Indian Ocean analyses

NASA Technical Reports Server (NTRS)

Meyers, Gary

1992-01-01

The background and goals of Indian Ocean thermal sampling are discussed from the perspective of a national project which has research goals relevant to variation of climate in Australia. The critical areas of SST variation are identified. The first goal of thermal sampling at this stage is to develop a climatology of thermal structure in the areas and a description of the annual variation of major currents. The sampling strategy is reviewed. Dense XBT sampling is required to achieve accurate, monthly maps of isotherm-depth because of the high level of noise in the measurements caused by aliasing of small scale variation. In the Indian Ocean ship routes dictate where adequate sampling can be achieved. An efficient sampling rate on available routes is determined based on objective analysis. The statistical structure required for objective analysis is described and compared at 95 locations in the tropical Pacific and 107 in the tropical Indian Oceans. XBT data management and quality control methods at CSIRO are reviewed. Results on the mean and annual variation of temperature and baroclinic structure in the South Equatorial Current and Pacific/Indian Ocean Throughflow are presented for the region between northwest Australia and Java-Timor. The mean relative geostrophic transport (0/400 db) of Throughflow is approximately 5 x 106 m3/sec. A nearly equal volume transport is associated with the reference velocity at 400 db. The Throughflow feeds the South Equatorial Current, which has maximum westward flow in August/September, at the end of the southeasterly Monsoon season. A strong semiannual oscillation in the South Java Current is documented. The results are in good agreement with the Semtner and Chervin (1988) ocean general circulation model. The talk concludes with comments on data inadequacies (insufficient coverage, timeliness) particular to the Indian Ocean and suggestions on the future role that can be played by Data Centers, particularly with regard to quality control of data as research bodies are replaced by operational bodies in the Global Ocean Observing System.

Rotational coherent anti-stokes Raman spectroscopy measurements in a rotating cavity with axial throughflow of cooling air: oxygen concentration measurements.

PubMed

Black, J D; Long, C A

1992-07-20

In a rotating cavity rig, which models cooling air flow in the spaces between disks of a gas turbine compressor, the buildup of oxygen concentration after the cooling gas was changed from nitrogen to air was monitored using rotational coherent anti-Stokes Raman spectroscopy (CARS). From this information an estimate of the fraction of the throughflow entering the rotating cavity was obtained. This demonstrates that rotational CARS can be applied as a nonintrusive concentration-measurement technique in a rotating engineering test rig.

Coral radiocarbon constraints on the source of the Indonesian throughflow

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

Moore, M.D.; Schrag, D.P.; Kashgarian, M.

1997-06-01

Radiocarbon variability in {ital Porites} spp. corals from Guam and the Makassar Strait (Indonesian Seaway) was used to identify the source waters contributing to the Indonesian throughflow. Time series with bimonthly resolution were constructed using accelerator mass spectrometry. The seasonal variability ranges from 15 to 60{per_thousand}, with large interannual variability. {Delta}{sup 14}C values from Indonesia and Guam have a nearly identical range. Annual mean {Delta}{sup 14}C values from Indonesia are 50 to 60{per_thousand} higher than in corals from Canton in the South Equatorial Current [{ital Druffel}, 1987]. These observations support a year-round North Pacific source for the Indonesian throughflow andmore » imply negligible contribution by South Equatorial Current water. The large seasonality in {Delta}{sup 14}C values from both sites emphasizes the dynamic behavior of radiocarbon in the surface ocean and suggests that {Delta}{sup 14}C time series of similar resolution can help constrain seasonal and interannual changes in ocean circulation in the Pacific over the last several decades.{copyright} 1997 American Geophysical Union« less

Experimental and computational results from a large low-speed centrifugal impeller

NASA Technical Reports Server (NTRS)

Hathaway, M. D.; Chriss, R. M.; Wood, J. R.; Strazisar, A. J.

1993-01-01

An experimental and computational investigation of the NASA Low-Speed Centrifugal Compressor (LSCC) flow field has been conducted using laser anemometry and Dawes' 3D viscous code. The experimental configuration consists of a backswept impeller followed by a vaneless diffuser. Measurements of the three-dimensional velocity field were acquired at several measurement planes through the compressor. The measurements describe both the throughflow and secondary velocity field along each measurement plane and in several cases provide details of the flow within the blade boundary layers. The experimental and computational results provide a clear understanding of the development of the throughflow momentum wake which is characteristic of centrifugal compressors.

Porous structure, permeability, and mechanical properties of polyolefin microporous films

NASA Astrophysics Data System (ADS)

Elyashevich, G. K.; Kuryndin, I. S.; Lavrentyev, V. K.; Bobrovsky, A. Yu.; Bukošek, V.

2012-09-01

Microporous films of polyolefins, namely, polyethylene and polypropylene, have been prepared using the process based on the extrusion of the melt with the subsequent annealing, uniaxial extension, and thermal fixation. The influence of the conditions used for preparation of the films on their morphology, porosity, number and sizes of through-flow channels, and mechanical properties has been investigated. It has been found that a significant influence on the characteristics of the porous structure of the films is exerted by the degree of orientation of the melt at extrusion, the annealing temperature, and the degree of uniaxial extension of the films. The threshold values of these parameters, at which through-flow channels are formed in the films, have been determined. It has been shown using filtration porosimetry that polyethylene films have a higher permeability to liquids as compared to the polypropylene samples (240 and 180 L/(m2 h atm), respectively). The porous structure of the polyethylene films is characterized by larger sizes of through pores than those of the polypropylene samples (the average pore sizes are 210 and 160 nm, respectively), whereas the polypropylene films contain a larger number of through-flow channels.

Performance potential of air turbo-ramjet employing supersonic through-flow fan

NASA Technical Reports Server (NTRS)

Kepler, C. E.; Champagne, G. A.

1989-01-01

A study was conducted to assess the performance potential of a supersonic through-flow fan in an advanced engine designed to power a Mach-5 cruise vehicle. It included a preliminary evaluation of fan performance requirements and the desirability of supersonic versus subsonic combustion, the design and performance of supersonic fans, and the conceptual design of a single-pass air-turbo-rocket/ramjet engine for a Mach 5 cruise vehicle. The study results showed that such an engine could provide high thrust over the entire speed range from sea-level takeoff to Mach 5 cruise, especially over the transonic speed range, and high fuel specific impulse at the Mach 5 cruise condition, with the fan windmilling.

Operational procedure for computer program for design point characteristics of a compressed-air generator with through-flow combustor for V/STOL applications

NASA Technical Reports Server (NTRS)

Krebs, R. P.

1971-01-01

The computer program described in this report calculates the design-point characteristics of a compressed-air generator for use in V/STOL applications such as systems with a tip-turbine-driven lift fan. The program computes the dimensions and mass, as well as the thermodynamic performance of a model air generator configuration which involves a straight through-flow combustor. Physical and thermodynamic characteristics of the air generator components are also given. The program was written in FORTRAN IV language. Provision has been made so that the program will accept input values in either SI units or U.S. customary units. Each air generator design-point calculation requires about 1.5 seconds of 7094 computer time for execution.

Measurements within the Pacific-Indian oceans throughflow region

NASA Astrophysics Data System (ADS)

Fieux, M.; Andrié, C.; Delecluse, P.; Ilahude, A. G.; Kartavtseff, A.; Mantisi, F.; Molcard, R.; Swallow, J. C.

1994-07-01

Two hydrographic (θ, S, O 2) and trichlorofluoromethane (F-11) sections were carried out between the Australian continental shelf and Indonesia, in August 1989, on board the R.V. Marion Dufresne. The sections lie in the easternmost part of the Indian Ocean where the throughflow between the Pacific Ocean and the Indian Ocean emerges. They allow us to describe the features of the water-property and circulation fields of the throughflow at its entrance in the Indian Ocean. Between the Australian continental shelf and Bali, the Subtropical and Central waters are separated from the waters of the Indonesian seas by a sharp hydrological front, located around 13°30 S, below the thermocline down to 700 m. Near the coast of Bali, upwelling occurs in the near-surface layer under the effect of the southeast monsoon; at depth, between 300 m to more than 800 m, a water mass of northern Indian Ocean origin was present. From the characteristics of the bottom water found in the Lombok basin, the maximum depth of the Java ridge which separates the Lombok basin from the Northwest Australian basin lies around 3650 m. Off Sumba, Savu, Roti and Timor channels a core of low salinity and high oxygen content near-surface water was found in the axis of each channel, which suggests strong currents from the interior Indonesian seas towards the Indian Ocean. The entrance of the deep water flowing in the opposite direction, from the Indian Ocean to the Timor basin, was marked below 1400 m to the sill depth, through an increase of salinity and oxygen content. The flow reversal, observed briefly by a Pegasus direct current profiler in the Timor strait, was located at 1200 m depth. During the southeast monsoon, the net (geostrophic + Ekman) transport calculated on the section Australia-Bali give an estimate of the throughflow between 0 and 500 m of 22 ± 4 × 10 6 m 3 s -1 towards the Indian Ocean, with a concentration of the transport in the upper layers (19 × 10 6 m 3 s -1 in 0-200 m) and near the Indonesian coast, north of 13°30 S. In this region of intense mixing, attempts to make a salinity budget were inconclusive but did not imply any reduction in estimated throughflow transport. Below 500 m the net transport is of the order of the uncertainty. The total estimated transport (0-1900 dbar, deepest sill depth) is 18.6 × 10 6 m 3 s -1 (±7) with a mean temperature of 23°C and a mean salinity of 34.0 psu (but may be as large as 23 × 10 6 m 3 s -1, with mean temperature of 20°C and mean salinity of 34.1 psu).

Supersonic through-flow fan engine and aircraft mission performance

NASA Technical Reports Server (NTRS)

Franciscus, Leo C.; Maldonado, Jaime J.

1989-01-01

A study was made to evaluate potential improvement to a commercial supersonic transport by powering it with supersonic through-flow fan turbofan engines. A Mach 3.2 mission was considered. The three supersonic fan engines considered were designed to operate at bypass ratios of 0.25, 0.5, and 0.75 at supersonic cruise. For comparison a turbine bypass turbojet was included in the study. The engines were evaluated on the basis of aircraft takeoff gross weight with a payload of 250 passengers for a fixed range of 5000 N.MI. The installed specific fuel consumption of the supersonic fan engines was 7 to 8 percent lower than that of the turbine bypass engine. The aircraft powered by the supersonic fan engines had takeoff gross weights 9 to 13 percent lower than aircraft powered by turbine bypass engines.

Glacial reduction and millennial-scale variations in Drake Passage throughflow.

PubMed

Lamy, Frank; Arz, Helge W; Kilian, Rolf; Lange, Carina B; Lembke-Jene, Lester; Wengler, Marc; Kaiser, Jérôme; Baeza-Urrea, Oscar; Hall, Ian R; Harada, Naomi; Tiedemann, Ralf

2015-11-03

The Drake Passage (DP) is the major geographic constriction for the Antarctic Circumpolar Current (ACC) and exerts a strong control on the exchange of physical, chemical, and biological properties between the Atlantic, Pacific, and Indian Ocean basins. Resolving changes in the flow of circumpolar water masses through this gateway is, therefore, crucial for advancing our understanding of the Southern Ocean's role in global ocean and climate variability. Here, we reconstruct changes in DP throughflow dynamics over the past 65,000 y based on grain size and geochemical properties of sediment records from the southernmost continental margin of South America. Combined with published sediment records from the Scotia Sea, we argue for a considerable total reduction of DP transport and reveal an up to ∼ 40% decrease in flow speed along the northernmost ACC pathway entering the DP during glacial times. Superimposed on this long-term decrease are high-amplitude, millennial-scale variations, which parallel Southern Ocean and Antarctic temperature patterns. The glacial intervals of strong weakening of the ACC entering the DP imply an enhanced export of northern ACC surface and intermediate waters into the South Pacific Gyre and reduced Pacific-Atlantic exchange through the DP ("cold water route"). We conclude that changes in DP throughflow play a critical role for the global meridional overturning circulation and interbasin exchange in the Southern Ocean, most likely regulated by variations in the westerly wind field and changes in Antarctic sea ice extent.

Glacial reduction and millennial-scale variations in Drake Passage throughflow

PubMed Central

Lamy, Frank; Arz, Helge W.; Kilian, Rolf; Lange, Carina B.; Lembke-Jene, Lester; Wengler, Marc; Kaiser, Jérôme; Baeza-Urrea, Oscar; Hall, Ian R.; Harada, Naomi; Tiedemann, Ralf

2015-01-01

The Drake Passage (DP) is the major geographic constriction for the Antarctic Circumpolar Current (ACC) and exerts a strong control on the exchange of physical, chemical, and biological properties between the Atlantic, Pacific, and Indian Ocean basins. Resolving changes in the flow of circumpolar water masses through this gateway is, therefore, crucial for advancing our understanding of the Southern Ocean’s role in global ocean and climate variability. Here, we reconstruct changes in DP throughflow dynamics over the past 65,000 y based on grain size and geochemical properties of sediment records from the southernmost continental margin of South America. Combined with published sediment records from the Scotia Sea, we argue for a considerable total reduction of DP transport and reveal an up to ∼40% decrease in flow speed along the northernmost ACC pathway entering the DP during glacial times. Superimposed on this long-term decrease are high-amplitude, millennial-scale variations, which parallel Southern Ocean and Antarctic temperature patterns. The glacial intervals of strong weakening of the ACC entering the DP imply an enhanced export of northern ACC surface and intermediate waters into the South Pacific Gyre and reduced Pacific–Atlantic exchange through the DP (“cold water route”). We conclude that changes in DP throughflow play a critical role for the global meridional overturning circulation and interbasin exchange in the Southern Ocean, most likely regulated by variations in the westerly wind field and changes in Antarctic sea ice extent. PMID:26417070

ECOSYSTEM GROWTH AND DEVELOPMENT

EPA Science Inventory

Thermodynamically, ecosystem growth and development is the process by which energy throughflow and stored biomass increase. Several proposed hypotheses describe the natural tendencies that occur as an ecosystem matures, and here, we consider five: minimum entropy production, maxi...

Vapor-dominated zones within hydrothermal systems: evolution and natural state

USGS Publications Warehouse

Ingebritsen, S.E.; Sorey, M.L.

1988-01-01

Three conceptual models illustrate the range of hydrothermal systems in which vapor-dominated conditions are found. The first model (model I) represents a system with an extensive near-vaporstatic vapor-dominated zone and limited liquid throughflow and is analogous to systems such as The Geysers, California. Models II and III represent systems with significant liquid throughflow and include steam-heated discharge features at higher elevations and high-chloride springs at lower elevations connected to and fed by a single circulation system at depth. In model II, as in model I, the vapor-dominated zone has a near-vaporstatic vertical pressure gradient and is generally underpressured with respect to local hydrostatic pressure. The vapor-dominated zone in model III is quite different, in that phase separation takes place at pressures close to local hydrostatic and the overall pressure gradient is near hydrostatic. -from Authors

Modelling the influence of elevation and snow regime on winter stream temperature in the rain-on-snow zone

NASA Astrophysics Data System (ADS)

Leach, J.; Moore, D.

2015-12-01

Winter stream temperature of coastal mountain catchments influences fish growth and development. Transient snow cover and advection associated with lateral throughflow inputs are dominant controls on stream thermal regimes in these regions. Existing stream temperature models lack the ability to properly simulate these processes. Therefore, we developed and evaluated a conceptual-parametric catchment-scale stream temperature model that includes the role of transient snow cover and lateral advection associated with throughflow. The model provided reasonable estimates of observed stream temperature at three test catchments. We used the model to simulate winter stream temperature for virtual catchments located at different elevations within the rain-on-snow zone. The modelling exercise examined stream temperature response associated with interactions between elevation, snow regime, and changes in air temperature. Modelling results highlight that the sensitivity of winter stream temperature response to changes in climate may be dependent on catchment elevation and landscape position.

Sensitivity of equatorial Pacific and Indian Ocean watermasses to the position of the Indonesian Throughflow

NASA Astrophysics Data System (ADS)

Rodgers, Keith B.; Latif, Mojib; Legutke, Stephanie

2000-09-01

The sensitivity of the thermal structure of the equatorial Pacific and Indian Ocean pycnoclines to a model's representation of the Indonesian Straits connecting the two basins is investigated. Two integrations are performed using the global HOPE ocean model. The initial conditions and surface forcing for both cases are identical; the only difference between the runs is that one has an opening for the Indonesian Straits which spans the equator on the Pacific side, and the other has an opening which lies fully north of the equator. The resulting sensitivity throughout much of the upper ocean is greater than 0.5°C for both the equatorial Indian and Pacific. A realistic simulation of net Indonesian Throughflow (ITF) transport (measured in Sverdrups) is not sufficient for an adequate simulation of equatorial watermasses. The ITF must also contain a realistic admixture of northern and southern Pacific source water.

Ecosystem growth and development.

PubMed

Fath, Brian D; Jørgensen, Sven E; Patten, Bernard C; Straskraba, Milan

2004-11-01

One of the most important features of biosystems is how they are able to maintain local order (low entropy) within their system boundaries. At the ecosystem scale, this organization can be observed in the thermodynamic parameters that describe it, such that these parameters can be used to track ecosystem growth and development during succession. Thermodynamically, ecosystem growth is the increase of energy throughflow and stored biomass, and ecosystem development is the internal reorganization of these energy mass stores, which affect transfers, transformations, and time lags within the system. Several proposed hypotheses describe thermodynamically the orientation or natural tendency that ecosystems follow during succession, and here, we consider five: minimize specific entropy production, maximize dissipation, maximize exergy storage (includes biomass and information), maximize energy throughflow, and maximize retention time. These thermodynamic orientors were previously all shown to occur to some degree during succession, and here we present a refinement by observing them during different stages of succession. We view ecosystem succession as a series of four growth and development stages: boundary, structural, network, and informational. We demonstrate how each of these ecological thermodynamic orientors behaves during the different growth and development stages, and show that while all apply during some stages only maximizing energy throughflow and maximizing exergy storage are applicable during all four stages. Therefore, we conclude that the movement away from thermodynamic equilibrium, and the subsequent increase in organization during ecosystem growth and development, is a result of system components and configurations that maximize the flux of useful energy and the amount of stored exergy. Empirical data and theoretical models support these conclusions.

Monthly Variation of Taiwan Strait Through-flow Transports and Associated Water Masses

NASA Astrophysics Data System (ADS)

Jan, S.; Sheu, D.; Kuo, H.

2005-05-01

Through-flow transports and associated water masses are analyzed using current data measured by bottom-mounted and ship-board ADCP (1999-2001) across the central Taiwan Strait and strait-wide hydrographic data acquired from 79 CTD survey cruises (1986-2003). The East Asian monsoon, from southwest in July to August and northeast in October to March, controls the transport fluctuation which peaks in August (2.34 Sv northward), is hampered by the northeast monsoon after September and diminishes to the minimum (0.26 Sv southward) in December. The standard deviation of the calculated transport ranges from 0.56 to 1.05 Sv during northeast monsoon months and is relatively small in other months. A cluster analysis together with conventional T-S diagrams identifies the saline and warm Kuroshio Branch Water (KBW), the less saline South China Sea Surface Water (SCSSW), the brackish and cold China Coastal Water (CCW), the saline Subsurface Water (SW) (depth > 100 m) and the Diluted Coastal Water (DCW). The majority of the northward transport in summer carries the SCSSW to the East China Sea. Meanwhile, the DCW appears off the northwest bank of the strait and the SW resides in the bottom layer of a deep trench in the southeastern strait. The onset of the northeast monsoon in September drives the CCW from the Yangtze river mouth to the northern strait. In the southern strait, the northward-moving KBW replaces the SCSSW and meets the southward-intruding CCW in the middle strait during November to April.

Role of the Indonesian Throughflow in controlling regional mean climate and rainfall variability

NASA Astrophysics Data System (ADS)

England, Matthew H.; Santoso, Agus; Phipps, Steven; Ummenhofer, Caroline

2017-04-01

The role of the Indonesian Throughflow (ITF) in controlling regional mean climate and rainfall is examined using a coupled ocean-atmosphere general circulation model. Experiments employing both a closed and open ITF are equilibrated to steady state and then 200 years of natural climatic variability is assessed within each model run, with a particular focus on the Indian Ocean region. Opening of the ITF results in a mean Pacific-to-Indian throughflow of 21 Sv (1 Sv = 106 m3 sec-1), which advects warm west Pacific waters into the east Indian Ocean. This warm signature is propagated westward by the mean ocean flow, however it never reaches the west Indian Ocean, as an ocean-atmosphere feedback in the tropics generates a weakened trade wind field that is reminiscent of the negative phase of the Indian Ocean Dipole (IOD). This is in marked contrast to the Indian Ocean response to an open ITF when examined in ocean-only model experiments; which sees a strengthening of both the Indian Ocean South Equatorial Current and the Agulhas Current. The coupled feedback in contrast leads to cooler conditions over the west Indian Ocean, and an anomalous zonal atmospheric pressure gradient that enhances the advection of warm moist air toward south Asia and Australia. This leaves the African continent significantly drier, and much of Australia and southern Asia significantly wetter, in response to the opening of the ITF. Given the substantial interannual variability that the ITF exhibits in the present-day climate system, and the restriction of the ITF gateway in past climate eras, this could have important implications for understanding past and present regional rainfall patterns around the Indian Ocean and over neighbouring land-masses.

Long-term Variation of the East Sea Throughflow and its Possible Influences on the East Sea Warming

NASA Astrophysics Data System (ADS)

Kang, H.; Lee, H.; Kang, S.; Jung, K.

2006-12-01

The prominent long-term change of the East Sea (Japan Sea) is the deep water warming and the depletion of oxygen in the deep layer during the last 40 years. The cause of this phenomena explained mainly by the slow down of the deep convection in the northern region influenced by the global warming. A distinguished feature of the East Sea is the upper layer flow through the three major straits connected to the Pacific Ocean. Generally, East Sea Throughflow (EST) supplies the warm water through the Korea Strait and drains relatively cold water through the Tsugaru and the Soya Straits. In this study, the role of the EST transport variation on the East Sea warming has been investigated. To understand the EST transport variablililty, monthly mean EST transport time series extracted from the Simple Ocean Data Assimilation (SODA 1.4.2) data during the period of 1958 to 2001. It shows that winter time transport anomaly seems to have overall increasing trend with PDO (Pacific Decadal Oscillation) like fluctuation. The relation between the EST transport anomaly and the local or remote wind stress anomaly has been studied. We have also carried out a numerical experiment using a three-dimensional regional model to understand the East Sea response to the long-term EST transport change. Though the throughflow confined in the upper layer, it is interesting to note that the EST can affect on the meridional overturning strength by way of changing the heat transport amount to the convection favorable region. Possible influences of the EST transport variablity on the East Sea warming are discussed.

The herbicide glyphosate and its metabolite AMPA in the Lavaux vineyard area, western Switzerland: proof of widespread export to surface waters. Part II: the role of infiltration and surface runoff.

PubMed

Daouk, Silwan; De Alencastro, Luiz F; Pfeifer, Hans-Rudolf

2013-01-01

Two parcels of the Lavaux vineyard area, western Switzerland, were studied to assess to which extent the widely used herbicide, glyphosate, and its metabolite aminomethylphosphonic acid (AMPA) were retained in the soil or exported to surface waters. They were equipped at their bottom with porous ceramic cups and runoff collectors, which allowed retrieving water samples for the growing seasons 2010 and 2011. The role of slope, soil properties and rainfall regime in their export was examined and the surface runoff/throughflows ratio was determined with a mass balance. Our results revealed elevated glyphosate and AMPA concentrations at 60 and 80 cm depth at parcel bottoms, suggesting their infiltration in the upper parts of the parcels and the presence of preferential flows in the studied parcels. Indeed, the succession of rainy days induced the gradual saturation of the soil porosity, leading to rapid infiltration through macropores, as well as surface runoff formation. Furthermore, the presence of more impervious weathered marls at 100 cm depth induced throughflows, the importance of which in the lateral transport of the herbicide molecules was determined by the slope steepness. Mobility of glyphosate and AMPA into the unsaturated zone was thus likely driven by precipitation regime and soil characteristics, such as slope, porosity structure and layer permeability discrepancy. Important rainfall events (>10 mm/day) were clearly exporting molecules from the soil top layer, as indicated by important concentrations in runoff samples. The mass balance showed that total loss (10-20%) mainly occurred through surface runoff (96%) and, to a minor extent, by throughflows in soils (4%), with subsequent exfiltration to surface waters.

Rate dependent fractionation of sulfur isotopes in through-flowing systems

NASA Astrophysics Data System (ADS)

Giannetta, M.; Sanford, R. A.; Druhan, J. L.

2017-12-01

The fidelity of reactive transport models in quantifying microbial activity in the subsurface is often improved through the use stable isotopes. However, the accuracy of current predictions for microbially mediated isotope fractionations within open through-flowing systems typically depends on nutrient availability. This disparity arises from the common application of a single `effective' fractionation factor assigned to a given system, despite extensive evidence for variability in the fractionation factor between eutrophic environments and many naturally occurring, nutrient-limited environments. Here, we demonstrate a reactive transport model with the capacity to simulate a variable fractionation factor over a range of microbially mediated reduction rates and constrain the model with experimental data for nutrient limited conditions. Two coupled isotope-specific Monod rate laws for 32S and 34S, constructed to quantify microbial sulfate reduction and predict associated S isotope partitioning, were parameterized using a series of batch reactor experiments designed to minimize microbial growth. In the current study, we implement these parameterized isotope-specific rate laws within an open, through-flowing system to predict variable fractionation with distance as a function of sulfate reduction rate. These predictions are tested through a supporting laboratory experiment consisting of a flow-through column packed with homogenous porous media inoculated with the same species of sulfate reducing bacteria used in the previous batch reactors, Desulfovibrio vulgaris. The collective results of batch reactor and flow-through column experiments support a significant improvement for S isotope predictions in isotope-sensitive multi-component reactive transport models through treatment of rate-dependent fractionation. Such an update to the model will better equip reactive transport software for isotope informed characterization of microbial activity within energy and nutrient limited environments.

A proposed through-flow inverse method for the design of mixed-flow pumps

NASA Technical Reports Server (NTRS)

Borges, Joao Eduardo

1991-01-01

A through-flow (hub-to-shroud) truly inverse method is proposed and described. It uses an imposition of mean swirl, i.e., radius times mean tangential velocity, given throughout the meridional section of the turbomachine as an initial design specification. In the present implementation, it is assumed that the fluid is inviscid, incompressible, and irrotational at inlet and that the blades are supposed to have zero thickness. Only blade rows that impart to the fluid a constant work along the space are considered. An application of this procedure to design the rotor of a mixed-flow pump is described in detail. The strategy used to find a suitable mean swirl distribution and the other design inputs is also described. The final blade shape and pressure distributions on the blade surface are presented, showing that it is possible to obtain feasible designs using this technique. Another advantage of this technique is the fact that it does not require large amounts of CPU time.

SPCZ zonal events and downstream influence on surface ocean conditions in the Indonesian Throughflow region

NASA Astrophysics Data System (ADS)

Linsley, Braddock K.; Wu, Henry C.; Rixen, Tim; Charles, Christopher D.; Gordon, Arnold L.; Moore, Michael D.

2017-01-01

Seasonal surface freshening of the Makassar Strait, the main conduit of the Indonesian Throughflow (ITF), is a key factor controlling the ITF. Here we present a 262 year reconstruction of seasonal sea-surface-salinity variability from 1742 to 2004 Common Era by using coral δ18O records from the central Makassar Strait. Our record reveals persistent seasonal freshening and also years with significant truncations of seasonal freshening that correlate exactly with South Pacific Convergence Zone (SPCZ) zonal events >4000 km to the east. During these events, the SPCZ dramatically rotates 15° north to near the equator and stronger westward flowing South Pacific boundary currents force higher-salinity water through the Makassar Strait in February-May halting the normal seasonal freshening in the strait. By these teleconnections, our Makassar coral δ18O series provides the first record of the recurrence interval of these zonal SPCZ events and demonstrates that they have occurred on a semiregular basis since the mid-1700s.

Marine Isotope Stage (MIS) M2 ( 3.3 Ma) in the southern hemisphere: constraining the climatic drivers of a short-term glaciation event during the Pliocene warm Period.

NASA Astrophysics Data System (ADS)

De Vleeschouwer, D.; Auer, G.; Bogus, K.; Groeneveld, J.; Henderiks, J.; Jatiningrum, R. S.; Christensen, B. A.

2017-12-01

Global climate was characterized by intriguing climate variability during the Late Pliocene (3.6 to 2.59 Ma): a brief (<100 kyr) but intense glaciation (MIS M2) interrupted the relatively warm climate state around 3.3 Ma. Until today, different hypotheses exist to explain why this glaciation event was so intense, and why the global climate system returned to warm Pliocene conditions relatively quickly. One of these proposed mechanisms is a reduced equator-to-pole heat transfer, in response to a tectonically reduced Indonesian Throughflow (ITF; De Schepper et al., 2014; Karas et al., 2011a, b). However, the scarcity of orbital-scale continuous climate archives in the outflow of the Indonesian Seaway hampers testing this hypothesis. To assess the supposed relationship between mid-Pliocene glaciations and latitudinal heat transport through the Indonesian Throughflow, we constructed a 3-kyr resolution planktonic δ18OG.sacculiferrecord for the 3.9 - 2.7 Ma interval from Site U1463 (18°59'S, 117°37'E; Northwestern Australian Shelf; IODP Expedition 356 "Indonesian Throughflow"). The U1463 oxygen isotope record concurs exceptionally well with the sea surface temperature (SST) record from Site 806 (0°19'N, 159°22'E) in the West Pacific Warm Pool (Wara et al., 2005), even during MIS M2. Hence, Site U1463 suggests an uninterrupted ITF signal during Pliocene glaciations. Surprisingly though, the U1463 δ18OG.sacculifer record exhibits a 0.5‰ offset with the nearby Site 763 record (20°35'S, 112°12'E) around MIS M2. This implies that Site 763, which lies a bit further offshore than U1463, fits better with Indian Ocean SST records (e.g. Site 214; Karas et al., 2009) across MIS M2. In conclusion, the U1463 data reveal that heat-transport through the Indonesian Throughflow did not shut down completely during MIS M2. However, its intensity decreased during MIS M2, causing Site 763 to temporarily reflect an Indian Ocean, rather than an ITF signal. References De Schepper, S. et al. 2014, Earth-Science Reviews, v. 135, p. 83-102. Karas, C. et al. 2009, Nature Geosci, v. 2, no. 6, p. 434-438. Karas, C. et al. 2011a, Earth and Planetary Science Letters, v. 301, no. 1-2, p. 117-124. -, 2011b, Paleoceanography, v. 26. Wara, M. W. et al., 2005, Science, v. 309, no. 5735, p. 758-761.

The 3-D viscous flow CFD analysis of the propeller effect on an advanced ducted propeller subsonic inlet

NASA Technical Reports Server (NTRS)

Iek, Chanthy; Boldman, Donald R.; Ibrahim, Mounir

1993-01-01

A time marching Navier-Stokes code called PARC3D was used to study the 3-D viscous flow associated with an advanced ducted propeller (ADP) subsonic inlet at take-off operating conditions. At a free stream Mach number of 0.2, experimental data for the inlet-with-propeller test model indicated that the airflow was attached on the cowl windward lip at an angle of attack of 25 degrees became unstable at 29 degrees, and separated at 30 degrees. An experimental study with a similar inlet and with no propeller (through-flow) indicated that flow separation occurred at an angle of attack a few degrees below the value observed when the inlet was tested with the propeller. This tends to indicate that the propeller exerts a favorable effect on the inlet performance. During the through-flow experiment a stationary blockage device was used to successfully simulate the propeller effect on the inlet flow field at angles of attack. In the present numerical study, this flow blockage was modeled via a PARC3D computational boundary condition (BC) called the screen BC. The principle formulation of this BC was based on the one-and-half dimension actuator disk theory. This screen BC was applied at the inlet propeller face station of the computational grid. Numerical results were obtained with and without the screen BC. The application of the screen BC in this numerical study provided results which are similar to the results of past experimental efforts in which either the blockage device or the propeller was used.

Parametric Study of a Mach 2.4 Transport Engine with Supersonic Through-Flow Rotor and Supersonic Counter-Rotating Diffuser (SSTR/SSCRD)

NASA Technical Reports Server (NTRS)

Tran, Donald H.

2004-01-01

A parametric study is conducted to evaluate a mixed-flow turbofan equipped with a supersonic through-flow rotor and a supersonic counter-rotating diffuser (SSTR/SSCRD) for a Mach 2.4 civil transport. Engine cycle, weight, and mission analyses are performed to obtain a minimum takeoff gross weight aircraft. With the presence of SSTR/SSCRD, the inlet can be shortened to provide better pressure recovery. For the same engine airflow, the inlet, nacelle, and pylon weights are estimated to be 73 percent lighter than those of a conventional inlet. The fan weight is 31 percent heavier, but overall the installed engine pod weight is 11 percent lighter than the current high-speed civil transport baseline conventional mixed-flow turbofan. The installed specific fuel consumption of the supersonic fan engine is 2 percent higher than that of the baseline turbofan at supersonic cruise. Finally, the optimum SSTR/SSCRD airplane meets the FAR36 Stage 3 noise limit and is within 7 percent of the baseline turbofan airplane takeoff gross weight over a 5000-n mi mission.

Numerical Assessment of Four-Port Through-Flow Wave Rotor Cycles with Passage Height Variation

NASA Technical Reports Server (NTRS)

Paxson, D. E.; Lindau, Jules W.

1997-01-01

The potential for improved performance of wave rotor cycles through the use of passage height variation is examined. A Quasi-one-dimensional CFD code with experimentally validated loss models is used to determine the flowfield in the wave rotor passages. Results indicate that a carefully chosen passage height profile can produce substantial performance gains. Numerical performance data are presented for a specific profile, in a four-port, through-flow cycle design which yielded a computed 4.6% increase in design point pressure ratio over a comparably sized rotor with constant passage height. In a small gas turbine topping cycle application, this increased pressure ratio would reduce specific fuel consumption to 22% below the un-topped engine; a significant improvement over the already impressive 18% reductions predicted for the constant passage height rotor. The simulation code is briefly described. The method used to obtain rotor passage height profiles with enhanced performance is presented. Design and off-design results are shown using two different computational techniques. The paper concludes with some recommendations for further work.

A Modified Through-Flow Wave Rotor Cycle with Combustor Bypass Ducts

NASA Technical Reports Server (NTRS)

Paxson Daniel E.; Nalim, M. Razi

1998-01-01

A wave rotor cycle is described which avoids the inherent problem of combustor exhaust gas recirculation (EGR) found in four-port, through-flow wave rotor cycles currently under consideration for topping gas turbine engines. The recirculated hot gas is eliminated by the judicious placement of a bypass duct which transfers gas from one end of the rotor to the other. The resulting cycle, when analyzed numerically, yields an absolute mean rotor temperature 18% below the already impressive value of the conventional four-port cycle (approximately the turbine inlet temperature). The absolute temperature of the gas leading to the combustor is also reduced from the conventional four-port design by 22%. The overall design point pressure ratio of this new bypass cycle is approximately the same as the conventional four-port cycle. This paper will describe the EGR problem and the bypass cycle solution including relevant wave diagrams. Performance estimates of design and off-design operation of a specific wave rotor will be presented. The results were obtained using a one-dimensional numerical simulation and design code.

The Indian Ocean as a Connector

NASA Astrophysics Data System (ADS)

Durgadoo, J. V.; Biastoch, A.; Boning, C. W.

2016-02-01

The Indian Ocean is a conduit for the upper ocean flow of the global thermohaline circulation. It receives water from the Pacific Ocean through the Indonesian throughflow and the Tasman leakage, and exports water into the Atlantic by means of Agulhas leakage. A small contribution from the northern Indian Ocean is also detectable within Agulhas leakage. Changes on different timescales in the various components of the Pacific inflows and the Atlantic outflow have been reported. Little is known on the role of the Indian Ocean circulation in communicating changes from the Pacific into the Atlantic, let alone any eventual alterations in response to climate change. The precise routes and timescales of Indonesian throughflow, Tasman leakage, Red Sea and Persian Gulf Waters towards the Atlantic are examined in a Lagrangian framework within a high-resolution global ocean model. In this presentation, the following questions are addressed: How are Pacific waters modified in the Indian Ocean before reaching the Agulhas system? On what timescale is water that enters the Indian Ocean from the Pacific flushed out? How important are detours in the Bay of Bengal and Arabian Sea?

Validation of the flow-through chamber (FTC) and steady-state (SS) methods for clearance rate measurements in bivalves

PubMed Central

Larsen, Poul S.; Riisgård, Hans Ulrik

2012-01-01

Summary To obtain precise and reliable laboratory clearance rate (filtration rate) measurements with the ‘flow-through chamber method’ (FTC) the design must ensure that only inflow water reaches the bivalve's inhalant aperture and that exit flow is fully mixed. As earlier recommended these prerequisites can be checked by a plot of clearance rate (CR) versus increasing through-flow (Fl) to reach a plateau, which is the true CR, but we also recommend to plot percent particles cleared versus reciprocal through-flow where the plateau becomes the straight line CR/Fl, and we emphasize that the percent of particles cleared is in itself neither a criterion for valid CR measurement, nor an indicator of appropriate ‘chamber geometry’ as hitherto adapted in many studies. For the ‘steady-state method’ (SS), the design must ensure that inflow water becomes fully mixed with the bivalve's excurrent flow to establish a uniform chamber concentration prevailing at its incurrent flow and at the chamber outlet. These prerequisites can be checked by a plot of CR versus increasing Fl, which should give the true CR at all through-flows. Theoretically, the experimental uncertainty of CR for a given accuracy of concentration measurements depends on the percent reduction in particle concentration (100×P) from inlet to outlet of the ideal ‘chamber geomety’. For FTC, it decreases with increasing values of P while for SS it first decreases but then increases again, suggesting the use of an intermediate value of P. In practice, the optimal value of P may depend on the given ‘chamber geometry’. The fundamental differences between the FTC and the SS methods and practical guidelines for their use are pointed out, and new data on CR for the blue mussel, Mytilus edulis, illustrate a design and use of the SS method which may be employed in e.g. long-term growth experiments at constant algal concentrations. PMID:23213362

Circulation and oxygenation of the glacial South China Sea

NASA Astrophysics Data System (ADS)

Li, Dawei; Chiang, Tzu-Ling; Kao, Shuh-Ji; Hsin, Yi-Chia; Zheng, Li-Wei; Yang, Jin-Yu Terence; Hsu, Shih-Chieh; Wu, Chau-Ron; Dai, Minhan

2017-05-01

Degree of oxygenation in intermediate water modulates the downward transferring efficiency of primary productivity (PP) from surface water to deep water for carbon sequestration, consequently, the storage of nutrients versus the delivery and sedimentary burial fluxes of organic matter and associated biomarkers. To better decipher the PP history of the South China Sea (SCS), appreciation about the glacial-interglacial variation of the Luzon Strait (LS) throughflow, which determines the mean residence time and oxygenation of water mass in the SCS interior, is required. Based on a well-established physical model, we conducted a 3-D modeling exercise to quantify the effects of sea level drop and monsoon wind intensity on glacial circulation pattern, thus, to evaluate effects of productivity and circulation-induced oxygenation on the burial of organic matter. Under modern climatology wind conditions, a 135 m sea-level drop results in a greater basin closeness and a ∼24% of reduction in the LS intermediate westward throughflow, consequently, an increase in the mean water residence time (from 19.0 to 23.0 years). However, when the wind intensity was doubled during glacial low sea-level conditon, the throughflow restored largely to reach a similar residence time (18.4 years) as today regardless its closeness. Comparing with present day SCS, surface circulation pattern in glacial model exhibits (1) stronger upwelling at the west off Luzon Island, and (2) an intensified southwestward jet current along the western boundary of the SCS basin. Superimposed hypothetically by stronger monsoon wind, the glacial SCS conditions facilitate greater primary productivity in the northern part. Manganese, a redox sensitive indicator, in IMAGES core MD972142 at southeastern SCS revealed a relatively reducing environment in glacial periods. Considering the similarity in the mean water residence time between modern and glacial cases, the reducing environment of the glacial southeastern SCS was thus ascribed to a productivity-induced rather than ventilation-induced consequence.

The role of the Indonesian Throughflow in equatorial Pacific thermocline ventilation

NASA Astrophysics Data System (ADS)

Rodgers, Keith B.; Cane, Mark A.; Naik, Naomi H.; Schrag, Daniel P.

1999-09-01

The role of the Indonesian Throughflow (ITF) in the thermocline circulation of the low-latitude Pacific Ocean is explored using a high-resolution primitive equation ocean circulation model. Seasonally forced runs for a domain with an open Indonesian passage are compared with seasonally forced runs for a closed Pacific domain. Three cases are considered: one with no throughflow, one with 10 Sv of imposed ITF transport, and one with 20 Sv of ITF transport. Two idealized tracers, one that tags northern component subtropical water and another that tags southern component subtropical water, are used to diagnose the mixing ratio of northern and southern component waters in the equatorial thermocline. It is found that the mixing ratio of north/south component waters in the equatorial thermocline is highly sensitive to whether the model accounts for an ITF. Without an ITF, the source of equatorial undercurrent water is primarily of North Pacific origin, with the ratio of northern to southern component water being approximately 2.75 to 1. The ratio of northern to southern component water in the Equatorial Undercurrent with 10 Sv of ITF is approximately 1.4 to 1, and the ratio with 20 Sv of imposed ITF is 1 to 1.25. Estimates from data suggest a mean mixing ratio of northern to southern component water of less than 1 to 1. Assuming that the mixing ratio changes approximately linearly as the ITF transport varies between 10 and 20 Sv, an approximate balance between northern and southern component water is reached when the ITF transport is approximately 16 Sv. It is also shown that for the isopycnal surfaces within the core of the equatorial undercurrent, a 2°C temperature front exists across the equator in the western equatorial Pacific, beneath the warm pool. The implications of the model results and the temperature data for the heat budget of the equatorial Pacific are considered.

Seasonal variation of the South Indian tropical gyre

NASA Astrophysics Data System (ADS)

Aguiar-González, Borja; Ponsoni, Leandro; Ridderinkhof, Herman; van Aken, Hendrik M.; de Ruijter, Will P. M.; Maas, Leo R. M.

2016-04-01

Based on satellite altimeter data and global atlases of temperature, salinity, wind stress and wind-driven circulation we investigate the seasonal variation of the South Indian tropical gyre and its associated open-ocean upwelling system, known as the Seychelles-Chagos Thermocline Ridge (SCTR). Results show a year-round, altimeter-derived cyclonic gyre where the upwelling regime appears closely related to seasonality of the ocean gyre, a relationship that has not been previously explored in this region. An analysis of major forcing mechanisms suggests that the thermocline ridge results from the constructive interaction of basin-scale wind stress curl, local-scale wind stress forcing and remote forcing driven by Rossby waves of different periodicity: semiannual in the west, under the strong influence of monsoonal winds; and, annual in the east, where the southeasterlies prevail. One exception occurs during winter, when the well-known westward intensification of the upwelling core, the Seychelles Dome, is shown to be largely a response of the wind-driven circulation. At basin-scale, the most outstanding feature is the seasonal shrinkage of the ocean gyre and the SCTR. From late autumn to spring, the eastward South Equatorial Countercurrent (SECC) recirculates early in the east on feeding the westward South Equatorial Current, therefore closing the gyre before arrival to Sumatra. We find this recirculation longitude migrates over 20° and collocates with the westward advance of a zonal thermohaline front emerging from the encounter between (upwelled) Indian Equatorial Water and relatively warmer and fresher Indonesian Throughflow Water. We suggest this front, which we call the Indonesian Throughflow Front, plays an important role as remote forcing to the tropical gyre, generating southward geostrophic flows that contribute to the early recirculation of the SECC.

Control of the Diurnal Pattern of Methane Emission from Emergent Aquatic Macrophytes by Gas Transport Mechanisms

NASA Technical Reports Server (NTRS)

Whiting, Gary J.; Chanton, Jeffrey P.

1995-01-01

Methane emissions from Typha latifolia (L.) showed a large mid-morning transient peak associated with rising light levels. This peak was also associated with a steep decline in lacunal CH, concentrations near the stem base. This pattern contrasted sharply with emissions from Peltandra virginica (L.) that gradually rose to a peak in the mid-afternoon corresponding to elevated air temperatures. Internal CH4 concentrations within P. virginica stems did not change significantly over the diurnal period. Stomatal conductance appeared to correlate directly with light levels in both plant types and were not associated with peak CH4 emission events in either plant. These patterns are consistent with a convective throughflow and diffusive gas ventilation systems for Typha and Peltandra, respectively. Further effects of the convective throughflow in T. latifolia were evident in the elevated CH4 concentrations measured within brown leaves as contrasted to the near ambient levels measured within live green leaves. Experimental manipulation of elevated and reduced CO2 levels in the atmosphere surrounding the plants and of light/dark periods suggested that stomatal aperture has little or no control of methane emissions from T. latifolia.

Timing and pacing of Pliocene climate and paleoenvironmental change in southwestern Australia (IODP Exp. 356, Site U1459).

NASA Astrophysics Data System (ADS)

De Vleeschouwer, D.; Bogus, K.; Auer, G.; Christensen, B. A.; Baranwal, S.; Fulthorpe, C.; Gallagher, S. J.; Groeneveld, J.; Henderiks, J.; Mamo, B. L.; Petrick, B.

2016-12-01

The Pliocene Epoch was a globally-warm, high-CO2 period, which nevertheless experienced four globally-recognized glacial events (De Schepper et al., 2014). Brief (<100 kyr) but intense glacials interrupted the relatively warm Pliocene climate at 4.9, 4.0, 3.6 and 3.3 Ma. Different hypotheses exist to explain why these glaciation events were so intense, and why the global climate system returned to warm conditions relatively quickly. Some of these hypotheses ascribe a key-role to the Indonesian Throughflow, as a regulator of equator-to-pole heat transfer. IODP Site U1459 (28°40'S, 113°34'E; Perth Basin) lies directly seaward of the Houtman-Abrolhos main reef complex. The development of a reef complex at 28°S is possible because of the "modern" Leeuwin Current, which is mainly fed by the Indonesian Throughflow. The Leeuwin Current transports warm, low-salinity, nutrient-deficient water southward along the west coast of Australia. However, the Pliocene oceanography of southwest Australia and the possible influence of a Leeuwin-like current are not well known. Here, we present orbital scale elemental data, obtained by X-ray fluorescence (XRF) core scanning to provide insight into the long-term evolution of the Leeuwin Current. The XRF-derived calcium-iron ratio time-series exhibits two distinct minima, marking two intervals where the unlithified packstones and grainstones have relatively low carbonate content. These intervals are dated at 4.0 and 3.3 Ma and thus correspond with two globally-recognized Pliocene glaciation events. During these glacials, the equator-to-pole heat transfer was likely reduced due to a restriction of the Indonesian Throughflow, which could imply that Site U1459 was under the relatively stronger influence of a colder, northwards-flowing West Australian Current at 4.0 and 3.3 Ma. De Schepper, S., et al. (2014). "A global synthesis of the marine and terrestrial evidence for glaciation during the Pliocene Epoch." Earth-Science Reviews 135: 83-102.

The experimental verification of a streamline curvature numerical analysis method applied to the flow through an axial flow fan

NASA Technical Reports Server (NTRS)

Pierzga, M. J.

1981-01-01

The experimental verification of an inviscid, incompressible through-flow analysis method is presented. The primary component of this method is an axisymmetric streamline curvature technique which is used to compute the hub-to-tip flow field of a given turbomachine. To analyze the flow field in the blade-to-blade plane of the machine, the potential flow solution of an infinite cascade of airfoils is also computed using a source model technique. To verify the accuracy of such an analysis method an extensive experimental verification investigation was conducted using an axial flow research fan. Detailed surveys of the blade-free regions of the machine along with intra-blade surveys using rotating pressure sensing probes and blade surface static pressure taps provide a one-to-one relationship between measured and predicted data. The results of this investigation indicate the ability of this inviscid analysis method to predict the design flow field of the axial flow fan test rotor to within a few percent of the measured values.

Three-dimensional flow field measurements in a radial inflow turbine scroll using LDV

NASA Technical Reports Server (NTRS)

Malak, M. F.; Hamed, A.; Tabakoff, W.

1986-01-01

The results of an experimental study of the three-dimensional flow field in a radial inflow turbine scroll are presented. A two-color LDV system was used in the measurement of three orthogonal velocity components at 758 points located throughout the scroll and the unvaned portion of the nozzle. The cold flow experimental results are presented for through-flow velocity contours and the cross velocity vectors.

Method and apparatus for cold gas reinjection in through-flow and reverse-flow wave rotors

NASA Technical Reports Server (NTRS)

Nalim, M. Razi (Inventor); Paxson, Daniel E. (Inventor)

1999-01-01

A method and apparatus for cold gas reinjection in through-flow and reverse-flow wave rotors having a plurality of channels formed around a periphery thereof. A first port injects a supply of cool air into the channels. A second port allows the supply of cool air to exit the channels and flow to a combustor. A third port injects a supply of hot gas from the combustor into the channels. A fourth port allows the supply of hot gas to exit the channels and flow to a turbine. A diverting port and a reinjection port are connected to the second and third ports, respectively. The diverting port diverts a portion of the cool air exiting through the second port as reinjection air. The diverting port is fluidly connected to the reinjection port which reinjects the reinjection air back into the channels. The reinjection air evacuates the channels of the hot gas resident therein and cools the channel walls, a pair of end walls of the rotor, ducts communicating with the rotor and subsequent downstream components. In a second embodiment, the second port receives all of the cool air exiting the channels and the diverting port diverts a portion of the cool air just prior to the cool air flowing to the combustor.

Surface water processes in the Indonesian throughflow as documented by a high-resolution coral Δ14C record

NASA Astrophysics Data System (ADS)

Fallon, Stewart J.; Guilderson, Thomas P.

2008-09-01

To explore the seasonal to decadal variability in surface water masses that contribute to the Indonesian throughflow, we have generated a 115-year bimonthly coral-based radiocarbon time series from a coral in the Makassar Straits. In the pre-bomb (pre-1955) era from 1890 to 1954, the radiocarbon time series occasionally displays a small seasonal signal (10-15‰). After 1954 the radiocarbon record increases rapidly, in response to the increased atmospheric 14C content caused by nuclear weapons testing. From 1957 to 1986 the record displays clear seasonal variability from 15 to 60‰ and the post-bomb peak (163 per mil) occurred in 1974. The seasonal cycle of radiocarbon can be attributed to variations of surface waters passing through the South Makassar Strait. Southern Makassar is under the influence of the Northwest Monsoon, which is responsible for the high austral summer radiocarbon (North Pacific waters) and the Southeast Monsoon that flushes back a mixture of low (South Pacific and upwelling altered) radiocarbon water from the Banda Sea. The coral record also shows a significant 14C peak in 1955 due to the bomb-14C water advected into this region from nuclear weapons tests in the Marshall Islands in 1954.

Rapid runoff via shallow throughflow and deeper preferential flow in a boreal catchment underlain by frozen silt (Alaska, USA)

USGS Publications Warehouse

Koch, Joshua C.; Ewing, Stephanie A.; Striegl, Robert G.; McKnight, Diane M.

2013-01-01

In high-latitude catchments where permafrost is present, runoff dynamics are complicated by seasonal active-layer thaw, which may cause a change in the dominant flowpaths as water increasingly contacts mineral soils of low hydraulic conductivity. A 2-year study, conducted in an upland catchment in Alaska (USA) underlain by frozen, well-sorted eolian silt, examined changes in infiltration and runoff with thaw. It was hypothesized that rapid runoff would be maintained by flow through shallow soils during the early summer and deeper preferential flow later in the summer. Seasonal changes in soil moisture, infiltration, and runoff magnitude, location, and chemistry suggest that transport is rapid, even when soils are thawed to their maximum extent. Between June and September, a shift occurred in the location of runoff, consistent with subsurface preferential flow in steep and wet areas. Uranium isotopes suggest that late summer runoff erodes permafrost, indicating that substantial rapid flow may occur along the frozen boundary. Together, throughflow and deep preferential flow may limit upland boreal catchment water and solute storage, and subsequently biogeochemical cycling on seasonal to annual timescales. Deep preferential flow may be important for stream incision, network drainage development, and the release of ancient carbon to ecosystems

Computational analysis of a multistage axial compressor

NASA Astrophysics Data System (ADS)

Mamidoju, Chaithanya

Turbomachines are used extensively in Aerospace, Power Generation, and Oil & Gas Industries. Efficiency of these machines is often an important factor and has led to the continuous effort to improve the design to achieve better efficiency. The axial flow compressor is a major component in a gas turbine with the turbine's overall performance depending strongly on compressor performance. Traditional analysis of axial compressors involves throughflow calculations, isolated blade passage analysis, Quasi-3D blade-to-blade analysis, single-stage (rotor-stator) analysis, and multi-stage analysis involving larger design cycles. In the current study, the detailed flow through a 15 stage axial compressor is analyzed using a 3-D Navier Stokes CFD solver in a parallel computing environment. Methodology is described for steady state (frozen rotor stator) analysis of one blade passage per component. Various effects such as mesh type and density, boundary conditions, tip clearance and numerical issues such as turbulence model choice, advection model choice, and parallel processing performance are analyzed. A high sensitivity of the predictions to the above was found. Physical explanation to the flow features observed in the computational study are given. The total pressure rise verses mass flow rate was computed.

Millennial-scale ocean current intensity changes off southernmost Chile and implications for Drake Passage throughflow

NASA Astrophysics Data System (ADS)

Lamy, F.; Arz, H. W.; Kilian, R.; Baeza Urrea, O.; Caniupan, M.; Kissel, C.; Lange, C.

2012-04-01

The Antarctic Circumpolar Current (ACC) plays an essential role in the thermohaline circulation and global climate. Today a large volume of ACC water passes through the Drake Passage, a major geographic constrain for the circumpolar flow. Satellite tracked surface drifters have shown that Subantarctic Surface water of the ACC is transported northeastward across the Southeast Pacific from ~53°S/100°W towards the Chilean coast at ~40°S/75°W where surface waters bifurcate and flow northward into the Peru Chile Current (PCC) finally reaching the Eastern Tropical Pacific, and southwards into the Cape Horn Current (CHC). The CHC thus transports a significant amount of northern ACC water towards the Drake Passage and reaches surface current velocities of up to 35 cm/s within a narrow belt of ~100-150 km width off the coast. Also at deeper water levels, an accelerated southward flow occurs along the continental slope off southernmost South America that likewise substantially contributes to the Drake Passage throughflow. Here we report on high resolution geochemical and grain-size records from core MD07-3128 (53°S; 1032 m water depth) which has been retrieved from the upper continental slope off the Pacific entrance of the Magellan Strait beneath the CHC. Magnetic grain-sizes and grain-size distributions of the terrigenous fraction reveal large amplitude changes between the Holocene and the last glacial, as well as millennial-scale variability (most pronounced during Marine Isotope Stage). Magnetic grain-sizes, silt/clay ratios, fine sand contents, sortable silt contents, and sortable silt mean grain-sizes are substantially higher during the Holocene suggesting strongly enhanced current activity. The high absolute values imply flow speeds larger than 25 cm/s as currently observed in the CHC surface current. Furthermore, winnowing processes through bottom current activity and changes in the availability of terrigenous material (ice-sheet extension and related supply of silt/clay, efficiency of the fjords in trapping sediment) might have contributed to the observed grain-size variations. Assuming that surface and bottom current strength changes are the major controlling factors, our data suggest a strongly enhanced CHC and deeper flow during the Holocene compared to the mean of the last glacial. During MIS 3, several phases of stronger current flow mostly correlate with warm sea surface temperatures at the site and, within age uncertainties, with millennial-scale warm phases in Antarctic ice cores. Taken together our data can be interpreted in terms of strongly reduced contributions of northern ACC water to the Drake Passage throughflow during the glacial in general and during millennial-scale cold phases in particular. At the same time, advection of northern ACC water into the PCC was probably enhanced. These results are consistent with model runs showing largely reduced volume transport through the Drake Passage during the last glacial maximum and an increasing throughflow during the last deglaciation that might have affected the strengthening of the Atlantic Meridional Overturning Circulation.

A calculation procedure for viscous flow in turbomachines, volume 3. [computer programs

NASA Technical Reports Server (NTRS)

Khalil, I.; Sheoran, Y.; Tabakoff, W.

1980-01-01

A method for analyzing the nonadiabatic viscous flow through turbomachine blade passages was developed. The field analysis is based upon the numerical integration of the full incompressible Navier-Stokes equations, together with the energy equation on the blade-to-blade surface. A FORTRAN IV computer program was written based on this method. The numerical code used to solve the governing equations employs a nonorthogonal boundary fitted coordinate system. The flow may be axial, radial or mixed and there may be a change in stream channel thickness in the through-flow direction. The inputs required for two FORTRAN IV programs are presented. The first program considers laminar flows and the second can handle turbulent flows. Numerical examples are included to illustrate the use of the program, and to show the results that are obtained.

Analysis of turbulent mixing in Dewakang Sill, Southern Makassar Strait

NASA Astrophysics Data System (ADS)

Risko; Atmadipoera, A. S.; Jaya, I.; Sudjono, E. H.

2017-01-01

Dewakang Sill is located in southern Makassar Strait, conveying major path of Indonesian Throughflow (ITF), as a confluence region of different water masses, such as salty Pacific water and fresh Java Sea water. Its depth is about 680 m which blocks the ITF flow below this depth into Flores Sea. This research aimed to estimate turbulent mixing in the Dewakang Sill by applying Thorpe analysis using 24 hours “yoyo” CTD data sets, acquired from MAJAFLOX Cruise in August 2015. The results showed that stratification of water masses is dominated by Pacific water origin. Those are North Pacific Subtropical thermocline and Intermediate water masses. Mean dissipation of turbulent kinetic energy (ɛ) and turbulent vertical diffusivity (Kρ ) value in the Dewakang Sill are of O(1.08 × 10-6)Wkg-1, and O(2.84 × 10-4) m2s-1 respectively. High correlation between epsilon and internal waves oscillation suggested that internal tidal waves activities are the major forcing for turbulent mixing in the study area.

Indonesian Throughflow drove Australian climate from humid Pliocene to arid Pleistocene

NASA Astrophysics Data System (ADS)

Christensen, B. A.; Renema, W.; Henderiks, J.; De Vleeschouwer, D.; Groeneveld, J.; Castañeda, I. S.; Reuning, L.; Bogus, K.; Auer, G.; Ishiwa, T.; McHugh, C.; Gallagher, S. J.; Fulthorpe, C.; Expedition 356 Scientists, I.

2016-12-01

Our understanding of the onset of aridity in Australia and associated mechanisms is limited by the availability of long, continuous climate archives, particularly for the NW shelf in the Pliocene. Five sites were cored and logged on IODP Expedition 356, western Australian margin. Analysis of the natural gamma ray (NGR) suite of downhole logs, provide insights to the timing and rate of climate change. NGR data provide an outstanding tool to assess continental humidity (K%) and aridity (Th/K, Uppm); interpretations are supported with clay mineral data. We show progressive constriction of the Indonesian Throughflow (ITF) and the emerging Maritime Continent drove Australian climate to become drier and more variable. We identify 3 intervals of latest Miocene through early Pleistocene change: sudden onset of humidity at 5.5 Ma (Humid Interval), followed by decreased humidity (Transition Interval) and establishment of the NW dust pathway (Arid Interval) at 2.3 Ma. The Humid Interval is associated with the Western Pacific Warm Pool (WPWP) expansion west to the South China Sea and higher Indian Ocean SSTs. Our study of the NW region confirms wetter climates ringed the arid center during the early Pliocene. Reduced moisture availability began at 3.3 Ma, coincident with cooling in the WPWP and elsewhere, global atmospheric circulation constriction and Indian Ocean subsurface freshening and cooling, a direct response to ITF constriction. Greatest aridity and the onset of the modern dust pathway, documented in Th/K and Uppm logs beginning 2.3 Ma, is coincident with orbitally- controlled climatic change, and reorganization of Indian Ocean circulation. Our data indicate Australian climate is driven by tectonic and oceanographic changes in the ITF. Such changes altered regional atmospheric moisture transport and Indian Ocean circulation patterns and led to a shift from Pacific to Indian Ocean influence on theNW Australian climate, well after the intensification of northern hemisphere glaciation. We conclude that the Maritime Continent is the switchboard modulating teleconnections between monsoonal and glacial climate systems.

Compilation of Abstracts of Theses Submitted by Candidates for Degrees: October 1988 to September 1989

DTIC Science & Technology

1989-09-30

to accommodate peripherally non -uniform flow modelling free of experimental uncertainties. It was effects (blockage) in the throughflow code...combines that experimental control functions with a detail in this thesis, and the results of a computer menu-driven, diagnostic subsystem to ensure...equations and design a complete (DSL) for both linear and non -linear models and automatic control system for the three dimensional compared. Cross

Euler solutions for an unbladed jet engine configuration

NASA Technical Reports Server (NTRS)

Stewart, Mark E. M.

1991-01-01

A Euler solution for an axisymmetric jet engine configuration without blade effects is presented. The Euler equations are solved on a multiblock grid which covers a domain including the inlet, bypass duct, core passage, nozzle, and the far field surrounding the engine. The simulation is verified by considering five theoretical properties of the solution. The solution demonstrates both multiblock grid generation techniques and a foundation for a full jet engine throughflow calculation.

Seasonal variation of the South Indian tropical gyre

NASA Astrophysics Data System (ADS)

Aguiar-González, Borja; Ponsoni, Leandro; Ridderinkhof, Herman; van Aken, Hendrik M.; de Ruijter, Will P. M.; Maas, Leo R. M.

2016-04-01

The South Indian tropical gyre receives and redistributes water masses from the Indonesian Throughflow (ITF), a source of Pacific Ocean water which represents the only low-latitude connector between the world oceans and, therefore, a key component in the global ocean circulation and climate system. We investigate the seasonal variation of the South Indian tropical gyre and its associated open-ocean upwelling system, known as the Seychelles-Chagos Thermocline Ridge (SCTR), based on satellite altimeter data (AVISO) and global atlases of temperature and salinity (CARS09), wind stress (SCOW) and wind-driven circulation. Two novel large-scale features governing the upper geostrophic circulation of the South Indian tropical gyre are revealed. First, the seasonal shrinkage of the ocean gyre. This occurs when the South Equatorial Countercurrent (SECC) recirculates before arrival to Sumatra from winter to spring, in apparent synchronization with the annual cycle of the ITF. Second, the open-ocean upwelling is found to vary following seasonality of the overlying geostrophic ocean gyre, a relationship that has not been previously shown for this region. An analysis of major forcing mechanisms suggests that the thermocline ridge results from the constructive interaction of basin-scale wind stress curl, local-scale wind stress forcing and remote forcing driven by Rossby waves of different periodicity: semiannual in the west, under the strong influence of monsoonal winds; and, annual in the east, where the southeasterlies prevail. One exception occurs during winter, when the well-known westward intensification of the upwelling core, the Seychelles Dome, is shown to be largely a response of the wind-driven circulation. Broadly speaking, the seasonal shrinkage of the ocean gyre (and the SCTR) is the one feature that differs most when the geostrophic circulation is compared to the wind-driven Sverdrup circulation. From late autumn to spring, the eastward SECC recirculates early in the east on feeding the westward South Equatorial Current, therefore closing the gyre before arrival to Sumatra. We find this recirculation longitude migrates over 20° and collocates with the westward advance of a zonal thermohaline front emerging from the encounter between (upwelled) Indian Equatorial Water and relatively warmer and fresher Indonesian Throughflow Water. We suggest this front, which we call the Indonesian Throughflow Front, plays an important role as forcing to the tropical gyre, generating southward geostrophic flows that contribute to the early recirculation of the SECC at longitudes more westward than predicted from the barotropic wind-driven circulation. Because our findings are based on time-averaged seasonal fields from 22 years of satellite altimeter data and from about 60 years of non-systematic sampling of ocean temperature and salinity data (CARS09), we stress the importance of further study on the possibility that interanual variability in the seasonal ITF may cause changes in the seasonal resizing of the ocean gyre and its associated upwelling ridge.

Controls on the chemistry of runoff from an upland peat catchment

NASA Astrophysics Data System (ADS)

Worrall, Fred; Burt, Tim; Adamson, John

2003-07-01

This study uses 2 years of data from a detailed weekly water sampling programme in a 11·4 km2 upland peat catchment in the Northern Pennines, UK. The sampling comprised precipitation, soil-water samples and a number of streams, including the basin outlet. Samples were analysed for: pH, conductivity, alkalinity, Na, K, Ca, Mg, Fe, Al, Total N, SO4, Cl and colour. Principal component analysis (PCA) was used to identify end-members and compositional trends in order to identify controls on the development of water composition. The study showed that the direct use of PCA had several advantages over the use of end-member mixing analysis (EMMA) as it combines an analysis of mixing and evolving waters without the assumption of having to know the compositional sources of the water. In its application to an upland peat catchment, the study supports the view that shallow throughflow at the catotelm/acrotelm boundary is responsible for storm runoff generation and shows that baseflow is controlled by cation exchange in the catotelm and mixing with a base-rich groundwater.

An 8,000 year oxygen isotope record of hydroclimatic change from Paradise Lake, central British Columbia

NASA Astrophysics Data System (ADS)

Hillman, A. L.; Abbott, M. B.; Steinman, B. A.; Pompeani, D. P.; Cwiklik, J. P.

2013-12-01

Climate in the Pacific Northwest over the Holocene has primarily been controlled by the position of the Aleutian Low (AL), which is interconnected to the Pacific Decadal Oscillation (PDO) and the El Nino Southern Oscillation (ENSO). Stable isotopes of authigenic calcite precipitated from lake water and archived as lake sediment can be used to reconstruct changes in precipitation/evaporation (P/E) balance over timescales ranging from individual years to millennia. Several records of this type from southern British Columbia and northern Washington (e.g., Castor and Cleland Lakes), as well as from the southern Yukon Territory (e.g., Marcella and Rantin Lakes) have been produced, but few records from between these two regions exist. Here, we present a record of δ18O and δ13C measurements of authigenic calcite from Paradise Lake, British Columbia (54.68259°N, 122.61154°W), a surficially closed basin, groundwater throughflow lake located in the central interior of British Columbia. A total of 14 AMS radiocarbon dates were used to provide age control for the Paradise Lake record. In sediment from 8,000-4,500 years BP, oxygen isotope values vary around a mean value of -18.0‰. From 4,500-2,000 years BP, a general trend towards more positive oxygen isotope values occurs, with increased variability in both δ18O and δ13C. A gradual shift of ~2‰ in δ18O measurements (to a mean value of -16.0‰) occurs over the last 2,000 years of the record, likely due to lower lake levels. The large magnitude mean state shifts in oxygen isotopes over the last 8,000 years are similar to that observed in the Marcella Lake record (Anderson et al., 2007), although they are of a smaller magnitude. We hypothesize that significant groundwater throughflow at Paradise Lake likely causes a muted hydrologic and isotopic response to climate forcing relative to Marcella Lake, which has more isotopically enriched water and loses a greater proportion of water via evaporation. The Paradise lake δ18O record provides insight into the response of surficially closed, throughflow lakes to changes in hydroclimatic conditions and suggests that centennial to millennial changes in Holocene precipitation-evaporation balance forced by synoptic Pacific Ocean dynamics were coherently expressed across the greater Pacific Northwest region.

Simulated and Observed Circulation in the Indonesian Seas: 1/12 deg Global HYCOM and the INSTANT Observations

DTIC Science & Technology

2010-04-14

for inter- basin exchange, including the net throughflow transport. The simulated total ITF transport (-13.4 Sv) is similar to the observational...May 2004 and 2005, November 2004, 2005 and 2006) appear to be associated with coastally-trapped Kelvin waves propagating eastward along Sumatra coast...in global HYCOM, this submerged multi-passage plateau causes the flow to separate into three branches, an eastern and central branch that feeds the

Through-Flow Calculations in Axial Turbomachinery

DTIC Science & Technology

1976-10-01

coilditions should be next on the agenda. Authors’ response: I think the process is essentially iterative between SI and S2 solutions. If SI surfaces...secondary flows in high Mach number situations. Concerning Gelder’s approach, i think that your remark is rather optimistic. We use a method based on...my remarks on Gelder’s work were based on calculations made by Gelder himself. One or two other people have managed to get the calculation through

Simulated and Observed Circulation in the Indonesian Seas: 1/12 degree Global HYCOM and the INSTANT Observations

DTIC Science & Technology

2010-01-01

Circulation in the Indonesian Seas: 1/12 degree Global HYCOM and the INSTANT Observations 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM...SUPPLEMENTARY NOTES 14. ABSTRACT A l/l 2 global version of the HYbrid Coordinate Ocean Model (HYCOM) using 3-hourly atmospheric forcing is analyzed and...TERMS Indonesian Throughflow, global HYCOM, INSTANT, Inter-ocean exchange, ocean modeling 16. SECURITY CLASSIFICATION OF: a. REPORT Unclassified b

Variability of Indonesian Throughflow and Borneo Runoff During the Last 14 kyr

NASA Astrophysics Data System (ADS)

Hendrizan, Marfasran; Kuhnt, Wolfgang; Holbourn, Ann

2017-10-01

We present a high-resolution ( 20 to 100 years temporal resolution) reconstruction of hydrological changes in the Makassar Strait over the last 14 kyr from Core SO217-18517 retrieved off the Mahakam Delta (1°32.198'S, 117°33.756'E; 698 m water depth) during the SO217 Makassar-Java Cruise. Sea surface temperatures, based on Mg/Ca of Globigerinoides ruber and alkenone UK'37, and seawater δ18O reconstructions, based on G. ruber δ18O and Mg/Ca, in combination with sortable silt grain size measurements and X-ray fluorescence (XRF) core scanner derived elemental data provide evidence for increased precipitation during the Bølling-Allerød (BA) and early Holocene and for warmer and more saline surface waters and a decrease in the intensity of the Indonesian Throughflow (ITF) during the Younger Dryas (YD). XRF derived Log (Zr/Rb) records, sortable silt data and increased sedimentation rates indicate decreased winnowing, interpreted as a slowdown of the ITF thermocline flow during the YD. We attribute this decline in ITF intensity to slowdown of the Atlantic meridional overturning circulation during the YD. We suggest that changes in Makassar Strait surface hydrology during this interval of Northern Hemisphere cooling and Southern Hemisphere warming were related to a southward displacement of the Intertropical Convergence Zone.

General specifications for the development of a USL NASA PC R and D statistical analysis support package

NASA Technical Reports Server (NTRS)

Dominick, Wayne D. (Editor); Bassari, Jinous; Triantafyllopoulos, Spiros

1984-01-01

The University of Southwestern Louisiana (USL) NASA PC R and D statistical analysis support package is designed to be a three-level package to allow statistical analysis for a variety of applications within the USL Data Base Management System (DBMS) contract work. The design addresses usage of the statistical facilities as a library package, as an interactive statistical analysis system, and as a batch processing package.

Experimental and computational investigation of the NASA Low-Speed Centrifugal Compressor flow field

NASA Technical Reports Server (NTRS)

Hathaway, M. D.; Chriss, R. M.; Wood, J. R.; Strazisar, A. J.

1992-01-01

An experimental and computational investigation of the NASA Low-Speed Centrifugal Compressor (LSCC) flow field has been conducted using laser anemometry and Dawes' 3D viscous code. The experimental configuration consists of a backswept impeller followed by a vaneless diffuser. Measurements of the three-dimensional velocity field were acquired at several measurement planes through the compressor. The measurements describe both the throughflow and secondary velocity field along each measurement plane. In several cases the measurements provide details of the flow within the blade boundary layers. Insight into the complex flow physics within centrifugal compressors is provided by the computational analysis, and assessment of the CFD predictions is provided by comparison with the measurements. Five-hole probe and hot-wire surveys at the inlet and exit to the rotor as well as surface flow visualization along the impeller blade surfaces provide independent confirmation of the laser measurement technique.

Vorticity Dynamics in Axial Compressor Flow Diagnosis and Design.

NASA Astrophysics Data System (ADS)

Wu, Jie-Zhi; Yang, Yan-Tao; Wu, Hong; Li, Qiu-Shi; Mao, Feng; Zhou, Sheng

2007-11-01

It is well recognized that vorticity and vortical structures appear inevitably in viscous compressor flows and have strong influence on the compressor performance. But conventional analysis and design procedure cannot pinpoint the quantitative contribution of each individual vortical structure to the integrated performance of a compressor, such as the stagnation-pressure ratio and efficiency. We fill this gap by using the so-called derivative-moment transformation which has been successfully applied to external aerodynamics. We show that the compressor performance is mainly controlled by the radial distribution of azimuthal vorticity, of which an optimization in the through-flow design stage leads to a simple Abel equation of the second kind. Solving the equation yields desired circulation distribution that optimizes the blade geometry. The advantage of this new procedure is demonstrated by numerical examples, including the posterior performance check by 3-D Navier-Stokes simulation.

Nonlinear stability analysis of Darcy’s flow with viscous heating

PubMed Central

Alves, Leonardo S. de B.; Barletta, Antonio

2016-01-01

The nonlinear stability of a rectangular porous channel saturated by a fluid is here investigated. The aspect ratio of the channel is assumed to be variable. The channel walls are considered impermeable and adiabatic except for the horizontal top which is assumed to be isothermal. The viscous dissipation is acting inside the channel as internal heat generator. A basic throughflow is imposed, and the nonlinear convective stability is investigated by means of the generalized integral transform technique. The neutral stability curve is compared with the one obtained by the linear stability analysis already present in the literature. The growth rate analysis of different unstable modes is performed. The Nusselt number is investigated for several supercritical configurations in order to better understand how the system behaves when conditions far away from neutral stability are considered. The patterns of the neutrally stable convective cells are also reported. Nonlinear simulations support the results obtained by means of the linear stability analysis, confirming that viscous dissipation alone is indeed capable of inducing mixed convection. Low Gebhart or high Péclet numbers lead to a transient overheating of the originally motionless fluid before it settles in its convective steady state. PMID:27279772

Seasonal Variation of the Indonesian Throughflow in Makassar Strait

DTIC Science & Technology

2012-07-01

HYCOM). Twenty-eight years (1981–2008) of 1/38 Indo-Pacific basin HYCOM simulations and three years (2004–06) from a 1/128 global HYCOM simulation are...eight years (1981?2008) of 1/ 38 Indo-Pacific basin HYCOM simulations and three years (2004?06) from a 1/ 128 global HYCOM simulation are analyzed...Wyrtki 1973) and the propa- gation of Kelvin waves along the coasts of Sumatra and Java, such as observed and modeled during May 1997 (Sprintall et

Preliminary Cultural Resource Survey and Geomorphological Assessment of Selected Areas in Navigation Pool 16, Mississippi River.

DTIC Science & Technology

1982-06-01

Dated Sites in Pool 16 .............. 28 OR 2. Stream Gauge Data for Historical - Floods, Illinois and Mississippi Canal Lock 32 (U. S. Corps of...the ridge was 30 TABLE 2 STREAM GAUGE DATA FOR HISTORICAL FLOODS, ILLINOIS AND MISSISSIPPI CANAL LOCK 32 (U. S. CORPS OF ENGINEERS 1981) Rank Order of...result of back- water activity rather than active throughflow similar to that experienced in the 1890s. Judging from river gauge records dating from

Why Do Intrathermocline Eddies Form in the Japan/East Sea? A Modeling Perspective

DTIC Science & Technology

2006-09-01

no longer be las sihied a, IT Fs. Both (a) and (b) are from Gordon et al. (2002). 136 Occanoyraphiy I Vol. 19, No. 3, Sept. 2006 retains particular...advantages associated Tsushima Strait and out through the Table 1. Layer Numbers and with the different vertical coordinate Tsugaru and Soya Straits...when it is deep- and through Soya , 0.7 Sv. Thus, the total ocean-topographical coupling via the est. Sigma (terrain-following) coordi- throughflow

Kinematics Simulation Analysis of Packaging Robot with Joint Clearance

NASA Astrophysics Data System (ADS)

Zhang, Y. W.; Meng, W. J.; Wang, L. Q.; Cui, G. H.

2018-03-01

Considering the influence of joint clearance on the motion error, repeated positioning accuracy and overall position of the machine, this paper presents simulation analysis of a packaging robot — 2 degrees of freedom(DOF) planar parallel robot based on the characteristics of high precision and fast speed of packaging equipment. The motion constraint equation of the mechanism is established, and the analysis and simulation of the motion error are carried out in the case of turning the revolute clearance. The simulation results show that the size of the joint clearance will affect the movement accuracy and packaging efficiency of the packaging robot. The analysis provides a reference point of view for the packaging equipment design and selection criteria and has a great significance on the packaging industry automation.

Corner flow control in high through-flow axial commercial fan/booster using blade 3-D optimization

NASA Astrophysics Data System (ADS)

Zhu, Fang; Jin, Donghai; Gui, Xingmin

2012-02-01

This study is aimed at using blade 3-D optimization to control corner flows in the high through-flow fan/booster of a high bypass ratio commercial turbofan engine. Two kinds of blade 3-D optimization, end-bending and bow, are focused on. On account of the respective operation mode and environment, the approach to 3-D aerodynamic modeling of rotor blades is different from stator vanes. Based on the understanding of the mechanism of the corner flow and the consideration of intensity problem for rotors, this paper uses a variety of blade 3-D optimization approaches, such as loading distribution optimization, perturbation of departure angles and stacking-axis manipulation, which are suitable for rotors and stators respectively. The obtained 3-D blades and vanes can improve the corner flow features by end-bending and bow effects. The results of this study show that flows in corners of the fan/booster, such as the fan hub region, the tip and hub of the vanes of the booster, are very complex and dominated by 3-D effects. The secondary flows there are found to have a strong detrimental effect on the compressor performance. The effects of both end-bending and bow can improve the flow separation in corners, but the specific ways they work and application scope are somewhat different. Redesigning the blades via blade 3-D optimization to control the corner flow has effectively reduced the loss generation and improved the stall margin by a large amount.

XAPiir: A recursive digital filtering package

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

Harris, D.

1990-09-21

XAPiir is a basic recursive digital filtering package, containing both design and implementation subroutines. XAPiir was developed for the experimental array processor (XAP) software package, and is written in FORTRAN. However, it is intended to be incorporated into any general- or special-purpose signal analysis program. It replaces the older package RECFIL, offering several enhancements. RECFIL is used in several large analysis programs developed at LLNL, including the seismic analysis package SAC, several expert systems (NORSEA and NETSEA), and two general purpose signal analysis packages (SIG and VIEW). This report is divided into two sections: the first describes the use ofmore » the subroutine package, and the second, its internal organization. In the first section, the filter design problem is briefly reviewed, along with the definitions of the filter design parameters and their relationship to the subroutine input parameters. In the second section, the internal organization is documented to simplify maintenance and extensions to the package. 5 refs., 9 figs.« less

The Importance of Take-Out Food Packaging Attributes: Conjoint Analysis and Quality Function Deployment Approach

NASA Astrophysics Data System (ADS)

Lestari Widaningrum, Dyah

2014-03-01

This research aims to investigate the importance of take-out food packaging attributes, using conjoint analysis and QFD approach among consumers of take-out food products in Jakarta, Indonesia. The conjoint results indicate that perception about packaging material (such as paper, plastic, and polystyrene foam) plays the most important role overall in consumer perception. The clustering results that there is strong segmentation in which take-out food packaging material consumer consider most important. Some consumers are mostly oriented toward the colour of packaging, while another segment of customers concerns on packaging shape and packaging information. Segmentation variables based on packaging response can provide very useful information to maximize image of products through the package's impact. The results of House of Quality development described that Conjoint Analysis - QFD is a useful combination of the two methodologies in product development, market segmentation, and the trade off between customers' requirements in the early stages of HOQ process

Summary of Conference

NASA Technical Reports Server (NTRS)

Morrison, Jonathan

2010-01-01

Environmental issues are a key driver. The need for better mechanisms to enable discipline hopping/crossover (materials (MEMS), control, fluids). Better sensors and actuators and better communication for these to be developed. Better understanding of the needs of the turbomachinery industry, especially in identifying where flow control can be beneficial (e.g., variable intake geometry). Challenge for flow control to be fail-safe, or to be developed for non-critical control gains (e.g., noise). more detailed information on stage through-flow behaviour (with/without control) increased use of laser interrogation (PIV, PTV, MTV).

The Centennial and Millennial Variability of the IndoPacific Warm Pool and the Indonesian Throughflow

DTIC Science & Technology

2012-02-01

proxy  is  required.  The  G.  ruber  Mg/Ca  results  suggest  that  the...interpretations,  indicating   further  work  on  this   proxy  is  required.  The  G.  ruber  Mg/Ca  results  suggest  that...the  ITCZ  would  lose  some  of  its   northward  bias.  Our  hydrologic   proxies  show  exactly  that.  Our

Experimental study of cassava sun drying

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

Njie, D.N.; Rumsey, T.R.

1997-03-01

Sun drying experiments were performed to compare drying of cassava chips in sheet-metal trays with drying on mesh wire trays. In the sheet-metal trays, there was air flow across the top of the bed chips, while the mesh wire trays permitted air to flow through the bed. Drying rate was faster and more uniform in the trays with through-flow air circulation. Higher temperatures were reached by chips in the sheet-metal trays than those in the mesh trays because of contact heating, but the drying rate was lower because of the reduced air flow.

Synchronized Schlieren method for vortex shedding in cascade during acoustic resonance

NASA Astrophysics Data System (ADS)

Nagashima, T.; Tanida, Y.

1986-10-01

An evaluation is made of synchronized schlieren optical system methods for the simultaneous visualization of both the acoustic wave and vortex shedding phenomena encountered during acoustic resonance excited by vortex shedding from the trailing edges of cascade blades. Attention is given to the case of parallel flat plate blades in throughflow velocities of up to 100 m/s. The acoustic wavefront is found to appear in the trailing edge region and travel upstream when a pair of vortices of opposite sign are fully developed at the trailing edge.

Safety analysis report for packaging (onsite) steel drum

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

McCormick, W.A.

This Safety Analysis Report for Packaging (SARP) provides the analyses and evaluations necessary to demonstrate that the steel drum packaging system meets the transportation safety requirements of HNF-PRO-154, Responsibilities and Procedures for all Hazardous Material Shipments, for an onsite packaging containing Type B quantities of solid and liquid radioactive materials. The basic component of the steel drum packaging system is the 208 L (55-gal) steel drum.

Imaging and modeling of flow in porous media using clinical nuclear emission tomography systems and computational fluid dynamics

NASA Astrophysics Data System (ADS)

Boutchko, Rostyslav; Rayz, Vitaliy L.; Vandehey, Nicholas T.; O'Neil, James P.; Budinger, Thomas F.; Nico, Peter S.; Druhan, Jennifer L.; Saloner, David A.; Gullberg, Grant T.; Moses, William W.

2012-01-01

This paper presents experimental and modeling aspects of applying nuclear emission tomography to study fluid flow in laboratory packed porous media columns of the type frequently used in geophysics, geochemistry and hydrology research. Positron emission tomography (PET) and single photon emission computed tomography (SPECT) are used as non-invasive tools to obtain dynamic 3D images of radioactive tracer concentrations. Dynamic sequences obtained using 18F-FDG PET are used to trace flow through a 5 cm diameter × 20 cm tall sand packed column with and without an impermeable obstacle. In addition, a custom-made rotating column setup placed in a clinical two-headed SPECT camera is used to image 99mTc-DTPA tracer propagation in a through-flowing column (10 cm diameter × 30 cm tall) packed with recovered aquifer sediments. A computational fluid dynamics software package FLUENT is used to model the observed flow dynamics. Tracer distributions obtained in the simulations in the smaller column uniformly packed with sand and in the column with an obstacle are remarkably similar to the reconstructed images in the PET experiments. SPECT results demonstrate strongly non-uniform flow patterns for the larger column slurry-packed with sub-surface sediment and slow upward flow. In the numerical simulation of the SPECT study, two symmetric channels with increased permeability are prescribed along the column walls, which result in the emergence of two well-defined preferential flow paths. Methods and results of this work provide new opportunities in hydrologic and biogeochemical research. The primary target application for developed technologies is non-destructive, non-perturbing, quantitative imaging of flow dynamics within laboratory scale porous media systems.

Imaging and modeling of flow in porous media using clinical nuclear emission tomography systems and computational fluid dynamics.

PubMed

Boutchko, Rostyslav; Rayz, Vitaliy L; Vandehey, Nicholas T; O'Neil, James P; Budinger, Thomas F; Nico, Peter S; Druhan, Jennifer L; Saloner, David A; Gullberg, Grant T; Moses, William W

2012-01-01

This paper presents experimental and modeling aspects of applying nuclear emission tomography to study fluid flow in laboratory packed porous media columns of the type frequently used in geophysics, geochemistry and hydrology research. Positron emission tomography (PET) and single photon emission computed tomography (SPECT) are used as non-invasive tools to obtain dynamic 3D images of radioactive tracer concentrations. Dynamic sequences obtained using 18 F-FDG PET are used to trace flow through a 5 cm diameter × 20 cm tall sand packed column with and without an impermeable obstacle. In addition, a custom-made rotating column setup placed in a clinical two-headed SPECT camera is used to image 99m Tc-DTPA tracer propagation in a through-flowing column (10 cm diameter × 30 cm tall) packed with recovered aquifer sediments. A computational fluid dynamics software package FLUENT is used to model the observed flow dynamics. Tracer distributions obtained in the simulations in the smaller column uniformly packed with sand and in the column with an obstacle are remarkably similar to the reconstructed images in the PET experiments. SPECT results demonstrate strongly non-uniform flow patterns for the larger column slurry-packed with sub-surface sediment and slow upward flow. In the numerical simulation of the SPECT study, two symmetric channels with increased permeability are prescribed along the column walls, which result in the emergence of two well-defined preferential flow paths. Methods and results of this work provide new opportunities in hydrologic and biogeochemical research. The primary target application for developed technologies is non-destructive, non-perturbing, quantitative imaging of flow dynamics within laboratory scale porous media systems.

Skills Analysis. Workshop Package on Skills Analysis, Skills Audit and Training Needs Analysis.

ERIC Educational Resources Information Center

Hayton, Geoff; And Others

This four-part package is designed to assist Australian workshop leaders running 2-day workshops on skills analysis, skills audit, and training needs analysis. Part A contains information on how to use the package and a list of workshop aims. Parts B, C, and D consist, respectively, of the workshop leader's guide; overhead transparency sheets and…

PLATSIM: A Simulation and Analysis Package for Large-Order Flexible Systems. Version 2.0

NASA Technical Reports Server (NTRS)

Maghami, Peiman G.; Kenny, Sean P.; Giesy, Daniel P.

1997-01-01

The software package PLATSIM provides efficient time and frequency domain analysis of large-order generic space platforms. PLATSIM can perform open-loop analysis or closed-loop analysis with linear or nonlinear control system models. PLATSIM exploits the particular form of sparsity of the plant matrices for very efficient linear and nonlinear time domain analysis, as well as frequency domain analysis. A new, original algorithm for the efficient computation of open-loop and closed-loop frequency response functions for large-order systems has been developed and is implemented within the package. Furthermore, a novel and efficient jitter analysis routine which determines jitter and stability values from time simulations in a very efficient manner has been developed and is incorporated in the PLATSIM package. In the time domain analysis, PLATSIM simulates the response of the space platform to disturbances and calculates the jitter and stability values from the response time histories. In the frequency domain analysis, PLATSIM calculates frequency response function matrices and provides the corresponding Bode plots. The PLATSIM software package is written in MATLAB script language. A graphical user interface is developed in the package to provide convenient access to its various features.

Multiple-Group Analysis Using the sem Package in the R System

ERIC Educational Resources Information Center

Evermann, Joerg

2010-01-01

Multiple-group analysis in covariance-based structural equation modeling (SEM) is an important technique to ensure the invariance of latent construct measurements and the validity of theoretical models across different subpopulations. However, not all SEM software packages provide multiple-group analysis capabilities. The sem package for the R…

User's manual for the coupled rotor/airframe vibration analysis graphic package

NASA Technical Reports Server (NTRS)

Studwell, R. E.

1982-01-01

User instructions for a graphics package for coupled rotor/airframe vibration analysis are presented. Responses to plot package messages which the user must make to activate plot package operations and options are described. Installation instructions required to set up the program on the CDC system are included. The plot package overlay structure and subroutines which have to be modified for the CDC system are also described. Operating instructions for CDC applications are included.

SPCZ Zonal Events and Downstream Influence on Surface Ocean Conditions in the Indonesian Throughflow Region: Implications for SPCZ Mean Position Effects on the ITF

NASA Astrophysics Data System (ADS)

Linsley, B. K.; Wu, H. C.; Rixen, T.; Charles, C. D.; Gordon, A. L.; Moore, M.

2017-12-01

Seasonal surface freshening of the Makassar Strait, the main conduit of the Indonesian Throughflow (ITF), is a key factor controlling the temperature and salinity characteristics of ITF transport to the Indian Ocean. Here we present a 262-year reconstruction of seasonal sea-surface-salinity (SSS) variability from 1742-2004 C.E. using coral oxygen isotope (δ18O) records from the central Makassar Strait. Our record reveals persistent seasonal freshening and also years with significant truncations of seasonal freshening that correlate exactly with South Pacific Convergence Zone (SPCZ) zonal events >4,000 km to the east. During these newly identified events, the SPCZ dramatically rotates 15° north to near the equator and stronger westward flowing South Pacific boundary currents transport salty water north across the equator and force higher salinity water through the Makassar Strait in February-May halting the normal seasonal freshening in the strait. By these teleconnections, our Makassar coral δ18O series provides the first record of the recurrence interval of these zonal SPCZ events and demonstrates that they have occurred on a semi-regular basis since the mid-1700s. The deeper time implications of these results suggest that long-term changes in the position of the SPCZ and ITCZ in the central equatorial Pacific would affect Pacific western boundary currents and the transport of South Pacific water north across the equator and into the ITF. Preliminary results and plans underway to evaluate this hypothesis over the last 2.5 Ma will also be presented.

Climate variability and predictability associated with the Indo-Pacific Oceanic Channel Dynamics in the CCSM4 Coupled System Model

NASA Astrophysics Data System (ADS)

Yuan, Dongliang; Xu, Peng; Xu, Tengfei

2017-01-01

An experiment using the Community Climate System Model (CCSM4), a participant of the Coupled Model Intercomparison Project phase-5 (CMIP5), is analyzed to assess the skills of this model in simulating and predicting the climate variabilities associated with the oceanic channel dynamics across the Indo-Pacific Oceans. The results of these analyses suggest that the model is able to reproduce the observed lag correlation between the oceanic anomalies in the southeastern tropical Indian Ocean and those in the cold tongue in the eastern equatorial Pacific Ocean at a time lag of 1 year. This success may be largely attributed to the successful simulation of the interannual variations of the Indonesian Throughflow, which carries the anomalies of the Indian Ocean Dipole (IOD) into the western equatorial Pacific Ocean to produce subsurface temperature anomalies, which in turn propagate to the eastern equatorial Pacific to generate ENSO. This connection is termed the "oceanic channel dynamics" and is shown to be consistent with the observational analyses. However, the model simulates a weaker connection between the IOD and the interannual variability of the Indonesian Throughflow transport than found in the observations. In addition, the model overestimates the westerly wind anomalies in the western-central equatorial Pacific in the year following the IOD, which forces unrealistic upwelling Rossby waves in the western equatorial Pacific and downwelling Kelvin waves in the east. This assessment suggests that the CCSM4 coupled climate system has underestimated the oceanic channel dynamics and overestimated the atmospheric bridge processes.

Water mass characteristic in the outflow region of the Indonesian throughflow during and post 2016 negative Indian ocean dipole event

NASA Astrophysics Data System (ADS)

Bayhaqi, A.; Iskandar, I.; Surinati, D.; Budiman, A. S.; Wardhana, A. K.; Dirhamsyah; Yuan, D.; Lestari, D. O.

2018-05-01

Strong El Niño and positive Indian Ocean Dipole (pIOD) events in 2015/2016 followed by relatively strong negative Indian Ocean Dipole (nIOD) and weak La Niña in 2016 events have affected hydrography conditions in the Indonesian Throughflow (ITF) region. Two research cruises were conducted using RV Baruna Jaya VIII in August and November 2016. These cruises aim to evaluate possible impact of those two climate mode events on the water mass characteristic in the outflow region of the ITF. Hydrographic data from those two cruises were combined with the sea surface temperature (SST) from the Advanced Very High Resolution Radiometer (AVHRR) and surface wind data from the European Centre for Medium-Range Weather Forecasts (ECMWF). The results showed that in the 2016 anomaly year, the cooler sea surface temperature was observed during the negative IOD (nIOD) event while the warmer temperature was found in the post of nIOD event. The observed water mass characteristics in the outflow region of the ITF revealed that the upper layer was dominated by the Indian Ocean water mass, while the Pacific Ocean water mass was observed in the deeper layer. The observed current data across the Sumba Strait showed that the South Java Coastal Current (SJCC) was observed in the upper layer, propagating eastward toward the Savu Sea. A few days later, the observed currents in the upper layer of the Ombai Strait revealed the ITF flow towards the Indian Ocean. Meanwhile, the lower layer showed an eastward flow towards the Ombai Strait.

clusterProfiler: an R package for comparing biological themes among gene clusters.

PubMed

Yu, Guangchuang; Wang, Li-Gen; Han, Yanyan; He, Qing-Yu

2012-05-01

Increasing quantitative data generated from transcriptomics and proteomics require integrative strategies for analysis. Here, we present an R package, clusterProfiler that automates the process of biological-term classification and the enrichment analysis of gene clusters. The analysis module and visualization module were combined into a reusable workflow. Currently, clusterProfiler supports three species, including humans, mice, and yeast. Methods provided in this package can be easily extended to other species and ontologies. The clusterProfiler package is released under Artistic-2.0 License within Bioconductor project. The source code and vignette are freely available at http://bioconductor.org/packages/release/bioc/html/clusterProfiler.html.

Poppr: an R package for genetic analysis of populations with mixed (clonal/sexual) reproduction

USDA-ARS?s Scientific Manuscript database

Poppr is an R package for analysis of population genetic data. It extends the adegenet package and provides several novel tools, particularly with regard to analysis of data from admixed, clonal, and/or sexual populations. Currently, poppr can be used for dominant/codominant and haploid/diploid gene...

A comparison of InVivoStat with other statistical software packages for analysis of data generated from animal experiments.

PubMed

Clark, Robin A; Shoaib, Mohammed; Hewitt, Katherine N; Stanford, S Clare; Bate, Simon T

2012-08-01

InVivoStat is a free-to-use statistical software package for analysis of data generated from animal experiments. The package is designed specifically for researchers in the behavioural sciences, where exploiting the experimental design is crucial for reliable statistical analyses. This paper compares the analysis of three experiments conducted using InVivoStat with other widely used statistical packages: SPSS (V19), PRISM (V5), UniStat (V5.6) and Statistica (V9). We show that InVivoStat provides results that are similar to those from the other packages and, in some cases, are more advanced. This investigation provides evidence of further validation of InVivoStat and should strengthen users' confidence in this new software package.

New Mexico Play Fairway Analysis: Particle Tracking ArcGIS Map Packages

DOE Data Explorer

Jeff Pepin

2015-11-15

These are map packages used to visualize geochemical particle-tracking analysis results in ArcGIS. It includes individual map packages for several regions of New Mexico including: Acoma, Rincon, Gila, Las Cruces, Socorro and Truth or Consequences.

PresenceAbsence: An R package for presence absence analysis

Treesearch

Elizabeth A. Freeman; Gretchen Moisen

2008-01-01

The PresenceAbsence package for R provides a set of functions useful when evaluating the results of presence-absence analysis, for example, models of species distribution or the analysis of diagnostic tests. The package provides a toolkit for selecting the optimal threshold for translating a probability surface into presence-absence maps specifically tailored to their...

An unconditionally stable Runge-Kutta method for unsteady flows

NASA Technical Reports Server (NTRS)

Jorgenson, Philip C. E.; Chima, Rodrick V.

1988-01-01

A quasi-three dimensional analysis was developed for unsteady rotor-stator interaction in turbomachinery. The analysis solves the unsteady Euler or thin-layer Navier-Stokes equations in a body fitted coordinate system. It accounts for the effects of rotation, radius change, and stream surface thickness. The Baldwin-Lomax eddy viscosity model is used for turbulent flows. The equations are integrated in time using a four stage Runge-Kutta scheme with a constant time step. Implicit residual smoothing was employed to accelerate the solution of the time accurate computations. The scheme is described and accuracy analyses are given. Results are shown for a supersonic through-flow fan designed for NASA Lewis. The rotor:stator blade ratio was taken as 1:1. Results are also shown for the first stage of the Space Shuttle Main Engine high pressure fuel turbopump. Here the blade ratio is 2:3. Implicit residual smoothing was used to increase the time step limit of the unsmoothed scheme by a factor of six with negligible differences in the unsteady results. It is felt that the implicitly smoothed Runge-Kutta scheme is easily competitive with implicit schemes for unsteady flows while retaining the simplicity of an explicit scheme.

MODEL 9977 B(M)F-96 SAFETY ANALYSIS REPORT FOR PACKAGING

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

Abramczyk, G; Paul Blanton, P; Kurt Eberl, K

2006-05-18

This Safety Analysis Report for Packaging (SARP) documents the analysis and testing performed on and for the 9977 Shipping Package, referred to as the General Purpose Fissile Package (GPFP). The performance evaluation presented in this SARP documents the compliance of the 9977 package with the regulatory safety requirements for Type B packages. Per 10 CFR 71.59, for the 9977 packages evaluated in this SARP, the value of ''N'' is 50, and the Transport Index based on nuclear criticality control is 1.0. The 9977 package is designed with a high degree of single containment. The 9977 complies with 10 CFR 71more » (2002), Department of Energy (DOE) Order 460.1B, DOE Order 460.2, and 10 CFR 20 (2003) for As Low As Reasonably Achievable (ALARA) principles. The 9977 also satisfies the requirements of the Regulations for the Safe Transport of Radioactive Material--1996 Edition (Revised)--Requirements. IAEA Safety Standards, Safety Series No. TS-R-1 (ST-1, Rev.), International Atomic Energy Agency, Vienna, Austria (2000). The 9977 package is designed, analyzed and fabricated in accordance with Section III of the American Society of Mechanical Engineers (ASME) Boiler and Pressure Vessel (B&PV) Code, 1992 edition.« less

Temperature and salinity variability in the exit passages of the Indonesian Throughflow

NASA Astrophysics Data System (ADS)

Sprintall, Janet; Potemra, James T.; Hautala, Susan L.; Bray, Nancy A.; Pandoe, Wahyu W.

2003-07-01

The Indonesian Throughflow was monitored from December 1995 until May 1999 in the five major exit passages of the Lesser Sunda Islands, as it flows from the Indonesian interior seas into the southeast Indian Ocean. The monitoring array included pairs of shallow pressure gauges at each side of the straits, equipped with temperature and salinity sensors. As in the inferred geostrophic velocity from the cross-strait pressure gauge data, the temperature and salinity data show strong variability over all time scales related to the local regional and remote forcing mechanisms of heat, freshwater and wind. The annual cycle dominates the temperature time series, with warmest temperatures occurring during the austral summer northwest monsoon, except in Lombok Strait where the semi-annual signal is dominant, and related to the Indian Ocean westerly wind-forced Kelvin waves during the monsoon transitions that supply Indian Ocean warmer surface water to the strait. In the salinity data, the annual signal again dominates the time series in all straits, with a distinct freshening occurring in March-May. This is partly related to the rainfall and resultant voluminous river runoff impacting the region, one month after the wetter northwest monsoon ends in March. The fresh, warm water from the monsoon-transition Indian Ocean Kelvin wave also contributes to the freshening observed in May. There is little cross-strait gradient in near-surface temperature and salinity through the outflow straits, except in Lombok Strait, where Lombok is warmer (except during the northwest monsoon) and fresher than the Bali site (especially during March through May). A fortnightly signal in temperature is found in Ombai and Sumba Straits, and is probably related to the proximity of these straits to the interior Banda Sea where the fortnightly tidal signal is strong. The fortnightly signal is also evident at the Bali site, although not at the Lombok site. Numerous ADCP surveys taken during the survey period suggest a western intensification of the flow through Lombok Strait, such that the Bali site also may be more influenced by the internal Indonesian seas. Finally, there is regional variability in temperature and salinity on interannual time scales. From mid-1997 through early 1998, the region is cooler and saltier than normal. These property changes are related to both the strong 1997-1998 El Niño event in the Pacific, and the strong 1997 Dipole Mode in the Indian Ocean, which together can result in lower regional precipitation; lower transport of the fresh, warm Throughflow water; and changes in the upwelling regime along the Lesser Sunda Island chain. From mid-1998 on, warmer conditions returned to the region probably related to the La Niña event.

DESIGN ANALYSIS FOR THE DEFENSE HIGH-LEVEL WASTE DISPOSAL CONTAINER

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

G. Radulesscu; J.S. Tang

The purpose of ''Design Analysis for the Defense High-Level Waste Disposal Container'' analysis is to technically define the defense high-level waste (DHLW) disposal container/waste package using the Waste Package Department's (WPD) design methods, as documented in ''Waste Package Design Methodology Report'' (CRWMS M&O [Civilian Radioactive Waste Management System Management and Operating Contractor] 2000a). The DHLW disposal container is intended for disposal of commercial high-level waste (HLW) and DHLW (including immobilized plutonium waste forms), placed within disposable canisters. The U.S. Department of Energy (DOE)-managed spent nuclear fuel (SNF) in disposable canisters may also be placed in a DHLW disposal container alongmore » with HLW forms. The objective of this analysis is to demonstrate that the DHLW disposal container/waste package satisfies the project requirements, as embodied in Defense High Level Waste Disposal Container System Description Document (SDD) (CRWMS M&O 1999a), and additional criteria, as identified in Waste Package Design Sensitivity Report (CRWMS M&Q 2000b, Table 4). The analysis briefly describes the analytical methods appropriate for the design of the DHLW disposal contained waste package, and summarizes the results of the calculations that illustrate the analytical methods. However, the analysis is limited to the calculations selected for the DHLW disposal container in support of the Site Recommendation (SR) (CRWMS M&O 2000b, Section 7). The scope of this analysis is restricted to the design of the codisposal waste package of the Savannah River Site (SRS) DHLW glass canisters and the Training, Research, Isotopes General Atomics (TRIGA) SNF loaded in a short 18-in.-outer diameter (OD) DOE standardized SNF canister. This waste package is representative of the waste packages that consist of the DHLW disposal container, the DHLW/HLW glass canisters, and the DOE-managed SNF in disposable canisters. The intended use of this analysis is to support Site Recommendation reports and to assist in the development of WPD drawings. Activities described in this analysis were conducted in accordance with the Development Plan ''Design Analysis for the Defense High-Level Waste Disposal Container'' (CRWMS M&O 2000c) with no deviations from the plan.« less

Network Meta-Analysis Using R: A Review of Currently Available Automated Packages

PubMed Central

Neupane, Binod; Richer, Danielle; Bonner, Ashley Joel; Kibret, Taddele; Beyene, Joseph

2014-01-01

Network meta-analysis (NMA) – a statistical technique that allows comparison of multiple treatments in the same meta-analysis simultaneously – has become increasingly popular in the medical literature in recent years. The statistical methodology underpinning this technique and software tools for implementing the methods are evolving. Both commercial and freely available statistical software packages have been developed to facilitate the statistical computations using NMA with varying degrees of functionality and ease of use. This paper aims to introduce the reader to three R packages, namely, gemtc, pcnetmeta, and netmeta, which are freely available software tools implemented in R. Each automates the process of performing NMA so that users can perform the analysis with minimal computational effort. We present, compare and contrast the availability and functionality of different important features of NMA in these three packages so that clinical investigators and researchers can determine which R packages to implement depending on their analysis needs. Four summary tables detailing (i) data input and network plotting, (ii) modeling options, (iii) assumption checking and diagnostic testing, and (iv) inference and reporting tools, are provided, along with an analysis of a previously published dataset to illustrate the outputs available from each package. We demonstrate that each of the three packages provides a useful set of tools, and combined provide users with nearly all functionality that might be desired when conducting a NMA. PMID:25541687

Network meta-analysis using R: a review of currently available automated packages.

PubMed

Neupane, Binod; Richer, Danielle; Bonner, Ashley Joel; Kibret, Taddele; Beyene, Joseph

2014-01-01

Network meta-analysis (NMA)--a statistical technique that allows comparison of multiple treatments in the same meta-analysis simultaneously--has become increasingly popular in the medical literature in recent years. The statistical methodology underpinning this technique and software tools for implementing the methods are evolving. Both commercial and freely available statistical software packages have been developed to facilitate the statistical computations using NMA with varying degrees of functionality and ease of use. This paper aims to introduce the reader to three R packages, namely, gemtc, pcnetmeta, and netmeta, which are freely available software tools implemented in R. Each automates the process of performing NMA so that users can perform the analysis with minimal computational effort. We present, compare and contrast the availability and functionality of different important features of NMA in these three packages so that clinical investigators and researchers can determine which R packages to implement depending on their analysis needs. Four summary tables detailing (i) data input and network plotting, (ii) modeling options, (iii) assumption checking and diagnostic testing, and (iv) inference and reporting tools, are provided, along with an analysis of a previously published dataset to illustrate the outputs available from each package. We demonstrate that each of the three packages provides a useful set of tools, and combined provide users with nearly all functionality that might be desired when conducting a NMA.

Environmental assessment of packaging: Sense and sensibility

NASA Astrophysics Data System (ADS)

Kooijman, Jan M.

1993-09-01

The functions of packaging are derived from product requirements, thus for insight into the environmental effects of packaging the actual combination of product and package has to be evaluated along the production and distribution system. This extension to all related environmental aspects adds realism to the environmental analysis and provides guidance for design while preventing a too detailed investigation of parts of the production system. This approach is contrary to current environmental studies where packaging is always treated as an independent object, neglecting the more important environmental effects of the product that are influenced by packaging. The general analysis and quantification stages for this approach are described, and the currently available methods for the assessment of environmental effects are reviewed. To limit the workload involved in an environmental assessment, a step-by-step analysis and the use of feedback is recommended. First the dominant environmental effects of a particular product and its production and distribution are estimated. Then, on the basis of these preliminary results, the appropriate system boundaries are chosen and the need for further or more detailed environmental analysis is determined. For typical food and drink applications, the effect of different system boundaries on the outcome of environmental assessments and the advantage of the step-by-step analysis of the food supply system is shown. It appears that, depending on the consumer group, different advice for reduction of environmental effects has to be given. Furthermore, because of interrelated environmental effects of the food supply system, the continuing quest for more detailed and accurate analysis of the package components is not necessary for improved management of the environmental effects of packaging.

Safety analysis report -- Packages LP-50 tritium package (Packaging of fissile and other radioactive materials)

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

Gates, A.A.; McCarthy, P.G.; Edl, J.W.

1975-05-01

Elemental tritium is shipped at low pressure in a stainless steel container (LP-50) surrounded by an aluminum vessel and Celotex insulation at least 4 in. thick in a steel drum. Each package contains a large quantity (greater than a Type A quantity) of nonfissile material, as defined in AECM 0529. This report provides the details of the safety analysis performed for this type container.

Comparison of requirements and capabilities of major multipurpose software packages.

PubMed

Igo, Robert P; Schnell, Audrey H

2012-01-01

The aim of this chapter is to introduce the reader to commonly used software packages and illustrate their input requirements, analysis options, strengths, and limitations. We focus on packages that perform more than one function and include a program for quality control, linkage, and association analyses. Additional inclusion criteria were (1) programs that are free to academic users and (2) currently supported, maintained, and developed. Using those criteria, we chose to review three programs: Statistical Analysis for Genetic Epidemiology (S.A.G.E.), PLINK, and Merlin. We will describe the required input format and analysis options. We will not go into detail about every possible program in the packages, but we will give an overview of the packages requirements and capabilities.

Basic analysis of reflectometry data software package for the analysis of multilayered structures according to reflectometry data

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

Astaf'ev, S. B., E-mail: bard@ns.crys.ras.ru; Shchedrin, B. M.; Yanusova, L. G.

2012-01-15

The main principles of developing the Basic Analysis of Reflectometry Data (BARD) software package, which is aimed at obtaining a unified (standardized) tool for analyzing the structure of thin multilayer films and nanostructures of different nature based on reflectometry data, are considered. This software package contains both traditionally used procedures for processing reflectometry data and the authors' original developments on the basis of new methods for carrying out and analyzing reflectometry experiments. The structure of the package, its functional possibilities, examples of application, and prospects of development are reviewed.

The Indonesian Throughflow (ITF) and its impacts on the Indian Ocean during the global warming slowdown period

NASA Astrophysics Data System (ADS)

Makarim, S.; Liu, Z.; Yu, W.; Yan, X.; Sprintall, J.

2016-12-01

The global warming slowdown indicated by a slower warming rate at the surface layer accompanied by stronger heat transport into the deeper layers has been explored in the Indian Ocean. Although the mechanisms of the global warming slowdown are still under warm debate, some clues have been recognized that decadal La Nina like-pattern induced decadal cooling in the Pacific Ocean and generated an increase of the Indonesian Throughflow (ITF) transport in 2004-2010. However, how the ITF spreading to the interior of the Indian Ocean and the impact of ITF changes on the Indian Ocean, in particular its water mass transformation and current system are still unknown. To this end, we analyzed thermohaline structure and current system at different depths in the Indian Ocean both during and just before the global warming slowdown period using the ORAS4 and ARGO dataset. Here, we found the new edge of ITF at off Sumatra presumably as northward deflection of ITF Lombok Strait, and The Monsoon Onset Monitoring and Social Ecology Impact (MOMSEI) and Java Upwelling Variation Observation (JUVO) dataset confirmed this evident. An isopycnal mixing method initially proposed by Du et al. (2013) is adopted to quantify the spreading of ITF water in the Indian Ocean, and therefore the impacts of ITF changes on the variation of the Agulhas Current, Leuween Current, Bay of Bengal Water. This study also prevailed the fresher salinity in the Indian Ocean during the slowdown warming period were not only contributed by stronger transport of the ITF, but also by freshening Arabian Sea and infiltrating Antartic Intermediate Water (AAIW).

Interhemispheric teleconnections: Late Pliocene change in Mediterranean outflow water linked to changes in Indonesian Through-Flow and Atlantic Meridional Overturning Circulation, a review and update

NASA Astrophysics Data System (ADS)

Sarnthein, Michael; Grunert, Patrick; Khélifi, Nabil; Frank, Martin; Nürnberg, Dirk

2018-03-01

The ultimate, possibly geodynamic control and potential impact of changes in circulation activity and salt discharge of Mediterranean outflow waters (MOW) on Atlantic meridional overturning circulation have formed long-standing objectives in paleoceanography. Late Pliocene changes in the distal advection of MOW were reconstructed on orbital timescales for northeast Atlantic DSDP/ODP sites 548 and 982 off Brittany and on Rockall Plateau, supplemented by a proximal record from Site U1389 west off Gibraltar, and compared to Western Mediterranean surface and deep-water records of Alboran Sea Site 978. From 3.43 to 3.3 Ma, MOW temperatures and salinities form a prominent rise by 2-4 °C and 3 psu, induced by a preceding and coeval rise in sea surface and deep-water salinity and increased summer aridity in the Mediterranean Sea. We speculate that these changes triggered an increased MOW flow and were ultimately induced by a persistent 2.5 °C cooling of Indonesian Through-Flow waters. The temperature drop resulted from the northward drift of Australia that crossed a threshold value near 3.6-3.3 Ma and led to a large-scale cooling of the eastern subtropical Indian Ocean and in turn, to a reduction of African monsoon rains. Vice versa, we show that the distinct rise in Mediterranean salt export after 3.4 Ma induced a unique long-term rise in the formation of Upper North Atlantic Deep Water, that followed with a phase lag of 100 ky. In summary, we present evidence for an interhemispheric teleconnection of processes in the Indonesian Gateways, the Mediterranean and Labrador Seas, jointly affecting Pliocene climate.

The IOD-ENSO precursory teleconnection over the tropical Indo-Pacific Ocean: dynamics and long-term trends under global warming

NASA Astrophysics Data System (ADS)

Yuan, Dongliang; Hu, Xiaoyue; Xu, Peng; Zhao, Xia; Masumoto, Yukio; Han, Weiqing

2018-01-01

The dynamics of the teleconnection between the Indian Ocean Dipole (IOD) in the tropical Indian Ocean and El Niño-Southern Oscillation (ENSO) in the tropical Pacific Ocean at the time lag of one year are investigated using lag correlations between the oceanic anomalies in the southeastern tropical Indian Ocean in fall and those in the tropical Indo-Pacific Ocean in the following winter-fall seasons in the observations and in high-resolution global ocean model simulations. The lag correlations suggest that the IOD-forced interannual transport anomalies of the Indonesian Throughflow generate thermocline anomalies in the western equatorial Pacific Ocean, which propagate to the east to induce ocean-atmosphere coupled evolution leading to ENSO. In comparison, lag correlations between the surface zonal wind anomalies over the western equatorial Pacific in fall and the Indo-Pacific oceanic anomalies at time lags longer than a season are all insignificant, suggesting the short memory of the atmospheric bridge. A linear continuously stratified model is used to investigate the dynamics of the oceanic connection between the tropical Indian and Pacific Oceans. The experiments suggest that interannual equatorial Kelvin waves from the Indian Ocean propagate into the equatorial Pacific Ocean through the Makassar Strait and the eastern Indonesian seas with a penetration rate of about 10%-15% depending on the baroclinic modes. The IOD-ENSO teleconnection is found to get stronger in the past century or so. Diagnoses of the CMIP5 model simulations suggest that the increased teleconnection is associated with decreased Indonesian Throughflow transports in the recent century, which is found sensitive to the global warming forcing.

The Holocene history of Nares Strait: Transition from glacial bay to Arctic-Atlantic throughflow

USGS Publications Warehouse

Jennings, Anne E.; Sheldon, Christina; Cronin, Thomas M.; Francus, Pierre; Stoner, Joseph; Andrews, John

2011-01-01

Retreat of glacier ice from Nares Strait and other straits in the Canadian Arctic Archipelago after the end of the last Ice Age initiated an important connection between the Arctic and the North Atlantic Oceans, allowing development of modern ocean circulation in Baffin Bay and the Labrador Sea. As low-salinity, nutrient-rich Arctic Water began to enter Baffin Bay, it contributed to the Baffin and Labrador currents flowing southward. This enhanced freshwater inflow must have influenced the sea ice regime and likely is responsible for poor calcium carbonate preservation that characterizes the Baffin Island margin today. Sedimentologic and paleoceanographic data from radiocarbon-dated core HLY03-05GC, Hall Basin, northern Nares Strait, document the timing and paleoenvironments surrounding the retreat of waning ice sheets from Nares Strait and opening of this connection between the Arctic Ocean and Baffin Bay. Hall Basin was deglaciated soon before 10,300 cal BP (calibrated years before present) and records ice-distal sedimentation in a glacial bay facing the Arctic Ocean until about 9,000 cal BP. Atlantic Water was present in Hall Basin during deglaciation, suggesting that it may have promoted ice retreat. A transitional unit with high ice-rafted debris content records the opening of Nares Strait at approximately 9,000 cal BP. High productivity in Hall Basin between 9,000 and 6,000 cal BP reflects reduced sea ice cover and duration as well as throughflow of nutrient-rich Pacific Water. The later Holocene is poorly resolved in the core, but slow sedimentation rates and heavier carbon isotope values support an interpretation of increased sea ice cover and decreased productivity during the Neoglacial period.

Seasonal circulation patterns of the Yellow and East China Seas derived from satellite-tracked drifter trajectories and hydrographic observations

NASA Astrophysics Data System (ADS)

Lie, Heung-Jae; Cho, Cheol-Ho

2016-08-01

We investigated seasonal circulation patterns of the Yellow and East China Seas (YECS), by reviewing previous works on the circulation and its dominant currents, and taking into account newly-compiled trajectories of satellite-tracked drifters collected between the 1980s and 2000s. The circulation patterns suggested before the 1990s can be categorized into two groups, depending on the identified origin of the Tsushima Warm Current in the Korea-Tsushima Straits: (i) branching from the Kuroshio southwest of Kyushu, or (ii) northeastward continuation of the Taiwan Strait throughflow. The branching of the Kuroshio southwest of Kyushu and northeast of Taiwan was clearly evidenced by current measurements and concurrent hydrographic surveys. However, there is still no clear evidence for the northeastward pathway of Taiwan Strait throughflow across the mid-shelf area of the East China Sea. Target-oriented surveys in the 1990s and 2000s employing advanced instruments, such as drifter tracking and acoustic Doppler current profiler measurements, now provide decisive proof of the clockwise rounding of the Cheju Warm Current around Jeju-do throughout the year, of the northeastward extension of Changjiang discharge in summer, and of the presence of the Yellow Sea Warm Current only in winter. Thus, both coastal currents in shallow water and secondary branch currents of the Kuroshio (such as the Yellow Sea Warm Current) are found to significantly change from winter to summer. To better present the basic pattern of YECS circulation and its seasonality, we have constructed seasonal circulations patterns, based on review results, on the newly-compiled drifter trajectories, and on hydrographic observations. Further investigations should be carried out in future, with support of comprehensive current measurements on shelf areas and through elaborate numerical modeling.

Intraseasonal flow and its impact on the chlorophyll-a concentration in the Sunda Strait and its vicinity

NASA Astrophysics Data System (ADS)

Xu, Tengfei; Li, Shujiang; Hamzah, Faisal; Setiawan, Agus; Susanto, R. Dwi; Cao, Guojiao; Wei, Zexun

2018-06-01

Sunda Strait is the outflow strait of the South China Sea branch of the Pacific to Indian Ocean Throughflow. The annual mean volume transport through the Sunda Strait is around 0.25 Sv from the Java Sea to the eastern Indian Ocean, only 2.5% of the IndonesianThroughflow, and thus has been ignored by previous investigations. However, the Nutrient concentrations in the Sunda Strait and its vicinity are found highly related to the water transport through the Sunda Strait. Particularly, our observation shows significant intraseasonal variability (ISV) of currents at period around 25-45 days in the Sunda Strait. Both remote and local wind forcing contribute to the ISVs in the Sunda Strait. The intraseasonal oscillation of sea surface wind in the central Indian Ocean drives upwelling/downwelling equatorial Kelvin waves to propagate along the equator and subsequently along the Sumatra-Java coasts, resulting in negative/positive sea level anomalies in the south of the Sunda Strait. The local intraseasonal sea surface wind anomalies also tend to induce negative/positive sea level anomalies in the south of the Sunda Strait by offshore/onshore Ekman transport while there are upwelling/downwelling events. The ensuring sea level gradient associated with the sea level anomalies in the south of the Sunda Strait induces intraseasonal outflow (from Indian Ocean to Java Sea) and inflow (from Java Sea to Indian Ocean) through the strait. Analyses also show that the chlorophyll-a concentrations in the south of the Sunda Strait are lower/higher during the inflow/outflow period of the ISV events in March through May. The mechanism attributes to both the nutrient-rich water transported by the intraseasonal flow in the Sunda Strait and by the upwelling and Ekman transport driven by the local sea surface wind anomalies.

PharmacoGx: an R package for analysis of large pharmacogenomic datasets.

PubMed

Smirnov, Petr; Safikhani, Zhaleh; El-Hachem, Nehme; Wang, Dong; She, Adrian; Olsen, Catharina; Freeman, Mark; Selby, Heather; Gendoo, Deena M A; Grossmann, Patrick; Beck, Andrew H; Aerts, Hugo J W L; Lupien, Mathieu; Goldenberg, Anna; Haibe-Kains, Benjamin

2016-04-15

Pharmacogenomics holds great promise for the development of biomarkers of drug response and the design of new therapeutic options, which are key challenges in precision medicine. However, such data are scattered and lack standards for efficient access and analysis, consequently preventing the realization of the full potential of pharmacogenomics. To address these issues, we implemented PharmacoGx, an easy-to-use, open source package for integrative analysis of multiple pharmacogenomic datasets. We demonstrate the utility of our package in comparing large drug sensitivity datasets, such as the Genomics of Drug Sensitivity in Cancer and the Cancer Cell Line Encyclopedia. Moreover, we show how to use our package to easily perform Connectivity Map analysis. With increasing availability of drug-related data, our package will open new avenues of research for meta-analysis of pharmacogenomic data. PharmacoGx is implemented in R and can be easily installed on any system. The package is available from CRAN and its source code is available from GitHub. bhaibeka@uhnresearch.ca or benjamin.haibe.kains@utoronto.ca Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Solvation Structure and Thermodynamic Mapping (SSTMap): An Open-Source, Flexible Package for the Analysis of Water in Molecular Dynamics Trajectories.

PubMed

Haider, Kamran; Cruz, Anthony; Ramsey, Steven; Gilson, Michael K; Kurtzman, Tom

2018-01-09

We have developed SSTMap, a software package for mapping structural and thermodynamic water properties in molecular dynamics trajectories. The package introduces automated analysis and mapping of local measures of frustration and enhancement of water structure. The thermodynamic calculations are based on Inhomogeneous Fluid Solvation Theory (IST), which is implemented using both site-based and grid-based approaches. The package also extends the applicability of solvation analysis calculations to multiple molecular dynamics (MD) simulation programs by using existing cross-platform tools for parsing MD parameter and trajectory files. SSTMap is implemented in Python and contains both command-line tools and a Python module to facilitate flexibility in setting up calculations and for automated generation of large data sets involving analysis of multiple solutes. Output is generated in formats compatible with popular Python data science packages. This tool will be used by the molecular modeling community for computational analysis of water in problems of biophysical interest such as ligand binding and protein function.

Lin4Neuro: a customized Linux distribution ready for neuroimaging analysis

PubMed Central

2011-01-01

Background A variety of neuroimaging software packages have been released from various laboratories worldwide, and many researchers use these packages in combination. Though most of these software packages are freely available, some people find them difficult to install and configure because they are mostly based on UNIX-like operating systems. We developed a live USB-bootable Linux package named "Lin4Neuro." This system includes popular neuroimaging analysis tools. The user interface is customized so that even Windows users can use it intuitively. Results The boot time of this system was only around 40 seconds. We performed a benchmark test of inhomogeneity correction on 10 subjects of three-dimensional T1-weighted MRI scans. The processing speed of USB-booted Lin4Neuro was as fast as that of the package installed on the hard disk drive. We also installed Lin4Neuro on a virtualization software package that emulates the Linux environment on a Windows-based operation system. Although the processing speed was slower than that under other conditions, it remained comparable. Conclusions With Lin4Neuro in one's hand, one can access neuroimaging software packages easily, and immediately focus on analyzing data. Lin4Neuro can be a good primer for beginners of neuroimaging analysis or students who are interested in neuroimaging analysis. It also provides a practical means of sharing analysis environments across sites. PMID:21266047

Lin4Neuro: a customized Linux distribution ready for neuroimaging analysis.

PubMed

Nemoto, Kiyotaka; Dan, Ippeita; Rorden, Christopher; Ohnishi, Takashi; Tsuzuki, Daisuke; Okamoto, Masako; Yamashita, Fumio; Asada, Takashi

2011-01-25

A variety of neuroimaging software packages have been released from various laboratories worldwide, and many researchers use these packages in combination. Though most of these software packages are freely available, some people find them difficult to install and configure because they are mostly based on UNIX-like operating systems. We developed a live USB-bootable Linux package named "Lin4Neuro." This system includes popular neuroimaging analysis tools. The user interface is customized so that even Windows users can use it intuitively. The boot time of this system was only around 40 seconds. We performed a benchmark test of inhomogeneity correction on 10 subjects of three-dimensional T1-weighted MRI scans. The processing speed of USB-booted Lin4Neuro was as fast as that of the package installed on the hard disk drive. We also installed Lin4Neuro on a virtualization software package that emulates the Linux environment on a Windows-based operation system. Although the processing speed was slower than that under other conditions, it remained comparable. With Lin4Neuro in one's hand, one can access neuroimaging software packages easily, and immediately focus on analyzing data. Lin4Neuro can be a good primer for beginners of neuroimaging analysis or students who are interested in neuroimaging analysis. It also provides a practical means of sharing analysis environments across sites.

Effect of Various Packaging Methods on Small-Scale Hanwoo (Korean Native Cattle) during Refrigerated Storage

PubMed Central

Yu, Hwan Hee; Song, Myung Wook; Kim, Tae-Kyung; Choi, Yun-Sang; Cho, Gyu Yong; Lee, Na-Kyoung; Paik, Hyun-Dong

2018-01-01

Abstract The objective of this study was to investigate comparison of physicochemical, microbiological, and sensory characteristics of Hanwoo eye of round by various packaging methods [wrapped packaging (WP), modified atmosphere packaging (MAP), vacuum packaging (VP) with three different vacuum films, and vacuum skin packaging (VSP)] at a small scale. Packaged Hanwoo beef samples were stored in refrigerated conditions (4±1°C) for 28 days. Packaged beef was sampled on days 0, 7, 14, 21, and 28. Physicochemical [pH, surface color, thiobarbituric acid reactive substances (TBARS), and volatile basic nitrogen (VBN) values], microbiological, and sensory analysis of packaged beef samples were performed. VP and VSP samples showed low TBARS and VBN values, and pH and surface color did not change substantially during the 28-day period. For VSP, total viable bacteria, psychrotrophic bacteria, lactic acid bacteria, and coliform counts were lower than those for other packaging systems. Salmonella spp. and Escherichia coli O157:H7 were not detected in any packaged beef samples. A sensory analysis showed that the scores for appearance, flavor, color, and overall acceptability did not change significantly until day 7. In total, VSP was effective with respect to significantly higher a* values, physicochemical stability, and microbial safety in Hanwoo packaging (p<0.05). PMID:29805283

A Description and Analysis of the German Packaging Take-Back System

ERIC Educational Resources Information Center

Nakajima, Nina; Vanderburg, Willem H.

2006-01-01

The German packaging ordinance is an example of legislated extended producer responsibility (also known as product take-back). Consumers can leave packaging with retailers, and packagers are required to pay for their recycling and disposal. It can be considered to be successful in reducing waste, spurring the redesign of packaging to be more…

DESIGN ANALYSIS FOR THE NAVAL SNF WASTE PACKAGE

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

T.L. Mitchell

2000-05-31

The purpose of this analysis is to demonstrate the design of the naval spent nuclear fuel (SNF) waste package (WP) using the Waste Package Department's (WPD) design methodologies and processes described in the ''Waste Package Design Methodology Report'' (CRWMS M&O [Civilian Radioactive Waste Management System Management and Operating Contractor] 2000b). The calculations that support the design of the naval SNF WP will be discussed; however, only a sub-set of such analyses will be presented and shall be limited to those identified in the ''Waste Package Design Sensitivity Report'' (CRWMS M&O 2000c). The objective of this analysis is to describe themore » naval SNF WP design method and to show that the design of the naval SNF WP complies with the ''Naval Spent Nuclear Fuel Disposal Container System Description Document'' (CRWMS M&O 1999a) and Interface Control Document (ICD) criteria for Site Recommendation. Additional criteria for the design of the naval SNF WP have been outlined in Section 6.2 of the ''Waste Package Design Sensitivity Report'' (CRWMS M&O 2000c). The scope of this analysis is restricted to the design of the naval long WP containing one naval long SNF canister. This WP is representative of the WPs that will contain both naval short SNF and naval long SNF canisters. The following items are included in the scope of this analysis: (1) Providing a general description of the applicable design criteria; (2) Describing the design methodology to be used; (3) Presenting the design of the naval SNF waste package; and (4) Showing compliance with all applicable design criteria. The intended use of this analysis is to support Site Recommendation reports and assist in the development of WPD drawings. Activities described in this analysis were conducted in accordance with the technical product development plan (TPDP) ''Design Analysis for the Naval SNF Waste Package (CRWMS M&O 2000a).« less

Pse-Analysis: a python package for DNA/RNA and protein/ peptide sequence analysis based on pseudo components and kernel methods.

PubMed

Liu, Bin; Wu, Hao; Zhang, Deyuan; Wang, Xiaolong; Chou, Kuo-Chen

2017-02-21

To expedite the pace in conducting genome/proteome analysis, we have developed a Python package called Pse-Analysis. The powerful package can automatically complete the following five procedures: (1) sample feature extraction, (2) optimal parameter selection, (3) model training, (4) cross validation, and (5) evaluating prediction quality. All the work a user needs to do is to input a benchmark dataset along with the query biological sequences concerned. Based on the benchmark dataset, Pse-Analysis will automatically construct an ideal predictor, followed by yielding the predicted results for the submitted query samples. All the aforementioned tedious jobs can be automatically done by the computer. Moreover, the multiprocessing technique was adopted to enhance computational speed by about 6 folds. The Pse-Analysis Python package is freely accessible to the public at http://bioinformatics.hitsz.edu.cn/Pse-Analysis/, and can be directly run on Windows, Linux, and Unix.

Safety analysis report for packaging (onsite) multicanister overpack cask

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

Edwards, W.S.

1997-07-14

This safety analysis report for packaging (SARP) documents the safety of shipments of irradiated fuel elements in the MUlticanister Overpack (MCO) and MCO Cask for a highway route controlled quantity, Type B fissile package. This SARP evaluates the package during transfers of (1) water-filled MCOs from the K Basins to the Cold Vacuum Drying Facility (CVDF) and (2) sealed and cold vacuum dried MCOs from the CVDF in the 100 K Area to the Canister Storage Building in the 200 East Area.

MWASTools: an R/bioconductor package for metabolome-wide association studies.

PubMed

Rodriguez-Martinez, Andrea; Posma, Joram M; Ayala, Rafael; Neves, Ana L; Anwar, Maryam; Petretto, Enrico; Emanueli, Costanza; Gauguier, Dominique; Nicholson, Jeremy K; Dumas, Marc-Emmanuel

2018-03-01

MWASTools is an R package designed to provide an integrated pipeline to analyse metabonomic data in large-scale epidemiological studies. Key functionalities of our package include: quality control analysis; metabolome-wide association analysis using various models (partial correlations, generalized linear models); visualization of statistical outcomes; metabolite assignment using statistical total correlation spectroscopy (STOCSY); and biological interpretation of metabolome-wide association studies results. The MWASTools R package is implemented in R (version  > =3.4) and is available from Bioconductor: https://bioconductor.org/packages/MWASTools/. m.dumas@imperial.ac.uk. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Structural constraints in the packaging of bluetongue virus genomic segments

PubMed Central

Burkhardt, Christiane; Sung, Po-Yu; Celma, Cristina C.

2014-01-01

The mechanism used by bluetongue virus (BTV) to ensure the sorting and packaging of its 10 genomic segments is still poorly understood. In this study, we investigated the packaging constraints for two BTV genomic segments from two different serotypes. Segment 4 (S4) of BTV serotype 9 was mutated sequentially and packaging of mutant ssRNAs was investigated by two newly developed RNA packaging assay systems, one in vivo and the other in vitro. Modelling of the mutated ssRNA followed by biochemical data analysis suggested that a conformational motif formed by interaction of the 5′ and 3′ ends of the molecule was necessary and sufficient for packaging. A similar structural signal was also identified in S8 of BTV serotype 1. Furthermore, the same conformational analysis of secondary structures for positive-sense ssRNAs was used to generate a chimeric segment that maintained the putative packaging motif but contained unrelated internal sequences. This chimeric segment was packaged successfully, confirming that the motif identified directs the correct packaging of the segment. PMID:24980574

Novel Techniques for Millimeter-Wave Packages

NASA Technical Reports Server (NTRS)

Herman, Martin I.; Lee, Karen A.; Kolawa, Elzbieta A.; Lowry, Lynn E.; Tulintseff, Ann N.

1995-01-01

A new millimeter-wave package architecture with supporting electrical, mechanical and material science experiment and analysis is presented. This package is well suited for discrete devices, monolithic microwave integrated circuits (MMIC's) and multichip module (MCM) applications. It has low-loss wide-band RF transitions which are necessary to overcome manufacturing tolerances leading to lower per unit cost Potential applications of this new packaging architecture which go beyond the standard requirements of device protection include integration of antennas, compatibility to photonic networks and direct transitions to waveguide systems. Techniques for electromagnetic analysis, thermal control and hermetic sealing were explored. Three dimensional electromagnetic analysis was performed using a finite difference time-domain (FDTD) algorithm and experimentally verified for millimeter-wave package input and output transitions. New multi-material system concepts (AlN, Cu, and diamond thin films) which allow excellent surface finishes to be achieved with enhanced thermal management have been investigated. A new approach utilizing block copolymer coatings was employed to hermetically seal packages which met MIL STD-883.

dartr: An r package to facilitate analysis of SNP data generated from reduced representation genome sequencing.

PubMed

Gruber, Bernd; Unmack, Peter J; Berry, Oliver F; Georges, Arthur

2018-05-01

Although vast technological advances have been made and genetic software packages are growing in number, it is not a trivial task to analyse SNP data. We announce a new r package, dartr, enabling the analysis of single nucleotide polymorphism data for population genomic and phylogenomic applications. dartr provides user-friendly functions for data quality control and marker selection, and permits rigorous evaluations of conformation to Hardy-Weinberg equilibrium, gametic-phase disequilibrium and neutrality. The package reports standard descriptive statistics, permits exploration of patterns in the data through principal components analysis and conducts standard F-statistics, as well as basic phylogenetic analyses, population assignment, isolation by distance and exports data to a variety of commonly used downstream applications (e.g., newhybrids, faststructure and phylogeny applications) outside of the r environment. The package serves two main purposes: first, a user-friendly approach to lower the hurdle to analyse such data-therefore, the package comes with a detailed tutorial targeted to the r beginner to allow data analysis without requiring deep knowledge of r. Second, we use a single, well-established format-genlight from the adegenet package-as input for all our functions to avoid data reformatting. By strictly using the genlight format, we hope to facilitate this format as the de facto standard of future software developments and hence reduce the format jungle of genetic data sets. The dartr package is available via the r CRAN network and GitHub. © 2017 John Wiley & Sons Ltd.

Toward the greening of nuclear energy: A content analysis of nuclear energy frames from 1991 to 2008

NASA Astrophysics Data System (ADS)

Miller, Sonya R.

Framing theory has emerged as one of the predominant theories employed in mass communications research in the 21st century. Frames are identified as interpretive packages for content where some issue attributes are highlighted over other attributes. While framing effects studies appear plentiful, longitudinal studies assessing trends in dominant framing packages and story elements for an issue appear to be less understood. Through content analysis, this study examines dominant frame packages, story elements, headline tone, story tone, stereotypes, and source attribution for nuclear energy from 1991-2008 in the New York Times, USA Today, the Wall Street Journal, and the Washington Post. Unlike many content analysis studies, this study compares intercoder reliability among three indices---percentage agreement, proportional reduction of loss and Scott's Pi. The newspapers represented in this study possess a commonality in the types of dominant frames packages employed. Significant dominant frame packages among the four newspapers include human/health, proliferation, procedural, and marketplace. While the procedural frame package was more likely to appear prior to the 1997 Kyoto Protocol, the proliferation frame packaged was more likely to appear after the Kyoto Protol. Over time, the sustainable frame package demonstrated increased significance. This study is part of the growing literature regarding the function of frames over time.

East Europe Report, Economic and Industrial Affairs

DTIC Science & Technology

1984-09-13

and weekend cottages are becoming places of the "second ownership pro- cess": 40-50 percent of them are permanently furnished with electric or gas ...stove 15.9 8.2 10.3 19.3 16.6 18.6 4. Gas stove 27.1 30.3 29.7 36.8 47.- 47.4 5. Electric blender X 27.2 29.4 36.1 45.7 49.6 6. Electric food pro...30.8 31.4 38.- 10. Gas through-flow heater 10.6 13.7 12.6 14.- 14.9 18.8 11. Nonautomatic washing machine 80.1 85.4 88.2 77.8 73.7 70.8 12

Pacific western boundary currents and their roles in climate.

PubMed

Hu, Dunxin; Wu, Lixin; Cai, Wenju; Gupta, Alex Sen; Ganachaud, Alexandre; Qiu, Bo; Gordon, Arnold L; Lin, Xiaopei; Chen, Zhaohui; Hu, Shijian; Wang, Guojian; Wang, Qingye; Sprintall, Janet; Qu, Tangdong; Kashino, Yuji; Wang, Fan; Kessler, William S

2015-06-18

Pacific Ocean western boundary currents and the interlinked equatorial Pacific circulation system were among the first currents of these types to be explored by pioneering oceanographers. The widely accepted but poorly quantified importance of these currents-in processes such as the El Niño/Southern Oscillation, the Pacific Decadal Oscillation and the Indonesian Throughflow-has triggered renewed interest. Ongoing efforts are seeking to understand the heat and mass balances of the equatorial Pacific, and possible changes associated with greenhouse-gas-induced climate change. Only a concerted international effort will close the observational, theoretical and technical gaps currently limiting a robust answer to these elusive questions.

Energy efficient engine high-pressure turbine detailed design report

NASA Technical Reports Server (NTRS)

Thulin, R. D.; Howe, D. C.; Singer, I. D.

1982-01-01

The energy efficient engine high-pressure turbine is a single stage system based on technology advancements in the areas of aerodynamics, structures and materials to achieve high performance, low operating economics and durability commensurate with commercial service requirements. Low loss performance features combined with a low through-flow velocity approach results in a predicted efficiency of 88.8 for a flight propulsion system. Turbine airfoil durability goals are achieved through the use of advanced high-strength and high-temperature capability single crystal materials and effective cooling management. Overall, this design reflects a considerable extension in turbine technology that is applicable to future, energy efficient gas-turbine engines.

Gesellschaft fuer angewandte Mathematik und Mechanik, Scientific Annual Meeting, Universitaet Hannover, Hanover, Federal Republic of Germany, Apr. 8-12, 1990, Reports

NASA Astrophysics Data System (ADS)

Various papers on applied mathematics and mechanics are presented. Among the individual topics addressed are: dynamical systems with time-varying or unsteady structure, micromechanical modeling of creep rupture, forced vibrations of elastic sandwich plates with thick surface layers, postbuckling of a complete spherical shell under a line load, differential-geometric approach to the multibody system dynamics, stability of an oscillator with stochastic parametric excitation, identification strategies for crack-formation in rotors, identification of physical parameters of FEMs, impact model for elastic and partly plastic impacts on objects, varying delay and stability in dynamical systems. Also discussed are: parameter identification of a hybrid model for vibration analysis using the FEM, vibration behavior of a labyrinth seal with through-flow, similarities in the boundary layer of fiber composite materials, distortion parameter in shell theories, elastoplastic crack problem at finite strain, algorithm for computing effective stiffnesses of plates with periodic structure, plasticity of metal-matrix composites in a mixed stress-strain space formation, constitutive equations in directly formulated plate theories, microbuckling and homogenization for long fiber composites.

Residual gas analysis device

DOEpatents

Thornberg, Steven M [Peralta, NM

2012-07-31

A system is provided for testing the hermeticity of a package, such as a microelectromechanical systems package containing a sealed gas volume, with a sampling device that has the capability to isolate the package and breach the gas seal connected to a pulse valve that can controllably transmit small volumes down to 2 nanoliters to a gas chamber for analysis using gas chromatography/mass spectroscopy diagnostics.

Unlocking the potential of publicly available microarray data using inSilicoDb and inSilicoMerging R/Bioconductor packages.

PubMed

Taminau, Jonatan; Meganck, Stijn; Lazar, Cosmin; Steenhoff, David; Coletta, Alain; Molter, Colin; Duque, Robin; de Schaetzen, Virginie; Weiss Solís, David Y; Bersini, Hugues; Nowé, Ann

2012-12-24

With an abundant amount of microarray gene expression data sets available through public repositories, new possibilities lie in combining multiple existing data sets. In this new context, analysis itself is no longer the problem, but retrieving and consistently integrating all this data before delivering it to the wide variety of existing analysis tools becomes the new bottleneck. We present the newly released inSilicoMerging R/Bioconductor package which, together with the earlier released inSilicoDb R/Bioconductor package, allows consistent retrieval, integration and analysis of publicly available microarray gene expression data sets. Inside the inSilicoMerging package a set of five visual and six quantitative validation measures are available as well. By providing (i) access to uniformly curated and preprocessed data, (ii) a collection of techniques to remove the batch effects between data sets from different sources, and (iii) several validation tools enabling the inspection of the integration process, these packages enable researchers to fully explore the potential of combining gene expression data for downstream analysis. The power of using both packages is demonstrated by programmatically retrieving and integrating gene expression studies from the InSilico DB repository [https://insilicodb.org/app/].

Which community care for patients with schizophrenic disorders? Packages of care provided by Departments of Mental Health in Lombardy (Italy).

PubMed

Lora, Antonio; Cosentino, Ugo; Gandini, Anna; Zocchetti, Carlo

2007-01-01

The treatment of schizophrenic disorders is the most important challenge for community care. The analysis focuses on packages of care provided to 23.602 patients with a ICD-10 diagnosis of schizophrenic disorder and treated in 2001 by the Departments of Mental Health in Lombardy, Italy. Packages of care refer to a mix of treatments provided to each patient during the year by different settings. Direct costs of the packages were calculated. Linear Discriminant Analysis has been used to link socio-demographic and diagnostic sub-groups of the patients to packages of care. People with schizophrenic disorders received relatively few care packages: only four packages involved more than 5%. Two thirds of the patients received only care provided by Community Mental Health Centres. In the other two packages with a percentage over 5%, the activity was provided by CMHCs, jointly with General Hospitals or Day Care Facilities. Complex care packages were rare (only 6%). As well as the intensity, also the variety of care provided by CMHCs increased with the complexity of care packages. In Lombardy more than half of the resources were spent for schizophrenia. The range of the costs per package was very wide. LDA failed to link characteristics of the patients to packages of care. Care packages are useful tools to understand better how mental health system works, how resources have been spent and to point out problems in the quality of care.

The gputools package enables GPU computing in R.

PubMed

Buckner, Joshua; Wilson, Justin; Seligman, Mark; Athey, Brian; Watson, Stanley; Meng, Fan

2010-01-01

By default, the R statistical environment does not make use of parallelism. Researchers may resort to expensive solutions such as cluster hardware for large analysis tasks. Graphics processing units (GPUs) provide an inexpensive and computationally powerful alternative. Using R and the CUDA toolkit from Nvidia, we have implemented several functions commonly used in microarray gene expression analysis for GPU-equipped computers. R users can take advantage of the better performance provided by an Nvidia GPU. The package is available from CRAN, the R project's repository of packages, at http://cran.r-project.org/web/packages/gputools More information about our gputools R package is available at http://brainarray.mbni.med.umich.edu/brainarray/Rgpgpu

Differential maneuvering simulator data reduction and analysis software

NASA Technical Reports Server (NTRS)

Beasley, G. P.; Sigman, R. S.

1972-01-01

A multielement data reduction and analysis software package has been developed for use with the Langley differential maneuvering simulator (DMS). This package, which has several independent elements, was developed to support all phases of DMS aircraft simulation studies with a variety of both graphical and tabular information. The overall software package is considered unique because of the number, diversity, and sophistication of the element programs available for use in a single study. The purpose of this paper is to discuss the overall DMS data reduction and analysis package by reviewing the development of the various elements of the software, showing typical results that can be obtained, and discussing how each element can be used.

The role of the Atlantic Water in multidecadal ocean variability in the Nordic and Barents Seas

NASA Astrophysics Data System (ADS)

Yashayaev, Igor; Seidov, Dan

2015-03-01

The focus of this work is on the temporal and spatial variability of the Atlantic Water (AW). We analyze the existing historic hydrographic data from the World Ocean Database to document the long-term variability of the AW throughflow across the Norwegian Sea to the western Barents Sea. Interannual-to-multidecadal variability of water temperature, salinity and density are analyzed along six composite sections crossing the AW flow and coastal currents at six selected locations. The stations are lined up from southwest to northeast - from the northern North Sea (69°N) throughout the Norwegian Sea to the Kola Section in the Barents Sea (33°30‧E). The changing volume and characteristics of the AW throughflow dominate the hydrographic variability on decadal and longer time scales in the studied area. We examine the role of fluctuations of the volume of inflow versus the variable local factors, such as the air-sea interaction and mixing with the fresh coastal and cold Arctic waters, in controlling the long-term regional variability. It is shown that the volume of the AW, passing through the area and affecting the position of the outer edge of the warm and saline core, correlates well with temperature and salinity averaged over the central portions of the studied sections. The coastal flow (mostly associated with the Norwegian Coastal Current flowing over the continental shelf) is largely controlled by seasonal local heat and freshwater impacts. Temperature records at all six lines show a warming trend superimposed on a series of relatively warm and cold periods, which in most cases follow, with a delay of four to five years, the periods of relatively low and high North Atlantic Oscillation (NAO), and the periods of relatively high and low Atlantic Multidecadal Oscillation (AMO), respectively. In general, there is a relatively high correlation between the year-to-year changes of the NAO and AMO indices, which is to some extent reflected in the (delayed) AW temperature fluctuations. It takes about two years for freshening and salinification events and a much shorter time (of about a year or less) for cooling and warming episodes to propagate or spread across the region. This significant difference in the propagation rates of salinity and temperature anomalies is explained by the leading role of horizontal advection in the propagation of salinity anomalies, whereas temperature is also controlled by the competing air-sea interaction along the AW throughflow. Therefore, although a water parcel moves within the flow as a whole, the temperature, salinity and density anomalies split and propagate separately, with the temperature and density signals leading relative to the salinity signal. A new hydrographic index, coastal-to-offshore density step, is introduced to capture variability in the strength of the AW volume transport. This index shows the same cycles of variability as observed in temperature, NAO and AMO but without an obvious trend.

The Role of Packaging in Solid Waste Management 1966 to 1976.

ERIC Educational Resources Information Center

Darnay, Arsen; Franklin, William E.

The goals of waste processors and packagers obviously differ: the packaging industry seeks durable container material that will be unimpaired by external factors. Until recently, no systematic analysis of the relationship between packaging and solid waste disposal had been undertaken. This three-part document defines these interactions, and the…

Cyrface: An interface from Cytoscape to R that provides a user interface to R packages.

PubMed

Gonçalves, Emanuel; Mirlach, Franz; Saez-Rodriguez, Julio

2013-01-01

There is an increasing number of software packages to analyse biological experimental data in the R environment. In particular, Bioconductor, a repository of curated R packages, is one of the most comprehensive resources for bioinformatics and biostatistics. The use of these packages is increasing, but it requires a basic understanding of the R language, as well as the syntax of the specific package used. The availability of user graphical interfaces for these packages would decrease the learning curve and broaden their application. Here, we present a Cytoscape app termed Cyrface that allows Cytoscape apps to connect to any function and package developed in R. Cyrface can be used to run R packages from within the Cytoscape environment making use of a graphical user interface. Moreover, it can link R packages with the capabilities of Cytoscape and its apps, in particular network visualization and analysis. Cyrface's utility has been demonstrated for two Bioconductor packages ( CellNOptR and DrugVsDisease), and here we further illustrate its usage by implementing a workflow of data analysis and visualization. Download links, installation instructions and user guides can be accessed from the Cyrface's homepage ( http://www.ebi.ac.uk/saezrodriguez/cyrface/) and from the Cytoscape app store ( http://apps.cytoscape.org/apps/cyrface).

Analysis of Variance: What Is Your Statistical Software Actually Doing?

ERIC Educational Resources Information Center

Li, Jian; Lomax, Richard G.

2011-01-01

Users assume statistical software packages produce accurate results. In this article, the authors systematically examined Statistical Package for the Social Sciences (SPSS) and Statistical Analysis System (SAS) for 3 analysis of variance (ANOVA) designs, mixed-effects ANOVA, fixed-effects analysis of covariance (ANCOVA), and nested ANOVA. For each…

49 CFR 109.9 - Transportation for examination and analysis.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 2 2011-10-01 2011-10-01 false Transportation for examination and analysis. 109.9... analysis. (a) An agent may direct a package to be transported to a facility for examination and analysis... the package conforms to subchapter C of this chapter; (2) Conflicting information concerning the...

Learn by Yourself: The Self-Learning Tools for Qualitative Analysis Software Packages

ERIC Educational Resources Information Center

Freitas, Fábio; Ribeiro, Jaime; Brandão, Catarina; Reis, Luís Paulo; de Souza, Francislê Neri; Costa, António Pedro

2017-01-01

Computer Assisted Qualitative Data Analysis Software (CAQDAS) are tools that help researchers to develop qualitative research projects. These software packages help the users with tasks such as transcription analysis, coding and text interpretation, writing and annotation, content search and analysis, recursive abstraction, grounded theory…

Resilience Among Students at the Basic Enlisted Submarine School

DTIC Science & Technology

2016-12-01

reported resilience. The Hayes’ Macro in the Statistical Package for the Social Sciences (SSPS) was used to uncover factors relevant to mediation analysis... Statistical Package for the Social Sciences (SPSS) was used to uncover factors relevant to mediation analysis. Findings suggest that the encouragement of...to Stressful Experiences Scale RTC Recruit Training Command SPSS Statistical Package for the Social Sciences SS Social Support SWB Subjective Well

Technical Review Report for the Model 9978-96 Package Safety Analysis Report for Packaging (S-SARP-G-00002, Revision 1, March 2009)

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

West, M

2009-03-06

This Technical Review Report (TRR) documents the review, performed by Lawrence Livermore National Laboratory (LLNL) Staff, at the request of the Department of Energy (DOE), on the 'Safety Analysis Report for Packaging (SARP), Model 9978 B(M)F-96', Revision 1, March 2009 (S-SARP-G-00002). The Model 9978 Package complies with 10 CFR 71, and with 'Regulations for the Safe Transport of Radioactive Material-1996 Edition (As Amended, 2000)-Safety Requirements', International Atomic Energy Agency (IAEA) Safety Standards Series No. TS-R-1. The Model 9978 Packaging is designed, analyzed, fabricated, and tested in accordance with Section III of the American Society of Mechanical Engineers Boiler and Pressuremore » Vessel Code (ASME B&PVC). The review presented in this TRR was performed using the methods outlined in Revision 3 of the DOE's 'Packaging Review Guide (PRG) for Reviewing Safety Analysis Reports for Packages'. The format of the SARP follows that specified in Revision 2 of the Nuclear Regulatory Commission's Regulatory Guide 7.9, i.e., 'Standard Format and Content of Part 71 Applications for Approval of Packages for Radioactive Material'. Although the two documents are similar in their content, they are not identical. Formatting differences have been noted in this TRR, where appropriate. The Model 9978 Packaging is a single containment package, using a 5-inch containment vessel (5CV). It uses a nominal 35-gallon drum package design. In comparison, the Model 9977 Packaging uses a 6-inch containment vessel (6CV). The Model 9977 and Model 9978 Packagings were developed concurrently, and they were referred to as the General Purpose Fissile Material Package, Version 1 (GPFP). Both packagings use General Plastics FR-3716 polyurethane foam as insulation and as impact limiters. The 5CV is used as the Primary Containment Vessel (PCV) in the Model 9975-96 Packaging. The Model 9975-96 Packaging also has the 6CV as its Secondary Containment Vessel (SCV). In comparison, the Model 9975 Packagings use Celotex{trademark} for insulation and as impact limiters. To provide a historical perspective, it is noted that the Model 9975-96 Packaging is a 35-gallon drum package design that has evolved from a family of packages designed by DOE contractors at the Savannah River Site. Earlier package designs, i.e., the Model 9965, the Model 9966, the Model 9967, and the Model 9968 Packagings, were originally designed and certified in the early 1980s. In the 1990s, updated package designs that incorporated design features consistent with the then-newer safety requirements were proposed. The updated package designs at the time were the Model 9972, the Model 9973, the Model 9974, and the Model 9975 Packagings, respectively. The Model 9975 Package was certified by the Packaging Certification Program, under the Office of Safety Management and Operations. The Model 9978 Package has six Content Envelopes: C.1 ({sup 238}Pu Heat Sources), C.2 ( Pu/U Metals), C.3 (Pu/U Oxides, Reserved), C.4 (U Metal or Alloy), C.5 (U Compounds), and C.6 (Samples and Sources). Per 10 CFR 71.59 (Code of Federal Regulations), the value of N is 50 for the Model 9978 Package leading to a Criticality Safety Index (CSI) of 1.0. The Transport Index (TI), based on dose rate, is calculated to be a maximum of 4.1.« less

Efficient analysis of large-scale genome-wide data with two R packages: bigstatsr and bigsnpr.

PubMed

Privé, Florian; Aschard, Hugues; Ziyatdinov, Andrey; Blum, Michael G B

2017-03-30

Genome-wide datasets produced for association studies have dramatically increased in size over the past few years, with modern datasets commonly including millions of variants measured in dozens of thousands of individuals. This increase in data size is a major challenge severely slowing down genomic analyses, leading to some software becoming obsolete and researchers having limited access to diverse analysis tools. Here we present two R packages, bigstatsr and bigsnpr, allowing for the analysis of large scale genomic data to be performed within R. To address large data size, the packages use memory-mapping for accessing data matrices stored on disk instead of in RAM. To perform data pre-processing and data analysis, the packages integrate most of the tools that are commonly used, either through transparent system calls to existing software, or through updated or improved implementation of existing methods. In particular, the packages implement fast and accurate computations of principal component analysis and association studies, functions to remove SNPs in linkage disequilibrium and algorithms to learn polygenic risk scores on millions of SNPs. We illustrate applications of the two R packages by analyzing a case-control genomic dataset for celiac disease, performing an association study and computing Polygenic Risk Scores. Finally, we demonstrate the scalability of the R packages by analyzing a simulated genome-wide dataset including 500,000 individuals and 1 million markers on a single desktop computer. https://privefl.github.io/bigstatsr/ & https://privefl.github.io/bigsnpr/. florian.prive@univ-grenoble-alpes.fr & michael.blum@univ-grenoble-alpes.fr. Supplementary materials are available at Bioinformatics online.

MethVisual - visualization and exploratory statistical analysis of DNA methylation profiles from bisulfite sequencing.

PubMed

Zackay, Arie; Steinhoff, Christine

2010-12-15

Exploration of DNA methylation and its impact on various regulatory mechanisms has become a very active field of research. Simultaneously there is an arising need for tools to process and analyse the data together with statistical investigation and visualisation. MethVisual is a new application that enables exploratory analysis and intuitive visualization of DNA methylation data as is typically generated by bisulfite sequencing. The package allows the import of DNA methylation sequences, aligns them and performs quality control comparison. It comprises basic analysis steps as lollipop visualization, co-occurrence display of methylation of neighbouring and distant CpG sites, summary statistics on methylation status, clustering and correspondence analysis. The package has been developed for methylation data but can be also used for other data types for which binary coding can be inferred. The application of the package, as well as a comparison to existing DNA methylation analysis tools and its workflow based on two datasets is presented in this paper. The R package MethVisual offers various analysis procedures for data that can be binarized, in particular for bisulfite sequenced methylation data. R/Bioconductor has become one of the most important environments for statistical analysis of various types of biological and medical data. Therefore, any data analysis within R that allows the integration of various data types as provided from different technological platforms is convenient. It is the first and so far the only specific package for DNA methylation analysis, in particular for bisulfite sequenced data available in R/Bioconductor enviroment. The package is available for free at http://methvisual.molgen.mpg.de/ and from the Bioconductor Consortium http://www.bioconductor.org.

MethVisual - visualization and exploratory statistical analysis of DNA methylation profiles from bisulfite sequencing

PubMed Central

2010-01-01

Background Exploration of DNA methylation and its impact on various regulatory mechanisms has become a very active field of research. Simultaneously there is an arising need for tools to process and analyse the data together with statistical investigation and visualisation. Findings MethVisual is a new application that enables exploratory analysis and intuitive visualization of DNA methylation data as is typically generated by bisulfite sequencing. The package allows the import of DNA methylation sequences, aligns them and performs quality control comparison. It comprises basic analysis steps as lollipop visualization, co-occurrence display of methylation of neighbouring and distant CpG sites, summary statistics on methylation status, clustering and correspondence analysis. The package has been developed for methylation data but can be also used for other data types for which binary coding can be inferred. The application of the package, as well as a comparison to existing DNA methylation analysis tools and its workflow based on two datasets is presented in this paper. Conclusions The R package MethVisual offers various analysis procedures for data that can be binarized, in particular for bisulfite sequenced methylation data. R/Bioconductor has become one of the most important environments for statistical analysis of various types of biological and medical data. Therefore, any data analysis within R that allows the integration of various data types as provided from different technological platforms is convenient. It is the first and so far the only specific package for DNA methylation analysis, in particular for bisulfite sequenced data available in R/Bioconductor enviroment. The package is available for free at http://methvisual.molgen.mpg.de/ and from the Bioconductor Consortium http://www.bioconductor.org. PMID:21159174

Automotive Exterior Noise Optimization Using Grey Relational Analysis Coupled with Principal Component Analysis

NASA Astrophysics Data System (ADS)

Chen, Shuming; Wang, Dengfeng; Liu, Bo

This paper investigates optimization design of the thickness of the sound package performed on a passenger automobile. The major characteristics indexes for performance selected to evaluate the processes are the SPL of the exterior noise and the weight of the sound package, and the corresponding parameters of the sound package are the thickness of the glass wool with aluminum foil for the first layer, the thickness of the glass fiber for the second layer, and the thickness of the PE foam for the third layer. In this paper, the process is fundamentally with multiple performances, thus, the grey relational analysis that utilizes grey relational grade as performance index is especially employed to determine the optimal combination of the thickness of the different layers for the designed sound package. Additionally, in order to evaluate the weighting values corresponding to various performance characteristics, the principal component analysis is used to show their relative importance properly and objectively. The results of the confirmation experiments uncover that grey relational analysis coupled with principal analysis methods can successfully be applied to find the optimal combination of the thickness for each layer of the sound package material. Therefore, the presented method can be an effective tool to improve the vehicle exterior noise and lower the weight of the sound package. In addition, it will also be helpful for other applications in the automotive industry, such as the First Automobile Works in China, Changan Automobile in China, etc.

InterFace: A software package for face image warping, averaging, and principal components analysis.

PubMed

Kramer, Robin S S; Jenkins, Rob; Burton, A Mike

2017-12-01

We describe InterFace, a software package for research in face recognition. The package supports image warping, reshaping, averaging of multiple face images, and morphing between faces. It also supports principal components analysis (PCA) of face images, along with tools for exploring the "face space" produced by PCA. The package uses a simple graphical user interface, allowing users to perform these sophisticated image manipulations without any need for programming knowledge. The program is available for download in the form of an app, which requires that users also have access to the (freely available) MATLAB Runtime environment.

Selection of software for mechanical engineering undergraduates

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

Cheah, C. T.; Yin, C. S.; Halim, T.

A major problem with the undergraduate mechanical course is the limited exposure of students to software packages coupled with the long learning curve on the existing software packages. This work proposes the use of appropriate software packages for the entire mechanical engineering curriculum to ensure students get sufficient exposure real life design problems. A variety of software packages are highlighted as being suitable for undergraduate work in mechanical engineering, e.g. simultaneous non-linear equations; uncertainty analysis; 3-D modeling software with the FEA; analysis tools for the solution of problems in thermodynamics, fluid mechanics, mechanical system design, and solid mechanics.

Safety analysis report for packaging, Oak Ridge Y-12 Plant, model DC-1 package with HEU oxide contents. Change pages for Rev.1

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

NONE

This Safety Analysis Report for Packaging for the Oak Ridge Y-12 Plant for the Model DC-1 package with highly enriched uranium (HEU) oxide contents has been prepared in accordance with governing regulations form the Nuclear Regulatory Commission and the Department of Transportation and orders from the Department of energy. The fundamental safety requirements addressed by these regulations and orders pertain to the containment of radioactive material, radiation shielding, and nuclear subcriticality. This report demonstrates how these requirements are met.

Image analysis to evaluate the browning degree of banana (Musa spp.) peel.

PubMed

Cho, Jeong-Seok; Lee, Hyeon-Jeong; Park, Jung-Hoon; Sung, Jun-Hyung; Choi, Ji-Young; Moon, Kwang-Deog

2016-03-01

Image analysis was applied to examine banana peel browning. The banana samples were divided into 3 treatment groups: no treatment and normal packaging (Cont); CO2 gas exchange packaging (CO); normal packaging with an ethylene generator (ET). We confirmed that the browning of banana peels developed more quickly in the CO group than the other groups based on sensory test and enzyme assay. The G (green) and CIE L(∗), a(∗), and b(∗) values obtained from the image analysis sharply increased or decreased in the CO group. And these colour values showed high correlation coefficients (>0.9) with the sensory test results. CIE L(∗)a(∗)b(∗) values using a colorimeter also showed high correlation coefficients but comparatively lower than those of image analysis. Based on this analysis, browning of the banana occurred more quickly for CO2 gas exchange packaging, and image analysis can be used to evaluate the browning of banana peels. Copyright © 2015 Elsevier Ltd. All rights reserved.

PIVOT: platform for interactive analysis and visualization of transcriptomics data.

PubMed

Zhu, Qin; Fisher, Stephen A; Dueck, Hannah; Middleton, Sarah; Khaladkar, Mugdha; Kim, Junhyong

2018-01-05

Many R packages have been developed for transcriptome analysis but their use often requires familiarity with R and integrating results of different packages requires scripts to wrangle the datatypes. Furthermore, exploratory data analyses often generate multiple derived datasets such as data subsets or data transformations, which can be difficult to track. Here we present PIVOT, an R-based platform that wraps open source transcriptome analysis packages with a uniform user interface and graphical data management that allows non-programmers to interactively explore transcriptomics data. PIVOT supports more than 40 popular open source packages for transcriptome analysis and provides an extensive set of tools for statistical data manipulations. A graph-based visual interface is used to represent the links between derived datasets, allowing easy tracking of data versions. PIVOT further supports automatic report generation, publication-quality plots, and program/data state saving, such that all analysis can be saved, shared and reproduced. PIVOT will allow researchers with broad background to easily access sophisticated transcriptome analysis tools and interactively explore transcriptome datasets.

iGC-an integrated analysis package of gene expression and copy number alteration.

PubMed

Lai, Yi-Pin; Wang, Liang-Bo; Wang, Wei-An; Lai, Liang-Chuan; Tsai, Mong-Hsun; Lu, Tzu-Pin; Chuang, Eric Y

2017-01-14

With the advancement in high-throughput technologies, researchers can simultaneously investigate gene expression and copy number alteration (CNA) data from individual patients at a lower cost. Traditional analysis methods analyze each type of data individually and integrate their results using Venn diagrams. Challenges arise, however, when the results are irreproducible and inconsistent across multiple platforms. To address these issues, one possible approach is to concurrently analyze both gene expression profiling and CNAs in the same individual. We have developed an open-source R/Bioconductor package (iGC). Multiple input formats are supported and users can define their own criteria for identifying differentially expressed genes driven by CNAs. The analysis of two real microarray datasets demonstrated that the CNA-driven genes identified by the iGC package showed significantly higher Pearson correlation coefficients with their gene expression levels and copy numbers than those genes located in a genomic region with CNA. Compared with the Venn diagram approach, the iGC package showed better performance. The iGC package is effective and useful for identifying CNA-driven genes. By simultaneously considering both comparative genomic and transcriptomic data, it can provide better understanding of biological and medical questions. The iGC package's source code and manual are freely available at https://www.bioconductor.org/packages/release/bioc/html/iGC.html .

Variations in algorithm implementation among quantitative texture analysis software packages

NASA Astrophysics Data System (ADS)

Foy, Joseph J.; Mitta, Prerana; Nowosatka, Lauren R.; Mendel, Kayla R.; Li, Hui; Giger, Maryellen L.; Al-Hallaq, Hania; Armato, Samuel G.

2018-02-01

Open-source texture analysis software allows for the advancement of radiomics research. Variations in texture features, however, result from discrepancies in algorithm implementation. Anatomically matched regions of interest (ROIs) that captured normal breast parenchyma were placed in the magnetic resonance images (MRI) of 20 patients at two time points. Six first-order features and six gray-level co-occurrence matrix (GLCM) features were calculated for each ROI using four texture analysis packages. Features were extracted using package-specific default GLCM parameters and using GLCM parameters modified to yield the greatest consistency among packages. Relative change in the value of each feature between time points was calculated for each ROI. Distributions of relative feature value differences were compared across packages. Absolute agreement among feature values was quantified by the intra-class correlation coefficient. Among first-order features, significant differences were found for max, range, and mean, and only kurtosis showed poor agreement. All six second-order features showed significant differences using package-specific default GLCM parameters, and five second-order features showed poor agreement; with modified GLCM parameters, no significant differences among second-order features were found, and all second-order features showed poor agreement. While relative texture change discrepancies existed across packages, these differences were not significant when consistent parameters were used.

Statistical principle and methodology in the NISAN system.

PubMed Central

Asano, C

1979-01-01

The NISAN system is a new interactive statistical analysis program package constructed by an organization of Japanese statisticans. The package is widely available for both statistical situations, confirmatory analysis and exploratory analysis, and is planned to obtain statistical wisdom and to choose optimal process of statistical analysis for senior statisticians. PMID:540594

PyPathway: Python Package for Biological Network Analysis and Visualization.

PubMed

Xu, Yang; Luo, Xiao-Chun

2018-05-01

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

An experimental analysis of the effectiveness and sustainability of a Chinese tutoring package.

PubMed

Wu, Hang; Miller, L Keith

2012-01-01

This experiment evaluated the effects of training tutors to use an instructional package to teach pronunciation and translation of the Chinese language. Tutors' correct use of the package increased from 68% of trials to 92% after training, and student correct pronunciation increased from 45% to 90%, with similar effects for translation. Continued use of the package, high social validity, and extended follow-up suggest that use of the package may be sustainable.

AN EXPERIMENTAL ANALYSIS OF THE EFFECTIVENESS AND SUSTAINABILITY OF A CHINESE TUTORING PACKAGE

PubMed Central

Wu, Hang; Miller, L. Keith

2012-01-01

This experiment evaluated the effects of training tutors to use an instructional package to teach pronunciation and translation of the Chinese language. Tutors' correct use of the package increased from 68% of trials to 92% after training, and student correct pronunciation increased from 45% to 90%, with similar effects for translation. Continued use of the package, high social validity, and extended follow-up suggest that use of the package may be sustainable. PMID:22403470

Regional Morphology Analysis Package (RMAP): Empirical Orthogonal Function Analysis, Background and Examples

DTIC Science & Technology

2007-10-01

1984. Complex principal component analysis : Theory and examples. Journal of Climate and Applied Meteorology 23: 1660-1673. Hotelling, H. 1933...Sediments 99. ASCE: 2,566-2,581. Von Storch, H., and A. Navarra. 1995. Analysis of climate variability. Applications of statistical techniques. Berlin...ERDC TN-SWWRP-07-9 October 2007 Regional Morphology Empirical Analysis Package (RMAP): Orthogonal Function Analysis , Background and Examples by

Determining Permissible Oxygen and Water Vapor Transmission Rate for Non-Retort Military Ration Packaging

DTIC Science & Technology

2011-11-01

OXYGEN AND WATER VAPOR TRANSMISSION RATE FOR NON- RETORT MILITARY RATION PACKAGING by Danielle Froio Alan Wright Nicole Favreau and Sarah...ANSI Std. Z39.18 RETORT STORAGE SHELF LIFE RETORT POUCHES SENSORY ANALYSIS OXYGEN CRACKERS PACKAGING SENSORY... Packaging for MRE. (a) MRE Retort Pouch Quad-Laminate Structure; (b) MRE Non- retort Pouch Tri-Laminate Structure

AOP: An R Package For Sufficient Causal Analysis in Pathway ...

EPA Pesticide Factsheets

Summary: How can I quickly find the key events in a pathway that I need to monitor to predict that a/an beneficial/adverse event/outcome will occur? This is a key question when using signaling pathways for drug/chemical screening in pharma-cology, toxicology and risk assessment. By identifying these sufficient causal key events, we have fewer events to monitor for a pathway, thereby decreasing assay costs and time, while maximizing the value of the information. I have developed the “aop” package which uses backdoor analysis of causal net-works to identify these minimal sets of key events that are suf-ficient for making causal predictions. Availability and Implementation: The source and binary are available online through the Bioconductor project (http://www.bioconductor.org/) as an R package titled “aop”. The R/Bioconductor package runs within the R statistical envi-ronment. The package has functions that can take pathways (as directed graphs) formatted as a Cytoscape JSON file as input, or pathways can be represented as directed graphs us-ing the R/Bioconductor “graph” package. The “aop” package has functions that can perform backdoor analysis to identify the minimal set of key events for making causal predictions.Contact: burgoon.lyle@epa.gov This paper describes an R/Bioconductor package that was developed to facilitate the identification of key events within an AOP that are the minimal set of sufficient key events that need to be tested/monit

Software design for analysis of multichannel intracardial and body surface electrocardiograms.

PubMed

Potse, Mark; Linnenbank, André C; Grimbergen, Cornelis A

2002-11-01

Analysis of multichannel ECG recordings (body surface maps (BSMs) and intracardial maps) requires special software. We created a software package and a user interface on top of a commercial data analysis package (MATLAB) by a combination of high-level and low-level programming. Our software was created to satisfy the needs of a diverse group of researchers. It can handle a large variety of recording configurations. It allows for interactive usage through a fast and robust user interface, and batch processing for the analysis of large amounts of data. The package is user-extensible, includes routines for both common and experimental data processing tasks, and works on several computer platforms. The source code is made intelligible using software for structured documentation and is available to the users. The package is currently used by more than ten research groups analysing ECG data worldwide.

Analysis of reference transactions using packaged computer programs.

PubMed

Calabretta, N; Ross, R

1984-01-01

Motivated by a continuing education class attended by the authors on the measurement of reference desk activities, the reference department at Scott Memorial Library initiated a project to gather data on reference desk transactions and to analyze the data by using packaged computer programs. The programs utilized for the project were SPSS (Statistical Package for the Social Sciences) and SAS (Statistical Analysis System). The planning, implementation and development of the project are described.

Supersonic fan engines for military aircraft

NASA Technical Reports Server (NTRS)

Franciscus, L. C.

1983-01-01

Engine performance and mission studies were performed for turbofan engines with supersonic through-flow fans. A Mach 2.4 CTOL aircraft was used in the study. Two missions were considered: a long range penetrator mission and a long range intercept mission. The supersonic fan engine is compared with an augmented mixed flow turbofan in terms of mission radius for a fixed takeoff gross weight of 75,000 lbm. The mission radius of aircraft powered by supersonic fan engines could be 15 percent longer than aircraft powered with conventional turbofan engines at moderate thrust to gross weight ratios. The climb and acceleration performance of the supersonic fan engines is better than that of the conventional turbofan engines.

A Review of Meta-Analysis Packages in R

ERIC Educational Resources Information Center

Polanin, Joshua R.; Hennessy, Emily A.; Tanner-Smith, Emily E.

2017-01-01

Meta-analysis is a statistical technique that allows an analyst to synthesize effect sizes from multiple primary studies. To estimate meta-analysis models, the open-source statistical environment R is quickly becoming a popular choice. The meta-analytic community has contributed to this growth by developing numerous packages specific to…

Propensity Score Analysis in R: A Software Review

ERIC Educational Resources Information Center

Keller, Bryan; Tipton, Elizabeth

2016-01-01

In this article, we review four software packages for implementing propensity score analysis in R: "Matching, MatchIt, PSAgraphics," and "twang." After briefly discussing essential elements for propensity score analysis, we apply each package to a data set from the Early Childhood Longitudinal Study in order to estimate the…

Environmental Assessment of Packaging: The Consumer Point of View

PubMed

Van Dam YK

1996-09-01

When marketing environmentally responsible packaged products, the producer is confronted with consumer beliefs concerning the environmental friendliness of packaging materials. When making environmentally conscious packaging decisions, these consumer beliefs should be taken into account alongside the technical guidelines. Dutch consumer perceptions of the environmental friendliness of packaged products are reported and compared with the results of a life-cycle analysis assessment. It is shown that consumers judge environmental friendliness mainly from material and returnability. Furthermore, the consumer perception of the environmental friendliness of packaging material is based on the postconsumption waste, whereas the environmental effects of production are ignored. From the consumer beliefs concerning environmental friendliness implications are deduced for packaging policy and for environmental policy.KEY WORDS: Consumer behavior; Environment; Food; Packaging; Perception; Waste

Analysis of counting data: Development of the SATLAS Python package

NASA Astrophysics Data System (ADS)

Gins, W.; de Groote, R. P.; Bissell, M. L.; Granados Buitrago, C.; Ferrer, R.; Lynch, K. M.; Neyens, G.; Sels, S.

2018-01-01

For the analysis of low-statistics counting experiments, a traditional nonlinear least squares minimization routine may not always provide correct parameter and uncertainty estimates due to the assumptions inherent in the algorithm(s). In response to this, a user-friendly Python package (SATLAS) was written to provide an easy interface between the data and a variety of minimization algorithms which are suited for analyzinglow, as well as high, statistics data. The advantage of this package is that it allows the user to define their own model function and then compare different minimization routines to determine the optimal parameter values and their respective (correlated) errors. Experimental validation of the different approaches in the package is done through analysis of hyperfine structure data of 203Fr gathered by the CRIS experiment at ISOLDE, CERN.

scraps: An open-source Python-based analysis package for analyzing and plotting superconducting resonator data

DOE PAGES

Carter, Faustin Wirkus; Khaire, Trupti S.; Novosad, Valentyn; ...

2016-11-07

We present "scraps" (SuperConducting Analysis and Plotting Software), a Python package designed to aid in the analysis and visualization of large amounts of superconducting resonator data, specifically complex transmission as a function of frequency, acquired at many different temperatures and driving powers. The package includes a least-squares fitting engine as well as a Monte-Carlo Markov Chain sampler for sampling the posterior distribution given priors, marginalizing over nuisance parameters, and estimating covariances. A set of plotting tools for generating publication-quality figures is also provided in the package. Lastly, we discuss the functionality of the software and provide some examples of itsmore » utility on data collected from a niobium-nitride coplanar waveguide resonator fabricated at Argonne National Laboratory.« less

ANALYSIS/PLOT: a graphics package for use with the SORT/ANALYSIS data bases

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

Sady, C.A.

1983-08-01

This report describes a graphics package that is used with the SORT/ANALYSIS data bases. The data listed by the SORT/ANALYSIS program can be presented in pie, bar, line, or Gantt chart form. Instructions for the use of the plotting program and descriptions of the subroutines are given in the report.

Dualities in the analysis of phage DNA packaging motors

PubMed Central

Serwer, Philip; Jiang, Wen

2012-01-01

The DNA packaging motors of double-stranded DNA phages are models for analysis of all multi-molecular motors and for analysis of several fundamental aspects of biology, including early evolution, relationship of in vivo to in vitro biochemistry and targets for anti-virals. Work on phage DNA packaging motors both has produced and is producing dualities in the interpretation of data obtained by use of both traditional techniques and the more recently developed procedures of single-molecule analysis. The dualities include (1) reductive vs. accretive evolution, (2) rotation vs. stasis of sub-assemblies of the motor, (3) thermal ratcheting vs. power stroking in generating force, (4) complete motor vs. spark plug role for the packaging ATPase, (5) use of previously isolated vs. new intermediates for analysis of the intermediate states of the motor and (6) a motor with one cycle vs. a motor with two cycles. We provide background for these dualities, some of which are under-emphasized in the literature. We suggest directions for future research. PMID:23532204

Safety analysis report for the SR-101 inert reservoir package

DOT National Transportation Integrated Search

1998-11-01

Department of Energy (DOE) AL Weapons Surety Division (WSD) requires the SR-101 Inert Reservoir Package to : meet applicable hazardous material transportation requirements. This Safety Analysis Report (SAR) is based on : requirements in place at the ...

WGCNA: an R package for weighted correlation network analysis.

PubMed

Langfelder, Peter; Horvath, Steve

2008-12-29

Correlation networks are increasingly being used in bioinformatics applications. For example, weighted gene co-expression network analysis is a systems biology method for describing the correlation patterns among genes across microarray samples. Weighted correlation network analysis (WGCNA) can be used for finding clusters (modules) of highly correlated genes, for summarizing such clusters using the module eigengene or an intramodular hub gene, for relating modules to one another and to external sample traits (using eigengene network methodology), and for calculating module membership measures. Correlation networks facilitate network based gene screening methods that can be used to identify candidate biomarkers or therapeutic targets. These methods have been successfully applied in various biological contexts, e.g. cancer, mouse genetics, yeast genetics, and analysis of brain imaging data. While parts of the correlation network methodology have been described in separate publications, there is a need to provide a user-friendly, comprehensive, and consistent software implementation and an accompanying tutorial. The WGCNA R software package is a comprehensive collection of R functions for performing various aspects of weighted correlation network analysis. The package includes functions for network construction, module detection, gene selection, calculations of topological properties, data simulation, visualization, and interfacing with external software. Along with the R package we also present R software tutorials. While the methods development was motivated by gene expression data, the underlying data mining approach can be applied to a variety of different settings. The WGCNA package provides R functions for weighted correlation network analysis, e.g. co-expression network analysis of gene expression data. The R package along with its source code and additional material are freely available at http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA.

WGCNA: an R package for weighted correlation network analysis

PubMed Central

Langfelder, Peter; Horvath, Steve

2008-01-01

Background Correlation networks are increasingly being used in bioinformatics applications. For example, weighted gene co-expression network analysis is a systems biology method for describing the correlation patterns among genes across microarray samples. Weighted correlation network analysis (WGCNA) can be used for finding clusters (modules) of highly correlated genes, for summarizing such clusters using the module eigengene or an intramodular hub gene, for relating modules to one another and to external sample traits (using eigengene network methodology), and for calculating module membership measures. Correlation networks facilitate network based gene screening methods that can be used to identify candidate biomarkers or therapeutic targets. These methods have been successfully applied in various biological contexts, e.g. cancer, mouse genetics, yeast genetics, and analysis of brain imaging data. While parts of the correlation network methodology have been described in separate publications, there is a need to provide a user-friendly, comprehensive, and consistent software implementation and an accompanying tutorial. Results The WGCNA R software package is a comprehensive collection of R functions for performing various aspects of weighted correlation network analysis. The package includes functions for network construction, module detection, gene selection, calculations of topological properties, data simulation, visualization, and interfacing with external software. Along with the R package we also present R software tutorials. While the methods development was motivated by gene expression data, the underlying data mining approach can be applied to a variety of different settings. Conclusion The WGCNA package provides R functions for weighted correlation network analysis, e.g. co-expression network analysis of gene expression data. The R package along with its source code and additional material are freely available at . PMID:19114008

Application of the Finite Elemental Analysis to Modeling Temperature Change of the Vaccine in an Insulated Packaging Container during Transport.

PubMed

Ge, Changfeng; Cheng, Yujie; Shen, Yan

2013-01-01

This study demonstrated an attempt to predict temperatures of a perishable product such as vaccine inside an insulated packaging container during transport through finite element analysis (FEA) modeling. In order to use the standard FEA software for simulation, an equivalent heat conduction coefficient is proposed and calculated to describe the heat transfer of the air trapped inside the insulated packaging container. The three-dimensional, insulated packaging container is regarded as a combination of six panels, and the heat flow at each side panel is a one-dimension diffusion process. The transit-thermal analysis was applied to simulate the heat transition process from ambient environment to inside the container. Field measurements were carried out to collect the temperature during transport, and the collected data were compared to the FEA simulation results. Insulated packaging containers are used to transport temperature-sensitive products such as vaccine and other pharmaceutical products. The container is usually made of an extruded polystyrene foam filled with gel packs. World Health Organization guidelines recommend that all vaccines except oral polio vaccine be distributed in an environment where the temperature ranges between +2 to +8 °C. The primary areas of concern in designing the packaging for vaccine are how much of the foam thickness and gel packs should be used in order to keep the temperature in a desired range, and how to prevent the vaccine from exposure to freezing temperatures. This study uses numerical simulation to predict temperature change within an insulated packaging container in vaccine cold chain. It is our hope that this simulation will provide the vaccine industries with an alternative engineering tool to validate vaccine packaging and project thermal equilibrium within the insulated packaging container.

GOplot: an R package for visually combining expression data with functional analysis.

PubMed

Walter, Wencke; Sánchez-Cabo, Fátima; Ricote, Mercedes

2015-09-01

Despite the plethora of methods available for the functional analysis of omics data, obtaining comprehensive-yet detailed understanding of the results remains challenging. This is mainly due to the lack of publicly available tools for the visualization of this type of information. Here we present an R package called GOplot, based on ggplot2, for enhanced graphical representation. Our package takes the output of any general enrichment analysis and generates plots at different levels of detail: from a general overview to identify the most enriched categories (bar plot, bubble plot) to a more detailed view displaying different types of information for molecules in a given set of categories (circle plot, chord plot, cluster plot). The package provides a deeper insight into omics data and allows scientists to generate insightful plots with only a few lines of code to easily communicate the findings. The R package GOplot is available via CRAN-The Comprehensive R Archive Network: http://cran.r-project.org/web/packages/GOplot. The shiny web application of the Venn diagram can be found at: https://wwalter.shinyapps.io/Venn/. A detailed manual of the package with sample figures can be found at https://wencke.github.io/ fscabo@cnic.es or mricote@cnic.es. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Large space telescope, phase A. Volume 4: Scientific instrument package

NASA Technical Reports Server (NTRS)

1972-01-01

The design and characteristics of the scientific instrument package for the Large Space Telescope are discussed. The subjects include: (1) general scientific objectives, (2) package system analysis, (3) scientific instrumentation, (4) imaging photoelectric sensors, (5) environmental considerations, and (6) reliability and maintainability.

The Analysis of the Regression-Discontinuity Design in R

ERIC Educational Resources Information Center

Thoemmes, Felix; Liao, Wang; Jin, Ze

2017-01-01

This article describes the analysis of regression-discontinuity designs (RDDs) using the R packages rdd, rdrobust, and rddtools. We discuss similarities and differences between these packages and provide directions on how to use them effectively. We use real data from the Carolina Abecedarian Project to show how an analysis of an RDD can be…

Examining the role of unmeasured confounding in mediation analysis with genetic and genomic applications.

PubMed

Lutz, Sharon M; Thwing, Annie; Schmiege, Sarah; Kroehl, Miranda; Baker, Christopher D; Starling, Anne P; Hokanson, John E; Ghosh, Debashis

2017-07-19

In mediation analysis if unmeasured confounding is present, the estimates for the direct and mediated effects may be over or under estimated. Most methods for the sensitivity analysis of unmeasured confounding in mediation have focused on the mediator-outcome relationship. The Umediation R package enables the user to simulate unmeasured confounding of the exposure-mediator, exposure-outcome, and mediator-outcome relationships in order to see how the results of the mediation analysis would change in the presence of unmeasured confounding. We apply the Umediation package to the Genetic Epidemiology of Chronic Obstructive Pulmonary Disease (COPDGene) study to examine the role of unmeasured confounding due to population stratification on the effect of a single nucleotide polymorphism (SNP) in the CHRNA5/3/B4 locus on pulmonary function decline as mediated by cigarette smoking. Umediation is a flexible R package that examines the role of unmeasured confounding in mediation analysis allowing for normally distributed or Bernoulli distributed exposures, outcomes, mediators, measured confounders, and unmeasured confounders. Umediation also accommodates multiple measured confounders, multiple unmeasured confounders, and allows for a mediator-exposure interaction on the outcome. Umediation is available as an R package at https://github.com/SharonLutz/Umediation A tutorial on how to install and use the Umediation package is available in the Additional file 1.

The Geomorphic Road Analysis and Inventory Package (GRAIP) Volume 2: Office Procedures

Treesearch

Richard M. Cissel; Thomas A. Black; Kimberly A. T. Schreuders; Ajay Prasad; Charles H. Luce; David G. Tarboton; Nathan A. Nelson

2012-01-01

An important first step in managing forest roads for improved water quality and aquatic habitat is the performance of an inventory. The Geomorphic Roads Analysis and Inventory Package (GRAIP) was developed as a tool for making a comprehensive inventory and analysis of the effects of forest roads on watersheds. This manual describes the data analysis and process of a...

psygenet2r: a R/Bioconductor package for the analysis of psychiatric disease genes.

PubMed

Gutiérrez-Sacristán, Alba; Hernández-Ferrer, Carles; González, Juan R; Furlong, Laura I

2017-12-15

Psychiatric disorders have a great impact on morbidity and mortality. Genotype-phenotype resources for psychiatric diseases are key to enable the translation of research findings to a better care of patients. PsyGeNET is a knowledge resource on psychiatric diseases and their genes, developed by text mining and curated by domain experts. We present psygenet2r, an R package that contains a variety of functions for leveraging PsyGeNET database and facilitating its analysis and interpretation. The package offers different types of queries to the database along with variety of analysis and visualization tools, including the study of the anatomical structures in which the genes are expressed and gaining insight of gene's molecular function. Psygenet2r is especially suited for network medicine analysis of psychiatric disorders. The package is implemented in R and is available under MIT license from Bioconductor (http://bioconductor.org/packages/release/bioc/html/psygenet2r.html). juanr.gonzalez@isglobal.org or laura.furlong@upf.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Fragman: an R package for fragment analysis.

PubMed

Covarrubias-Pazaran, Giovanny; Diaz-Garcia, Luis; Schlautman, Brandon; Salazar, Walter; Zalapa, Juan

2016-04-21

Determination of microsatellite lengths or other DNA fragment types is an important initial component of many genetic studies such as mutation detection, linkage and quantitative trait loci (QTL) mapping, genetic diversity, pedigree analysis, and detection of heterozygosity. A handful of commercial and freely available software programs exist for fragment analysis; however, most of them are platform dependent and lack high-throughput applicability. We present the R package Fragman to serve as a freely available and platform independent resource for automatic scoring of DNA fragment lengths diversity panels and biparental populations. The program analyzes DNA fragment lengths generated in Applied Biosystems® (ABI) either manually or automatically by providing panels or bins. The package contains additional tools for converting the allele calls to GenAlEx, JoinMap® and OneMap software formats mainly used for genetic diversity and generating linkage maps in plant and animal populations. Easy plotting functions and multiplexing friendly capabilities are some of the strengths of this R package. Fragment analysis using a unique set of cranberry (Vaccinium macrocarpon) genotypes based on microsatellite markers is used to highlight the capabilities of Fragman. Fragman is a valuable new tool for genetic analysis. The package produces equivalent results to other popular software for fragment analysis while possessing unique advantages and the possibility of automation for high-throughput experiments by exploiting the power of R.

Nonstationary Extreme Value Analysis in a Changing Climate: A Software Package

NASA Astrophysics Data System (ADS)

Cheng, L.; AghaKouchak, A.; Gilleland, E.

2013-12-01

Numerous studies show that climatic extremes have increased substantially in the second half of the 20th century. For this reason, analysis of extremes under a nonstationary assumption has received a great deal of attention. This paper presents a software package developed for estimation of return levels, return periods, and risks of climatic extremes in a changing climate. This MATLAB software package offers tools for analysis of climate extremes under both stationary and non-stationary assumptions. The Nonstationary Extreme Value Analysis (hereafter, NEVA) provides an efficient and generalized framework for analyzing extremes using Bayesian inference. NEVA estimates the extreme value parameters using a Differential Evolution Markov Chain (DE-MC) which utilizes the genetic algorithm Differential Evolution (DE) for global optimization over the real parameter space with the Markov Chain Monte Carlo (MCMC) approach and has the advantage of simplicity, speed of calculation and convergence over conventional MCMC. NEVA also offers the confidence interval and uncertainty bounds of estimated return levels based on the sampled parameters. NEVA integrates extreme value design concepts, data analysis tools, optimization and visualization, explicitly designed to facilitate analysis extremes in geosciences. The generalized input and output files of this software package make it attractive for users from across different fields. Both stationary and nonstationary components of the package are validated for a number of case studies using empirical return levels. The results show that NEVA reliably describes extremes and their return levels.

Data Packages for the Hanford Immobilized Low Activity Tank Waste Performance Assessment 2001 Version [SEC 1 THRU 5

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

MANN, F.M.

Data package supporting the 2001 Immobilized Low-Activity Waste Performance Analysis. Geology, hydrology, geochemistry, facility, waste form, and dosimetry data based on recent investigation are provided. Verification and benchmarking packages for selected software codes are provided.

Wave Engine Topping Cycle Assessment

NASA Technical Reports Server (NTRS)

Welch, Gerard E.

1996-01-01

The performance benefits derived by topping a gas turbine engine with a wave engine are assessed. The wave engine is a wave rotor that produces shaft power by exploiting gas dynamic energy exchange and flow turning. The wave engine is added to the baseline turboshaft engine while keeping high-pressure-turbine inlet conditions, compressor pressure ratio, engine mass flow rate, and cooling flow fractions fixed. Related work has focused on topping with pressure-exchangers (i.e., wave rotors that provide pressure gain with zero net shaft power output); however, more energy can be added to a wave-engine-topped cycle leading to greater engine specific-power-enhancement The energy addition occurs at a lower pressure in the wave-engine-topped cycle; thus the specific-fuel-consumption-enhancement effected by ideal wave engine topping is slightly lower than that effected by ideal pressure-exchanger topping. At a component level, however, flow turning affords the wave engine a degree-of-freedom relative to the pressure-exchanger that enables a more efficient match with the baseline engine. In some cases, therefore, the SFC-enhancement by wave engine topping is greater than that by pressure-exchanger topping. An ideal wave-rotor-characteristic is used to identify key wave engine design parameters and to contrast the wave engine and pressure-exchanger topping approaches. An aerodynamic design procedure is described in which wave engine design-point performance levels are computed using a one-dimensional wave rotor model. Wave engines using various wave cycles are considered including two-port cycles with on-rotor combustion (valved-combustors) and reverse-flow and through-flow four-port cycles with heat addition in conventional burners. A through-flow wave cycle design with symmetric blading is used to assess engine performance benefits. The wave-engine-topped turboshaft engine produces 16% more power than does a pressure-exchanger-topped engine under the specified topping constraints. Positive and negative aspects of wave engine topping in gas turbine engines are identified.

Evaluation of an operational ocean model configuration at 1/12° spatial resolution for the Indonesian seas - Part 1: Ocean physics

NASA Astrophysics Data System (ADS)

Tranchant, B.; Reffray, G.; Greiner, E.; Nugroho, D.; Koch-Larrouy, A.; Gaspar, P.

2015-08-01

INDO12, a 1/12° regional version of the NEMO physical ocean model covering the whole Indonesian EEZ has been developed and is now running every week in the framework of the INDESO project (Infrastructure Development of Space Oceanography) implemented by the Indonesian Ministry of Marine Affairs and Fisheries. The initial hydrographic conditions as well as open boundary conditions are derived from the operational global ocean forecasting system at 1/4° operated by Mercator Ocean. Atmospheric forcing fields (3 hourly ECMWF analyses) are used to force the regional model. INDO12 is also forced by tidal currents and elevations, and by the inverse barometer effect. The turbulent mixing induced by internal tides is taken into account through a specific parameterization. In this study we evaluate the model skill through comparisons with various datasets including outputs of the parent model, climatologies, in situ temperature and salinity measurements, and satellite data. The simulated and altimeter-derived Eddy Kinetic Energy fields display similar patterns and confirm that tides are a dominant forcing in the area. The volume transport of the Indonesian ThroughFlow is in good agreement with the INSTANT current meter estimates while the transport through Luzon Strait is, on average, westward but probably too weak. Significant water mass transformation occurs along the main routes of the Indonesian Throughflow (ITF) and compares well with observations. Vertical mixing is able to erode the South and North Pacific subtropical waters salinity maximum as seen in TS diagrams. Compared to satellite data, surface salinity and temperature fields display marked biases in the South China Sea. Altogether, INDO12 proves to be able to provide a very realistic simulation of the ocean circulation and water mass transformation through the Indonesian Archipelago. A few weaknesses are also detected. Work is on-going to reduce or eliminate these problems in the second INDO12 version.

Relationship between the Bering Strait Throughflow and Salinity in the Bering Sea in an Atmosphere-Ocean-Ice Coupled Model

NASA Astrophysics Data System (ADS)

Kawai, Y.; Osafune, S.; Masuda, S.; Komuro, Y.

2016-12-01

The relationship between the volumetric transport of the Bering Strait throughflow (BTF) and sea surface salinity (SSS) in the Bering Sea was investigated using an atmosphere-ocean-ice coupled model, MIROC4h, which includes an eddy-permitting ocean model. The MIROC4h simulated well the seasonal cycle of BTF transport, although it overestimated the transport compared with previous studies. The interannual variations of SSS in the Bering Sea were correlated with those of BTF transport: SSS in the northwestern Bering Sea was high when BTF transport was large. The SSS anomaly associated with the BTF anomaly became evident from late autumn to spring, and SSS lagged behind the BTF by a few months. The BTF transport was strongly correlated with the SSH in the eastern Bering Sea, the southwestern Chukchi Sea, and the East Siberian Sea. The low SSH along the Russian coast in the Arctic Ocean was uncorrelated with the high SSH in the Bering Sea. The Arctic SSH affected BTF transport and the SSS in the northwestern Bering Sea independently of the SSH in the Bering Sea. We evaluated the salt budget in the northwestern Bering Sea, including Anadyr Bay. When the BTF transport in October-March was large, the horizontal convergence of salt increased and sea-ice melting decreased; both changes contributed to the increase of salinity. In contrast, evaporation-minus-precipitation and the residual component had the opposite effect. The sea-ice retreat was closely related to meridional wind anomalies that also raised the SSH in the eastern Bering Sea. Changes in upper-layer currents caused by the southerly wind anomalies in the Bering Sea contributed to the increase of the horizontal convergence of salt. In addition, the SSH anomalies in the Arctic Ocean independently affected the currents in the Bering Strait and the northwestern Bering Sea, perhaps through the propagation of shelf waves, which also led to salinization.

AMS 14 C dating controlled records of monsoon and Indonesian throughflow variability from the eastern Indian Ocean of the past 32,000 years

NASA Astrophysics Data System (ADS)

Li, Z. Y.; Chen, M. T.; Shi, X.; Liu, S.; Wang, H.

2015-12-01

Zi-Ye Li a, Min-Te Chen b, Hou-Jie Wang a, Sheng-Fa Liu c, Xue-Fa Shi ca College of Marine Geosciences, Ocean University of China, Qingdao 266100, P.R. Chinab Institute of Applied Geosciences, National Taiwan Ocean University, Keelung, Taiwan 20224, ROCc First Institute of Oceanography, SOA, Qingdao 266100, P.R. China Indonesian throughflow (ITF) is one of the most important currents responsible for transporting heat and moisture from the western Pacific to the Indian Oceans. The ITF is also well-known as effectively in modulating the global climate change with the interactions among ENSO and Asian monsoons. Here we present an AMS 14C dating controlled sea surface temperature (SST) record from core SO184-10043 (07°18.57'S, 105°03.53'E), which was retrieved from 2171m water depth at a north-south depression located at the southeastern offshore area of Sumatera in the eastern Indian Ocean. Based on our high-resolution SST using Mg/Ca analyses based on planktonic foraminifera shells of Globigerinoides ruber and alkenone index, U k'37-SST, oxygen isotope stratigraphy, and AMC 14C age-controls, our records show that, during the past 32,000 years, the SSTs were decreased which imply weaker ITF during Marine Isotope Stage (MIS) 2 and 3. The weaker UTF may respond to strengthened northeast monsoon during the boreal winter. During 21 to 15ka, the southeast monsoon had been stronger and the northeast monsoon was relatively weaker. During 15 to 8ka, rapid sea level rising may allow the opening of the gateways in the Makassar Strait and Lombok Strait that may have further strengthened the ITF. During the early Holocene, the northeast and southeast monsoons seem to be both strengthened. We will discuss the implications of the hydrographic variability and their age uncertainties in this paper during the meeting.

INTERFACING SAS TO ORACLE IN THE UNIX ENVIRONMENT

EPA Science Inventory

SAS is an EPA standard data and statistical analysis software package while ORACLE is EPA's standard data base management system software package. RACLE has the advantage over SAS in data retrieval and storage capabilities but has limited data and statistical analysis capability....

Neural Network Prototyping Package Within IRAF

NASA Technical Reports Server (NTRS)

Bazell, David

1997-01-01

The purpose of this contract was to develop a neural network package within the IRAF environment to allow users to easily understand and use different neural network algorithms the analysis of astronomical data. The package was developed for use within IRAF to allow portability to different computing environments and to provide a familiar and easy to use interface with the routines. In addition to developing the software and supporting documentation, we planned to use the system for the analysis of several sample problems to prove its viability and usefulness.

An Interactive Computer Aided Design and Analysis Package.

DTIC Science & Technology

1986-03-01

Al-A167 114 AN INTERACTIVE COMPUTER AIDED DESIGN MUD ANAILYSIS 1/𔃼 PACKAGE(U) NAVAL POSTGRADUATE SCHOOL NONTEREY CA T L EUALD "AR 86 UNCLSSIFIED F... SCHOOL Monterey, California DTIC .LECTE MAYOS THESIS AN INTERACTIVE COMPUTER AIDED DESIGN AND ANALYSIS PACKAGE by Terrence L. Ewald March 1986 jThesis...ORGANIZATION Naval Postgraduate School (if dAp90h81111) Naval Postgraduate School . 62A 6C. ADDRESS (0ty. State, and ZIP Code) 7b. ADDRESS (City State. and

The LARSYS educational package: Instructor's notes. [instructional materials for training people to analyze remotely sensed data

NASA Technical Reports Server (NTRS)

Lindenlaub, J. C.; Davis, S. M.

1974-01-01

Materials are presented for assisting instructors in teaching the LARSYS Educational Package, which is a set of instructional materials to train people to analyze remotely sensed multispectral data. The seven units of the package are described. These units are: quantitative remote sensing, overview of the LARSYS software system, the 2780 remote terminal, demonstration of LARSYS on the 2780 remote terminal, exercises, guide to multispectral data analysis, and a case study using LARSYS for analysis of LANDSAT data.

Long duration exposure facility solar illumination data package

NASA Technical Reports Server (NTRS)

Berrios, William M.; Sampair, Thomas

1990-01-01

A post flight solar illumination data package was created by the LDEF thermal analysis data group in support of the LDEF science office data group. The data presented was prepared with the Thermal Radiation Analysis System (TRASYS) program. Ground tracking data was used to calculate daily orbital beta angles for the calculation of resultant fluxes. This data package will be useful in calculation of solar illumination fluent for a variety of beta angle orbital conditions encountered during the LDEF mission.

PLATSIM: An efficient linear simulation and analysis package for large-order flexible systems

NASA Technical Reports Server (NTRS)

Maghami, Periman; Kenny, Sean P.; Giesy, Daniel P.

1995-01-01

PLATSIM is a software package designed to provide efficient time and frequency domain analysis of large-order generic space platforms implemented with any linear time-invariant control system. Time domain analysis provides simulations of the overall spacecraft response levels due to either onboard or external disturbances. The time domain results can then be processed by the jitter analysis module to assess the spacecraft's pointing performance in a computationally efficient manner. The resulting jitter analysis algorithms have produced an increase in speed of several orders of magnitude over the brute force approach of sweeping minima and maxima. Frequency domain analysis produces frequency response functions for uncontrolled and controlled platform configurations. The latter represents an enabling technology for large-order flexible systems. PLATSIM uses a sparse matrix formulation for the spacecraft dynamics model which makes both the time and frequency domain operations quite efficient, particularly when a large number of modes are required to capture the true dynamics of the spacecraft. The package is written in MATLAB script language. A graphical user interface (GUI) is included in the PLATSIM software package. This GUI uses MATLAB's Handle graphics to provide a convenient way for setting simulation and analysis parameters.

An Examination of the Effects of a Video-Based Training Package on Professional Staff's Implementation of a Brief Functional Analysis and Data Analysis

ERIC Educational Resources Information Center

Fleming, Courtney V.

2011-01-01

Minimal research has investigated training packages used to teach professional staff how to implement functional analysis procedures and to interpret data gathered during functional analysis. The current investigation used video-based training with role-play and feedback to teach six professionals in a clinical setting to implement procedures of a…

Evaluation of the Field Test of Project Information Packages: Volume III--Resource Cost Analysis.

ERIC Educational Resources Information Center

Al-Salam, Nabeel; And Others

The third of three volumes evaluating the first year field test of the Project Information Packages (PIPs) provides a cost analysis study as a key element in the total evaluation. The resource approach to cost analysis is explained and the specific resource methodology used in the main cost analysis of the 19 PIP field-test projects detailed. The…

GRAFLAB 2.3 for UNIX - A MATLAB database, plotting, and analysis tool: User`s guide

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

Dunn, W.N.

1998-03-01

This report is a user`s manual for GRAFLAB, which is a new database, analysis, and plotting package that has been written entirely in the MATLAB programming language. GRAFLAB is currently used for data reduction, analysis, and archival. GRAFLAB was written to replace GRAFAID, which is a FORTRAN database, analysis, and plotting package that runs on VAX/VMS.

GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, miRNA, and mRNA data in GDC.

PubMed

Li, Ruidong; Qu, Han; Wang, Shibo; Wei, Julong; Zhang, Le; Ma, Renyuan; Lu, Jianming; Zhu, Jianguo; Zhong, Wei-De; Jia, Zhenyu

2018-03-02

The large-scale multidimensional omics data in the Genomic Data Commons (GDC) provides opportunities to investigate the crosstalk among different RNA species and their regulatory mechanisms in cancers. Easy-to-use bioinformatics pipelines are needed to facilitate such studies. We have developed a user-friendly R/Bioconductor package, named GDCRNATools, for downloading, organizing, and analyzing RNA data in GDC with an emphasis on deciphering the lncRNA-mRNA related competing endogenous RNAs (ceRNAs) regulatory network in cancers. Many widely used bioinformatics tools and databases are utilized in our package. Users can easily pack preferred downstream analysis pipelines or integrate their own pipelines into the workflow. Interactive shiny web apps built in GDCRNATools greatly improve visualization of results from the analysis. GDCRNATools is an R/Bioconductor package that is freely available at Bioconductor (http://bioconductor.org/packages/devel/bioc/html/GDCRNATools.html). Detailed instructions, manual and example code are also available in Github (https://github.com/Jialab-UCR/GDCRNATools). arthur.jia@ucr.edu or zhongwd2009@live.cn or doctorzhujianguo@163.com.

Impact of policy changes on infant feeding decisions among low-income women participating in the Special Supplemental Nutrition Program for Women, Infants, and Children.

PubMed

Whaley, Shannon E; Koleilat, Maria; Whaley, Mike; Gomez, Judy; Meehan, Karen; Saluja, Kiran

2012-12-01

We present infant feeding data before and after the 2009 Special Supplemental Nutrition Program for Women, Infants, and Children (WIC) food package change that supported and incentivized breastfeeding. We describe the key role of California WIC staff in supporting these policy changes. We analyzed WIC data on more than 180,000 infants in Southern California. We employed the analysis of variance and Tukey (honestly significant difference) tests to compare issuance rates of postpartum and infant food packages before and after the changes. We used analysis of covariance to adjust for poverty status changes as a potential confounder. Issuance rates of the "fully breastfeeding" package at infant WIC enrollment increased by 86% with the package changes. Rates also increased significantly for 2- and 6-month-old infants. Issuance rates of packages that included formula decreased significantly. All outcomes remained highly significant in the adjusted model. Policy changes, training of front-line WIC staff, and participant education influenced issuance rates of WIC food packages. In California, the issuance rates of packages that include formula have significantly decreased and the rate for those that include no formula has significantly increased.

SIMA: Python software for analysis of dynamic fluorescence imaging data.

PubMed

Kaifosh, Patrick; Zaremba, Jeffrey D; Danielson, Nathan B; Losonczy, Attila

2014-01-01

Fluorescence imaging is a powerful method for monitoring dynamic signals in the nervous system. However, analysis of dynamic fluorescence imaging data remains burdensome, in part due to the shortage of available software tools. To address this need, we have developed SIMA, an open source Python package that facilitates common analysis tasks related to fluorescence imaging. Functionality of this package includes correction of motion artifacts occurring during in vivo imaging with laser-scanning microscopy, segmentation of imaged fields into regions of interest (ROIs), and extraction of signals from the segmented ROIs. We have also developed a graphical user interface (GUI) for manual editing of the automatically segmented ROIs and automated registration of ROIs across multiple imaging datasets. This software has been designed with flexibility in mind to allow for future extension with different analysis methods and potential integration with other packages. Software, documentation, and source code for the SIMA package and ROI Buddy GUI are freely available at http://www.losonczylab.org/sima/.

Space shuttle/food system. Volume 2, Appendix C: Food cooling techniques analysis. Appendix D: Package and stowage: Alternate concepts analysis

NASA Technical Reports Server (NTRS)

1974-01-01

The relative penalties associated with various techniques for providing an onboard cold environment for storage of perishable food items, and for the development of packaging and vehicle stowage parameters were investigated in terms of the overall food system design analysis of space shuttle. The degrees of capability for maintaining both a 40 F to 45 F refrigerated temperature and a 0 F and 20 F frozen environment were assessed for the following cooling techniques: (1) phase change (heat sink) concept; (2) thermoelectric concept; (3) vapor cycle concept; and (4) expendable ammonia concept. The parameters considered in the analysis were weight, volume, and spacecraft power restrictions. Data were also produced for packaging and vehicle stowage parameters which are compatible with vehicle weight and volume specifications. Certain assumptions were made for food packaging sizes based on previously generated space shuttle menus. The results of the study are shown, along with the range of meal choices considered.

Numerical simulations of flying and swimming of biological systems with the viscous vortex particle method

NASA Astrophysics Data System (ADS)

Eldredge, Jeff

2005-11-01

Many biological mechanisms of locomotion involve the interaction of a fluid with a deformable surface undergoing large unsteady motion. Analysis of such problems poses a significant challenge to conventional grid-based computational approaches. Particularly in the moderate Reynolds number regime where many insects and fish function, viscous and inertial processes are both important, and vorticity serves a crucial role. In this work, the viscous vortex particle method is shown to provide an efficient, intuitive simulation approach for investigation of these biological systems. In contrast with a grid-based approach, the method solves the Navier--Stokes equations by tracking computational particles that carry smooth blobs of vorticity and exchange strength with one another to account for viscous diffusion. Thus, computational resources are focused on the physically relevant features of the flow, and there is no need for artificial boundary conditions. Building from previously-developed techniques for the creation of vorticity to enforce no-throughflow and no-slip conditions, the present method is extended to problems of coupled fluid--body dynamics by enforcement of global conservation of momenta. The application to several two-dimensional model problems is demonstrated, including single and multiple flapping wings and free swimming of a three-linkage fish.

3-D viscous flow CFD analysis of the propeller effect on an advanced ducted propeller subsonic inlet

NASA Technical Reports Server (NTRS)

Iek, Chanthy; Boldman, Donald R.; Ibrahim, Mounir

1993-01-01

The time-marching Navier-Stokes code PARC3D was used to study the 3D viscous flow associated with an advanced ducted propeller subsonic inlet at take-off operating conditions. At a free stream Mach number of 0.2, experimental data for the inlet-with-propeller test model indicated that the airflow was attached on the cowl windward lip at an angle of attack of 25 deg became unstable at 29 deg, and separated at 30 deg. An experimental study with a similar inlet and without propeller (through-flow) indicated that flow separation occurred at an angle of attack a few degrees below the value observed when the inlet was tested with the propeller, indicating the propeller's favorable effect on inlet performance. In the present numerical study, flow blockage analogous to the propeller was modeled via a PARC3D computational boundary condition (BC), the 'screen BC', based on 1-1/2 dimension actuator disk theory. The application of the screen BC in this numerical study provided results similar to those of past experimental efforts in which either the blockage device or the propeller was used.

A Three-Dimensional Unsteady CFD Model of Compressor Stability

NASA Technical Reports Server (NTRS)

Chima, Rodrick V.

2006-01-01

A three-dimensional unsteady CFD code called CSTALL has been developed and used to investigate compressor stability. The code solved the Euler equations through the entire annulus and all blade rows. Blade row turning, losses, and deviation were modeled using body force terms which required input data at stations between blade rows. The input data was calculated using a separate Navier-Stokes turbomachinery analysis code run at one operating point near stall, and was scaled to other operating points using overall characteristic maps. No information about the stalled characteristic was used. CSTALL was run in a 2-D throughflow mode for very fast calculations of operating maps and estimation of stall points. Calculated pressure ratio characteristics for NASA stage 35 agreed well with experimental data, and results with inlet radial distortion showed the expected loss of range. CSTALL was also run in a 3-D mode to investigate inlet circumferential distortion. Calculated operating maps for stage 35 with 120 degree distortion screens showed a loss in range and pressure rise. Unsteady calculations showed rotating stall with two part-span stall cells. The paper describes the body force formulation in detail, examines the computed results, and concludes with observations about the code.

CFD Design and Analysis of a Passively Suspended Tesla Pump Left Ventricular Assist Device

PubMed Central

Medvitz, Richard B.; Boger, David A.; Izraelev, Valentin; Rosenberg, Gerson; Paterson, Eric G.

2012-01-01

This paper summarizes the use of computational fluid dynamics (CFD) to design a novelly suspended Tesla LVAD. Several design variants were analyzed to study the parameters affecting device performance. CFD was performed at pump speeds of 6500, 6750 and 7000 RPM and at flow rates varying from 3 to 7 liter-per-minute (LPM). The CFD showed that shortening the plates nearest the pump inlet reduced the separations formed beneath the upper plate leading edges and provided a more uniform flow distribution through the rotor gaps, both of which positively affected the device hydrodynamic performance. The final pump design was found to produce a head rise of 77 mmHg with a hydraulic efficiency of 16% at the design conditions of 6 LPM throughflow and a 6750 RPM rotation rate. To assess the device hemodynamics the strain rate fields were evaluated. The wall shear stresses demonstrated that the pump wall shear stresses were likely adequate to inhibit thrombus deposition. Finally, an integrated field hemolysis model was applied to the CFD results to assess the effects of design variation and operating conditions on the device hemolytic performance. PMID:21595722

Electro-Microfluidic Packaging

NASA Astrophysics Data System (ADS)

Benavides, G. L.; Galambos, P. C.

2002-06-01

There are many examples of electro-microfluidic products that require cost effective packaging solutions. Industry has responded to a demand for products such as drop ejectors, chemical sensors, and biological sensors. Drop ejectors have consumer applications such as ink jet printing and scientific applications such as patterning self-assembled monolayers or ejecting picoliters of expensive analytes/reagents for chemical analysis. Drop ejectors can be used to perform chemical analysis, combinatorial chemistry, drug manufacture, drug discovery, drug delivery, and DNA sequencing. Chemical and biological micro-sensors can sniff the ambient environment for traces of dangerous materials such as explosives, toxins, or pathogens. Other biological sensors can be used to improve world health by providing timely diagnostics and applying corrective measures to the human body. Electro-microfluidic packaging can easily represent over fifty percent of the product cost and, as with Integrated Circuits (IC), the industry should evolve to standard packaging solutions. Standard packaging schemes will minimize cost and bring products to market sooner.

Versatile Software Package For Near Real-Time Analysis of Experimental Data

NASA Technical Reports Server (NTRS)

Wieseman, Carol D.; Hoadley, Sherwood T.

1998-01-01

This paper provides an overview of a versatile software package developed for time- and frequency-domain analyses of experimental wind-tunnel data. This package, originally developed for analyzing data in the NASA Langley Transonic Dynamics Tunnel (TDT), is applicable for analyzing any time-domain data. A Matlab-based software package, TDT-analyzer, provides a compendium of commonly-required dynamic analysis functions in a user-friendly interactive and batch processing environment. TDT-analyzer has been used extensively to provide on-line near real-time and post-test examination and reduction of measured data acquired during wind tunnel tests of aeroelastically-scaled models of aircraft and rotorcraft as well as a flight test of the NASA High Alpha Research Vehicle (HARV) F-18. The package provides near real-time results in an informative and timely manner far exceeding prior methods of data reduction at the TDT.

Material flow analysis for an industry - A case study in packaging

USGS Publications Warehouse

Amey, E.B.; Sandgren, K.

1996-01-01

The basic materials used in packaging are glass, metals (primarily aluminum and steel), an ever-growing range of plastics, paper and paperboard, wood, textiles for bags, and miscellaneous other materials (such as glues, inks, and other supplies). They are fabricated into rigid, semi-rigid, or flexible containers. The most common forms of these containers include cans, drums, bottles, cartons, boxes, bags, pouches, and wraps. Packaging products are, for the most part, low cost, bulky products that are manufactured close to their customers. There is virtually no import or export of packaging products. A material flow analysis can be developed that looks at all inputs to an industrial sector, inventories the losses in processing, and tracks the fate of the material after its useful life. An example is presented that identifies the material inputs to the packaging industry, and addresses the ultimate fate of the materials used. ?? 1996 International Association for Mathematical Geology.

A Systematic Review and Meta-Analysis of Fecal Contamination and Inadequate Treatment of Packaged Water

PubMed Central

Williams, Ashley R.; Bain, Robert E. S.; Fisher, Michael B.; Cronk, Ryan; Kelly, Emma R.; Bartram, Jamie

2015-01-01

Background Packaged water products provide an increasingly important source of water for consumption. However, recent studies raise concerns over their safety. Objectives To assess the microbial safety of packaged water, examine differences between regions, country incomes, packaged water types, and compare packaged water with other water sources. Methods We performed a systematic review and meta-analysis. Articles published in English, French, Portuguese, Spanish and Turkish, with no date restrictions were identified from online databases and two previous reviews. Studies published before April 2014 that assessed packaged water for the presence of Escherichia coli, thermotolerant or total coliforms were included provided they tested at least ten samples or brands. Results A total of 170 studies were included in the review. The majority of studies did not detect fecal indicator bacteria in packaged water (78/141). Compared to packaged water from upper-middle and high-income countries, packaged water from low and lower-middle-income countries was 4.6 (95% CI: 2.6–8.1) and 13.6 (95% CI: 6.9–26.7) times more likely to contain fecal indicator bacteria and total coliforms, respectively. Compared to all other packaged water types, water from small bottles was less likely to be contaminated with fecal indicator bacteria (OR = 0.32, 95%CI: 0.17–0.58) and total coliforms (OR = 0.10, 95%CI: 0.05, 0.22). Packaged water was less likely to contain fecal indicator bacteria (OR = 0.35, 95%CI: 0.20, 0.62) compared to other water sources used for consumption. Conclusions Policymakers and regulators should recognize the potential benefits of packaged water in providing safer water for consumption at and away from home, especially for those who are otherwise unlikely to gain access to a reliable, safe water supply in the near future. To improve the quality of packaged water products they should be integrated into regulatory and monitoring frameworks. PMID:26505745

A Systematic Review and Meta-Analysis of Fecal Contamination and Inadequate Treatment of Packaged Water.

PubMed

Williams, Ashley R; Bain, Robert E S; Fisher, Michael B; Cronk, Ryan; Kelly, Emma R; Bartram, Jamie

2015-01-01

Packaged water products provide an increasingly important source of water for consumption. However, recent studies raise concerns over their safety. To assess the microbial safety of packaged water, examine differences between regions, country incomes, packaged water types, and compare packaged water with other water sources. We performed a systematic review and meta-analysis. Articles published in English, French, Portuguese, Spanish and Turkish, with no date restrictions were identified from online databases and two previous reviews. Studies published before April 2014 that assessed packaged water for the presence of Escherichia coli, thermotolerant or total coliforms were included provided they tested at least ten samples or brands. A total of 170 studies were included in the review. The majority of studies did not detect fecal indicator bacteria in packaged water (78/141). Compared to packaged water from upper-middle and high-income countries, packaged water from low and lower-middle-income countries was 4.6 (95% CI: 2.6-8.1) and 13.6 (95% CI: 6.9-26.7) times more likely to contain fecal indicator bacteria and total coliforms, respectively. Compared to all other packaged water types, water from small bottles was less likely to be contaminated with fecal indicator bacteria (OR = 0.32, 95%CI: 0.17-0.58) and total coliforms (OR = 0.10, 95%CI: 0.05, 0.22). Packaged water was less likely to contain fecal indicator bacteria (OR = 0.35, 95%CI: 0.20, 0.62) compared to other water sources used for consumption. Policymakers and regulators should recognize the potential benefits of packaged water in providing safer water for consumption at and away from home, especially for those who are otherwise unlikely to gain access to a reliable, safe water supply in the near future. To improve the quality of packaged water products they should be integrated into regulatory and monitoring frameworks.

RSEIS and RFOC: Seismic Analysis in R

NASA Astrophysics Data System (ADS)

Lees, J. M.

2015-12-01

Open software is essential for reproducible scientific exchange. R-packages provide a platform for development of seismological investigation software that can be properly documented and traced for data processing. A suite of R packages designed for a wide range of seismic analysis is currently available in the free software platform called R. R is a software platform based on the S-language developed at Bell Labs decades ago. Routines in R can be run as standalone function calls, or developed in object-oriented mode. R comes with a base set of routines, and thousands of user developed packages. The packages developed at UNC include subroutines and interactive codes for processing seismic data, analyzing geographic information (GIS) and inverting data involved in a variety of geophysical applications. On CRAN (Comprehensive R Archive Network, http://www.r-project.org/) currently available packages related to seismic analysis are RSEIS, Rquake, GEOmap, RFOC, zoeppritz, RTOMO, and geophys, Rwave, PEIP, hht, rFDSN. These include signal processing, data management, mapping, earthquake location, deconvolution, focal mechanisms, wavelet transforms, Hilbert-Huang Transforms, tomographic inversion, and Mogi deformation among other useful functionality. All software in R packages is required to have detailed documentation, making the exchange and modification of existing software easy. In this presentation, I will focus on packages RSEIS and RFOC, showing examples from a variety of seismic analyses. The R approach has similarities to the popular (and expensive) MATLAB platform, although R is open source and free to down load.

An R package for the design, analysis and operation of reservoir systems

NASA Astrophysics Data System (ADS)

Turner, Sean; Ng, Jia Yi; Galelli, Stefano

2016-04-01

We present a new R package - named "reservoir" - which has been designed for rapid and easy routing of runoff through storage. The package comprises well-established tools for capacity design (e.g., the sequent peak algorithm), performance analysis (storage-yield-reliability and reliability-resilience-vulnerability analysis) and release policy optimization (Stochastic Dynamic Programming). Operating rules can be optimized for water supply, flood control and amenity objectives, as well as for maximum hydropower production. Storage-depth-area relationships are in-built, allowing users to incorporate evaporation from the reservoir surface. We demonstrate the capabilities of the software for global studies using thousands of reservoirs from the Global Reservoir and Dam (GRanD) database fed by historical monthly inflow time series from a 0.5 degree gridded global runoff dataset. The package is freely available through the Comprehensive R Archive Network (CRAN).

Probablistic Analyses of Waste Package Quantities Impacted by Potential Igneous Disruption at Yucca Mountain

NASA Astrophysics Data System (ADS)

Wallace, M. G.; Iuzzolina, H.

2005-12-01

A probabilistic analysis was conducted to estimate ranges for the numbers of waste packages that could be damaged in a potential future igneous event through a repository at Yucca Mountain. The analysis includes disruption from an intrusive igneous event and from an extrusive volcanic event. This analysis supports the evaluation of the potential consequences of future igneous activity as part of the total system performance assessment for the license application for the Yucca Mountain Project (YMP). The first scenario, igneous intrusion, investigated the case where one or more igneous dikes intersect the repository. A swarm of dikes was characterized by distributions of length, width, azimuth, and number of dikes and the spacings between them. Through the use in part of a latin hypercube simulator and a modified video game engine, mathematical relationships were built between those parameters and the number of waste packages hit. Corresponding cumulative distribution function curves (CDFs) for the number of waste packages hit under several different scenarios were calculated. Variations in dike thickness ranges, as well as in repository magma bulkhead positions were examined through sensitivity studies. It was assumed that all waste packages in an emplacement drift would be impacted if that drift was intersected by a dike. Over 10,000 individual simulations were performed. Based on these calculations, out of a total of over 11,000 planned waste packages distributed over an area of approximately 5.5 km2 , the median number of waste packages impacted was roughly 1/10 of the total. Individual cases ranged from 0 waste packages to the entire inventory being impacted. The igneous intrusion analysis involved an explicit characterization of dike-drift intersections, built upon various distributions that reflect the uncertainties associated with the inputs. The second igneous scenario, volcanic eruption (eruptive conduits), considered the effects of conduits formed in association with a volcanic eruption through the repository. Mathematical relations were built between the resulting conduit areas and the fraction of the repository area occupied by waste packages. This relation was used in conjunction with a joint distribution incorporating variability in eruptive conduit diameters and in the number of eruptive conduits that could intersect the repository.

puma: a Bioconductor package for propagating uncertainty in microarray analysis.

PubMed

Pearson, Richard D; Liu, Xuejun; Sanguinetti, Guido; Milo, Marta; Lawrence, Neil D; Rattray, Magnus

2009-07-09

Most analyses of microarray data are based on point estimates of expression levels and ignore the uncertainty of such estimates. By determining uncertainties from Affymetrix GeneChip data and propagating these uncertainties to downstream analyses it has been shown that we can improve results of differential expression detection, principal component analysis and clustering. Previously, implementations of these uncertainty propagation methods have only been available as separate packages, written in different languages. Previous implementations have also suffered from being very costly to compute, and in the case of differential expression detection, have been limited in the experimental designs to which they can be applied. puma is a Bioconductor package incorporating a suite of analysis methods for use on Affymetrix GeneChip data. puma extends the differential expression detection methods of previous work from the 2-class case to the multi-factorial case. puma can be used to automatically create design and contrast matrices for typical experimental designs, which can be used both within the package itself but also in other Bioconductor packages. The implementation of differential expression detection methods has been parallelised leading to significant decreases in processing time on a range of computer architectures. puma incorporates the first R implementation of an uncertainty propagation version of principal component analysis, and an implementation of a clustering method based on uncertainty propagation. All of these techniques are brought together in a single, easy-to-use package with clear, task-based documentation. For the first time, the puma package makes a suite of uncertainty propagation methods available to a general audience. These methods can be used to improve results from more traditional analyses of microarray data. puma also offers improvements in terms of scope and speed of execution over previously available methods. puma is recommended for anyone working with the Affymetrix GeneChip platform for gene expression analysis and can also be applied more generally.

Interfaces between statistical analysis packages and the ESRI geographic information system

NASA Technical Reports Server (NTRS)

Masuoka, E.

1980-01-01

Interfaces between ESRI's geographic information system (GIS) data files and real valued data files written to facilitate statistical analysis and display of spatially referenced multivariable data are described. An example of data analysis which utilized the GIS and the statistical analysis system is presented to illustrate the utility of combining the analytic capability of a statistical package with the data management and display features of the GIS.

TYPE A FISSILE PACKAGING FOR AIR TRANSPORT PROJECT OVERVIEW

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

Eberl, K.; Blanton, P.

2013-10-11

This paper presents the project status of the Model 9980, a new Type A fissile packaging for use in air transport. The Savannah River National Laboratory (SRNL) developed this new packaging to be a light weight (<150-lb), drum-style package and prepared a Safety Analysis for Packaging (SARP) for submission to the DOE/EM. The package design incorporates unique features and engineered materials specifically designed to minimize packaging weight and to be in compliance with 10CFR71 requirements. Prototypes were fabricated and tested to evaluate the design when subjected to Normal Conditions of Transport (NCT) and Hypothetical Accident Conditions (HAC). An overview ofmore » the design details, results of the regulatory testing, and lessons learned from the prototype fabrication for the 9980 will be presented.« less

A large column analog experiment of stable isotope variations during reactive transport: II. Carbon mass balance, microbial community structure and predation

NASA Astrophysics Data System (ADS)

Druhan, Jennifer L.; Bill, Markus; Lim, HsiaoChien; Wu, Cindy; Conrad, Mark E.; Williams, Kenneth H.; DePaolo, Donald J.; Brodie, Eoin L.

2014-01-01

Here we report a combined analysis of carbon mass balance based on isotopic labeling and microbiological characterization during organic carbon stimulated bioreduction of a subsurface sediment in a large laboratory column experimental system. This combination of approaches allows quantification of both the cycling of carbon through multiple redox pathways and the associated spatial and temporal evolution of bacterial communities in response to this nutrient source. Carbon isotope mass balance facilitated by the use of 13C-labeled acetate as the electron donor showed evidence for a net loss of sediment organic carbon over the course of the amendment experiment. Furthermore, these data clearly demonstrated a source of isotopically labeled inorganic carbon that was not attributable to primary metabolism by acetate-oxidizing microorganisms. Fluid samples collected weekly over the duration of the 43-day amendment at <20 cm intervals along the flow path were analyzed for microbial composition by pyrosequencing of ribosomal RNA genes. The microbial community composition was transient, with distinct occurrences of Azoarcus, Geobacter and multiple sulfate reducing species over the course of the experiment. In combination with DNA sequencing data, the anomalous carbon cycling process is shown to occur exclusively during the period of predominant Geobacter species growth. Pyrosequencing indicated, and targeted cloning and sequencing confirmed the presence of several bacteriovorous protozoa, including species of the Breviata, Planococcus and Euplotes genera. Cloning and qPCR analysis demonstrated that Euplotes species were most abundant and displayed a growth trajectory that closely followed that of the Geobacter population. These results suggest a previously undocumented secondary turnover of biomass carbon related to protozoan grazing that was not sufficiently prevalent to be observed in bulk concentrations of carbon species in the system, but was clearly identified in the partitioning of carbon isotopes. This study demonstrates evidence for predator-prey relationships that impact subsurface microbial community dynamics and provides a novel indication of the impact of this relationship on the flux of carbon through a system via the microbial biomass pool. Overall, our approach provides high temporal and spatial sampling resolution at field relevant flow rates, while minimizing effects of mixing and transverse dispersion. The result is a quantitative carbon budget accounting for a diversity of processes that should be considered for inclusion in reactive transport models that aim to predict carbon turnover, nutrient flux, and redox reactions in natural and stimulated subsurface systems. the mobilization of previously stabilized, sediment-bound carbon; a carbon mass balance for a through-flowing sediment column over the course of a 43-day amendment using 13C-labeled acetate; a phylogenetic microbial community structure at <20 cm sampling resolution with distance away from the organic carbon source weekly over the 43-day amendment; protozoan grazing on the active Geobacteraceae population and the rapid turnover of microbial biomass carbon as a secondary cycling pathway. Such a high resolution, combined analysis of microbial populations and the associated carbon mass balance in a through-flowing system at field relevant flow rates provides novel, quantitative insights into the interface between biogeochemical cycling and bulk carbon fluxes in the near-surface environment.

Observed strengthening of interbasin exchange via the Indonesian seas due to rainfall intensification

PubMed Central

Sprintall, Janet

2017-01-01

Abstract A proxy of the Indonesian Throughflow (ITF) transport, developed using in situ hydrographic measurements along with assimilations, shows a significant strengthening trend during the past decade. This trend is due to a freshening and subsequent increase in the halosteric component of the ITF transport associated with enhanced rainfall over the Maritime Continent over the same period. The strengthening of the ITF transport leads to a significant change in heat and freshwater exchange between the Pacific and Indian Oceans and contributes to the warming and freshening of the eastern Indian Ocean. The combined effect of the ITF transport of mass and freshwater along with tropical rainfall plays a very important role in the climate system. PMID:28405053

Supersonic fan engines for military aircraft

NASA Technical Reports Server (NTRS)

Franciscus, L. C.

1983-01-01

Engine performance and mission studies were performed for turbofan engines with supersonic through-flow fans. A Mach 2.4 CTOL aircraft was used in the study. Two missions were considered: a long range penetrator mission and a long range intercept mission. The supersonic fan engine is compared with an augmented mixed flow turbofan in terms of mission radius for a fixed takeoff gross weight of 75,000 lbm. The mission radius of aircraft powered by supersonic fan engines could be 15 percent longer than aircraft powered with conventional turbofan engines at moderate thrust to gross weight ratios. The climb and acceleration performance of the supersonic fan engines is better than that of the conventional turbofan engines. Previously announced in STAR as N83-34947

Computer program for calculating full potential transonic, quasi-three-dimensional flow through a rotating turbomachinery blade row

NASA Technical Reports Server (NTRS)

Farrell, C. A.

1982-01-01

A fast, reliable computer code is described for calculating the flow field about a cascade of arbitrary two dimensional airfoils. The method approximates the three dimensional flow in a turbomachinery blade row by correcting for stream tube convergence and radius change in the throughflow direction. A fully conservative solution of the full potential equation is combined with the finite volume technique on a body-fitted periodic mesh, with an artificial density imposed in the transonic region to insure stability and the capture of shock waves. The instructions required to set up and use the code are included. The name of the code is QSONIC. A numerical example is also given to illustrate the output of the program.

High speed civil transport

NASA Technical Reports Server (NTRS)

Bogardus, Scott; Loper, Brent; Nauman, Chris; Page, Jeff; Parris, Rusty; Steinbach, Greg

1990-01-01

The design process of the High Speed Civil Transport (HSCT) combines existing technology with the expectation of future technology to create a Mach 3.0 transport. The HSCT was designed to have a range in excess of 6000 nautical miles and carry up to 300 passengers. This range will allow the HSCT to service the economically expanding Pacific Basin region. Effort was made in the design to enable the aircraft to use conventional airports with standard 12,000 foot runways. With a takeoff thrust of 250,000 pounds, the four supersonic through-flow engines will accelerate the HSCT to a cruise speed of Mach 3.0. The 679,000 pound (at takeoff) HSCT is designed to cruise at an altitude of 70,000 feet, flying above most atmospheric disturbances.

AMModels: An R package for storing models, data, and metadata to facilitate adaptive management

PubMed Central

Katz, Jonathan E.

2018-01-01

Agencies are increasingly called upon to implement their natural resource management programs within an adaptive management (AM) framework. This article provides the background and motivation for the R package, AMModels. AMModels was developed under R version 3.2.2. The overall goal of AMModels is simple: To codify knowledge in the form of models and to store it, along with models generated from numerous analyses and datasets that may come our way, so that it can be used or recalled in the future. AMModels facilitates this process by storing all models and datasets in a single object that can be saved to an .RData file and routinely augmented to track changes in knowledge through time. Through this process, AMModels allows the capture, development, sharing, and use of knowledge that may help organizations achieve their mission. While AMModels was designed to facilitate adaptive management, its utility is far more general. Many R packages exist for creating and summarizing models, but to our knowledge, AMModels is the only package dedicated not to the mechanics of analysis but to organizing analysis inputs, analysis outputs, and preserving descriptive metadata. We anticipate that this package will assist users hoping to preserve the key elements of an analysis so they may be more confidently revisited at a later date. PMID:29489825

AMModels: An R package for storing models, data, and metadata to facilitate adaptive management.

PubMed

Donovan, Therese M; Katz, Jonathan E

2018-01-01

Agencies are increasingly called upon to implement their natural resource management programs within an adaptive management (AM) framework. This article provides the background and motivation for the R package, AMModels. AMModels was developed under R version 3.2.2. The overall goal of AMModels is simple: To codify knowledge in the form of models and to store it, along with models generated from numerous analyses and datasets that may come our way, so that it can be used or recalled in the future. AMModels facilitates this process by storing all models and datasets in a single object that can be saved to an .RData file and routinely augmented to track changes in knowledge through time. Through this process, AMModels allows the capture, development, sharing, and use of knowledge that may help organizations achieve their mission. While AMModels was designed to facilitate adaptive management, its utility is far more general. Many R packages exist for creating and summarizing models, but to our knowledge, AMModels is the only package dedicated not to the mechanics of analysis but to organizing analysis inputs, analysis outputs, and preserving descriptive metadata. We anticipate that this package will assist users hoping to preserve the key elements of an analysis so they may be more confidently revisited at a later date.

Dynamic Modeling Using MCSim and R (SOT 2016 Biological Modeling Webinar Series)

EPA Science Inventory

MCSim is a stand-alone software package for simulating and analyzing dynamic models, with a focus on Bayesian analysis using Markov Chain Monte Carlo. While it is an extremely powerful package, it is somewhat inflexible, and offers only a limited range of analysis options, with n...

Technical Review Report for the Mound 1KW Package Safety Analysis Report for Packaging Waiver for the Use of Modified Primary Containment Vessel (PCV)

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

West, M; Hafner, R

2008-05-05

This Technical Review Report (TRR) documents the review, performed by the Lawrence Livermore National Laboratory (LLNL) staff, at the request of the U.S. Department of Energy (DOE), on the Waiver for the Use of Modified Primary Containment Vessels (PCV). The waiver is to be used to support a limited number of shipments of fuel for the Multi-Mission Radioisotope Thermoelectric Generator (MMRTG) Project in support of the National Aeronautics and Space Administration's (NASA's) Mars Science Laboratory (MSL) mission. Under the waiver, an inventory of existing national security PCVs will be converted to standard PCVs. Both types of PCVs are currently approvedmore » for use by the Office of Nuclear Energy. LLNL has previously reviewed the national security PCVs under Mound 1KW Package Safety Analysis Report for Packaging, Addendum No. 1, Revision c, dated June 2007 (Addendum 1). The safety analysis of the package is documented in the Safety Analysis Report for Packaging (SARP) for the Mound 1KW Package (i.e., the Mound 1KW SARP, or the SARP) where the standard PCVs have been reviewed by LLNL. The Mound 1KW Package is certified by DOE Certificate of Compliance (CoC) number USA/9516/B(U)F-85 for the transportation of Type B quantities of plutonium heat source material. The waiver requests an exemption, claiming safety equivalent to the requirements specified in 10 CFR 71.12, Specific Exemptions, and will lead to a letter amendment to the CoC. Under the waiver, the Office of Radioisotope Power Systems, NE-34, is seeking an exemption from 10 CFR 71.19(d)(1), Previously Approved Package,[5] which states: '(d) NRC will approve modifications to the design and authorized contents of a Type B package, or a fissile material package, previously approved by NRC, provided--(1) The modifications of a Type B package are not significant with respect to the design, operating characteristics, or safe performance of the containment system, when the package is subjected to the tests specified in {section}71.71 and 71.73.' The LLNL staff had previously reviewed a request from Idaho National Laboratory (INL) to reconfigure national security PCVs to standard PCVs. With a nominal 50% reduction in both the height and the volume, the LLNL staff initially deemed the modifications to be significant, which would not be allowed under the provisions of 10 CFR 71.19(d)(1)--see above. As a follow-up, the DOE requested additional clarification from the Nuclear Regulatory Commission (NRC). The NRC concluded that the reconfiguration would be a new fabrication, and that an exemption to the regulations would be required to allow its use, as per the requirements specified in 10 CFR 71.19(c)(1), Previously Approved Package: '(c) A Type B(U) package, a Type B(M) package, or a fissile material package previously approved by the NRC with the designation '-85' in the identification number of the NRC CoC, may be used under the general license of {section}71.17 with the following additional conditions: (1) Fabrication of the package must be satisfactorily completed by December 31, 2006, as demonstrated by application of its model number in accordance with 71.85(c).' Although the preferred approach toward the resolution of this issue would be for the applicant to submit an updated SARP, the applicant has stated that the process of updating the Model Mound 1KW Package SARP is a work that is in progress, but that the updated SARP is not yet ready for submittal. The applicant has to provide a submittal, proving that the package meets the '-96' requirements of International Atomic Energy Agency (IAEA) Safety Standards Series No. TS-R-1, in order to fabricate approved packagings after December 31, 2006. The applicant has further stated that all other packaging features, as described in the currently approved Model Mound 1KW Package SARP, remain unchanged. This report documents the LLNL review of the waiver request. The specific review for each SARP Chapter is documented.« less

MeV+R: using MeV as a graphical user interface for Bioconductor applications in microarray analysis

PubMed Central

Chu, Vu T; Gottardo, Raphael; Raftery, Adrian E; Bumgarner, Roger E; Yeung, Ka Yee

2008-01-01

We present MeV+R, an integration of the JAVA MultiExperiment Viewer program with Bioconductor packages. This integration of MultiExperiment Viewer and R is easily extensible to other R packages and provides users with point and click access to traditionally command line driven tools written in R. We demonstrate the ability to use MultiExperiment Viewer as a graphical user interface for Bioconductor applications in microarray data analysis by incorporating three Bioconductor packages, RAMA, BRIDGE and iterativeBMA. PMID:18652698

Drought: A comprehensive R package for drought monitoring, prediction and analysis

NASA Astrophysics Data System (ADS)

Hao, Zengchao; Hao, Fanghua; Singh, Vijay P.; Cheng, Hongguang

2015-04-01

Drought may impose serious challenges to human societies and ecosystems. Due to complicated causing effects and wide impacts, a universally accepted definition of drought does not exist. The drought indicator is commonly used to characterize drought properties such as duration or severity. Various drought indicators have been developed in the past few decades for the monitoring of a certain aspect of drought condition along with the development of multivariate drought indices for drought characterizations from multiple sources or hydro-climatic variables. Reliable drought prediction with suitable drought indicators is critical to the drought preparedness plan to reduce potential drought impacts. In addition, drought analysis to quantify the risk of drought properties would provide useful information for operation drought managements. The drought monitoring, prediction and risk analysis are important components in drought modeling and assessments. In this study, a comprehensive R package "drought" is developed to aid the drought monitoring, prediction and risk analysis (available from R-Forge and CRAN soon). The computation of a suite of univariate and multivariate drought indices that integrate drought information from various sources such as precipitation, temperature, soil moisture, and runoff is available in the drought monitoring component in the package. The drought prediction/forecasting component consists of statistical drought predictions to enhance the drought early warning for decision makings. Analysis of drought properties such as duration and severity is also provided in this package for drought risk assessments. Based on this package, a drought monitoring and prediction/forecasting system is under development as a decision supporting tool. The package will be provided freely to the public to aid the drought modeling and assessment for researchers and practitioners.

Implementation of interconnect simulation tools in spice

NASA Technical Reports Server (NTRS)

Satsangi, H.; Schutt-Aine, J. E.

1993-01-01

Accurate computer simulation of high speed digital computer circuits and communication circuits requires a multimode approach to simulate both the devices and the interconnects between devices. Classical circuit analysis algorithms (lumped parameter) are needed for circuit devices and the network formed by the interconnected devices. The interconnects, however, have to be modeled as transmission lines which incorporate electromagnetic field analysis. An approach to writing a multimode simulator is to take an existing software package which performs either lumped parameter analysis or field analysis and add the missing type of analysis routines to the package. In this work a traditionally lumped parameter simulator, SPICE, is modified so that it will perform lossy transmission line analysis using a different model approach. Modifying SPICE3E2 or any other large software package is not a trivial task. An understanding of the programming conventions used, simulation software, and simulation algorithms is required. This thesis was written to clarify the procedure for installing a device into SPICE3E2. The installation of three devices is documented and the installations of the first two provide a foundation for installation of the lossy line which is the third device. The details of discussions are specific to SPICE, but the concepts will be helpful when performing installations into other circuit analysis packages.

A streamlined Python framework for AT-TPC data analysis

NASA Astrophysics Data System (ADS)

Taylor, J. Z.; Bradt, J.; Bazin, D.; Kuchera, M. P.

2017-09-01

User-friendly data analysis software has been developed for the Active-Target Time Projection Chamber (AT-TPC) experiment at the National Superconducting Cyclotron Laboratory at Michigan State University. The AT-TPC, commissioned in 2014, is a gas-filled detector that acts as both the detector and target for high-efficiency detection of low-intensity, exotic nuclear reactions. The pytpc framework is a Python package for analyzing AT-TPC data. The package was developed for the analysis of 46Ar(p, p) data. The existing software was used to analyze data produced by the 40Ar(p, p) experiment that ran in August, 2015. Usage of the package was documented in an analysis manual both to improve analysis steps and aid in the work of future AT-TPC users. Software features and analysis methods in the pytpc framework will be presented along with the 40Ar results.

Model-based gene set analysis for Bioconductor.

PubMed

Bauer, Sebastian; Robinson, Peter N; Gagneur, Julien

2011-07-01

Gene Ontology and other forms of gene-category analysis play a major role in the evaluation of high-throughput experiments in molecular biology. Single-category enrichment analysis procedures such as Fisher's exact test tend to flag large numbers of redundant categories as significant, which can complicate interpretation. We have recently developed an approach called model-based gene set analysis (MGSA), that substantially reduces the number of redundant categories returned by the gene-category analysis. In this work, we present the Bioconductor package mgsa, which makes the MGSA algorithm available to users of the R language. Our package provides a simple and flexible application programming interface for applying the approach. The mgsa package has been made available as part of Bioconductor 2.8. It is released under the conditions of the Artistic license 2.0. peter.robinson@charite.de; julien.gagneur@embl.de.

Agarose Gel Electrophoresis Reveals Structural Fluidity of a Phage T3 DNA Packaging Intermediate

PubMed Central

Serwer, Philip; Wright, Elena T.

2012-01-01

We find a new aspect of DNA packaging-associated structural fluidity for phage T3 capsids. The procedure is (1) glutaraldehyde cross-linking of in vivo DNA packaging intermediates for stabilization of structure and then (2) determining of effective radius by two-dimensional agarose gel electrophoresis (2d-AGE). The intermediates are capsids with incompletely packaged DNA (ipDNA) and without an external DNA segment; these intermediates are called ipDNA-capsids. We initially increase production of ipDNA-capsids by raising NaCl concentration during in vivo DNA packaging. By 2d-AGE, we find a new state of contracted shell for some particles of one previously identified ipDNA-capsid. The contracted shell-state is found when ipDNA length/mature DNA length (F) is above 0.17, but not at lower F. Some contracted-shell ipDNA-capsids have the phage tail; others do not. The contracted-shell ipDNA-capsids are explained by premature DNA maturation cleavage that makes accessible a contracted-shell intermediate of a cycle of the T3 DNA packaging motor. The analysis of ipDNA-capsids, rather than intermediates with uncleaved DNA, provides a simplifying strategy for a complete biochemical analysis of in vivo DNA packaging. PMID:22222979

Impact of Policy Changes on Infant Feeding Decisions Among Low-Income Women Participating in the Special Supplemental Nutrition Program for Women, Infants, and Children

PubMed Central

Koleilat, Maria; Whaley, Mike; Gomez, Judy; Meehan, Karen; Saluja, Kiran

2012-01-01

Objectives. We present infant feeding data before and after the 2009 Special Supplemental Nutrition Program for Women, Infants, and Children (WIC) food package change that supported and incentivized breastfeeding. We describe the key role of California WIC staff in supporting these policy changes. Methods. We analyzed WIC data on more than 180 000 infants in Southern California. We employed the analysis of variance and Tukey (honestly significant difference) tests to compare issuance rates of postpartum and infant food packages before and after the changes. We used analysis of covariance to adjust for poverty status changes as a potential confounder. Results. Issuance rates of the “fully breastfeeding” package at infant WIC enrollment increased by 86% with the package changes. Rates also increased significantly for 2- and 6-month-old infants. Issuance rates of packages that included formula decreased significantly. All outcomes remained highly significant in the adjusted model. Conclusions. Policy changes, training of front-line WIC staff, and participant education influenced issuance rates of WIC food packages. In California, the issuance rates of packages that include formula have significantly decreased and the rate for those that include no formula has significantly increased. PMID:23078467

Program Package for the Analysis of High Resolution High Signal-To-Noise Stellar Spectra

NASA Astrophysics Data System (ADS)

Piskunov, N.; Ryabchikova, T.; Pakhomov, Yu.; Sitnova, T.; Alekseeva, S.; Mashonkina, L.; Nordlander, T.

2017-06-01

The program package SME (Spectroscopy Made Easy), designed to perform an analysis of stellar spectra using spectral fitting techniques, was updated due to adding new functions (isotopic and hyperfine splittins) in VALD and including grids of NLTE calculations for energy levels of few chemical elements. SME allows to derive automatically stellar atmospheric parameters: effective temperature, surface gravity, chemical abundances, radial and rotational velocities, turbulent velocities, taking into account all the effects defining spectral line formation. SME package uses the best grids of stellar atmospheres that allows us to perform spectral analysis with the similar accuracy in wide range of stellar parameters and metallicities - from dwarfs to giants of BAFGK spectral classes.

The Geomorphic Road Analysis and Inventory Package (GRAIP) Volume 1: Data Collection Method

Treesearch

Thomas A. Black; Richard M. Cissel; Charles H. Luce

2012-01-01

An important first step in managing forest roads for improved water quality and aquatic habitat is the performance of an inventory. The Geomorphic Roads Analysis and Inventory Package (GRAIP) was developed as a tool for making a comprehensive inventory and analysis of the effects of forest roads on watersheds. This manual describes the data collection and process of a...

Item Response Data Analysis Using Stata Item Response Theory Package

ERIC Educational Resources Information Center

Yang, Ji Seung; Zheng, Xiaying

2018-01-01

The purpose of this article is to introduce and review the capability and performance of the Stata item response theory (IRT) package that is available from Stata v.14, 2015. Using a simulated data set and a publicly available item response data set extracted from Programme of International Student Assessment, we review the IRT package from…

MGtoolkit: A python package for implementing metagraphs

NASA Astrophysics Data System (ADS)

Ranathunga, D.; Nguyen, H.; Roughan, M.

In this paper we present MGtoolkit: an open-source Python package for implementing metagraphs - a first of its kind. Metagraphs are commonly used to specify and analyse business and computer-network policies alike. MGtoolkit can help verify such policies and promotes learning and experimentation with metagraphs. The package currently provides purely textual output for visualising metagraphs and their analysis results.

77 FR 67678 - Content Specifications and Shielding Evaluations for Type B Transportation Packages

Federal Register 2010, 2011, 2012, 2013, 2014

2012-11-13

...The U.S. Nuclear Regulatory Commission (NRC or the Commission) is issuing for public comment Draft Regulatory Issue Summary (RIS) 2012-XX, ``Content Specifications and Shielding Evaluations for Type B Transportation Packages.'' This RIS clarifies the NRC's use of staff guidance in NUREG-1609, ``Standard Review Plan for Transport Packages for Radioactive Material,'' for the review of content specifications and shielding evaluations included in the Certificates of Compliance (CoC) and safety analysis reports (SARs) for Type B transportation packages.

Design requirements for SRB production control system. Volume 3: Package evaluation, modification and hardware

NASA Technical Reports Server (NTRS)

1981-01-01

The software package evaluation was designed to analyze commercially available, field-proven, production control or manufacturing resource planning management technology and software package. The analysis was conducted by comparing SRB production control software requirements and conceptual system design to software package capabilities. The methodology of evaluation and the findings at each stage of evaluation are described. Topics covered include: vendor listing; request for information (RFI) document; RFI response rate and quality; RFI evaluation process; and capabilities versus requirements.

ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data

PubMed Central

Morgan, Martin; Anders, Simon; Lawrence, Michael; Aboyoun, Patrick; Pagès, Hervé; Gentleman, Robert

2009-01-01

Summary: ShortRead is a package for input, quality assessment, manipulation and output of high-throughput sequencing data. ShortRead is provided in the R and Bioconductor environments, allowing ready access to additional facilities for advanced statistical analysis, data transformation, visualization and integration with diverse genomic resources. Availability and Implementation: This package is implemented in R and available at the Bioconductor web site; the package contains a ‘vignette’ outlining typical work flows. Contact: mtmorgan@fhcrc.org PMID:19654119

Improving packaged food quality and safety. Part 1: synchrotron X-ray analysis.

PubMed

López-Rubio, A; Hernandez-Muñoz, P; Catala, R; Gavara, R; Lagarón, J M

2005-10-01

The objective was to demonstrate, as an example of an application, the potential of synchrotron X-ray analysis to detect morphological alterations that can occur in barrier packaging materials and structures. These changes can affect the packaging barrier characteristics when conventional food preservation treatments are applied to packaged food. The paper presents the results of a number of experiments where time-resolved combined wide-angle X-ray scattering and small-angle X-ray scattering analysis as a function of temperature and humidity were applied to ethylene-vinyl alcohol co-polymers (EVOH), polypropylene (PP)/EVOH/PP structures, aliphatic polyketone terpolymer (PK) and amorphous polyamide (aPA) materials. A comparison between conventional retorting and high-pressure processing treatments in terms of morphologic alterations are also presented for EVOH. The impact of retorting on the EVOH structure contrasts with the good behaviour of the PK during this treatment and with that of aPA. However, no significant structural changes were observed by wide-angle X-ray scattering in the EVOH structures after high-pressure processing treatment. These structural observations have also been correlated with oxygen permeability measurements that are of importance when guaranteeing the intended levels of safety and quality of packaged food.

Re-design of apple pia packaging using quality function deployment method

NASA Astrophysics Data System (ADS)

Pulungan, M. H.; Nadira, N.; Dewi, I. A.

2018-03-01

This study was aimed to identify the attributes for premium apple pia packaging, to determine the technical response to be carried out by Permata Agro Mandiri Small and Medium Enterprise (SME) and to design a new apple pie packaging acceptable by the SME. The Quality Function Deployment (QFD) method was employed to improve the apple pia packaging design, which consisted of seven stages in data analysis. The results indicated that whats attribute required by the costumers include graphic design, dimensions, capacity, shape, strength, and resistance of packaging. While, the technical responses to be conducted by the SMEs were as follows: attractive visual packaging designs, attractive colors, clear images and information, packaging size dimensions, a larger capacity packaging (more product content), ergonomic premium packaging, not easily torn, and impact resistant packaging materials. The findings further confirmed that the design of premium apple pia packaging accepted by the SMES was the one with the capacity of ten apple pia or 200 g weight, and with rectangular or beam shape form. The packaging material used was a duplex carton with 400 grammage (g/m2), the outer part of the packaging was coated with plastic and the inside was added with duplex carton. The acceptable packaging dimension was 30 cm x 5 cm x 3 cm (L x W x H) with a mix of black and yellow color in the graphical design.

Language Analysis Package (L.A.P.) Version I System Design.

ERIC Educational Resources Information Center

Porch, Ann

To permit researchers to use the speed and versatility of the computer to process natural language text as well as numerical data without undergoing special training in programing or computer operations, a language analysis package has been developed partially based on several existing programs. An overview of the design is provided and system…

The aquamet Package for R: A Tool for Use with the National Rivers and Streams Assessment

EPA Science Inventory

The use of R software in environmental data analysis has become increasingly common because it is very powerful, versatile and available free of charge, with hundreds of contributed add-on packages available that perform almost every conceivable type of analysis or task. The Envi...

Calibration data Analysis Package (CAP): An IDL based widget application for analysis of X-ray calibration data

NASA Astrophysics Data System (ADS)

Vaishali, S.; Narendranath, S.; Sreekumar, P.

An IDL (interactive data language) based widget application developed for the calibration of C1XS (Narendranath et al., 2010) instrument on Chandrayaan-1 is modified to provide a generic package for the analysis of data from x-ray detectors. The package supports files in ascii as well as FITS format. Data can be fitted with a list of inbuilt functions to derive the spectral redistribution function (SRF). We have incorporated functions such as `HYPERMET' (Philips & Marlow 1976) including non Gaussian components in the SRF such as low energy tail, low energy shelf and escape peak. In addition users can incorporate additional models which may be required to model detector specific features. Spectral fits use a routine `mpfit' which uses Leven-Marquardt least squares fitting method. The SRF derived from this tool can be fed into an accompanying program to generate a redistribution matrix file (RMF) compatible with the X-ray spectral analysis package XSPEC. The tool provides a user friendly interface of help to beginners and also provides transparency and advanced features for experts.

RAPIDR: an analysis package for non-invasive prenatal testing of aneuploidy

PubMed Central

Lo, Kitty K.; Boustred, Christopher; Chitty, Lyn S.; Plagnol, Vincent

2014-01-01

Non-invasive prenatal testing (NIPT) of fetal aneuploidy using cell-free fetal DNA is becoming part of routine clinical practice. RAPIDR (Reliable Accurate Prenatal non-Invasive Diagnosis R package) is an easy-to-use open-source R package that implements several published NIPT analysis methods. The input to RAPIDR is a set of sequence alignment files in the BAM format, and the outputs are calls for aneuploidy, including trisomies 13, 18, 21 and monosomy X as well as fetal sex. RAPIDR has been extensively tested with a large sample set as part of the RAPID project in the UK. The package contains quality control steps to make it robust for use in the clinical setting. Availability and implementation: RAPIDR is implemented in R and can be freely downloaded via CRAN from here: http://cran.r-project.org/web/packages/RAPIDR/index.html. Contact: kitty.lo@ucl.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24990604

PAT-1 safety analysis report addendum.

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

Weiner, Ruth F.; Schmale, David T.; Kalan, Robert J.

2010-09-01

The Plutonium Air Transportable Package, Model PAT-1, is certified under Title 10, Code of Federal Regulations Part 71 by the U.S. Nuclear Regulatory Commission (NRC) per Certificate of Compliance (CoC) USA/0361B(U)F-96 (currently Revision 9). The purpose of this SAR Addendum is to incorporate plutonium (Pu) metal as a new payload for the PAT-1 package. The Pu metal is packed in an inner container (designated the T-Ampoule) that replaces the PC-1 inner container. The documentation and results from analysis contained in this addendum demonstrate that the replacement of the PC-1 and associated packaging material with the T-Ampoule and associated packaging withmore » the addition of the plutonium metal content are not significant with respect to the design, operating characteristics, or safe performance of the containment system and prevention of criticality when the package is subjected to the tests specified in 10 CFR 71.71, 71.73 and 71.74.« less

Appearance Matters: Neural Correlates of Food Choice and Packaging Aesthetics

PubMed Central

Van der Laan, Laura N.; De Ridder, Denise T. D.; Viergever, Max A.; Smeets, Paul A. M.

2012-01-01

Neuro-imaging holds great potential for predicting choice behavior from brain responses. In this study we used both traditional mass-univariate and state-of-the-art multivariate pattern analysis to establish which brain regions respond to preferred packages and to what extent neural activation patterns can predict realistic low-involvement consumer choices. More specifically, this was assessed in the context of package-induced binary food choices. Mass-univariate analyses showed that several regions, among which the bilateral striatum, were more strongly activated in response to preferred food packages. Food choices could be predicted with an accuracy of up to 61.2% by activation patterns in brain regions previously found to be involved in healthy food choices (superior frontal gyrus) and visual processing (middle occipital gyrus). In conclusion, this study shows that mass-univariate analysis can detect small package-induced differences in product preference and that MVPA can successfully predict realistic low-involvement consumer choices from functional MRI data. PMID:22848586

Generic Degraded Congiguration Probability Analysis for DOE Codisposal Waste Package

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

S.F.A. Deng; M. Saglam; L.J. Gratton

2001-05-23

In accordance with the technical work plan, ''Technical Work Plan For: Department of Energy Spent Nuclear Fuel Work Packages'' (CRWMS M&O 2000c), this Analysis/Model Report (AMR) is developed for the purpose of screening out degraded configurations for U.S. Department of Energy (DOE) spent nuclear fuel (SNF) types. It performs the degraded configuration parameter and probability evaluations of the overall methodology specified in the ''Disposal Criticality Analysis Methodology Topical Report'' (YMP 2000, Section 3) to qualifying configurations. Degradation analyses are performed to assess realizable parameter ranges and physical regimes for configurations. Probability calculations are then performed for configurations characterized by k{submore » eff} in excess of the Critical Limit (CL). The scope of this document is to develop a generic set of screening criteria or models to screen out degraded configurations having potential for exceeding a criticality limit. The developed screening criteria include arguments based on physical/chemical processes and probability calculations and apply to DOE SNF types when codisposed with the high-level waste (HLW) glass inside a waste package. The degradation takes place inside the waste package and is long after repository licensing has expired. The emphasis of this AMR is on degraded configuration screening and the probability analysis is one of the approaches used for screening. The intended use of the model is to apply the developed screening criteria to each DOE SNF type following the completion of the degraded mode criticality analysis internal to the waste package.« less

An R package for the integrated analysis of metabolomics and spectral data.

PubMed

Costa, Christopher; Maraschin, Marcelo; Rocha, Miguel

2016-06-01

Recently, there has been a growing interest in the field of metabolomics, materialized by a remarkable growth in experimental techniques, available data and related biological applications. Indeed, techniques as nuclear magnetic resonance, gas or liquid chromatography, mass spectrometry, infrared and UV-visible spectroscopies have provided extensive datasets that can help in tasks as biological and biomedical discovery, biotechnology and drug development. However, as it happens with other omics data, the analysis of metabolomics datasets provides multiple challenges, both in terms of methodologies and in the development of appropriate computational tools. Indeed, from the available software tools, none addresses the multiplicity of existing techniques and data analysis tasks. In this work, we make available a novel R package, named specmine, which provides a set of methods for metabolomics data analysis, including data loading in different formats, pre-processing, metabolite identification, univariate and multivariate data analysis, machine learning, and feature selection. Importantly, the implemented methods provide adequate support for the analysis of data from diverse experimental techniques, integrating a large set of functions from several R packages in a powerful, yet simple to use environment. The package, already available in CRAN, is accompanied by a web site where users can deposit datasets, scripts and analysis reports to be shared with the community, promoting the efficient sharing of metabolomics data analysis pipelines. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

AMModels: An R package for storing models, data, and metadata to facilitate adaptive management

USGS Publications Warehouse

Donovan, Therese M.; Katz, Jonathan

2018-01-01

Agencies are increasingly called upon to implement their natural resource management programs within an adaptive management (AM) framework. This article provides the background and motivation for the R package, AMModels. AMModels was developed under R version 3.2.2. The overall goal of AMModels is simple: To codify knowledge in the form of models and to store it, along with models generated from numerous analyses and datasets that may come our way, so that it can be used or recalled in the future. AMModels facilitates this process by storing all models and datasets in a single object that can be saved to an .RData file and routinely augmented to track changes in knowledge through time. Through this process, AMModels allows the capture, development, sharing, and use of knowledge that may help organizations achieve their mission. While AMModels was designed to facilitate adaptive management, its utility is far more general. Many R packages exist for creating and summarizing models, but to our knowledge, AMModels is the only package dedicated not to the mechanics of analysis but to organizing analysis inputs, analysis outputs, and preserving descriptive metadata. We anticipate that this package will assist users hoping to preserve the key elements of an analysis so they may be more confidently revisited at a later date.

An initial investigation into methods of computing transonic aerodynamic sensitivity coefficients

NASA Technical Reports Server (NTRS)

Carlson, Leland A.

1991-01-01

The three dimensional quasi-analytical sensitivity analysis and the ancillary driver programs are developed needed to carry out the studies and perform comparisons. The code is essentially contained in one unified package which includes the following: (1) a three dimensional transonic wing analysis program (ZEBRA); (2) a quasi-analytical portion which determines the matrix elements in the quasi-analytical equations; (3) a method for computing the sensitivity coefficients from the resulting quasi-analytical equations; (4) a package to determine for comparison purposes sensitivity coefficients via the finite difference approach; and (5) a graphics package.

Analysis pipelines and packages for Infinium HumanMethylation450 BeadChip (450k) data

PubMed Central

Morris, Tiffany J.; Beck, Stephan

2015-01-01

The Illumina HumanMethylation450 BeadChip has become a popular platform for interrogating DNA methylation in epigenome-wide association studies (EWAS) and related projects as well as resource efforts such as the International Cancer Genome Consortium (ICGC) and the International Human Epigenome Consortium (IHEC). This has resulted in an exponential increase of 450k data in recent years and triggered the development of numerous integrated analysis pipelines and stand-alone packages. This review will introduce and discuss the currently most popular pipelines and packages and is particularly aimed at new 450k users. PMID:25233806

The CASA Software Package

NASA Astrophysics Data System (ADS)

Petry, Dirk

2018-03-01

CASA is the standard science data analysis package for ALMA and VLA but it can also be used for the analysis of data from other observatories. In this talk, I will give an overview of the structure and features of CASA, who develops it, and the present status and plans, and then show typical analysis workflows for ALMA data with special emphasis on the handling of single dish data and its combination with interferometric data.

Reviews.

ERIC Educational Resources Information Center

Science Teacher, 1988

1988-01-01

Reviews four software packages available for IBM PC or Apple II. Includes "Graphical Analysis III"; "Space Max: Space Station Construction Simulation"; "Guesstimation"; and "Genetic Engineering Toolbox." Focuses on each packages' strengths in a high school context. (CW)

Assessing direct analysis in real-time-mass spectrometry (DART-MS) for the rapid identification of additives in food packaging.

PubMed

Ackerman, L K; Noonan, G O; Begley, T H

2009-12-01

The ambient ionization technique direct analysis in real time (DART) was characterized and evaluated for the screening of food packaging for the presence of packaging additives using a benchtop mass spectrometer (MS). Approximate optimum conditions were determined for 13 common food-packaging additives, including plasticizers, anti-oxidants, colorants, grease-proofers, and ultraviolet light stabilizers. Method sensitivity and linearity were evaluated using solutions and characterized polymer samples. Additionally, the response of a model additive (di-ethyl-hexyl-phthalate) was examined across a range of sample positions, DART, and MS conditions (temperature, voltage and helium flow). Under optimal conditions, molecular ion (M+H+) was the major ion for most additives. Additive responses were highly sensitive to sample and DART source orientation, as well as to DART flow rates, temperatures, and MS inlet voltages, respectively. DART-MS response was neither consistently linear nor quantitative in this setting, and sensitivity varied by additive. All additives studied were rapidly identified in multiple food-packaging materials by DART-MS/MS, suggesting this technique can be used to screen food packaging rapidly. However, method sensitivity and quantitation requires further study and improvement.

An open-source software package for multivariate modeling and clustering: applications to air quality management.

PubMed

Wang, Xiuquan; Huang, Guohe; Zhao, Shan; Guo, Junhong

2015-09-01

This paper presents an open-source software package, rSCA, which is developed based upon a stepwise cluster analysis method and serves as a statistical tool for modeling the relationships between multiple dependent and independent variables. The rSCA package is efficient in dealing with both continuous and discrete variables, as well as nonlinear relationships between the variables. It divides the sample sets of dependent variables into different subsets (or subclusters) through a series of cutting and merging operations based upon the theory of multivariate analysis of variance (MANOVA). The modeling results are given by a cluster tree, which includes both intermediate and leaf subclusters as well as the flow paths from the root of the tree to each leaf subcluster specified by a series of cutting and merging actions. The rSCA package is a handy and easy-to-use tool and is freely available at http://cran.r-project.org/package=rSCA . By applying the developed package to air quality management in an urban environment, we demonstrate its effectiveness in dealing with the complicated relationships among multiple variables in real-world problems.

MNE software for processing MEG and EEG data

PubMed Central

Gramfort, A.; Luessi, M.; Larson, E.; Engemann, D.; Strohmeier, D.; Brodbeck, C.; Parkkonen, L.; Hämäläinen, M.

2013-01-01

Magnetoencephalography and electroencephalography (M/EEG) measure the weak electromagnetic signals originating from neural currents in the brain. Using these signals to characterize and locate brain activity is a challenging task, as evidenced by several decades of methodological contributions. MNE, whose name stems from its capability to compute cortically-constrained minimum-norm current estimates from M/EEG data, is a software package that provides comprehensive analysis tools and workflows including preprocessing, source estimation, time–frequency analysis, statistical analysis, and several methods to estimate functional connectivity between distributed brain regions. The present paper gives detailed information about the MNE package and describes typical use cases while also warning about potential caveats in analysis. The MNE package is a collaborative effort of multiple institutes striving to implement and share best methods and to facilitate distribution of analysis pipelines to advance reproducibility of research. Full documentation is available at http://martinos.org/mne. PMID:24161808

European consumer response to packaging technologies for improved beef safety.

PubMed

Van Wezemael, Lynn; Ueland, Øydis; Verbeke, Wim

2011-09-01

Beef packaging can influence consumer perceptions of beef. Although consumer perceptions and acceptance are considered to be among the most limiting factors in the application of new technologies, there is a lack of knowledge about the acceptability to consumers of beef packaging systems aimed at improved safety. This paper explores European consumers' acceptance levels of different beef packaging technologies. An online consumer survey was conducted in five European countries (n=2520). Acceptance levels among the sample ranged between 23% for packaging releasing preservative additives up to 73% for vacuum packaging. Factor analysis revealed that familiar packaging technologies were clearly preferred over non-familiar technologies. Four consumer segments were identified: the negative (31% of the sample), cautious (30%), conservative (17%) and enthusiast (22%) consumers, which were profiled based on their attitudes and beef consumption behaviour. Differences between consumer acceptance levels should be taken into account while optimising beef packaging and communicating its benefits. Copyright © 2011 Elsevier Ltd. All rights reserved.

An R package for analyzing and modeling ranking data

PubMed Central

2013-01-01

Background In medical informatics, psychology, market research and many other fields, researchers often need to analyze and model ranking data. However, there is no statistical software that provides tools for the comprehensive analysis of ranking data. Here, we present pmr, an R package for analyzing and modeling ranking data with a bundle of tools. The pmr package enables descriptive statistics (mean rank, pairwise frequencies, and marginal matrix), Analytic Hierarchy Process models (with Saaty’s and Koczkodaj’s inconsistencies), probability models (Luce model, distance-based model, and rank-ordered logit model), and the visualization of ranking data with multidimensional preference analysis. Results Examples of the use of package pmr are given using a real ranking dataset from medical informatics, in which 566 Hong Kong physicians ranked the top five incentives (1: competitive pressures; 2: increased savings; 3: government regulation; 4: improved efficiency; 5: improved quality care; 6: patient demand; 7: financial incentives) to the computerization of clinical practice. The mean rank showed that item 4 is the most preferred item and item 3 is the least preferred item, and significance difference was found between physicians’ preferences with respect to their monthly income. A multidimensional preference analysis identified two dimensions that explain 42% of the total variance. The first can be interpreted as the overall preference of the seven items (labeled as “internal/external”), and the second dimension can be interpreted as their overall variance of (labeled as “push/pull factors”). Various statistical models were fitted, and the best were found to be weighted distance-based models with Spearman’s footrule distance. Conclusions In this paper, we presented the R package pmr, the first package for analyzing and modeling ranking data. The package provides insight to users through descriptive statistics of ranking data. Users can also visualize ranking data by applying a thought multidimensional preference analysis. Various probability models for ranking data are also included, allowing users to choose that which is most suitable to their specific situations. PMID:23672645

An R package for analyzing and modeling ranking data.

PubMed

Lee, Paul H; Yu, Philip L H

2013-05-14

In medical informatics, psychology, market research and many other fields, researchers often need to analyze and model ranking data. However, there is no statistical software that provides tools for the comprehensive analysis of ranking data. Here, we present pmr, an R package for analyzing and modeling ranking data with a bundle of tools. The pmr package enables descriptive statistics (mean rank, pairwise frequencies, and marginal matrix), Analytic Hierarchy Process models (with Saaty's and Koczkodaj's inconsistencies), probability models (Luce model, distance-based model, and rank-ordered logit model), and the visualization of ranking data with multidimensional preference analysis. Examples of the use of package pmr are given using a real ranking dataset from medical informatics, in which 566 Hong Kong physicians ranked the top five incentives (1: competitive pressures; 2: increased savings; 3: government regulation; 4: improved efficiency; 5: improved quality care; 6: patient demand; 7: financial incentives) to the computerization of clinical practice. The mean rank showed that item 4 is the most preferred item and item 3 is the least preferred item, and significance difference was found between physicians' preferences with respect to their monthly income. A multidimensional preference analysis identified two dimensions that explain 42% of the total variance. The first can be interpreted as the overall preference of the seven items (labeled as "internal/external"), and the second dimension can be interpreted as their overall variance of (labeled as "push/pull factors"). Various statistical models were fitted, and the best were found to be weighted distance-based models with Spearman's footrule distance. In this paper, we presented the R package pmr, the first package for analyzing and modeling ranking data. The package provides insight to users through descriptive statistics of ranking data. Users can also visualize ranking data by applying a thought multidimensional preference analysis. Various probability models for ranking data are also included, allowing users to choose that which is most suitable to their specific situations.

Radio Astronomy Tools in Python: Spectral-cube, pvextractor, and more

NASA Astrophysics Data System (ADS)

Ginsburg, A.; Robitaille, T.; Beaumont, C.; Rosolowsky, E.; Leroy, A.; Brogan, C.; Hunter, T.; Teuben, P.; Brisbin, D.

2015-12-01

The radio-astro-tools organization has been established to facilitate development of radio and millimeter analysis tools by the scientific community. The first packages developed under its umbrella are: • The spectral-cube package, for reading, writing, and analyzing spectral data cubes • The pvextractor package for extracting position-velocity slices from position-position-velocity cubes along aribitrary paths • The radio-beam package to handle gaussian beams in the context of the astropy quantity and unit framework • casa-python to enable installation of these packages - and any other - into users' CASA environments without conflicting with the underlying CASA package. Community input in the form of code contributions, suggestions, questions and commments is welcome on all of these tools. They can all be found at http://radio-astro-tools.github.io.

Introduction to Political Risk Analysis. Learning Packages in the Policy Sciences, PS-24.

ERIC Educational Resources Information Center

Coplin, William D.; O'Leary, Michael K.

This package introduces college students to the kind of analysis that multinational corporations undertake to assess risks to their business operations due to political and economic conditions. Designed to be completed in 3 weeks, the four exercises enable students to (1) identify the major sources of political risk; (2) determine what social,…

Development of program package for investigation and modeling of carbon nanostructures in diamond like carbon films with the help of Raman scattering and infrared absorption spectra line resolving

NASA Astrophysics Data System (ADS)

Hayrapetyan, David B.; Hovhannisyan, Levon; Mantashyan, Paytsar A.

2013-04-01

The analysis of complex spectra is an actual problem for modern science. The work is devoted to the creation of a software package, which analyzes spectrum in the different formats, possesses by dynamic knowledge database and self-study mechanism, performs automated analysis of the spectra compound based on knowledge database by application of certain algorithms. In the software package as searching systems, hyper-spherical random search algorithms, gradient algorithms and genetic searching algorithms were used. The analysis of Raman and IR spectrum of diamond-like carbon (DLC) samples were performed by elaborated program. After processing the data, the program immediately displays all the calculated parameters of DLC.

GUIDEseq: a bioconductor package to analyze GUIDE-Seq datasets for CRISPR-Cas nucleases.

PubMed

Zhu, Lihua Julie; Lawrence, Michael; Gupta, Ankit; Pagès, Hervé; Kucukural, Alper; Garber, Manuel; Wolfe, Scot A

2017-05-15

Genome editing technologies developed around the CRISPR-Cas9 nuclease system have facilitated the investigation of a broad range of biological questions. These nucleases also hold tremendous promise for treating a variety of genetic disorders. In the context of their therapeutic application, it is important to identify the spectrum of genomic sequences that are cleaved by a candidate nuclease when programmed with a particular guide RNA, as well as the cleavage efficiency of these sites. Powerful new experimental approaches, such as GUIDE-seq, facilitate the sensitive, unbiased genome-wide detection of nuclease cleavage sites within the genome. Flexible bioinformatics analysis tools for processing GUIDE-seq data are needed. Here, we describe an open source, open development software suite, GUIDEseq, for GUIDE-seq data analysis and annotation as a Bioconductor package in R. The GUIDEseq package provides a flexible platform with more than 60 adjustable parameters for the analysis of datasets associated with custom nuclease applications. These parameters allow data analysis to be tailored to different nuclease platforms with different length and complexity in their guide and PAM recognition sequences or their DNA cleavage position. They also enable users to customize sequence aggregation criteria, and vary peak calling thresholds that can influence the number of potential off-target sites recovered. GUIDEseq also annotates potential off-target sites that overlap with genes based on genome annotation information, as these may be the most important off-target sites for further characterization. In addition, GUIDEseq enables the comparison and visualization of off-target site overlap between different datasets for a rapid comparison of different nuclease configurations or experimental conditions. For each identified off-target, the GUIDEseq package outputs mapped GUIDE-Seq read count as well as cleavage score from a user specified off-target cleavage score prediction algorithm permitting the identification of genomic sequences with unexpected cleavage activity. The GUIDEseq package enables analysis of GUIDE-data from various nuclease platforms for any species with a defined genomic sequence. This software package has been used successfully to analyze several GUIDE-seq datasets. The software, source code and documentation are freely available at http://www.bioconductor.org/packages/release/bioc/html/GUIDEseq.html .

MetaboAnalystR: an R package for flexible and reproducible analysis of metabolomics data.

PubMed

Chong, Jasmine; Xia, Jianguo

2018-06-28

The MetaboAnalyst web application has been widely used for metabolomics data analysis and interpretation. Despite its user-friendliness, the web interface has presented its inherent limitations (especially for advanced users) with regard to flexibility in creating customized workflow, support for reproducible analysis, and capacity in dealing with large data. To address these limitations, we have developed a companion R package (MetaboAnalystR) based on the R code base of the web server. The package has been thoroughly tested to ensure that the same R commands will produce identical results from both interfaces. MetaboAnalystR complements the MetaboAnalyst web server to facilitate transparent, flexible and reproducible analysis of metabolomics data. MetaboAnalystR is freely available from https://github.com/xia-lab/MetaboAnalystR. Supplementary data are available at Bioinformatics online.

Mesoscale and severe storms (Mass) data management and analysis system

NASA Technical Reports Server (NTRS)

Hickey, J. S.; Karitani, S.; Dickerson, M.

1984-01-01

Progress on the Mesoscale and Severe Storms (MASS) data management and analysis system is described. An interactive atmospheric data base management software package to convert four types of data (Sounding, Single Level, Grid, Image) into standard random access formats is implemented and integrated with the MASS AVE80 Series general purpose plotting and graphics display data analysis software package. An interactive analysis and display graphics software package (AVE80) to analyze large volumes of conventional and satellite derived meteorological data is enhanced to provide imaging/color graphics display utilizing color video hardware integrated into the MASS computer system. Local and remote smart-terminal capability is provided by installing APPLE III computer systems within individual scientist offices and integrated with the MASS system, thus providing color video display, graphics, and characters display of the four data types.

78 FR 26090 - Content Specifications and Shielding Evaluations for Type B Transportation Packages

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-03

...The U.S. Nuclear Regulatory Commission (NRC) is issuing Regulatory Issue Summary (RIS) 2013-04, ``Content Specifications and Shielding Evaluations for Type B Transportation Packages.'' This RIS clarifies the NRC's use of staff guidance in NUREG-1609, ``Standard Review Plan for Transport Packages for Radioactive Material,'' for the review of content specifications and shielding evaluations included in the Certificates of Compliance (CoC) and safety analysis reports (SARs) for Type B transportation packages. The RIS does not impose any additional regulatory requirements on NRC licensees.

A convenient and adaptable package of DNA sequence analysis programs for microcomputers.

PubMed Central

Pustell, J; Kafatos, F C

1982-01-01

We describe a package of DNA data handling and analysis programs designed for microcomputers. The package is convenient for immediate use by persons with little or no computer experience, and has been optimized by trial in our group for a year. By typing a single command, the user enters a system which asks questions or gives instructions in English. The system will enter, alter, and manage sequence files or a restriction enzyme library. It generates the reverse complement, translates, calculates codon usage, finds restriction sites, finds homologies with various degrees of mismatch, and graphs amino acid composition or base frequencies. A number of options for data handling and printing can be used to produce figures for publication. The package will be available in ANSI Standard FORTRAN for use with virtually any FORTRAN compiler. PMID:6278412

QFASAR: Quantitative fatty acid signature analysis with R

USGS Publications Warehouse

Bromaghin, Jeffrey F.

2017-01-01

Knowledge of predator diets provides essential insights into their ecology, yet diet estimation is challenging and remains an active area of research.Quantitative fatty acid signature analysis (QFASA) is a popular method of estimating diet composition that continues to be investigated and extended. However, software to implement QFASA has only recently become publicly available.I summarize a new R package, qfasar, for diet estimation using QFASA methods. The package also provides functionality to evaluate and potentially improve the performance of a library of prey signature data, compute goodness-of-fit diagnostics, and support simulation-based research. Several procedures in the package have not previously been published.qfasar makes traditional and recently published QFASA diet estimation methods accessible to ecologists for the first time. Use of the package is illustrated with signature data from Chukchi Sea polar bears and potential prey species.

Distributed analysis at LHCb

NASA Astrophysics Data System (ADS)

Williams, Mike; Egede, Ulrik; Paterson, Stuart; LHCb Collaboration

2011-12-01

The distributed analysis experience to date at LHCb has been positive: job success rates are high and wait times for high-priority jobs are low. LHCb users access the grid using the GANGA job-management package, while the LHCb virtual organization manages its resources using the DIRAC package. This clear division of labor has benefitted LHCb and its users greatly; it is a major reason why distributed analysis at LHCb has been so successful. The newly formed LHCb distributed analysis support team has also proved to be a success.

Some current research in rotating-disc systems.

PubMed

Owen, J M; Wilson, M

2001-05-01

Rotating-disc systems are used to model the flow and heat transfer that occurs inside the cooling-air systems of gas-turbine engines. In this paper, recent computational and experimental research in three systems is discussed: rotor-stator systems, rotating cavities with superposed flow and buoyancy-induced flow in a rotating cavity. Discussion of the first two systems concentrates respectively on pre-swirl systems and rotating cavities with a peripheral inflow and outflow of cooling air. Buoyancy-induced flow in a rotating cavity is one of the most difficult problems facing computationalists and experimentalists, and there are similarities between the circulation in the Earth's atmosphere and the flow inside gas-turbine rotors. For this case, results are presented for heat transfer in sealed annuli and in rotating cavities with an axial throughflow of cooling air.

Rio Grande valley Colorado new Mexico and Texas

USGS Publications Warehouse

Ellis, Sherman R.; Levings, Gary W.; Carter, Lisa F.; Richey, Steven F.; Radell, Mary Jo

1993-01-01

Two structural settings are found in the study unit: alluvial basins and bedrock basins. The alluvial basins can have through-flowing surface water or be closed basins. The discussion of streamflow and water quality for the surface-water system is based on four river reaches for the 750 miles of the main stem. the quality of the ground water is affected by both natural process and human activities and by nonpoint and point sources. Nonpoint sources for surface water include agriculture, hydromodification, and mining operations; point sources are mainly discharge from wastewater treatment plants. Nonpoint sources for ground water include agriculture and septic tanks and cesspools; point sources include leaking underground storage tanks, unlined or manure-lined holding ponds used for disposal of dairy wastes, landfills, and mining operations.

Influence of packaging information on consumer liking of chocolate milk.

PubMed

Kim, M K; Lopetcharat, K; Drake, M A

2013-08-01

Chocolate milk varies widely in flavor, color, and viscosity, and liking is influenced by these properties. Additionally, package labels (declared fat content) and brand are some of the extrinsic factors that may influence consumer perception. The objective of this study was to evaluate the effects of packaging labels and brand name on consumer liking and purchase intent of chocolate milk. A consumer acceptance test, conjoint analysis survey, and Kano analysis were conducted. One hundred eight consumers evaluated 7 chocolate milks with and without brand or package information in a 2-d crossover design. A conjoint analysis survey and Kano analysis were conducted after the consumer acceptance test. Results were evaluated by 2-way ANOVA and multivariate analyses. Declared fat content and brand influenced overall liking and purchase intent for chocolate milks to differing degrees. A subsequent conjoint analysis (n=250) revealed that fat content was a driver of choice for purchasing chocolate milk followed by sugar content and brand. Brand name was less important for purchase intent of chocolate milk than fat or sugar content. Among fat content of chocolate milk, 2 and 1% fat level were most appealing to consumers, and reduced sugar and regular sugar were equally important for purchase intent. Kano analysis confirmed that fat content (whole milk, 1, or 2% fat chocolate milk) was an attractive attribute for consumer satisfaction, more so than brand. Organic labeling did not affect the purchase decision of chocolate milk; however, Kano results revealed that having an organic label on a package positively influenced consumer satisfaction. Findings from this study can help chocolate milk producers as well as food marketers better target their product labels with attributes that drive consumer choice of chocolate milk. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Oufti: An integrated software package for high-accuracy, high-throughput quantitative microscopy analysis

PubMed Central

Paintdakhi, Ahmad; Parry, Bradley; Campos, Manuel; Irnov, Irnov; Elf, Johan; Surovtsev, Ivan; Jacobs-Wagner, Christine

2016-01-01

Summary With the realization that bacteria display phenotypic variability among cells and exhibit complex subcellular organization critical for cellular function and behavior, microscopy has re-emerged as a primary tool in bacterial research during the last decade. However, the bottleneck in today’s single-cell studies is quantitative image analysis of cells and fluorescent signals. Here, we address current limitations through the development of Oufti, a stand-alone, open-source software package for automated measurements of microbial cells and fluorescence signals from microscopy images. Oufti provides computational solutions for tracking touching cells in confluent samples, handles various cell morphologies, offers algorithms for quantitative analysis of both diffraction and non-diffraction-limited fluorescence signals, and is scalable for high-throughput analysis of massive datasets, all with subpixel precision. All functionalities are integrated in a single package. The graphical user interface, which includes interactive modules for segmentation, image analysis, and post-processing analysis, makes the software broadly accessible to users irrespective of their computational skills. PMID:26538279

From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline.

PubMed

Chen, Yunshun; Lun, Aaron T L; Smyth, Gordon K

2016-01-01

In recent years, RNA sequencing (RNA-seq) has become a very widely used technology for profiling gene expression. One of the most common aims of RNA-seq profiling is to identify genes or molecular pathways that are differentially expressed (DE) between two or more biological conditions. This article demonstrates a computational workflow for the detection of DE genes and pathways from RNA-seq data by providing a complete analysis of an RNA-seq experiment profiling epithelial cell subsets in the mouse mammary gland. The workflow uses R software packages from the open-source Bioconductor project and covers all steps of the analysis pipeline, including alignment of read sequences, data exploration, differential expression analysis, visualization and pathway analysis. Read alignment and count quantification is conducted using the Rsubread package and the statistical analyses are performed using the edgeR package. The differential expression analysis uses the quasi-likelihood functionality of edgeR.

Definition of Small Gram Quantity Contents for Type B Radioactive Material Transportation Packages: Activity-Based Content Limitations

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

Sitaraman, S; Kim, S; Biswas, D

2010-10-27

Since the 1960's, the Department of Transportation Specification (DOT Spec) 6M packages have been used extensively for transportation of Type B quantities of radioactive materials between Department of Energy (DOE) facilities, laboratories, and productions sites. However, due to the advancement of packaging technology, the aging of the 6M packages, and variability in the quality of the packages, the DOT implemented a phased elimination of the 6M specification packages (and other DOT Spec packages) in favor of packages certified to meet federal performance requirements. DOT issued the final rule in the Federal Register on October 1, 2004 requiring that use ofmore » the DOT Specification 6M be discontinued as of October 1, 2008. A main driver for the change was the fact that the 6M specification packagings were not supported by a Safety Analysis Report for Packaging (SARP) that was compliant with Title 10 of the Code of Federal Regulations part 71 (10 CFR 71). Therefore, materials that would have historically been shipped in 6M packages are being identified as contents in Type B (and sometimes Type A fissile) package applications and addenda that are to be certified under the requirements of 10 CFR 71. The requirements in 10 CFR 71 include that the Safety Analysis Report for Packaging (SARP) must identify the maximum radioactivity of radioactive constituents and maximum quantities of fissile constituents (10 CFR 71.33(b)(1) and 10 CFR 71.33(b)(2)), and that the application (i.e., SARP submittal or SARP addendum) demonstrates that the external dose rate (due to the maximum radioactivity of radioactive constituents and maximum quantities of fissile constituents) on the surface of the packaging (i.e., package and contents) not exceed 200 mrem/hr (10 CFR 71.35(a), 10 CFR 71.47(a)). It has been proposed that a 'Small Gram Quantity' of radioactive material be defined, such that, when loaded in a transportation package, the dose rates at external points of an unshielded packaging not exceed the regulatory limits prescribed by 10 CFR 71 for non-exclusive shipments. The mass of each radioisotope presented in this paper is limited by the radiation dose rate on the external surface of the package, which per the regulatory limit should not exceed 200 mrem/hr. The results presented are a compendium of allowable masses of a variety of different isotopes (with varying impurity levels of beryllium in some of the actinide isotopes) that, when loaded in an unshielded packaging, do not result in an external dose rate on the surface of the package that exceeds 190 mrem/hr (190 mrem/hr was chosen to provide 5% conservatism relative to the regulatory limit). These mass limits define the term 'Small Gram Quantity' (SGQ) contents in the context of radioactive material transportation packages. The term SGQ is isotope-specific and pertains to contents in radioactive material transportation packages that do not require shielding and still satisfy the external dose rate requirements. Since these calculated mass limits are for contents without shielding, they are conservative for packaging materials that provide some limited shielding or if the contents are placed into a shielded package. The isotopes presented in this paper were chosen as the isotopes that Department of Energy (DOE) sites most likely need to ship. Other more rarely shipped isotopes, along with industrial and medical isotopes, are planned to be included in subsequent extensions of this work.« less

Computer Lab Tools for Science: An Analysis of Commercially Available Science Interfacing Software for Microcomputers. A Quarterly Report.

ERIC Educational Resources Information Center

Weaver, Dave

Science interfacing packages (also known as microcomputer-based laboratories or probeware) generally consist of a set of programs on disks, a user's manual, and hardware which includes one or more sensory devices. Together with a microcomputer they combine to make a powerful data acquisition and analysis tool. Packages are available for accurately…

Designing a User-Friendly Microcomputer-Based Laboratory Package through the Factor Analysis of Teacher Evaluations

ERIC Educational Resources Information Center

Lavonen, Jari; Juuti, Kalle; Meisalo, Veijo

2003-01-01

In this study we analyse how the experiences of chemistry teachers on the use of a Microcomputer-Based Laboratory (MBL), gathered by a Likert-scale instrument, can be utilized to develop the new package "Empirica 2000." We used exploratory factor analysis to identify the essential features in a large set of questionnaire data to see how…

Space shuttle/food system study. Volume 2, Appendix F: Flight food and primary packaging

NASA Technical Reports Server (NTRS)

1974-01-01

The analysis and selection of food items and primary packaging, the development of menus, the nutritional analysis of diet, and the analyses of alternate food mixes and contingency foods is reported in terms of the overall food system design for space shuttle flight. Stowage weights and cubic volumes associated with each alternate mix were also evaluated.

Using FIESTA , an R-based tool for analysts, to look at temporal trends in forest estimates

Treesearch

Tracey S. Frescino; Paul L. Patterson; Elizabeth A. Freeman; Gretchen G. Moisen

2012-01-01

FIESTA (Forest Inventory Estimation for Analysis) is a user-friendly R package that supports the production of estimates for forest resources based on procedures from Bechtold and Patterson (2005). The package produces output consistent with current tools available for the Forest Inventory and Analysis National Program, such as FIDO (Forest Inventory Data Online) and...

Analysis of half diallel mating designs I: a practical analysis procedure for ANOVA approximation.

Treesearch

G.R. Johnson; J.N. King

1998-01-01

Procedures to analyze half-diallel mating designs using the SAS statistical package are presented. The procedure requires two runs of PROC and VARCOMP and results in estimates of additive and non-additive genetic variation. The procedures described can be modified to work on most statistical software packages which can compute variance component estimates. The...

The U. S. Department of Energy SARP review training program

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

Mauck, C.J.

1988-01-01

In support of its radioactive material packaging certification program, the U.S. Department of Energy (DOE) has established a special training workshop. The purpose of the two-week workshop is to develop skills in reviewing Safety Analysis Reports for Packagings (SARPs) and performing confirmatory analyses. The workshop, conducted by the Lawrence Livermore National Laboratory (LLNL) for DOE, is divided into two parts: methods of review and methods of analysis. The sessions covering methods of review are based on the DOE document, ''Packaging Review Guide for Reviewing Safety Analysis Reports for Packagings'' (PRG). The sessions cover relevant DOE Orders and all areas ofmore » review in the applicable Nuclear Regulatory Commission (NRC) Regulatory Guides. The technical areas addressed include structural and thermal behavior, materials, shielding, criticality, and containment. The course sessions on methods of analysis provide hands-on experience in the use of calculational methods and codes for reviewing SARPs. Analytical techniques and computer codes are discussed and sample problems are worked. Homework is assigned each night and over the included weekend; at the conclusion, a comprehensive take-home examination is given requiring six to ten hours to complete.« less

The `TTIME' Package: Performance Evaluation in a Cluster Computing Environment

NASA Astrophysics Data System (ADS)

Howe, Marico; Berleant, Daniel; Everett, Albert

2011-06-01

The objective of translating developmental event time across mammalian species is to gain an understanding of the timing of human developmental events based on known time of those events in animals. The potential benefits include improvements to diagnostic and intervention capabilities. The CRAN `ttime' package provides the functionality to infer unknown event timings and investigate phylogenetic proximity utilizing hierarchical clustering of both known and predicted event timings. The original generic mammalian model included nine eutherian mammals: Felis domestica (cat), Mustela putorius furo (ferret), Mesocricetus auratus (hamster), Macaca mulatta (monkey), Homo sapiens (humans), Mus musculus (mouse), Oryctolagus cuniculus (rabbit), Rattus norvegicus (rat), and Acomys cahirinus (spiny mouse). However, the data for this model is expected to grow as more data about developmental events is identified and incorporated into the analysis. Performance evaluation of the `ttime' package across a cluster computing environment versus a comparative analysis in a serial computing environment provides an important computational performance assessment. A theoretical analysis is the first stage of a process in which the second stage, if justified by the theoretical analysis, is to investigate an actual implementation of the `ttime' package in a cluster computing environment and to understand the parallelization process that underlies implementation.

SuperSegger: robust image segmentation, analysis and lineage tracking of bacterial cells.

PubMed

Stylianidou, Stella; Brennan, Connor; Nissen, Silas B; Kuwada, Nathan J; Wiggins, Paul A

2016-11-01

Many quantitative cell biology questions require fast yet reliable automated image segmentation to identify and link cells from frame-to-frame, and characterize the cell morphology and fluorescence. We present SuperSegger, an automated MATLAB-based image processing package well-suited to quantitative analysis of high-throughput live-cell fluorescence microscopy of bacterial cells. SuperSegger incorporates machine-learning algorithms to optimize cellular boundaries and automated error resolution to reliably link cells from frame-to-frame. Unlike existing packages, it can reliably segment microcolonies with many cells, facilitating the analysis of cell-cycle dynamics in bacteria as well as cell-contact mediated phenomena. This package has a range of built-in capabilities for characterizing bacterial cells, including the identification of cell division events, mother, daughter and neighbouring cells, and computing statistics on cellular fluorescence, the location and intensity of fluorescent foci. SuperSegger provides a variety of postprocessing data visualization tools for single cell and population level analysis, such as histograms, kymographs, frame mosaics, movies and consensus images. Finally, we demonstrate the power of the package by analyzing lag phase growth with single cell resolution. © 2016 John Wiley & Sons Ltd.

Poor-quality antimalarial drugs in southeast Asia and sub-Saharan Africa.

PubMed

Nayyar, Gaurvika M L; Breman, Joel G; Newton, Paul N; Herrington, James

2012-06-01

Poor-quality antimalarial drugs lead to drug resistance and inadequate treatment, which pose an urgent threat to vulnerable populations and jeopardise progress and investments in combating malaria. Emergence of artemisinin resistance or tolerance in Plasmodium falciparum on the Thailand-Cambodia border makes protection of the effectiveness of the drug supply imperative. We reviewed published and unpublished studies reporting chemical analyses and assessments of packaging of antimalarial drugs. Of 1437 samples of drugs in five classes from seven countries in southeast Asia, 497 (35%) failed chemical analysis, 423 (46%) of 919 failed packaging analysis, and 450 (36%) of 1260 were classified as falsified. In 21 surveys of drugs from six classes from 21 countries in sub-Saharan Africa, 796 (35%) of 2297 failed chemical analysis, 28 (36%) of 77 failed packaging analysis, and 79 (20%) of 389 were classified as falsified. Data were insufficient to identify the frequency of substandard (products resulting from poor manufacturing) antimalarial drugs, and packaging analysis data were scarce. Concurrent interventions and a multifaceted approach are needed to define and eliminate criminal production, distribution, and poor manufacturing of antimalarial drugs. Empowering of national medicine regulatory authorities to protect the global drug supply is more important than ever. Copyright © 2012 Elsevier Ltd. All rights reserved.

Powerlaw: a Python package for analysis of heavy-tailed distributions.

PubMed

Alstott, Jeff; Bullmore, Ed; Plenz, Dietmar

2014-01-01

Power laws are theoretically interesting probability distributions that are also frequently used to describe empirical data. In recent years, effective statistical methods for fitting power laws have been developed, but appropriate use of these techniques requires significant programming and statistical insight. In order to greatly decrease the barriers to using good statistical methods for fitting power law distributions, we developed the powerlaw Python package. This software package provides easy commands for basic fitting and statistical analysis of distributions. Notably, it also seeks to support a variety of user needs by being exhaustive in the options available to the user. The source code is publicly available and easily extensible.

ddpcr: an R package and web application for analysis of droplet digital PCR data.

PubMed

Attali, Dean; Bidshahri, Roza; Haynes, Charles; Bryan, Jennifer

2016-01-01

Droplet digital polymerase chain reaction (ddPCR) is a novel platform for exact quantification of DNA which holds great promise in clinical diagnostics. It is increasingly popular due to its digital nature, which provides more accurate quantification and higher sensitivity than traditional real-time PCR. However, clinical adoption has been slowed in part by the lack of software tools available for analyzing ddPCR data. Here, we present ddpcr - a new R package for ddPCR visualization and analysis. In addition, ddpcr includes a web application (powered by the Shiny R package) that allows users to analyze ddPCR data using an interactive graphical interface.

FTOOLS: A FITS Data Processing and Analysis Software Package

NASA Astrophysics Data System (ADS)

Blackburn, J. K.

FTOOLS, a highly modular collection of over 110 utilities for processing and analyzing data in the FITS (Flexible Image Transport System) format, has been developed in support of the HEASARC (High Energy Astrophysics Science Archive Research Center) at NASA's Goddard Space Flight Center. Each utility performs a single simple task such as presentation of file contents, extraction of specific rows or columns, appending or merging tables, binning values in a column or selecting subsets of rows based on a boolean expression. Individual utilities can easily be chained together in scripts to achieve more complex operations such as the generation and displaying of spectra or light curves. The collection of utilities provides both generic processing and analysis utilities and utilities specific to high energy astrophysics data sets used for the ASCA, ROSAT, GRO, and XTE missions. A core set of FTOOLS providing support for generic FITS data processing, FITS image analysis and timing analysis can easily be split out of the full software package for users not needing the high energy astrophysics mission utilities. The FTOOLS software package is designed to be both compatible with IRAF and completely stand alone in a UNIX or VMS environment. The user interface is controlled by standard IRAF parameter files. The package is self documenting through the IRAF help facility and a stand alone help task. Software is written in ANSI C and \\fortran to provide portability across most computer systems. The data format dependencies between hardware platforms are isolated through the FITSIO library package.

ChAMP: updated methylation analysis pipeline for Illumina BeadChips.

PubMed

Tian, Yuan; Morris, Tiffany J; Webster, Amy P; Yang, Zhen; Beck, Stephan; Feber, Andrew; Teschendorff, Andrew E

2017-12-15

The Illumina Infinium HumanMethylationEPIC BeadChip is the new platform for high-throughput DNA methylation analysis, effectively doubling the coverage compared to the older 450 K array. Here we present a significantly updated and improved version of the Bioconductor package ChAMP, which can be used to analyze EPIC and 450k data. Many enhanced functionalities have been added, including correction for cell-type heterogeneity, network analysis and a series of interactive graphical user interfaces. ChAMP is a BioC package available from https://bioconductor.org/packages/release/bioc/html/ChAMP.html. a.teschendorff@ucl.ac.uk or s.beck@ucl.ac.uk or a.feber@ucl.ac.uk. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

What's New in GSAS-II

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

Toby, Brian H.; Von Dreele, Robert B.

The General Structure and Analysis Software II (GSAS-II) package is an all-new crystallographic analysis package written to replace and extend the capabilities of the universal and widely used GSAS and EXPGUI packages. GSAS-II was described in a 2013 article, but considerable work has been completed since then. This paper describes the advances, which include: rigid body fitting and structure solution modules; improved treatment for parametric refinements and equation of state fitting; and small-angle scattering data reduction and analysis. GSAS-II offers versatile and extensible modules for import and export of data and results. Capabilities are provided for users to select anymore » version of the code. Code documentation has reached 150 pages and 17 web-tutorials are offered. © 2014 International Centre for Diffraction Data.« less

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

PubMed

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

2018-03-07

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

Packaging- and transportation-related occurrence reports : FY 1994 annual report

DOT National Transportation Integrated Search

1995-03-01

The Oak Ridge National Laboratory, through its support to the Department of Energys Office of Facility Safety Analysis, EH-32, retrieves reports and information pertaining to transportation and : packaging occurrences from the centralized Occurrence ...

On the release of cppxfel for processing X-ray free-electron laser images.

PubMed

Ginn, Helen Mary; Evans, Gwyndaf; Sauter, Nicholas K; Stuart, David Ian

2016-06-01

As serial femtosecond crystallography expands towards a variety of delivery methods, including chip-based methods, and smaller collected data sets, the requirement to optimize the data analysis to produce maximum structure quality is becoming increasingly pressing. Here cppxfel , a software package primarily written in C++, which showcases several data analysis techniques, is released. This software package presently indexes images using DIALS (diffraction integration for advanced light sources) and performs an initial orientation matrix refinement, followed by post-refinement of individual images against a reference data set. Cppxfel is released with the hope that the unique and useful elements of this package can be repurposed for existing software packages. However, as released, it produces high-quality crystal structures and is therefore likely to be also useful to experienced users of X-ray free-electron laser (XFEL) software who wish to maximize the information extracted from a limited number of XFEL images.

Design and analysis study of a spacecraft optical transceiver package

NASA Technical Reports Server (NTRS)

Lambert, S. G.

1985-01-01

A detailed system level design of an Optical Transceiver Package (OPTRANSPAC) for a deep space vehicle whose mission is outer planet exploration is developed. In addition to the terminal design, this study provides estimates of the dynamic environments to be encountered by the transceiver throughout its mission life. Optical communication link analysis, optical thin lens design, electronic functional design and mechanical layout and packaging are employed in the terminal design. Results of the study describe an Optical Transceiver Package capable of communicating to an Earth Orbiting Relay Station at a distance of 10 Astronomical Units (AU) and data rates up to 100 KBPS. The transceiver is also capable of receiving 1 KBPS of command data from the Earth Relay. The physical dimensions of the terminal are contained within a 3.5' x 1.5' x 2.0' envelope and the transceiver weight and power are estimated at 52.2 Kg (115 pounds) and 57 watts, respectively.

On the release of cppxfel for processing X-ray free-electron laser images

DOE PAGES

Ginn, Helen Mary; Evans, Gwyndaf; Sauter, Nicholas K.; ...

2016-05-11

As serial femtosecond crystallography expands towards a variety of delivery methods, including chip-based methods, and smaller collected data sets, the requirement to optimize the data analysis to produce maximum structure quality is becoming increasingly pressing. Herecppxfel, a software package primarily written in C++, which showcases several data analysis techniques, is released. This software package presently indexes images using DIALS (diffraction integration for advanced light sources) and performs an initial orientation matrix refinement, followed by post-refinement of individual images against a reference data set.Cppxfelis released with the hope that the unique and useful elements of this package can be repurposed formore » existing software packages. However, as released, it produces high-quality crystal structures and is therefore likely to be also useful to experienced users of X-ray free-electron laser (XFEL) software who wish to maximize the information extracted from a limited number of XFEL images.« less

NORTICA—a new code for cyclotron analysis

NASA Astrophysics Data System (ADS)

Gorelov, D.; Johnson, D.; Marti, F.

2001-12-01

The new package NORTICA (Numerical ORbit Tracking In Cyclotrons with Analysis) of computer codes for beam dynamics simulations is under development at NSCL. The package was started as a replacement for the code MONSTER [1] developed in the laboratory in the past. The new codes are capable of beam dynamics simulations in both CCF (Coupled Cyclotron Facility) accelerators, the K500 and K1200 superconducting cyclotrons. The general purpose of this package is assisting in setting and tuning the cyclotrons taking into account the main field and extraction channel imperfections. The computer platform for the package is Alpha Station with UNIX operating system and X-Windows graphic interface. A multiple programming language approach was used in order to combine the reliability of the numerical algorithms developed over the long period of time in the laboratory and the friendliness of modern style user interface. This paper describes the capability and features of the codes in the present state.

Solving PDEs with Intrepid

DOE PAGES

Bochev, P.; Edwards, H. C.; Kirby, R. C.; ...

2012-01-01

Intrepid is a Trilinos package for advanced discretizations of Partial Differential Equations (PDEs). The package provides a comprehensive set of tools for local, cell-based construction of a wide range of numerical methods for PDEs. This paper describes the mathematical ideas and software design principles incorporated in the package. We also provide representative examples showcasing the use of Intrepid both in the context of numerical PDEs and the more general context of data analysis.

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

Anderson, James; Goins, Monty; Paul, Pran

This safety analysis report for packaging (SARP) presents the results of the safety analysis prepared in support of the Consolidated Nuclear Security, LLC (CNS) request for licensing of the Model ES-3100 package with bulk highly enriched uranium (HEU) contents and issuance of a Type B(U) Fissile Material Certificate of Compliance. This SARP, published in the format specified in the Nuclear Regulatory Commission (NRC) Regulatory Guide 7.9 and using information provided in UCID-21218 and NRC Regulatory Guide 7.10, demonstrates that the Y-12 National Security Complex (Y-12) ES-3100 package with bulk HEU contents meets the established NRC regulations for packaging, preparation formore » shipment, and transportation of radioactive materials given in Title 10, Part 71, of the Code of Federal Regulations (CFR) [10 CFR 71] as well as U.S. Department of Transportation (DOT) regulations for packaging and shipment of hazardous materials given in Title 49 CFR. To protect the health and safety of the public, shipments of adioactive materials are made in packaging that is designed, fabricated, assembled, tested, procured, used, maintained, and repaired in accordance with the provisions cited above. Safety requirements addressed by the regulations that must be met when transporting radioactive materials are containment of radioactive materials, radiation shielding, and assurance of nuclear subcriticality.« less

Variability of upper ocean thermohaline structure during a MJO event from DYNAMO aircraft observations

NASA Astrophysics Data System (ADS)

Alappattu, Denny P.; Wang, Qing; Kalogiros, John; Guy, Nick; Jorgensen, David P.

2017-02-01

This paper reports upper ocean thermohaline structure and variability observed during the life cycle of an intense Madden Julian Oscillation (MJO) event occurred in the southern tropical Indian Ocean (14°S-Eq, 70°E-81°E). Water column measurements for this study were collected using airborne expendable probes deployed from NOAA's WP-3D Orion aircraft operated as a part of Dynamics of MJO field experiment conducted during November-December 2011. Purpose of the study is twofold; (1) to provide a statistical analysis of the upper ocean properties observed during different phases of MJO and, (2) to investigate how the upper ocean thermohaline structure evolved in the study region in response to the MJO induced perturbation. During the active phase of MJO, mixed layer depth (MLD) had a characteristic bimodal distribution. Primary and secondary modes were at ˜34 m and ˜65 m, respectively. Spatial heterogeneity of the upper ocean response to the MJO forcing was the plausible reason for bimodal distribution. Thermocline and isothermal layer depth deepened, respectively, by 13 and 19 m from the suppressed through the restoring phase of MJO. Thicker (>30 m) barrier layers were found to occur more frequently in the active phase of MJO, associated with convective rainfalls. Additionally, the water mass analysis indicated that, in the active phase of this MJO event the subsurface was dominated by Indonesian throughflow, nonetheless intrusion of Arabian Sea high saline water was also noted near the equator.

Nonlinear detection of large-scale transitions in Plio-Pleistocene African climate

NASA Astrophysics Data System (ADS)

Donges, J. F.; Donner, R. V.; Trauth, M. H.; Marwan, N.; Schellnhuber, H. J.; Kurths, J.

2011-12-01

Potential paleoclimatic driving mechanisms acting on human development present an open problem of cross-disciplinary scientific interest. The analysis of paleoclimate archives encoding the environmental variability in East Africa during the last 5 Ma (million years) has triggered an ongoing debate about possible candidate processes and evolutionary mechanisms. In this work, we apply a novel nonlinear statistical technique, recurrence network analysis, to three distinct marine records of terrigenous dust flux. Our method enables us to identify three epochs with transitions between qualitatively different types of environmental variability in North and East Africa during the (i) Mid-Pliocene (3.35-3.15 Ma BP (before present)), (ii) Early Pleistocene (2.25-1.6 Ma BP), and (iii) Mid-Pleistocene (1.1-0.7 Ma BP). A deeper examination of these transition periods reveals potential climatic drivers, including (i) large-scale changes in ocean currents due to a spatial shift of the Indonesian throughflow in combination with an intensification of Northern Hemisphere glaciation, (ii) a global reorganization of the atmospheric Walker circulation induced in the tropical Pacific and Indian Ocean, and (iii) shifts in the dominating temporal variability pattern of glacial activity during the Mid-Pleistocene, respectively. A statistical reexamination of the available fossil record demonstrates a remarkable coincidence between the detected transition periods and major steps in hominin evolution. This suggests that the observed shifts between more regular and more erratic environmental variability have acted as a trigger for rapid change in the development of humankind in Africa.

Nonlinear detection of paleoclimate-variability transitions possibly related to human evolution

NASA Astrophysics Data System (ADS)

Donges, J. F.; Donner, R. V.; Trauth, M. H.; Marwan, N.; Schellnhuber, H. J.; Kurths, J.

2012-04-01

Potential paleoclimatic driving mechanisms acting on human evolution present an open problem of cross-disciplinary scientific interest. The analysis of paleoclimate archives encoding the environmental variability in East Africa during the last 5 Ma (million years) has triggered an ongoing debate about possible candidate processes and evolutionary mechanisms. In this work, we apply a novel nonlinear statistical technique, recurrence network analysis, to three distinct marine records of terrigenous dust flux. Our method enables us to identify three epochs with transitions between qualitatively different types of environmental variability in North and East Africa during the (i) Mid-Pliocene (3.35-3.15 Ma BP (before present)), (ii) Early Pleistocene (2.25-1.6 Ma BP), and (iii) Mid-Pleistocene (1.1-0.7 Ma BP). A deeper examination of these transition periods reveals potential climatic drivers, including (i) large-scale changes in ocean currents due to a spatial shift of the Indonesian throughflow in combination with an intensification of Northern Hemisphere glaciation, (ii) a global reorganization of the atmospheric Walker circulation induced in the tropical Pacific and Indian Ocean, and (iii) shifts in the dominating temporal variability pattern of glacial activity during the Mid-Pleistocene, respectively. A reexamination of the available fossil record demonstrates statistically significant coincidences between the detected transition periods and major steps in hominin evolution. This suggests that the observed shifts between more regular and more erratic environmental variability may have acted as a trigger for rapid change in the development of humankind in Africa.

Effecting aging time of epoxy molding compound to molding process for integrated circuit packaging

NASA Astrophysics Data System (ADS)

Tachapitunsuk, Jirayu; Ugsornrat, Kessararat; Srisuwitthanon, Warayoot; Thonglor, Panakamon

2017-09-01

This research studied about effecting aging time of epoxy molding compound (EMC) that effect to reliability performance of integrated circuit (IC) package in molding process. Molding process is so important of IC packaging process for protecting IC chip (or die) from temperature and humidity environment using encapsulated EMC. For general molding process, EMC are stored in the frozen at 5°C and left at room temperature at 25 °C for aging time on self before molding of die onto lead frame is 24 hours. The aging time effect to reliability performance of IC package due to different temperature and humidity inside the package. In experiment, aging time of EMC were varied from 0 to 24 hours for molding process of SOIC-8L packages. For analysis, these packages were tested by x-ray and scanning acoustic microscope to analyze properties of EMC with an aging time and also analyzed delamination, internal void, and wire sweep inside the packages with different aging time. The results revealed that different aging time of EMC effect to properties and reliability performance of molding process.

On the Rocks: Microbiological Quality and Microbial Diversity of Packaged Ice in Southern California.

PubMed

Lee, Kun Ho; Ab Samad, Liana S; Lwin, Phillip M; Riedel, Stefan F; Magin, Ashley; Bashir, Mina; Vaishampayan, Parag A; Lin, Wei-Jen

2017-06-01

Ice is defined as a food and is frequently used in direct contact with food and beverages. Packaged ice is commercially produced and can be easily found in grocery and convenience stores. However, the quality and safety of packaged ice products is not consistent. The Packaged Ice Quality Control Standards manual (PIQCS) published by the International Packaged Ice Association provides the quality and processing standards for packaged ice produced by its members. Packaged ice produced on the premise of stores (on-site packaged ice) is not required to be in compliance with these standards. In this study, packaged ice produced by manufacturing plants or by in-store bagger (ISB) machines and on-site packaged ice were compared for their microbiological quality and microbial diversity. Our results revealed that 19% of the 120 on-site packaged ice samples did not meet the PIQCS microbial limit of 500 CFU/mL (or g) and also the absence of coliforms and Escherichia coli . Staphylococci were found in 34% of the on-site packaged ice samples, most likely through contamination from the packaging workers. None of the ISB and manufactured packaged ice samples had unacceptable microbial levels, and all were devoid of staphylococci. Salmonella was absent in all samples analyzed in this study. Microbial community analysis of ice based on 16S/18S rRNA targeted sequencing revealed a much higher microbial diversity and abundance in the on-site packaged ice than in the ISB ice. Proteobacteria, especially Alphaproteobacteria and Betaproteobacteria, were the dominant bacterial groups in all samples tested. Most of these bacteria were oligotrophic; however, a few opportunistic or potential pathogens were found at low levels in the on-site packaged ice but not in the ISB packaged ice. The types of microbes identified may provide information needed to investigate potential sources of contamination. Our data also suggest a need for enforcement of processing standards during the on-site packaging of ice.

Instrument Packages for the Cold, Dark, High Radiation Environments

NASA Technical Reports Server (NTRS)

Clark, P. E.; Millar, P. S.; Yeh, P. S.; Beamna, B.; Brigham, D.; Feng, S.

2011-01-01

We are developing a small cold temperature instrument package concept that integrates a cold temperature power system and radhard ultra low temperature ultra low power electronics components and power supplies now under development into a cold temperature surface operational version of a planetary surface instrument package. We are already in the process of developing a lower power lower tem-perature version for an instrument of mutual interest to SMD and ESMD to support the search for volatiles (the mass spectrometer VAPoR, Volatile Analysis by Pyrolysis of Regolith) both as a stand alone instrument and as part of an environmental monitoring package.

Implementation of radiation shielding calculation methods. Volume 1: Synopsis of methods and summary of results

NASA Technical Reports Server (NTRS)

Capo, M. A.; Disney, R. K.

1971-01-01

The work performed in the following areas is summarized: (1) Analysis of Realistic nuclear-propelled vehicle was analyzed using the Marshall Space Flight Center computer code package. This code package includes one and two dimensional discrete ordinate transport, point kernel, and single scatter techniques, as well as cross section preparation and data processing codes, (2) Techniques were developed to improve the automated data transfer in the coupled computation method of the computer code package and improve the utilization of this code package on the Univac-1108 computer system. (3) The MSFC master data libraries were updated.

Nmrglue: an open source Python package for the analysis of multidimensional NMR data.

PubMed

Helmus, Jonathan J; Jaroniec, Christopher P

2013-04-01

Nmrglue, an open source Python package for working with multidimensional NMR data, is described. When used in combination with other Python scientific libraries, nmrglue provides a highly flexible and robust environment for spectral processing, analysis and visualization and includes a number of common utilities such as linear prediction, peak picking and lineshape fitting. The package also enables existing NMR software programs to be readily tied together, currently facilitating the reading, writing and conversion of data stored in Bruker, Agilent/Varian, NMRPipe, Sparky, SIMPSON, and Rowland NMR Toolkit file formats. In addition to standard applications, the versatility offered by nmrglue makes the package particularly suitable for tasks that include manipulating raw spectrometer data files, automated quantitative analysis of multidimensional NMR spectra with irregular lineshapes such as those frequently encountered in the context of biomacromolecular solid-state NMR, and rapid implementation and development of unconventional data processing methods such as covariance NMR and other non-Fourier approaches. Detailed documentation, install files and source code for nmrglue are freely available at http://nmrglue.com. The source code can be redistributed and modified under the New BSD license.

Nmrglue: An Open Source Python Package for the Analysis of Multidimensional NMR Data

PubMed Central

Helmus, Jonathan J.; Jaroniec, Christopher P.

2013-01-01

Nmrglue, an open source Python package for working with multidimensional NMR data, is described. When used in combination with other Python scientific libraries, nmrglue provides a highly flexible and robust environment for spectral processing, analysis and visualization and includes a number of common utilities such as linear prediction, peak picking and lineshape fitting. The package also enables existing NMR software programs to be readily tied together, currently facilitating the reading, writing and conversion of data stored in Bruker, Agilent/Varian, NMRPipe, Sparky, SIMPSON, and Rowland NMR Toolkit file formats. In addition to standard applications, the versatility offered by nmrglue makes the package particularly suitable for tasks that include manipulating raw spectrometer data files, automated quantitative analysis of multidimensional NMR spectra with irregular lineshapes such as those frequently encountered in the context of biomacromolecular solid-state NMR, and rapid implementation and development of unconventional data processing methods such as covariance NMR and other non-Fourier approaches. Detailed documentation, install files and source code for nmrglue are freely available at http://nmrglue.com. The source code can be redistributed and modified under the New BSD license. PMID:23456039

SWMPr: An R Package for Retrieving, Organizing, and ...

EPA Pesticide Factsheets

The System-Wide Monitoring Program (SWMP) was implemented in 1995 by the US National Estuarine Research Reserve System. This program has provided two decades of continuous monitoring data at over 140 fixed stations in 28 estuaries. However, the increasing quantity of data provided by the monitoring network has complicated broad-scale comparisons between systems and, in some cases, prevented simple trend analysis of water quality parameters at individual sites. This article describes the SWMPr package that provides several functions that facilitate data retrieval, organization, andanalysis of time series data in the reserve estuaries. Previously unavailable functions for estuaries are also provided to estimate rates of ecosystem metabolism using the open-water method. The SWMPr package has facilitated a cross-reserve comparison of water quality trends and links quantitative information with analysis tools that have use for more generic applications to environmental time series. The manuscript describes a software package that was recently developed to retrieve, organize, and analyze monitoring data from the National Estuarine Research Reserve System. Functions are explained in detail, including recent applications for trend analysis of ecosystem metabolism.

Easing access to R using 'shiny' to create graphical user interfaces: An example for the R package 'Luminescence'

NASA Astrophysics Data System (ADS)

Burow, Christoph; Kreutzer, Sebastian; Dietze, Michael; Fuchs, Margret C.; Schmidt, Christoph; Fischer, Manfred; Brückner, Helmut

2017-04-01

Since the release of the R package 'Luminescence' (Kreutzer et al., 2012) the functionality of the package has been greatly enhanced by implementing further functions for measurement data processing, statistical analysis and graphical output. Despite its capabilities for complex and non-standard analysis of luminescence data, working with the command-line interface (CLI) of R can be tedious at best and overwhelming at worst, especially for users without experience in programming languages. Even though much work is put into simplifying the usage of the package to continuously lower the entry threshold, at least basic knowledge of R will always be required. Thus, the potential user base of the package cannot be exhausted, at least as long as the CLI is the only means of utilising the 'Luminescence' package. But even experienced users may find it tedious to iteratively run a function until a satisfying results is produced. For example, plotting data is also at least partly subject to personal aesthetic tastes in accordance with the information it is supposed to convey and iterating through all the possible options in the R CLI can be a time-consuming task. An alternative approach to the CLI is the graphical user interface (GUI), which allows direct, interactive manipulation and interaction with the underlying software. For users with little or no experience with command-lines a GUI offers intuitive access that counteracts the perceived steep learning curve of a CLI. Even though R lacks native support for GUI functions, its capabilities of linking it to other programming languages allows to utilise external frameworks to build graphical user interfaces. A recent attempt to provide a GUI toolkit for R was the introduction of the 'shiny' package (Chang et al., 2016), which allows automatic construction of HTML, CSS and JavaScript based user interfaces straight from R. Here, we give (1) a brief introduction to the 'shiny' framework for R, before we (2) present a GUI for the R package 'Luminescence' in the form of interactive web applications. These applications can be accessed online so that a user is not even required to have a local installation of R and which provide access to most of the plotting functions of the R package 'Luminescence'. These functionalities will be demonstrated live during the PICO session. References Chang, W., Cheng, J., Allaire, JJ., Xie, Y., McPherson, J., 2016. shiny: Web Application Framework for R. R package version 0.13.2. https://CRAN.R-project.org/package=shiny Kreutzer, S., Schmidt, C., Fuchs, M.C., Dietze, M., Fischer, M., Fuchs, M., 2012. Introducing an R package for luminescence dating analysis. Ancient TL, 30: 1-8, 2012.

Indonesian Throughflow variability over the last glacial cycle (Invited)

NASA Astrophysics Data System (ADS)

Holbourn, A. E.; Kuhnt, W.; Regenberg, M.; Xu, J.; Hendrizan, M.; Schröder, J.

2013-12-01

The transfer of surface and intermediate waters from the Pacific Ocean to the Indian Ocean through the Indonesian archipelago (Indonesian Throughflow: ITF) strongly influences the heat and freshwater budgets of tropical water masses, in turn affecting global climate. Key areas for monitoring past ITF variations through this critical gateway are the narrow passages through the Makassar Strait and Flores Sea and the main outflow area within the Timor Sea. Here, we integrate high-resolution sea surface temperature and salinity reconstructions (based on paired planktic foraminiferal Mg/Ca and δ18O) with X-ray fluorescence runoff data and benthic isotopes from marine sediment cores retrieved in these regions during several cruises with RV'Sonne' and RV'Marion Dufresne'. Our results show that high latitude climate variability strongly influenced ITF intensity on millennial to centennial timescales as well as on longer glacial-interglacial timescales. Marked declines in ITF strength occurred during Heinrich events and the Younger Dryas, most likely related to slowdown of the global thermohaline circulation during colder northern hemisphere climate spells, when deep water production decreased and the deep ocean became more stratified. Additionally, the surface component of the ITF strongly reflects regional windstress and rainfall patterns, and thus the spatial extent and intensity of the tropical convection over the Indonesian archipelago. Our runoff and salinity estimates reveal that the development of the tropical convection was intricately linked to the latitudinal migration of the Inter Tropical Convergence Zone (ITCZ). In particular, our data show that the Australian monsoon intensified during the major deglacial atmospheric CO2 rise through the Younger Dryas and earliest Holocene (12.9-10 ka). This massive intensification of the Australian monsoon coincided with a southward shift of the ITCZ, linked to southern hemisphere warming and enhanced greenhouse forcing over the Australian continent. However, the development of the monsoon was asynchronous over the region, which we relate to changes in landmass exposure during deglacial sea-level rise. Thus, we find that sea-level exerted a major control on ITF properties through the last glacial termination by altering gateway configuration and precipitation-evaporation budgets over the Indonesian archipelago.

Reliability and accuracy of three imaging software packages used for 3D analysis of the upper airway on cone beam computed tomography images.

PubMed

Chen, Hui; van Eijnatten, Maureen; Wolff, Jan; de Lange, Jan; van der Stelt, Paul F; Lobbezoo, Frank; Aarab, Ghizlane

2017-08-01

The aim of this study was to assess the reliability and accuracy of three different imaging software packages for three-dimensional analysis of the upper airway using CBCT images. To assess the reliability of the software packages, 15 NewTom 5G ® (QR Systems, Verona, Italy) CBCT data sets were randomly and retrospectively selected. Two observers measured the volume, minimum cross-sectional area and the length of the upper airway using Amira ® (Visage Imaging Inc., Carlsbad, CA), 3Diagnosys ® (3diemme, Cantu, Italy) and OnDemand3D ® (CyberMed, Seoul, Republic of Korea) software packages. The intra- and inter-observer reliability of the upper airway measurements were determined using intraclass correlation coefficients and Bland & Altman agreement tests. To assess the accuracy of the software packages, one NewTom 5G ® CBCT data set was used to print a three-dimensional anthropomorphic phantom with known dimensions to be used as the "gold standard". This phantom was subsequently scanned using a NewTom 5G ® scanner. Based on the CBCT data set of the phantom, one observer measured the volume, minimum cross-sectional area, and length of the upper airway using Amira ® , 3Diagnosys ® , and OnDemand3D ® , and compared these measurements with the gold standard. The intra- and inter-observer reliability of the measurements of the upper airway using the different software packages were excellent (intraclass correlation coefficient ≥0.75). There was excellent agreement between all three software packages in volume, minimum cross-sectional area and length measurements. All software packages underestimated the upper airway volume by -8.8% to -12.3%, the minimum cross-sectional area by -6.2% to -14.6%, and the length by -1.6% to -2.9%. All three software packages offered reliable volume, minimum cross-sectional area and length measurements of the upper airway. The length measurements of the upper airway were the most accurate results in all software packages. All software packages underestimated the upper airway dimensions of the anthropomorphic phantom.

SFAP: Scan-Tron Forms Analysis Package for the IBM-PC. User's Guide, Version 2.0.

ERIC Educational Resources Information Center

Harnisch, Delwyn L.; And Others

The Scan-Tron Forms Analysis Package (SFAP) is a collection of integrated programs that allow an IBM-PC (or compatible) to collect data from a Scan-Tron 1200 forms reader. In addition to the basic data acquisition capability, the SFAP has additional capabilities related to the viewing and formatting of incoming data. When used in combination with…

Analyzing a Career. The Wisconsin Guide to Local Curriculum Improvement in Industrial Education, K-12.

ERIC Educational Resources Information Center

Loeffler, Gordon

The intent of this field tested instructional package is to acquaint the student with a method of career analysis to enable him to determine whether a career is in harmony with his future employment goals. The package provides behavioral objectives, a student self-test, a basic information section, and a career analysis study to aid the student in…

Packaging- and transportation-related occurrence reports : FY 1995 annual report

DOT National Transportation Integrated Search

1996-03-01

The Oak Ridge National Laboratory, through its support to the U.S. Department of Energys (DOEs) Office of Facility Safety Analysis, EH-32, retrieves reports and information pertaining to transportation and packaging occurrences from the centralized O...

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories.

PubMed

McGibbon, Robert T; Beauchamp, Kyle A; Harrigan, Matthew P; Klein, Christoph; Swails, Jason M; Hernández, Carlos X; Schwantes, Christian R; Wang, Lee-Ping; Lane, Thomas J; Pande, Vijay S

2015-10-20

As molecular dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use software tools for the analysis of these simulations is growing. We have developed MDTraj, a modern, lightweight, and fast software package for analyzing MD simulations. MDTraj reads and writes trajectory data in a wide variety of commonly used formats. It provides a large number of trajectory analysis capabilities including minimal root-mean-square-deviation calculations, secondary structure assignment, and the extraction of common order parameters. The package has a strong focus on interoperability with the wider scientific Python ecosystem, bridging the gap between MD data and the rapidly growing collection of industry-standard statistical analysis and visualization tools in Python. MDTraj is a powerful and user-friendly software package that simplifies the analysis of MD data and connects these datasets with the modern interactive data science software ecosystem in Python. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

SNPassoc: an R package to perform whole genome association studies.

PubMed

González, Juan R; Armengol, Lluís; Solé, Xavier; Guinó, Elisabet; Mercader, Josep M; Estivill, Xavier; Moreno, Víctor

2007-03-01

The popularization of large-scale genotyping projects has led to the widespread adoption of genetic association studies as the tool of choice in the search for single nucleotide polymorphisms (SNPs) underlying susceptibility to complex diseases. Although the analysis of individual SNPs is a relatively trivial task, when the number is large and multiple genetic models need to be explored it becomes necessary a tool to automate the analyses. In order to address this issue, we developed SNPassoc, an R package to carry out most common analyses in whole genome association studies. These analyses include descriptive statistics and exploratory analysis of missing values, calculation of Hardy-Weinberg equilibrium, analysis of association based on generalized linear models (either for quantitative or binary traits), and analysis of multiple SNPs (haplotype and epistasis analysis). Package SNPassoc is available at CRAN from http://cran.r-project.org. A tutorial is available on Bioinformatics online and in http://davinci.crg.es/estivill_lab/snpassoc.

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

PubMed Central

McGibbon, Robert T.; Beauchamp, Kyle A.; Harrigan, Matthew P.; Klein, Christoph; Swails, Jason M.; Hernández, Carlos X.; Schwantes, Christian R.; Wang, Lee-Ping; Lane, Thomas J.; Pande, Vijay S.

2015-01-01

As molecular dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use software tools for the analysis of these simulations is growing. We have developed MDTraj, a modern, lightweight, and fast software package for analyzing MD simulations. MDTraj reads and writes trajectory data in a wide variety of commonly used formats. It provides a large number of trajectory analysis capabilities including minimal root-mean-square-deviation calculations, secondary structure assignment, and the extraction of common order parameters. The package has a strong focus on interoperability with the wider scientific Python ecosystem, bridging the gap between MD data and the rapidly growing collection of industry-standard statistical analysis and visualization tools in Python. MDTraj is a powerful and user-friendly software package that simplifies the analysis of MD data and connects these datasets with the modern interactive data science software ecosystem in Python. PMID:26488642

Chandra Interactive Analysis of Observations (CIAO)

NASA Technical Reports Server (NTRS)

Dobrzycki, Adam

2000-01-01

The Chandra (formerly AXAF) telescope, launched on July 23, 1999, provides X-rays data with unprecedented spatial and spectral resolution. As part of the Chandra scientific support, the Chandra X-ray Observatory Center provides a new data analysis system, CIAO ("Chandra Interactive Analysis of Observations"). We will present the main components of the system: "First Look" analysis; SHERPA: a multi-dimensional, multi-mission modeling and fitting application; Chandra Imaging and Plotting System; Detect package-source detection algorithms; and DM package generic data manipulation tools, We will set up a demonstration of the portable version of the system and show examples of Chandra Data Analysis.

Bird impact analysis package for turbine engine fan blades

NASA Technical Reports Server (NTRS)

Hirschbein, M. S.

1982-01-01

A computer program has been developed to analyze the gross structural response of turbine engine fan blades subjected to bird strikes. The program couples a NASTRAN finite element model and modal analysis of a fan blade with a multi-mode bird impact analysis computer program. The impact analysis uses the NASTRAN blade model and a fluid jet model of the bird to interactively calculate blade loading during a bird strike event. The analysis package is computationaly efficient, easy to use and provides a comprehensive history of the gross structual blade response. Example cases are presented for a representative fan blade.

Tree Classification Software

NASA Technical Reports Server (NTRS)

Buntine, Wray

1993-01-01

This paper introduces the IND Tree Package to prospective users. IND does supervised learning using classification trees. This learning task is a basic tool used in the development of diagnosis, monitoring and expert systems. The IND Tree Package was developed as part of a NASA project to semi-automate the development of data analysis and modelling algorithms using artificial intelligence techniques. The IND Tree Package integrates features from CART and C4 with newer Bayesian and minimum encoding methods for growing classification trees and graphs. The IND Tree Package also provides an experimental control suite on top. The newer features give improved probability estimates often required in diagnostic and screening tasks. The package comes with a manual, Unix 'man' entries, and a guide to tree methods and research. The IND Tree Package is implemented in C under Unix and was beta-tested at university and commercial research laboratories in the United States.

Global review of open access risk assessment software packages valid for global or continental scale analysis

NASA Astrophysics Data System (ADS)

Daniell, James; Simpson, Alanna; Gunasekara, Rashmin; Baca, Abigail; Schaefer, Andreas; Ishizawa, Oscar; Murnane, Rick; Tijssen, Annegien; Deparday, Vivien; Forni, Marc; Himmelfarb, Anne; Leder, Jan

2015-04-01

Over the past few decades, a plethora of open access software packages for the calculation of earthquake, volcanic, tsunami, storm surge, wind and flood have been produced globally. As part of the World Bank GFDRR Review released at the Understanding Risk 2014 Conference, over 80 such open access risk assessment software packages were examined. Commercial software was not considered in the evaluation. A preliminary analysis was used to determine whether the 80 models were currently supported and if they were open access. This process was used to select a subset of 31 models that include 8 earthquake models, 4 cyclone models, 11 flood models, and 8 storm surge/tsunami models for more detailed analysis. By using multi-criteria analysis (MCDA) and simple descriptions of the software uses, the review allows users to select a few relevant software packages for their own testing and development. The detailed analysis evaluated the models on the basis of over 100 criteria and provides a synopsis of available open access natural hazard risk modelling tools. In addition, volcano software packages have since been added making the compendium of risk software tools in excess of 100. There has been a huge increase in the quality and availability of open access/source software over the past few years. For example, private entities such as Deltares now have an open source policy regarding some flood models (NGHS). In addition, leaders in developing risk models in the public sector, such as Geoscience Australia (EQRM, TCRM, TsuDAT, AnuGA) or CAPRA (ERN-Flood, Hurricane, CRISIS2007 etc.), are launching and/or helping many other initiatives. As we achieve greater interoperability between modelling tools, we will also achieve a future wherein different open source and open access modelling tools will be increasingly connected and adapted towards unified multi-risk model platforms and highly customised solutions. It was seen that many software tools could be improved by enabling user-defined exposure and vulnerability. Without this function, many tools can only be used regionally and not at global or continental scale. It is becoming increasingly easy to use multiple packages for a single region and/or hazard to characterize the uncertainty in the risk, or use as checks for the sensitivities in the analysis. There is a potential for valuable synergy between existing software. A number of open source software packages could be combined to generate a multi-risk model with multiple views of a hazard. This extensive review has simply attempted to provide a platform for dialogue between all open source and open access software packages and to hopefully inspire collaboration between developers, given the great work done by all open access and open source developers.

Wide-field Imaging System and Rapid Direction of Optical Zoom (WOZ)

DTIC Science & Technology

2010-09-25

commercial software packages: SolidWorks, COMSOL Multiphysics, and ZEMAX optical design. SolidWorks is a computer aided design package, which as a live...interface to COMSOL. COMSOL is a finite element analysis/partial differential equation solver. ZEMAX is an optical design package. Both COMSOL and... ZEMAX have live interfaces to MatLab. Our initial investigations have enabled a model in SolidWorks to be updated in COMSOL, an FEA calculation

snpGeneSets: An R Package for Genome-Wide Study Annotation

PubMed Central

Mei, Hao; Li, Lianna; Jiang, Fan; Simino, Jeannette; Griswold, Michael; Mosley, Thomas; Liu, Shijian

2016-01-01

Genome-wide studies (GWS) of SNP associations and differential gene expressions have generated abundant results; next-generation sequencing technology has further boosted the number of variants and genes identified. Effective interpretation requires massive annotation and downstream analysis of these genome-wide results, a computationally challenging task. We developed the snpGeneSets package to simplify annotation and analysis of GWS results. Our package integrates local copies of knowledge bases for SNPs, genes, and gene sets, and implements wrapper functions in the R language to enable transparent access to low-level databases for efficient annotation of large genomic data. The package contains functions that execute three types of annotations: (1) genomic mapping annotation for SNPs and genes and functional annotation for gene sets; (2) bidirectional mapping between SNPs and genes, and genes and gene sets; and (3) calculation of gene effect measures from SNP associations and performance of gene set enrichment analyses to identify functional pathways. We applied snpGeneSets to type 2 diabetes (T2D) results from the NHGRI genome-wide association study (GWAS) catalog, a Finnish GWAS, and a genome-wide expression study (GWES). These studies demonstrate the usefulness of snpGeneSets for annotating and performing enrichment analysis of GWS results. The package is open-source, free, and can be downloaded at: https://www.umc.edu/biostats_software/. PMID:27807048

SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data.

PubMed

Varet, Hugo; Brillet-Guéguen, Loraine; Coppée, Jean-Yves; Dillies, Marie-Agnès

2016-01-01

Several R packages exist for the detection of differentially expressed genes from RNA-Seq data. The analysis process includes three main steps, namely normalization, dispersion estimation and test for differential expression. Quality control steps along this process are recommended but not mandatory, and failing to check the characteristics of the dataset may lead to spurious results. In addition, normalization methods and statistical models are not exchangeable across the packages without adequate transformations the users are often not aware of. Thus, dedicated analysis pipelines are needed to include systematic quality control steps and prevent errors from misusing the proposed methods. SARTools is an R pipeline for differential analysis of RNA-Seq count data. It can handle designs involving two or more conditions of a single biological factor with or without a blocking factor (such as a batch effect or a sample pairing). It is based on DESeq2 and edgeR and is composed of an R package and two R script templates (for DESeq2 and edgeR respectively). Tuning a small number of parameters and executing one of the R scripts, users have access to the full results of the analysis, including lists of differentially expressed genes and a HTML report that (i) displays diagnostic plots for quality control and model hypotheses checking and (ii) keeps track of the whole analysis process, parameter values and versions of the R packages used. SARTools provides systematic quality controls of the dataset as well as diagnostic plots that help to tune the model parameters. It gives access to the main parameters of DESeq2 and edgeR and prevents untrained users from misusing some functionalities of both packages. By keeping track of all the parameters of the analysis process it fits the requirements of reproducible research.

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

Carter, Faustin Wirkus; Khaire, Trupti S.; Novosad, Valentyn

We present "scraps" (SuperConducting Analysis and Plotting Software), a Python package designed to aid in the analysis and visualization of large amounts of superconducting resonator data, specifically complex transmission as a function of frequency, acquired at many different temperatures and driving powers. The package includes a least-squares fitting engine as well as a Monte-Carlo Markov Chain sampler for sampling the posterior distribution given priors, marginalizing over nuisance parameters, and estimating covariances. A set of plotting tools for generating publication-quality figures is also provided in the package. Lastly, we discuss the functionality of the software and provide some examples of itsmore » utility on data collected from a niobium-nitride coplanar waveguide resonator fabricated at Argonne National Laboratory.« less

Analysis pipelines and packages for Infinium HumanMethylation450 BeadChip (450k) data.

PubMed

Morris, Tiffany J; Beck, Stephan

2015-01-15

The Illumina HumanMethylation450 BeadChip has become a popular platform for interrogating DNA methylation in epigenome-wide association studies (EWAS) and related projects as well as resource efforts such as the International Cancer Genome Consortium (ICGC) and the International Human Epigenome Consortium (IHEC). This has resulted in an exponential increase of 450k data in recent years and triggered the development of numerous integrated analysis pipelines and stand-alone packages. This review will introduce and discuss the currently most popular pipelines and packages and is particularly aimed at new 450k users. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

The ssWavelets package

Treesearch

Jeffrey H. Gove

2017-01-01

This package adds several classes, generics and associated methods as well as a few various functions to help with wavelet decomposition of sampling surfaces generated using sampSurf. As such, it can be thought of as an extension to sampSurf for wavelet analysis.

Preliminary design package for Sunair SEC-601 solar collector

NASA Technical Reports Server (NTRS)

1978-01-01

The preliminary design of the Owens-Illinois model Sunair SEC-601 tubular air solar collector is presented. Information in this package includes the subsystem design and development approaches, hazard analysis, and detailed drawings available as the preliminary design review.

Hera - The HEASARC's New Data Analysis Service

NASA Technical Reports Server (NTRS)

Pence, William

2006-01-01

Hera is the new computer service provided by the HEASARC at the NASA Goddard Space Flight Center that enables qualified student and professional astronomical researchers to immediately begin analyzing scientific data from high-energy astrophysics missions. All the necessary resources needed to do the data analysis are freely provided by Hera, including: * the latest version of the hundreds of scientific analysis programs in the HEASARC's HEASOFT package, as well as most of the programs in the Chandra CIAO package and the XMM-Newton SAS package. * high speed access to the terabytes of data in the HEASARC's high energy astrophysics Browse data archive. * a cluster of fast Linw workstations to run the software * ample local disk space to temporarily store the data and results. Some of the many features and different modes of using Hera are illustrated in this poster presentation.

Computational methods for evaluation of cell-based data assessment--Bioconductor.

PubMed

Le Meur, Nolwenn

2013-02-01

Recent advances in miniaturization and automation of technologies have enabled cell-based assay high-throughput screening, bringing along new challenges in data analysis. Automation, standardization, reproducibility have become requirements for qualitative research. The Bioconductor community has worked in that direction proposing several R packages to handle high-throughput data including flow cytometry (FCM) experiment. Altogether, these packages cover the main steps of a FCM analysis workflow, that is, data management, quality assessment, normalization, outlier detection, automated gating, cluster labeling, and feature extraction. Additionally, the open-source philosophy of R and Bioconductor, which offers room for new development, continuously drives research and improvement of theses analysis methods, especially in the field of clustering and data mining. This review presents the principal FCM packages currently available in R and Bioconductor, their advantages and their limits. Copyright © 2012 Elsevier Ltd. All rights reserved.

pcr: an R package for quality assessment, analysis and testing of qPCR data

PubMed Central

Ahmed, Mahmoud

2018-01-01

Background Real-time quantitative PCR (qPCR) is a broadly used technique in the biomedical research. Currently, few different analysis models are used to determine the quality of data and to quantify the mRNA level across the experimental conditions. Methods We developed an R package to implement methods for quality assessment, analysis and testing qPCR data for statistical significance. Double Delta CT and standard curve models were implemented to quantify the relative expression of target genes from CT in standard qPCR control-group experiments. In addition, calculation of amplification efficiency and curves from serial dilution qPCR experiments are used to assess the quality of the data. Finally, two-group testing and linear models were used to test for significance of the difference in expression control groups and conditions of interest. Results Using two datasets from qPCR experiments, we applied different quality assessment, analysis and statistical testing in the pcr package and compared the results to the original published articles. The final relative expression values from the different models, as well as the intermediary outputs, were checked against the expected results in the original papers and were found to be accurate and reliable. Conclusion The pcr package provides an intuitive and unified interface for its main functions to allow biologist to perform all necessary steps of qPCR analysis and produce graphs in a uniform way. PMID:29576953

The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again.

PubMed

González-Beltrán, Alejandra; Neumann, Steffen; Maguire, Eamonn; Sansone, Susanna-Assunta; Rocca-Serra, Philippe

2014-01-01

The ISA-Tab format and software suite have been developed to break the silo effect induced by technology-specific formats for a variety of data types and to better support experimental metadata tracking. Experimentalists seldom use a single technique to monitor biological signals. Providing a multi-purpose, pragmatic and accessible format that abstracts away common constructs for describing Investigations, Studies and Assays, ISA is increasingly popular. To attract further interest towards the format and extend support to ensure reproducible research and reusable data, we present the Risa package, which delivers a central component to support the ISA format by enabling effortless integration with R, the popular, open source data crunching environment. The Risa package bridges the gap between the metadata collection and curation in an ISA-compliant way and the data analysis using the widely used statistical computing environment R. The package offers functionality for: i) parsing ISA-Tab datasets into R objects, ii) augmenting annotation with extra metadata not explicitly stated in the ISA syntax; iii) interfacing with domain specific R packages iv) suggesting potentially useful R packages available in Bioconductor for subsequent processing of the experimental data described in the ISA format; and finally v) saving back to ISA-Tab files augmented with analysis specific metadata from R. We demonstrate these features by presenting use cases for mass spectrometry data and DNA microarray data. The Risa package is open source (with LGPL license) and freely available through Bioconductor. By making Risa available, we aim to facilitate the task of processing experimental data, encouraging a uniform representation of experimental information and results while delivering tools for ensuring traceability and provenance tracking. The Risa package is available since Bioconductor 2.11 (version 1.0.0) and version 1.2.1 appeared in Bioconductor 2.12, both along with documentation and examples. The latest version of the code is at the development branch in Bioconductor and can also be accessed from GitHub https://github.com/ISA-tools/Risa, where the issue tracker allows users to report bugs or feature requests.

The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again

PubMed Central

2014-01-01

Background The ISA-Tab format and software suite have been developed to break the silo effect induced by technology-specific formats for a variety of data types and to better support experimental metadata tracking. Experimentalists seldom use a single technique to monitor biological signals. Providing a multi-purpose, pragmatic and accessible format that abstracts away common constructs for describing Investigations, Studies and Assays, ISA is increasingly popular. To attract further interest towards the format and extend support to ensure reproducible research and reusable data, we present the Risa package, which delivers a central component to support the ISA format by enabling effortless integration with R, the popular, open source data crunching environment. Results The Risa package bridges the gap between the metadata collection and curation in an ISA-compliant way and the data analysis using the widely used statistical computing environment R. The package offers functionality for: i) parsing ISA-Tab datasets into R objects, ii) augmenting annotation with extra metadata not explicitly stated in the ISA syntax; iii) interfacing with domain specific R packages iv) suggesting potentially useful R packages available in Bioconductor for subsequent processing of the experimental data described in the ISA format; and finally v) saving back to ISA-Tab files augmented with analysis specific metadata from R. We demonstrate these features by presenting use cases for mass spectrometry data and DNA microarray data. Conclusions The Risa package is open source (with LGPL license) and freely available through Bioconductor. By making Risa available, we aim to facilitate the task of processing experimental data, encouraging a uniform representation of experimental information and results while delivering tools for ensuring traceability and provenance tracking. Software availability The Risa package is available since Bioconductor 2.11 (version 1.0.0) and version 1.2.1 appeared in Bioconductor 2.12, both along with documentation and examples. The latest version of the code is at the development branch in Bioconductor and can also be accessed from GitHub https://github.com/ISA-tools/Risa, where the issue tracker allows users to report bugs or feature requests. PMID:24564732

Putting the 1991 census sample of anonymised records on your Unix workstation.

PubMed

Turton, I; Openshaw, S

1995-03-01

"The authors describe the development of a customised computer software package for easing the analysis of the U.K. 1991 Sample of Anonymised Records. The resulting USAR [Unix Sample of Anonymised Records] package is designed to be portable within the Unix environment. It offers a number of features such as interactive table design, intelligent data interpretation, and fuzzy query. An example of SAR analysis is provided." excerpt

A predictive transport modeling code for ICRF-heated tokamaks

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

Phillips, C.K.; Hwang, D.Q.; Houlberg, W.

In this report, a detailed description of the physic included in the WHIST/RAZE package as well as a few illustrative examples of the capabilities of the package will be presented. An in depth analysis of ICRF heating experiments using WHIST/RAZE will be discussed in a forthcoming report. A general overview of philosophy behind the structure of the WHIST/RAZE package, a summary of the features of the WHIST code, and a description of the interface to the RAZE subroutines are presented in section 2 of this report. Details of the physics contained in the RAZE code are examined in section 3.more » Sample results from the package follow in section 4, with concluding remarks and a discussion of possible improvements to the package discussed in section 5.« less

modlAMP: Python for antimicrobial peptides.

PubMed

Müller, Alex T; Gabernet, Gisela; Hiss, Jan A; Schneider, Gisbert

2017-09-01

We have implemented the lecular esign aboratory's nti icrobial eptides package ( ), a Python-based software package for the design, classification and visual representation of peptide data. modlAMP offers functions for molecular descriptor calculation and the retrieval of amino acid sequences from public or local sequence databases, and provides instant access to precompiled datasets for machine learning. The package also contains methods for the analysis and representation of circular dichroism spectra. The modlAMP Python package is available under the BSD license from URL http://doi.org/10.5905/ethz-1007-72 or via pip from the Python Package Index (PyPI). gisbert.schneider@pharma.ethz.ch. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

A predictive transport modeling code for ICRF-heated tokamaks

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

Phillips, C.K.; Hwang, D.Q.; Houlberg, W.

1992-02-01

In this report, a detailed description of the physic included in the WHIST/RAZE package as well as a few illustrative examples of the capabilities of the package will be presented. An in depth analysis of ICRF heating experiments using WHIST/RAZE will be discussed in a forthcoming report. A general overview of philosophy behind the structure of the WHIST/RAZE package, a summary of the features of the WHIST code, and a description of the interface to the RAZE subroutines are presented in section 2 of this report. Details of the physics contained in the RAZE code are examined in section 3.more » Sample results from the package follow in section 4, with concluding remarks and a discussion of possible improvements to the package discussed in section 5.« less

UPLC-Q-TOF-MS analysis of non-volatile migrants from new active packaging materials.

PubMed

Aznar, M; Rodriguez-Lafuente, A; Alfaro, P; Nerin, C

2012-10-01

Ultra-performance liquid chromatography (UPLC) coupled to mass spectrometry (MS) is a useful tool in the analysis of non-volatile compounds, and the use of a quadrupole-time-of-flight (Q-TOF) mass analyzer allows a high sensitivity and accuracy when acquiring full fragment mode, providing a high assurance of correct identification of unknown compounds. In this work, UPLC-Q-TOF-MS technology has been applied to the analysis of non-volatile migrants from new active packaging materials. The materials tested were based on polypropylene (PP), ethylene-vinyl alcohol copolymer (EVOH), and poly(ethylene terephthalate) (PET). The active packaging materials studied were one PP film containing a natural antioxidant, and two PP/EVOH films, two PET/EVOH films and one coextruded PP/EVOH/PP film containing natural antimicrobials. The chemical structure of several compounds was unequivocally identified. The analysis revealed the migration of some of the active substances used in the manufacture of active packaging, such as caffeine (0.07 ± 0.01 μg/g), carvacrol (0.31 ± 0.03 μg/g) and citral (0.20 ± 0.01 μg/g). Unintentionally added substances were also found, such as citral reaction compounds, or citral impurities present in the raw materials.

Multiscale analysis of river networks using the R package linbin

USGS Publications Warehouse

Welty, Ethan Z.; Torgersen, Christian E.; Brenkman, Samuel J.; Duda, Jeffrey J.; Armstrong, Jonathan B.

2015-01-01

Analytical tools are needed in riverine science and management to bridge the gap between GIS and statistical packages that were not designed for the directional and dendritic structure of streams. We introduce linbin, an R package developed for the analysis of riverscapes at multiple scales. With this software, riverine data on aquatic habitat and species distribution can be scaled and plotted automatically with respect to their position in the stream network or—in the case of temporal data—their position in time. The linbin package aggregates data into bins of different sizes as specified by the user. We provide case studies illustrating the use of the software for (1) exploring patterns at different scales by aggregating variables at a range of bin sizes, (2) comparing repeat observations by aggregating surveys into bins of common coverage, and (3) tailoring analysis to data with custom bin designs. Furthermore, we demonstrate the utility of linbin for summarizing patterns throughout an entire stream network, and we analyze the diel and seasonal movements of tagged fish past a stationary receiver to illustrate how linbin can be used with temporal data. In short, linbin enables more rapid analysis of complex data sets by fisheries managers and stream ecologists and can reveal underlying spatial and temporal patterns of fish distribution and habitat throughout a riverscape.

Groundwater flow and solute transport modelling from within R: Development of the RMODFLOW and RMT3DMS packages.

NASA Astrophysics Data System (ADS)

Rogiers, Bart

2015-04-01

Since a few years, an increasing number of contributed R packages is becoming available, in the field of hydrology. Hydrological time series analysis packages, lumped conceptual rainfall-runoff models, distributed hydrological models, weather generators, and different calibration and uncertainty estimation methods are all available. Also a few packages are available for solving partial differential equations. Subsurface hydrological modelling is however still seldomly performed in R, or with codes interfaced with R, despite the fact that excellent geostatistical packages, model calibration/inversion options and state-of-the-art visualization libraries are available. Moreover, other popular scientific programming languages like matlab and python have packages for pre- and post-processing files of MODFLOW (Harbaugh 2005) and MT3DMS (Zheng 2010) models. To fill this gap, we present here the development versions of the RMODFLOW and RMT3DMS packages, which allow pre- and post-processing MODFLOW and MT3DMS input and output files from within R. File reading and writing functions are currently available for different packages, and plotting functions are foreseen making use of the ggplot2 package (plotting system based on the grammar of graphics; Wickham 2009). The S3 generic-function object oriented programming style is used for this. An example is provided, making modifications to an existing model, and visualization of the model output. References Harbaugh, A. (2005). MODFLOW-2005: The US Geological Survey Modular Ground-water Model--the Ground-water Flow Process, U.S. Geological Survey Techniques and Methods 6-A16 (p. 253). Wickham, H. (2009). ggplot2: elegant graphics for data analysis. Springer New York, 2009. Zheng, C. (2010). MT3DMS v5.3, a modular three-dimensional multispecies transport model for simulation of advection, dispersion and chemical reactions of contaminants in groundwater systems. Supplemental User's Guide. (p. 56).

MAVTgsa: An R Package for Gene Set (Enrichment) Analysis

DOE PAGES

Chien, Chih-Yi; Chang, Ching-Wei; Tsai, Chen-An; ...

2014-01-01

Gene semore » t analysis methods aim to determine whether an a priori defined set of genes shows statistically significant difference in expression on either categorical or continuous outcomes. Although many methods for gene set analysis have been proposed, a systematic analysis tool for identification of different types of gene set significance modules has not been developed previously. This work presents an R package, called MAVTgsa, which includes three different methods for integrated gene set enrichment analysis. (1) The one-sided OLS (ordinary least squares) test detects coordinated changes of genes in gene set in one direction, either up- or downregulation. (2) The two-sided MANOVA (multivariate analysis variance) detects changes both up- and downregulation for studying two or more experimental conditions. (3) A random forests-based procedure is to identify gene sets that can accurately predict samples from different experimental conditions or are associated with the continuous phenotypes. MAVTgsa computes the P values and FDR (false discovery rate) q -value for all gene sets in the study. Furthermore, MAVTgsa provides several visualization outputs to support and interpret the enrichment results. This package is available online.« less

Warpage of QFN Package in Post Mold Cure Process of integrated circuit packaging

NASA Astrophysics Data System (ADS)

Sriwithoon, Nattha; Ugsornrat, Kessararat; Srisuwitthanon, Warayoot; Thonglor, Panakamon

2017-09-01

This research studied about warpage of QFN package in post mold cure process of integrated circuit (IC) packages using pre-plated (PPF) leadframe. For IC package, epoxy molding compound (EMC) are molded by cross linking of compound stiffness but incomplete crosslinked network and leading the fully cured thermoset by post mold cure (PMC) process. The cure temperature of PMC can change microstructure of EMC in term of stress inside the package and effect to warpage of the package due to coefficient of thermal expansion (CTE) between EMC and leadframe. In experiment, cure temperatures were varied to check the effect of internal stress due to different cure temperature after completed post mold cure for TDFN 2×3 8L. The cure temperature were varied with 180 °C, 170 °C, 160 °C, and 150°C with cure time 4 and 6 hours, respectively. For analysis, the TDFN 2×3 8L packages were analyzed the warpage by thickness gauge and scanning acoustic microscope (SAM) after take the test samples out from the oven cure. The results confirmed that effect of different CTE between EMC and leadframe due to different cure temperature resulting to warpage of the TDFN 2×3 8L packages.

Validation of thermal effects of LED package by using Elmer finite element simulation method

NASA Astrophysics Data System (ADS)

Leng, Lai Siang; Retnasamy, Vithyacharan; Mohamad Shahimin, Mukhzeer; Sauli, Zaliman; Taniselass, Steven; Bin Ab Aziz, Muhamad Hafiz; Vairavan, Rajendaran; Kirtsaeng, Supap

2017-02-01

The overall performance of the Light-emitting diode, LED package is critically affected by the heat attribution. In this study, open source software - Elmer FEM has been utilized to study the thermal analysis of the LED package. In order to perform a complete simulation study, both Salome software and ParaView software were introduced as Pre and Postprocessor. The thermal effect of the LED package was evaluated by this software. The result has been validated with commercially licensed software based on previous work. The percentage difference from both simulation results is less than 5% which is tolerable and comparable.

smwrData—An R package of example hydrologic data, version 1.1.1

USGS Publications Warehouse

Lorenz, David L.

2015-11-06

A collection of 24 datasets, including streamflow, well characteristics, groundwater elevations, and discrete water-quality concentrations, is provided to produce a consistent set of example data to demonstrate typical data manipulations or statistical analysis of hydrologic data. These example data are provided in an R package called smwrData. The data in the package have been collected by the U.S. Geological Survey or published in its reports, for example Helsel and Hirsch (2002). The R package provides a convenient mechanism for distributing the data to users of R within the U.S. Geological Survey and other users in the R community.

Laser Anemometer Measurements of the Three-Dimensional Rotor Flow Field in the NASA Low-Speed Centrifugal Compressor

NASA Technical Reports Server (NTRS)

Hathaway, Michael D.; Chriss, Randall M.; Strazisar, Anthony J.; Wood, Jerry R.

1995-01-01

A laser anemometer system was used to provide detailed surveys of the three-dimensional velocity field within the NASA low-speed centrifugal impeller operating with a vaneless diffuser. Both laser anemometer and aerodynamic performance data were acquired at the design flow rate and at a lower flow rate. Floor path coordinates, detailed blade geometry, and pneumatic probe survey results are presented in tabular form. The laser anemometer data are presented in the form of pitchwise distributions of axial, radial, and relative tangential velocity on blade-to-blade stream surfaces at 5-percent-of-span increments, starting at 95-percent-of-span from the hub. The laser anemometer data are also presented as contour and wire-frame plots of throughflow velocity and vector plots of secondary velocities at all measurement stations through the impeller.

Partitioning of zinc among common ferromagnesian minerals and implications for hydrothermal mobilization

USGS Publications Warehouse

Johnson, C.A.

1994-01-01

In systems where metals are scavenging from crystalline rocks by through-flowing fluids, the important host minerals must be dissolved or must undergo cation-exchange reactions with the fluid. Whereas copper resides in sulfides, zinc resides in magnetic and, to a lesser extent, in biotite, clinopyroxene and olivine. Magnetite is known from petrographic studies to be more resistant to alteration than sulfides. For metals extracted from crystalline rocks, the Cu:Zn mass ratio may thus decrease with progressive alteration. In systems where metals are scavenged from cooling magmas by exsolving fluids, the metals are partitioned among melt, fluid and any crystals that have fractionated. For zinc, crystal fractionation may be an important sink if magnetite or biotite crystallize before fluid saturation. The zinc concentrations of magmatic fluids will thus be reduced. -from Author

Unified functional network and nonlinear time series analysis for complex systems science: The pyunicorn package

NASA Astrophysics Data System (ADS)

Donges, Jonathan; Heitzig, Jobst; Beronov, Boyan; Wiedermann, Marc; Runge, Jakob; Feng, Qing Yi; Tupikina, Liubov; Stolbova, Veronika; Donner, Reik; Marwan, Norbert; Dijkstra, Henk; Kurths, Jürgen

2016-04-01

We introduce the pyunicorn (Pythonic unified complex network and recurrence analysis toolbox) open source software package for applying and combining modern methods of data analysis and modeling from complex network theory and nonlinear time series analysis. pyunicorn is a fully object-oriented and easily parallelizable package written in the language Python. It allows for the construction of functional networks such as climate networks in climatology or functional brain networks in neuroscience representing the structure of statistical interrelationships in large data sets of time series and, subsequently, investigating this structure using advanced methods of complex network theory such as measures and models for spatial networks, networks of interacting networks, node-weighted statistics, or network surrogates. Additionally, pyunicorn provides insights into the nonlinear dynamics of complex systems as recorded in uni- and multivariate time series from a non-traditional perspective by means of recurrence quantification analysis, recurrence networks, visibility graphs, and construction of surrogate time series. The range of possible applications of the library is outlined, drawing on several examples mainly from the field of climatology. pyunicorn is available online at https://github.com/pik-copan/pyunicorn. Reference: J.F. Donges, J. Heitzig, B. Beronov, M. Wiedermann, J. Runge, Q.-Y. Feng, L. Tupikina, V. Stolbova, R.V. Donner, N. Marwan, H.A. Dijkstra, and J. Kurths, Unified functional network and nonlinear time series analysis for complex systems science: The pyunicorn package, Chaos 25, 113101 (2015), DOI: 10.1063/1.4934554, Preprint: arxiv.org:1507.01571 [physics.data-an].

Cost-effectiveness Analysis in R Using a Multi-state Modeling Survival Analysis Framework: A Tutorial.

PubMed

Williams, Claire; Lewsey, James D; Briggs, Andrew H; Mackay, Daniel F

2017-05-01

This tutorial provides a step-by-step guide to performing cost-effectiveness analysis using a multi-state modeling approach. Alongside the tutorial, we provide easy-to-use functions in the statistics package R. We argue that this multi-state modeling approach using a package such as R has advantages over approaches where models are built in a spreadsheet package. In particular, using a syntax-based approach means there is a written record of what was done and the calculations are transparent. Reproducing the analysis is straightforward as the syntax just needs to be run again. The approach can be thought of as an alternative way to build a Markov decision-analytic model, which also has the option to use a state-arrival extended approach. In the state-arrival extended multi-state model, a covariate that represents patients' history is included, allowing the Markov property to be tested. We illustrate the building of multi-state survival models, making predictions from the models and assessing fits. We then proceed to perform a cost-effectiveness analysis, including deterministic and probabilistic sensitivity analyses. Finally, we show how to create 2 common methods of visualizing the results-namely, cost-effectiveness planes and cost-effectiveness acceptability curves. The analysis is implemented entirely within R. It is based on adaptions to functions in the existing R package mstate to accommodate parametric multi-state modeling that facilitates extrapolation of survival curves.

MSUSTAT.

ERIC Educational Resources Information Center

Mauriello, David

1984-01-01

Reviews an interactive statistical analysis package (designed to run on 8- and 16-bit machines that utilize CP/M 80 and MS-DOS operating systems), considering its features and uses, documentation, operation, and performance. The package consists of 40 general purpose statistical procedures derived from the classic textbook "Statistical…

Nuclear criticality safety evaluation of SRS 9971 shipping package

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

Vescovi, P.J.

1993-02-01

This evaluation is requested to revise the criticality evaluation used to generate Chapter 6 (Criticality Evaluation) of the Safety Analysis Report for Packaging (SARP) for shipment Of UO{sub 3} product from the Uranium Solidification Facility (USF) in the SRS 9971 shipping package. The pertinent document requesting this evaluation is included as Attachment I. The results of the evaluation are given in Attachment II which is written as Chapter 6 of a NRC format SARP.

Wavelet analysis to decompose a vibration simulation signal to improve pre-distribution testing of packaging

NASA Astrophysics Data System (ADS)

Griffiths, K. R.; Hicks, B. J.; Keogh, P. S.; Shires, D.

2016-08-01

In general, vehicle vibration is non-stationary and has a non-Gaussian probability distribution; yet existing testing methods for packaging design employ Gaussian distributions to represent vibration induced by road profiles. This frequently results in over-testing and/or over-design of the packaging to meet a specification and correspondingly leads to wasteful packaging and product waste, which represent 15bn per year in the USA and €3bn per year in the EU. The purpose of the paper is to enable a measured non-stationary acceleration signal to be replaced by a constructed signal that includes as far as possible any non-stationary characteristics from the original signal. The constructed signal consists of a concatenation of decomposed shorter duration signals, each having its own kurtosis level. Wavelet analysis is used for the decomposition process into inner and outlier signal components. The constructed signal has a similar PSD to the original signal, without incurring excessive acceleration levels. This allows an improved and more representative simulated input signal to be generated that can be used on the current generation of shaker tables. The wavelet decomposition method is also demonstrated experimentally through two correlation studies. It is shown that significant improvements over current international standards for packaging testing are achievable; hence the potential for more efficient packaging system design is possible.

Assessing contamination of smoked sprats (Sprattus sprattus) with polycyclic aromatic hydrocarbons (PAHs) and changes in its level during storage in various types of packaging.

PubMed

Kuźmicz, Kamila; Ciemniak, Artur

2018-01-02

The analysis of material used in this study demonstrated that the amount of polycyclic aromatic hydrocarbons (PAHs) in smoked sprats varies from the level below the lowest detection limit in muscles up to 9.99 µg kg -1 of benzo[a]pyrene (BaP) in fish skin. Such a high level of PAHs in skin was reported only in one of six batches of sprats, while mean BaP level was at 1.69 µg kg -1 . Regardless such a high BaP level in skin, its concentration in muscles did not exceed the maximum acceptable level. The study objective was to assess to what extent packaging materials adsorb PAH compounds from food. Changes in the PAH levels were monitored in fish during their storage in packages made of various materials. The storage time was from 0 to 168 hours. The obtained results varied considerably, therefore their scatter did not allow to confirm unequivocally the preliminary hypothesis about the reduction of PAHs due to their migration to packaging material. However, analysis of the packaging used in this study demonstrated a significant increase in the level of total 16 PAHs. When high-density polyethylene (HDPE) packaging was analysed, a six-fold increase in the total 16 PAHs was observed comparing to the blank sample.

Association of Time between Surgery and Adjuvant Therapy with Survival in Oral Cavity Cancer.

PubMed

Chen, Michelle M; Harris, Jeremy P; Orosco, Ryan K; Sirjani, Davud; Hara, Wendy; Divi, Vasu

2018-06-01

Objective The National Cancer Center Network recommends starting radiation therapy within 6 weeks after surgery for oral cavity squamous cell carcinoma (OCSCC), but there is limited evidence of the importance of the total time from surgery to completion of radiation therapy (package time). We set out to determine if there was an association between package time and survival in OCSCC and to evaluate the impact of treatment location on outcomes. Study Design Retrospective cohort study. Setting Tertiary academic medical center. Subjects and Methods We reviewed the records of patients with OCSCC who completed postoperative radiation therapy at an academic medical center from 2008 to 2016. The primary endpoints were overall survival and recurrence-free survival. Statistical analysis included χ 2 tests and Cox proportional hazards regressions. Results We identified 132 patients with an average package time of 12.6 weeks. On multivariate analysis, package time >11 weeks was independently associated with decreased overall survival (hazard ratio, 6.68; 95% CI, 1.42-31.44) and recurrence-free survival (hazard ratio, 2.94; 95% CI, 1.20-7.18). Patients who received radiation therapy at outside facilities were more likely to have treatment delays (90.2% vs 62.9%, P = .001). Conclusions Prolonged package times are associated with decreased overall and recurrence-free survival among patients with OCSCC. Patients who received radiation therapy at outside facilities are more likely to have prolonged package times.

ReadqPCR and NormqPCR: R packages for the reading, quality checking and normalisation of RT-qPCR quantification cycle (Cq) data.

PubMed

Perkins, James R; Dawes, John M; McMahon, Steve B; Bennett, David L H; Orengo, Christine; Kohl, Matthias

2012-07-02

Measuring gene transcription using real-time reverse transcription polymerase chain reaction (RT-qPCR) technology is a mainstay of molecular biology. Technologies now exist to measure the abundance of many transcripts in parallel. The selection of the optimal reference gene for the normalisation of this data is a recurring problem, and several algorithms have been developed in order to solve it. So far nothing in R exists to unite these methods, together with other functions to read in and normalise the data using the chosen reference gene(s). We have developed two R/Bioconductor packages, ReadqPCR and NormqPCR, intended for a user with some experience with high-throughput data analysis using R, who wishes to use R to analyse RT-qPCR data. We illustrate their potential use in a workflow analysing a generic RT-qPCR experiment, and apply this to a real dataset. Packages are available from http://www.bioconductor.org/packages/release/bioc/html/ReadqPCR.htmland http://www.bioconductor.org/packages/release/bioc/html/NormqPCR.html These packages increase the repetoire of RT-qPCR analysis tools available to the R user and allow them to (amongst other things) read their data into R, hold it in an ExpressionSet compatible R object, choose appropriate reference genes, normalise the data and look for differential expression between samples.

Packaging Technology for Dielectric-Coating-Less Heavy Ion Radiation Testing of High-Voltage (HV) Electronic Parts

NASA Technical Reports Server (NTRS)

Woodworth, Andrew; Chen, Liangyu

2017-01-01

Testing high voltage (HV) electronic parts (greater than 300 V) for sudden event effects (SEE) caused by cosmic rays in the space environment, consisting of energetic heavy-ions, and neutron radiation in the upper atmosphere is a crucial step towards using these parts in spacecraft and aircraft. Due to the nature of cosmic radiation and neutrons, electronic parts are tested for SEE without any packaging and/or shielding over the top of the device. In the case of commercial HV parts, the top of the packaging is etched off and then a thin dielectric coating is placed over the part in order to avoid electrical arcing between the device surface and wire bonds and other components. Even though the effects of the thin dielectric layer on SEE testing can be accounted for, the dielectric layer significantly hinders post testing failure analysis. Replicating the test capability of state-of-the-art packaging while eliminating the need for post radiation test processing of the die surface (that obscures failure analysis) is the goal. To that end, a new packaging concept for HV parts has been developed that requires no dielectric coating over the part. Testing of prototype packages used with Schottky diodes (rated at 1200V) has shown no electrical arcing during testing and leakage currents during reverse bias testing are within the manufactures specifications.

Antimicrobial, antioxidant and sensory features of eugenol, carvacrol and trans-anethole in active packaging for organic ready-to-eat iceberg lettuce.

PubMed

Wieczyńska, Justyna; Cavoski, Ivana

2018-09-01

In this study, bio-based emitting sachets containing eugenol (EUG), carvacrol (CAR) and trans-anethole (ANT) were inserted into cellulose (CE) and polypropylene (PP) pillow packages of organic ready-to-eat (RTE) iceberg lettuce to investigate their functional features. EUG, CAR and ANT sachets in CE; and CAR in PP packages showed antimicrobial activities against coliforms (Δlog CFU g -1 of -1.38, -0.91, -0.93 and -0.93, respectively). EUG and ANT sachets in both packages reduced discoloration (ΔE of 9.5, 1.8, 9.4 and 5.6, respectively). ANT in both, and EUG only in PP packages induced biosynthesis of caffeoyl derivatives (C a T A , D i C a T A , D i C a Q A ), total phenolics and antioxidant activity (FRAP). Also, ANT and EUG in both packages improved overall freshness and odor. Principal component analysis separated ANT and EUG from CAR in both packages. The Pearson correlation confirmed that overall quality improvements were more pronounced by ANT inside the packages in comparison to EUG and CAR. Copyright © 2018 Elsevier Ltd. All rights reserved.

Integrating environmental management into food safety and food packaging in Malaysia: review of the food regulation 1985

NASA Astrophysics Data System (ADS)

Nordin, N. H.; Hara, H.; Kaida, N.

2017-05-01

Food safety is an important issue that is related to public safety to prevent the toxicity threats of the food. Management through legal approach has been used in Malaysia as one of the predominant approaches to manage the environment. In this regard, the Food Regulation 1985 has been one of the mechanisms of environmental management through legal approach in controlling the safety of packaged food in food packaging industry in Malaysia. The present study aims to analyse and to explain the implementation of the Food Regulation 1985 in controlling the safety of packaged food in Malaysia and to integrate the concept of environmental management into the food safety issue. Qualitative analysis on the regulation document revealed that there are two main themes, general and specific, while their seven sub themes are included harmful packages, safety packages, reuse packages, polyvinyl chloride (PVC), alcoholic bottle, toys, money and others and iron powder. The implementation of the Food Regulation 1985 in controlling the safety of packaged food should not be regarded solely for regulation purposes but should be further developed for a broader sense of food safety from overcoming the food poisoning.

2011 drug packaging review: too many dangers and too many patients overlooked.

PubMed

2012-05-01

Every year, Prescrire's analysis of drug packaging confirms the importance of taking packaging into account in assessing a drug's harm-benefit balance. Safe, tried and true options are available, yet the quality of most of the drug packaging Prescrire examined in 2011 left much to be desired. Few of the packaging items examined help prevent medication errors and many actually increase the risks: misleading and confusing labelling, dosing devices that create a risk of overdose, bottles without a child-proof cap, and inadequate or dangerous patient information leaflets. Umbrella brands continue to expand and are a potential source of medication errors. Some patients are at greater risk: the patient leaflets for NSAIDs endanger pregnant women and their unborn babies; children are insufficiently protected by paediatric packaging and are at risk due to the lack of child-proof caps on too many bottles. The raft of regulatory measures taken by the French drug regulatory agency (Afssaps) in the aftermath of the Mediator disaster overlooked the importance of packaging. Until drug regulatory agencies tackle the vast issue of drug packaging, it is up to healthcare professionals to protect patients from harm.

MC-GenomeKey: a multicloud system for the detection and annotation of genomic variants.

PubMed

Elshazly, Hatem; Souilmi, Yassine; Tonellato, Peter J; Wall, Dennis P; Abouelhoda, Mohamed

2017-01-20

Next Generation Genome sequencing techniques became affordable for massive sequencing efforts devoted to clinical characterization of human diseases. However, the cost of providing cloud-based data analysis of the mounting datasets remains a concerning bottleneck for providing cost-effective clinical services. To address this computational problem, it is important to optimize the variant analysis workflow and the used analysis tools to reduce the overall computational processing time, and concomitantly reduce the processing cost. Furthermore, it is important to capitalize on the use of the recent development in the cloud computing market, which have witnessed more providers competing in terms of products and prices. In this paper, we present a new package called MC-GenomeKey (Multi-Cloud GenomeKey) that efficiently executes the variant analysis workflow for detecting and annotating mutations using cloud resources from different commercial cloud providers. Our package supports Amazon, Google, and Azure clouds, as well as, any other cloud platform based on OpenStack. Our package allows different scenarios of execution with different levels of sophistication, up to the one where a workflow can be executed using a cluster whose nodes come from different clouds. MC-GenomeKey also supports scenarios to exploit the spot instance model of Amazon in combination with the use of other cloud platforms to provide significant cost reduction. To the best of our knowledge, this is the first solution that optimizes the execution of the workflow using computational resources from different cloud providers. MC-GenomeKey provides an efficient multicloud based solution to detect and annotate mutations. The package can run in different commercial cloud platforms, which enables the user to seize the best offers. The package also provides a reliable means to make use of the low-cost spot instance model of Amazon, as it provides an efficient solution to the sudden termination of spot machines as a result of a sudden price increase. The package has a web-interface and it is available for free for academic use.

Specifying a State Guaranteed Health Benefits package for Kazakhstan: lessons for emerging economies and middle-income countries.

PubMed

Jones, Michael; Chanturidze, Tata; Franzen, Sam; Manu, Alex; Naylor, Mike

2017-10-01

The Government of Kazakhstan is engaged in a "root and branch" modernisation of the health care sector. One aspect of the raft of modernisation programmes was to revisit the State Guaranteed Health Benefits Package, with the aim to review citizen entitlements to healthcare. This paper reviews the ongoing evolution of the planning of the health benefits package in Kazakhstan, with the main challenges encountered, and critical lessons learned, to be considered for similar attempts elsewhere. The main conclusions are that: the design process requires a blend of technical and socio-political analysis, because it attracts public interest, and therefore political risks; the scale and burden of analysis need to be kept to manageable proportions; and the relationship between the benefits package and funding modalities needs to be carefully managed by the State, to ensure access to declared entitlements to all members, including the most vulnerable, while keeping the package financially feasible. © 2017 The Authors. International Journal of Health Planning and Management published by John Wiley & Sons, Ltd. © 2017 The Authors. International Journal of Health Planning and Management published by John Wiley & Sons, Ltd.

SimHap GUI: an intuitive graphical user interface for genetic association analysis.

PubMed

Carter, Kim W; McCaskie, Pamela A; Palmer, Lyle J

2008-12-25

Researchers wishing to conduct genetic association analysis involving single nucleotide polymorphisms (SNPs) or haplotypes are often confronted with the lack of user-friendly graphical analysis tools, requiring sophisticated statistical and informatics expertise to perform relatively straightforward tasks. Tools, such as the SimHap package for the R statistics language, provide the necessary statistical operations to conduct sophisticated genetic analysis, but lacks a graphical user interface that allows anyone but a professional statistician to effectively utilise the tool. We have developed SimHap GUI, a cross-platform integrated graphical analysis tool for conducting epidemiological, single SNP and haplotype-based association analysis. SimHap GUI features a novel workflow interface that guides the user through each logical step of the analysis process, making it accessible to both novice and advanced users. This tool provides a seamless interface to the SimHap R package, while providing enhanced functionality such as sophisticated data checking, automated data conversion, and real-time estimations of haplotype simulation progress. SimHap GUI provides a novel, easy-to-use, cross-platform solution for conducting a range of genetic and non-genetic association analyses. This provides a free alternative to commercial statistics packages that is specifically designed for genetic association analysis.

DOE-EM-45 PACKAGING OPERATIONS AND MAINTENANCE COURSE

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

Watkins, R.; England, J.

2010-05-28

Savannah River National Laboratory - Savannah River Packaging Technology (SRNL-SRPT) delivered the inaugural offering of the Packaging Operations and Maintenance Course for DOE-EM-45's Packaging Certification Program (PCP) at the University of South Carolina Aiken on September 1 and 2, 2009. Twenty-nine students registered, attended, and completed this training. The DOE-EM-45 Packaging Certification Program (PCP) sponsored the presentation of a new training course, Packaging Maintenance and Operations, on September 1-2, 2009 at the University of South Carolina Aiken (USC-Aiken) campus in Aiken, SC. The premier offering of the course was developed and presented by the Savannah River National Laboratory, and attendedmore » by twenty-nine students across the DOE, NNSA and private industry. This training informed package users of the requirements associated with handling shipping containers at a facility (user) level and provided a basic overview of the requirements typically outlined in Safety Analysis Report for Packaging (SARP) Chapters 1, 7, and 8. The course taught packaging personnel about the regulatory nature of SARPs to help reduce associated and often costly packaging errors. Some of the topics covered were package contents, loading, unloading, storage, torque requirements, maintaining records, how to handle abnormal conditions, lessons learned, leakage testing (including demonstration), and replacement parts. The target audience for this course was facility operations personnel, facility maintenance personnel, and field quality assurance personnel who are directly involved in the handling of shipping containers. The training also aimed at writers of SARP Chapters 1, 7, and 8, package designers, and anyone else involved in radioactive material packaging and transportation safety. Student feedback and critiques of the training were very positive. SRNL will offer the course again at USC Aiken in September 2010.« less

Prevalence of Campylobacter, Salmonella, and Escherichia coli on the external packaging of raw meat.

PubMed

Burgess, F; Little, C L; Allen, G; Williamson, K; Mitchelli, R T

2005-03-01

During September and October 2002, 3,662 prepackaged raw meat samples were collected to evaluate the extent and nature of microbiological contamination on external surfaces of the packaging, which could potentially cross-contaminate ready-to-eat foods during and after purchase. Salmonella was detected on two (<1%) samples of external packaging (both from raw chicken), and Campylobacter was detected on 41 (1.1%) samples of external packaging. The external packaging of game fowl exhibited the highest Campylobacter contamination (3.6%), followed by raw chicken (3.0%), lamb (1.6%), turkey (0.8%), pork (0.2%), and beef (0.1%); Campylobacter jejuni and Campylobacter coli accounted for 59% (24 of 41) and 24% (10 of 41) of the contaminating Campylobacter species, respectively. C. coli isolates from the external packaging were more multiresistant to antimicrobial drugs, including quinolones such as ciprofloxacin, than was C. jejuni. Escherichia coli (an indicator of fecal contamination) was isolated from the external packaging on 4% of the raw meat samples at levels of 40 to 10(5) CFU per swab. The external packaging of raw meats is a vehicle for potential cross-contamination by Campylobacter, Salmonella, and E. coli in retail premises and consumers' homes. The external surface of heat-sealed packaging was less frequently contaminated with Campylobacter and E. coli compared with other types of packaging (e.g., overwrapping, bag, and tie tape) (P < 0.0001 to 0.01). In addition, external packaging of raw meats was contaminated less frequently with Campylobacter and E. coli when packaging was intact, packaging and display areas were visually clean, display temperatures were below 8 degrees C, and hazard analysis systems were in place.

Diagnostic packages can be assigned accurately in emergency departments. A multi-centre cohort study.

PubMed

Nørgaard, Birgitte; Mogensen, Christian Backer; Teglbjærg, Lars Stubbe; Brabrand, Mikkel; Lassen, Annmarie Touborg

2016-06-01

In the Region of Southern Denmark, the emergency departments categorise patients based on presenting symptoms and a proposed diagnostic package (n = 40) within each category. The diagnostic packages describe relevant clinical information and standard laboratory and other investigations to be performed. Allocation to the right diagnostic package is assumed to be associated with a higher quality. The aim of this study was to describe to which degree the assigned symptom-based diagnostic packages are related to relevant discharge diagnoses. This was a descriptive cohort study. The analysis was based on data on assigned diagnostic package, patient discharge diagnosis, hospital, gender, age, time of admission and discharge, length of stay, diagnostic package assigned, discharge diagnosis and co-morbidity. An acceptable standard for what would be an appropriate primarily diagnostic package was developed using a modified Delphi method. A total of 16,543 patient contacts were identified. Women constituted 52.2% (n = 8,925) of the patients. The median age was 64 years and the median length of stay was one day. All diagnostic packages were represented. A total of 68% of the included patients had been assigned an acceptable diagnostic package (95% confidence interval: 67.2-68.7). We found an appropriate use of one of 30 diagnostic packages in more than 50% of the cases. We found that 68% of the included patients were assigned an acceptable diagnostic package and that about 80% of all acute pathways were covered by 14 diagnostic packages. The study was funded by Region of Southern Denmark. The study was registered with the Danish Data Protection Agency (No. 2008-58-0035). No further approval was required.

Patient assessment within the context of healthcare delivery packages: A comparative analysis.

PubMed

Rossen, Camilla Blach; Buus, Niels; Stenager, Egon; Stenager, Elsebeth

2016-01-01

Due to an increased focus on productivity and cost-effectiveness, many countries across the world have implemented a variety of tools for standardizing diagnostics and treatment. In Denmark, healthcare delivery packages are increasingly used for assessment of patients. A package is a tool for creating coordination, continuity and efficient pathways; each step is pre-booked, and the package has a well-defined content within a predefined category of diseases. The aim of this study was to investigate how assessment processes took place within the context of healthcare delivery packages. The study used a constructivist Grounded Theory approach. Ethnographic fieldwork was carried out in three specialized units: a mental health unit and two multiple sclerosis clinics in Southern Denmark, which all used assessment packages. Several types of data were sampled through theoretical sampling. Participant observation was conducted for a total of 126h. Formal and informal interviews were conducted with 12 healthcare professionals and 13 patients. Furthermore, audio recordings were made of 9 final consultations between physicians and patients; 193min of recorded consultations all in all. Lastly, the medical records of 13 patients and written information about packages were collected. The comparative, abductive analysis focused on the process of assessment and the work made by all the actors involved. In this paper, we emphasized the work of healthcare professionals. We constructed five interrelated categories: 1. "Standardized assessing", 2. "Flexibility", which has two sub-categories, 2.1. "Diagnostic options" and 2.2. "Time and organization", and, finally, 3. "Resisting the frames". The process of assessment required all participants to perform the predefined work in the specified way at the specified time. Multidisciplinary teamwork was essential for the success of the process. The local organization of the packages influenced the assessment process, most notably the pre-defined scope of relevant diseases targeted by the package. The inflexible frames of the assessment package could cause resistance among clinicians. Moreover, expert knowledge was an important factor for the efficiency of the process. Some types of organizational work processes resulted in many patients being assessed, but without being diagnosed with at package-relevant disease. Limiting the grounds for using specialist knowledge in structured health care delivery may affect specialists' sense of professional autonomy and can result in professionals employing strategies to resist the frames of the packages. Finally, when organizing healthcare delivery packages, it seems important to consider how to make the optimal use of specialist knowledge. Copyright © 2015 Elsevier Ltd. All rights reserved.

Predictive Utility of Marketed Volumetric Software Tools in Subjects at Risk for Alzheimer's: Do Regions Outside the Hippocampus Matter?

PubMed Central

Tanpitukpongse, Teerath P.; Mazurowski, Maciej A.; Ikhena, John; Petrella, Jeffrey R.

2016-01-01

Background and Purpose To assess prognostic efficacy of individual versus combined regional volumetrics in two commercially-available brain volumetric software packages for predicting conversion of patients with mild cognitive impairment to Alzheimer's disease. Materials and Methods Data was obtained through the Alzheimer's Disease Neuroimaging Initiative. 192 subjects (mean age 74.8 years, 39% female) diagnosed with mild cognitive impairment at baseline were studied. All had T1WI MRI sequences at baseline and 3-year clinical follow-up. Analysis was performed with NeuroQuant® and Neuroreader™. Receiver operating characteristic curves assessing the prognostic efficacy of each software package were generated using a univariable approach employing individual regional brain volumes, as well as two multivariable approaches (multiple regression and random forest), combining multiple volumes. Results On univariable analysis of 11 NeuroQuant® and 11 Neuroreader™ regional volumes, hippocampal volume had the highest area under the curve for both software packages (0.69 NeuroQuant®, 0.68 Neuroreader™), and was not significantly different (p > 0.05) between packages. Multivariable analysis did not increase the area under the curve for either package (0.63 logistic regression, 0.60 random forest NeuroQuant®; 0.65 logistic regression, 0.62 random forest Neuroreader™). Conclusion Of the multiple regional volume measures available in FDA-cleared brain volumetric software packages, hippocampal volume remains the best single predictor of conversion of mild cognitive impairment to Alzheimer's disease at 3-year follow-up. Combining volumetrics did not add additional prognostic efficacy. Therefore, future prognostic studies in MCI, combining such tools with demographic and other biomarker measures, are justified in using hippocampal volume as the only volumetric biomarker. PMID:28057634

Review and analysis of dense linear system solver package for distributed memory machines

NASA Technical Reports Server (NTRS)

Narang, H. N.

1993-01-01

A dense linear system solver package recently developed at the University of Texas at Austin for distributed memory machine (e.g. Intel Paragon) has been reviewed and analyzed. The package contains about 45 software routines, some written in FORTRAN, and some in C-language, and forms the basis for parallel/distributed solutions of systems of linear equations encountered in many problems of scientific and engineering nature. The package, being studied by the Computer Applications Branch of the Analysis and Computation Division, may provide a significant computational resource for NASA scientists and engineers in parallel/distributed computing. Since the package is new and not well tested or documented, many of its underlying concepts and implementations were unclear; our task was to review, analyze, and critique the package as a step in the process that will enable scientists and engineers to apply it to the solution of their problems. All routines in the package were reviewed and analyzed. Underlying theory or concepts which exist in the form of published papers or technical reports, or memos, were either obtained from the author, or from the scientific literature; and general algorithms, explanations, examples, and critiques have been provided to explain the workings of these programs. Wherever the things were still unclear, communications were made with the developer (author), either by telephone or by electronic mail, to understand the workings of the routines. Whenever possible, tests were made to verify the concepts and logic employed in their implementations. A detailed report is being separately documented to explain the workings of these routines.

Larger and More Prominent Graphic Health Warnings on Plain-Packaged Tobacco Products and Avoidant Responses in Current Smokers: a Qualitative Study.

PubMed

Hardcastle, Sarah J; Chan, Derwin C K; Caudwell, Kim M; Sultan, Sarwat; Cranwell, Jo; Chatzisarantis, Nikos L D; Hagger, Martin S

2016-02-01

The introduction of tobacco plain packaging legislation in Australia meant that all tobacco products were to be sold in plain dark-brown packaging with 75% front-of-pack graphic health warnings and standardised font type and size for brand name and product variant. The change in the size and prominence of the warnings has been proposed as a reason for behaviour change in smokers in terms of increased intentions to quit and quit attempts. The current research examined attitudes and beliefs of cigarette smokers toward the increased size and prominence of the warnings and effects on their behaviour. Participants (N = 160) completed open-ended responses to questions on beliefs, attitudes and responses to plain packaging. Responses were subjected to inductive thematic content analysis for key themes. Four themes emerged from the analysis: emotional response to packaging, scepticism of health warnings, warnings and cessation behaviour, and avoidant coping behaviours. Participants reported increased negative emotional responses to the packaging and made specific reference to the graphic health warnings. Some participants attempted to discredit the messages. Others reported increased intentions to quit or quitting attempts. There were pervasive reports of avoidant responses including covering or hiding the warnings. Consistent with theories of illness perceptions and coping, current findings indicate that the larger, prominent graphic health warnings on plain-packaged tobacco products had pervasive effects on threat perceptions and subsequent behavioural responses. While some of the reported responses were adaptive (e.g. attempts to quit), others were maladaptive (e.g. avoiding the warnings).

Optimal packaging of FIV genomic RNA depends upon a conserved long-range interaction and a palindromic sequence within gag.

PubMed

Rizvi, Tahir A; Kenyon, Julia C; Ali, Jahabar; Aktar, Suriya J; Phillip, Pretty S; Ghazawi, Akela; Mustafa, Farah; Lever, Andrew M L

2010-10-15

The feline immunodeficiency virus (FIV) is a lentivirus that is related to human immunodeficiency virus (HIV), causing a similar pathology in cats. It is a potential small animal model for AIDS and the FIV-based vectors are also being pursued for human gene therapy. Previous studies have mapped the FIV packaging signal (ψ) to two or more discontinuous regions within the 5' 511 nt of the genomic RNA and structural analyses have determined its secondary structure. The 5' and 3' sequences within ψ region interact through extensive long-range interactions (LRIs), including a conserved heptanucleotide interaction between R/U5 and gag. Other secondary structural elements identified include a conserved 150 nt stem-loop (SL2) and a small palindromic stem-loop within gag open reading frame that might act as a viral dimerization initiation site. We have performed extensive mutational analysis of these sequences and structures and ascertained their importance in FIV packaging using a trans-complementation assay. Disrupting the conserved heptanucleotide LRI to prevent base pairing between R/U5 and gag reduced packaging by 2.8-5.5 fold. Restoration of pairing using an alternative, non-wild type (wt) LRI sequence restored RNA packaging and propagation to wt levels, suggesting that it is the structure of the LRI, rather than its sequence, that is important for FIV packaging. Disrupting the palindrome within gag reduced packaging by 1.5-3-fold, but substitution with a different palindromic sequence did not restore packaging completely, suggesting that the sequence of this region as well as its palindromic nature is important. Mutation of individual regions of SL2 did not have a pronounced effect on FIV packaging, suggesting that either it is the structure of SL2 as a whole that is necessary for optimal packaging, or that there is redundancy within this structure. The mutational analysis presented here has further validated the previously predicted RNA secondary structure of FIV ψ. Copyright © 2010 Elsevier Ltd. All rights reserved.

Flat-plate solar collector - installation package

NASA Technical Reports Server (NTRS)

1978-01-01

Package includes installation, operation and maintenance manual for collector, analysis of safety hazards, special handling instructions, materials list, installation drawings, and warranty and certification statement. Manual includes instructions for roof preparation and for preparing collector for installation. Several pages are devoted to major and minor repairs.

Rcupcake: an R package for querying and analyzing biomedical data through the BD2K PIC-SURE RESTful API.

PubMed

Gutiérrez-Sacristán, Alba; Guedj, Romain; Korodi, Gabor; Stedman, Jason; Furlong, Laura I; Patel, Chirag J; Kohane, Isaac S; Avillach, Paul

2018-04-15

In the era of big data and precision medicine, the number of databases containing clinical, environmental, self-reported and biochemical variables is increasing exponentially. Enabling the experts to focus on their research questions rather than on computational data management, access and analysis is one of the most significant challenges nowadays. We present Rcupcake, an R package that contains a variety of functions for leveraging different databases through the BD2K PIC-SURE RESTful API and facilitating its query, analysis and interpretation. The package offers a variety of analysis and visualization tools, including the study of the phenotype co-occurrence and prevalence, according to multiple layers of data, such as phenome, exposome or genome. The package is implemented in R and is available under Mozilla v2 license from GitHub (https://github.com/hms-dbmi/Rcupcake). Two reproducible case studies are also available (https://github.com/hms-dbmi/Rcupcake-case-studies/blob/master/SSCcaseStudy_v01.ipynb, https://github.com/hms-dbmi/Rcupcake-case-studies/blob/master/NHANEScaseStudy_v01.ipynb). paul_avillach@hms.harvard.edu. Supplementary data are available at Bioinformatics online.

Quantiprot - a Python package for quantitative analysis of protein sequences.

PubMed

Konopka, Bogumił M; Marciniak, Marta; Dyrka, Witold

2017-07-17

The field of protein sequence analysis is dominated by tools rooted in substitution matrices and alignments. A complementary approach is provided by methods of quantitative characterization. A major advantage of the approach is that quantitative properties defines a multidimensional solution space, where sequences can be related to each other and differences can be meaningfully interpreted. Quantiprot is a software package in Python, which provides a simple and consistent interface to multiple methods for quantitative characterization of protein sequences. The package can be used to calculate dozens of characteristics directly from sequences or using physico-chemical properties of amino acids. Besides basic measures, Quantiprot performs quantitative analysis of recurrence and determinism in the sequence, calculates distribution of n-grams and computes the Zipf's law coefficient. We propose three main fields of application of the Quantiprot package. First, quantitative characteristics can be used in alignment-free similarity searches, and in clustering of large and/or divergent sequence sets. Second, a feature space defined by quantitative properties can be used in comparative studies of protein families and organisms. Third, the feature space can be used for evaluating generative models, where large number of sequences generated by the model can be compared to actually observed sequences.

New generation of exploration tools: interactive modeling software and microcomputers

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

Krajewski, S.A.

1986-08-01

Software packages offering interactive modeling techniques are now available for use on microcomputer hardware systems. These packages are reasonably priced for both company and independent explorationists; they do not require users to have high levels of computer literacy; they are capable of rapidly completing complex ranges of sophisticated geologic and geophysical modeling tasks; and they can produce presentation-quality output for comparison with real-world data. For example, interactive packages are available for mapping, log analysis, seismic modeling, reservoir studies, and financial projects as well as for applying a variety of statistical and geostatistical techniques to analysis of exploration data. More importantly,more » these packages enable explorationists to directly apply their geologic expertise when developing and fine-tuning models for identifying new prospects and for extending producing fields. As a result of these features, microcomputers and interactive modeling software are becoming common tools in many exploration offices. Gravity and magnetics software programs illustrate some of the capabilities of such exploration tools.« less

Promoter classifier: software package for promoter database analysis.

PubMed

Gershenzon, Naum I; Ioshikhes, Ilya P

2005-01-01

Promoter Classifier is a package of seven stand-alone Windows-based C++ programs allowing the following basic manipulations with a set of promoter sequences: (i) calculation of positional distributions of nucleotides averaged over all promoters of the dataset; (ii) calculation of the averaged occurrence frequencies of the transcription factor binding sites and their combinations; (iii) division of the dataset into subsets of sequences containing or lacking certain promoter elements or combinations; (iv) extraction of the promoter subsets containing or lacking CpG islands around the transcription start site; and (v) calculation of spatial distributions of the promoter DNA stacking energy and bending stiffness. All programs have a user-friendly interface and provide the results in a convenient graphical form. The Promoter Classifier package is an effective tool for various basic manipulations with eukaryotic promoter sequences that usually are necessary for analysis of large promoter datasets. The program Promoter Divider is described in more detail as a representative component of the package.

Influence of some packaging materials and of natural tocopherols on the sensory properties of breakfast cereals.

PubMed

Paradiso, Vito M; Caponio, Francesco; Summo, Carmine; Gomes, Tommaso

2014-04-01

The combined effect of natural antioxidants and packaging materials on the quality decay of breakfast cereals during storage was evaluated. Corn flakes were produced on industrial scale, using different packages and adding natural tocopherols to the ingredients, and stored for 1 year. The samples were then submitted to sensory analysis and HS-solid phase microextraction/gas chromatography/mass spectrometry (SPME/GC/MS) analysis. The packaging had a significant influence on the sensory profile of the aged product: metallized polypropylene gave the highest levels of oxidation compounds and sensory defects. The sensory profile was improved using polypropylene and especially high-density polyethylene. Natural tocopherols reduced the sensory decay of the flakes and the oxidative evolution of the volatile profile. They gave the most remarkable improvement in polypropylene (either metallized or not) packs. Polypropylene showed a barrier effect on the scalping of volatiles outside of the pack. This led to higher levels of oxidation volatiles and faster rates of the further oxidative processes involving the volatiles.

DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq experiments.

PubMed

Vrahatis, Aristidis G; Balomenos, Panos; Tsakalidis, Athanasios K; Bezerianos, Anastasios

2016-12-15

DEsubs is a network-based systems biology R package that extracts disease-perturbed subpathways within a pathway network as recorded by RNA-seq experiments. It contains an extensive and customized framework with a broad range of operation modes at all stages of the subpathway analysis, enabling so a case-specific approach. The operation modes include pathway network construction and processing, subpathway extraction, visualization and enrichment analysis with regard to various biological and pharmacological features. Its capabilities render DEsubs a tool-guide for both the modeler and experimentalist for the identification of more robust systems-level drug targets and biomarkers for complex diseases. DEsubs is implemented as an R package following Bioconductor guidelines: http://bioconductor.org/packages/DEsubs/ CONTACT: tassos.bezerianos@nus.edu.sgSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Scripting MODFLOW model development using Python and FloPy

USGS Publications Warehouse

Bakker, Mark; Post, Vincent E. A.; Langevin, Christian D.; Hughes, Joseph D.; White, Jeremy; Starn, Jeffrey; Fienen, Michael N.

2016-01-01

Graphical user interfaces (GUIs) are commonly used to construct and postprocess numerical groundwater flow and transport models. Scripting model development with the programming language Python is presented here as an alternative approach. One advantage of Python is that there are many packages available to facilitate the model development process, including packages for plotting, array manipulation, optimization, and data analysis. For MODFLOW-based models, the FloPy package was developed by the authors to construct model input files, run the model, and read and plot simulation results. Use of Python with the available scientific packages and FloPy facilitates data exploration, alternative model evaluations, and model analyses that can be difficult to perform with GUIs. Furthermore, Python scripts are a complete, transparent, and repeatable record of the modeling process. The approach is introduced with a simple FloPy example to create and postprocess a MODFLOW model. A more complicated capture-fraction analysis with a real-world model is presented to demonstrate the types of analyses that can be performed using Python and FloPy.

Interactive graphical system for small-angle scattering analysis of polydisperse systems

NASA Astrophysics Data System (ADS)

Konarev, P. V.; Volkov, V. V.; Svergun, D. I.

2016-09-01

A program suite for one-dimensional small-angle scattering analysis of polydisperse systems and multiple data sets is presented. The main program, POLYSAS, has a menu-driven graphical user interface calling computational modules from ATSAS package to perform data treatment and analysis. The graphical menu interface allows one to process multiple (time, concentration or temperature-dependent) data sets and interactively change the parameters for the data modelling using sliders. The graphical representation of the data is done via the Winteracter-based program SASPLOT. The package is designed for the analysis of polydisperse systems and mixtures, and permits one to obtain size distributions and evaluate the volume fractions of the components using linear and non-linear fitting algorithms as well as model-independent singular value decomposition. The use of the POLYSAS package is illustrated by the recent examples of its application to study concentration-dependent oligomeric states of proteins and time kinetics of polymer micelles for anticancer drug delivery.

Power Analysis of an Automated Dynamic Cone Penetrometer

DTIC Science & Technology

2015-09-01

temperature and b) as a function of load current at 21 °C ..3 Fig. 4 K33 stepper motor candidate in the standard NEMA 34 package .........5 Fig. 5 Analytical...will be assessed. Fig. 4 K33 stepper motor candidate in the standard NEMA 34 package 3. Analyses Analysis of the mechanical system begins with the...DCP dynamic cone penetrometer EMF electromotive force NEMA National Electrical Manufacturers Association 20 1 DEFENSE TECH INFO CTR

Safety analysis report for packaging, onsite, long-length contaminated equipment transport system

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

McCormick, W.A.

1997-05-09

This safety analysis report for packaging describes the components of the long-length contaminated equipment (LLCE) transport system (TS) and provides the analyses, evaluations, and associated operational controls necessary for the safe use of the LLCE TS on the Hanford Site. The LLCE TS will provide a standardized, comprehensive approach for the disposal of approximately 98% of LLCE scheduled to be removed from the 200 Area waste tanks.

Software Package Completed for Alloy Design at the Atomic Level

NASA Technical Reports Server (NTRS)

Bozzolo, Guillermo H.; Noebe, Ronald D.; Abel, Phillip B.; Good, Brian S.

2001-01-01

As a result of a multidisciplinary effort involving solid-state physics, quantum mechanics, and materials and surface science, the first version of a software package dedicated to the atomistic analysis of multicomponent systems was recently completed. Based on the BFS (Bozzolo, Ferrante, and Smith) method for the calculation of alloy and surface energetics, this package includes modules devoted to the analysis of many essential features that characterize any given alloy or surface system, including (1) surface structure analysis, (2) surface segregation, (3) surface alloying, (4) bulk crystalline material properties and atomic defect structures, and (5) thermal processes that allow us to perform phase diagram calculations. All the modules of this Alloy Design Workbench 1.0 (ADW 1.0) are designed to run in PC and workstation environments, and their operation and performance are substantially linked to the needs of the user and the specific application.

EXP-PAC: providing comparative analysis and storage of next generation gene expression data.

PubMed

Church, Philip C; Goscinski, Andrzej; Lefèvre, Christophe

2012-07-01

Microarrays and more recently RNA sequencing has led to an increase in available gene expression data. How to manage and store this data is becoming a key issue. In response we have developed EXP-PAC, a web based software package for storage, management and analysis of gene expression and sequence data. Unique to this package is SQL based querying of gene expression data sets, distributed normalization of raw gene expression data and analysis of gene expression data across experiments and species. This package has been populated with lactation data in the international milk genomic consortium web portal (http://milkgenomics.org/). Source code is also available which can be hosted on a Windows, Linux or Mac APACHE server connected to a private or public network (http://mamsap.it.deakin.edu.au/~pcc/Release/EXP_PAC.html). Copyright © 2012 Elsevier Inc. All rights reserved.

PLACE: an open-source python package for laboratory automation, control, and experimentation.

PubMed

Johnson, Jami L; Tom Wörden, Henrik; van Wijk, Kasper

2015-02-01

In modern laboratories, software can drive the full experimental process from data acquisition to storage, processing, and analysis. The automation of laboratory data acquisition is an important consideration for every laboratory. When implementing a laboratory automation scheme, important parameters include its reliability, time to implement, adaptability, and compatibility with software used at other stages of experimentation. In this article, we present an open-source, flexible, and extensible Python package for Laboratory Automation, Control, and Experimentation (PLACE). The package uses modular organization and clear design principles; therefore, it can be easily customized or expanded to meet the needs of diverse laboratories. We discuss the organization of PLACE, data-handling considerations, and then present an example using PLACE for laser-ultrasound experiments. Finally, we demonstrate the seamless transition to post-processing and analysis with Python through the development of an analysis module for data produced by PLACE automation. © 2014 Society for Laboratory Automation and Screening.

MPTinR: analysis of multinomial processing tree models in R.

PubMed

Singmann, Henrik; Kellen, David

2013-06-01

We introduce MPTinR, a software package developed for the analysis of multinomial processing tree (MPT) models. MPT models represent a prominent class of cognitive measurement models for categorical data with applications in a wide variety of fields. MPTinR is the first software for the analysis of MPT models in the statistical programming language R, providing a modeling framework that is more flexible than standalone software packages. MPTinR also introduces important features such as (1) the ability to calculate the Fisher information approximation measure of model complexity for MPT models, (2) the ability to fit models for categorical data outside the MPT model class, such as signal detection models, (3) a function for model selection across a set of nested and nonnested candidate models (using several model selection indices), and (4) multicore fitting. MPTinR is available from the Comprehensive R Archive Network at http://cran.r-project.org/web/packages/MPTinR/ .

Power Extension Package (PEP) system definition extension, orbital service module systems analysis study. Volume 3: PEP analysis and tradeoffs

NASA Technical Reports Server (NTRS)

1979-01-01

The objectives, conclusions, and approaches for accomplishing 19 specific design and analysis activities related to the installation of the power extension package (PEP) into the Orbiter cargo bay are described as well as those related to its deployment, extension, and retraction. The proposed cable handling system designed to transmit power from PEP to the Orbiter by way of the shuttle remote manipulator system is described and a preliminary specification for the gimbal assembly, solar array drive is included.

Probabilistic Design and Analysis Framework

NASA Technical Reports Server (NTRS)

Strack, William C.; Nagpal, Vinod K.

2010-01-01

PRODAF is a software package designed to aid analysts and designers in conducting probabilistic analysis of components and systems. PRODAF can integrate multiple analysis programs to ease the tedious process of conducting a complex analysis process that requires the use of multiple software packages. The work uses a commercial finite element analysis (FEA) program with modules from NESSUS to conduct a probabilistic analysis of a hypothetical turbine blade, disk, and shaft model. PRODAF applies the response surface method, at the component level, and extrapolates the component-level responses to the system level. Hypothetical components of a gas turbine engine are first deterministically modeled using FEA. Variations in selected geometrical dimensions and loading conditions are analyzed to determine the effects of the stress state within each component. Geometric variations include the cord length and height for the blade, inner radius, outer radius, and thickness, which are varied for the disk. Probabilistic analysis is carried out using developing software packages like System Uncertainty Analysis (SUA) and PRODAF. PRODAF was used with a commercial deterministic FEA program in conjunction with modules from the probabilistic analysis program, NESTEM, to perturb loads and geometries to provide a reliability and sensitivity analysis. PRODAF simplified the handling of data among the various programs involved, and will work with many commercial and opensource deterministic programs, probabilistic programs, or modules.

Introduction in IND and recursive partitioning

NASA Technical Reports Server (NTRS)

Buntine, Wray; Caruana, Rich

1991-01-01

This manual describes the IND package for learning tree classifiers from data. The package is an integrated C and C shell re-implementation of tree learning routines such as CART, C4, and various MDL and Bayesian variations. The package includes routines for experiment control, interactive operation, and analysis of tree building. The manual introduces the system and its many options, gives a basic review of tree learning, contains a guide to the literature and a glossary, and lists the manual pages for the routines and instructions on installation.

KMgene: a unified R package for gene-based association analysis for complex traits.

PubMed

Yan, Qi; Fang, Zhou; Chen, Wei; Stegle, Oliver

2018-02-09

In this report, we introduce an R package KMgene for performing gene-based association tests for familial, multivariate or longitudinal traits using kernel machine (KM) regression under a generalized linear mixed model (GLMM) framework. Extensive simulations were performed to evaluate the validity of the approaches implemented in KMgene. http://cran.r-project.org/web/packages/KMgene. qi.yan@chp.edu or wei.chen@chp.edu. Supplementary data are available at Bioinformatics online. © The Author(s) 2018. Published by Oxford University Press.

A User-Friendly Software Package for HIFU Simulation

NASA Astrophysics Data System (ADS)

Soneson, Joshua E.

2009-04-01

A freely-distributed, MATLAB (The Mathworks, Inc., Natick, MA)-based software package for simulating axisymmetric high-intensity focused ultrasound (HIFU) beams and their heating effects is discussed. The package (HIFU_Simulator) consists of a propagation module which solves the Khokhlov-Zabolotskaya-Kuznetsov (KZK) equation and a heating module which solves Pennes' bioheat transfer (BHT) equation. The pressure, intensity, heating rate, temperature, and thermal dose fields are computed, plotted, the output is released to the MATLAB workspace for further user analysis or postprocessing.

Control Systems

NASA Technical Reports Server (NTRS)

1984-01-01

Boeing Commercial Airplane Company's Flight Control Department engineers relied on Langley developed software package known as ORACLS to develop an advanced control synthesis package for both continuous and discrete control system. Package was used by Boeing for computerized analysis of new system designs. Resulting applications include a multiple input/output control system for the terrain-following navigation equipment of the Air Forces B-1 Bomber, and another for controlling in flight changes of wing camber on an experimental airplane. ORACLS is one of 1,300 computer programs available from COSMIC.

An Analysis of an R&D Program Selection Process at the Aeronautical Systems Division.

DTIC Science & Technology

1980-09-01

Without the help of the Defense Wide Management and Support panel members, this research effort would have been impossible. They provided valuable personal ...decision packages. Next, the DWMS panel members were interviewed in order to obtain their personal interpretation of the evaluation cri- teria used by...packages (McCandless, 1978:46). The state of Georgia had over 11,000 packages to evaluate, and it would be impossible for one person to evaluate all the

Nuclear criticality safety evaluation of SRS 9971 shipping package. [SRS (Savannah River Site)

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

Vescovi, P.J.

1993-02-01

This evaluation is requested to revise the criticality evaluation used to generate Chapter 6 (Criticality Evaluation) of the Safety Analysis Report for Packaging (SARP) for shipment Of UO[sub 3] product from the Uranium Solidification Facility (USF) in the SRS 9971 shipping package. The pertinent document requesting this evaluation is included as Attachment I. The results of the evaluation are given in Attachment II which is written as Chapter 6 of a NRC format SARP.

The MHOST finite element program: 3-D inelastic analysis methods for hot section components. Volume 2: User's manual

NASA Technical Reports Server (NTRS)

Nakazawa, Shohei

1989-01-01

The user options available for running the MHOST finite element analysis package is described. MHOST is a solid and structural analysis program based on the mixed finite element technology, and is specifically designed for 3-D inelastic analysis. A family of 2- and 3-D continuum elements along with beam and shell structural elements can be utilized, many options are available in the constitutive equation library, the solution algorithms and the analysis capabilities. The outline of solution algorithms is discussed along with the data input and output, analysis options including the user subroutines and the definition of the finite elements implemented in the program package.

The Decoding Toolbox (TDT): a versatile software package for multivariate analyses of functional imaging data

PubMed Central

Hebart, Martin N.; Görgen, Kai; Haynes, John-Dylan

2015-01-01

The multivariate analysis of brain signals has recently sparked a great amount of interest, yet accessible and versatile tools to carry out decoding analyses are scarce. Here we introduce The Decoding Toolbox (TDT) which represents a user-friendly, powerful and flexible package for multivariate analysis of functional brain imaging data. TDT is written in Matlab and equipped with an interface to the widely used brain data analysis package SPM. The toolbox allows running fast whole-brain analyses, region-of-interest analyses and searchlight analyses, using machine learning classifiers, pattern correlation analysis, or representational similarity analysis. It offers automatic creation and visualization of diverse cross-validation schemes, feature scaling, nested parameter selection, a variety of feature selection methods, multiclass capabilities, and pattern reconstruction from classifier weights. While basic users can implement a generic analysis in one line of code, advanced users can extend the toolbox to their needs or exploit the structure to combine it with external high-performance classification toolboxes. The toolbox comes with an example data set which can be used to try out the various analysis methods. Taken together, TDT offers a promising option for researchers who want to employ multivariate analyses of brain activity patterns. PMID:25610393

Type of packaging affects the colour stability of vitamin E enriched beef.

PubMed

Nassu, Renata T; Uttaro, Bethany; Aalhus, Jennifer L; Zawadski, Sophie; Juárez, Manuel; Dugan, Michael E R

2012-12-01

Colour stability is a very important parameter for meat retail display, as appearance of the product is the deciding factor for consumers at time of purchase. This study investigated the possibility of extending appearance shelf-life through the combined use of packaging method (overwrapping - OVER, modified atmosphere - MAP, vacuum skin packaging - VSP and a combination of modified atmosphere and vacuum skin packaging - MAPVSP) and antioxidants (vitamin E enriched beef). Retail attributes (appearance, lean colour, % surface discolouration), as well as colour space analysis of images for red, green and blue parameters were measured over 18days. MAPVSP provided the most desirable retail appearance during the first 4days of retail display, while VSP-HB had the best colour stability. Overall, packaging type was more influential than α-tocopherol levels on meat colour stability, although α-tocopherol levels (>4μgg(-1) meat) had a protective effect when using high oxygen packaging methods. Crown Copyright © 2012. Published by Elsevier Ltd. All rights reserved.

Unified functional network and nonlinear time series analysis for complex systems science: The pyunicorn package

NASA Astrophysics Data System (ADS)

Donges, Jonathan F.; Heitzig, Jobst; Beronov, Boyan; Wiedermann, Marc; Runge, Jakob; Feng, Qing Yi; Tupikina, Liubov; Stolbova, Veronika; Donner, Reik V.; Marwan, Norbert; Dijkstra, Henk A.; Kurths, Jürgen

2015-11-01

We introduce the pyunicorn (Pythonic unified complex network and recurrence analysis toolbox) open source software package for applying and combining modern methods of data analysis and modeling from complex network theory and nonlinear time series analysis. pyunicorn is a fully object-oriented and easily parallelizable package written in the language Python. It allows for the construction of functional networks such as climate networks in climatology or functional brain networks in neuroscience representing the structure of statistical interrelationships in large data sets of time series and, subsequently, investigating this structure using advanced methods of complex network theory such as measures and models for spatial networks, networks of interacting networks, node-weighted statistics, or network surrogates. Additionally, pyunicorn provides insights into the nonlinear dynamics of complex systems as recorded in uni- and multivariate time series from a non-traditional perspective by means of recurrence quantification analysis, recurrence networks, visibility graphs, and construction of surrogate time series. The range of possible applications of the library is outlined, drawing on several examples mainly from the field of climatology.

Melanie II--a third-generation software package for analysis of two-dimensional electrophoresis images: I. Features and user interface.

PubMed

Appel, R D; Palagi, P M; Walther, D; Vargas, J R; Sanchez, J C; Ravier, F; Pasquali, C; Hochstrasser, D F

1997-12-01

Although two-dimensional electrophoresis (2-DE) computer analysis software packages have existed ever since 2-DE technology was developed, it is only now that the hardware and software technology allows large-scale studies to be performed on low-cost personal computers or workstations, and that setting up a 2-DE computer analysis system in a small laboratory is no longer considered a luxury. After a first attempt in the seventies and early eighties to develop 2-DE analysis software systems on hardware that had poor or even no graphical capabilities, followed in the late eighties by a wave of innovative software developments that were possible thanks to new graphical interface standards such as XWindows, a third generation of 2-DE analysis software packages has now come to maturity. It can be run on a variety of low-cost, general-purpose personal computers, thus making the purchase of a 2-DE analysis system easily attainable for even the smallest laboratory that is involved in proteome research. Melanie II 2-D PAGE, developed at the University Hospital of Geneva, is such a third-generation software system for 2-DE analysis. Based on unique image processing algorithms, this user-friendly object-oriented software package runs on multiple platforms, including Unix, MS-Windows 95 and NT, and Power Macintosh. It provides efficient spot detection and quantitation, state-of-the-art image comparison, statistical data analysis facilities, and is Internet-ready. Linked to proteome databases such as those available on the World Wide Web, it represents a valuable tool for the "Virtual Lab" of the post-genome area.

Using R to implement spatial analysis in open source environment

NASA Astrophysics Data System (ADS)

Shao, Yixi; Chen, Dong; Zhao, Bo

2007-06-01

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

ULFEM time series analysis package

USGS Publications Warehouse

Karl, Susan M.; McPhee, Darcy K.; Glen, Jonathan M. G.; Klemperer, Simon L.

2013-01-01

This manual describes how to use the Ultra-Low-Frequency ElectroMagnetic (ULFEM) software package. Casual users can read the quick-start guide and will probably not need any more information than this. For users who may wish to modify the code, we provide further description of the routines.

Death by heroin intoxication in a body pusher with an innovative packaging technique: case report and review of the literature.

PubMed

Visentin, Sindi; Bevilacqua, Greta; Giraudo, Chiara; Dengo, Caterina; Nalesso, Alessandro; Montisci, Massimo

2017-11-01

Death due to mechanical or chemical intoxication of heroin body packers, thanks to the continuous improvement in packaging techniques, are increasingly rare, and almost all the cases reported in the literature refer to drug swallowers. A case of fatal acute heroin intoxication in a body pusher with an unreported packaging technique is presented, and previous deaths due to heroin body packing are reviewed, taking into consideration imaging techniques performed, cause of death, toxicological analysis on biological and non-biological samples, as well as number, position and type of drug packages identified at the dissection of the body. The innovative packaging technique found in the present case, constituted by an external multilayer cellophane casing containing 16 smaller packages of hardened heroin powder, each one covered with cigarette paper and multiple layers of heat-sealed cellophane, was probably used to avoid both chemical complications of package rupture and to create a package with morphological and radiological features different from those reported by previous studies. Drug dealers, in fact, are continually looking for packaging methods that, besides being safer, minimize the risk of detection at the radiological examinations performed, thus increasing the number of false negative findings. The identification of new types of package is therefore important, in order to identify packages that do not have the typical radiological signs, both in order to protect the patient's health and to avoid the non-recognition of a drug carrier. Despite the presence of multilayer composition of both the smaller and the bigger external coverage, these new types of package did not guarantee the greater safety of the drug dealer. Copyright © 2017 Elsevier B.V. All rights reserved.

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

Loftin, B.; Abramczyk, G.; Koenig, R.

Radioactive materials are stored in a variety of locations throughout the DOE complex. At the Savannah River Site (SRS), materials are stored within dedicated facilities. Each of those facilities has a documented safety analysis (DSA) that describes accidents that the facility and the materials within it may encounter. Facilities at the SRS are planning on utilizing the certified Model 9977 Shipping Package as a long term storage package and one of these facilities required ballistics testing. Specifically, in order to meet the facility DSA, the radioactive materials (RAM) must be contained within the storage package after impact by a .223more » caliber round. In order to qualify the Model 9977 Shipping Package for storage in this location, the package had to be tested under these conditions. Over the past two years, the Model 9977 Shipping Package has been subjected to a series of ballistics tests. The purpose of the testing was to determine if the 9977 would be suitable for use as a storage package at a Savannah River Site facility. The facility requirements are that the package must not release any of its contents following the impact in its most vulnerable location by a .223 caliber round. A package, assembled to meet all of the design requirements for a certified 9977 shipping configuration and using simulated contents, was tested at the Savannah River Site in March of 2011. The testing was completed and the package was examined. The results of the testing and examination are presented in this paper.« less

Physics of Failure Analysis of Xilinx Flip Chip CCGA Packages: Effects of Mission Environments on Properties of LP2 Underfill and ATI Lid Adhesive Materials

NASA Technical Reports Server (NTRS)

Suh, Jong-ook

2013-01-01

The Xilinx Virtex 4QV and 5QV (V4 and V5) are next-generation field-programmable gate arrays (FPGAs) for space applications. However, there have been concerns within the space community regarding the non-hermeticity of V4/V5 packages; polymeric materials such as the underfill and lid adhesive will be directly exposed to the space environment. In this study, reliability concerns associated with the non-hermeticity of V4/V5 packages were investigated by studying properties and behavior of the underfill and the lid adhesvie materials used in V4/V5 packages.

Robust hard-solder packaging of conduction cooled laser diode bars

NASA Astrophysics Data System (ADS)

Schleuning, David; Griffin, Mike; James, Phillip; McNulty, John; Mendoza, Dan; Morales, John; Nabors, David; Peters, Mike; Zhou, Hailong; Reed, Murray

2007-02-01

We present the reliability of high-power laser diodes utilizing hard solder (AuSn) on a conduction-cooled package (HCCP). We present results of 50 W hard-pulse operation at 8xx nm and demonstrate a reliability of MTTF > 27 khrs (90% CL), which is an order of magnitude improvement over traditional packaging. We also present results at 9xx nm with a reliability of MTTF >17 khrs (90% CL) at 75 W. We discuss finite element analysis (FEA) modeling and time dependent temperature measurements combined with experimental life-test data to quantify true hard-pulse operation. We also discuss FEA and measured stress profiles across laser bars comparing soft and hard solder packaging.

Modeling, design, packing and experimental analysis of liquid-phase shear-horizontal surface acoustic wave sensors

NASA Astrophysics Data System (ADS)

Pollard, Thomas B

Recent advances in microbiology, computational capabilities, and microelectromechanical-system fabrication techniques permit modeling, design, and fabrication of low-cost, miniature, sensitive and selective liquid-phase sensors and lab-on-a-chip systems. Such devices are expected to replace expensive, time-consuming, and bulky laboratory-based testing equipment. Potential applications for devices include: fluid characterization for material science and industry; chemical analysis in medicine and pharmacology; study of biological processes; food analysis; chemical kinetics analysis; and environmental monitoring. When combined with liquid-phase packaging, sensors based on surface-acoustic-wave (SAW) technology are considered strong candidates. For this reason such devices are focused on in this work; emphasis placed on device modeling and packaging for liquid-phase operation. Regarding modeling, topics considered include mode excitation efficiency of transducers; mode sensitivity based on guiding structure materials/geometries; and use of new piezoelectric materials. On packaging, topics considered include package interfacing with SAW devices, and minimization of packaging effects on device performance. In this work novel numerical models are theoretically developed and implemented to study propagation and transduction characteristics of sensor designs using wave/constitutive equations, Green's functions, and boundary/finite element methods. Using developed simulation tools that consider finite-thickness of all device electrodes, transduction efficiency for SAW transducers with neighboring uniform or periodic guiding electrodes is reported for the first time. Results indicate finite electrode thickness strongly affects efficiency. Using dense electrodes, efficiency is shown to approach 92% and 100% for uniform and periodic electrode guiding, respectively; yielding improved sensor detection limits. A numerical sensitivity analysis is presented targeting viscosity using uniform-electrode and shear-horizontal mode configurations on potassium-niobate, langasite, and quartz substrates. Optimum configurations are determined yielding maximum sensitivity. Results show mode propagation-loss and sensitivity to viscosity are correlated by a factor independent of substrate material. The analysis is useful for designing devices meeting sensitivity and signal level requirements. A novel, rapid and precise microfluidic chamber alignment/bonding method was developed for SAW platforms. The package is shown to have little effect on device performance and permits simple macrofluidic interfacing. Lastly, prototypes were designed, fabricated, and tested for viscosity and biosensor applications; results show ability to detect as low as 1% glycerol in water and surface-bound DNA crosslinking.

Net costs of health worker rural incentive packages: an example from the Lao People's Democratic Republic.

PubMed

Keuffel, Eric; Jaskiewicz, Wanda; Paphassarang, Chanthakhath; Tulenko, Kate

2013-11-01

Many developing countries are examining whether to institute incentive packages that increase the share of health workers who opt to locate in rural settings; however, uncertainty exists with respect to the expected net cost (or benefit) from these packages. We utilize the findings from the discrete choice experiment surveys applied to students training to be health professionals and costing analyses in Lao People's Democratic Republic to model the anticipated effect of incentive packages on new worker location decisions and direct costs. Incorporating evidence on health worker density and health outcomes, we then estimate the expected 5-year net cost (or benefit) of each incentive packages for 3 health worker cadres--physicians, nurses/midwives, and medical assistants. Under base case assumptions, the optimal incentive package for each cadre produced a 5-year net benefit (maximum net benefit for physicians: US$ 44,000; nurses/midwives: US$ 5.6 million; medical assistants: US$ 485,000). After accounting for health effects, the expected net cost of select incentive packages would be substantially less than the original estimate of direct costs. In the case of Lao People's Democratic Republic, incentive packages that do not invest in capital-intensive components generally should produce larger net benefits. Combining discrete choice experiment surveys, costing surveys and cost-benefit analysis methods may be replicated by other developing countries to calculate whether health worker incentive packages are viable policy options.

An Innovative Learning Model for Computation in First Year Mathematics

ERIC Educational Resources Information Center

Tonkes, E. J.; Loch, B. I.; Stace, A. W.

2005-01-01

MATLAB is a sophisticated software tool for numerical analysis and visualization. The University of Queensland has adopted Matlab as its official teaching package across large first year mathematics courses. In the past, the package has met severe resistance from students who have not appreciated their computational experience. Several main…

PyPedal, an open source software package for pedigree analysis

USDA-ARS?s Scientific Manuscript database

The open source software package PyPedal (http://pypedal.sourceforge.net/) was first released in 2002, and provided users with a set of simple tools for manipulating pedigrees. Its flexibility has been demonstrated by its used in a number of settings for large and small populations. After substantia...

Effectiveness of Simulation in a Hybrid and Online Networking Course.

ERIC Educational Resources Information Center

Cameron, Brian H.

2003-01-01

Reports on a study that compares the performance of students enrolled in two sections of a Web-based computer networking course: one utilizing a simulation package and the second utilizing a static, graphical software package. Analysis shows statistically significant improvements in performance in the simulation group compared to the…

Microcomputer Applications in Local Assessment Systems.

ERIC Educational Resources Information Center

Harnisch, Delwyn L.; And Others

The capabilities and hardware requirements of four microcomputer software packages produced by the Office of Educational Testing, Research and Service at the University of Illinois at Urbana-Champaign are described. These programs are: (1) the Scan-Tron Forms Analysis Package Version 2.0, an interface between an IBM-compatible and a Scan-Tron…

COLDMON -- Cold File Analysis Package

NASA Astrophysics Data System (ADS)

Rawlinson, D. J.

The COLDMON package has been written to allow system managers to identify those items of software that are not used (or used infrequently) on their systems. It consists of a few command procedures and a Fortran program to analyze the results. It makes use of the AUDIT facility and security ACLs in VMS.

Scientific Software: How to Find What You Need and Get What You Pay for.

ERIC Educational Resources Information Center

Gabaldon, Diana J.

1984-01-01

Provides examples of software for the sciences, including: packages for pathology/toxicology laboratories (costing over $15,000), DNA sequencing, and data acquisition/analysis; general-purpose software for scientific uses; and "custom" packages, including a program to maintain a listing of "Escherichia coli" strains and a…

16 CFR 700.1 - Products covered.

Code of Federal Regulations, 2010 CFR

2010-01-01

... the purchase transaction. An analysis of the transaction will determine whether the goods are real or..., but which have been packaged in a manner that does not permit breaking the package to purchase an item... sale at $12 must be designated, even though identical items may be offered in smaller quantities at...

Features of free software packages in flow cytometry: a comparison between four non-commercial software sources.

PubMed

Sahraneshin Samani, Fazel; Moore, Jodene K; Khosravani, Pardis; Ebrahimi, Marzieh

2014-08-01

Flow cytometers designed to analyze large particles are enabling new applications in biology. Data analysis is a critical component of the process FCM. In this article we compare features of four free software packages including WinMDI, Cyflogic, Flowing software, and Cytobank.

An Overview of Software for Conducting Dimensionality Assessment in Multidimensional Models

ERIC Educational Resources Information Center

Svetina, Dubravka; Levy, Roy

2012-01-01

An overview of popular software packages for conducting dimensionality assessment in multidimensional models is presented. Specifically, five popular software packages are described in terms of their capabilities to conduct dimensionality assessment with respect to the nature of analysis (exploratory or confirmatory), types of data (dichotomous,…

Maximizing Enrollment Yield through Financial Aid Packaging Policies

ERIC Educational Resources Information Center

Spaulding, Randy; Olswang, Steven

2005-01-01

Using institutional data, this paper presents a model to enable researchers and enrollment managers to assess the effectiveness of financial aid packaging policies in light of student characteristics and institutional market position. The model uses discriminant analysis and a series of hypothetical financial aid award scenarios to predict the…

A qualitative analysis of New Zealand retailers’ responses to standardised packaging legislation and tobacco industry opposition

PubMed Central

Guthrie, John; Hoek, Janet; Darroch, Ella; Wood, Zoë

2015-01-01

Objectives Many of the approximately 8000 New Zealand retailers selling tobacco are small stores that tobacco companies have represented as victims of policy measures designed to reduce smoking. Despite this depiction, many retailers experience considerable ambivalence in selling tobacco, a product they know harms their customers. We explored how retailers perceived the proposed introduction of standardised (or ‘plain’) packaging and their assessment of arguments made by tobacco companies in submissions on proposed standardised packaging legislation. Participants Using qualitative in-depth interviews, we recruited and interviewed 23 retailers of dairies (small convenience stores), small supermarkets, and service stations. Analyses Data were analysed using a protocol-driven approach; this stance enabled direct analysis of tobacco companies’ arguments, particularly those purporting to represent retailers’ concerns. Results Retailers were concerned about the financial implications of standardised packaging and the effects it may have on their ability to provide rapid and efficient customer service. However, few thought standardised packaging would foster illicit trade or spawn further regulation; most placed public health goals ahead of tobacco companies’ ‘rights’, and many supported government intervention to protect population health. Conclusions Retailers held ambivalent views on standardised packaging; while they were concerned about short-term effects on their business, they recognised the harm smoking causes. Policymakers and health researchers could collaborate more effectively with retailers by assisting them to create financially viable roles more compatible with public health objectives. PMID:26553840

Impact of Nisin-Activated Packaging on Microbiota of Beef Burgers during Storage

PubMed Central

Ferrocino, Ilario; Greppi, Anna; La Storia, Antonietta; Rantsiou, Kalliopi; Ercolini, Danilo

2015-01-01

Beef burgers were stored at 4°C in a vacuum in nisin-activated antimicrobial packaging. Microbial ecology analyses were performed on samples collected between days 0 and 21 of storage to discover the population diversity. Two batches were analyzed using RNA-based denaturing gradient gel electrophoresis (DGGE) and pyrosequencing. The active packaging retarded the growth of the total viable bacteria and lactic acid bacteria. Culture-independent analysis by pyrosequencing of RNA extracted directly from meat showed that Photobacterium phosphoreum, Lactococcus piscium, Lactobacillus sakei, and Leuconostoc carnosum were the major operational taxonomic units (OTUs) shared between control and treated samples. Beta diversity analysis of the 16S rRNA sequence data and RNA-DGGE showed a clear separation between two batches based on the microbiota. Control samples from batch B showed a significant high abundance of some taxa sensitive to nisin, such as Kocuria rhizophila, Staphylococcus xylosus, Leuconostoc carnosum, and Carnobacterium divergens, compared to control samples from batch A. However, only from batch B was it possible to find a significant difference between controls and treated samples during storage due to the active packaging. Predicted metagenomes confirmed differences between the two batches and indicated that the use of nisin-based antimicrobial packaging can determine a reduction in the abundance of specific metabolic pathways related to spoilage. The present study aimed to assess the viable bacterial communities in beef burgers stored in nisin-based antimicrobial packaging, and it highlights the efficacy of this strategy to prolong beef burger shelf life. PMID:26546424

ReadqPCR and NormqPCR: R packages for the reading, quality checking and normalisation of RT-qPCR quantification cycle (Cq) data

PubMed Central

2012-01-01

Background Measuring gene transcription using real-time reverse transcription polymerase chain reaction (RT-qPCR) technology is a mainstay of molecular biology. Technologies now exist to measure the abundance of many transcripts in parallel. The selection of the optimal reference gene for the normalisation of this data is a recurring problem, and several algorithms have been developed in order to solve it. So far nothing in R exists to unite these methods, together with other functions to read in and normalise the data using the chosen reference gene(s). Results We have developed two R/Bioconductor packages, ReadqPCR and NormqPCR, intended for a user with some experience with high-throughput data analysis using R, who wishes to use R to analyse RT-qPCR data. We illustrate their potential use in a workflow analysing a generic RT-qPCR experiment, and apply this to a real dataset. Packages are available from http://www.bioconductor.org/packages/release/bioc/html/ReadqPCR.htmland http://www.bioconductor.org/packages/release/bioc/html/NormqPCR.html Conclusions These packages increase the repetoire of RT-qPCR analysis tools available to the R user and allow them to (amongst other things) read their data into R, hold it in an ExpressionSet compatible R object, choose appropriate reference genes, normalise the data and look for differential expression between samples. PMID:22748112

The R package 'Luminescence': a history of unexpected complexity and concepts to deal with it

NASA Astrophysics Data System (ADS)

Kreutzer, Sebastian; Burow, Christoph; Dietze, Michael; Fuchs, Margret C.; Friedrich, Johannes; Fischer, Manfred; Schmidt, Christoph

2017-04-01

Overcoming limitations in the so far used standard software, developing an efficient solution of low weight for a very specific task or creating graphs of high quality: the reasons that may had initially lead a scientist to work with R are manifold. And as long as developed solutions, e.g., R scripts, are needed for personal use only, code can remain unstructured and a documentation is not compulsory. However, this changes with the first friendly request for help after the code has been reused by others. In contrast to single scripts, written without intention to ever get published, for R packages the CRAN policy demands a more structured and elaborated approach including a minimum of documentation. Nevertheless, growing projects with thousands of lines of code that need to be maintained can become overwhelming, in particular as researchers are not by definition experts on managing software projects. The R package 'Luminescence' (Kreutzer et al., 2017), a collection of tools dealing with the analysis of luminescence data in a geoscientific, geochronological context, started as one single R script, but quickly evolved into a comprehensive solution connected with various other R packages. We present (1) a very brief development history of the package 'Luminescence', before we (2) sketch technical challenges encountered over time and solutions that have been found to deal with it by using various open source tools. Our presentation is considered as a collection of concepts and approaches to set up R projects in geosciences. References. Kreutzer, S., Dietze, M., Burow, C., Fuchs, M. C., Schmidt, C., Fischer, M., Friedrich, J., 2017. Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.6.4. https://CRAN.R-project.org/package=Luminescence

Investigation of the Finite Element Software Packages at KSC

NASA Technical Reports Server (NTRS)

Lu, Chu-Ho

1991-01-01

The useful and powerful features of NASTRAN and three real world problems for the testing of the capabilities of different NASTRAN versions are discussed. The test problems involve direct transient analysis, nonlinear analysis, and static analysis. The experiences in using graphics software packages are also discussed. It was found that MSC/XL can be more useful if it can be improved to generate picture files of the analysis results and to extend its capabilities to support finite element codes other than MSC/NASTRAN. It was found that the current version of SDRC/I-DEAS (version VI) may have bugs in the module 'Data Loader'.

REPRODUCIBLE RESEARCH WORKFLOW IN R FOR THE ANALYSIS OF PERSONALIZED HUMAN MICROBIOME DATA.

PubMed

Callahan, Benjamin; Proctor, Diana; Relman, David; Fukuyama, Julia; Holmes, Susan

2016-01-01

This article presents a reproducible research workflow for amplicon-based microbiome studies in personalized medicine created using Bioconductor packages and the knitr markdown interface.We show that sometimes a multiplicity of choices and lack of consistent documentation at each stage of the sequential processing pipeline used for the analysis of microbiome data can lead to spurious results. We propose its replacement with reproducible and documented analysis using R packages dada2, knitr, and phyloseq. This workflow implements both key stages of amplicon analysis: the initial filtering and denoising steps needed to construct taxonomic feature tables from error-containing sequencing reads (dada2), and the exploratory and inferential analysis of those feature tables and associated sample metadata (phyloseq). This workow facilitates reproducible interrogation of the full set of choices required in microbiome studies. We present several examples in which we leverage existing packages for analysis in a way that allows easy sharing and modification by others, and give pointers to articles that depend on this reproducible workflow for the study of longitudinal and spatial series analyses of the vaginal microbiome in pregnancy and the oral microbiome in humans with healthy dentition and intra-oral tissues.

WebArray: an online platform for microarray data analysis

PubMed Central

Xia, Xiaoqin; McClelland, Michael; Wang, Yipeng

2005-01-01

Background Many cutting-edge microarray analysis tools and algorithms, including commonly used limma and affy packages in Bioconductor, need sophisticated knowledge of mathematics, statistics and computer skills for implementation. Commercially available software can provide a user-friendly interface at considerable cost. To facilitate the use of these tools for microarray data analysis on an open platform we developed an online microarray data analysis platform, WebArray, for bench biologists to utilize these tools to explore data from single/dual color microarray experiments. Results The currently implemented functions were based on limma and affy package from Bioconductor, the spacings LOESS histogram (SPLOSH) method, PCA-assisted normalization method and genome mapping method. WebArray incorporates these packages and provides a user-friendly interface for accessing a wide range of key functions of limma and others, such as spot quality weight, background correction, graphical plotting, normalization, linear modeling, empirical bayes statistical analysis, false discovery rate (FDR) estimation, chromosomal mapping for genome comparison. Conclusion WebArray offers a convenient platform for bench biologists to access several cutting-edge microarray data analysis tools. The website is freely available at . It runs on a Linux server with Apache and MySQL. PMID:16371165

Applications of decision analysis and related techniques to industrial engineering problems at KSC

NASA Technical Reports Server (NTRS)

Evans, Gerald W.

1995-01-01

This report provides: (1) a discussion of the origination of decision analysis problems (well-structured problems) from ill-structured problems; (2) a review of the various methodologies and software packages for decision analysis and related problem areas; (3) a discussion of how the characteristics of a decision analysis problem affect the choice of modeling methodologies, thus providing a guide as to when to choose a particular methodology; and (4) examples of applications of decision analysis to particular problems encountered by the IE Group at KSC. With respect to the specific applications at KSC, particular emphasis is placed on the use of the Demos software package (Lumina Decision Systems, 1993).

Software and package applicating for network meta-analysis: A usage-based comparative study.

PubMed

Xu, Chang; Niu, Yuming; Wu, Junyi; Gu, Huiyun; Zhang, Chao

2017-12-21

To compare and analyze the characteristics and functions of software applications for network meta-analysis (NMA). PubMed, EMbase, The Cochrane Library, the official websites of Bayesian inference Using Gibbs Sampling (BUGS), Stata and R, and Google were searched to collect the software and packages for performing NMA; software and packages published up to March 2016 were included. After collecting the software, packages, and their user guides, we used the software and packages to calculate a typical example. All characteristics, functions, and computed results were compared and analyzed. Ten types of software were included, including programming and non-programming software. They were developed mainly based on Bayesian or frequentist theory. Most types of software have the characteristics of easy operation, easy mastery, exact calculation, or excellent graphing. However, there was no single software that performed accurate calculations with superior graphing; this could only be achieved through the combination of two or more types of software. This study suggests that the user should choose the appropriate software according to personal programming basis, operational habits, and financial ability. Then, the choice of the combination of BUGS and R (or Stata) software to perform the NMA is considered. © 2017 Chinese Cochrane Center, West China Hospital of Sichuan University and John Wiley & Sons Australia, Ltd.

Community-based benchmarking of the CMIP DECK experiments

NASA Astrophysics Data System (ADS)

Gleckler, P. J.

2015-12-01

A diversity of community-based efforts are independently developing "diagnostic packages" with little or no coordination between them. A short list of examples include NCAR's Climate Variability Diagnostics Package (CVDP), ORNL's International Land Model Benchmarking (ILAMB), LBNL's Toolkit for Extreme Climate Analysis (TECA), PCMDI's Metrics Package (PMP), the EU EMBRACE ESMValTool, the WGNE MJO diagnostics package, and CFMIP diagnostics. The full value of these efforts cannot be realized without some coordination. As a first step, a WCRP effort has initiated a catalog to document candidate packages that could potentially be applied in a "repeat-use" fashion to all simulations contributed to the CMIP DECK (Diagnostic, Evaluation and Characterization of Klima) experiments. Some coordination of community-based diagnostics has the additional potential to improve how CMIP modeling groups analyze their simulations during model-development. The fact that most modeling groups now maintain a "CMIP compliant" data stream means that in principal without much effort they could readily adopt a set of well organized diagnostic capabilities specifically designed to operate on CMIP DECK experiments. Ultimately, a detailed listing of and access to analysis codes that are demonstrated to work "out of the box" with CMIP data could enable model developers (and others) to select those codes they wish to implement in-house, potentially enabling more systematic evaluation during the model development process.

SimHap GUI: An intuitive graphical user interface for genetic association analysis

PubMed Central

Carter, Kim W; McCaskie, Pamela A; Palmer, Lyle J

2008-01-01

Background Researchers wishing to conduct genetic association analysis involving single nucleotide polymorphisms (SNPs) or haplotypes are often confronted with the lack of user-friendly graphical analysis tools, requiring sophisticated statistical and informatics expertise to perform relatively straightforward tasks. Tools, such as the SimHap package for the R statistics language, provide the necessary statistical operations to conduct sophisticated genetic analysis, but lacks a graphical user interface that allows anyone but a professional statistician to effectively utilise the tool. Results We have developed SimHap GUI, a cross-platform integrated graphical analysis tool for conducting epidemiological, single SNP and haplotype-based association analysis. SimHap GUI features a novel workflow interface that guides the user through each logical step of the analysis process, making it accessible to both novice and advanced users. This tool provides a seamless interface to the SimHap R package, while providing enhanced functionality such as sophisticated data checking, automated data conversion, and real-time estimations of haplotype simulation progress. Conclusion SimHap GUI provides a novel, easy-to-use, cross-platform solution for conducting a range of genetic and non-genetic association analyses. This provides a free alternative to commercial statistics packages that is specifically designed for genetic association analysis. PMID:19109877

Application of Thermo-Mechanical Measurements of Plastic Packages for Reliability Evaluation of PEMS

NASA Technical Reports Server (NTRS)

Sharma, Ashok K.; Teverovsky, Alexander

2004-01-01

Thermo-mechanical analysis (TMA) is typically employed for measurements of the glass transition temperature (Tg) and coefficients of thermal expansion (CTE) in molding compounds used in plastic encapsulated microcircuits (PEMs). Application of TMA measurements directly to PEMs allows anomalies to be revealed in deformation of packages with temperature, and thus indicates possible reliability concerns related to thermo-mechanical integrity and stability of the devices. In this work, temperature dependencies of package deformation were measured in several types of PEMs that failed environmental stress testing including temperature cycling, highly accelerated stress testing (HAST) in humid environments, and bum-in (BI) testing. Comparison of thermo-mechanical characteristics of packages and molding compounds in the failed parts allowed for explanation of the observed failures. The results indicate that TMA of plastic packages might be used for quality evaluation of PEMs intended for high-reliability applications.

R-Based Software for the Integration of Pathway Data into Bioinformatic Algorithms

PubMed Central

Kramer, Frank; Bayerlová, Michaela; Beißbarth, Tim

2014-01-01

Putting new findings into the context of available literature knowledge is one approach to deal with the surge of high-throughput data results. Furthermore, prior knowledge can increase the performance and stability of bioinformatic algorithms, for example, methods for network reconstruction. In this review, we examine software packages for the statistical computing framework R, which enable the integration of pathway data for further bioinformatic analyses. Different approaches to integrate and visualize pathway data are identified and packages are stratified concerning their features according to a number of different aspects: data import strategies, the extent of available data, dependencies on external tools, integration with further analysis steps and visualization options are considered. A total of 12 packages integrating pathway data are reviewed in this manuscript. These are supplemented by five R-specific packages for visualization and six connector packages, which provide access to external tools. PMID:24833336

Seasonal water mass distribution in the Indonesian throughflow entering the Indian Ocean

NASA Astrophysics Data System (ADS)

Coatanoan, C.; Metzl, N.; Fieux, M.; Coste, B.

1999-09-01

A multiparametric approach is used to analyze the seasonal properties of water masses in the eastern Indian Ocean. The data were measured during two cruises of the Java Australia Dynamic Experiment (JADE) program carried out during two opposite seasons: August 1989 (SE monsoon) and February-March 1992 (NW monsoon). These cruises took place at the end of a La Niña event and during an El Niño episode, respectively. Seven sources have been identified in the studied region for the 200-800 m layer: the Subtropical Indian Water, the Indian Central Water, the modified Antarctic Intermediate Water, the Indonesian Subsurface Water, the Indonesian Intermediate Water, the Arabian Sea-Persian Gulf Water (AS-PGW), and the Arabian Sea-Red Sea Water (AS-RSW). The selected tracers are potential temperature, salinity and oxygen with mass conservation and positive mixing coefficients as constraints. The analysis indicates the proportion of each water source along the Australia-Bali section and into the Indonesian channels. Although no large changes are observed for Indonesian waters, significant seasonal variations are found for the southern and northern Indian Ocean water. During the NW monsoon, the contribution of the AS-RSW increases at the entrance of the Indonesian archipelago whereas the contribution of the south Indian waters decreases in the northwest Australia basin. In a complementary study, nutrients are introduced into the multiparametric analysis in order to more clearly separate the signature of the north Indian waters (AS-PGW, AS-RSW) and to provide supplementary information on the biological history of the water masses, which is compared to large-scale primary production estimates.

Xarray: multi-dimensional data analysis in Python

NASA Astrophysics Data System (ADS)

Hoyer, Stephan; Hamman, Joe; Maussion, Fabien

2017-04-01

xarray (http://xarray.pydata.org) is an open source project and Python package that provides a toolkit and data structures for N-dimensional labeled arrays, which are the bread and butter of modern geoscientific data analysis. Key features of the package include label-based indexing and arithmetic, interoperability with the core scientific Python packages (e.g., pandas, NumPy, Matplotlib, Cartopy), out-of-core computation on datasets that don't fit into memory, a wide range of input/output options, and advanced multi-dimensional data manipulation tools such as group-by and resampling. In this contribution we will present the key features of the library and demonstrate its great potential for a wide range of applications, from (big-)data processing on super computers to data exploration in front of a classroom.

Decontamination of food packaging using electron beam—status and prospects

NASA Astrophysics Data System (ADS)

Mittendorfer, J.; Bierbaumer, H. P.; Gratzl, F.; Kellauer, E.

2002-03-01

In this paper the status of food packaging disinfection decontamination using electron beam at Mediscan GmbH is presented. The first section of the paper describes the activities at the service center, where food packaging materials, e.g. yoghurt cups are decontaminated in their final shipment containers. As important step in the hazard analysis and critical control point of food processing, microbiological uncontaminated food packaging material is of public interest and attracts a lot of attention from packaging material producers and food processors. The dose ranges for different sterility assurance levels are discussed and results from microbiological test are presented. Studies at Mediscan have demonstrated, that an electron beam treatment at a dose of 5-7 kGy is most effective against yeast and mold, which are mainly responsible for spoilage and short shelf-life of a variety of products. The second section is devoted to the field of inline decontamination of food packaging and sterilization of pharmaceutical packaging material and the research currently conducted at Mediscan. The requirements for industrial inline electron beam systems are summarized and design concepts discussed in terms of beam energy, beam current, irradiation topology, product handling and shielding.

The results of pre-design studies on the development of a new design of gas turbine compressor package of GPA-C-16 type

NASA Astrophysics Data System (ADS)

Smirnov, A. V.; Chobenko, V. M.; Shcherbakov, O. M.; Ushakov, S. M.; Parafiynyk, V. P.; Sereda, R. M.

2017-08-01

The article summarizes the results of analysis of data concerning the operation of turbocompressor packages at compressor stations for the natural gas transmission system of Ukraine. The basic requirements for gas turbine compressor packages used for modernization and reconstruction of compressor stations are considered. Using a 16 MW gas turbine package GPA-C-16S/76-1,44M1 as an example, the results of pre-design studies and some technical solutions that improve the energy efficiency of gas turbine compressor packages and their reliability, as well as its environmental performance are given. In particular, the article deals with the matching of performance characteristics of a centrifugal compressor (hereinafter compressor) and gas turbine drive to reduce fuel gas consumption; as well as application of energy efficient technologies, in particular, exhaust gas heat recovery units and gas-oil heat exchangers in turbocompressor packages oil system; as well as reducing emissions of carbon monoxide into the atmosphere using a catalytic exhaust system. Described technical solutions can be used for development of other types of gas turbine compressor packages.

Computing and software

USGS Publications Warehouse

White, Gary C.; Hines, J.E.

2004-01-01

The reality is that the statistical methods used for analysis of data depend upon the availability of software. Analysis of marked animal data is no different than the rest of the statistical field. The methods used for analysis are those that are available in reliable software packages. Thus, the critical importance of having reliable, up–to–date software available to biologists is obvious. Statisticians have continued to develop more robust models, ever expanding the suite of potential analysis methodsavailable. But without software to implement these newer methods, they will languish in the abstract, and not be applied to the problems deserving them.In the Computers and Software Session, two new software packages are described, a comparison of implementation of methods for the estimation of nest survival is provided, and a more speculative paper about how the next generation of software might be structured is presented.Rotella et al. (2004) compare nest survival estimation with different software packages: SAS logistic regression, SAS non–linear mixed models, and Program MARK. Nests are assumed to be visited at various, possibly infrequent, intervals. All of the approaches described compute nest survival with the same likelihood, and require that the age of the nest is known to account for nests that eventually hatch. However, each approach offers advantages and disadvantages, explored by Rotella et al. (2004).Efford et al. (2004) present a new software package called DENSITY. The package computes population abundance and density from trapping arrays and other detection methods with a new and unique approach. DENSITY represents the first major addition to the analysis of trapping arrays in 20 years.Barker & White (2004) discuss how existing software such as Program MARK require that each new model’s likelihood must be programmed specifically for that model. They wishfully think that future software might allow the user to combine pieces of likelihood functions together to generate estimates. The idea is interesting, and maybe some bright young statistician can work out the specifics to implement the procedure.Choquet et al. (2004) describe MSURGE, a software package that implements the multistate capture–recapture models. The unique feature of MSURGE is that the design matrix is constructed with an interpreted language called GEMACO. Because MSURGE is limited to just multistate models, the special requirements of these likelihoods can be provided.The software and methods presented in these papers gives biologists and wildlife managers an expanding range of possibilities for data analysis. Although ease–of–use is generally getting better, it does not replace the need for understanding of the requirements and structure of the models being computed. The internet provides access to many free software packages as well as user–discussion groups to share knowledge and ideas. (A starting point for wildlife–related applications is (http://www.phidot.org).

DCGL v2.0: an R package for unveiling differential regulation from differential co-expression.

PubMed

Yang, Jing; Yu, Hui; Liu, Bao-Hong; Zhao, Zhongming; Liu, Lei; Ma, Liang-Xiao; Li, Yi-Xue; Li, Yuan-Yuan

2013-01-01

Differential co-expression analysis (DCEA) has emerged in recent years as a novel, systematic investigation into gene expression data. While most DCEA studies or tools focus on the co-expression relationships among genes, some are developing a potentially more promising research domain, differential regulation analysis (DRA). In our previously proposed R package DCGL v1.0, we provided functions to facilitate basic differential co-expression analyses; however, the output from DCGL v1.0 could not be translated into differential regulation mechanisms in a straightforward manner. To advance from DCEA to DRA, we upgraded the DCGL package from v1.0 to v2.0. A new module named "Differential Regulation Analysis" (DRA) was designed, which consists of three major functions: DRsort, DRplot, and DRrank. DRsort selects differentially regulated genes (DRGs) and differentially regulated links (DRLs) according to the transcription factor (TF)-to-target information. DRrank prioritizes the TFs in terms of their potential relevance to the phenotype of interest. DRplot graphically visualizes differentially co-expressed links (DCLs) and/or TF-to-target links in a network context. In addition to these new modules, we streamlined the codes from v1.0. The evaluation results proved that our differential regulation analysis is able to capture the regulators relevant to the biological subject. With ample functions to facilitate differential regulation analysis, DCGL v2.0 was upgraded from a DCEA tool to a DRA tool, which may unveil the underlying differential regulation from the observed differential co-expression. DCGL v2.0 can be applied to a wide range of gene expression data in order to systematically identify novel regulators that have not yet been documented as critical. DCGL v2.0 package is available at http://cran.r-project.org/web/packages/DCGL/index.html or at our project home page http://lifecenter.sgst.cn/main/en/dcgl.jsp.

Packaging of a unit-length viral genome: the role of nucleotides and the gpD decoration protein in stable nucleocapsid assembly in bacteriophage lambda.

PubMed

Yang, Qin; Maluf, Nasib Karl; Catalano, Carlos Enrique

2008-11-28

The developmental pathways for a variety of eukaryotic and prokaryotic double-stranded DNA viruses include packaging of viral DNA into a preformed procapsid structure, catalyzed by terminase enzymes and fueled by ATP hydrolysis. In most instances, a capsid expansion process accompanies DNA packaging, which significantly increases the volume of the capsid to accommodate the full-length viral genome. "Decoration" proteins add to the surface of the expanded capsid lattice, and the terminase motors tightly package DNA, generating up to approximately 20 atm of internal capsid pressure. Herein we describe biochemical studies on genome packaging using bacteriophage lambda as a model system. Kinetic analysis suggests that the packaging motor possesses at least four ATPase catalytic sites that act cooperatively to effect DNA translocation, and that the motor is highly processive. While not required for DNA translocation into the capsid, the phage lambda capsid decoration protein gpD is essential for the packaging of the penultimate 8-10 kb (15-20%) of the viral genome; virtually no DNA is packaged in the absence of gpD when large DNA substrates are used, most likely due to a loss of capsid structural integrity. Finally, we show that ATP hydrolysis is required to retain the genome in a packaged state subsequent to condensation within the capsid. Presumably, the packaging motor continues to "idle" at the genome end and to maintain a positive pressure towards the packaged state. Surprisingly, ADP, guanosine triphosphate, and the nonhydrolyzable ATP analog 5'-adenylyl-beta,gamma-imidodiphosphate (AMP-PNP) similarly stabilize the packaged viral genome despite the fact that they fail to support genome packaging. In contrast, the poorly hydrolyzed ATP analog ATP-gammaS only partially stabilizes the nucleocapsid, and a DNA is released in "quantized" steps. We interpret the ensemble of data to indicate that (i) the viral procapsid possesses a degree of plasticity that is required to accommodate the packaging of large DNA substrates; (ii) the gpD decoration protein is required to stabilize the fully expanded capsid; and (iii) nucleotides regulate high-affinity DNA binding interactions that are required to maintain DNA in the packaged state.

Summer monsoon response of the Northern Somali Current, 1995

NASA Astrophysics Data System (ADS)

Schott, Friedrich; Fischer, Jürgen; Garternicht, Ulf; Quadfasel, Detlef

Preliminary results on the development of the northern Somali Current regime and Great Whirl during the summer monsoon of 1995 are reported. They are based on the water mass and current profiling observations from three shipboard surveys of R/V Meteor and on the time series from a moored current-meter and ADCP array. The monsoon response of the GW was deep-reaching, to more than 1000m. involving large deep transports. The northern Somali Current was found to be disconnected from the interior Arabian Sea in latitude range 4°N-12°N in both, water mass properties and current fields. Instead, communication dominantly occurs through the passages between Socotra and the African continent. From moored stations in the main passage a northward throughflow from the Somali Current to the Gulf of Aden of about 5 Sv was determined for the summer monsoon of 1995.

Salinification in the South China Sea Since Late 2012: A Reversal of the Freshening Since the 1990s

NASA Astrophysics Data System (ADS)

Zeng, Lili; Chassignet, Eric P.; Schmitt, Raymond W.; Xu, Xiaobiao; Wang, Dongxiao

2018-03-01

Salinification has occurred in the South China Sea from late 2012 to the present, as shown by satellite Aquarius/Soil Moisture Active Passive data and Argo float data. This salinification follows a 20 year freshening trend that started in 1993. The salinification signal is strongest near the surface and extends downward under the seasonal thermocline to a depth of 150 m. The salinification occurs when the phase of the Pacific Decadal Oscillation switches from negative to positive. Diagnosis of the salinity budget suggests that an increasing net surface freshwater loss and the horizontal salt advection through the Luzon Strait driven by the South China Sea throughflow contributed to this ongoing salinification. In particular, a decrease in precipitation and enhanced Luzon Strait transport dominated the current intense salinification. Of particular interest is whether this salinification will continue until it reaches the previous maximum recorded in 1992.

Intraseasonal variability and tides in Makassar Strait

NASA Astrophysics Data System (ADS)

Susanto, R. Dwi; Gordon, Arnold L.; Sprintall, Janet; Herunadi, Bambang

2000-05-01

Intraseasonal variability and tides along the Makassar Strait, the major route of Indonesian throughflow, are investigated using spectral and time-frequency analyses which are applied to sea level, wind and mooring data. Semidiurnal and diurnal tides are dominant features, with higher (lower) semidiurnal (diurnal) energy in the north compared to the south. Sea levels and mooring data display intraseasonal variability which are probably a response to remotely forced Kelvin waves from the Indian Ocean through Lombok Strait and to Rossby waves from the Pacific Ocean. Sea levels in Tarakan and Balikpapan and Makassar mooring velocities reveal intraseasonal features with periods of 48-62 days associated with Rossby waves from the Sulawesi Sea. Kelvin wave features with periods of 67-100 days are seen in Bali (Lombok Strait), at the mooring sites and in Balikpapan, however, they are not seen in Tarakan, which implies that these waves diminish after passing through the Makassar Strait.

Role of the Bering Strait on the hysteresis of the ocean conveyor belt circulation and glacial climate stability.

PubMed

Hu, Aixue; Meehl, Gerald A; Han, Weiqing; Timmermann, Axel; Otto-Bliesner, Bette; Liu, Zhengyu; Washington, Warren M; Large, William; Abe-Ouchi, Ayako; Kimoto, Masahide; Lambeck, Kurt; Wu, Bingyi

2012-04-24

Abrupt climate transitions, known as Dansgaard-Oeschger and Heinrich events, occurred frequently during the last glacial period, specifically from 80-11 thousand years before present, but were nearly absent during interglacial periods and the early stages of glacial periods, when major ice-sheets were still forming. Here we show, with a fully coupled state-of-the-art climate model, that closing the Bering Strait and preventing its throughflow between the Pacific and Arctic Oceans during the glacial period can lead to the emergence of stronger hysteresis behavior of the ocean conveyor belt circulation to create conditions that are conducive to triggering abrupt climate transitions. Hence, it is argued that even for greenhouse warming, abrupt climate transitions similar to those in the last glacial time are unlikely to occur as the Bering Strait remains open.

Oceanic Fluxes of Mass, Heat and Freshwater: A Global Estimate and Perspective

NASA Technical Reports Server (NTRS)

MacDonald, Alison Marguerite

1995-01-01

Data from fifteen globally distributed, modern, high resolution, hydrographic oceanic transects are combined in an inverse calculation using large scale box models. The models provide estimates of the global meridional heat and freshwater budgets and are used to examine the sensitivity of the global circulation, both inter and intra-basin exchange rates, to a variety of external constraints provided by estimates of Ekman, boundary current and throughflow transports. A solution is found which is consistent with both the model physics and the global data set, despite a twenty five year time span and a lack of seasonal consistency among the data. The overall pattern of the global circulation suggested by the models is similar to that proposed in previously published local studies and regional reviews. However, significant qualitative and quantitative differences exist. These differences are due both to the model definition and to the global nature of the data set.

Digital PIV (DPIV) Software Analysis System

NASA Technical Reports Server (NTRS)

Blackshire, James L.

1997-01-01

A software package was developed to provide a Digital PIV (DPIV) capability for NASA LaRC. The system provides an automated image capture, test correlation, and autocorrelation analysis capability for the Kodak Megaplus 1.4 digital camera system for PIV measurements. The package includes three separate programs that, when used together with the PIV data validation algorithm, constitutes a complete DPIV analysis capability. The programs are run on an IBM PC/AT host computer running either Microsoft Windows 3.1 or Windows 95 using a 'quickwin' format that allows simple user interface and output capabilities to the windows environment.

Numerical analysis of laminar and turbulent incompressible flows using the finite element Fluid Dynamics Analysis Package (FIDAP)

NASA Technical Reports Server (NTRS)

Sohn, Jeong L.

1988-01-01

The purpose of the study is the evaluation of the numerical accuracy of FIDAP (Fluid Dynamics Analysis Package). Accordingly, four test problems in laminar and turbulent incompressible flows are selected and the computational results of these problems compared with other numerical solutions and/or experimental data. These problems include: (1) 2-D laminar flow inside a wall-driven cavity; (2) 2-D laminar flow over a backward-facing step; (3) 2-D turbulent flow over a backward-facing step; and (4) 2-D turbulent flow through a turn-around duct.

PCIPS 2.0: Powerful multiprofile image processing implemented on PCs

NASA Technical Reports Server (NTRS)

Smirnov, O. M.; Piskunov, N. E.

1992-01-01

Over the years, the processing power of personal computers has steadily increased. Now, 386- and 486-based PC's are fast enough for many image processing applications, and inexpensive enough even for amateur astronomers. PCIPS is an image processing system based on these platforms that was designed to satisfy a broad range of data analysis needs, while requiring minimum hardware and providing maximum expandability. It will run (albeit at a slow pace) even on a 80286 with 640K memory, but will take full advantage of bigger memory and faster CPU's. Because the actual image processing is performed by external modules, the system can be easily upgraded by the user for all sorts of scientific data analysis. PCIPS supports large format lD and 2D images in any numeric type from 8-bit integer to 64-bit floating point. The images can be displayed, overlaid, printed and any part of the data examined via an intuitive graphical user interface that employs buttons, pop-up menus, and a mouse. PCIPS automatically converts images between different types and sizes to satisfy the requirements of various applications. PCIPS features an API that lets users develop custom applications in C or FORTRAN. While doing so, a programmer can concentrate on the actual data processing, because PCIPS assumes responsibility for accessing images and interacting with the user. This also ensures that all applications, even custom ones, have a consistent and user-friendly interface. The API is compatible with factory programming, a metaphor for constructing image processing procedures that will be implemented in future versions of the system. Several application packages were created under PCIPS. The basic package includes elementary arithmetics and statistics, geometric transformations and import/export in various formats (FITS, binary, ASCII, and GIF). The CCD processing package and the spectral analysis package were successfully used to reduce spectra from the Nordic Telescope at La Palma. A photometry package is also available, and other packages are being developed. A multitasking version of PCIPS that utilizes the factory programming concept is currently under development. This version will remain compatible (on the source code level) with existing application packages and custom applications.

Introduction to IND and recursive partitioning, version 1.0

NASA Technical Reports Server (NTRS)

Buntine, Wray; Caruana, Rich

1991-01-01

This manual describes the IND package for learning tree classifiers from data. The package is an integrated C and C shell re-implementation of tree learning routines such as CART, C4, and various MDL and Bayesian variations. The package includes routines for experiment control, interactive operation, and analysis of tree building. The manual introduces the system and its many options, gives a basic review of tree learning, contains a guide to the literature and a glossary, lists the manual pages for the routines, and instructions on installation.

Parallel Climate Data Assimilation PSAS Package

NASA Technical Reports Server (NTRS)

Ding, Hong Q.; Chan, Clara; Gennery, Donald B.; Ferraro, Robert D.

1996-01-01

We have designed and implemented a set of highly efficient and highly scalable algorithms for an unstructured computational package, the PSAS data assimilation package, as demonstrated by detailed performance analysis of systematic runs on up to 512node Intel Paragon. The equation solver achieves a sustained 18 Gflops performance. As the results, we achieved an unprecedented 100-fold solution time reduction on the Intel Paragon parallel platform over the Cray C90. This not only meets and exceeds the DAO time requirements, but also significantly enlarges the window of exploration in climate data assimilations.

Recent developments with the ORSER system

NASA Technical Reports Server (NTRS)

Baumer, G. M.; Turner, B. J.; Myers, W. L.

1981-01-01

Additions to the ORSER remote sensing data processing package are described. The ORSER package consists of about 35 individual programs that are grouped into preprocessing, data analysis, and display subsystems. Additional data formats and data management, data transformation, and geometric correlation programs were supplemented to the preprocessing subsystem. Enhancements to the data analysis techniques include a maximum likelihood classifier (MAXCLASS) and a new version of the STATS program which makes delineation of training areas easier and allows for detection of outlier points. Ongoing developments are also described.

Analysis of microgravity space experiments Space Shuttle programmatic safety requirements

NASA Technical Reports Server (NTRS)

Terlep, Judith A.

1996-01-01

This report documents the results of an analysis of microgravity space experiments space shuttle programmatic safety requirements and recommends the creation of a Safety Compliance Data Package (SCDP) Template for both flight and ground processes. These templates detail the programmatic requirements necessary to produce a complete SCDP. The templates were developed from various NASA centers' requirement documents, previously written guidelines on safety data packages, and from personal experiences. The templates are included in the back as part of this report.

Orchestrating high-throughput genomic analysis with Bioconductor

PubMed Central

Huber, Wolfgang; Carey, Vincent J.; Gentleman, Robert; Anders, Simon; Carlson, Marc; Carvalho, Benilton S.; Bravo, Hector Corrada; Davis, Sean; Gatto, Laurent; Girke, Thomas; Gottardo, Raphael; Hahne, Florian; Hansen, Kasper D.; Irizarry, Rafael A.; Lawrence, Michael; Love, Michael I.; MacDonald, James; Obenchain, Valerie; Oleś, Andrzej K.; Pagès, Hervé; Reyes, Alejandro; Shannon, Paul; Smyth, Gordon K.; Tenenbaum, Dan; Waldron, Levi; Morgan, Martin

2015-01-01

Bioconductor is an open-source, open-development software project for the analysis and comprehension of high-throughput data in genomics and molecular biology. The project aims to enable interdisciplinary research, collaboration and rapid development of scientific software. Based on the statistical programming language R, Bioconductor comprises 934 interoperable packages contributed by a large, diverse community of scientists. Packages cover a range of bioinformatic and statistical applications. They undergo formal initial review and continuous automated testing. We present an overview for prospective users and contributors. PMID:25633503

A CAD approach to magnetic bearing design

NASA Technical Reports Server (NTRS)

Jeyaseelan, M.; Anand, D. K.; Kirk, J. A.

1988-01-01

A design methodology has been developed at the Magnetic Bearing Research Laboratory for designing magnetic bearings using a CAD approach. This is used in the algorithm of an interactive design software package. The package is a design tool developed to enable the designer to simulate the entire process of design and analysis of the system. Its capabilities include interactive input/modification of geometry, finding any possible saturation at critical sections of the system, and the design and analysis of a control system that stabilizes and maintains magnetic suspension.

An econometric analysis of regional differences in household waste collection: the case of plastic packaging waste in Sweden.

PubMed

Hage, Olle; Söderholm, Patrik

2008-01-01

The Swedish producer responsibility ordinance mandates producers to collect and recycle packaging materials. This paper investigates the main determinants of collection rates of household plastic packaging waste in Swedish municipalities. This is done by the use of a regression analysis based on cross-sectional data for 252 Swedish municipalities. The results suggest that local policies, geographic/demographic variables, socio-economic factors and environmental preferences all help explain inter-municipality collection rates. For instance, the collection rate appears to be positively affected by increases in the unemployment rate, the share of private houses, and the presence of immigrants (unless newly arrived) in the municipality. The impacts of distance to recycling industry, urbanization rate and population density on collection outcomes turn out, though, to be both statistically and economically insignificant. A reasonable explanation for this is that the monetary compensation from the material companies to the collection entrepreneurs vary depending on region and is typically higher in high-cost regions. This implies that the plastic packaging collection in Sweden may be cost ineffective. Finally, the analysis also shows that municipalities that employ weight-based waste management fees generally experience higher collection rates than those municipalities in which flat and/or volume-based fees are used.

Cantera Integration with the Toolbox for Modeling and Analysis of Thermodynamic Systems (T-MATS)

NASA Technical Reports Server (NTRS)

Lavelle, Thomas M.; Chapman, Jeffryes W.; May, Ryan D.; Litt, Jonathan S.; Guo, Ten-Huei

2014-01-01

NASA Glenn Research Center (GRC) has recently developed a software package for modeling generic thermodynamic systems called the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS). T-MATS is a library of building blocks that can be assembled to represent any thermodynamic system in the Simulink(Registered TradeMark) (The MathWorks, Inc.) environment. These elements, along with a Newton Raphson solver (also provided as part of the T-MATS package), enable users to create models of a wide variety of systems. The current version of T-MATS (v1.0.1) uses tabular data for providing information about a specific mixture of air, water (humidity), and hydrocarbon fuel in calculations of thermodynamic properties. The capabilities of T-MATS can be expanded by integrating it with the Cantera thermodynamic package. Cantera is an object-oriented analysis package that calculates thermodynamic solutions for any mixture defined by the user. Integration of Cantera with T-MATS extends the range of systems that may be modeled using the toolbox. In addition, the library of elements released with Cantera were developed using MATLAB native M-files, allowing for quicker prototyping of elements. This paper discusses how the new Cantera-based elements are created and provides examples for using T-MATS integrated with Cantera.

Cantera Integration with the Toolbox for Modeling and Analysis of Thermodynamic Systems (T-MATS)

NASA Technical Reports Server (NTRS)

Lavelle, Thomas M.; Chapman, Jeffryes W.; May, Ryan D.; Litt, Jonathan S.; Guo, Ten-Huei

2014-01-01

NASA Glenn Research Center (GRC) has recently developed a software package for modeling generic thermodynamic systems called the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS). T-MATS is a library of building blocks that can be assembled to represent any thermodynamic system in the Simulink (The MathWorks, Inc.) environment. These elements, along with a Newton Raphson solver (also provided as part of the T-MATS package), enable users to create models of a wide variety of systems. The current version of T-MATS (v1.0.1) uses tabular data for providing information about a specific mixture of air, water (humidity), and hydrocarbon fuel in calculations of thermodynamic properties. The capabilities of T-MATS can be expanded by integrating it with the Cantera thermodynamic package. Cantera is an object-oriented analysis package that calculates thermodynamic solutions for any mixture defined by the user. Integration of Cantera with T-MATS extends the range of systems that may be modeled using the toolbox. In addition, the library of elements released with Cantera were developed using MATLAB native M-files, allowing for quicker prototyping of elements. This paper discusses how the new Cantera-based elements are created and provides examples for using T-MATS integrated with Cantera.

An econometric analysis of regional differences in household waste collection: The case of plastic packaging waste in Sweden

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

Hage, Olle; Soederholm, Patrik

2008-07-01

The Swedish producer responsibility ordinance mandates producers to collect and recycle packaging materials. This paper investigates the main determinants of collection rates of household plastic packaging waste in Swedish municipalities. This is done by the use of a regression analysis based on cross-sectional data for 252 Swedish municipalities. The results suggest that local policies, geographic/demographic variables, socio-economic factors and environmental preferences all help explain inter-municipality collection rates. For instance, the collection rate appears to be positively affected by increases in the unemployment rate, the share of private houses, and the presence of immigrants (unless newly arrived) in the municipality. Themore » impacts of distance to recycling industry, urbanization rate and population density on collection outcomes turn out, though, to be both statistically and economically insignificant. A reasonable explanation for this is that the monetary compensation from the material companies to the collection entrepreneurs vary depending on region and is typically higher in high-cost regions. This implies that the plastic packaging collection in Sweden may be cost ineffective. Finally, the analysis also shows that municipalities that employ weight-based waste management fees generally experience higher collection rates than those municipalities in which flat and/or volume-based fees are used.« less

Numeric analysis of terahertz wave propagation in familiar packaging materials

NASA Astrophysics Data System (ADS)

Zhang, Lihong; Yang, Guang

2015-10-01

To assess the potential application of terahertz waves in security examination, the transmission characteristics of terahertz waves in packaging materials should be studied. This paper simulates the propagation of terahertz waves in cloth and paper, studies the changes of shape and position of crest of terahertz waves before and after these materials, and gets the law of these changes, which has potential applications in thickness measurement for the thin insulated materials; gives reflected and transmitted wave of terahertz waves, and computes reflected and transmitted coefficient, indicates the good transmission properties of these materials for terahertz waves, which provides the theoretical basis for the realization of contactless security examination of packaged post, package and people pass the important passageway (such as airport and station).

Effectiveness of foam-based and traditional green roofs in reducing nitrogen, phosphorus, organic carbon and suspended solids in urban installations

NASA Astrophysics Data System (ADS)

MacAvoy, S. E.; Mucha, S.; Williamson, G.

2017-12-01

While green roofs have well understood benefits for retaining runoff, there is less of a consensus regarding the potential for retaining and absorbing nutrients or suspended solids from roof runoff that would otherwise travel to waterways. Additionally, there are numerous designs, materials and maintenance plans associated with "green" roofs/surfaces that may greatly impact not only their hydrological benefit but also their pollution mitigation potential. Here we examine the NO3, NH4, total organic carbon (TOC), total phosphorus (TP) and total suspended solids (TSS) retention potential from planted and unplanted foam roofs and traditional soil roofs. Direct precipitation, untreated runoff and throughflow from the different roof types were collected for 3 to 11 rain events over a year (depending on roof). Unplanted and traditional roofs reduced TSS by 80% or better relative to runoff. Traditional roofs showed 50% lower TP than runoff or other roof types. TOC was higher than direct precipitation for all treatments, although there were no differences among the treatments themselves. Taken as averages over the 11 events, NO3 and NH4 concentrations were highly variable for runoff and treatments and significant differences were not detected. Preliminary analysis suggests there were no differences between performance of traditional versus foam-based roofs, although a greater sample size is required to be definitive.

Ceramic ball grid array package stress analysis

NASA Astrophysics Data System (ADS)

Badri, S. H. B. S.; Aziz, M. H. A.; Ong, N. R.; Sauli, Z.; Alcain, J. B.; Retnasamy, V.

2017-09-01

The ball grid array (BGA), a form of chip scale package (CSP), was developed as one of the most advanced surface mount devices, which may be assembled by an ordinary surface ball bumps are used instead of plated nickel and gold (Ni/Au) bumps. Assembly and reliability of the BGA's printed circuit board (PCB), which is soldered by conventional surface mount technology is considered in this study. The Ceramic Ball Grid Array (CBGA) is a rectangular ceramic package or square-shaped that will use the solder ball for external electrical connections instead of leads or wire for connections. The solder balls will be arranged in an array or grid at the bottom of the ceramic package body. In this study, ANSYS software is used to investigate the stress on the package for 2 balls and 4 balls of the CBGA package with the various force range of 1-3 Newton applied to the top of the die, top of the substrate and side of the substrate. The highest maximum stress was analyzed and the maximum equivalent stress was observed on the solder ball and the die. From the simulation result, the CBGA package with less solder balls experience higher stress compared to the package with many solder balls. Therefore, less number of solder ball on the CBGA package results higher stress and critically affect the reliability of the solder balls itself, substrate and die which can lead to the solder crack and also die crack.

The role of assessment packages for diagnostic consultations: A conversation analytic perspective.

PubMed

Rossen, Camilla B; Buus, Niels; Stenager, Egon; Stenager, Elsebeth

2015-05-01

This article reports a conversation analysis of assessment package consultations. Healthcare delivery packages belong to a highly structured mode of healthcare delivery, in which specific courses of healthcare interventions related to assessment and treatment are predefined, both as to timing and content. Assessment packages are widely used in an increasing number of medical specialities; however, there is a lack of knowledge about how packaged assessment influences the interaction between doctor and patient. In this study, we investigate the final consultation in assessment packages, which is when the final clarification of the patient's symptoms takes place. The primary data of the study were eight audio recordings of consultations, and the secondary data were ethnographic field descriptions. In most consultations, packaged assessment was a resource as it provided fast and efficient clarification. In most cases, clarification was treated as good news since it either confirmed the absence of a serious disease or resulted in a diagnosis leading to relevant treatment offers. However, in some cases, clarification was not perceived as good news. This was the case in consultations with patients whose goal was to leave the consultation with clarification in the form of a definite diagnosis, but who were not offered such clarification. These patients negotiated the outcome of the consultation by applying implicit and explicit pressure, which induced the doctors to disregard the boundaries of the package and offer the patient more tests. The study highlights some of the problems related to introducing narrow, specialized package assessment. © The Author(s) 2014.

Application of humidity-controlled dynamic mechanical analysis (DMA-RH) to moisture-sensitive edible casein films for use in food packaging

USDA-ARS?s Scientific Manuscript database

Protein-based and other hydrophilic thin films are promising materials for the manufacture of edible food packaging and other food and non-food applications. Calcium caseinate (CaCas) films are highly hygroscopic and physical characterization under broad environmental conditions is critical to appli...

An Analysis of U.S. Business Schools' Catalogs, Application Packages, and Program Materials from an International Perspective.

ERIC Educational Resources Information Center

Webb, Marion S.; Mayer, Kenneth R.; Pioche, Virginie

1999-01-01

Catalogs, application packages, and program materials from 106 business schools were analyzed to determine the degree of international coverage in business schools' curricula. Findings indicated a trend to require international functional courses, such as international finance, in the traditional Master in business administration programs and to…

Rheological behaviors of edible casein-based packaging films under extreme environmental conditions, using humidity-controlled dynamic mechanical analysis

USDA-ARS?s Scientific Manuscript database

Thin casein films for food packaging applications possess good strength and low oxygen permeability but low water-resistance and elasticity. Customizing the mechanical properties of the films to target specific behaviors depending on temperature and humidity changes would enable a variety of commerc...

Beyond the Fringe: A Framework for Assessing Teach-Yourself Materials for ab initio English-Speaking Learners.

ERIC Educational Resources Information Center

Jones, Francis R.

1993-01-01

A detailed, nonimpressionistic assessment checklist is presented for teach-yourself language packages. Two example research applications are given: a survey of a range of course packages, and an analysis of the patterns of materials used by an individual learner of Hungarian. (39 references) (Author/LB)

Chemistry [Sahuarita High School Career Curriculum Project].

ERIC Educational Resources Information Center

Lane, Robert

This course entitled "Chemistry" is one of a series of instructional guides prepared by teachers for the Sahuarita High School (Arizona) Career Curriculum Project. It consists of three packages, the first dealing with solids, liquids and solutions, the second with acids, bases and anions, and the third with cation analysis. These packages are…

Power Extension Package (PEP) system definition extension, orbital service module systems analysis study. Volume 12: PEP data item descriptions

NASA Technical Reports Server (NTRS)

1979-01-01

Contractor information requirements necessary to support the power extension package project of the space shuttle program are specified for the following categories of data: project management; configuration management; systems engineering and test; manufacturing; reliability, quality assurance and safety; logistics; training; and operations.

Power Extension Package (PEP) system definition extension, orbital service module systems analysis study. Volume 11: PEP, cost, schedules, and work breakdown structure dictionary

NASA Technical Reports Server (NTRS)

1979-01-01

Cost scheduling and funding data are presented for the reference design of the power extension package. Major schedule milestones are correlated with current Spacelab flight dates. Funding distributions provide for minimum expenditure during the first year of the project.

Object-Oriented Analysis and Design of the Saber Wargame

DTIC Science & Technology

1991-12-01

coordinates for an aircraft package moving right when the starting x value is even. It is called by GO.NE, GOSE , and GONW. 108 - MOVERIGHTODD. This... GOSE , and GONW. - MOVEUPRIGHTEVEN. This procedure determines the new x and y air hex coordinates for an aircraft package moving up and right when the

Water-mass formation and Sverdrup dynamics; a comparison between climatology and a coupled ocean-atmosphere model

NASA Astrophysics Data System (ADS)

England, Matthew H.; Tomczak, Matthias; Stuart Godfrey, J.

1992-06-01

The coupled ocean-atmosphere model integrations of Manabe and Stouffer (1988) are compared with climatological distributions of depth-integrated flow and water-mass formation. The description of the ocean circulation in their two quasi-stable equilibria is extended to include an analysis of the horizontal and meridional transport as well as the water-mass formation and vertical motion in the model. In particular, the wind-driven Sverdrup flow is computed and compared with the actual mass transport streamfunction of the model. It is found that a Sverdrup model of depth-integrated flow captures the major features of the coupled model's ocean circulation, except near region of deep water formation, where the thermohaline field drives ocean currents and wind-driven flow becomes secondary. The coupled model fails to allow for a barotropic mass transport through the Indonesian Passage. Instead, only baroclinically driven fluxes of heat and freshwater are resolved through the Indonesian Archipelago. The Sverdrup model suggests that a barotropic throughflow would transport about 16 Sv from the Pacific to Indian Oceans. According to Sverdrup dynamics, this would serve to weaken the East Australian Current by about 16 Sv and strengthen the Agulhas Current by the same amount. Recent integrations of a World Ocean model with and without a barotropic throughflow in the Indonesian Passage suggest that the modelled heat transport is sensitive to the nature of flow through the Indonesian Archipelago. From' a comparison of observed and simulated water mass properties, it is shown that some major aspects of the global-scale water masses are not captured by the coupled model. This reveals a shortcoming of the model's ability to represent the global-scale heat and freshwater balances. For example, there is an unrealistically intense halocline in the immediate vicinity of Antartica, prohibiting the formation of bottom water in the Weddell and Ross Seas. Also, no low salinity traces of Antarctic or North Pacific Intermediate Water appear in the model integrations, primarily because there is no source of sufficiently dense bottom water adjacent to Antarctica. Without this dense bottom water, the "would-be" intermediate water at 60°S sinks to great depths and actually becomes the model ocean's bottom water. Then, the simulated bottom water is too fresh and warm in the climate model, matching the temperature—salinity signature of Antarctic Intermediate Water. In the North Atlantic, whilst deep water formation appears in one of the climate states of Manabe and Stouffer (1988), its downward penetration is not as deep as observed. This is because their deep North Atlantic is not ventilated by the thermohaline overturning of warm salty North Atlantic Deep Water. Instead, a deep overturning cell centred near the equator transports relatively fresh water into the region. In contrast, the location and strength of Central Water formation agrees well with climatology.

Visible spectroscopy as a tool for the assessment of storage conditions of fresh pork packaged in modified atmosphere.

PubMed

Spanos, Dimitrios; Christensen, Mette; Tørngren, Mari Ann; Baron, Caroline P

2016-03-01

The storage conditions of fresh meat are known to impact its colour and microbial shelf life. In the present study, visible spectroscopy was evaluated as a method to assess meat storage conditions and its optimisation. Fresh pork steaks (longissimus thoracis et lumborum and semimembranosus) were placed in modified atmosphere packaging using gas mixtures containing 0, 40, 50, and 80% oxygen, and stored with or without light for up to 9days. Principal component analysis of visible reflectance spectra (400-700nm) showed that the colour of the different meat cuts was affected by presence of oxygen, illumination, and storage time. Differences in the oxygen levels did not contribute to the observed variance. Predictive models based on partial least squares regression-discriminant analysis exhibited high potency in the classification of the storage parameters of meat cuts packaged in modified atmosphere. The study demonstrates the applicability of visible spectroscopy as a tool to assess the storage conditions of meat cuts packaged in modified atmosphere. Copyright © 2015 Elsevier Ltd. All rights reserved.

Scripting MODFLOW Model Development Using Python and FloPy.

PubMed

Bakker, M; Post, V; Langevin, C D; Hughes, J D; White, J T; Starn, J J; Fienen, M N

2016-09-01

Graphical user interfaces (GUIs) are commonly used to construct and postprocess numerical groundwater flow and transport models. Scripting model development with the programming language Python is presented here as an alternative approach. One advantage of Python is that there are many packages available to facilitate the model development process, including packages for plotting, array manipulation, optimization, and data analysis. For MODFLOW-based models, the FloPy package was developed by the authors to construct model input files, run the model, and read and plot simulation results. Use of Python with the available scientific packages and FloPy facilitates data exploration, alternative model evaluations, and model analyses that can be difficult to perform with GUIs. Furthermore, Python scripts are a complete, transparent, and repeatable record of the modeling process. The approach is introduced with a simple FloPy example to create and postprocess a MODFLOW model. A more complicated capture-fraction analysis with a real-world model is presented to demonstrate the types of analyses that can be performed using Python and FloPy. © 2016, National Ground Water Association.

MEANS: python package for Moment Expansion Approximation, iNference and Simulation

PubMed Central

Fan, Sisi; Geissmann, Quentin; Lakatos, Eszter; Lukauskas, Saulius; Ale, Angelique; Babtie, Ann C.; Kirk, Paul D. W.; Stumpf, Michael P. H.

2016-01-01

Motivation: Many biochemical systems require stochastic descriptions. Unfortunately these can only be solved for the simplest cases and their direct simulation can become prohibitively expensive, precluding thorough analysis. As an alternative, moment closure approximation methods generate equations for the time-evolution of the system’s moments and apply a closure ansatz to obtain a closed set of differential equations; that can become the basis for the deterministic analysis of the moments of the outputs of stochastic systems. Results: We present a free, user-friendly tool implementing an efficient moment expansion approximation with parametric closures that integrates well with the IPython interactive environment. Our package enables the analysis of complex stochastic systems without any constraints on the number of species and moments studied and the type of rate laws in the system. In addition to the approximation method our package provides numerous tools to help non-expert users in stochastic analysis. Availability and implementation: https://github.com/theosysbio/means Contacts: m.stumpf@imperial.ac.uk or e.lakatos13@imperial.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153663

MEANS: python package for Moment Expansion Approximation, iNference and Simulation.

PubMed

Fan, Sisi; Geissmann, Quentin; Lakatos, Eszter; Lukauskas, Saulius; Ale, Angelique; Babtie, Ann C; Kirk, Paul D W; Stumpf, Michael P H

2016-09-15

Many biochemical systems require stochastic descriptions. Unfortunately these can only be solved for the simplest cases and their direct simulation can become prohibitively expensive, precluding thorough analysis. As an alternative, moment closure approximation methods generate equations for the time-evolution of the system's moments and apply a closure ansatz to obtain a closed set of differential equations; that can become the basis for the deterministic analysis of the moments of the outputs of stochastic systems. We present a free, user-friendly tool implementing an efficient moment expansion approximation with parametric closures that integrates well with the IPython interactive environment. Our package enables the analysis of complex stochastic systems without any constraints on the number of species and moments studied and the type of rate laws in the system. In addition to the approximation method our package provides numerous tools to help non-expert users in stochastic analysis. https://github.com/theosysbio/means m.stumpf@imperial.ac.uk or e.lakatos13@imperial.ac.uk Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments.

PubMed

Wen, Bo; Xu, Shaohang; Sheynkman, Gloria M; Feng, Qiang; Lin, Liang; Wang, Quanhui; Xu, Xun; Wang, Jun; Liu, Siqi

2014-11-01

Single nucleotide variations (SNVs) located within a reading frame can result in single amino acid polymorphisms (SAPs), leading to alteration of the corresponding amino acid sequence as well as function of a protein. Accurate detection of SAPs is an important issue in proteomic analysis at the experimental and bioinformatic level. Herein, we present sapFinder, an R software package, for detection of the variant peptides based on tandem mass spectrometry (MS/MS)-based proteomics data. This package automates the construction of variation-associated databases from public SNV repositories or sample-specific next-generation sequencing (NGS) data and the identification of SAPs through database searching, post-processing and generation of HTML-based report with visualized interface. sapFinder is implemented as a Bioconductor package in R. The package and the vignette can be downloaded at http://bioconductor.org/packages/devel/bioc/html/sapFinder.html and are provided under a GPL-2 license. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Active packaging from chitosan-titanium dioxide nanocomposite film for prolonging storage life of tomato fruit.

PubMed

Kaewklin, Patinya; Siripatrawan, Ubonrat; Suwanagul, Anawat; Lee, Youn Suk

2018-06-01

The feasibility of active packaging from chitosan (CS) and chitosan containing nanosized titanium dioxide (CT) to maintain quality and extend storage life of climacteric fruit was investigated. The CT nanocomposite film and CS film were fabricated using a solution casting method and used as active packaging to delay ripening process of cherry tomatoes. Changes in firmness, weight loss, a*/b* color, lycopene content, total soluble solid, ascorbic acid, and concentration of ethylene and carbon dioxide of the tomatoes packaged in CT film, CS film, and control (without CT or CS films) were monitored during storage at 20°C. Classification of fruit quality as a function of different packaging treatments was visualized using linear discriminant analysis. Tomatoes packaged in the CT film evolved lower quality changes than those in the CS film and control. The results suggested that the CT film exhibited ethylene photodegradation activity when exposed to UV light and consequently delayed the ripening process and changes in the quality of the tomatoes. Copyright © 2018 Elsevier B.V. All rights reserved.

Iron chelating active packaging: Influence of competing ions and pH value on effectiveness of soluble and immobilized hydroxamate chelators.

PubMed

Ogiwara, Yoshiko; Roman, Maxine J; Decker, Eric A; Goddard, Julie M

2016-04-01

Many packaged foods utilize synthetic chelators (e.g. ethylenediaminetetraacetic acid, EDTA) to inhibit iron-promoted oxidation or microbial growth which would result in quality loss. To address consumer demands for all natural products, we have previously developed a non-migratory iron chelating active packaging material by covalent immobilization of polyhydroxamate and demonstrated its efficacy in delaying lipid oxidation. Herein, we demonstrate the ability of this hydroxamate-functionalized iron chelating active packaging to retain iron chelating capacity; even in the presence of competing ions common in food. Both immobilized and soluble hydroxamate chelators retained iron chelating capacity in the presence of calcium, magnesium, and sodium competing ions, although at pH 5.0 the presence of calcium reduced immobilized hydroxamate iron chelation. A strong correlation was found between colorimetric and mass spectral analysis of iron chelation by the chelating packaging material. Such chelating active packaging may support reducing additive use in product formulations, while retaining quality and shelf life. Copyright © 2015 Elsevier Ltd. All rights reserved.

27 CFR 25.195 - Removals for analysis.

Code of Federal Regulations, 2011 CFR

2011-04-01

..., DEPARTMENT OF THE TREASURY LIQUORS BEER Removals Without Payment of Tax Removals for Analysis, Research... analysis in packages or in bulk containers. The brewer shall record beer removed for analysis in daily...

27 CFR 25.195 - Removals for analysis.

Code of Federal Regulations, 2010 CFR

2010-04-01

..., DEPARTMENT OF THE TREASURY LIQUORS BEER Removals Without Payment of Tax Removals for Analysis, Research... analysis in packages or in bulk containers. The brewer shall record beer removed for analysis in daily...

SNP_tools: A compact tool package for analysis and conversion of genotype data for MS-Excel

PubMed Central

Chen, Bowang; Wilkening, Stefan; Drechsel, Marion; Hemminki, Kari

2009-01-01

Background Single nucleotide polymorphism (SNP) genotyping is a major activity in biomedical research. Scientists prefer to have a facile access to the results which may require conversions between data formats. First hand SNP data is often entered in or saved in the MS-Excel format, but this software lacks genetic and epidemiological related functions. A general tool to do basic genetic and epidemiological analysis and data conversion for MS-Excel is needed. Findings The SNP_tools package is prepared as an add-in for MS-Excel. The code is written in Visual Basic for Application, embedded in the Microsoft Office package. This add-in is an easy to use tool for users with basic computer knowledge (and requirements for basic statistical analysis). Conclusion Our implementation for Microsoft Excel 2000-2007 in Microsoft Windows 2000, XP, Vista and Windows 7 beta can handle files in different formats and converts them into other formats. It is a free software. PMID:19852806

SNP_tools: A compact tool package for analysis and conversion of genotype data for MS-Excel.

PubMed

Chen, Bowang; Wilkening, Stefan; Drechsel, Marion; Hemminki, Kari

2009-10-23

Single nucleotide polymorphism (SNP) genotyping is a major activity in biomedical research. Scientists prefer to have a facile access to the results which may require conversions between data formats. First hand SNP data is often entered in or saved in the MS-Excel format, but this software lacks genetic and epidemiological related functions. A general tool to do basic genetic and epidemiological analysis and data conversion for MS-Excel is needed. The SNP_tools package is prepared as an add-in for MS-Excel. The code is written in Visual Basic for Application, embedded in the Microsoft Office package. This add-in is an easy to use tool for users with basic computer knowledge (and requirements for basic statistical analysis). Our implementation for Microsoft Excel 2000-2007 in Microsoft Windows 2000, XP, Vista and Windows 7 beta can handle files in different formats and converts them into other formats. It is a free software.

JGromacs: a Java package for analyzing protein simulations.

PubMed

Münz, Márton; Biggin, Philip C

2012-01-23

In this paper, we introduce JGromacs, a Java API (Application Programming Interface) that facilitates the development of cross-platform data analysis applications for Molecular Dynamics (MD) simulations. The API supports parsing and writing file formats applied by GROMACS (GROningen MAchine for Chemical Simulations), one of the most widely used MD simulation packages. JGromacs builds on the strengths of object-oriented programming in Java by providing a multilevel object-oriented representation of simulation data to integrate and interconvert sequence, structure, and dynamics information. The easy-to-learn, easy-to-use, and easy-to-extend framework is intended to simplify and accelerate the implementation and development of complex data analysis algorithms. Furthermore, a basic analysis toolkit is included in the package. The programmer is also provided with simple tools (e.g., XML-based configuration) to create applications with a user interface resembling the command-line interface of GROMACS applications. JGromacs and detailed documentation is freely available from http://sbcb.bioch.ox.ac.uk/jgromacs under a GPLv3 license .

Migration from printing inks in multilayer food packaging materials by GC-MS analysis and pattern recognition with chemometrics.

PubMed

Clemente, Isabel; Aznar, Margarita; Nerín, Cristina; Bosetti, Osvaldo

2016-01-01

Inks and varnishes used in food packaging multilayer materials can contain different substances that are potential migrants when packaging is in contact with food. Although printing inks are applied on the external layer, they can migrate due to set-off phenomena. In order to assess food safety, migration tests were performed from two materials sets: set A based on paper and set B based on PET; both contained inks. Migration was performed to four food simulants (EtOH 50%, isooctane, EtOH 95% and Tenax(®)) and the volatile compounds profile was analysed by GC-MS. The effect of presence/absence of inks and varnishes and also their position in the material was studied. A total of 149 volatile compounds were found in migration from set A and 156 from set B materials, some of them came from inks. Quantitative analysis and a principal component analysis were performed in order to identify patterns among sample groups.

Around and about an application of the GAMLSS package to non-stationary flood frequency analysis

NASA Astrophysics Data System (ADS)

Debele, S. E.; Bogdanowicz, E.; Strupczewski, W. G.

2017-08-01

The non-stationarity of hydrologic processes due to climate change or human activities is challenging for the researchers and practitioners. However, the practical requirements for taking into account non-stationarity as a support in decision-making procedures exceed the up-to-date development of the theory and the of software. Currently, the most popular and freely available software package that allows for non-stationary statistical analysis is the GAMLSS (generalized additive models for location, scale and shape) package. GAMLSS has been used in a variety of fields. There are also several papers recommending GAMLSS in hydrological problems; however, there are still important issues which have not previously been discussed concerning mainly GAMLSS applicability not only for research and academic purposes, but also in a design practice. In this paper, we present a summary of our experiences in the implementation of GAMLSS to non-stationary flood frequency analysis, highlighting its advantages and pointing out weaknesses with regard to methodological and practical topics.

Thermal Analysis of the NASA Integrated Vehicle Health Monitoring Experiment Technology for X-Vehicles (NITEX)

NASA Technical Reports Server (NTRS)

Hegab, Hisham E.

2002-01-01

The purpose of this project was to perform a thermal analysis for the NASA Integrated Vehicle Health Monitoring (IVHM) Technology Experiment for X-vehicles (NITEX). This electronics package monitors vehicle sensor information in flight and downlinks vehicle health summary information via telemetry. The experiment will be tested on the X-34 in an unpressurized compartment, in the vicinity of one of the vehicle's liquid oxygen tanks. The transient temperature profile for the electronics package has been determined using finite element analysis for possible mission profiles that will most likely expose the package to the most extreme hot and cold environmental conditions. From the analyses, it was determined that temperature limits for the electronics would be exceeded for the worst case cold environment mission profile. The finite element model used for the analyses was modified to examine the use of insulation to address this problem. Recommendations for insulating the experiment for the cold environment are presented, and were analyzed to determine their effect on a nominal mission profile.

Thermal Analysis Of The NASA Integrated Vehicle Health Monitoring Experiment Technology For X-Vehicles (NITEX)

NASA Technical Reports Server (NTRS)

Hegab, Hisham E.

2001-01-01

The purpose of this project was to perform a thermal analysis for the NASA Integrated Vehicle Health Monitoring (IVHM) Technology Experiment for X-vehicles (NITEX). This electronics package monitors vehicle sensor information in flight and downlinks vehicle health summary information via telemetry. The experiment will be tested on the X-34 in an unpressurized compartment, in the vicinity of one of the vehicle's liquid oxygen tanks. The transient temperature profile for the electronics package has been determined using finite element analysis for possible mission profiles that will most likely expose the package to the most extreme hot and cold environmental conditions. From the analyses, it was determined that temperature limits for the electronics would be exceeded for the worst case cold environment mission profile. The finite element model used for the analyses was modified to examine the use of insulation to address this problem. Recommendations for insulating the experiment for the cold environment are presented, and were analyzed to determine their effect on a nominal mission profile.

Motofit - integrating neutron reflectometry acquisition, reduction and analysis into one, easy to use, package

NASA Astrophysics Data System (ADS)

Nelson, Andrew

2010-11-01

The efficient use of complex neutron scattering instruments is often hindered by the complex nature of their operating software. This complexity exists at each experimental step: data acquisition, reduction and analysis, with each step being as important as the previous. For example, whilst command line interfaces are powerful at automated acquisition they often reduce accessibility by novice users and sometimes reduce the efficiency for advanced users. One solution to this is the development of a graphical user interface which allows the user to operate the instrument by a simple and intuitive "push button" approach. This approach was taken by the Motofit software package for analysis of multiple contrast reflectometry data. Here we describe the extension of this package to cover the data acquisition and reduction steps for the Platypus time-of-flight neutron reflectometer. Consequently, the complete operation of an instrument is integrated into a single, easy to use, program, leading to efficient instrument usage.

JGromacs: A Java Package for Analyzing Protein Simulations

PubMed Central

2011-01-01

In this paper, we introduce JGromacs, a Java API (Application Programming Interface) that facilitates the development of cross-platform data analysis applications for Molecular Dynamics (MD) simulations. The API supports parsing and writing file formats applied by GROMACS (GROningen MAchine for Chemical Simulations), one of the most widely used MD simulation packages. JGromacs builds on the strengths of object-oriented programming in Java by providing a multilevel object-oriented representation of simulation data to integrate and interconvert sequence, structure, and dynamics information. The easy-to-learn, easy-to-use, and easy-to-extend framework is intended to simplify and accelerate the implementation and development of complex data analysis algorithms. Furthermore, a basic analysis toolkit is included in the package. The programmer is also provided with simple tools (e.g., XML-based configuration) to create applications with a user interface resembling the command-line interface of GROMACS applications. Availability: JGromacs and detailed documentation is freely available from http://sbcb.bioch.ox.ac.uk/jgromacs under a GPLv3 license. PMID:22191855

'spup' - an R package for uncertainty propagation analysis in spatial environmental modelling

NASA Astrophysics Data System (ADS)

Sawicka, Kasia; Heuvelink, Gerard

2017-04-01

Computer models have become a crucial tool in engineering and environmental sciences for simulating the behaviour of complex static and dynamic systems. However, while many models are deterministic, the uncertainty in their predictions needs to be estimated before they are used for decision support. Currently, advances in uncertainty propagation and assessment have been paralleled by a growing number of software tools for uncertainty analysis, but none has gained recognition for a universal applicability and being able to deal with case studies with spatial models and spatial model inputs. Due to the growing popularity and applicability of the open source R programming language we undertook a project to develop an R package that facilitates uncertainty propagation analysis in spatial environmental modelling. In particular, the 'spup' package provides functions for examining the uncertainty propagation starting from input data and model parameters, via the environmental model onto model predictions. The functions include uncertainty model specification, stochastic simulation and propagation of uncertainty using Monte Carlo (MC) techniques, as well as several uncertainty visualization functions. Uncertain environmental variables are represented in the package as objects whose attribute values may be uncertain and described by probability distributions. Both numerical and categorical data types are handled. Spatial auto-correlation within an attribute and cross-correlation between attributes is also accommodated for. For uncertainty propagation the package has implemented the MC approach with efficient sampling algorithms, i.e. stratified random sampling and Latin hypercube sampling. The design includes facilitation of parallel computing to speed up MC computation. The MC realizations may be used as an input to the environmental models called from R, or externally. Selected visualization methods that are understandable by non-experts with limited background in statistics can be used to summarize and visualize uncertainty about the measured input, model parameters and output of the uncertainty propagation. We demonstrate that the 'spup' package is an effective and easy tool to apply and can be used in multi-disciplinary research and model-based decision support.

Predictive Utility of Marketed Volumetric Software Tools in Subjects at Risk for Alzheimer Disease: Do Regions Outside the Hippocampus Matter?

PubMed

Tanpitukpongse, T P; Mazurowski, M A; Ikhena, J; Petrella, J R

2017-03-01

Alzheimer disease is a prevalent neurodegenerative disease. Computer assessment of brain atrophy patterns can help predict conversion to Alzheimer disease. Our aim was to assess the prognostic efficacy of individual-versus-combined regional volumetrics in 2 commercially available brain volumetric software packages for predicting conversion of patients with mild cognitive impairment to Alzheimer disease. Data were obtained through the Alzheimer's Disease Neuroimaging Initiative. One hundred ninety-two subjects (mean age, 74.8 years; 39% female) diagnosed with mild cognitive impairment at baseline were studied. All had T1-weighted MR imaging sequences at baseline and 3-year clinical follow-up. Analysis was performed with NeuroQuant and Neuroreader. Receiver operating characteristic curves assessing the prognostic efficacy of each software package were generated by using a univariable approach using individual regional brain volumes and 2 multivariable approaches (multiple regression and random forest), combining multiple volumes. On univariable analysis of 11 NeuroQuant and 11 Neuroreader regional volumes, hippocampal volume had the highest area under the curve for both software packages (0.69, NeuroQuant; 0.68, Neuroreader) and was not significantly different ( P > .05) between packages. Multivariable analysis did not increase the area under the curve for either package (0.63, logistic regression; 0.60, random forest NeuroQuant; 0.65, logistic regression; 0.62, random forest Neuroreader). Of the multiple regional volume measures available in FDA-cleared brain volumetric software packages, hippocampal volume remains the best single predictor of conversion of mild cognitive impairment to Alzheimer disease at 3-year follow-up. Combining volumetrics did not add additional prognostic efficacy. Therefore, future prognostic studies in mild cognitive impairment, combining such tools with demographic and other biomarker measures, are justified in using hippocampal volume as the only volumetric biomarker. © 2017 by American Journal of Neuroradiology.

Packaging interventions to increase medication adherence: systematic review and meta-analysis

PubMed Central

Conn, Vicki S.; Ruppar, Todd M.; Chan, Keith C.; Dunbar-Jacob, Jacqueline; Pepper, Ginette A.; De Geest, Sabina

2015-01-01

Objective Inadequate medication adherence is a widespread problem that contributes to increase chronic disease complications and health care expenditures. Packaging interventions using pill boxes and blister packs have been widely recommended to address the medication adherence issue. This meta-analysis review determined the overall effect of packaging interventions on medication adherence and health outcomes. In addition, we tested whether effects vary depending on intervention, sample, and design characteristics. Research design and methods Extensive literature search strategies included examination of 13 computerized databases and 19 research registries, hand searches of 57 journal, and author and ancestry searches. Eligible studies included either pill-boxes or blister packaging interventions to increase medication adherence. Primary study characteristics and outcomes were reliably coded. Random-effects analyses were used to calculate overall effect sizes and conduct moderator analyses. Results Data were synthesized across 22,858 subjects from 52 reports. The overall mean weighted standardized difference effect size for two-group comparisons was 0.593 (favoring treatment over control), which is consistent with the mean of 71% adherence for treatment subjects compared to 63% among control subjects. We found using moderator analyses that interventions were most effective when they used blister packs and were delivered in pharmacies, while interventions were less effective when studies included older subjects and those with cognitive impairment. Methodological moderator analyses revealed significantly larger effect sizes in studies reporting continuous data outcomes instead of dichotomous results and in studies using pharmacy refill medication adherence measures as compared to studies with self-report measures. Conclusions Overall, meta-analysis findings support the use of packaging interventions to effectively increase medication adherence. Limitations of the study include the exclusion of packaging interventions other than pill boxes and blister packs, evidence of publication bias, and primary study sparse reporting of health outcomes and potentially interesting moderating variables such as the number of prescribed medications. PMID:25333709

User guide to Exploration and Graphics for RivEr Trends (EGRET) and dataRetrieval: R packages for hydrologic data

USGS Publications Warehouse

Hirsch, Robert M.; De Cicco, Laura A.

2015-01-01

Evaluating long-term changes in river conditions (water quality and discharge) is an important use of hydrologic data. To carry out such evaluations, the hydrologist needs tools to facilitate several key steps in the process: acquiring the data records from a variety of sources, structuring it in ways that facilitate the analysis, processing the data with routines that extract information about changes that may be happening, and displaying findings with graphical techniques. A pair of tightly linked R packages, called dataRetrieval and EGRET (Exploration and Graphics for RivEr Trends), have been developed for carrying out each of these steps in an integrated manner. They are designed to easily accept data from three sources: U.S. Geological Survey hydrologic data, U.S. Environmental Protection Agency (EPA) STORET data, and user-supplied flat files. The dataRetrieval package not only serves as a “front end” to the EGRET package, it can also be used to easily download many types of hydrologic data and organize it in ways that facilitate many other hydrologic applications. The EGRET package has components oriented towards the description of long-term changes in streamflow statistics (high flow, average flow, and low flow) as well as changes in water quality. For the water-quality analysis, it uses Weighted Regressions on Time, Discharge and Season (WRTDS) to describe long-term trends in both concentration and flux. EGRET also creates a wide range of graphical presentations of the water-quality data and of the WRTDS results. This report serves as a user guide to these two R packages, providing detailed guidance on installation and use of the software, documentation of the analysis methods used, as well as guidance on some of the kinds of questions and approaches that the software can facilitate.

ddPCRclust - An R package and Shiny app for automated analysis of multiplexed ddPCR data.

PubMed

Brink, Benedikt G; Meskas, Justin; Brinkman, Ryan R

2018-03-09

Droplet digital PCR (ddPCR) is an emerging technology for quantifying DNA. By partitioning the target DNA into ∼20000 droplets, each serving as its own PCR reaction compartment, a very high sensitivity of DNA quantification can be achieved. However, manual analysis of the data is time consuming and algorithms for automated analysis of non-orthogonal, multiplexed ddPCR data are unavailable, presenting a major bottleneck for the advancement of ddPCR transitioning from low-throughput to high- throughput. ddPCRclust is an R package for automated analysis of data from Bio-Rad's droplet digital PCR systems (QX100 and QX200). It can automatically analyse and visualise multiplexed ddPCR experiments with up to four targets per reaction. Results are on par with manual analysis, but only take minutes to compute instead of hours. The accompanying Shiny app ddPCRvis provides easy access to the functionalities of ddPCRclust through a web-browser based GUI. R package: https://github.com/bgbrink/ddPCRclust; Interface: https://github.com/bgbrink/ddPCRvis/; Web: https://bibiserv.cebitec.uni-bielefeld.de/ddPCRvis/. bbrink@cebitec.uni-bielefeld.de.

Vibration analysis of printed circuit boards: Effect of boundary condition

NASA Astrophysics Data System (ADS)

Prashanth, M. D.

2018-04-01

A spacecraft consists of a number of electronic packages to meet the functional requirements. An electronic package is generally an assembly of printed circuit boards placed in a mechanical housing. A number of electronic components are mounted on the printed circuit board (PCB). A spacecraft experiences various types of loads during its launch such as vibration, acoustic and shock loads. Prediction of response for printed circuit boards due to vibration loads is important for mechanical design and reliability of electronic packages. The modeling and analysis of printed circuit boards is required for accurate prediction of response due to vibration loads. The response of PCB is highly dependent on the mounting configuration of PCB. In addition, anti-vibration mounts or stiffeners are used to reduce the PCB response. Vibration analysis of printed circuit boards is carried out using finite element method. The objective of this paper is to determine the dynamic characteristics of a printed circuit board. Modeling and analysis of PCB shall be carried out to study the effect of boundary conditions on the vibration response. The modeling of stiffeners or ribs shall also be considered in detail. The analysis results shall be validated using vibration tests of PCB.

A Novel Method to Decontaminate Surgical Instruments for Operational and Austere Environments.

PubMed

Knox, Randy W; Demons, Samandra T; Cunningham, Cord W

2015-12-01

The purpose of this investigation was to test a field-expedient, cost-effective method to decontaminate, sterilize, and package surgical instruments in an operational (combat) or austere environment using chlorhexidine sponges, ultraviolet C (UVC) light, and commercially available vacuum sealing. This was a bench study of 4 experimental groups and 1 control group of 120 surgical instruments. Experimental groups were inoculated with a 10(6) concentration of common wound bacteria. The control group was vacuum sealed without inoculum. Groups 1, 2, and 3 were first scrubbed with a chlorhexidine sponge, rinsed, and dried. Group 1 was then packaged; group 2 was irradiated with UVC light, then packaged; group 3 was packaged, then irradiated with UVC light through the bag; and group 4 was packaged without chlorhexidine scrubbing or UVC irradiation. The UVC was not tested by itself, as it does not grossly clean. The instruments were stored overnight and tested for remaining colony forming units (CFU). Data analysis was conducted using analysis of variance and group comparisons using the Tukey method. Group 4 CFU was statistically greater (P < .001) than the control group and groups 1 through 3. There was no statistically significant difference between the control group and groups 1 through 3. Vacuum sealing of chlorhexidine-scrubbed contaminated instruments with and without handheld UVC irradiation appears to be an acceptable method of field decontamination. Chlorhexidine scrubbing alone achieved a 99.9% reduction in CFU, whereas adding UVC before packaging achieved sterilization or 100% reduction in CFU, and UVC through the bag achieved disinfection. Published by Elsevier Inc.

A qualitative analysis of New Zealand retailers' responses to standardised packaging legislation and tobacco industry opposition.

PubMed

Guthrie, John; Hoek, Janet; Darroch, Ella; Wood, Zoë

2015-11-09

Many of the approximately 8000 New Zealand retailers selling tobacco are small stores that tobacco companies have represented as victims of policy measures designed to reduce smoking. Despite this depiction, many retailers experience considerable ambivalence in selling tobacco, a product they know harms their customers. We explored how retailers perceived the proposed introduction of standardised (or 'plain') packaging and their assessment of arguments made by tobacco companies in submissions on proposed standardised packaging legislation. Using qualitative in-depth interviews, we recruited and interviewed 23 retailers of dairies (small convenience stores), small supermarkets, and service stations. Data were analysed using a protocol-driven approach; this stance enabled direct analysis of tobacco companies' arguments, particularly those purporting to represent retailers' concerns. Retailers were concerned about the financial implications of standardised packaging and the effects it may have on their ability to provide rapid and efficient customer service. However, few thought standardised packaging would foster illicit trade or spawn further regulation; most placed public health goals ahead of tobacco companies' 'rights', and many supported government intervention to protect population health. Retailers held ambivalent views on standardised packaging; while they were concerned about short-term effects on their business, they recognised the harm smoking causes. Policymakers and health researchers could collaborate more effectively with retailers by assisting them to create financially viable roles more compatible with public health objectives. 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/