicholas, Rachel; Radhakrishnan, Sheila; Sathia, Leena; Swarbrick, Helen; Blaikie, Dee; Rodger, Alison
2016-01-04
Domestic violence screening is advocated in some healthcare settings. Evidence that it increases referral to support agencies or improves health outcomes is limited. This study aimed to (1) investigate the proportion of hospital patients reporting domestic violence, (2) describe characteristics and previous hospital attendances of affected patients and (3) assess referrals to an in-house domestic violence advisor from Camden Safety Net. A series of observational studies. Three outpatient clinics at the Royal Free London NHS Foundation Trust. 10,158 patients screened for domestic violence in community gynaecology, genitourinary medicine (GUM) and HIV medicine clinics between 1 October 2013 and 30 June 2014. Also 2253 Camden Safety Net referrals over the same period. (1) Percentage reporting domestic violence by age group gender, ethnicity and clinic. (2) Rates of hospital attendances in the past 3 years for those screening positive and negative. (3) Characteristics, uptake and risk assessment results for hospital in-house domestic violence referrals compared with Camden Safety Net referrals from other sources. Of the 10,158 patients screened, 57.4% were female with a median age of 30 years. Overall, 7.1% reported ever-experiencing domestic violence, ranging from 5.7% in GUM to 29.4% in HIV services. People screening positive for domestic violence had higher rates of previous emergency department attendances (rate ratio (RR) 1.63, 95% CI 1.09 to 2.48), emergency inpatient admissions (RR 2.27, 95% CI 1.37 to 3.84) and day-case admissions (RR 2.03, 95% CI 1.23 to 3.43) than those screening negative. The 77 hospital referrals to the hospital-based domestic violence advisor during the study period were more likely to be taken up and to be classified as high risk than referrals from elsewhere. Selective screening for domestic violence in high-risk hospital clinic populations has the potential to identify affected patients and promote good uptake of referrals for in-house domestic violence support. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/
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Suarez-Almazor, M E; Kendall, C J; Dorgan, M
2001-01-01
In the past few years access to the Internet has become readily available. Patients are increasingly seeking and obtaining health information through the Internet, most often the World Wide Web (WWW). We assessed the content, authorship, and scope of the information available on WWW in relation to rheumatoid arthritis. In an attempt to replicate use by the average person, a broad search of the Internet was conducted for the phrase "rheumatoid arthritis" using WebCrawler, a commonly used search engine. All the "hits" were critically assessed after visiting and collecting information from the respective Web sites in relation to relevance, scope, authorship, type of publication, and financial objectives. The search returned 537 hits. We evaluated 531-2 did not exist, 2 could not be contacted, one was not in English, and one required a membership to access. The 531 hits originated from 388 Web sites. Only 198 (51%) were considered to be relevant and 7 (2%) were of doubtful relevance. Thirty-four (17%) were posted by an individual, 57 (28%) by a nonprofit organization, 104 (51%) by a profit industry, and 10 (5%) by universities. Ninety-one (44%) promoted alternative therapies, the most common including cetyl-myristoleate, colloidal minerals, Pycnogenol, shark cartilage, and Tahitian Noni. Of the 107 sites with financial interests, 76 (71%) promoted alternative medicine. The first 100 hits only identified about a third of the nonprofit organizations or university owned Web pages. Many sites easily accessed by consumers appear to be profit based companies advertising an alternative product claimed to be effective for many conditions. These findings emphasize the need for critical evaluation of Web site contents.
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NASA Astrophysics Data System (ADS)
Löptien, U.; Dietze, H.
2014-06-01
The Baltic Sea is a seasonally ice-covered, marginal sea, situated in central northern Europe. It is an essential waterway connecting highly industrialised countries. Because ship traffic is intermittently hindered by sea ice, the local weather services have been monitoring sea ice conditions for decades. In the present study we revisit a historical monitoring data set, covering the winters 1960/1961. This data set, dubbed Data Bank for Baltic Sea Ice and Sea Surface Temperatures (BASIS) ice, is based on hand-drawn maps that were collected and then digitised 1981 in a joint project of the Finnish Institute of Marine Research (today Finish Meteorological Institute (FMI)) and the Swedish Meteorological and Hydrological Institute (SMHI). BASIS ice was designed for storage on punch cards and all ice information is encoded by five digits. This makes the data hard to access. Here we present a post-processed product based on the original five-digit code. Specifically, we convert to standard ice quantities (including information on ice types), which we distribute in the current and free Network Common Data Format (NetCDF). Our post-processed data set will help to assess numerical ice models and provide easy-to-access unique historical reference material for sea ice in the Baltic Sea. In addition we provide statistics showcasing the data quality. The website www.baltic-ocean.org hosts the post-prossed data and the conversion code. The data are also archived at the Data Publisher for Earth & Environmental Science PANGEA (doi:10.1594/PANGEA.832353).
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NASA Astrophysics Data System (ADS)
Boulanger, Damien; Gautron, Benoit; Thouret, Valérie; Fontaine, Alain
2016-04-01
IAGOS (In-service Aircraft for a Global Observing System) is a European Research Infrastructure which aims at the provision of long-term, regular and spatially resolved in situ observations of the atmospheric composition. IAGOS observation systems are deployed on a fleet of commercial aircraft. The IAGOS database is an essential part of the global atmospheric monitoring network. It contains IAGOS-core data and IAGOS-CARIBIC (Civil Aircraft for the Regular Investigation of the Atmosphere Based on an Instrument Container) data. The IAGOS Database Portal (http://www.iagos.fr, damien.boulanger@obs-mip.fr) is part of the French atmospheric chemistry data center AERIS (http://www.aeris-data.fr). The new IAGOS Database Portal has been released in December 2015. The main improvement is the interoperability implementation with international portals or other databases in order to improve IAGOS data discovery. In the frame of the IGAS project (IAGOS for the Copernicus Atmospheric Service), a data network has been setup. It is composed of three data centers: the IAGOS database in Toulouse; the HALO research aircraft database at DLR (https://halo-db.pa.op.dlr.de); and the CAMS data center in Jülich (http://join.iek.fz-juelich.de). The CAMS (Copernicus Atmospheric Monitoring Service) project is a prominent user of the IGAS data network. The new portal provides improved and new services such as the download in NetCDF or NASA Ames formats, plotting tools (maps, time series, vertical profiles, etc.) and user management. Added value products are available on the portal: back trajectories, origin of air masses, co-location with satellite data, etc. The link with the CAMS data center, through JOIN (Jülich OWS Interface), allows to combine model outputs with IAGOS data for inter-comparison. Finally IAGOS metadata has been standardized (ISO 19115) and now provides complete information about data traceability and quality.
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Hosting an `Ask the Astronomer' Site on the Internet
NASA Astrophysics Data System (ADS)
Odenwald, S. F.
1996-12-01
Since 1995, the World Wide Web has explosively evolved into a significant medium for dispensing astronomical information to the general public. In addition to the numerous image archives that have proliferated, an increasing number of sites invite visitors to pose questions about astronomy and receive answers provided by professional astronomers. In this paper, I describe the operation of an Ask the Astronomer site that was opened on the WWW during August, 1995 as part of an astronomy education resource area called the "Astronomy Cafe" (URL=http://www2.ari.net/home/odenwald/cafe.html). The Astronomy Cafe includes a number of documents describing: a career in astronomy; how research papers are written; essays about cosmology, hyperspace and infrared astronomy; and the results from a 100-question, just for fun, personality test which distinguishes astronomers from non-astronomers. The Ask the Astronomer site is operated by a single astronomer through private donations and is now approaching its 500th day of operation. It contains over 2000+ questions and answers with a growth rate of 5 - 10 questions per day. It has attracted 70,000 visitors who are responsible for nearly 1 million 'hits' during the site's lifetime. The monthly statistics provide a unique survey of the kinds of individuals and organizations who visit Ask the Astronomer-type web sites, moreover, the accumulated questions provide a diagnostic X-ray into the public mind in the area of astronomy. I will present an analysis of the user demographics, and the types of questions that appear to be the most frequently asked. A paper copy of the complete index of these questions will be available for inspection.
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Hyporheic network (Hyporheisches Netzwerk)
NASA Astrophysics Data System (ADS)
Lewandowski, J.; Fleckenstein, J.; Hoehn, E.; Nützmann, G.; Radke, M.; Saenger, N.; Schmidt, C.
2009-04-01
The transition zone between surface waters like streams and rivers and the adjacent aquifers is a zone of paramount ecological importance. Due to the complexity of exchange processes, their temporal variability, and the spatial heterogeneity of the ecotone, the understanding and ability to modell the hydrodynamic, hydrochemical, and (micro-)biological processes is still limited. Therefore, a network of scientists and practitioners involved in research and management of hyporheic zones in German-speaking countries (Germany, Switzerland, Austria) is propsed in analogy to the hyporheic network (www.hyporheic.net) in the UK. The initiators of the network anticipate that an intense scientific exchange of knowledge and methods will improve our understanding of hyporheic processes and in turn our ability to manage them. The network will facilitate the formation of research groups to identify and understand key processes and their interactions. Research will be focused at a few major study sites, to bring together different expertise to allow more detailed, interdisciplinary investigations. Those sites can serve as crystallisation points for new research projects. Exchange within the network will be organized via an internet platform (www.hyporheisches-netzwerk.de), regular workshops, and several working groups dealing with different topics. A fast knowledge transfer is a further aim of the collaboration in order to shorten the time-lag between scientific findings and their implementation into management practice. Water resources management authorities should also be involved in the network to address urgent problems and direct some capacities to answer those questions. For instance, changes in geomorphology, water and temperature regimes as well as other anthropogenic impacts might increase the need for cold water refugia and altered flow regimes to maintain biodiversity. Additional qualitative improvements are required by the EU water framework directive.
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An integrative approach to ortholog prediction for disease-focused and other functional studies.
Hu, Yanhui; Flockhart, Ian; Vinayagam, Arunachalam; Bergwitz, Clemens; Berger, Bonnie; Perrimon, Norbert; Mohr, Stephanie E
2011-08-31
Mapping of orthologous genes among species serves an important role in functional genomics by allowing researchers to develop hypotheses about gene function in one species based on what is known about the functions of orthologs in other species. Several tools for predicting orthologous gene relationships are available. However, these tools can give different results and identification of predicted orthologs is not always straightforward. We report a simple but effective tool, the Drosophila RNAi Screening Center Integrative Ortholog Prediction Tool (DIOPT; http://www.flyrnai.org/diopt), for rapid identification of orthologs. DIOPT integrates existing approaches, facilitating rapid identification of orthologs among human, mouse, zebrafish, C. elegans, Drosophila, and S. cerevisiae. As compared to individual tools, DIOPT shows increased sensitivity with only a modest decrease in specificity. Moreover, the flexibility built into the DIOPT graphical user interface allows researchers with different goals to appropriately 'cast a wide net' or limit results to highest confidence predictions. DIOPT also displays protein and domain alignments, including percent amino acid identity, for predicted ortholog pairs. This helps users identify the most appropriate matches among multiple possible orthologs. To facilitate using model organisms for functional analysis of human disease-associated genes, we used DIOPT to predict high-confidence orthologs of disease genes in Online Mendelian Inheritance in Man (OMIM) and genes in genome-wide association study (GWAS) data sets. The results are accessible through the DIOPT diseases and traits query tool (DIOPT-DIST; http://www.flyrnai.org/diopt-dist). DIOPT and DIOPT-DIST are useful resources for researchers working with model organisms, especially those who are interested in exploiting model organisms such as Drosophila to study the functions of human disease genes.
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Development and implementation of an Integrated Water Resources Management System (IWRMS)
NASA Astrophysics Data System (ADS)
Flügel, W.-A.; Busch, C.
2011-04-01
One of the innovative objectives in the EC project BRAHMATWINN was the development of a stakeholder oriented Integrated Water Resources Management System (IWRMS). The toolset integrates the findings of the project and presents it in a user friendly way for decision support in sustainable integrated water resources management (IWRM) in river basins. IWRMS is a framework, which integrates different types of basin information and which supports the development of IWRM options for climate change mitigation. It is based on the River Basin Information System (RBIS) data models and delivers a graphical user interface for stakeholders. A special interface was developed for the integration of the enhanced DANUBIA model input and the NetSyMod model with its Mulino decision support system (mulino mDss) component. The web based IWRMS contains and combines different types of data and methods to provide river basin data and information for decision support. IWRMS is based on a three tier software framework which uses (i) html/javascript at the client tier, (ii) PHP programming language to realize the application tier, and (iii) a postgresql/postgis database tier to manage and storage all data, except the DANUBIA modelling raw data, which are file based and registered in the database tier. All three tiers can reside on one or different computers and are adapted to the local hardware infrastructure. IWRMS as well as RBIS are based on Open Source Software (OSS) components and flexible and time saving access to that database is guaranteed by web-based interfaces for data visualization and retrieval. The IWRMS is accessible via the BRAHMATWINN homepage: http://www.brahmatwinn.uni-jena.de and a user manual for the RBIS is available for download as well.
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Does Tropical Cyclone Modification Make Sense? A Decision-Analytic Assessment
NASA Astrophysics Data System (ADS)
Klima, K.; Morgan, M. G.; Grossmann, I.
2009-12-01
Since the demise of project Stormfury in 1983, little attention has been devoted to the possibility of intentionally modifying tropical cyclones (TC). However, following Hurricane Katrina and three other Category 5 hurricanes (Emily, Rita, and Wilma), which together resulted in at least 2,280 deaths and over $120-billion in damages (Blake et al., 2007), the U.S. Department of Homeland Security (DHS) has recently begun to support an effort to identify and evaluate hurricane mitigation strategies through Project HURRMIT ([http://www.ofcm.noaa.gov/ihc09/Presentations/Session10/s10-01Woodley.ppt]). Using a decision analytic framing and FEMA's HAZUS-MH MR3 damage model (http://www.fema.gov/plan/prevent/hazus/]), this paper asks, how sure must one be that an intervention will reduce TC damages before choosing to undertake a program of modification? The analysis is formulated in probabilistic terms, and assesses net benefits. In contrast to a much earlier application of decision analysis to TC-modification (Howard et al., 1972) , this work uses census data on the value of property at risk, and prior distributions on changing storm behavior based on data from hurricanes approaching the east coast of Florida since 1953. Even before considering both issues of liability that may arise from the fact that a modified storm is no longer "an act of God" as well as unforeseen environmental consequences, our results suggest that while TC modification techniques will likely alter TC behavior, one will have to be significantly more confident of the predictability and effectiveness of modification methods before their use can be justified. This work is supported by the Climate Decision Making Center through a cooperative agreement between the National Science Foundation (SES-0345798) and Carnegie Mellon University.
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Technical Data Exchange Software Tools Adapted to Distributed Microsatellite Design
NASA Astrophysics Data System (ADS)
Pache, Charly
2002-01-01
One critical issue concerning distributed design of satellites, is the collaborative work it requires. In particular, the exchange of data between each group responsible for each subsystem can be complex and very time-consuming. The goal of this paper is to present a design collaborative tool, the SSETI Design Model (SDM), specifically developed for enabling satellite distributed design. SDM is actually used in the ongoing Student Space Exploration &Technology (SSETI) initiative (www.sseti.net). SSETI is lead by European Space Agency (ESA) outreach office (http://www.estec.esa.nl/outreach), involving student groups from all over Europe for design, construction and launch of a microsatellite. The first part of this paper presents the current version of the SDM tool, a collection of Microsoft Excel linked worksheets, one for each subsystem. An overview of the project framework/structure is given, explaining the different actors, the flows between them, as well as the different types of data and the links - formulas - between data sets. Unified Modeling Language (UML) diagrams give an overview of the different parts . Then the SDM's functionalities, developed in VBA scripts (Visual Basic for Application), are introduced, as well as the interactive features, user interfaces and administration tools. The second part discusses the capabilities and limitations of SDM current version. Taking into account these capabilities and limitations, the third part outlines the next version of SDM, a web-oriented, database-driven evolution of the current version. This new approach will enable real-time data exchange and processing between the different actors of the mission. Comprehensive UML diagrams will guide the audience through the entire modeling process of such a system. Tradeoffs simulation capabilities, security, reliability, hardware and software issues will also be thoroughly discussed.
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Exploratory visualization of earth science data in a Semantic Web context
NASA Astrophysics Data System (ADS)
Ma, X.; Fox, P. A.
2012-12-01
Earth science data are increasingly unlocked from their local 'safes' and shared online with the global science community as well as the average citizen. The European Union (EU)-funded project OneGeology-Europe (1G-E, www.onegeology-europe.eu) is a typical project that promotes works in that direction. The 1G-E web portal provides easy access to distributed geological data resources across participating EU member states. Similar projects can also be found in other countries or regions, such as the geoscience information network USGIN (www.usgin.org) in United States, the groundwater information network GIN-RIES (www.gw-info.net) in Canada and the earth science infrastructure AuScope (www.auscope.org.au) in Australia. While data are increasingly made available online, we currently face a shortage of tools and services that support information and knowledge discovery with such data. One reason is that earth science data are recorded in professional language and terms, and people without background knowledge cannot understand their meanings well. The Semantic Web provides a new context to help computers as well as users to better understand meanings of data and conduct applications. In this study we aim to chain up Semantic Web technologies (e.g., vocabularies/ontologies and reasoning), data visualization (e.g., an animation underpinned by an ontology) and online earth science data (e.g., available as Web Map Service) to develop functions for information and knowledge discovery. We carried out a case study with data of the 1G-E project. We set up an ontology of geological time scale using the encoding languages of SKOS (Simple Knowledge Organization System) and OWL (Web Ontology Language) from W3C (World Wide Web Consortium, www.w3.org). Then we developed a Flash animation of geological time scale by using the ActionScript language. The animation is underpinned by the ontology and the interrelationships between concepts of geological time scale are visualized in the animation. We linked the animation and the ontology to the online geological data of 1G-E project and developed interactive applications. The animation was used to show legends of rock age layers in geological maps dynamically. In turn, these legends were used as control panels to filter out and generalize geospatial features of certain rock ages on map layers. We tested the functions with maps of various EU member states. As a part of the initial results, legends for rock age layers of EU individual national maps were generated respectively, and the functions for filtering and generalization were examined with the map of United Kingdom. Though new challenges are rising in the tests, like those caused by synonyms (e.g., 'Lower Cambrian' and 'Terreneuvian'), the initial results achieved the designed goals of information and knowledge discovery by using the ontology-underpinned animation. This study shows that (1) visualization lowers the barrier of ontologies, (2) integrating ontologies and visualization adds value to online earth science data services, and (3) exploratory visualization supports the procedure of data processing as well as the display of results.
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NASA Astrophysics Data System (ADS)
Schaap, Dick M. A.; Maudire, Gilbert
2010-05-01
SeaDataNet is a leading infrastructure in Europe for marine & ocean data management. It is actively operating and further developing a Pan-European infrastructure for managing, indexing and providing access to ocean and marine data sets and data products, acquired via research cruises and other observational activities, in situ and remote sensing. The basis of SeaDataNet is interconnecting 40 National Oceanographic Data Centres and Marine Data Centers from 35 countries around European seas into a distributed network of data resources with common standards for metadata, vocabularies, data transport formats, quality control methods and flags, and access. Thereby most of the NODC's operate and/or are developing national networks to other institutes in their countries to ensure national coverage and long-term stewardship of available data sets. The majority of data managed by SeaDataNet partners concerns physical oceanography, marine chemistry, hydrography, and a substantial volume of marine biology and geology and geophysics. These are partly owned by the partner institutes themselves and for a major part also owned by other organizations from their countries. The SeaDataNet infrastructure is implemented with support of the EU via the EU FP6 SeaDataNet project to provide the Pan-European data management system adapted both to the fragmented observation system and the users need for an integrated access to data, meta-data, products and services. The SeaDataNet project has a duration of 5 years and started in 2006, but builds upon earlier data management infrastructure projects, undertaken over a period of 20 years by an expanding network of oceanographic data centres from the countries around all European seas. Its predecessor project Sea-Search had a strict focus on metadata. SeaDataNet maintains significant interest in the further development of the metadata infrastructure, extending its services with the provision of easy data access and generic data products. Version 1 of its infrastructure upgrade was launched in April 2008 and is now well underway to include all 40 data centres at V1 level. It comprises the network of 40 interconnected data centres (NODCs) and a central SeaDataNet portal. V1 provides users a unified and transparent overview of the metadata and controlled access to the large collections of data sets, that are managed at these data centres. The SeaDataNet V1 infrastructure comprises the following middleware services: • Discovery services = Metadata directories and User interfaces • Vocabulary services = Common vocabularies and Governance • Security services = Authentication, Authorization & Accounting • Delivery services = Requesting and Downloading of data sets • Viewing services = Mapping of metadata • Monitoring services = Statistics on system usage and performance and Registration of data requests and transactions • Maintenance services = Entry and updating of metadata by data centres Also good progress is being made with extending the SeaDataNet infrastructure with V2 services: • Viewing services = Quick views and Visualisation of data and data products • Product services = Generic and standard products • Exchange services = transformation of SeaDataNet portal CDI output to INSPIRE compliance As a basis for the V1 services, common standards have been defined for metadata and data formats, common vocabularies, quality flags, and quality control methods, based on international standards, such as ISO 19115, OGC, NetCDF (CF), ODV, best practices from IOC and ICES, and following INSPIRE developments. An important objective of the SeaDataNet V1 infrastructure is to provide transparent access to the distributed data sets via a unique user interface and download service. In the SeaDataNet V1 architecture the Common Data Index (CDI) V1 metadata service provides the link between discovery and delivery of data sets. The CDI user interface enables users to have a detailed insight of the availability and geographical distribution of marine data, archived at the connected data centres. It provides sufficient information to allow the user to assess the data relevance. Moreover the CDI user interface provides the means for downloading data sets in common formats via a transaction mechanism. The SeaDataNet portal provides registered users access to these distributed data sets via the CDI V1 Directory and a shopping basket mechanism. This allows registered users to locate data of interest and submit their data requests. The requests are forwarded automatically from the portal to the relevant SeaDataNet data centres. This process is controlled via the Request Status Manager (RSM) Web Service at the portal and a Download Manager (DM) java software module, implemented at each of the data centres. The RSM also enables registered users to check regularly the status of their requests and download data sets, after access has been granted. Data centres can follow all transactions for their data sets online and can handle requests which require their consent. The actual delivery of data sets is done between the user and the selected data centre. Very good progress is being made with connecting all SeaDataNet data centres and their data sets to the CDI V1 system. At present the CDI V1 system provides users functionality to discover and download more than 500.000 data sets, a number which is steadily increasing. The SeaDataNet architecture provides a coherent system of the various V1 services and inclusion of the V2 services. For the implementation, a range of technical components have been defined and developed. These make use of recent web technologies, and also comprise Java components, to provide multi-platform support and syntactic interoperability. To facilitate sharing of resources and interoperability, SeaDataNet has adopted the technology of SOAP Web services for various communication tasks. The SeaDataNet architecture has been designed as a multi-disciplinary system from the beginning. It is able to support a wide variety of data types and to serve several sector communities. SeaDataNet is willing to share its technologies and expertise, to spread and expand its approach, and to build bridges to other well established infrastructures in the marine domain. Therefore SeaDataNet has developed a strategy of seeking active cooperation on a national scale with other data holding organisations via its NODC networks and on an international scale with other European and international data management initiatives and networks. This is done with the objective to achieve a wider coverage of data sources and an overall interoperability between data infrastructures in the marine and ocean domains. Recent examples are e.g. the EU FP7 projects Geo-Seas for geology and geophysical data sets, UpgradeBlackSeaScene for a Black Sea data management infrastructure, CaspInfo for a Caspian Sea data management infrastructure, the EU EMODNET pilot projects, for hydrographic, chemical, and biological data sets. All projects are adopting the SeaDataNet standards and extending its services. Also active cooperation takes place with EuroGOOS and MyOcean in the domain of real-time and delayed mode metocean monitoring data. SeaDataNet Partners: IFREMER (France), MARIS (Netherlands), HCMR/HNODC (Greece), ULg (Belgium), OGS (Italy), NERC/BODC (UK), BSH/DOD (Germany), SMHI (Sweden), IEO (Spain), RIHMI/WDC (Russia), IOC (International), ENEA (Italy), INGV (Italy), METU (Turkey), CLS (France), AWI (Germany), IMR (Norway), NERI (Denmark), ICES (International), EC-DG JRC (International), MI (Ireland), IHPT (Portugal), RIKZ (Netherlands), RBINS/MUMM (Belgium), VLIZ (Belgium), MRI (Iceland), FIMR (Finland ), IMGW (Poland), MSI (Estonia), IAE/UL (Latvia), CMR (Lithuania), SIO/RAS (Russia), MHI/DMIST (Ukraine), IO/BAS (Bulgaria), NIMRD (Romania), TSU (Georgia), INRH (Morocco), IOF (Croatia), PUT (Albania), NIB (Slovenia), UoM (Malta), OC/UCY (Cyprus), IOLR (Israel), NCSR/NCMS (Lebanon), CNR-ISAC (Italy), ISMAL (Algeria), INSTM (Tunisia)
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NASA Astrophysics Data System (ADS)
Vukics, András
2012-06-01
C++QED is a versatile framework for simulating open quantum dynamics. It allows to build arbitrarily complex quantum systems from elementary free subsystems and interactions, and simulate their time evolution with the available time-evolution drivers. Through this framework, we introduce a design which should be generic for high-level representations of composite quantum systems. It relies heavily on the object-oriented and generic programming paradigms on one hand, and on the other hand, compile-time algorithms, in particular C++ template-metaprogramming techniques. The core of the design is the data structure which represents the state vectors of composite quantum systems. This data structure models the multi-array concept. The use of template metaprogramming is not only crucial to the design, but with its use all computations pertaining to the layout of the simulated system can be shifted to compile time, hence cutting on runtime. Program summaryProgram title: C++QED Catalogue identifier: AELU_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AELU_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions:http://cpc.cs.qub.ac.uk/licence/aelu_v1_0.html. The C++QED package contains other software packages, Blitz, Boost and FLENS, all of which may be distributed freely but have individual license requirements. Please see individual packages for license conditions. No. of lines in distributed program, including test data, etc.: 597 974 No. of bytes in distributed program, including test data, etc.: 4 874 839 Distribution format: tar.gz Programming language: C++ Computer: i386-i686, x86_64 Operating system: In principle cross-platform, as yet tested only on UNIX-like systems (including Mac OS X). RAM: The framework itself takes about 60 MB, which is fully shared. The additional memory taken by the program which defines the actual physical system (script) is typically less than 1 MB. The memory storing the actual data scales with the system dimension for state-vector manipulations, and the square of the dimension for density-operator manipulations. This might easily be GBs, and often the memory of the machine limits the size of the simulated system. Classification: 4.3, 4.13, 6.2, 20 External routines: Boost C++ libraries (http://www.boost.org/), GNU Scientific Library (http://www.gnu.org/software/gsl/), Blitz++ (http://www.oonumerics.org/blitz/), Linear Algebra Package - Flexible Library for Efficient Numerical Solutions (http://flens.sourceforge.net/). Nature of problem: Definition of (open) composite quantum systems out of elementary building blocks [1]. Manipulation of such systems, with emphasis on dynamical simulations such as Master-equation evolution [2] and Monte Carlo wave-function simulation [3]. Solution method: Master equation, Monte Carlo wave-function method. Restrictions: Total dimensionality of the system. Master equation - few thousands. Monte Carlo wave-function trajectory - several millions. Unusual features: Because of the heavy use of compile-time algorithms, compilation of programs written in the framework may take a long time and much memory (up to several GBs). Additional comments: The framework is not a program, but provides and implements an application-programming interface for developing simulations in the indicated problem domain. Supplementary information: http://cppqed.sourceforge.net/. Running time: Depending on the magnitude of the problem, can vary from a few seconds to weeks.
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NASA Astrophysics Data System (ADS)
Schaap, D. M. A.; Maudire, G.
2009-04-01
SeaDataNet is an Integrated research Infrastructure Initiative (I3) in EU FP6 (2006 - 2011) to provide the data management system adapted both to the fragmented observation system and the users need for an integrated access to data, meta-data, products and services. Therefore SeaDataNet insures the long term archiving of the large number of multidisciplinary data (i.e. temperature, salinity current, sea level, chemical, physical and biological properties) collected by many different sensors installed on board of research vessels, satellite and the various platforms of the marine observing system. The SeaDataNet project started in 2006, but builds upon earlier data management infrastructure projects, undertaken over a period of 20 years by an expanding network of oceanographic data centres from the countries around all European seas. Its predecessor project Sea-Search had a strict focus on metadata. SeaDataNet maintains significant interest in the further development of the metadata infrastructure, but its primary objective is the provision of easy data access and generic data products. SeaDataNet is a distributed infrastructure that provides transnational access to marine data, meta-data, products and services through 40 interconnected Trans National Data Access Platforms (TAP) from 35 countries around the Black Sea, Mediterranean, North East Atlantic, North Sea, Baltic and Arctic regions. These include: National Oceanographic Data Centres (NODC's) Satellite Data Centres. Furthermore the SeaDataNet consortium comprises a number of expert modelling centres, SME's experts in IT, and 3 international bodies (ICES, IOC and JRC). Planning: The SeaDataNet project is delivering and operating the infrastructure in 3 versions: Version 0: maintenance and further development of the metadata systems developed by the Sea-Search project plus the development of a new metadata system for indexing and accessing to individual data objects managed by the SeaDataNet data centres. This is known as the Common Data Index (CDI) V0 system Version 1: harmonisation and upgrading of the metadatabases through adoption of the ISO 19115 metadata standard and provision of transparent data access and download services from all partner data centres through upgrading the Common Data Index and deployment of a data object delivery service. Version 2: adding data product services and OGC compliant viewing services and further virtualisation of data access. SeaDataNet Version 0: The SeaDataNet portal has been set up at http://www.seadatanet.org and it provides a platform for all SeaDataNet services and standards as well as background information about the project and its partners. It includes discovery services via the following catalogues: CSR - Cruise Summary Reports of research vessels; EDIOS - Locations and details of monitoring stations and networks / programmes; EDMED - High level inventory of Marine Environmental Data sets collected and managed by research institutes and organisations; EDMERP - Marine Environmental Research Projects ; EDMO - Marine Organisations. These catalogues are interrelated, where possible, to facilitate cross searching and context searching. These catalogues connect to the Common Data Index (CDI). Common Data Index (CDI) The CDI gives detailed insight in available datasets at partners databases and paves the way to direct online data access or direct online requests for data access / data delivery. The CDI V0 metadatabase contains more than 340.000 individual data entries from 36 CDI partners from 29 countries across Europe, covering a broad scope and range of data, held by these organisations. For purposes of standardisation and international exchange the ISO19115 metadata standard has been adopted. The CDI format is defined as a dedicated subset of this standard. A CDI XML format supports the exchange between CDI-partners and the central CDI manager, and ensures interoperability with other systems and networks. CDI XML entries are generated by participating data centres, directly from their databases. CDI-partners can make use of dedicated SeaDataNet Tools to generate CDI XML files automatically. Approach for SeaDataNet V1 and V2: The approach for SeaDataNet V1 and V2, which is in line with the INSPIRE Directive, comprises the following services: Discovery services = Metadata directories Security services = Authentication, Authorization & Accounting (AAA) Delivery services = Data access & downloading of datasets Viewing services = Visualisation of metadata, data and data products Product services = Generic and standard products Monitoring services = Statistics on usage and performance of the system Maintenance services = Updating of metadata by SeaDataNet partners The services will be operated over a distributed network of interconnected Data Centres accessed through a central Portal. In addition to service access the portal will provide information on data management standards, tools and protocols. The architecture has been designed to provide a coherent system based on V1 services, whilst leaving the pathway open for later extension with V2 services. For the implementation, a range of technical components have been defined. Some are already operational with the remainder in the final stages of development and testing. These make use of recent web technologies, and also comprise Java components, to provide multi-platform support and syntactic interoperability. To facilitate sharing of resources and interoperability, SeaDataNet has adopted SOAP Web Service technology. The SeaDataNet architecture and components have been designed to handle all kinds of oceanographic and marine environmental data including both in-situ measurements and remote sensing observations. The V1 technical development is ready and the V1 system is now being implemented and adopted by all participating data centres in SeaDataNet. Interoperability: Interoperability is the key to distributed data management system success and it is achieved in SeaDataNet V1 by: Using common quality control protocols and flag scale Using controlled vocabularies from a single source that have been developed using international content governance Adopting the ISO 19115 metadata standard for all metadata directories Providing XML Validation Services to quality control the metadata maintenance, including field content verification based on Schematron. Providing standard metadata entry tools Using harmonised Data Transport Formats (NetCDF, ODV ASCII and MedAtlas ASCII) for data sets delivery Adopting of OGC standards for mapping and viewing services Using SOAP Web Services in the SeaDataNet architecture SeaDataNet V1 Delivery Services: An important objective of the V1 system is to provide transparent access to the distributed data sets via a unique user interface at the SeaDataNet portal and download service. In the SeaDataNet V1 architecture the Common Data Index (CDI) V1 provides the link between discovery and delivery. The CDI user interface enables users to have a detailed insight of the availability and geographical distribution of marine data, archived at the connected data centres, and it provides the means for downloading data sets in common formats via a transaction mechanism. The SeaDataNet portal provides registered users access to these distributed data sets via the CDI V1 Directory and a shopping basket mechanism. This allows registered users to locate data of interest and submit their data requests. The requests are forwarded automatically from the portal to the relevant SeaDataNet data centres. This process is controlled via the Request Status Manager (RSM) Web Service at the portal and a Download Manager (DM) java software module, implemented at each of the data centres. The RSM also enables registered users to check regularly the status of their requests and download data sets, after access has been granted. Data centres can follow all transactions for their data sets online and can handle requests which require their consent. The actual delivery of data sets is done between the user and the selected data centre. The CDI V1 system is now being populated by all participating data centres in SeaDataNet, thereby phasing out CDI V0. 0.1 SeaDataNet Partners: IFREMER (France), MARIS (Netherlands), HCMR/HNODC (Greece), ULg (Belgium), OGS (Italy), NERC/BODC (UK), BSH/DOD (Germany), SMHI (Sweden), IEO (Spain), RIHMI/WDC (Russia), IOC (International), ENEA (Italy), INGV (Italy), METU (Turkey), CLS (France), AWI (Germany), IMR (Norway), NERI (Denmark), ICES (International), EC-DG JRC (International), MI (Ireland), IHPT (Portugal), RIKZ (Netherlands), RBINS/MUMM (Belgium), VLIZ (Belgium), MRI (Iceland), FIMR (Finland ), IMGW (Poland), MSI (Estonia), IAE/UL (Latvia), CMR (Lithuania), SIO/RAS (Russia), MHI/DMIST (Ukraine), IO/BAS (Bulgaria), NIMRD (Romania), TSU (Georgia), INRH (Morocco), IOF (Croatia), PUT (Albania), NIB (Slovenia), UoM (Malta), OC/UCY (Cyprus), IOLR (Israel), NCSR/NCMS (Lebanon), CNR-ISAC (Italy), ISMAL (Algeria), INSTM (Tunisia)
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Papatheodorou, Irene; Ziehm, Matthias; Wieser, Daniela; Alic, Nazif; Partridge, Linda; Thornton, Janet M.
2012-01-01
A challenge of systems biology is to integrate incomplete knowledge on pathways with existing experimental data sets and relate these to measured phenotypes. Research on ageing often generates such incomplete data, creating difficulties in integrating RNA expression with information about biological processes and the phenotypes of ageing, including longevity. Here, we develop a logic-based method that employs Answer Set Programming, and use it to infer signalling effects of genetic perturbations, based on a model of the insulin signalling pathway. We apply our method to RNA expression data from Drosophila mutants in the insulin pathway that alter lifespan, in a foxo dependent fashion. We use this information to deduce how the pathway influences lifespan in the mutant animals. We also develop a method for inferring the largest common sub-paths within each of our signalling predictions. Our comparisons reveal consistent homeostatic mechanisms across both long- and short-lived mutants. The transcriptional changes observed in each mutation usually provide negative feedback to signalling predicted for that mutation. We also identify an S6K-mediated feedback in two long-lived mutants that suggests a crosstalk between these pathways in mutants of the insulin pathway, in vivo. By formulating the problem as a logic-based theory in a qualitative fashion, we are able to use the efficient search facilities of Answer Set Programming, allowing us to explore larger pathways, combine molecular changes with pathways and phenotype and infer effects on signalling in in vivo, whole-organism, mutants, where direct signalling stimulation assays are difficult to perform. Our methods are available in the web-service NetEffects: http://www.ebi.ac.uk/thornton-srv/software/NetEffects. PMID:23251396
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Papatheodorou, Irene; Ziehm, Matthias; Wieser, Daniela; Alic, Nazif; Partridge, Linda; Thornton, Janet M
2012-01-01
A challenge of systems biology is to integrate incomplete knowledge on pathways with existing experimental data sets and relate these to measured phenotypes. Research on ageing often generates such incomplete data, creating difficulties in integrating RNA expression with information about biological processes and the phenotypes of ageing, including longevity. Here, we develop a logic-based method that employs Answer Set Programming, and use it to infer signalling effects of genetic perturbations, based on a model of the insulin signalling pathway. We apply our method to RNA expression data from Drosophila mutants in the insulin pathway that alter lifespan, in a foxo dependent fashion. We use this information to deduce how the pathway influences lifespan in the mutant animals. We also develop a method for inferring the largest common sub-paths within each of our signalling predictions. Our comparisons reveal consistent homeostatic mechanisms across both long- and short-lived mutants. The transcriptional changes observed in each mutation usually provide negative feedback to signalling predicted for that mutation. We also identify an S6K-mediated feedback in two long-lived mutants that suggests a crosstalk between these pathways in mutants of the insulin pathway, in vivo. By formulating the problem as a logic-based theory in a qualitative fashion, we are able to use the efficient search facilities of Answer Set Programming, allowing us to explore larger pathways, combine molecular changes with pathways and phenotype and infer effects on signalling in in vivo, whole-organism, mutants, where direct signalling stimulation assays are difficult to perform. Our methods are available in the web-service NetEffects: http://www.ebi.ac.uk/thornton-srv/software/NetEffects.
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Autoplot: a Browser for Science Data on the Web
NASA Astrophysics Data System (ADS)
Faden, J.; Weigel, R. S.; West, E. E.; Merka, J.
2008-12-01
Autoplot (www.autoplot.org) is software for plotting data from many different sources and in many different file formats. Data from CDF, CEF, Fits, NetCDF, and OpenDAP can be plotted, along with many other sources such as ASCII tables and Excel spreadsheets. This is done by adapting these various data formats and APIs into a common data model that borrows from the netCDF and CDF data models. Autoplot uses a web browser metaphor to simplify use. The user specifies a parameter URL, for example a CDF file accessible via http with a parameter name appended, and the file resource is downloaded and the parameter is rendered in a scientifically meaningful way. When data span multiple files, the user can use a file name template in the URL to aggregate (combine) a set of remote files. So the problem of aggregating data across file boundaries is handled on the client side, allowing simple web servers to be used. The das2 graphics library provides rich controls for exploring the data. Scripting is supported through Python, providing not just programmatic control, but for calculating new parameters in a language that will look familiar to IDL and Matlab users. Autoplot is Java-based software, and will run on most computers without a burdensome installation process. It can also used as an applet or as a servlet that serves static images. Autoplot was developed as part of the Virtual Radiation Belt Observatory (ViRBO) project, and is also being used for the Virtual Magnetospheric Observatory (VMO). It is expected that this flexible, general-purpose plotting tool will be useful for allowing a data provider to add instant visualization capabilities to a directory of files or for general use in the Virtual Observatory environment.
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How much incisor decompensation is achieved prior to orthognathic surgery?
McNeil, Calum; McIntyre, Grant T; Laverick, Sean
2014-07-01
To quantify incisor decompensation in preparation for orthognathic surgery. Pre-treatment and pre-surgery lateral cephalograms for 86 patients who had combined orthodontic and orthognathic treatment were digitised using OPAL 2.1 [http://www.opalimage.co.uk]. To assess intra-observer reproducibility, 25 images were re-digitised one month later. Random and systematic error were assessed using the Dahlberg formula and a two-sample t-test, respectively. Differences in the proportions of cases where the maxillary (1100 +/- 60) or mandibular (900 +/- 60) incisors were fully decomensated were assessed using a Chi-square test (p<0.05). Mann-Whitney U tests were used to identify if there were any differences in the amount of net decompensation for maxillary and mandibular incisors between the Class II combined and Class III groups (p<0.05). Random and systematic error were less than 0.5 degrees and p<0.05, respectively. A greater proportion of cases had decompensated mandibular incisors (80%) than maxillary incisors (62%) and this difference was statistically significant (p=0.029). The amount of maxillary incisor decompensation in the Class II and Class III groups did not statistically differ (p=0.45) whereas the mandibular incisors in the Class III group underwent statistically significantly greater decompensation (p=0.02). Mandibular incisors were decompensated for a greater proportion of cases than maxillary incisors in preparation for orthognathic surgery. There was no difference in the amount of maxillary incisor decompensation between Class II and Class III cases. There was a greater net decompensation for mandibular incisors in Class III cases when compared to Class II cases. Key words:Decompensation, orthognathic, pre-surgical orthodontics, surgical-orthodontic.
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Slipping through the net: the paradox of nursing's electronic theses and dissertations.
Macduff, C; Goodfellow, L M; Nolfi, D; Copeland, S; Leslie, G D; Blackwood, D
2016-06-01
The study's main aim was to gain in-depth understanding of how nurse scholars engage with electronic theses and dissertations. Through elicitation of opinions about challenges and opportunities, and perceptions of future development, the study also aimed to influence the design of a new international web-based forum for learning and sharing information on this topic. Electronic theses and dissertations provide an opportunity to radically change the way in which graduate student research is presented, disseminated and used internationally. However, as revealed by a multi-national survey in 2011, many nurse scholars in vanguard universities have little awareness of how to find and exploit this ever-expanding global knowledge resource that is increasingly available free in full text format. Within this context more detailed understandings of nurse scholars' thinking and actions are required. A qualitative approach using a semi-structured interview guide was utilized to elicit perceptions from 14 nurse scholars. Thematic analysis of the interviewees' responses identified six major themes: initial exposure and effect; searching; accessing; handling; using; and evaluation. Insights were gained about the value of these resources and behaviours in using them as exemplars for structure, format and methodology. Despite the small study size, the findings added valuable new insights to the overview gained from the 2011 survey. These have been used to inform development of a new global initiative: the International Network for Electronic Theses and Dissertations in Nursing. Featuring an educational website (www.inetdin.net), this initiative aims to support and challenge nursing's policy makers, practitioners and especially educators to utilize this neglected but exponentially increasing wellspring of international nursing knowledge. © 2016 International Council of Nurses.
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Eysenbach, Gunther; Yihune, Gabriel; Lampe, Kristian; Cross, Phil; Brickley, Dan
2000-01-01
MedCERTAIN (MedPICS Certification and Rating of Trustworthy Health Information on the Net, http://www.medcertain.org/) is a recently launched international project funded under the European Union's (EU) "Action Plan for safer use of the Internet". It provides a technical infrastructure and a conceptual basis for an international system of "quality seals", ratings and self-labelling of Internet health information, with the final aim to establish a global "trustmark" for networked health information. Digital "quality seals" are evaluative metadata (using standards such as PICS=Platform for Internet Content Selection, now being replaced by RDF/XML) assigned by trusted third-party raters. The project also enables and encourages self-labelling with descriptive metainformation by web authors. Together these measures will help consumers as well as professionals to identify high-quality information on the Internet. MedCERTAIN establishes a fully functional demonstrator for a self- and third-party rating system enabling consumers and professionals to filter harmful health information and to positively identify and select high quality information. We aim to provide a trustmark system which allows citizens to place greater confidence in networked information, to encourage health information providers to follow best practices guidelines such as the Washington eHealth Code of Ethics, to provide effective feedback and law enforcement channels to handle user complaints, and to stimulate medical societies to develop standard for patient information. The project further proposes and identifies standards for interoperability of rating and description services (such as libraries or national health portals) and fosters a worldwide collaboration to guide consumers to high-quality information on the web.
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Loubet, Paul; Guerrisi, Caroline; Turbelin, Clément; Blondel, Béatrice; Launay, Odile; Bardou, Marc; Blanchon, Thierry; Bonmarin, Isabelle; Goffinet, François; Ancel, Pierre-Yves; Colizza, Vittoria; Hanslik, Thomas; Kernéis, Solen
2016-03-11
Pregnancy is a risk factor for severe influenza resulting in increased risks of hospitalisation and death in mothers and their new-borns. Our objective was to assess the representativeness and participation of French women to a new web-based collaborative tool for data collection and monitoring of Influenza Like Illness (ILI) during pregnancy. During the 2014/2015 influenza season, pregnant women living in metropolitan France were enrolled through a web platform ( https://www.grippenet.fr/). Then throughout the season, participants were asked to report, on a weekly basis, if they had experienced symptoms of ILI. Representativeness was assessed by comparing the characteristics of participants to those of the French National Perinatal Survey. For each participant, the participation rate was the number of weekly questionnaires completed, divided by the length of follow-up (in weeks). Predictors of active participation (participation rate >15%) were assessed by multivariate logistic regression. A total of 153 women were enrolled. Participants were older (mean age 34 years vs. 29 years) and more highly educated (high school level 89% versus 52%) than the general population of pregnant women in France, but the sample did not differ on pregnancy-related characteristics (parity, history of hospitalisation during a previous pregnancy). The median rate of participation was high (78%, interquartile range: 34-96). Higher educational level and participation to a previous GrippeNet.fr season were associated with active participation. Despite small sample size and lack of representativeness, the retention rate was high, suggesting that pregnant women are prone to adhere to a longitudinal follow-up of their health status via the Internet.
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NASA Astrophysics Data System (ADS)
Kimura, H.; Asano, Y.; Matsumoto, T.
2012-12-01
The rapid determination of hypocentral parameters and their transmission to the public are valuable components of disaster mitigation. We have operated an automatic system for this purpose—termed the Accurate and QUick Analysis system for source parameters (AQUA)—since 2005 (Matsumura et al., 2006). In this system, the initial hypocenter, the moment tensor (MT), and the centroid moment tensor (CMT) solutions are automatically determined and posted on the NIED Hi-net Web site (www.hinet.bosai.go.jp). This paper describes improvements made to the AQUA to overcome limitations that became apparent after the 2011 Tohoku Earthquake (05:46:17, March 11, 2011 in UTC). The improvements included the processing of NIED F-net velocity-type strong motion records, because NIED F-net broadband seismographs are saturated for great earthquakes such as the 2011 Tohoku Earthquake. These velocity-type strong motion seismographs provide unsaturated records not only for the 2011 Tohoku Earthquake, but also for recording stations located close to the epicenters of M>7 earthquakes. We used 0.005-0.020 Hz records for M>7.5 earthquakes, in contrast to the 0.01-0.05 Hz records employed in the original system. The initial hypocenters determined based on arrival times picked by using seismograms recorded by NIED Hi-net stations can have large errors in terms of magnitude and hypocenter location, especially for great earthquakes or earthquakes located far from the onland Hi-net network. The size of the 2011 Tohoku Earthquake was initially underestimated in the AQUA to be around M5 at the initial stage of rupture. Numerous aftershocks occurred at the outer rise east of the Japan trench, where a great earthquake is anticipated to occur. Hence, we modified the system to repeat the MT analyses assuming a larger size, for all earthquakes for which the magnitude was initially underestimated. We also broadened the search range of centroid depth for earthquakes located far from the onland Hi-net network. After implementing the above improvements, the CMT solution for the 2011 Tohoku Earthquake was successfully determined with a moment magnitude (Mw) of 8.6 (9.04 × 10^21 Nm). The focal mechanisms and centroid depths of the 2011 Tohoku Earthquake and M>7 aftershocks, as obtained using the improved system, are in agreement with those from the GlobalCMT. The sizes of these earthquakes are also consistent with those of GlobalCMT, with differences of less than Mw 0.1 except for the mainshock (Mw9.1, 5.31 × 10^22 Nm, GlobalCMT). This discrepancy may indicate that the bandwidth used in the analysis is insufficient for an earthquake of this size. To address this shortcoming, we used 0.0025-0.0100 Hz records and obtained a magnitude of Mw8.9 (3.35 × 10^22 Nm). This result is consistent with the GlobalCMT and other results (e.g., Mw 9.0, 3.43 × 10^22 Nm reported by Ozawa et al., 2011; Mw9.0, 4.42 × 10^22 Nm reported by Suzuki et al., 2011). Using the improved system, the CMT analysis for the 2011 Tohoku Earthquake is estimated to be completed within 12 minutes of the origin time.
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NASA Astrophysics Data System (ADS)
Hautière, Nicolas; Bourquin, Frédéric
2017-04-01
Through the centuries, the roads - which today constitute in France a huge transport network of 1 millions kilometers length - have always been able to cope with society needs and challenges. As a consequence, the next generation road infrastructure will have to take into account at least three societal transitions: ecological, energetic and digital. The goal of the 5th generation road project (R5G©) [1], led by Ifsttar in France, aligned with the Forever Open program [2], is to design and build demonstrators of such future road infrastructures. The goal of this presentation is to present different results related to the greening of road materials [3], the design of energy-positive roads [4, 5], the test of roads that self-diagnose [6], the design of roads adapted for connected [7], autonomous [8] and electrified vehicles [9], etc. In terms of perspectives, we will demonstrate that the road infrastructures will soon become a complex system: On one side road users will benefit from new services, on the other side such massively connected and instrumented infrastructures will potentially become an opportune sensor for knowledge development in geoscience, such as air quality, visibility and fog monitoring. References: [1] R5G project. r5g.ifsttar.fr [2] Forever Open Road project. www.foreveropenroad.eu [3] Biorepavation project. www.infravation.net/projects/BIOREPAVATION [4] N. Le Touz, J. Dumoulin. Numerical study of the thermal behavior of a new deicing road structure design with energy harvesting capabilities. EGU General Assembly 2015, Apr 2015, Vienne, Austria. [5] S. Asfour, F. Bernardin, E. Toussaint, J.-M. Piau. Hydrothermal modeling of porous pavement for its surface de-freezing. Applied Thermal Engineering. Volume 107, 25 August 2016, Pages 493-500 [6] LGV BPL Instrumentation. http://railenium.eu/wp-content/uploads/2016/08/INSTRUMENTATION-BPL-FR.pdf [7] SCOOP@F project. https://ec.europa.eu/inea/en/connecting-europe-facility/cef-transport/projects-by-country/multi-country/2014-eu-ta-0669-s [8] J. Ehrlich, D. Gruyer, O. Orfila, N. Hautière. Autonomous vehicle : The concept of high quality of service highway. FISITA World congress, Busan, Korea, 2016. [9] FABRIC project. www.fabric-project.eu
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NASA Astrophysics Data System (ADS)
Foucar, Lutz; Barty, Anton; Coppola, Nicola; Hartmann, Robert; Holl, Peter; Hoppe, Uwe; Kassemeyer, Stephan; Kimmel, Nils; Küpper, Jochen; Scholz, Mirko; Techert, Simone; White, Thomas A.; Strüder, Lothar; Ullrich, Joachim
2012-10-01
The Max Planck Advanced Study Group (ASG) at the Center for Free Electron Laser Science (CFEL) has created the CFEL-ASG Software Suite CASS to view, process and analyse multi-parameter experimental data acquired at Free Electron Lasers (FELs) using the CFEL-ASG Multi Purpose (CAMP) instrument Strüder et al. (2010) [6]. The software is based on a modular design so that it can be adjusted to accommodate the needs of all the various experiments that are conducted with the CAMP instrument. In fact, this allows the use of the software in all experiments where multiple detectors are involved. One of the key aspects of CASS is that it can be used either 'on-line', using a live data stream from the free-electron laser facility's data acquisition system to guide the experiment, and 'off-line', on data acquired from a previous experiment which has been saved to file. Program summary Program title: CASS Catalogue identifier: AEMP_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEMP_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public Licence, version 3 No. of lines in distributed program, including test data, etc.: 167073 No. of bytes in distributed program, including test data, etc.: 1065056 Distribution format: tar.gz Programming language: C++. Computer: Intel x86-64. Operating system: GNU/Linux (for information about restrictions see outlook). RAM: >8 GB Classification: 2.3, 3, 15, 16.4. External routines: Qt-Framework[1], SOAP[2], (optional HDF5[3], VIGRA[4], ROOT[5], QWT[6]) Nature of problem: Analysis and visualisation of scientific data acquired at Free-Electron-Lasers Solution method: Generalise data access and storage so that a variety of small programming pieces can be linked to form a complex analysis chain. Unusual features: Complex analysis chains can be built without recompiling the program Additional comments: An updated extensive documentation of CASS is available at [7]. Running time: Depending on the data size and complexity of analysis algorithms. References: [1] http://qt.nokia.com [2] http://www.cs.fsu.edu/~engelen/soap.html [3] http://www.hdfgroup.org/HDF5/ [4] http://hci.iwr.uni-heidelberg.de/vigra/ [5] http://root.cern.ch [6] http://qwt.sourceforge.net/ [7] http://www.mpi-hd.mpg.de/personalhomes/gitasg/cass
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NASA Astrophysics Data System (ADS)
Seamon, E.; Gessler, P. E.; Flathers, E.; Sheneman, L.; Gollberg, G.
2013-12-01
The Regional Approaches to Climate Change for Pacific Northwest Agriculture (REACCH PNA) is a five-year USDA/NIFA-funded coordinated agriculture project to examine the sustainability of cereal crop production systems in the Pacific Northwest, in relationship to ongoing climate change. As part of this effort, an extensive data management system has been developed to enable researchers, students, and the public, to upload, manage, and analyze various data. The REACCH PNA data management team has developed three core systems to encompass cyberinfrastructure and data management needs: 1) the reacchpna.org portal (https://www.reacchpna.org) is the entry point for all public and secure information, with secure access by REACCH PNA members for data analysis, uploading, and informational review; 2) the REACCH PNA Data Repository is a replicated, redundant database server environment that allows for file and database storage and access to all core data; and 3) the REACCH PNA Libraries which are functional groupings of data for REACCH PNA members and the public, based on their access level. These libraries are accessible thru our https://www.reacchpna.org portal. The developed system is structured in a virtual server environment (data, applications, web) that includes a geospatial database/geospatial web server for web mapping services (ArcGIS Server), use of ESRI's Geoportal Server for data discovery and metadata management (under the ISO 19115-2 standard), Thematic Realtime Environmental Distributed Data Services (THREDDS) for data cataloging, and Interactive Python notebook server (IPython) technology for data analysis. REACCH systems are housed and maintained by the Northwest Knowledge Network project (www.northwestknowledge.net), which provides data management services to support research. Initial project data harvesting and meta-tagging efforts have resulted in the interrogation and loading of over 10 terabytes of climate model output, regional entomological data, agricultural and atmospheric information, as well as imagery, publications, videos, and other soft content. In addition, the outlined data management approach has focused on the integration and interconnection of hard data (raw data output) with associated publications, presentations, or other narrative documentation - through metadata lineage associations. This harvest-and-consume data management methodology could additionally be applied to other research team environments that involve large and divergent data.
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Pöschl, Ulrich
2012-01-01
The traditional forms of scientific publishing and peer review do not live up to all demands of efficient communication and quality assurance in today’s highly diverse and rapidly evolving world of science. They need to be advanced and complemented by interactive and transparent forms of review, publication, and discussion that are open to the scientific community and to the public. The advantages of open access, public peer review, and interactive discussion can be efficiently and flexibly combined with the strengths of traditional scientific peer review. Since 2001 the benefits and viability of this approach are clearly demonstrated by the highly successful interactive open access journal Atmospheric Chemistry and Physics (ACP, www.atmos-chem-phys.net) and a growing number of sister journals launched and operated by the European Geosciences Union (EGU, www.egu.eu) and the open access publisher Copernicus (www.copernicus.org). The interactive open access journals are practicing an integrative multi-stage process of publication and peer review combined with interactive public discussion, which effectively resolves the dilemma between rapid scientific exchange and thorough quality assurance. Key features and achievements of this approach are: top quality and impact, efficient self-regulation and low rejection rates, high attractivity and rapid growth, low costs, and financial sustainability. In fact, ACP and the EGU interactive open access sister journals are by most if not all standards more successful than comparable scientific journals with traditional or alternative forms of peer review (editorial statistics, publication statistics, citation statistics, economic costs, and sustainability). The high efficiency and predictive validity of multi-stage open peer review have been confirmed in a series of dedicated studies by evaluation experts from the social sciences, and the same or similar concepts have recently also been adopted in other disciplines, including the life sciences and economics. Multi-stage open peer review can be flexibly adjusted to the needs and peculiarities of different scientific communities. Due to the flexibility and compatibility with traditional structures of scientific publishing and peer review, the multi-stage open peer review concept enables efficient evolution in scientific communication and quality assurance. It has the potential for swift replacement of hidden peer review as the standard of scientific quality assurance, and it provides a basis for open evaluation in science. PMID:22783183
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... Association -- www.csaceliacs.org Gluten Intolerance Group -- www.gluten.org National Institute of Diabetes and Digestive and Kidney Disease -- www.niddk.nih.gov/health-information/digestive-diseases/celiac-disease Beyond Celiac -- www. ...
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2015-01-12
VANDENBERG AIR FORCE BASE, Calif. – In the Astrotech payload processing facility on Vandenberg Air Force Base in California, NASA's Soil Moisture Active Passive, or SMAP, spacecraft, has been secured inside a transportation canister and secured onto a transporter for its move to the launch pad. SMAP will launch on a United Launch Alliance Delta II 7320 configuration vehicle featuring a United Launch Alliance first stage booster powered by an Aerojet Rocketdyne RS-27A main engine and three Alliant Techsystems, or ATK, strap-on solid rocket motors. Once on station in Earth orbit, SMAP will provide global measurements of soil moisture and its freeze/thaw state. These measurements will be used to enhance understanding of processes that link the water, energy and carbon cycles, and to extend the capabilities of weather and climate prediction models. SMAP data also will be used to quantify net carbon flux in boreal landscapes and to develop improved flood prediction and drought monitoring capabilities. Launch from Space Launch Complex 2 is targeted for Jan. 29. To learn more about SMAP, visit http://www.nasa.gov/smap. Photo credit: NASA/U.S. Air Force Photo Squadron
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2015-01-12
VANDENBERG AIR FORCE BASE, Calif. – In the Astrotech payload processing facility on Vandenberg Air Force Base in California, technicians enclose a transportation canister containing NASA's Soil Moisture Active Passive, or SMAP, spacecraft in an environmentally protective wrap for its move to the launch pad. SMAP will launch on a United Launch Alliance Delta II 7320 configuration vehicle featuring a United Launch Alliance first stage booster powered by an Aerojet Rocketdyne RS-27A main engine and three Alliant Techsystems, or ATK, strap-on solid rocket motors. Once on station in Earth orbit, SMAP will provide global measurements of soil moisture and its freeze/thaw state. These measurements will be used to enhance understanding of processes that link the water, energy and carbon cycles, and to extend the capabilities of weather and climate prediction models. SMAP data also will be used to quantify net carbon flux in boreal landscapes and to develop improved flood prediction and drought monitoring capabilities. Launch from Space Launch Complex 2 is targeted for Jan. 29. To learn more about SMAP, visit http://www.nasa.gov/smap. Photo credit: NASA/U.S. Air Force Photo Squadron
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2015-01-12
VANDENBERG AIR FORCE BASE, Calif. – In the Astrotech payload processing facility on Vandenberg Air Force Base in California, technicians secure a transportation canister around NASA's Soil Moisture Active Passive, or SMAP, spacecraft for its move to the launch pad. SMAP will launch on a United Launch Alliance Delta II 7320 configuration vehicle featuring a United Launch Alliance first stage booster powered by an Aerojet Rocketdyne RS-27A main engine and three Alliant Techsystems, or ATK, strap-on solid rocket motors. Once on station in Earth orbit, SMAP will provide global measurements of soil moisture and its freeze/thaw state. These measurements will be used to enhance understanding of processes that link the water, energy and carbon cycles, and to extend the capabilities of weather and climate prediction models. SMAP data also will be used to quantify net carbon flux in boreal landscapes and to develop improved flood prediction and drought monitoring capabilities. Launch from Space Launch Complex 2 is targeted for Jan. 29. To learn more about SMAP, visit http://www.nasa.gov/smap. Photo credit: NASA/U.S. Air Force Photo Squadron
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2015-01-12
VANDENBERG AIR FORCE BASE, Calif. – In the Astrotech payload processing facility on Vandenberg Air Force Base in California, NASA's Soil Moisture Active Passive, or SMAP, spacecraft, secured inside a transportation canister is lowered onto a transporter for its move to the launch pad. SMAP will launch on a United Launch Alliance Delta II 7320 configuration vehicle featuring a United Launch Alliance first stage booster powered by an Aerojet Rocketdyne RS-27A main engine and three Alliant Techsystems, or ATK, strap-on solid rocket motors. Once on station in Earth orbit, SMAP will provide global measurements of soil moisture and its freeze/thaw state. These measurements will be used to enhance understanding of processes that link the water, energy and carbon cycles, and to extend the capabilities of weather and climate prediction models. SMAP data also will be used to quantify net carbon flux in boreal landscapes and to develop improved flood prediction and drought monitoring capabilities. Launch from Space Launch Complex 2 is targeted for Jan. 29. To learn more about SMAP, visit http://www.nasa.gov/smap. Photo credit: NASA/U.S. Air Force Photo Squadron
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2015-01-12
VANDENBERG AIR FORCE BASE, Calif. – In the Astrotech payload processing facility on Vandenberg Air Force Base in California, a technician ensures the transportation canister containing NASA's Soil Moisture Active Passive, or SMAP, spacecraft is ready for its move to the launch pad. SMAP will launch on a United Launch Alliance Delta II 7320 configuration vehicle featuring a United Launch Alliance first stage booster powered by an Aerojet Rocketdyne RS-27A main engine and three Alliant Techsystems, or ATK, strap-on solid rocket motors. Once on station in Earth orbit, SMAP will provide global measurements of soil moisture and its freeze/thaw state. These measurements will be used to enhance understanding of processes that link the water, energy and carbon cycles, and to extend the capabilities of weather and climate prediction models. SMAP data also will be used to quantify net carbon flux in boreal landscapes and to develop improved flood prediction and drought monitoring capabilities. Launch from Space Launch Complex 2 is targeted for Jan. 29. To learn more about SMAP, visit http://www.nasa.gov/smap. Photo credit: NASA/U.S. Air Force Photo Squadron
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2015-01-12
VANDENBERG AIR FORCE BASE, Calif. – In the Astrotech payload processing facility on Vandenberg Air Force Base in California, technicians enclose a transportation canister containing NASA's Soil Moisture Active Passive, or SMAP, spacecraft in an environmentally protective wrap for its move to the launch pad. SMAP will launch on a United Launch Alliance Delta II 7320 configuration vehicle featuring a United Launch Alliance first stage booster powered by an Aerojet Rocketdyne RS-27A main engine and three Alliant Techsystems, or ATK, strap-on solid rocket motors. Once on station in Earth orbit, SMAP will provide global measurements of soil moisture and its freeze/thaw state. These measurements will be used to enhance understanding of processes that link the water, energy and carbon cycles, and to extend the capabilities of weather and climate prediction models. SMAP data also will be used to quantify net carbon flux in boreal landscapes and to develop improved flood prediction and drought monitoring capabilities. Launch from Space Launch Complex 2 is targeted for Jan. 29. To learn more about SMAP, visit http://www.nasa.gov/smap. Photo credit: NASA/U.S. Air Force Photo Squadron
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2014-12-12
VANDENBERG AIR FORCE BASE, Calif. – In the Astrotech payload processing facility on Vandenberg Air Force Base in California, technicians secure a transportation canister around NASA's Soil Moisture Active Passive, or SMAP, spacecraft for its move to the launch pad. SMAP will launch on a United Launch Alliance Delta II 7320 configuration vehicle featuring a United Launch Alliance first stage booster powered by an Aerojet Rocketdyne RS-27A main engine and three Alliant Techsystems, or ATK, strap-on solid rocket motors. Once on station in Earth orbit, SMAP will provide global measurements of soil moisture and its freeze/thaw state. These measurements will be used to enhance understanding of processes that link the water, energy and carbon cycles, and to extend the capabilities of weather and climate prediction models. SMAP data also will be used to quantify net carbon flux in boreal landscapes and to develop improved flood prediction and drought monitoring capabilities. Launch from Space Launch Complex 2 is targeted for Jan. 29. To learn more about SMAP, visit http://www.nasa.gov/smap. Photo credit: NASA/U.S. Air Force Photo Squadron
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2015-01-12
VANDENBERG AIR FORCE BASE, Calif. – In the Astrotech payload processing facility on Vandenberg Air Force Base in California, technicians enclose a transportation canister containing NASA's Soil Moisture Active Passive, or SMAP, spacecraft in an environmentally protective wrap for its move to the launch pad. SMAP will launch on a United Launch Alliance Delta II 7320 configuration vehicle featuring a United Launch Alliance first stage booster powered by an Aerojet Rocketdyne RS-27A main engine and three Alliant Techsystems, or ATK, strap-on solid rocket motors. Once on station in Earth orbit, SMAP will provide global measurements of soil moisture and its freeze/thaw state. These measurements will be used to enhance understanding of processes that link the water, energy and carbon cycles, and to extend the capabilities of weather and climate prediction models. SMAP data also will be used to quantify net carbon flux in boreal landscapes and to develop improved flood prediction and drought monitoring capabilities. Launch from Space Launch Complex 2 is targeted for Jan. 29. To learn more about SMAP, visit http://www.nasa.gov/smap. Photo credit: NASA/U.S. Air Force Photo Squadron
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2015-01-12
VANDENBERG AIR FORCE BASE, Calif. – In the Astrotech payload processing facility on Vandenberg Air Force Base in California, NASA's Soil Moisture Active Passive, or SMAP, spacecraft has had the appropriate logos affixed to its transportation canister before its move to the launch pad. SMAP will launch on a United Launch Alliance Delta II 7320 configuration vehicle featuring a United Launch Alliance first stage booster powered by an Aerojet Rocketdyne RS-27A main engine and three Alliant Techsystems, or ATK, strap-on solid rocket motors. Once on station in Earth orbit, SMAP will provide global measurements of soil moisture and its freeze/thaw state. These measurements will be used to enhance understanding of processes that link the water, energy and carbon cycles, and to extend the capabilities of weather and climate prediction models. SMAP data also will be used to quantify net carbon flux in boreal landscapes and to develop improved flood prediction and drought monitoring capabilities. Launch from Space Launch Complex 2 is targeted for Jan. 29. To learn more about SMAP, visit http://www.nasa.gov/smap. Photo credit: NASA/U.S. Air Force Photo Squadron
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Unobtrusive integration of data management with fMRI analysis.
Poliakov, Andrew V; Hertzenberg, Xenia; Moore, Eider B; Corina, David P; Ojemann, George A; Brinkley, James F
2007-01-01
This note describes a software utility, called X-batch which addresses two pressing issues typically faced by functional magnetic resonance imaging (fMRI) neuroimaging laboratories (1) analysis automation and (2) data management. The first issue is addressed by providing a simple batch mode processing tool for the popular SPM software package (http://www.fil.ion. ucl.ac.uk/spm/; Welcome Department of Imaging Neuroscience, London, UK). The second is addressed by transparently recording metadata describing all aspects of the batch job (e.g., subject demographics, analysis parameters, locations and names of created files, date and time of analysis, and so on). These metadata are recorded as instances of an extended version of the Protégé-based Experiment Lab Book ontology created by the Dartmouth fMRI Data Center. The resulting instantiated ontology provides a detailed record of all fMRI analyses performed, and as such can be part of larger systems for neuroimaging data management, sharing, and visualization. The X-batch system is in use in our own fMRI research, and is available for download at http://X-batch.sourceforge.net/.
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Identification of common, unique and polymorphic microsatellites among 73 cyanobacterial genomes.
Kabra, Ritika; Kapil, Aditi; Attarwala, Kherunnisa; Rai, Piyush Kant; Shanker, Asheesh
2016-04-01
Microsatellites also known as Simple Sequence Repeats are short tandem repeats of 1-6 nucleotides. These repeats are found in coding as well as non-coding regions of both prokaryotic and eukaryotic genomes and play a significant role in the study of gene regulation, genetic mapping, DNA fingerprinting and evolutionary studies. The availability of 73 complete genome sequences of cyanobacteria enabled us to mine and statistically analyze microsatellites in these genomes. The cyanobacterial microsatellites identified through bioinformatics analysis were stored in a user-friendly database named CyanoSat, which is an efficient data representation and query system designed using ASP.net. The information in CyanoSat comprises of perfect, imperfect and compound microsatellites found in coding, non-coding and coding-non-coding regions. Moreover, it contains PCR primers with 200 nucleotides long flanking region. The mined cyanobacterial microsatellites can be freely accessed at www.compubio.in/CyanoSat/home.aspx. In addition to this 82 polymorphic, 13,866 unique and 2390 common microsatellites were also detected. These microsatellites will be useful in strain identification and genetic diversity studies of cyanobacteria.
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Must research benefit human subjects if it is to be permissible?
Wikler, Daniel
2017-02-01
Must medical experiments with human subjects offer them a 'favourable risk-benefit ratio', that is, more expectation of benefit than harm or burden, if they are to be judged as ethically justified? Ethical justification is easier for experiments that do offer net benefit to subjects, but ethical justification is possible also for some experiments that do not. Basic science experiments with healthy volunteers and 'Phase I' drug trials that seek to determine tolerable dosage levels are routinely approved by ethical review committees; moreover, guidance they receive from government funding agencies specifically asks them to weigh risks to subjects against benefits to subjects and also benefits to those who may benefit from the knowledge gained in the experiment. If a puzzle remains, it is why there remains any assumption that research ethics requires a 'favourable risk-benefit ratio' for the individual research subject. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.
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Prediction of β-turns in proteins from multiple alignment using neural network
Kaur, Harpreet; Raghava, Gajendra Pal Singh
2003-01-01
A neural network-based method has been developed for the prediction of β-turns in proteins by using multiple sequence alignment. Two feed-forward back-propagation networks with a single hidden layer are used where the first-sequence structure network is trained with the multiple sequence alignment in the form of PSI-BLAST–generated position-specific scoring matrices. The initial predictions from the first network and PSIPRED-predicted secondary structure are used as input to the second structure-structure network to refine the predictions obtained from the first net. A significant improvement in prediction accuracy has been achieved by using evolutionary information contained in the multiple sequence alignment. The final network yields an overall prediction accuracy of 75.5% when tested by sevenfold cross-validation on a set of 426 nonhomologous protein chains. The corresponding Qpred, Qobs, and Matthews correlation coefficient values are 49.8%, 72.3%, and 0.43, respectively, and are the best among all the previously published β-turn prediction methods. The Web server BetaTPred2 (http://www.imtech.res.in/raghava/betatpred2/) has been developed based on this approach. PMID:12592033
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Vigg, Steven; Johnson, John
In this annual Monitoring & Evaluation (M&E) report to the Bonneville Power Administration (BPA), we summarize significant activities and performance measures resultant from enhanced protection by Columbia River Inter-Tribal Fisheries Enforcement (CRITFE) in the mainstem corridor (BPA Project 2000-056). This report covers the Fiscal Year (FY) 2000 performance period -- May 15, 2000 to May 14, 2001. Quarterly progress reports have previously been submitted to BPA and are posted on the M&E Web site (www.Eco-Law.net) -- for the time period April-December 2000 (Vigg 2000b,c,d) and for the period January-June 2001 (Vigg 2001a,b). We also present comprehensive data representing the firstmore » quarter of year 2000 in this report for a pre-project comparison. In addition, we have analyzed specific annual enforcement statistics to evaluate trends during the baseline period 1996-2000. Additional statistics and more years of comprehensive baseline data are now being summarized, and will be presented in future M&E annual reports--to provide a longer time series for evaluation of trends in input, output and outcome performance standards.« less
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Stensæth, Karette
2013-08-07
The point of departure in this text is the ongoing qualitative interdisciplinary research project RHYME (www.RHYME.no), which addresses the lack of health-promoting interactive and musical Information and Communications Technology (ICT) for families with children with severe disabilities. The project explores a new treatment paradigm based on collaborative, tangible, interactive net-based musical "smart things" with multimedia capabilities. The goal in RHYME is twofold: (1) to reduce isolation and passivity, and (2) to promote health and well-being. Co-creation is suggested as a possible path to achieving these goals, by evoking feelings, for example, or accommodating the needs to act and to create social relations; co-creation also motivates users to communicate and collaborate within (new) social relations. This article engages co-creation by incorporating aspects connected to interaction design and the field of music and health. Empirical observations will be referred to. The research question is as follows: What might co-creation imply for families of children with disabilities when musical and interactive tangibles are used as health-promoting implements?
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2013-01-01
The point of departure in this text is the ongoing qualitative interdisciplinary research project RHYME (www.RHYME.no), which addresses the lack of health-promoting interactive and musical Information and Communications Technology (ICT) for families with children with severe disabilities. The project explores a new treatment paradigm based on collaborative, tangible, interactive net-based musical “smart things” with multimedia capabilities. The goal in RHYME is twofold: (1) to reduce isolation and passivity, and (2) to promote health and well-being. Co-creation is suggested as a possible path to achieving these goals, by evoking feelings, for example, or accommodating the needs to act and to create social relations; co-creation also motivates users to communicate and collaborate within (new) social relations. This article engages co-creation by incorporating aspects connected to interaction design and the field of music and health. Empirical observations will be referred to. The research question is as follows: What might co-creation imply for families of children with disabilities when musical and interactive tangibles are used as health-promoting implements? PMID:23930992
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FNV: light-weight flash-based network and pathway viewer.
Dannenfelser, Ruth; Lachmann, Alexander; Szenk, Mariola; Ma'ayan, Avi
2011-04-15
Network diagrams are commonly used to visualize biochemical pathways by displaying the relationships between genes, proteins, mRNAs, microRNAs, metabolites, regulatory DNA elements, diseases, viruses and drugs. While there are several currently available web-based pathway viewers, there is still room for improvement. To this end, we have developed a flash-based network viewer (FNV) for the visualization of small to moderately sized biological networks and pathways. Written in Adobe ActionScript 3.0, the viewer accepts simple Extensible Markup Language (XML) formatted input files to display pathways in vector graphics on any web-page providing flexible layout options, interactivity with the user through tool tips, hyperlinks and the ability to rearrange nodes on the screen. FNV was utilized as a component in several web-based systems, namely Genes2Networks, Lists2Networks, KEA, ChEA and PathwayGenerator. In addition, FVN can be used to embed pathways inside pdf files for the communication of pathways in soft publication materials. FNV is available for use and download along with the supporting documentation and sample networks at http://www.maayanlab.net/FNV. avi.maayan@mssm.edu.
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Real-time Interplanetary Shock Prediciton System
NASA Astrophysics Data System (ADS)
Vandegriff, J.; Ho, G.; Plauger, J.
A system is being developed to predict the arrival times and maximum intensities of energetic storm particle (ESP) events at the earth. Measurements of particle flux values at L1 being made by the Electron, Proton, and Alpha Monitor (EPAM) instrument aboard NASA's ACE spacecraft are made available in real-time by the NOAA Space Environment Center as 5 minute averages of several proton and electron energy channels. Past EPAM flux measurements can be used to train forecasting algorithms which then run on the real-time data. Up to 3 days before the arrival of the interplanetary shock associated with an ESP event, characteristic changes in the particle intensities (such as decreased spectral slope and increased overall flux level) are easily discernable. Once the onset of an event is detected, a neural net is used to forecast the arrival time and flux level for the event. We present results obtained with this technique for forecasting the largest of the ESP events detected by EPAM. Forecasting information will be made publicly available through http://sd-www.jhuapl.edu/ACE/EPAM/, the Johns Hopkins University Applied Physics Lab web site for the ACE/EPAM instrument.
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Computational Search for Specific Magnetoelectronic Characteristics
NASA Astrophysics Data System (ADS)
Pickett, Warren E.
1997-08-01
Many aspects of the coupling between magnetic state (ferro- or antiferromagnetic) and the electronic properties of a material can be predicted reliably from local spin density (LSD) calculations. Such calculations are routinely used to interpret data, but so far little actual prediction of new materials has been attempted. We present here the application of LSD methods to look for half-metallic (HM) antiferromagnetic (AFM) compounds. These materials will have unusual properties, such as 100% spin-polarized transport with no net magnetic field, and the possibility of a novel type of superconductivity. The double perovskite crystal structure was chosen, due to some experience with it and its simplicity, and magnetic ions M',M'' were chosen in the expectation that their moments in the La_2M'M''O6 compound would be equal in magnitude and could be induced to align in an antiparallel manner, giving zero total magnetization. Results for six compounds, with magnetic ions chosen from the 3d transition series, will be described. Three HM AFM states have been found, as well as several HM ferromagnetic states.
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Lee, Imchang; Chalita, Mauricio; Ha, Sung-Min; Na, Seong-In; Yoon, Seok-Hwan; Chun, Jongsik
2017-06-01
Thanks to the recent advancement of DNA sequencing technology, the cost and time of prokaryotic genome sequencing have been dramatically decreased. It has repeatedly been reported that genome sequencing using high-throughput next-generation sequencing is prone to contaminations due to its high depth of sequencing coverage. Although a few bioinformatics tools are available to detect potential contaminations, these have inherited limitations as they only use protein-coding genes. Here we introduce a new algorithm, called ContEst16S, to detect potential contaminations using 16S rRNA genes from genome assemblies. We screened 69 745 prokaryotic genomes from the NCBI Assembly Database using ContEst16S and found that 594 were contaminated by bacteria, human and plants. Of the predicted contaminated genomes, 8 % were not predicted by the existing protein-coding gene-based tool, implying that both methods can be complementary in the detection of contaminations. A web-based service of the algorithm is available at www.ezbiocloud.net/tools/contest16s.
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Harewood, G C; Hendrick, L M
2010-03-01
The ability to critically appraise the calibre of studies in medical literature is increasingly important for medical professionals. This prospective controlled study evaluated the impact of a 6-h Evidence Based Medicine (EBM) Workshop on the critical appraisal skills of medical trainees. Individuals attended three 2-h workshops over a 3-week period, incorporating didactic lectures in statistics, clinical trial design, appraising research papers and practical examples. Appraisal skills were assessed pre- and post-training based on grading the quality of randomised control studies (level 1 evidence), cohort studies (level 2 evidence) and case-control studies (level 3 evidence) [From Oxford Centre for Evidence Based Medicine Levels of Evidence (2001), http://www.cebm.net/critical_appraisal.asp ]. Overall grading improved from 39% (pre-course) to 74% (post-course), P = 0.002, with grading of levels 1, 2 and 3 studies improving from 42 to 75%, 53 to 61% and 21 to 84%, respectively. We conclude that a 6-h formal EBM workshop is effective in enhancing the critical appraisal skills of medical trainees.
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Numerical simulation of NQR/NMR: Applications in quantum computing.
Possa, Denimar; Gaudio, Anderson C; Freitas, Jair C C
2011-04-01
A numerical simulation program able to simulate nuclear quadrupole resonance (NQR) as well as nuclear magnetic resonance (NMR) experiments is presented, written using the Mathematica package, aiming especially applications in quantum computing. The program makes use of the interaction picture to compute the effect of the relevant nuclear spin interactions, without any assumption about the relative size of each interaction. This makes the program flexible and versatile, being useful in a wide range of experimental situations, going from NQR (at zero or under small applied magnetic field) to high-field NMR experiments. Some conditions specifically required for quantum computing applications are implemented in the program, such as the possibility of use of elliptically polarized radiofrequency and the inclusion of first- and second-order terms in the average Hamiltonian expansion. A number of examples dealing with simple NQR and quadrupole-perturbed NMR experiments are presented, along with the proposal of experiments to create quantum pseudopure states and logic gates using NQR. The program and the various application examples are freely available through the link http://www.profanderson.net/files/nmr_nqr.php. Copyright © 2011 Elsevier Inc. All rights reserved.
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MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.
Kumar, Sudhir; Stecher, Glen; Tamura, Koichiro
2016-07-01
We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been optimized for use on 64-bit computing systems for analyzing larger datasets. Researchers can now explore and analyze tens of thousands of sequences in Mega The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees. The 64-bit Mega is made available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OS X. The command line Mega is available as native applications for Windows, Linux, and Mac OS X. They are intended for use in high-throughput and scripted analysis. Both versions are available from www.megasoftware.net free of charge. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
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Andrews, Steven S
2017-03-01
Smoldyn is a spatial and stochastic biochemical simulator. It treats each molecule of interest as an individual particle in continuous space, simulating molecular diffusion, molecule-membrane interactions and chemical reactions, all with good accuracy. This article presents several new features. Smoldyn now supports two types of rule-based modeling. These are a wildcard method, which is very convenient, and the BioNetGen package with extensions for spatial simulation, which is better for complicated models. Smoldyn also includes new algorithms for simulating the diffusion of surface-bound molecules and molecules with excluded volume. Both are exact in the limit of short time steps and reasonably good with longer steps. In addition, Smoldyn supports single-molecule tracking simulations. Finally, the Smoldyn source code can be accessed through a C/C ++ language library interface. Smoldyn software, documentation, code, and examples are at http://www.smoldyn.org . steven.s.andrews@gmail.com. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com
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NASA Astrophysics Data System (ADS)
Doran, Rosa; Ferlet, Roger; Gómez de Castro, Ana I.; Hill, Robert; Horellou, Cathy; Mankiewicz, Lech; Melchior, Anne-Laure; Metaxa, Margarita; Zanazzi, Alessandra
2007-08-01
Hands-on Universe is a project born at UC@Berkeley. A project devoted to enrich the teaching of Astronomy within the classroom environment with a different approach, more connected to the new technologies. Its main goals are not only to promote the use of such technologies but also to reawaken on students the taste for STEM (Science, technologies, engineering and math) related issues and also to increase their scientific culture. Eight countries in Europe decided to adopt the method and, funded by MINERVA, formed the European Hands-on Universe. Several resources were produced and a data reduction software developed http://www.euhou.net/.Other European countries are interested and should join this coordinated effort in the near future. At an international level there are 20 countries using this approach. There are plans to develop scientific cooperation among these countries. Pilot scientific research projects in schools are being tested in EU-HOU schools, Russia and USA. There is also a game being developed to be used as a new tool for teaching scientific content in the classroom environment. An effort to develop an international network of scientific / educational collaboration is the next step.
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Development of educational image databases and e-books for medical physics training.
Tabakov, S; Roberts, V C; Jonsson, B-A; Ljungberg, M; Lewis, C A; Wirestam, R; Strand, S-E; Lamm, I-L; Milano, F; Simmons, A; Deane, C; Goss, D; Aitken, V; Noel, A; Giraud, J-Y; Sherriff, S; Smith, P; Clarke, G; Almqvist, M; Jansson, T
2005-09-01
Medical physics education and training requires the use of extensive imaging material and specific explanations. These requirements provide an excellent background for application of e-Learning. The EU projects Consortia EMERALD and EMIT developed five volumes of such materials, now used in 65 countries. EMERALD developed e-Learning materials in three areas of medical physics (X-ray diagnostic radiology, nuclear medicine and radiotherapy). EMIT developed e-Learning materials in two further areas: ultrasound and magnetic resonance imaging. This paper describes the development of these e-Learning materials (consisting of e-books and educational image databases). The e-books include tasks helping studying of various equipment and methods. The text of these PDF e-books is hyperlinked with respective images. The e-books are used through the readers' own Internet browser. Each Image Database (IDB) includes a browser, which displays hundreds of images of equipment, block diagrams and graphs, image quality examples, artefacts, etc. Both the e-books and IDB are engraved on five separate CD-ROMs. Demo of these materials can be taken from www.emerald2.net.
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2015-01-12
VANDENBERG AIR FORCE BASE, Calif. – In the Astrotech payload processing facility on Vandenberg Air Force Base in California, technicians monitor the transportation canister containing NASA's Soil Moisture Active Passive, or SMAP, spacecraft as it is lowered onto a transporter for its move to the launch pad. SMAP will launch on a United Launch Alliance Delta II 7320 configuration vehicle featuring a United Launch Alliance first stage booster powered by an Aerojet Rocketdyne RS-27A main engine and three Alliant Techsystems, or ATK, strap-on solid rocket motors. Once on station in Earth orbit, SMAP will provide global measurements of soil moisture and its freeze/thaw state. These measurements will be used to enhance understanding of processes that link the water, energy and carbon cycles, and to extend the capabilities of weather and climate prediction models. SMAP data also will be used to quantify net carbon flux in boreal landscapes and to develop improved flood prediction and drought monitoring capabilities. Launch from Space Launch Complex 2 is targeted for Jan. 29. To learn more about SMAP, visit http://www.nasa.gov/smap. Photo credit: NASA/U.S. Air Force Photo Squadron
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21st century tools to prioritize contaminants for monitoring and ...
The webinar focused on ways that ToxCast high throughput screening data and the adverse outcome pathway framework, under development in the CSS program, can be used to prioritize environmental contaminants for monitoring and management. The webinar focused on ways that ToxCast high throughput screening data and the adverse outcome pathway framework, under development in the CSS program, can be used to prioritize environmental contaminants for monitoring and management. The work presented focused on case studies conducted in Region 8, in collaboration with EPA Region 8 and NEIC, as well as other federal (USGS, US FWS) and regional partners (Northern Colorado Plateau Network). The Consortium for Research and Education on Emerging Contaminants (CREEC) is a grass-roots 501(c)(3) non-profit organization comprised of world-class scientists and stakeholders with a shared interest in the source, fate, and physiological effects of contaminants of emerging concern (www.creec.net). As such, they represent an important group of stakeholders with an interest in applying the data, approaches, and tools that are being developed by the CSS program.
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Applying 21st century tools to watersheds of the western US ...
The webinar focused on ways that ToxCast high throughput screening data and the adverse outcome pathway framework, under development in the CSS program, can be used to prioritize environmental contaminants for monitoring and management. The webinar focused on ways that ToxCast high throughput screening data and the adverse outcome pathway framework, under development in the CSS program, can be used to prioritize environmental contaminants for monitoring and management. The work presented focused on case studies conducted in Region 8, in collaboration with EPA Region 8 and NEIC, as well as other federal (USGS, US FWS) and regional partners (Northern Colorado Plateau Network). The Consortium for Research and Education on Emerging Contaminants (CREEC) is a grass-roots 501(c)(3) non-profit organization comprised of world-class scientists and stakeholders with a shared interest in the source, fate, and physiological effects of contaminants of emerging concern (www.creec.net). As such, they represent an important group of stakeholders with an interest in applying the data, approaches, and tools that are being developed by the CSS program.
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GACD: Integrated Software for Genetic Analysis in Clonal F1 and Double Cross Populations.
Zhang, Luyan; Meng, Lei; Wu, Wencheng; Wang, Jiankang
2015-01-01
Clonal species are common among plants. Clonal F1 progenies are derived from the hybridization between 2 heterozygous clones. In self- and cross-pollinated species, double crosses can be made from 4 inbred lines. A clonal F1 population can be viewed as a double cross population when the linkage phase is determined. The software package GACD (Genetic Analysis of Clonal F1 and Double cross) is freely available public software, capable of building high-density linkage maps and mapping quantitative trait loci (QTL) in clonal F1 and double cross populations. Three functionalities are integrated in GACD version 1.0: binning of redundant markers (BIN); linkage map construction (CDM); and QTL mapping (CDQ). Output of BIN can be directly used as input of CDM. After adding the phenotypic data, the output of CDM can be used as input of CDQ. Thus, GACD acts as a pipeline for genetic analysis. GACD and example datasets are freely available from www.isbreeding.net. © The American Genetic Association. 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
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Informatics in radiology: radiology gamuts ontology: differential diagnosis for the Semantic Web.
Budovec, Joseph J; Lam, Cesar A; Kahn, Charles E
2014-01-01
The Semantic Web is an effort to add semantics, or "meaning," to empower automated searching and processing of Web-based information. The overarching goal of the Semantic Web is to enable users to more easily find, share, and combine information. Critical to this vision are knowledge models called ontologies, which define a set of concepts and formalize the relations between them. Ontologies have been developed to manage and exploit the large and rapidly growing volume of information in biomedical domains. In diagnostic radiology, lists of differential diagnoses of imaging observations, called gamuts, provide an important source of knowledge. The Radiology Gamuts Ontology (RGO) is a formal knowledge model of differential diagnoses in radiology that includes 1674 differential diagnoses, 19,017 terms, and 52,976 links between terms. Its knowledge is used to provide an interactive, freely available online reference of radiology gamuts ( www.gamuts.net ). A Web service allows its content to be discovered and consumed by other information systems. The RGO integrates radiologic knowledge with other biomedical ontologies as part of the Semantic Web. © RSNA, 2014.
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NASA Astrophysics Data System (ADS)
Moriarty, Patrick; Sanz Rodrigo, Javier; Gancarski, Pawel; Chuchfield, Matthew; Naughton, Jonathan W.; Hansen, Kurt S.; Machefaux, Ewan; Maguire, Eoghan; Castellani, Francesco; Terzi, Ludovico; Breton, Simon-Philippe; Ueda, Yuko
2014-06-01
Researchers within the International Energy Agency (IEA) Task 31: Wakebench have created a framework for the evaluation of wind farm flow models operating at the microscale level. The framework consists of a model evaluation protocol integrated with a web-based portal for model benchmarking (www.windbench.net). This paper provides an overview of the building-block validation approach applied to wind farm wake models, including best practices for the benchmarking and data processing procedures for validation datasets from wind farm SCADA and meteorological databases. A hierarchy of test cases has been proposed for wake model evaluation, from similarity theory of the axisymmetric wake and idealized infinite wind farm, to single-wake wind tunnel (UMN-EPFL) and field experiments (Sexbierum), to wind farm arrays in offshore (Horns Rev, Lillgrund) and complex terrain conditions (San Gregorio). A summary of results from the axisymmetric wake, Sexbierum, Horns Rev and Lillgrund benchmarks are used to discuss the state-of-the-art of wake model validation and highlight the most relevant issues for future development.
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PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods
2012-01-01
Background With the decrease of DNA sequencing costs, sequence-based typing methods are rapidly becoming the gold standard for epidemiological surveillance. These methods provide reproducible and comparable results needed for a global scale bacterial population analysis, while retaining their usefulness for local epidemiological surveys. Online databases that collect the generated allelic profiles and associated epidemiological data are available but this wealth of data remains underused and are frequently poorly annotated since no user-friendly tool exists to analyze and explore it. Results PHYLOViZ is platform independent Java software that allows the integrated analysis of sequence-based typing methods, including SNP data generated from whole genome sequence approaches, and associated epidemiological data. goeBURST and its Minimum Spanning Tree expansion are used for visualizing the possible evolutionary relationships between isolates. The results can be displayed as an annotated graph overlaying the query results of any other epidemiological data available. Conclusions PHYLOViZ is a user-friendly software that allows the combined analysis of multiple data sources for microbial epidemiological and population studies. It is freely available at http://www.phyloviz.net. PMID:22568821
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Mwalusepo, Sizah; Muli, Eliud; Faki, Asha; Raina, Suresh
2017-04-01
Land use and land cover changes will continue to affect resilient human communities and ecosystems as a result of climate change. However, an assessment of land use and land cover changes over time in Indian Ocean Islands is less documented. The land use/cover data changes over 10 years at smaller geographical scale across Unguja Island in Zanzibar were analyzed. Downscaling of the data was obtained from SERVIR through partnership with Kenya-based Regional Centre for Mapping of Resources for Development (RCMRD) database (http://www.servirglobal.net), and clipped down in ArcMap (Version 10.1) to Unguja Island. SERVIR and RCMRD Land Cover Dataset are mainly 30 m multispectral images include Landsat TM and ETM+Multispectral Images. Landscape ecology Statistics tool (LecoS) was used to analysis the land use and land cover changes. The data provide information on the status of the land use and land cover changes along the Unguja Island in Zanzibar. The data is of great significance to the future research on global change.
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The philosophical and pedagogical underpinnings of Active Learning in Engineering Education
NASA Astrophysics Data System (ADS)
Christie, Michael; de Graaff, Erik
2017-01-01
In this paper the authors draw on three sequential keynote addresses that they gave at Active Learning in Engineering Education (ALE) workshops in Copenhagen (2012), Caxias do Sol (2014) and San Sebastian (2015). Active Learning in Engineering Education is an informal international network of engineering educators dedicated to improving engineering education through active learning (http://www.ale-net.org/). The paper reiterates themes from those keynotes, namely, the philosophical and pedagogical underpinnings of Active Learning in Engineering Education, the scholarly questions that inspire engineering educators to go on improving their practice and exemplary models designed to activate the learning of engineering students. This paper aims to uncover the bedrock of established educational philosophies and theories that define and support active learning. The paper does not claim to present any new or innovative educational theory. There is already a surfeit of them. Rather, the aim is to assist Engineering Educators who wish to research how they can best activate the learning of their students by providing a readable, reasonable and solid underpinning for best practice in this field.
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Affective norms for 720 French words rated by children and adolescents (FANchild).
Monnier, Catherine; Syssau, Arielle
2017-10-01
FANchild (French Affective Norms for Children) provides norms of valence and arousal for a large corpus of French words (N = 720) rated by 908 French children and adolescents (ages 7, 9, 11, and 13). The ratings were made using the Self-Assessment Manikin (Lang, 1980). Because it combines evaluations of arousal and valence and includes ratings provided by 7-, 9-, 11-, and 13-year-olds, this database complements and extends existing French-language databases. Good response reliability was observed in each of the four age groups. Despite a significant level of consensus, we found age differences in both the valence and arousal ratings: Seven- and 9-year-old children gave higher mean valence and arousal ratings than did the other age groups. Moreover, the tendency to judge words positively (i.e., positive bias) decreased with age. This age- and sex-related database will enable French-speaking researchers to study how the emotional character of words influences their cognitive processing, and how this influence evolves with age. FANchild is available at https://www.researchgate.net/profile/Catherine_Monnier/contributions .
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43 CFR Appendix B to Part 2 - Internet Addresses
Code of Federal Regulations, 2010 CFR
2010-10-01
... Page: http://www.doi.gov 2. DOI FOIA Home Page: http://www.doi.gov/foia/ 3. DOI Reference Guide for Obtaining Information: http://www.doi.gov/foia/foitabl.htm 4. List of DOI Public Affairs Offices: http://www.doi.gov/foia/list.html 5. DOI FOIA Contacts: http://www.doi.gov/foia/contacts.html 6. DOI FOIA...
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43 CFR Appendix B to Part 2 - Internet Addresses
Code of Federal Regulations, 2012 CFR
2012-10-01
... Page: http://www.doi.gov 2. DOI FOIA Home Page: http://www.doi.gov/foia/ 3. DOI Reference Guide for Obtaining Information: http://www.doi.gov/foia/foitabl.htm 4. List of DOI Public Affairs Offices: http://www.doi.gov/foia/list.html 5. DOI FOIA Contacts: http://www.doi.gov/foia/contacts.html 6. DOI FOIA...
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NASA Astrophysics Data System (ADS)
EPL Management Team
2008-12-01
We would like to thank all our contributors, subscribers, reviewers, and readers for their interest in EPL during 2008. You each play an invaluable role in the promotion, prestige, development and success of the journal and therefore your continued support is greatly appreciated. The Directors' vision for EPL to become a leading home for global physics letters, to offer rapid publication of ground-breaking physics results from the international community, and to provide the broadest coverage of physics research, is beginning to take shape as increased submissions, reduced acceptance rates, raised scientific quality, rapid publication, and greater visibility amongst the community are achieved. The latest published articles will continue to be freely available for 30 days from their on-line publication. Those articles highlighted by the Co-Editors in 2008 will remain free-to-all for the entire of 2009. We invite you to visit the website regularly (http://www.epljournal.org) to stay up-to-date with the journal's latest developments and to read the most recent articles. Our most recent opportunity publicized on the EPL website and in the CERN SCOAP3 (Sponsoring Consortium for Open Access Publishing in Particle Physics) messages is below: Open Access Opportunity for Authors of Experimental and Theoretical HEP Articles EPL is delighted to offer open access free of charge to all authors submitting experimental and theoretical letters in PACS codes 10 and 20. This offer will remain open until the SCOAP3 agreement at CERN takes effect. Authors submitting any article to EPL will continue to be offered the opportunity to make their published letter open access for a one-off payment. However, with effect from 1 November 2008, any author who submits work related to subject areas within PACS 10 and 20 will benefit from open access at no charge, meaning their published article will be available free to all readers, forever. ``Physics of Elementary Particles and Fields'' and ``Nuclear Physics'' are two research areas focusing on the HEP community, that the EPLA Directors recognize as significant to the broadband development of EPL, and they endeavour to increase the number of high-quality research letters published in these fields, to engage more closely with the High Energy Physics community, and to strengthen and promote the journal. All submitted articles will still be subject to rigorous peer review to maintain the high standard of articles published in EPL, and will benefit from expert leadership within the Editorial Board and rapid publication in addition to open access. You are invited to submit your paper now on https://www.epletters.net to take advantage of this fantastic offer. If you have comments or questions about changes taking place in 2009, please e-mail us at info@epljournal.org or editorial.office@epletters.net. With our best wishes for 2009!