WorldWideScience

Sample records for profiles sampled flux

  1. The influence of humidity fluxes on offshore wind speed profiles

    DEFF Research Database (Denmark)

    Barthelmie, Rebecca Jane; Sempreviva, Anna Maria; Pryor, Sara

    2010-01-01

    extrapolation from lower measurements. With humid conditions and low mechanical turbulence offshore, deviations from the traditional logarithmic wind speed profile become significant and stability corrections are required. This research focuses on quantifying the effect of humidity fluxes on stability corrected...... wind speed profiles. The effect on wind speed profiles is found to be important in stable conditions where including humidity fluxes forces conditions towards neutral. Our results show that excluding humidity fluxes leads to average predicted wind speeds at 150 m from 10 m which are up to 4% higher...... than if humidity fluxes are included, and the results are not very sensitive to the method selected to estimate humidity fluxes....

  2. The influence of humidity fluxes on offshore wind speed profiles

    Directory of Open Access Journals (Sweden)

    R. J. Barthelmie

    2010-05-01

    Full Text Available Wind energy developments offshore focus on larger turbines to keep the relative cost of the foundation per MW of installed capacity low. Hence typical wind turbine hub-heights are extending to 100 m and potentially beyond. However, measurements to these heights are not usually available, requiring extrapolation from lower measurements. With humid conditions and low mechanical turbulence offshore, deviations from the traditional logarithmic wind speed profile become significant and stability corrections are required. This research focuses on quantifying the effect of humidity fluxes on stability corrected wind speed profiles. The effect on wind speed profiles is found to be important in stable conditions where including humidity fluxes forces conditions towards neutral. Our results show that excluding humidity fluxes leads to average predicted wind speeds at 150 m from 10 m which are up to 4% higher than if humidity fluxes are included, and the results are not very sensitive to the method selected to estimate humidity fluxes.

  3. Flux-profile relationships over a fetch limited beech forest

    DEFF Research Database (Denmark)

    Dellwik, E.; Jensen, N.O.

    2005-01-01

    The influence of an internal boundary layer and a roughness sublayer on flux-profile relationships for momentum and sensible heat have been investigated for a closed beech forest canopy with limited fetch conditions. The influence was quantified by derivation of local scaling functions for sensib...

  4. SNS Sample Activation Calculator Flux Recommendations and Validation

    Energy Technology Data Exchange (ETDEWEB)

    McClanahan, Tucker C. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Spallation Neutron Source (SNS); Gallmeier, Franz X. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Spallation Neutron Source (SNS); Iverson, Erik B. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Spallation Neutron Source (SNS); Lu, Wei [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Spallation Neutron Source (SNS)

    2015-02-01

    The Spallation Neutron Source (SNS) at Oak Ridge National Laboratory (ORNL) uses the Sample Activation Calculator (SAC) to calculate the activation of a sample after the sample has been exposed to the neutron beam in one of the SNS beamlines. The SAC webpage takes user inputs (choice of beamline, the mass, composition and area of the sample, irradiation time, decay time, etc.) and calculates the activation for the sample. In recent years, the SAC has been incorporated into the user proposal and sample handling process, and instrument teams and users have noticed discrepancies in the predicted activation of their samples. The Neutronics Analysis Team validated SAC by performing measurements on select beamlines and confirmed the discrepancies seen by the instrument teams and users. The conclusions were that the discrepancies were a result of a combination of faulty neutron flux spectra for the instruments, improper inputs supplied by SAC (1.12), and a mishandling of cross section data in the Sample Activation Program for Easy Use (SAPEU) (1.1.2). This report focuses on the conclusion that the SAPEU (1.1.2) beamline neutron flux spectra have errors and are a significant contributor to the activation discrepancies. The results of the analysis of the SAPEU (1.1.2) flux spectra for all beamlines will be discussed in detail. The recommendations for the implementation of improved neutron flux spectra in SAPEU (1.1.3) are also discussed.

  5. A LOFAR census of non-recycled pulsars: average profiles, dispersion measures, flux densities, and spectra

    Science.gov (United States)

    Bilous, A. V.; Kondratiev, V. I.; Kramer, M.; Keane, E. F.; Hessels, J. W. T.; Stappers, B. W.; Malofeev, V. M.; Sobey, C.; Breton, R. P.; Cooper, S.; Falcke, H.; Karastergiou, A.; Michilli, D.; Osłowski, S.; Sanidas, S.; ter Veen, S.; van Leeuwen, J.; Verbiest, J. P. W.; Weltevrede, P.; Zarka, P.; Grießmeier, J.-M.; Serylak, M.; Bell, M. E.; Broderick, J. W.; Eislöffel, J.; Markoff, S.; Rowlinson, A.

    2016-06-01

    We present first results from a LOFAR census of non-recycled pulsars. The census includes almost all such pulsars known (194 sources) at declinations Dec > 8° and Galactic latitudes |Gb| > 3°, regardless of their expected flux densities and scattering times. Each pulsar was observed for ≥20 min in the contiguous frequency range of 110-188 MHz. Full-Stokes data were recorded. We present the dispersion measures, flux densities, and calibrated total intensity profiles for the 158 pulsars detected in the sample. The median uncertainty in census dispersion measures (1.5 × 10-3 pc cm-3) is ten times smaller, on average, than in the ATNF pulsar catalogue. We combined census flux densities with those in the literature and fitted the resulting broadband spectra with single or broken power-law functions. For 48 census pulsars such fits are being published for the first time. Typically, thechoice between single and broken power-laws, as well as the location of the spectral break, were highly influenced by the spectral coverage of the available flux density measurements. In particular, the inclusion of measurements below 100 MHz appears essential for investigating the low-frequency turnover in the spectra for most of the census pulsars. For several pulsars, we compared the spectral indices from different works and found the typical spread of values to be within 0.5-1.5, suggesting a prevailing underestimation of spectral index errors in the literature. The census observations yielded some unexpected individual source results, as we describe in the paper. Lastly, we will provide this unique sample of wide-band, low-frequency pulse profiles via the European Pulsar Network Database. Tables B.1-B.4 are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/591/A134

  6. Linking evaporative fluxes from bare soils across surface viscous sublayer with the Monin-Obukhov atmospheric flux-profile estimates

    OpenAIRE

    Haghighi Erfan; Or Dani

    2015-01-01

    The Monin–Obukhov similarity theory (MOST) provides the theoretical basis for many “atmospheric based” methods (such as eddy covariance and flux profile methods) that are widely used for quantifying surface–atmosphere exchange processes. The turbulence driven and highly nonlinear profiles of momentum air temperature and vapor densities require complex resistance expressions applied to simple gradients deduced from a single or few height measurements. Notwithstanding the success of these atmos...

  7. Flux Calibration and Spectral Typing of the SPLASH Sample

    Science.gov (United States)

    Chang, Caroline; Vemuri, Nikita; Hamren, Katherine; Guhathakurta, Puragra

    2015-01-01

    We present the spectroscopic identification of M-stars in the disk of the Andromeda Galaxy (M31) and revised spectral types for the M-stars in the X-Shooter Library (XSL). Our dataset consists of optical spectra taken with the DEIMOS spectrograph on the Keck II 10-m telescope as part of the Spectroscopic Landscape of Andromeda's Stellar Halo (SPLASH) survey. We use stars from the MILES and X-Shooter Libraries to perform a first order flux calibration of these spectra, then use TiO-based indices from Fluks et al. 1994 to determine the probable M spectral subtype. While testing this procedure on the M-stars of the XSL, we find that the spectral subtypes derived from the spectra themselves are different from the spectral subtypes obtained from the literature and that XSL includes several spectra with subtypes seemingly later than M10. We suggest that this is due to stellar variability. We also identify ~2000 M-stars in the SPLASH sample. We present the distribution of subtypes here.This research was funded by grants from the National Science Foundation and the Space Telescope Science Institute. Some of the research presented here was conducted by high-school students under the auspices of the University of California Santa Cruz's Science Internship Program.

  8. Probing methane hydrate nucleation through the forward flux sampling method.

    Science.gov (United States)

    Bi, Yuanfei; Li, Tianshu

    2014-11-26

    Understanding the nucleation of hydrate is the key to developing effective strategies for controlling methane hydrate formation. Here we present a computational study of methane hydrate nucleation, by combining the forward flux sampling (FFS) method and the coarse-grained water model mW. To facilitate the application of FFS in studying the formation of methane hydrate, we developed an effective order parameter λ on the basis of the topological analysis of the tetrahedral network. The order parameter capitalizes the signature of hydrate structure, i.e., polyhedral cages, and is capable of efficiently distinguishing hydrate from ice and liquid water while allowing the formation of different hydrate phases, i.e., sI, sII, and amorphous. Integration of the order parameter λ with FFS allows explicitly computing hydrate nucleation rates and obtaining an ensemble of nucleation trajectories under conditions where spontaneous hydrate nucleation becomes too slow to occur in direct simulation. The convergence of the obtained hydrate nucleation rate was found to depend crucially on the convergence of the spatial distribution for the spontaneously formed hydrate seeds obtained from the initial sampling of FFS. The validity of the approach is also verified by the agreement between the calculated nucleation rate and that inferred from the direct simulation. Analyzing the obtained large ensemble of hydrate nucleation trajectories, we show hydrate formation at 220 K and 500 bar is initiated by the nucleation events occurring in the vicinity of water-methane interface, and facilitated by a gradual transition from amorphous to crystalline structure. The latter provides the direct support to the proposed two-step nucleation mechanism of methane hydrate.

  9. Wind profiles, momentum fluxes and roughness lengths at Cabauw revisited

    NARCIS (Netherlands)

    Verkaik, J.W.; Holtslag, A.A.M.

    2007-01-01

    We describe the results of an experiment focusing on wind speed and momentum fluxes in the atmospheric boundary layer up to 200 m. The measurements were conducted in 1996 at the Cabauw site in the Netherlands. Momentum fluxes are measured using the K-Gill Propeller Vane. Estimates of the roughness

  10. Determination of DNA profiling of siwak and toothbrush samples ...

    African Journals Online (AJOL)

    Background: DNA profiling is an integral part of forensic work. Enough and good samples for DNA quantification and profiling are mandatory. Aim of the study: To quantify and profile DNA from siwak and toothbrushes and study the effect of time on this process. Methodology: The present study included DNA profiling from ...

  11. Rapid measurement of charged particle beam profiles using a current flux grating

    Energy Technology Data Exchange (ETDEWEB)

    Paul, Samit; Chowdhury, Abhishek; Bhattacharjee, Sudeep [Department of Physics, Indian Institute of Technology, Kanpur 208016, UP (India)

    2015-02-15

    The principle and physics issues of charged particle beam diagnostics using a current flux grating are presented. Unidirectional array of conducting channels with interstitial insulating layers of spacing d is placed in the beam path to capture flux of charge and electronically reproduce an exact beam current profile with density variation. The role of secondary electrons due to the impinging particle beam (both electron and ion) on the probe is addressed and a correction factor is introduced. A 2-dimensional profile of the electron beam is obtained by rotating the probe about the beam axis. Finally, a comparison of measured beam profile with a Gaussian is presented.

  12. Estimation of dynamic flux profiles from metabolic time series data

    Directory of Open Access Journals (Sweden)

    Chou I-Chun

    2012-07-01

    Full Text Available Abstract Background Advances in modern high-throughput techniques of molecular biology have enabled top-down approaches for the estimation of parameter values in metabolic systems, based on time series data. Special among them is the recent method of dynamic flux estimation (DFE, which uses such data not only for parameter estimation but also for the identification of functional forms of the processes governing a metabolic system. DFE furthermore provides diagnostic tools for the evaluation of model validity and of the quality of a model fit beyond residual errors. Unfortunately, DFE works only when the data are more or less complete and the system contains as many independent fluxes as metabolites. These drawbacks may be ameliorated with other types of estimation and information. However, such supplementations incur their own limitations. In particular, assumptions must be made regarding the functional forms of some processes and detailed kinetic information must be available, in addition to the time series data. Results The authors propose here a systematic approach that supplements DFE and overcomes some of its shortcomings. Like DFE, the approach is model-free and requires only minimal assumptions. If sufficient time series data are available, the approach allows the determination of a subset of fluxes that enables the subsequent applicability of DFE to the rest of the flux system. The authors demonstrate the procedure with three artificial pathway systems exhibiting distinct characteristics and with actual data of the trehalose pathway in Saccharomyces cerevisiae. Conclusions The results demonstrate that the proposed method successfully complements DFE under various situations and without a priori assumptions regarding the model representation. The proposed method also permits an examination of whether at all, to what degree, or within what range the available time series data can be validly represented in a particular functional format of

  13. Profile Analysis of the Universal Nonverbal Intelligence Test Standardization Sample.

    Science.gov (United States)

    Wilhoit, Brian E.; McCallum, R. Steve

    2002-01-01

    A normative typology was developed and applied using multivariate profile analysis of subtest scores of the Universal Nonverbal Intelligence Test (UNIT) standardization sample. The results yielded a seven-profile cluster solution for the Extended Battery, and a six-profile cluster solution for the Standard Battery. Additionally, the results lend…

  14. Characterizing the height profile of the flux of wind-eroded sediment

    Science.gov (United States)

    Dong, Zhibao; Qian, Guangqiang

    2007-01-01

    Wind erosion causes severe environmental problems, such as aeolian desertification and dust storms, in arid and semiarid regions. Reliable prediction of the height profile of the wind-eroded sediment flux is crucial for estimation of transport rates, verification of computer models, understanding of particle-modified wind flows, and control of drifting sand. This study defined the basic height profile for the flux of wind-eroded sediment and the coefficients that characterize its equation. Nine grain-size populations of natural sand at different wind velocities were tested in a wind tunnel to measure the flux of sediment at different heights. The resulting flux profiles resemble a golf club with a small back-turn where the flux increases with increasing height within 20 mm above the surface. If the small back-turns are neglected, the flux profiles can be expressed by an exponential-decay function q_{{text{r}}} (z) = a{text{e}}^{{ - bzr }} , where q r( z) is the dimensionless relative flux of sediment at height z, which follows the exponential-decay law proposed by previous researchers for aeolian saltation. Three coefficients (a creep proportion, a relative decay rate, and an average saltation height) are proposed to characterize the height profile. Coefficients a and b in the above equation represent the creep proportion and relative decay rate as a function of height, respectively. Coefficient a varies widely, depending on grain size and wind velocity, but averages 0.09. It is suggested that the grain size and wind velocity must be specified when discussing creep proportion. Coefficients a and b are nearly linearly correlated and decrease as grain size and wind velocity increase. The average saltation height (the average height sediment particles can reach) was a function of grain size and wind velocity, and was well correlated with coefficients a and b.

  15. The effects of sample scheduling and sample numbers on estimates of the annual fluxes of suspended sediment in fluvial systems

    Science.gov (United States)

    Horowitz, Arthur J.; Clarke, Robin T.; Merten, Gustavo Henrique

    2015-01-01

    Since the 1970s, there has been both continuing and growing interest in developing accurate estimates of the annual fluvial transport (fluxes and loads) of suspended sediment and sediment-associated chemical constituents. This study provides an evaluation of the effects of manual sample numbers (from 4 to 12 year−1) and sample scheduling (random-based, calendar-based and hydrology-based) on the precision, bias and accuracy of annual suspended sediment flux estimates. The evaluation is based on data from selected US Geological Survey daily suspended sediment stations in the USA and covers basins ranging in area from just over 900 km2 to nearly 2 million km2 and annual suspended sediment fluxes ranging from about 4 Kt year−1 to about 200 Mt year−1. The results appear to indicate that there is a scale effect for random-based and calendar-based sampling schemes, with larger sample numbers required as basin size decreases. All the sampling schemes evaluated display some level of positive (overestimates) or negative (underestimates) bias. The study further indicates that hydrology-based sampling schemes are likely to generate the most accurate annual suspended sediment flux estimates with the fewest number of samples, regardless of basin size. This type of scheme seems most appropriate when the determination of suspended sediment concentrations, sediment-associated chemical concentrations, annual suspended sediment and annual suspended sediment-associated chemical fluxes only represent a few of the parameters of interest in multidisciplinary, multiparameter monitoring programmes. The results are just as applicable to the calibration of autosamplers/suspended sediment surrogates currently used to measure/estimate suspended sediment concentrations and ultimately, annual suspended sediment fluxes, because manual samples are required to adjust the sample data/measurements generated by these techniques so that they provide depth-integrated and cross

  16. Computing stationary distributions in equilibrium and nonequilibrium systems with forward flux sampling

    NARCIS (Netherlands)

    Valeriani, C.; Allen, R.J.; Morelli, M.J.; Frenkel, D.; Wolde, P.R. ten

    2007-01-01

    We present a method for computing stationary distributions for activated processes in equilibrium and nonequilibrium systems using forward flux sampling. In this method, the stationary distributions are obtained directly from the rate constant calculations for the forward and backward

  17. Dilation of force-free magnetic flux tubes. [solar magnetic field profiles

    Science.gov (United States)

    Frankenthal, S.

    1977-01-01

    A general study is presented of the mapping functions which relate the magnetic-field profiles across a force-free rope in segments subjected to various external pressures. The results reveal that if the external pressure falls below a certain critical level (dependent on the flux-current relation which defines the tube), the magnetic profile consists of an invariant core sheathed in a layer permeated by an azimuthal magnetic field.

  18. Shipboard Measurements of Surface Flux and Near Surface Profiles and Surface Flux Parameterization

    Science.gov (United States)

    2009-01-01

    overall project. Mr. Richard J. Lind worked on instrument preparation, calibration, and data sampling. Dr. John Kalogiros, an external research...temperature measured at the same time as the SST measurements where the multiple spike in the measurements are likely results of the ship plumes

  19. Toxic Metals Profiles in Hair Samples from Street Roaming Animals ...

    African Journals Online (AJOL)

    Assessment of toxic metals profiles in hair samples from street roaming animals in Yelwa-Yauri town, North Western, Nigeria was carried out. Hair samples for the analyses were collected from 108 animal (54 sheep and 54 goats) roaming the street of Yelwa-Yauri town and 45 samples from animals in the neighboring ...

  20. Modeling atmospheric CO2 concentration profiles and fluxes above sloping terrain at a boreal site

    Directory of Open Access Journals (Sweden)

    T. Aalto

    2006-01-01

    Full Text Available CO2 fluxes and concentrations were simulated in the planetary boundary layer above subarctic hilly terrain using a three dimensional model. The model solves the transport equations in the local scale and includes a vegetation sub-model. A WMO/GAW background concentration measurement site and an ecosystem flux measurement site are located inside the modeled region at a hilltop and above a mixed boreal forest, respectively. According to model results, the concentration measurement at the hill site was representative for continental background. However, this was not the case for the whole model domain. Concentration at few meters above active vegetation represented mainly local variation. Local variation became inseparable from the regional signal at about 60-100 m above ground. Flow over hills changed profiles of environmental variables and height of inversion layer, however CO2 profiles were more affected by upwind land use than topography. The hill site was above boundary layer during night and inside boundary layer during daytime. The CO2 input from model lateral boundaries dominated in both cases. Daily variation in the CO2 assimilation rate was clearly seen in the CO2 profiles. Concentration difference between the hill site and the forest site was about 5ppm during afternoon according to both model and measurements. The average modeled flux to the whole model region was about 40% of measured and modeled local flux at the forest site.

  1. A comprehensive metabolic profile of cultured astrocytes using isotopic transient metabolic flux analysis and 13C-labeled glucose

    Directory of Open Access Journals (Sweden)

    Ana I Amaral

    2011-09-01

    Full Text Available Metabolic models have been used to elucidate important aspects of brain metabolism in recent years. This work applies for the first time the concept of isotopic transient 13C metabolic flux analysis (MFA to estimate intracellular fluxes of cultured astrocytes. This methodology comprehensively explores the information provided by 13C labeling time-courses of intracellular metabolites after administration of a 13C labeled substrate. Cells were incubated with medium containing [1-13C]glucose for 24 h and samples of cell supernatant and extracts collected at different time-points were then analyzed by mass spectrometry and/or HPLC. Metabolic fluxes were estimated by fitting a carbon labeling network model to isotopomer profiles experimentally determined. Both the fast isotopic equilibrium of glycolytic metabolite pools and the slow labeling dynamics of TCA cycle intermediates are described well by the model. The large pools of glutamate and aspartate which are linked to the TCA cycle via reversible aminotransferase reactions are likely to be responsible for the observed delay in equilibration of TCA cycle intermediates. Furthermore, it was estimated that 11% of the glucose taken up by astrocytes was diverted to the pentose phosphate pathway. In addition, considerable fluxes through pyruvate carboxylase (PC (PC/pyruvate dehydrogenase (PDH ratio = 0.5, malic enzyme (5% of the total pyruvate production and catabolism of branched-chained amino acids (contributing with ~40% to total acetyl-CoA produced confirmed the significance of these pathways to astrocytic metabolism. Consistent with the need of maintaining cytosolic redox potential, the fluxes through the malate-aspartate shuttle and the PDH pathway were comparable. Finally, the estimated glutamate/α-ketoglutarate exchange rate (~0.7 µmol.mg prot-1.h-1 was similar to the TCA cycle flux. In conclusion, this work demonstrates the potential of isotopic transient MFA for a comprehensive analysis of

  2. Soil Greenhouse Gas Flux Measurements with Automated and Manual Static Chambers, Forced Diffusion Chamber, and Concentration Profiles

    Science.gov (United States)

    Ruan, L.; Oikawa, P. Y.; Géli, M.; Verfaillie, J. G.; Sturtevant, C. S.; Knox, S. H.; Nickerson, N.; McArthur, G.; Creelman, C.; Saad, N.; Alstad, K. P.; Arata, C.; Baldocchi, D. D.; Silver, W. L.

    2014-12-01

    Accurate measurements of soil greenhouse gas fluxes are critical for determining the role of ecosystem dynamics, both natural and managed, in climate change. We compared concentration profile methods with static, forced diffusion, and automated flux chambers using a combination of infrared gas analyzers (IRGA), gas chromatography, and cavity ring-down laser absorption spectroscopy (Picarro G2508) during field campaigns in managed ecosystems in California. At a drained peatland pasture site, we observed large differences between methods (fluxes ranged between 2-15 μmol CO2 m-2 s-1). However, low temporal/high spatial replication measurements (manual LI6400 chamber measurements; n=6 collars) encompassed the full range of CO2 fluxes observed across all other methods. This suggests that the majority of variability in CO2 emissions was due to high spatial variation in soil respiration and not due to methodological differences across measurement systems. At a dry upland pasture site, water, nitrate solution and manure were applied during the experimental period to expand the range of greenhouse fluxes. Preliminary results showed good agreement of gas fluxes between static and automatic chamber sampling. We observed large CO2 and N2O fluxes after manure application with both methods. The two chamber types were highly significantly correlated for N2O (slope=0.74, r2=0.94). Mean CH4 fluxes measured by static chambers was -0.36 μg cm-2 h-1, similar to the -0.57 μg cm-2 h-1 measured by the automatic chamber and Picarro analyzer during the study period. Overall, our results suggest that both automated and static chamber methods are in good agreement, but automated chambers are advantageous for capturing diel dynamics and pulse responses to experimental treatments. Our results also highlight the importance of spatial replication, which can be difficult to achieve using expensive automated chambers. We suggest future research efforts to seek a combination of high spatially

  3. Computing stationary distributions in equilibrium and non-equilibrium systems with Forward Flux Sampling

    NARCIS (Netherlands)

    Valeriani, C.; Allen, R.J.; Morelli, M.J.; Frenkel, D.; ten Wolde, P.R.

    2009-01-01

    We present a method for computing stationary distributions for activated processes in equilibrium and non-equilibrium systems using Forward Flux Sampling (FFS). In this method, the stationary distributions are obtained directly from the rate constant calculations for the forward and backward

  4. Flux

    DEFF Research Database (Denmark)

    Ravn, Ib

    Med udgangspunkt i kompleksistetsforskning og studiet af selvorganiserende systemer beskriver lb Ravn den fysiske og biologiske evolution og menneskets udvikling. Han fortolker begreber som kultur, sprog, frihed, værdier, mening, smerte og det ondes problem i lyset af en procesbaseret ontologi...... kanalisering af den flux eller energi, der strømmer igennem os og giver sig til kende i vore daglige aktiviteter. Skal vores tanker, handlinger, arbejde, samvær og politiske liv organiseres efter stramme og faste regelsæt, uden slinger i valsen? Eller skal de tværtimod forløbe ganske uhindret af regler og bånd...

  5. VizieR Online Data Catalog: GOALS sample PACS and SPIRE fluxes (Chu+, 2017)

    Science.gov (United States)

    Chu, J. K.; Sanders, D. B.; Larson, K. L.; Mazzarella, J. M.; Howell, J. H.; Diaz-Santos, T.; Xu, K. C.; Paladini, R.; Schulz, B.; Shupe, D.; Appleton, P.; Armus, L.; Billot, N.; Chan, B. H. P.; Evans, A. S.; Fadda, D.; Frayer, D. T.; Haan, S.; Ishida, C. M.; Iwasawa, K.; Kim, D.-C.; Lord, S.; Murphy, E.; Petric, A.; Privon, G. C.; Surace, J. A.; Treister, E.

    2017-06-01

    The IRAS RBGS contains 179 LIRGs (log(LIR/Lȯ)= 22 ultra-luminous infrared galaxies (ULIRGs: log(LIR/Lȯ)>=12.0); these 201 total objects comprise the GOALS sample (Armus et al. 2009), a statistically complete flux-limited sample of infrared-luminous galaxies in the local universe. This paper presents imaging and photometry for all 201 LIRGs and LIRG systems in the IRAS RBGS that were observed during our GOALS Herschel OT1 program. (4 data files).

  6. Photochemistry of solutes in/on ice: reaction rate dependence on sample orientation and photon flux

    Science.gov (United States)

    Hullar, T.; Anastasio, C.

    2015-12-01

    Particularly in polar regions, photochemical reactions in snowpacks can be an important mechanism for transforming organic and inorganic compounds. Chemicals within snow and ice are found in three different compartments: distributed in the bulk ice, concentrated in liquid-like regions (LLRs) within the ice matrix (such as at grain boundaries), or present in quasi-liquid layers (QLLs) at the air-ice interface. While some previous work suggested reaction rates may vary in these different compartments, our preliminary experiments found similar reaction rates in all three compartments, as well as in aqueous solution. Previous work also suggested reaction rate constants may be independent of photon flux under certain illumination conditions. Here, we extend our investigations to measure reaction rate constants in ice samples with different orientations to the illumination source, which our work thus far suggests may impact the measured rate constants. Polycyclic aromatic hydrocarbons (PAHs) are common pollutants in snow and ice. We first prepared aqueous solutions of a single PAH. We then froze these samples using various methods previously shown to segregate the solute into known locations in the ice matrix. With simulated polar sunlight, we illuminated these samples and measured photon flux (using 2-nitrobenzaldehyde as a chemical actinometer) and photodecay of the PAH. Using this information, we normalized the rate of PAH loss to the photon flux and calculated the rate constants for PAH photodegradation under various freezing conditions, photon fluxes, and sample orientations. We will report on the impact of these variables on PAH photodegradation as well as the effect of varying the photon flux.

  7. Comparison of soil solution sampling techniques to assess metal fluxes from contaminated soil to groundwater.

    Science.gov (United States)

    Coutelot, F; Sappin-Didier, V; Keller, C; Atteia, O

    2014-12-01

    The unsaturated zone plays a major role in elemental fluxes in terrestrial ecosystems. A representative chemical analysis of soil pore water is required for the interpretation of soil chemical phenomena and particularly to assess Trace Elements (TEs) mobility. This requires an optimal sampling system to avoid modification of the extracted soil water chemistry and allow for an accurate estimation of solute fluxes. In this paper, the chemical composition of soil solutions sampled by Rhizon® samplers connected to a standard syringe was compared to two other types of suction probes (Rhizon® + vacuum tube and Rhizon® + diverted flow system). We investigated the effects of different vacuum application procedures on concentrations of spiked elements (Cr, As, Zn) mixed as powder into the first 20 cm of 100-cm columns and non-spiked elements (Ca, Na, Mg) concentrations in two types of columns (SiO2 sand and a mixture of kaolinite + SiO2 sand substrates). Rhizon® was installed at different depths. The metals concentrations showed that (i) in sand, peak concentrations cannot be correctly sampled, thus the flux cannot be estimated, and the errors can easily reach a factor 2; (ii) in sand + clay columns, peak concentrations were larger, indicating that they could be sampled but, due to sorption on clay, it was not possible to compare fluxes at different depths. The different samplers tested were not able to reflect the elemental flux to groundwater and, although the Rhizon® + syringe device was more accurate, the best solution remains to be the use of a lysimeter, whose bottom is kept continuously at a suction close to the one existing in the soil.

  8. Impact of a hollow density profile on turbulent particle fluxes: Gyrokinetic and fluid simulations

    Science.gov (United States)

    Tegnered, D.; Oberparleiter, M.; Strand, P.; Nordman, H.

    2017-07-01

    Hollow density profiles may occur in connection with pellet fuelling and L to H transitions. A positive density gradient could potentially stabilize the turbulence or change the relation between convective and diffusive fluxes, thereby reducing the turbulent transport of particles towards the center, making the pellet fuelling scheme inefficient. In the present work, the particle transport driven by Ion Temperature Gradient/Trapped Electron (ITG/TE) mode turbulence in hollow density profiles is studied by fluid as well as gyrokinetic simulations. The fluid model used, an extended version of the Weiland transport model, Extended Drift Wave Model (EDWM), incorporates an arbitrary number of ion species in a multi-fluid description and an extended wavelength spectrum. The fluid model, which is fast and hence suitable for use in predictive simulations, is compared to gyrokinetic simulations using the code GENE. Typical tokamak parameters are used based on the Cyclone Base Case. Parameter scans in key plasma parameters like plasma β, R/LT, and magnetic shear are investigated. In addition, the effects of a fast species are studied and global ITG simulations in a simplified physics description are performed in order to investigate nonlocal effects. It is found that β in particular, has a stabilizing effect in the negative R/Ln region. Both nonlinear GENE and EDWM simulations show a decrease in inward flux for negative R/Ln and a change in the direction from inward to outward for positive R/Ln. Moreover, the addition of fast particles was shown to decrease the inward main ion particle flux in the positive gradient region further. This might have serious consequences for pellet fuelling of high β plasmas. Additionally, the heat flux in global ITG turbulence simulations indicates that nonlocal effects can play a different role from usual in connection with pellet fuelling.

  9. Choice of satellite-based CO2 product (XCO¬2, vertical profile) alters surface CO2 flux estimate

    Science.gov (United States)

    Liu, J.; Bowman, K. W.; Lee, M.; Henze, D. K.; Fisher, J. B.; Frankenberg, C.; Polhamus, A.

    2011-12-01

    The ACOS (Atmospheric CO2 Observations from Space) algorithm provides column-averaged CO2 products in units of dry-air mole fraction (XCO2) based on GOSAT radiances. However, XCO2 is derived from a linear transformation of the CO2 vertical profiles estimated from the ACOS retrieval algorithm. In theory, XCO2 vertical columns should provide no more information than the original CO2 profiles. However, the different sensitivities of either CO2 profiles or XCO2 to transport errors can significantly alter surface CO2 flux estimates. Though it has been argued that XCO2 may be less sensitive to transport error than CO2 vertical profiles, there is no study so far investigating the actual impact on surface CO2 flux estimation due to the choice of observation format, which could have significant impact on future satellite CO2 profile mission concepts. In this presentation, we will present the sensitivity of surface CO2 flux estimation to a suite of CO2 observation products, which includes CO2 vertical profiles, XCO2, and the lowest 3 levels of CO2 from CO2 vertical profiles. The CO2 observations are ACOS products covering from July 2009 to June 2010. We will present both OSSE and real observation experiments. In the OSSE experiments, we will present both perfect model experiments and experiments with model errors that are introduced by changing the planetary boundary height. In the real observations, we will show the annual and seasonal CO2 flux as function of regions from using the three observation products. The accuracy of CO2 flux estimation will be examined by comparing CO2 concentrations forced by posterior CO2 flux to independent CO2 observations. The surface CO2 flux estimation framework is based on GEOS-Chem adjoint model that is developed by the Carbon Monitoring Study flux pilot project.

  10. Chemical fluxes from time series sampling of the Irrawaddy and Salween Rivers, Myanmar

    OpenAIRE

    Chapman, Hazel; Bickle, Mike; Thaw, San Hla; Thiam, Hrin Nei

    2015-01-01

    The Irrawaddy and Salween rivers in Myanmar deliver water fluxes to the ocean equal to ~ 70% of the Ganges–Brahmaputra river system. Together these systems are thought to deliver about half the dissolved load from the tectonically active Himalayan–Tibetan orogen. Previously very little data was available on the dissolved load and isotopic compositions of these major rivers. Here we present time series data of 171 samples collected fortnightly at intervals throughout 2004 to 2007 from the Irra...

  11. Air-Sea Spray Airborne Radar Profiler Characterizes Energy Fluxes in Hurricanes

    Science.gov (United States)

    Durden, Stephen L.; Esteban-Fermandez, D.

    2010-01-01

    A report discusses ASAP (Air-sea Spray Airborne Profiler), a dual-wavelength radar profiler that provides measurement information about the droplet size distribution (DSD) of sea-spray, which can be used to estimate heat and moisture fluxes for hurricane research. Researchers have recently determined that sea spray can have a large effect on the magnitude and distribution of the air-sea energy flux at hurricane -force wind speeds. To obtain information about the DSD, two parameters of the DSD are required; for example, overall DSD amplitude and DSD mean diameter. This requires two measurements. Two frequencies are used, with a large enough separation that the differential frequency provides size information. One frequency is 94 GHz; the other is 220 GHz. These correspond to the Rayleigh and Mie regions. Above a surface wind speed of 10 m/ s, production of sea spray grows exponentially. Both the number of large droplets and the altitude they reach are a function of the surface wind speed.

  12. Defect profile estimation from magnetic flux leakage signal via efficient managing particle swarm optimization.

    Science.gov (United States)

    Han, Wenhua; Xu, Jun; Wang, Ping; Tian, Guiyun

    2014-06-12

    In this paper, efficient managing particle swarm optimization (EMPSO) for high dimension problem is proposed to estimate defect profile from magnetic flux leakage (MFL) signal. In the proposed EMPSO, in order to strengthen exchange of information among particles, particle pair model was built. For more efficient searching when facing different landscapes of problems, velocity updating scheme including three velocity updating models was also proposed. In addition, for more chances to search optimum solution out, automatic particle selection for re-initialization was implemented. The optimization results of six benchmark functions show EMPSO performs well when optimizing 100-D problems. The defect simulation results demonstrate that the inversing technique based on EMPSO outperforms the one based on self-learning particle swarm optimizer (SLPSO), and the estimated profiles are still close to the desired profiles with the presence of low noise in MFL signal. The results estimated from real MFL signal by EMPSO-based inversing technique also indicate that the algorithm is capable of providing an accurate solution of the defect profile with real signal. Both the simulation results and experiment results show the computing time of the EMPSO-based inversing technique is reduced by 20%-30% than that of the SLPSO-based inversing technique.

  13. Deep clonal profiling of formalin fixed paraffin embedded clinical samples.

    Directory of Open Access Journals (Sweden)

    Tara Holley

    Full Text Available Formalin fixed paraffin embedded (FFPE tissues are a vast resource of annotated clinical samples. As such, they represent highly desirable and informative materials for the application of high definition genomics for improved patient management and to advance the development of personalized therapeutics. However, a limitation of FFPE tissues is the variable quality of DNA extracted for analyses. Furthermore, admixtures of non-tumor and polyclonal neoplastic cell populations limit the number of biopsies that can be studied and make it difficult to define cancer genomes in patient samples. To exploit these valuable tissues we applied flow cytometry-based methods to isolate pure populations of tumor cell nuclei from FFPE tissues and developed a methodology compatible with oligonucleotide array CGH and whole exome sequencing analyses. These were used to profile a variety of tumors (breast, brain, bladder, ovarian and pancreas including the genomes and exomes of matching fresh frozen and FFPE pancreatic adenocarcinoma samples.

  14. Mineral Profile of Children's Fast Food Menu Samples.

    Science.gov (United States)

    Cervera, Maria Luisa; de la Guardia, Miguel; Ruiz-de-Cenzano, Manuela; Rochina-Marco, Arancha; López-Salazar, Óscar

    2017-05-26

    Children's fast food menus, including hamburgers served with french fries, dessert, and a soft drink, were analyzed to obtain the mineral profile of trace elements. The developed analytical methodology involved sample digestion under pressure inside a microwave oven with a mixture of HNO₃ and H₂O₂ and inductively coupled plasma-optical emission spectrometry. The method was validated by carrying out the analysis of certified reference materials (NIST 1570a spinach leaves, NCS ZC73016 chicken, and NIST 1568a rice flour) and using recovery experiments. Repeatability was verified by analyzing replicate samples. Twenty-six elements were studied, 12 of which-aluminum, barium, calcium, copper, iron, potassium, lithium, magnesium, manganese, sodium, strontium, and zinc-were quantitatively determined. Results were compared with other studies of fast food and children's menus published in the literature, and the nutritional value of samples was assessed with dietary intake guidelines.

  15. Fluxes of CO2, CH4 and N2O at two European beech forests: linking soil gas production profiles with soil and stem fluxes

    Science.gov (United States)

    Maier, Martin; Machacova, Katerina; Halaburt, Ellen; Haddad, Sally; Urban, Otmar; Lang, Friederike

    2016-04-01

    Soil and plant surfaces are known to exchange greenhouse gases with the atmosphere. Some gases like nitrous oxide (N2O) and methane (CH4) can be produced and re-consumed in different soil depths and soil compartments, so that elevated concentrations of CH4 or N2O in the soil do not necessarily mean a net efflux from the soil into the atmosphere. Soil aeration, and thus the oxygen status can underlay a large spatial variability within the soil on the plot and profile scale, but also within soil aggregates. Thus, conditions suitable for production and consumption of CH4 and N2O can vary on different scales in the soil. Plant surfaces can also emit or take up CH4 and N2O, and these fluxes can significantly contribute to the net ecosystem exchange. Since roots usually have large intercellular spaces or aerenchyma they may represent preferential transport ways for soil gases, linking possibly elevated soil gas concentrations in the subsoil in a "shortcut" to the atmosphere. We tested the hypothesis that the spatial variability of the soil-atmosphere fluxes of CO2, CH4 and N2O is caused by the heterogeneity in soil properties. Therefore, we measured soil-atmosphere gas fluxes, soil gas concentrations and soil diffusivity profiles and did a small scale field assessment of soil profiles on the measurments plots. We further tried to link vertical profiles of soil gas concentrations and diffusivity to derive the production and consumption profiles, and to link these profiles to the stem-atmosphere flux rates of individual trees. Measurements were conducted in two mountain beech forests with different geographical and climatic conditions (White Carpathians, Czech Republic; Black Forest, Germany). Gas fluxes at stem and soil levels were measured simultaneously using static chamber systems and chromatographic and continuous laser analyses. Monitoring simultaneously vertical soil gas profiles allowed to assess the within-soil gas fluxes, and thus to localize the production and

  16. Effect of spatial sampling from European flux towers for estimating carbon and water fluxes with artificial neural network

    DEFF Research Database (Denmark)

    Papale, D.; Black, T Andrew; Carvalhais, Nuno

    2015-01-01

    Empirical modeling approaches are frequently used to upscale local eddy covariance observations of carbon, water, and energy fluxes to regional and global scales. The predictive capacity of such models largely depends on the data used for parameterization and identification of input......-output relationships, while prediction for conditions outside the training domain is generally uncertain. In this work, artificial neural networks (ANNs) were used for the prediction of gross primary production (GPP) and latent heat flux (LE) on local and European scales with the aim to assess the portion...

  17. Headspace profiling of cocaine samples for intelligence purposes.

    Science.gov (United States)

    Dujourdy, Laurence; Besacier, Fabrice

    2008-08-06

    A method for determination of residual solvents in illicit hydrochloride cocaine samples using static headspace-gas chromatography (HS-GC) associated with a storage computerized procedure is described for the profiling and comparison of seizures. The system involves a gas chromatographic separation of 18 occluded solvents followed by fully automatic data analysis and transfer to a PHP/MySQL database. First, a fractional factorial design was used to evaluate the main effects of some critical method parameters (salt choice, vial agitation intensity, oven temperature, pressurization and loop equilibration) on the results with a minimum of experiments. The method was then validated for tactical intelligence purposes (batch comparison) via several studies: selection of solvents and mathematical comparison tool, reproducibility and "cutting" influence studies. The decision threshold to determine the similarity of two samples was set and false positives and negatives evaluated. Finally, application of the method to distinguish geographical origins is discussed.

  18. Effect of spatial sampling from European flux towers for estimating carbon and water fluxes with artificial neural networks

    NARCIS (Netherlands)

    Papale, Dario; Black, T.A.; Carvalhais, Nuno; Cescatti, Alessandro; Chen, Jiquan; Jung, Martin; Kiely, Gerard; Lasslop, Gitta; Mahecha, Miguel D.; Margolis, Hank; Merbold, Lutz; Montagnani, Leonardo; Moors, Eddy; Olesen, J.E.; Reichstein, Markus; Tramontana, Gianluca; Gorsel, Van Eva; Wohlfahrt, Georg; Ráduly, Botond

    2015-01-01

    Empirical modeling approaches are frequently used to upscale local eddy covariance observations of carbon, water, and energy fluxes to regional and global scales. The predictive capacity of such models largely depends on the data used for parameterization and identification of input-output

  19. Use of ordinary kriging to interpolate observations of fire radiative heat flux sampled with airborne imagery

    Science.gov (United States)

    Klauberg Silva, C.; Hudak, A. T.; Bright, B. C.; Dickinson, M. B.; Kremens, R.; Paugam, R.; Mell, W.

    2016-12-01

    Biomass burning has impacts on air pollution at local to regional scales and contributes to greenhouse gases and affects carbon balance at the global scale. Therefore, is important to accurately estimate and manage carbon pools (fuels) and fluxes (gases and particulate emissions having public health implications) associated with wildland fires. Fire radiative energy (FRE) has been shown to be linearly correlated with biomass burned in small-scale experimental fires but not at the landscape level. Characterization of FRE density (FRED) flux in J m-2 from a landscape-level fire presents an undersampling problem. Specifically, airborne acquisitions of long-wave infrared radiation (LWIR) from a nadir-viewing LWIR camera mounted on board fixed-wing aircraft provide only samples of FRED from a landscape-level fire, because of the time required to turn the plane around between passes, and a fire extent that is broader than the camera field of view. This undersampling in time and space produces apparent firelines in an image of observed FRED, capturing the fire spread only whenever and wherever the scene happened to be imaged. We applied ordinary kriging to images of observed FRED from five prescribed burns collected in forested and non-forested management units burned at Eglin Air Force Base in Florida USA in 2011 and 2012. The three objectives were to: 1. more realistically map FRED, 2. more accurately estimate total FRED as predicted from fuel consumption measurements, and 3. compare the sampled and kriged FRED maps to modeled estimates of fire rate of spread (ROS). Observed FRED was integrated from LWIR images calibrated to units of fire radiative flux density (FRFD) in W m-2. Iterating the kriging analysis 2-10 times (depending on the burn unit) led to more accurate FRED estimates, both in map form and in terms of total FRED, as corroborated by independent estimates of fuel consumption and ROS.

  20. Random sampling of elementary flux modes in large-scale metabolic networks.

    Science.gov (United States)

    Machado, Daniel; Soons, Zita; Patil, Kiran Raosaheb; Ferreira, Eugénio C; Rocha, Isabel

    2012-09-15

    The description of a metabolic network in terms of elementary (flux) modes (EMs) provides an important framework for metabolic pathway analysis. However, their application to large networks has been hampered by the combinatorial explosion in the number of modes. In this work, we develop a method for generating random samples of EMs without computing the whole set. Our algorithm is an adaptation of the canonical basis approach, where we add an additional filtering step which, at each iteration, selects a random subset of the new combinations of modes. In order to obtain an unbiased sample, all candidates are assigned the same probability of getting selected. This approach avoids the exponential growth of the number of modes during computation, thus generating a random sample of the complete set of EMs within reasonable time. We generated samples of different sizes for a metabolic network of Escherichia coli, and observed that they preserve several properties of the full EM set. It is also shown that EM sampling can be used for rational strain design. A well distributed sample, that is representative of the complete set of EMs, should be suitable to most EM-based methods for analysis and optimization of metabolic networks. Source code for a cross-platform implementation in Python is freely available at http://code.google.com/p/emsampler. dmachado@deb.uminho.pt Supplementary data are available at Bioinformatics online.

  1. Estimation of surface heat flux and surface temperature during inverse heat conduction under varying spray parameters and sample initial temperature.

    Science.gov (United States)

    Aamir, Muhammad; Liao, Qiang; Zhu, Xun; Aqeel-ur-Rehman; Wang, Hong; Zubair, Muhammad

    2014-01-01

    An experimental study was carried out to investigate the effects of inlet pressure, sample thickness, initial sample temperature, and temperature sensor location on the surface heat flux, surface temperature, and surface ultrafast cooling rate using stainless steel samples of diameter 27 mm and thickness (mm) 8.5, 13, 17.5, and 22, respectively. Inlet pressure was varied from 0.2 MPa to 1.8 MPa, while sample initial temperature varied from 600°C to 900°C. Beck's sequential function specification method was utilized to estimate surface heat flux and surface temperature. Inlet pressure has a positive effect on surface heat flux (SHF) within a critical value of pressure. Thickness of the sample affects the maximum achieved SHF negatively. Surface heat flux as high as 0.4024 MW/m(2) was estimated for a thickness of 8.5 mm. Insulation effects of vapor film become apparent in the sample initial temperature range of 900°C causing reduction in surface heat flux and cooling rate of the sample. A sensor location near to quenched surface is found to be a better choice to visualize the effects of spray parameters on surface heat flux and surface temperature. Cooling rate showed a profound increase for an inlet pressure of 0.8 MPa.

  2. Estimation of Surface Heat Flux and Surface Temperature during Inverse Heat Conduction under Varying Spray Parameters and Sample Initial Temperature

    Directory of Open Access Journals (Sweden)

    Muhammad Aamir

    2014-01-01

    Full Text Available An experimental study was carried out to investigate the effects of inlet pressure, sample thickness, initial sample temperature, and temperature sensor location on the surface heat flux, surface temperature, and surface ultrafast cooling rate using stainless steel samples of diameter 27 mm and thickness (mm 8.5, 13, 17.5, and 22, respectively. Inlet pressure was varied from 0.2 MPa to 1.8 MPa, while sample initial temperature varied from 600°C to 900°C. Beck’s sequential function specification method was utilized to estimate surface heat flux and surface temperature. Inlet pressure has a positive effect on surface heat flux (SHF within a critical value of pressure. Thickness of the sample affects the maximum achieved SHF negatively. Surface heat flux as high as 0.4024 MW/m2 was estimated for a thickness of 8.5 mm. Insulation effects of vapor film become apparent in the sample initial temperature range of 900°C causing reduction in surface heat flux and cooling rate of the sample. A sensor location near to quenched surface is found to be a better choice to visualize the effects of spray parameters on surface heat flux and surface temperature. Cooling rate showed a profound increase for an inlet pressure of 0.8 MPa.

  3. Estimation of Surface Heat Flux and Surface Temperature during Inverse Heat Conduction under Varying Spray Parameters and Sample Initial Temperature

    Science.gov (United States)

    Aamir, Muhammad; Liao, Qiang; Zhu, Xun; Aqeel-ur-Rehman; Wang, Hong

    2014-01-01

    An experimental study was carried out to investigate the effects of inlet pressure, sample thickness, initial sample temperature, and temperature sensor location on the surface heat flux, surface temperature, and surface ultrafast cooling rate using stainless steel samples of diameter 27 mm and thickness (mm) 8.5, 13, 17.5, and 22, respectively. Inlet pressure was varied from 0.2 MPa to 1.8 MPa, while sample initial temperature varied from 600°C to 900°C. Beck's sequential function specification method was utilized to estimate surface heat flux and surface temperature. Inlet pressure has a positive effect on surface heat flux (SHF) within a critical value of pressure. Thickness of the sample affects the maximum achieved SHF negatively. Surface heat flux as high as 0.4024 MW/m2 was estimated for a thickness of 8.5 mm. Insulation effects of vapor film become apparent in the sample initial temperature range of 900°C causing reduction in surface heat flux and cooling rate of the sample. A sensor location near to quenched surface is found to be a better choice to visualize the effects of spray parameters on surface heat flux and surface temperature. Cooling rate showed a profound increase for an inlet pressure of 0.8 MPa. PMID:24977219

  4. Methane, carbon dioxide and nitrous oxide fluxes in soil profile under a winter wheat-summer maize rotation in the North China Plain.

    Directory of Open Access Journals (Sweden)

    Yuying Wang

    Full Text Available The production and consumption of the greenhouse gases (GHGs methane (CH4, carbon dioxide (CO2 and nitrous oxide (N2O in soil profile are poorly understood. This work sought to quantify the GHG production and consumption at seven depths (0-30, 30-60, 60-90, 90-150, 150-200, 200-250 and 250-300 cm in a long-term field experiment with a winter wheat-summer maize rotation system, and four N application rates (0; 200; 400 and 600 kg N ha(-1 year(-1 in the North China Plain. The gas samples were taken twice a week and analyzed by gas chromatography. GHG production and consumption in soil layers were inferred using Fick's law. Results showed nitrogen application significantly increased N2O fluxes in soil down to 90 cm but did not affect CH4 and CO2 fluxes. Soil moisture played an important role in soil profile GHG fluxes; both CH4 consumption and CO2 fluxes in and from soil tended to decrease with increasing soil water filled pore space (WFPS. The top 0-60 cm of soil was a sink of atmospheric CH4, and a source of both CO2 and N2O, more than 90% of the annual cumulative GHG fluxes originated at depths shallower than 90 cm; the subsoil (>90 cm was not a major source or sink of GHG, rather it acted as a 'reservoir'. This study provides quantitative evidence for the production and consumption of CH4, CO2 and N2O in the soil profile.

  5. Numerical determination of vertical water flux based on soil temperature profiles

    Science.gov (United States)

    Tabbagh, Alain; Cheviron, Bruno; Henine, Hocine; Guérin, Roger; Bechkit, Mohamed-Amine

    2017-07-01

    High sensitivity temperature sensors (0.001 K sensitivity Pt100 thermistors), positioned at intervals of a few centimetres along a vertical soil profile, allow temperature measurements to be made which are sensitive to water flux through the soil. The development of high data storage capabilities now makes it possible to carry out in situ temperature recordings over long periods of time. By directly applying numerical models of convective and conductive heat transfer to experimental data recorded as a function of depth and time, it is possible to calculate Darcy's velocity from the convection transfer term, thus allowing water infiltration/exfiltration through the soil to be determined as a function of time between fixed depths. In the present study we consider temperature data recorded at the Boissy-le-Châtel (Seine et Marne, France) experimental station between April 16th, 2009 and March 8th, 2010, at six different depths and 10-min time intervals. We make use of two numerical finite element models to solve the conduction/convection heat transfer equation and compare their merits. These two models allow us to calculate the corresponding convective flux rate every day using a group of three sensors. The comparison of the two series of calculated values centred at 24 cm shows reliable results for periods longer than 8 days. These results are transformed in infiltration/exfiltration value after determining the soil volumetric heat capacity. The comparison with the rainfall and evaporation data for periods of ten days shows a close accordance with the behaviour of the system governed by rainfall evaporation rate during winter and spring.

  6. FANTOM5 CAGE profiles of human and mouse samples

    KAUST Repository

    Noguchi, Shuhei

    2017-08-29

    In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting of a variety of primary cells, tissues, cell lines, and time series samples during cell activation and development, were subjected to a uniform pipeline of CAGE data production. The analysis pipeline started by measuring RNA extracts to assess their quality, and continued to CAGE library production by using a robotic or a manual workflow, single molecule sequencing, and computational processing to generate frequencies of transcription initiation. Resulting data represents the consequence of transcriptional regulation in each analyzed state of mammalian cells. Non-overlapping peaks over the CAGE profiles, approximately 200,000 and 150,000 peaks for the human and mouse genomes, were identified and annotated to provide precise location of known promoters as well as novel ones, and to quantify their activities.

  7. Determination of DNA profiling of siwak and toothbrush samples ...

    African Journals Online (AJOL)

    Nagy Alfadaly

    2016-06-01

    Jun 1, 2016 ... Abstract Background: DNA profiling is an integral part of forensic work. Enough and good sam- ples for DNA quantification and profiling are mandatory. Aim of the study: To quantify and profile DNA from siwak and toothbrushes and study the effect of time on this process. Methodology: The present study ...

  8. A Faint Flux-Limited Lyman Alpha Emitter Sample at z=0.3

    Science.gov (United States)

    Wold, Isak; Finkelstein, Steven L.; Barger, Amy J.; Lauchlan Cowie, Lennox

    2017-06-01

    We present a flux-limited sample of z=0.3 Lya emitters (LAEs) from Galaxy Evolution Explorer (GALEX) grism spectroscopic data. The published GALEX z=0.3 LAE sample is pre-selected from continuum-bright objects and thus is biased against high equivalent width (EW) objects. We remove this continuum pre-selection and compute the EW distribution and the luminosity function of the Lya emission line from our sample. We examine the evolution of these quantities from z = 0.3 to 2.2 and find that the EW distribution shows little evidence for evolution over this redshift range. As shown by previous studies, the Lya luminosity density from star-forming galaxies declines rapidly with declining redshift. However, we find that the decline in Lya luminosity density from z=2.2 to z=0.3 may simply mirror the decline seen in the Ha luminosity density from z=2.2 to z=0.4, implying little change in the volumetric Lya escape fraction. Finally, we show that the observed Lya luminosity density from AGNs is comparable to the observed Lya luminosity density from star-forming galaxies at z=0.3. We suggest that this significant contribution from AGNs to the total observed Lya luminosity density persists out to z=2.2.

  9. The use of disjunct eddy sampling methods for the determination of ecosystem level fluxes of trace gases

    Directory of Open Access Journals (Sweden)

    A. A. Turnipseed

    2009-02-01

    Full Text Available The concept of disjunct eddy sampling (DES for use in measuring ecosystem-level micrometeorological fluxes is re-examined. The governing equations are discussed as well as other practical considerations and guidelines concerning this sampling method as it is applied to either the disjunct eddy covariance (DEC or disjunct eddy accumulation (DEA techniques. A disjunct eddy sampling system was constructed that could either be combined with relatively slow sensors (response time of 2 to 40 s to measure fluxes using DEC, or could also be used to accumulate samples in stable reservoirs for later laboratory analysis (DEA technique. Both the DEC and DEA modes of this sampler were tested against conventional eddy covariance (EC for fluxes of either CO2 (DEC or isoprene (DEA. Good agreement in both modes was observed relative to the EC systems. However, the uncertainty in a single DEA flux measurement was considerable (~40% due to both the reduced statistical sampling and the analytical precision of the concentration difference measurements. We have also re-investigated the effects of nonzero mean vertical wind velocity on accumulation techniques as it relates to our DEA measurements. Despite the higher uncertainty, disjunct eddy sampling can provide an alternative technique to eddy covariance for determining ecosystem-level fluxes for species where fast sensors do not currently exist.

  10. The use of disjunct eddy sampling methods for the determination of ecosystem level fluxes of trace gases

    Science.gov (United States)

    Turnipseed, A. A.; Pressley, S. N.; Karl, T.; Lamb, B.; Nemitz, E.; Allwine, E.; Cooper, W. A.; Shertz, S.; Guenther, A. B.

    2009-02-01

    The concept of disjunct eddy sampling (DES) for use in measuring ecosystem-level micrometeorological fluxes is re-examined. The governing equations are discussed as well as other practical considerations and guidelines concerning this sampling method as it is applied to either the disjunct eddy covariance (DEC) or disjunct eddy accumulation (DEA) techniques. A disjunct eddy sampling system was constructed that could either be combined with relatively slow sensors (response time of 2 to 40 s) to measure fluxes using DEC, or could also be used to accumulate samples in stable reservoirs for later laboratory analysis (DEA technique). Both the DEC and DEA modes of this sampler were tested against conventional eddy covariance (EC) for fluxes of either CO2 (DEC) or isoprene (DEA). Good agreement in both modes was observed relative to the EC systems. However, the uncertainty in a single DEA flux measurement was considerable (~40%) due to both the reduced statistical sampling and the analytical precision of the concentration difference measurements. We have also re-investigated the effects of nonzero mean vertical wind velocity on accumulation techniques as it relates to our DEA measurements. Despite the higher uncertainty, disjunct eddy sampling can provide an alternative technique to eddy covariance for determining ecosystem-level fluxes for species where fast sensors do not currently exist.

  11. In vivo metabolic flux profiling with stable isotopes discriminates sites and quantifies effects of mitochondrial dysfunction in C. elegans.

    Science.gov (United States)

    Vergano, Samantha Schrier; Rao, Meera; McCormack, Shana; Ostrovsky, Julian; Clarke, Colleen; Preston, Judith; Bennett, Michael J; Yudkoff, Marc; Xiao, Rui; Falk, Marni J

    2014-03-01

    Mitochondrial respiratory chain (RC) disease diagnosis is complicated both by an absence of biomarkers that sufficiently divulge all cases and limited capacity to quantify adverse effects across intermediary metabolism. We applied high performance liquid chromatography (HPLC) and mass spectrometry (MS) studies of stable-isotope based precursor-product relationships in the nematode, C. elegans, to interrogate in vivo differences in metabolic flux among distinct genetic models of primary RC defects and closely related metabolic disorders. C. elegans strains studied harbor single nuclear gene defects in complex I, II, or III RC subunits (gas-1, mev-1, isp-1); enzymes involved in coenzyme Q biosynthesis (clk-1), the tricarboxylic acid cycle (TCA, idh-1), or pyruvate metabolism (pdha-1); and central nodes of the nutrient-sensing signaling network that involve insulin response (daf-2) or the sirtuin homologue (sir-2.1). Synchronous populations of 2000 early larval stage worms were fed standard Escherichia coli on nematode growth media plates containing 1,6-(13)C2-glucose throughout their developmental period, with samples extracted on the first day of adult life in 4% perchloric acid with an internal standard. Quantitation of whole animal free amino acid concentrations and isotopic incorporation into amino and organic acids throughout development was performed in all strains by HPLC and isotope ratio MS, respectively. GC/MS analysis was also performed to quantify absolute isotopic incorporation in all molecular species of key TCA cycle intermediates in gas-1 and N2 adult worms. Genetic mutations within different metabolic pathways displayed distinct metabolic profiles. RC complex I (gas-1) and III (isp-1) subunit mutants, together with the coenzyme Q biosynthetic mutant (clk-1), shared a similar amino acid profile of elevated alanine and decreased glutamate. The metabolic signature of the complex II mutant (mev-1) was distinct from that of the other RC mutants but

  12. Investigation of Flux-Linkage Profile Measurement Methods for Switched-Reluctance Motors and Permanent-Magnet Motors

    DEFF Research Database (Denmark)

    Lu, Kaiyuan; Rasmussen, Peter Omand; Ritchie, Ewen

    2009-01-01

    Knowledge of actual flux linkage versus current profiles plays an important role in design verification and performance prediction for switched reluctance motors (SRM's) and permanent magnet motors (PMM's). Various measurement methods have been proposed and discussed so far but each method has its...... the described AC method on an SRM and on a PM motor. For these two motors, the measured flux-linkage-current curves are compared to those measured using other methods. The comparison results show good effectiveness of the proposed AC method for both the SRM and the PM motor....

  13. Forward flux sampling calculation of homogeneous nucleation rates from aqueous NaCl solutions

    Science.gov (United States)

    Jiang, Hao; Haji-Akbari, Amir; Debenedetti, Pablo G.; Panagiotopoulos, Athanassios Z.

    2018-01-01

    We used molecular dynamics simulations and the path sampling technique known as forward flux sampling to study homogeneous nucleation of NaCl crystals from supersaturated aqueous solutions at 298 K and 1 bar. Nucleation rates were obtained for a range of salt concentrations for the Joung-Cheatham NaCl force field combined with the Extended Simple Point Charge (SPC/E) water model. The calculated nucleation rates are significantly lower than the available experimental measurements. The estimates for the nucleation rates in this work do not rely on classical nucleation theory, but the pathways observed in the simulations suggest that the nucleation process is better described by classical nucleation theory than an alternative interpretation based on Ostwald's step rule, in contrast to some prior simulations of related models. In addition to the size of NaCl nucleus, we find that the crystallinity of a nascent cluster plays an important role in the nucleation process. Nuclei with high crystallinity were found to have higher growth probability and longer lifetimes, possibly because they are less exposed to hydration water.

  14. Tractable flux-driven temperature, density, and rotation profile evolution with the quasilinear gyrokinetic transport model QuaLiKiz

    Science.gov (United States)

    Citrin, J.; Bourdelle, C.; Casson, F. J.; Angioni, C.; Bonanomi, N.; Camenen, Y.; Garbet, X.; Garzotti, L.; Görler, T.; Gürcan, O.; Koechl, F.; Imbeaux, F.; Linder, O.; van de Plassche, K.; Strand, P.; Szepesi, G.; Contributors, JET

    2017-12-01

    Quasilinear turbulent transport models are a successful tool for prediction of core tokamak plasma profiles in many regimes. Their success hinges on the reproduction of local nonlinear gyrokinetic fluxes. We focus on significant progress in the quasilinear gyrokinetic transport model QuaLiKiz (Bourdelle et al 2016 Plasma Phys. Control. Fusion 58 014036), which employs an approximated solution of the mode structures to significantly speed up computation time compared to full linear gyrokinetic solvers. Optimisation of the dispersion relation solution algorithm within integrated modelling applications leads to flux calculations × {10}6-7 faster than local nonlinear simulations. This allows tractable simulation of flux-driven dynamic profile evolution including all transport channels: ion and electron heat, main particles, impurities, and momentum. Furthermore, QuaLiKiz now includes the impact of rotation and temperature anisotropy induced poloidal asymmetry on heavy impurity transport, important for W-transport applications. Application within the JETTO integrated modelling code results in 1 s of JET plasma simulation within 10 h using 10 CPUs. Simultaneous predictions of core density, temperature, and toroidal rotation profiles for both JET hybrid and baseline experiments are presented, covering both ion and electron turbulence scales. The simulations are successfully compared to measured profiles, with agreement mostly in the 5%–25% range according to standard figures of merit. QuaLiKiz is now open source and available at www.qualikiz.com.

  15. Constant Flux of Spatial Niche Partitioning through High-Resolution Sampling of Magnetotactic Bacteria.

    Science.gov (United States)

    He, Kuang; Gilder, Stuart A; Orsi, William D; Zhao, Xiangyu; Petersen, Nikolai

    2017-10-15

    Magnetotactic bacteria (MTB) swim along magnetic field lines in water. They are found in aquatic habitats throughout the world, yet knowledge of their spatial and temporal distribution remains limited. To help remedy this, we took MTB-bearing sediment from a natural pond, mixed the thoroughly homogenized sediment into two replicate aquaria, and then counted three dominant MTB morphotypes (coccus, spirillum, and rod-shaped MTB cells) at a high spatiotemporal sampling resolution: 36 discrete points in replicate aquaria were sampled every ∼30 days over 198 days. Population centers of the MTB coccus and MTB spirillum morphotypes moved in continual flux, yet they consistently inhabited separate locations, displaying significant anticorrelation. Rod-shaped MTB were initially concentrated toward the northern end of the aquaria, but at the end of the experiment, they were most densely populated toward the south. The finding that the total number of MTB cells increased over time during the experiment argues that population reorganization arose from relative changes in cell division and death and not from migration. The maximum net growth rates were 10, 3, and 1 doublings day -1 and average net growth rates were 0.24, 0.11, and 0.02 doublings day -1 for MTB cocci, MTB spirilla, and rod-shaped MTB, respectively; minimum growth rates for all three morphotypes were -0.03 doublings day -1 Our results suggest that MTB cocci and MTB spirilla occupy distinctly different niches: their horizontal positioning in sediment is anticorrelated and under constant flux. IMPORTANCE Little is known about the horizontal distribution of magnetotactic bacteria in sediment or how the distribution changes over time. We therefore measured three dominant magnetotactic bacterium morphotypes at 36 places in two replicate aquaria each month for 7 months. We found that the spatial positioning of population centers changed over time and that the two most abundant morphotypes (MTB cocci and MTB spirilla

  16. A Faint Flux-limited Lyα Emitter Sample at z ˜ 0.3

    Science.gov (United States)

    Wold, Isak G. B.; Finkelstein, Steven L.; Barger, Amy J.; Cowie, Lennox L.; Rosenwasser, Benjamin

    2017-10-01

    We present a flux-limited sample of z ˜ 0.3 Lyα emitters (LAEs) from Galaxy Evolution Explorer (GALEX) grism spectroscopic data. The published GALEX z ˜ 0.3 LAE sample is pre-selected from continuum-bright objects and thus is biased against high equivalent width (EW) LAEs. We remove this continuum pre-selection and compute the EW distribution and the luminosity function of the Lyα emission line directly from our sample. We examine the evolution of these quantities from z ˜ 0.3 to 2.2 and find that the EW distribution shows little evidence for evolution over this redshift range. As shown by previous studies, the Lyα luminosity density from star-forming (SF) galaxies declines rapidly with declining redshift. However, we find that the decline in Lyα luminosity density from z = 2.2 to z = 0.3 may simply mirror the decline seen in the Hα luminosity density from z = 2.2 to z = 0.4, implying little change in the volumetric Lyα escape fraction. Finally, we show that the observed Lyα luminosity density from AGNs is comparable to the observed Lyα luminosity density from SF galaxies at z = 0.3. We suggest that this significant contribution from AGNs to the total observed Lyα luminosity density persists out to z ˜ 2.2. Some of the data presented herein were obtained at the W.M. Keck Observatory, which is operated as a scientific partnership among the California Institute of Technology, the University of California, and the National Aeronautics and Space Administration. The Observatory was made possible by the generous financial support of the W.M. Keck Foundation.

  17. Expression and Genomic Profiling of Minute Breast Cancer Samples

    Science.gov (United States)

    2006-07-01

    Alteration of gene expression profiles of peripheral mononuclear blood cells by tobacco smoke : implications for periodontal diseases . Oral...potentially revolutionize (2) the existing cancer staging system and the management of early disease . Microarray- based gene expression profiling and...2002) Understanding disease cell by cell. Science, 296, 1329-1330. 15. Emmert-Buck, M.R., Bonner, R.F., Smith, P.D., Chuaqui, R.F., Zhuang, Z

  18. Effect of Sampling Depth on Air-Sea CO2 Flux Estimates in River-Stratified Arctic Coastal Waters

    Science.gov (United States)

    Miller, L. A.; Papakyriakou, T. N.

    2015-12-01

    In summer-time Arctic coastal waters that are strongly influenced by river run-off, extreme stratification severely limits wind mixing, making it difficult to effectively sample the surface 'mixed layer', which can be as shallow as 1 m, from a ship. During two expeditions in southwestern Hudson Bay, off the Nelson, Hayes, and Churchill River estuaries, we confirmed that sampling depth has a strong impact on estimates of 'surface' pCO2 and calculated air-sea CO2 fluxes. We determined pCO2 in samples collected from 5 m, using a typical underway system on the ship's seawater supply; from the 'surface' rosette bottle, which was generally between 1 and 3 m; and using a niskin bottle deployed at 1 m and just below the surface from a small boat away from the ship. Our samples confirmed that the error in pCO2 derived from typical ship-board versus small-boat sampling at a single station could be nearly 90 μatm, leading to errors in the calculated air-sea CO2 flux of more than 0.1 mmol/(m2s). Attempting to extrapolate such fluxes over the 6,000,000 km2 area of the Arctic shelves would generate an error approaching a gigamol CO2/s. Averaging the station data over a cruise still resulted in an error of nearly 50% in the total flux estimate. Our results have implications not only for the design and execution of expedition-based sampling, but also for placement of in-situ sensors. Particularly in polar waters, sensors are usually deployed on moorings, well below the surface, to avoid damage and destruction from drifting ice. However, to obtain accurate information on air-sea fluxes in these areas, it is necessary to deploy sensors on ice-capable buoys that can position the sensors in true 'surface' waters.

  19. Relative humidity effects on water vapour fluxes measured with closed-path eddy-covariance systems with short sampling lines

    DEFF Research Database (Denmark)

    Fratini, Gerardo; Ibrom, Andreas; Arriga, Nicola

    2012-01-01

    It has been formerly recognised that increasing relative humidity in the sampling line of closed-path eddy-covariance systems leads to increasing attenuation of water vapour turbulent fluctuations, resulting in strong latent heat flux losses. This occurrence has been analyzed for very long (50 m)...

  20. Arm retraction dynamics of entangled star polymers: A forward flux sampling method study.

    Science.gov (United States)

    Zhu, Jian; Likhtman, Alexei E; Wang, Zuowei

    2017-07-28

    The study of dynamics and rheology of well-entangled branched polymers remains a challenge for computer simulations due to the exponentially growing terminal relaxation times of these polymers with increasing molecular weights. We present an efficient simulation algorithm for studying the arm retraction dynamics of entangled star polymers by combining the coarse-grained slip-spring (SS) model with the forward flux sampling (FFS) method. This algorithm is first applied to simulate symmetric star polymers in the absence of constraint release (CR). The reaction coordinate for the FFS method is determined by finding good agreement of the simulation results on the terminal relaxation times of mildly entangled stars with those obtained from direct shooting SS model simulations with the relative difference between them less than 5%. The FFS simulations are then carried out for strongly entangled stars with arm lengths up to 16 entanglements that are far beyond the accessibility of brute force simulations in the non-CR condition. Apart from the terminal relaxation times, the same method can also be applied to generate the relaxation spectra of all entanglements along the arms which are desired for the development of quantitative theories of entangled branched polymers. Furthermore, we propose a numerical route to construct the experimentally measurable relaxation correlation functions by effectively linking the data stored at each interface during the FFS runs. The obtained star arm end-to-end vector relaxation functions Φ(t) and the stress relaxation function G(t) are found to be in reasonably good agreement with standard SS simulation results in the terminal regime. Finally, we demonstrate that this simulation method can be conveniently extended to study the arm-retraction problem in entangled star polymer melts with CR by modifying the definition of the reaction coordinate, while the computational efficiency will depend on the particular slip-spring or slip-link model

  1. Temperament profiles of Sasang typology in a child clinical sample

    Directory of Open Access Journals (Sweden)

    Soo Jin Lee

    2012-12-01

    Conclusion: These results demonstrated distinct temperament traits associated with traditional Korean Sasang types in children using an objective biopsychological personality inventory. With further investigation into the biopsychological profiles of the children, the longitudinal stability of the Sasang typology can be examined.

  2. Profiling critical cancer gene mutations in clinical tumor samples.

    Directory of Open Access Journals (Sweden)

    Laura E MacConaill

    2009-11-01

    Full Text Available Detection of critical cancer gene mutations in clinical tumor specimens may predict patient outcomes and inform treatment options; however, high-throughput mutation profiling remains underdeveloped as a diagnostic approach. We report the implementation of a genotyping and validation algorithm that enables robust tumor mutation profiling in the clinical setting.We developed and implemented an optimized mutation profiling platform ("OncoMap" to interrogate approximately 400 mutations in 33 known oncogenes and tumor suppressors, many of which are known to predict response or resistance to targeted therapies. The performance of OncoMap was analyzed using DNA derived from both frozen and FFPE clinical material in a diverse set of cancer types. A subsequent in-depth analysis was conducted on histologically and clinically annotated pediatric gliomas. The sensitivity and specificity of OncoMap were 93.8% and 100% in fresh frozen tissue; and 89.3% and 99.4% in FFPE-derived DNA. We detected known mutations at the expected frequencies in common cancers, as well as novel mutations in adult and pediatric cancers that are likely to predict heightened response or resistance to existing or developmental cancer therapies. OncoMap profiles also support a new molecular stratification of pediatric low-grade gliomas based on BRAF mutations that may have immediate clinical impact.Our results demonstrate the clinical feasibility of high-throughput mutation profiling to query a large panel of "actionable" cancer gene mutations. In the future, this type of approach may be incorporated into both cancer epidemiologic studies and clinical decision making to specify the use of many targeted anticancer agents.

  3. Chemical profiling of six samples of Brazilian propolis

    Directory of Open Access Journals (Sweden)

    Caroline C. Fernandes-Silva

    2013-01-01

    Full Text Available Six samples of Brazilian propolis from Minas Gerais and Paraná states were analyzed to identify the constituents (GC/MS and HPLC/MS and to determine their contents (HPLC and external standardization. All samples contained characteristic constituents of green propolis, but the samples from Minas Gerais had higher contents of prenylated phenylpropanoids and caffeoylquinic acids. Kaempferide and two other flavonoids were among the major constituents of the samples from Minas Gerais. Luteolin 5-O-methyl ether was detected only in samples from Paraná. Baccharis dracunculifolia was a source of resins for all samples analyzed, but the samples from Paraná had more complex plant origin.

  4. Expression and Genomic Profiling of Minute Breast Cancer Samples. Addendum

    Science.gov (United States)

    2007-07-01

    Alteration of gene expression profiles of peripheral mononuclear blood cells by tobacco smoke : implications for periodontal diseases . Oral Microbiol...promises to refine (1) and potentially revolutionize (2) the existing cancer staging system and the management of early disease . Microarray- based...14. Rubin, M.A. (2002) Understanding disease cell by cell. Science, 296, 1329-1330. 12 13 15. Emmert-Buck, M.R., Bonner, R.F., Smith, P.D

  5. 2010 OFES Joint Research TargetDivertor Heat Flux Profile Width Final Report DIII-D Contribution

    Energy Technology Data Exchange (ETDEWEB)

    Lasnier, C. J. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Makowski, M. A. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Boedo, J. A. [Univ. of California, San Diego, CA (United States); Hill, D. N. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Leonard, A. W. [General Atomics, San Diego, CA (United States); Porter, G. D. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Rensink, M. E. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Watkins, J. G. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2010-09-17

    Conduct experiments on major fusion facilities to improve understanding of the heat transport in the tokamak scrape-off layer (SOL) plasma, strengthening the basis for projecting divertor conditions in ITER. In FY10, FES will measure the divertor heat flux profiles and plasma characteristics in the tokamak scrape-off layer in multiple devices to investigate the underlying thermal transport processes. The unique characteristics of C-Mod, DIII-D, and NSTX will enable collection of data over a broad range of SOL and divertor parameters (e.g., collisionality, beta, parallel heat flux, and divertor geometry). Regimes similar to the ITER operating scenarios will be among those studied and characterized. Coordinated experiments using common analysis methods will generate a data set that will be compared with theory and simulation.

  6. Modification of SOL profiles and fluctuations with line-average density and divertor flux expansion in TCV

    DEFF Research Database (Denmark)

    Vianello, N.; Tsui, C.; Theiler, C.

    2017-01-01

    A set of Ohmic density ramp experiments addressing the role of parallel connection length in modifying scrape off layer (SOL) properties has been performed on the TCV tokamak. The parallel connection length has been modified by varying the poloidal flux expansion fx. It will be shown that this mo......A set of Ohmic density ramp experiments addressing the role of parallel connection length in modifying scrape off layer (SOL) properties has been performed on the TCV tokamak. The parallel connection length has been modified by varying the poloidal flux expansion fx. It will be shown...... that this modification does not influence neither the detachment density threshold, nor the development of a flat SOL density profile which instead depends strongly on the increase of the core line average density. The modification of the SOL upstream profile, with the appearance of what is generally called a density...... shoulder, has been related to the properties of filamentary blobs. Blob size increases with density, without any dependence on the parallel connection length both in the near and far SOL. The increase of the density decay length, corresponding to a profile flattening, has been related to the variation...

  7. Microbial community dynamics in soil aggregates shape biogeochemical gas fluxes from soil profiles - upscaling an aggregate biophysical model.

    Science.gov (United States)

    Ebrahimi, Ali; Or, Dani

    2016-09-01

    Microbial communities inhabiting soil aggregates dynamically adjust their activity and composition in response to variations in hydration and other external conditions. These rapid dynamics shape signatures of biogeochemical activity and gas fluxes emitted from soil profiles. Recent mechanistic models of microbial processes in unsaturated aggregate-like pore networks revealed a highly dynamic interplay between oxic and anoxic microsites jointly shaped by hydration conditions and by aerobic and anaerobic microbial community abundance and self-organization. The spatial extent of anoxic niches (hotspots) flicker in time (hot moments) and support substantial anaerobic microbial activity even in aerated soil profiles. We employed an individual-based model for microbial community life in soil aggregate assemblies represented by 3D angular pore networks. Model aggregates of different sizes were subjected to variable water, carbon and oxygen contents that varied with soil depth as boundary conditions. The study integrates microbial activity within aggregates of different sizes and soil depth to obtain estimates of biogeochemical fluxes from the soil profile. The results quantify impacts of dynamic shifts in microbial community composition on CO2 and N2 O production rates in soil profiles in good agreement with experimental data. Aggregate size distribution and the shape of resource profiles in a soil determine how hydration dynamics shape denitrification and carbon utilization rates. Results from the mechanistic model for microbial activity in aggregates of different sizes were used to derive parameters for analytical representation of soil biogeochemical processes across large scales of practical interest for hydrological and climate models. © 2016 John Wiley & Sons Ltd.

  8. Sample storage conditions significantly influence faecal microbiome profiles.

    Science.gov (United States)

    Choo, Jocelyn M; Leong, Lex E X; Rogers, Geraint B

    2015-11-17

    Sequencing-based studies of the human faecal microbiota are increasingly common. Appropriate storage of sample material is essential to avoid the introduction of post-collection bias in microbial community composition. Rapid freezing to -80 °C is commonly considered to be best-practice. However, this is not feasible in many studies, particularly those involving sample collection in participants' homes. We determined the extent to which a range of stabilisation and storage strategies maintained the composition of faecal microbial community structure relative to freezing to -80 °C. Refrigeration at 4 °C, storage at ambient temperature, and the use of several common preservative buffers (RNAlater, OMNIgene.GUT, Tris-EDTA) were assessed relative to freezing. Following 72 hours of storage, faecal microbial composition was assessed by 16 S rRNA amplicon sequencing. Refrigeration was associated with no significant alteration in faecal microbiota diversity or composition. However, samples stored using other conditions showed substantial divergence compared to -80 °C control samples. Aside from refrigeration, the use of OMNIgene.GUT resulted in the least alteration, while the greatest change was seen in samples stored in Tris-EDTA buffer. The commercially available OMNIgene.GUT kit may provide an important alternative where refrigeration and cold chain transportation is not available.

  9. Coupling soil Carbon Fluxes, Soil Microbes, and High-Resolution Carbon Profiling in Permafrost Transitions

    Science.gov (United States)

    Anderson, C.; Stegen, J.; Bond-Lamberty, B. P.; Tfaily, M. M.; Huang, M.; Liu, Y.

    2015-12-01

    Microbial communities play a central role in the functioning of natural ecosystems by heavily influencing biogeochemical cycles. Understanding how shifts in the environment are tied to shifts in biogeochemical rates via changes in microbial communities is particularly relevant in high latitude terrestrial systems underlain by permafrost due to vast carbon stocks currently stored within thawing permafrost. There is limited understanding, however, of the interplay among soil-atmosphere CO2 fluxes, microbial communities, and SOM chemical composition. To address this knowledge gap, we leverage the distinct spatial transitions in permafrost-affected soils at the Caribou Poker Creek Research Watershed, a 104 km2 boreal watershed ~50 km north of Fairbanks, AK. We integrate a variety of data to gain new knowledge of the factors that govern observed patterns in the rates of soil CO2 fluxes associated with permafrost to non-permafrost transition zones. We show that nonlinearities in fluxes are influenced by depth to permafrost, tree stand structure, and soil C composition. Further, using 16S sequencing methods we explore microbial community assembly processes and their connection to CO2 flux across spatial scales, and suggest a path to more mechanistically link microbes to large-scale biogeochemical cycles. Lastly, we use the Community Land Model (CLM) to compare Earth System Model predictions of soil C cycling with empirical measurements. Deviations between CLM predictions and field observations of CO2 flux and soil C stocks will provide insight for how the model may be improved through inclusion of additional biotic (e.g., microbial community composition) and abiotic (e.g., organic carbon composition) features, which will be critical to improve the predictive power of climate models in permafrost-affected regions.

  10. An information theory approach for evaluating earth radiation budget (ERB) measurements - Nonuniform sampling of diurnal longwave flux variations

    Science.gov (United States)

    Halyo, Nesim; Direskeneli, Haldun; Barkstrom, Bruce R.

    1991-01-01

    Satellite measurements are subject to a wide range of uncertainties due to their temporal, spatial, and directional sampling characteristics. An information-theory approach is suggested to examine the nonuniform temporal sampling of ERB measurements. The information (i.e., its entropy or uncertainty) before and after the measurements is determined, and information gain (IG) is defined as a reduction in the uncertainties involved. A stochastic model for the diurnal outgoing flux variations that affect the ERB is developed. Using Gaussian distributions for the a priori and measured radiant exitance fields, the IG is obtained by computing the a posteriori covariance. The IG for the monthly outgoing flux measurements is examined for different orbital parameters and orbital tracks, using the Earth Observing System orbital parameters as specific examples. Variations in IG due to changes in the orbit's inclination angle and the initial ascending node local time are investigated.

  11. Low-profile self-sealing sample transfer flexure box.

    Science.gov (United States)

    Simon, Kevin; Porz, Lukas; Swamy, Tushar; Chiang, Yet-Ming; Slocum, Alexander

    2017-08-01

    A flexural bearing mechanism has enabled the development of a self-sealing box for protecting air sensitive samples during transfer between glove boxes, micro-machining equipment, and microscopy equipment. The simplicity and self-actuating feature of this design makes it applicable to many devices that operate under vacuum conditions. The models used to design the flexural mechanism are presented in detail. The device has been tested in a Zeiss Merlin GEMINI II scanning electron microscope with Li 3 PS 4 samples, showing effective isolation from air and corrosion prevention.

  12. FANTOM5 CAGE profiles of human and mouse samples

    NARCIS (Netherlands)

    Noguchi, Shuhei; Arakawa, Takahiro; Fukuda, Shiro; Furuno, Masaaki; Hasegawa, Akira; Hori, Fumi; Ishikawa-Kato, Sachi; Kaida, Kaoru; Kaiho, Ai; Kanamori-Katayama, Mutsumi; Kawashima, Tsugumi; Kojima, Miki; Kubosaki, Atsutaka; Manabe, Ri-ichiroh; Murata, Mitsuyoshi; Nagao-Sato, Sayaka; Nakazato, Kenichi; Ninomiya, Noriko; Nishiyori-Sueki, Hiromi; Noma, Shohei; Saijyo, Eri; Saka, Akiko; Sakai, Mizuho; Simon, Christophe; Suzuki, Naoko; Tagami, Michihira; Watanabe, Shoko; Yoshida, Shigehiro; Arner, Peter; Axton, Richard A.; Babina, Magda; Baillie, J. Kenneth; Barnett, Timothy C.; Beckhouse, Anthony G.; Blumenthal, Antje; Bodega, Beatrice; Bonetti, Alessandro; Briggs, James; Brombacher, Frank; Carlisle, Ailsa J.; Clevers, Hans C.; Davis, Carrie A.; Detmar, Michael; Dohi, Taeko; Edge, Albert S. B.; Edinger, Matthias; Ehrlund, Anna; Ekwall, Karl; Endoh, Mitsuhiro; Enomoto, Hideki; Eslami, Afsaneh; Fagiolini, Michela; Fairbairn, Lynsey; Farach-Carson, Mary C.; Faulkner, Geoffrey J.; Ferrai, Carmelo; Fisher, Malcolm E.; Forrester, Lesley M.; Fujita, Rie; Furusawa, Jun-ichi; Geijtenbeek, Teunis B.; Gingeras, Thomas; Goldowitz, Daniel; Guhl, Sven; Guler, Reto; Gustincich, Stefano; Ha, Thomas J.; Hamaguchi, Masahide; Hara, Mitsuko; Hasegawa, Yuki; Herlyn, Meenhard; Heutink, Peter; Hitchens, Kelly J.; Hume, David A.; Ikawa, Tomokatsu; Ishizu, Yuri; Kai, Chieko; Kawamoto, Hiroshi; Kawamura, Yuki I.; Kempfle, Judith S.; Kenna, Tony J.; Kere, Juha; Khachigian, Levon M.; Kitamura, Toshio; Klein, Sarah; Klinken, S. Peter; Knox, Alan J.; Kojima, Soichi; Koseki, Haruhiko; Koyasu, Shigeo; Lee, Weonju; Lennartsson, Andreas; Mackay-sim, Alan; Mejhert, Niklas; Mizuno, Yosuke; Morikawa, Hiromasa; Morimoto, Mitsuru; Moro, Kazuyo; Morris, Kelly J.; Motohashi, Hozumi; Mummery, Christine L.; Nakachi, Yutaka; Nakahara, Fumio; Nakamura, Toshiyuki; Nakamura, Yukio; Nozaki, Tadasuke; Ogishima, Soichi; Ohkura, Naganari; Ohno, Hiroshi; Ohshima, Mitsuhiro; Okada-Hatakeyama, Mariko; Okazaki, Yasushi; Orlando, Valerio; Ovchinnikov, Dmitry A.; Passier, Robert; Patrikakis, Margaret; Pombo, Ana; Pradhan-Bhatt, Swati; Qin, Xian-Yang; Rehli, Michael; Rizzu, Patrizia; Roy, Sugata; Sajantila, Antti; Sakaguchi, Shimon; Sato, Hiroki; Satoh, Hironori; Savvi, Suzana; Saxena, Alka; Schmidl, Christian; Schneider, Claudio; Schulze-Tanzil, Gundula G.; Schwegmann, Anita; Sheng, Guojun; Shin, Jay W.; Sugiyama, Daisuke; Sugiyama, Takaaki; Summers, Kim M.; Takahashi, Naoko; Takai, Jun; Tanaka, Hiroshi; Tatsukawa, Hideki; Tomoiu, Andru; Toyoda, Hiroo; van de Wetering, Marc; van den Berg, Linda M.; Verardo, Roberto; Vijayan, Dipti; Wells, Christine A.; Winteringham, Louise N.; Wolvetang, Ernst; Yamaguchi, Yoko; Yamamoto, Masayuki; Yanagi-Mizuochi, Chiyo; Yoneda, Misako; Yonekura, Yohei; Zhang, Peter G.; Zucchelli, Silvia; Abugessaisa, Imad; Arner, Erik; Harshbarger, Jayson; Kondo, Atsushi; Lassmann, Timo; Lizio, Marina; Sahin, Serkan; Sengstag, Thierry; Severin, Jessica; Shimoji, Hisashi; Suzuki, Masanori; Suzuki, Harukazu; Kawai, Jun; Kondo, Naoto; Itoh, Masayoshi; Daub, Carsten O.; Kasukawa, Takeya; Kawaji, Hideya; Carninci, Piero; Forrest, Alistair R. R.; Hayashizaki, Yoshihide

    2017-01-01

    In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples,

  13. Modification of SOL profiles and fluctuations with line-average density and divertor flux expansion in TCV

    Science.gov (United States)

    Vianello, N.; Tsui, C.; Theiler, C.; Allan, S.; Boedo, J.; Labit, B.; Reimerdes, H.; Verhaegh, K.; Vijvers, W. A. J.; Walkden, N.; Costea, S.; Kovacic, J.; Ionita, C.; Naulin, V.; Nielsen, A. H.; Rasmussen, J. Juul; Schneider, B.; Schrittwieser, R.; Spolaore, M.; Carralero, D.; Madsen, J.; Lipschultz, B.; Militello, F.; The TCV Team; The EUROfusion MST1 Team

    2017-11-01

    A set of Ohmic density ramp experiments addressing the role of parallel connection length in modifying scrape off layer (SOL) properties has been performed on the TCV tokamak. The parallel connection length has been modified by varying the poloidal flux expansion f x . It will be shown that this modification does not influence neither the detachment density threshold, nor the development of a flat SOL density profile which instead depends strongly on the increase of the core line average density. The modification of the SOL upstream profile, with the appearance of what is generally called a density shoulder, has been related to the properties of filamentary blobs. Blob size increases with density, without any dependence on the parallel connection length both in the near and far SOL. The increase of the density decay length, corresponding to a profile flattening, has been related to the variation of the divertor normalized collisionality Λ_div (Myra et al 2006 Phys. Plasmas 13 112502, Carralero et al, ASDEX Upgrade Team, JET Contributors and EUROfusion MST1 Team 2015 Phys. Rev. Let. 115 215002), showing that in TCV the increase of Λ_div is not sufficient to guarantee the SOL upstream profile flattening.

  14. Metabolic flux profiling of recombinant protein secreting Pichia pastoris growing on glucose:methanol mixtures

    Directory of Open Access Journals (Sweden)

    Jordà Joel

    2012-05-01

    Full Text Available Abstract Background The methylotrophic yeast Pichia pastoris has emerged as one of the most promising yeast hosts for the production of heterologous proteins. Mixed feeds of methanol and a multicarbon source instead of methanol as sole carbon source have been shown to improve product productivities and alleviate metabolic burden derived from protein production. Nevertheless, systematic quantitative studies on the relationships between the central metabolism and recombinant protein production in P. pastoris are still rather limited, particularly when growing this yeast on mixed carbon sources, thus hampering future metabolic network engineering strategies for improved protein production. Results The metabolic flux distribution in the central metabolism of P. pastoris growing on a mixed feed of glucose and methanol was analyzed by Metabolic Flux Analysis (MFA using 13C-NMR-derived constraints. For this purpose, we defined new flux ratios for methanol assimilation pathways in P. pastoris cells growing on glucose:methanol mixtures. By using this experimental approach, the metabolic burden caused by the overexpression and secretion of a Rhizopus oryzae lipase (Rol in P. pastoris was further analyzed. This protein has been previously shown to trigger the unfolded protein response in P. pastoris. A series of 13C-tracer experiments were performed on aerobic chemostat cultivations with a control and two different Rol producing strains growing at a dilution rate of 0.09 h−1 using a glucose:methanol 80:20 (w/w mix as carbon source. The MFA performed in this study reveals a significant redistristribution of carbon fluxes in the central carbon metabolism when comparing the two recombinant strains vs the control strain, reflected in increased glycolytic, TCA cycle and NADH regeneration fluxes, as well as higher methanol dissimilation rates. Conclusions Overall, a further 13C-based MFA development to characterise the central metabolism of methylotrophic

  15. Metabolic flux profiling of recombinant protein secreting Pichia pastoris growing on glucose:methanol mixtures

    Science.gov (United States)

    2012-01-01

    Background The methylotrophic yeast Pichia pastoris has emerged as one of the most promising yeast hosts for the production of heterologous proteins. Mixed feeds of methanol and a multicarbon source instead of methanol as sole carbon source have been shown to improve product productivities and alleviate metabolic burden derived from protein production. Nevertheless, systematic quantitative studies on the relationships between the central metabolism and recombinant protein production in P. pastoris are still rather limited, particularly when growing this yeast on mixed carbon sources, thus hampering future metabolic network engineering strategies for improved protein production. Results The metabolic flux distribution in the central metabolism of P. pastoris growing on a mixed feed of glucose and methanol was analyzed by Metabolic Flux Analysis (MFA) using 13C-NMR-derived constraints. For this purpose, we defined new flux ratios for methanol assimilation pathways in P. pastoris cells growing on glucose:methanol mixtures. By using this experimental approach, the metabolic burden caused by the overexpression and secretion of a Rhizopus oryzae lipase (Rol) in P. pastoris was further analyzed. This protein has been previously shown to trigger the unfolded protein response in P. pastoris. A series of 13C-tracer experiments were performed on aerobic chemostat cultivations with a control and two different Rol producing strains growing at a dilution rate of 0.09 h−1 using a glucose:methanol 80:20 (w/w) mix as carbon source. The MFA performed in this study reveals a significant redistristribution of carbon fluxes in the central carbon metabolism when comparing the two recombinant strains vs the control strain, reflected in increased glycolytic, TCA cycle and NADH regeneration fluxes, as well as higher methanol dissimilation rates. Conclusions Overall, a further 13C-based MFA development to characterise the central metabolism of methylotrophic yeasts when growing on mixed

  16. Spectral sampling tools for vegetation biophysical parameters and flux measurements in Europe: the European ES0903 COST Action

    Science.gov (United States)

    Vescovo, L.

    2010-12-01

    The estimate of carbon sequestration by terrestrial ecosystems and the prediction of the global change impact on the ecosystem carbon balance are becoming urgent needs required by international agreements. To support the development of this knowledge, a deep insight into processes that regulate carbon exchanges between terrestrial ecosystems and the atmosphere is fundamental. Flux towers remain a primary tool for understanding ecosystem carbon fluxes within the global flux networks. International initiatives such as SpecNet are developing to fill the temporal and spatial gap between ecosystem measurements and remote sensing by means of scale-appropriate optical measurements. In this framework, a new EU COST Action project has started in Europe. Up to now, 16 countries are participating to the Action. The COST Action project is open to researchers from European Cost Countries, but also from Near-Neighbour and non-COST countries can participate to the Action and, in some cases, can obtain some specific national funding (e.g. Australia, New Zealand, South Africa, Argentina). According to the highlighted scientific questions, the objectives of ES0903 are i) to analyse the state of the art of the optical sampling research in Europe, ii) to standardize tools and methods in the optical sampling measurements, iii) to focus on the fluxes and biomass estimation problems as an input to the technological world for development of new sensors and iv) to involve the scientific instruments industries in designing and testing a common multi-band reflectance sensor for ground optical measurements in the European flux network. Thanks to the Action, the use of standardised protocols will be encouraged within a spectral measurements network, across site comparisons will be enabled and the use of new instruments and sensors will be promoted and tested. Some of the most common issues of the proximal sampling research, performed at ecosystem level, are: i)methods, protocols and

  17. Protein Profile study of clinical samples using Laser Induced Fluorescence as the detection method

    DEFF Research Database (Denmark)

    Karemore, Gopal Raghunath; Raja, Sujatha N.; Rai, Lavanya

    2009-01-01

      Protein profiles of tissue homogenates were recorded using HPLC separation and LIF detection method. The samples were collected from volunteers with clinically normal or cervical cancer conditions. It is shown that the protein profile can be classified as belonging to malignant or normal state ...

  18. A FLUX-LIMITED SAMPLE OF z {approx} 1 Ly{alpha} EMITTING GALAXIES IN THE CHANDRA DEEP FIELD SOUTH ,

    Energy Technology Data Exchange (ETDEWEB)

    Barger, A. J.; Wold, I. G. B. [Department of Astronomy, University of Wisconsin-Madison, 475 North Charter Street, Madison, WI 53706 (United States); Cowie, L. L. [Institute for Astronomy, University of Hawaii, 2680 Woodlawn Drive, Honolulu, HI 96822 (United States)

    2012-04-20

    We describe a method for obtaining a flux-limited sample of Ly{alpha} emitters from Galaxy Evolution Explorer (GALEX) grism data. We show that the multiple GALEX grism images can be converted into a three-dimensional (two spatial axes and one wavelength axis) data cube. The wavelength slices may then be treated as narrowband images and searched for emission-line galaxies. For the GALEX NUV grism data, the method provides a Ly{alpha} flux-limited sample over the redshift range z = 0.67-1.16. We test the method on the Chandra Deep Field South field, where we find 28 Ly{alpha} emitters with faint continuum magnitudes (NUV > 22) that are not present in the GALEX pipeline sample. We measure the completeness by adding artificial emitters and measuring the fraction recovered. We find that we have an 80% completeness above a Ly{alpha} flux of 10{sup -15} erg cm{sup -2} s{sup -1}. We use the UV spectra and the available X-ray data and optical spectra to estimate the fraction of active galactic nuclei in the selection. We report the first detection of a giant Ly{alpha} blob at z < 1, though we find that these objects are much less common at z = 1 than at z = 3. Finally, we compute limits on the z {approx} 1 Ly{alpha} luminosity function and confirm that there is a dramatic evolution in the luminosity function over the redshift range z = 0-1.

  19. Methane uptake in soils of Southern Spain estimated by two different techniques: Static chamber and 222radon flux and soil air concentration profiles

    Science.gov (United States)

    Dueñas, C.; Fernández, M. C.; Carretero, J.; Liger, E.

    Measurements of methane fluxes from four differing soils in the surroundings of Málaga (Spain) were carried out by two methods: a direct method using a static accumulation chamber at the soil surface and an indirect method obtained from simultaneously measured 222Rn flux from the soil surface in parallel with the concentration profile measurements of 222Rn and CH 4 in the air of soil. The directly measured methane flux at all the investigated soils was higher than the methane fluxes derived from the indirect method. Atmospheric methane was consumed by all the soils and mean direct flux to the atmosphere were 3.25 μmol m -2 h -1. The study showed no correlation between methane uptake and soil temperature, which might be due to the dry conditions prevailing during the study period.

  20. Adaptive autonomous sampling toward the study of microbial carbon and energy fluxes in a dynamic estuary

    Science.gov (United States)

    Herfort, L.; Seaton, C. M.; Wilkin, M.; Baptista, A. M.; Roman, B.; Preston, C. M.; Scholin, C. A.; Melançon, C.; Simon, H. M.

    2013-12-01

    An autonomous microbial sampling device was integrated with a long-term (endurance) environmental sensor system to investigate variation in microbial composition and activities related to complex estuarine dynamics. This integration was a part of ongoing efforts in the Center for Coastal Margin Observation and Prediction (CMOP) to study estuarine carbon and nitrogen cycling using an observation and prediction system (SATURN, http://www.stccmop.org/saturn) as foundational infrastructure. The two endurance stations fitted with physical and biogeochemical sensors that were used in this study are located in the SATURN observation network. The microbial sampler is the Environmental Sample Processor (ESP), a commercially available electromechanical/fluidic system designed for automated collection, preservation and in situ analyses of marine water samples. The primary goal of the integration was to demonstrate that the ESP, developed for sampling of pelagic oceanic environments, could be successfully deployed for autonomous sample acquisition in the highly dynamic and turbid Columbia River estuary. The ability of the ESP to collect material at both pre-determined times and automatically in response to local conditions was tested. Pre-designated samples were acquired at specific times to capture variability in the tidal cycle. Autonomous, adaptive sampling was triggered when conditions associated with specific water masses were detected in real-time by the SATURN station's sensors and then communicated to the ESP via the station computer to initiate sample collection. Triggering criteria were based on our understanding of estuary dynamics, as provided by the analysis of extensive archives of high-resolution, long-term SATURN observations and simulations. In this manner, we used the ESP to selectively sample various microbial consortia in the estuary to facilitate the study of ephemeral microbial-driven processes. For example, during the summer of 2013 the adaptive sampling

  1. A Faint Flux-Limited LAE Sample at z = 0.3

    Science.gov (United States)

    Wold, Isak; Finkelstein, Steven; Barger, Amy; cowie, lennox; Rosenwasser, Benjamin

    2018-01-01

    Observational surveys of Lya emitters (LAEs) have proven to be an efficient method to identify and study large numbers of galaxies over a wide redshift range. To understand what types of galaxies are selected in LAE surveys - and how this evolves with redshift - it is important to establish a low-redshift reference sample that can be directly compared to high-redshift samples. The lowest redshift where a direct Lya survey is currently possible is at a redshift of z~0.3 via the Galaxy Evolution Explorer (GALEX ) FUV grism data. Using the z~0.3 GALEX sample as an anchor point, it has been suggested that at low redshifts high equivalent width (EW) LAEs become less prevalent and that the amount of escaping Lya emission declines rapidly. A number of explanations for these trends have been suggested including increasing dust content, increasing neutral column density, and/or increasing metallicity of star-forming galaxies at lower redshifts. However, the published z~0.3 GALEX sample is pre-selected from bright NUV objects. Thus, objects with strong Lya emission but faint continuum (high-EW LAEs) could be missed. In this talk, I will present my efforts to re-reduce the deepest archival GALEX FUV grism data and obtain a sample that is not biased against high-EW LAEs. I will discuss the implications of this new sample on the evolutionary trends listed above.

  2. Bioenergetic profiling of Trypanosoma cruzi life stages using Seahorse extracellular flux technology.

    Science.gov (United States)

    Shah-Simpson, Sheena; Pereira, Camila F A; Dumoulin, Peter C; Caradonna, Kacey L; Burleigh, Barbara A

    2016-08-01

    Energy metabolism is an attractive target for the development of new therapeutics against protozoan pathogens, including Trypanosoma cruzi, the causative agent of human Chagas disease. Despite emerging evidence that mitochondrial electron transport is essential for the growth of intracellular T. cruzi amastigotes in mammalian cells, fundamental knowledge of mitochondrial energy metabolism in this parasite life stage remains incomplete. The Clark-type electrode, which measures the rate of oxygen consumption, has served as the traditional tool to study mitochondrial energetics and has contributed to our understanding of it in T. cruzi. Here, we evaluate the Seahorse XF(e)24 extracellular flux platform as an alternative method to assess mitochondrial bioenergetics in isolated T. cruzi parasites. We report optimized assay conditions used to perform mitochondrial stress tests with replicative life cycle stages of T. cruzi using the XF(e)24 instrument, and discuss the advantages and potential limitations of this methodology, as applied to T. cruzi and other trypanosomatids. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Mass Flux of Tephra Sampled Frequently During the Ongoing Halema`uma`u Eruption (Invited)

    Science.gov (United States)

    Swanson, D.; Wooten, K.; Orr, T. R.

    2009-12-01

    but falling back into the vent, where they resided until some later event lifted them to the crater rim. The daily juvenile mass flux, including recycled clasts but excluding 8 discrete explosive eruptions in 2008, ranged from 0 to 13,000 kg and was generally a few tens to a few hundreds of kilograms. We interpret the lithic clasts as derived from rock falls into the new vent and crater. Many have partial coatings of secondary minerals including anhydrite. The daily lithic mass flux varied from 1 to 6,900 kg. Much of the lithic material is perhaps better considered as rock-fall “dust” than as actual tephra. To date, about 400 tonnes of tephra have been ejected quasi-continuously, composing 18 percent of all tephra produced during the eruption. The rest resulted from the 8 discrete explosive eruptions, which ejected, in a few tens of seconds, masses more than ~7,000 kg (as high as ~ 800,000 kg). The total mass produced by these 8 eruptions is ~1,800 tonnes. The total mass of all tephra produced by the eruption is ~2,200 tonnes, with subequal amounts of juvenile and lithic components. The volume of lithic tephra (~1100 m3, assuming a deposit density of 1,000 kg/m3) is less than 1 percent of the volume of the new crater, currently ~130 m wide and 200 m deep. Clearly the crater has formed by collapse into underground void space.

  4. Comparative analysis of bacterial profiles in unstimulated and stimulated saliva samples

    Directory of Open Access Journals (Sweden)

    Daniel Belstrøm

    2016-03-01

    Full Text Available Background and objective: The microbial profiles of stimulated saliva samples have been shown to differentiate between patients with periodontitis, patients with dental caries, and orally healthy individuals. Saliva was stimulated to allow for easy and rapid collection; however, microbial composition may not reflect the more natural, unstimulated state. The purpose of this study was to validate whether stimulated saliva is an adequate surrogate for unstimulated saliva in determining salivary microbiomes. Design: Unstimulated (n=20 and stimulated (n=20 saliva samples were collected from 20 orally and systemically healthy, non-smoking participants. Salivary bacterial profiles were analyzed by means of the Human Oral Microbe Identification using Next Generation Sequencing (HOMINGS, and statistical analysis was performed using Mann–Whitney test with Benjamini–Hochberg's correction for multiple comparison, cluster analysis, principal component analysis, and correspondence analysis. Results: From a total of 40 saliva samples, 496 probe targets were identified with a mean number of targets per sample of 203 (range: 146–303, and a mean number of probe targets of 206 and 200 in unstimulated and stimulated saliva samples, respectively (p=0.62. Based on all statistical methods used for this study, the microbial profiles of unstimulated and stimulated saliva samples collected from the same person were not statistically significantly different. Conclusions: Analysis of bacterial salivary profiles in unstimulated and stimulated saliva samples collected from the same individual showed comparable results. Thus, the results verify that stimulated saliva is an adequate surrogate of unstimulated saliva for microbiome-related studies.

  5. Comparative analysis of bacterial profiles in unstimulated and stimulated saliva samples

    DEFF Research Database (Denmark)

    Belstrøm, Daniel; Holmstrup, Palle; Jensen, Allan Bardow

    2016-01-01

    BACKGROUND AND OBJECTIVE: The microbial profiles of stimulated saliva samples have been shown to differentiate between patients with periodontitis, patients with dental caries, and orally healthy individuals. Saliva was stimulated to allow for easy and rapid collection; however, microbial...... orally and systemically healthy, non-smoking participants. Salivary bacterial profiles were analyzed by means of the Human Oral Microbe Identification using Next Generation Sequencing (HOMINGS), and statistical analysis was performed using Mann-Whitney test with Benjamini-Hochberg's correction...

  6. Combining soil and tree-stem flux measurements and soil gas profiles to understand CH4 pathways in Fagus sylvatica forests

    Czech Academy of Sciences Publication Activity Database

    Maier, M.; Macháčová, Kateřina; Lang, F.; Svobodová, Kateřina; Urban, Otmar

    (2017) ISSN 1436-8730 R&D Projects: GA MŠk(CZ) LO1415 Institutional support: RVO:86652079 Keywords : ch4 * soil gas profile * gas flux * co2 * methanogenesis Subject RIV: ED - Physiology Impact factor: 2.102, year: 2016

  7. The impact of in-canopy wind profile formulations on heat flux estimation in an open orchard using the remote sensing-based two-source model

    Science.gov (United States)

    Cammalleri, C.; Anderson, M. C.; Ciraolo, G.; Durso, G.; Kustas, W. P.; La Loggia, G.; Minacapilli, M.

    2010-12-01

    For open orchard and vineyard canopies containing significant fractions of exposed soil (>50%), typical of Mediterranean agricultural regions, the energy balance of the vegetation elements is strongly influenced by heat exchange with the bare soil/substrate. For these agricultural systems a "two-source" approach, where radiation and turbulent exchange between the soil and canopy elements are explicitly modelled, appears to be the only suitable methodology for reliably assessing energy fluxes. In strongly clumped canopies, the effective wind speed profile inside and below the canopy layer can strongly influence the partitioning of energy fluxes between the soil and vegetation components. To assess the impact of in-canopy wind profile on model flux estimates, an analysis of three different formulations is presented, including algorithms from Goudriaan (1977), Massman (1987) and Lalic et al. (2003). The in-canopy wind profile formulations are applied to the thermal-based two-source energy balance (TSEB) model developed by Norman et al. (1995) and modified by Kustas and Norman (1999). High resolution airborne remote sensing images, collected over an agricultural area located in the western part of Sicily (Italy) comprised primarily of vineyards, olive and citrus orchards, are used to derive all the input parameters needed to apply the TSEB. The images were acquired from June to October 2008 and include a relatively wide range of meteorological and soil moisture conditions. A preliminary sensitivity analysis of the three wind profile algorithms highlights the dependence of wind speed just above the soil/substrate to leaf area index and canopy height over the typical range of canopy properties encountered in these agricultural areas. It is found that differences among the models in wind just above the soil surface are most significant under sparse and medium fractional cover conditions (15-50%). The TSEB model heat flux estimates are compared with micro

  8. The impact of in-canopy wind profile formulations on heat flux estimation in an open orchard using the remote sensing-based two-source model

    Directory of Open Access Journals (Sweden)

    C. Cammalleri

    2010-12-01

    Full Text Available For open orchard and vineyard canopies containing significant fractions of exposed soil (>50%, typical of Mediterranean agricultural regions, the energy balance of the vegetation elements is strongly influenced by heat exchange with the bare soil/substrate. For these agricultural systems a "two-source" approach, where radiation and turbulent exchange between the soil and canopy elements are explicitly modelled, appears to be the only suitable methodology for reliably assessing energy fluxes. In strongly clumped canopies, the effective wind speed profile inside and below the canopy layer can strongly influence the partitioning of energy fluxes between the soil and vegetation components. To assess the impact of in-canopy wind profile on model flux estimates, an analysis of three different formulations is presented, including algorithms from Goudriaan (1977, Massman (1987 and Lalic et al. (2003. The in-canopy wind profile formulations are applied to the thermal-based two-source energy balance (TSEB model developed by Norman et al. (1995 and modified by Kustas and Norman (1999. High resolution airborne remote sensing images, collected over an agricultural area located in the western part of Sicily (Italy comprised primarily of vineyards, olive and citrus orchards, are used to derive all the input parameters needed to apply the TSEB. The images were acquired from June to October 2008 and include a relatively wide range of meteorological and soil moisture conditions. A preliminary sensitivity analysis of the three wind profile algorithms highlights the dependence of wind speed just above the soil/substrate to leaf area index and canopy height over the typical range of canopy properties encountered in these agricultural areas. It is found that differences among the models in wind just above the soil surface are most significant under sparse and medium fractional cover conditions (15–50%. The TSEB model heat flux estimates are compared with micro

  9. Maternal influences on the transmission of leukocyte gene expression profiles in population samples from Brisbane, Australia.

    Directory of Open Access Journals (Sweden)

    Elizabeth Mason

    Full Text Available Two gene expression profiling studies designed to identify maternal influences on development of the neonate immune system and to address the population structure of the leukocyte transcriptome were carried out in Brisbane, Australia. In the first study, a comparison of 19 leukocyte samples obtained from mothers in the last three weeks of pregnancy with 37 umbilical cord blood samples documented differential expression of 7,382 probes at a false discovery rate of 1%, representing approximately half of the expressed transcriptome. An even larger component of the variation involving 8,432 probes, notably enriched for Vitamin E and methotrexate-responsive genes, distinguished two sets of individuals, with perfect transmission of the two profile types between each of 16 mother-child pairs in the study. A minor profile of variation was found to distinguish the gene expression profiles of obese mothers and children of gestational diabetic mothers from those of children born to obese mothers. The second study was of adult leukocyte profiles from a cross-section of Red Cross blood donors sampled throughout Brisbane. The first two axes in this study are related to the third and fourth axes of variation in the first study and also reflect variation in the abundance of CD4 and CD8 transcripts. One of the profiles associated with the third axis is largely excluded from samples from the central portion of the city. Despite enrichment of insulin signaling and aspects of central metabolism among the differentially expressed genes, there was little correlation between leukocyte expression profiles and body mass index overall. Our data is consistent with the notion that maternal health and cytokine milieu directly impact gene expression in fetal tissues, but that there is likely to be a complex interplay between cultural, genetic, and other environmental factors in the programming of gene expression in leukocytes of newborn children.

  10. Microbial profile comparisons of saliva, pooled and site-specific subgingival samples in periodontitis patients

    DEFF Research Database (Denmark)

    Belstrøm, Daniel; Sembler-Møller, Maria Lynn; Grande, Maria Anastasia

    2017-01-01

    OBJECTIVES: The purpose of this study was to compare microbial profiles of saliva, pooled and site-specific subgingival samples in patients with periodontitis. We tested the hypotheses that saliva can be an alternative to pooled subgingival samples, when screening for presence of periopathogens....... DESIGN: Site specific subgingival plaque samples (n = 54), pooled subgingival plaque samples (n = 18) and stimulated saliva samples (n = 18) were collected from 18 patients with generalized chronic periodontitis. Subgingival and salivary microbiotas were characterized by means of HOMINGS (Human Oral...... to an AUC of 0.76 (sensitivity: 0.56, specificity: 0.94) in pooled subgingival samples. CONCLUSIONS: Site-specific presence of periodontal pathogens was detected with comparable accuracy in stimulated saliva samples and pooled subgingival plaque samples. Consequently, saliva may be a reasonable surrogate...

  11. Different organochlorine contaminant profiles in groups of flounders (Platichthys flesus) from sampling locations around Denmark

    DEFF Research Database (Denmark)

    Vorkamp, Katrin; Svendsen, Tore Christian; Rønsholdt, Bent

    2012-01-01

    Flounders (Platichthys flesus) from the waters around Denmark were analysed for their organochlorine (OC) profile to study whether fish from the same genetic population could be separated into characteristic subpopulations, based on their feeding grounds. The chemical analysis of fish liver...... provided a data set of 16 OC compounds in 94 samples from 2004 to 2006. Except for hexachlorocyclohexane, OC compounds were intercorrelated, indicating similar environmental fate and bioaccumulation. OC profiles are less affected than absolute concentrations by potentially confounding biological factors...... and thus more suitable for studies of intrapopulation differences in relation to feeding grounds. Principal component analysis grouped the samples according to locations. All but three of the 94 samples could be reclassified. Samples from the same and additional locations collected in 2003 provided...

  12. Profiles of Chronic Illness Knowledge in a Community Sample of American Adults

    Science.gov (United States)

    Jackson, Todd

    2009-01-01

    The author identified profiles of chronic illness knowledge (i.e., heart disease, cancer, diabetes) in a community sample of American adults and examined the effect of sociodemographic influences on relations of illness knowledge to health practices and well-being. Participants were 181 women and 120 men who completed measures of illness…

  13. Microbial profile comparisons of saliva, pooled and site-specific subgingival samples in periodontitis patients

    DEFF Research Database (Denmark)

    Belstrøm, Daniel; Sembler-Møller, Maria Lynn; Grande, Maria Anastasia

    2017-01-01

    . DESIGN: Site specific subgingival plaque samples (n = 54), pooled subgingival plaque samples (n = 18) and stimulated saliva samples (n = 18) were collected from 18 patients with generalized chronic periodontitis. Subgingival and salivary microbiotas were characterized by means of HOMINGS (Human Oral......OBJECTIVES: The purpose of this study was to compare microbial profiles of saliva, pooled and site-specific subgingival samples in patients with periodontitis. We tested the hypotheses that saliva can be an alternative to pooled subgingival samples, when screening for presence of periopathogens...... by pooled subgingival samples. Presence of Porphyromonas gingivalis, Treponema denticola, Prevotella intermedia, Filifactor alocis, Tannerella forsythia and Parvimona micra in site-specific subgingival samples were detected in saliva with an AUC of 0.79 (sensitivity: 0.61, specificity: 0.94), compared...

  14. Sterile paper points as a bacterial DNA-contamination source in microbiome profiles of clinical samples.

    Science.gov (United States)

    van der Horst, Joyce; Buijs, Mark J; Laine, Marja L; Wismeijer, Daniël; Loos, Bruno G; Crielaard, Wim; Zaura, Egija

    2013-12-01

    High throughput sequencing of bacterial DNA from clinical samples provides untargeted, open-ended information on the entire microbial community. The downside of this approach is the vulnerability to DNA contamination from other sources than the clinical sample. Here we describe contamination from sterile paper points (PPs) used in microbial sample collection. Peri-implant samples from 48 individuals were collected using sterile PPs. Control samples contained only PPs or DNA extraction blank controls. 16S rRNA gene libraries were sequenced using 454 pyrosequencing. 16S rRNA gene copy numbers were measured by quantitative PCR. Nearly half of the sequencing reads belonged to two OTUs classified as Enterococcus (25% of reads) or Exiguobacterium (21%), which are not typical oral microorganisms. Of 87 peri-implant samples, only 10 samples (11%) contained neither of the two OTUs. The relative abundance of both unusual OTUs correlated with each other (pDNA equivalent to 1.2 × 10(3) and 1.1 × 10(4) cells respectively, which was within the range of DNA in the clinical samples (average 1.8 × 10(7), SD 4.8 × 10(7), min 4.4 × 10(2), max 2.8 × 10(8)). The microbial profile from these PPs was dominated (>83% of reads) by the two unusual OTUs. Sterile PPs can contain contaminating bacterial DNA. The use of PPs as a sampling tool for microbial profiling of clinical samples by open-ended techniques such as sequencing or DGGE should be avoided. Clinicians working with PPs as sampling tools for bacterial DNA should consider using an alternative sampling tool, because sterile unused PPs can be a considerable source of foreign bacterial DNA. We recommend sterile curettes for collecting clinical samples for open-ended techniques, such as sequencing or DGGE. Copyright © 2013 Elsevier Ltd. All rights reserved.

  15. Language profiles in young children with autism spectrum disorder: A community sample using multiple assessment instruments.

    Science.gov (United States)

    Nevill, Rose; Hedley, Darren; Uljarević, Mirko; Sahin, Ensu; Zadek, Johanna; Butter, Eric; Mulick, James A

    2017-11-01

    This study investigated language profiles in a community-based sample of 104 children aged 1-3 years who had been diagnosed with autism spectrum disorder using Diagnostic and Statistical Manual of Mental Disorders (5th ed.) diagnostic criteria. Language was assessed with the Mullen scales, Preschool Language Scale, fifth edition, and Vineland-II parent-report. The study aimed to determine whether the receptive-to-expressive language profile is independent from the assessment instrument used, and whether nonverbal cognition, early communicative behaviors, and autism spectrum disorder symptoms predict language scores. Receptive-to-expressive language profiles differed between assessment instruments and reporters, and Preschool Language Scale, fifth edition profiles were also dependent on developmental level. Nonverbal cognition and joint attention significantly predicted receptive language scores, and nonverbal cognition and frequency of vocalizations predicted expressive language scores. These findings support the administration of multiple direct assessment and parent-report instruments when evaluating language in young children with autism spectrum disorder, for both research and in clinical settings. Results also support that joint attention is a useful intervention target for improving receptive language skills in young children with autism spectrum disorder. Future research comparing language profiles of young children with autism spectrum disorder to children with non-autism spectrum disorder developmental delays and typical development will add to our knowledge of early language development in children with autism spectrum disorder.

  16. MicroRNA profiling of pericardial fluid samples from patients with heart failure.

    Directory of Open Access Journals (Sweden)

    Suvi M Kuosmanen

    Full Text Available Multicellular organisms maintain vital functions through intercellular communication. Release of extracellular vesicles that carry signals to even distant target organs is one way of accomplishing this communication. MicroRNAs can also be secreted from the cells in exosomes and act as paracrine signalling molecules. In addition, microRNAs have been implicated in the pathogenesis of a large number of diseases, including cardiovascular diseases, and are considered as promising candidate biomarkers due to their relative stability and easy quantification from clinical samples. Pericardial fluid contains hormones secreted by the heart and is known to reflect the cardiac function. In this study, we sought to investigate whether pericardial fluid contains microRNAs and if so, whether they could be used to distinguish between different cardiovascular pathologies and disease stages.Pericardial fluid was collected from heart failure patients during open-heart surgery. MicroRNA profiles of altogether 51 patients were measured by quantitative real-time PCR (qPCR using Exiqon human panels I and II. On the average, 256 microRNAs were detected per sample, and 70 microRNAs out of 742 profiled microRNAs were detected in every sample. The five most abundant microRNAs in pericardial fluid were miR-21-5p, miR-451a, miR-125b-5p, let-7b-5p and miR-16-5p. No specific signatures for cardiovascular pathologies or clinically assessed heart failure stages could be detected from the profiles and, overall, microRNA profiles of the samples were found to be very similar despite the heterogeneity in the study population.Measured microRNA profiles did not separate the samples according to the clinical features of the patients. However, several previously identified heart failure marker microRNAs were detected. The pericardial fluid microRNA profile appeared to be a result of an active and selective secretory process indicating that microRNAs may act as paracrine signalling

  17. Volatile organic compounds sources and sinks in a wheat canopy. Analysis based on combined eddy-covariance fluxes, in-canopy profiles and chamber measurements with a PTR-TOF-Qi-MS

    Science.gov (United States)

    Loubet, Benjamin; Gonzaga, Lais; Buysse, Pauline; Ciuraru, Raluca; Lafouge, Florence; Decuq, Céline; Zurfluh, Olivier; Fortineau, Alain; Fanucci, Olivier; Sarda-Esteve, Roland; Zannoni, Nora; Truong, Francois; Boissard, Christophe; Gros, Valérie

    2017-04-01

    Volatile organic compounds (VOC) are essential drivers of atmospheric chemistry. Many VOCs are emitted from and deposited to ecosystems. While forests and grasslands have already been substantially studied, exchanges of VOCs with crops are less known, although these ecosystems represent more than 50% of the surface in France. In this study, we analyze sources and sinks of VOCs in a wheat field (at the ICOS FR-GRI site near Paris) at anthesis based on measurements of fluxes, concentration profiles and branch chambers. The VOCs were measured using a PTR-TOF-Qi-MS (where Qi stands for Quad Ion guide). Air was successively sampled through lines located at different heights within and above the canopy, of which one was used for Eddy Covariance and located near a sonic anemometer. Additional measurements included the standard ICOS meteorological data as well as leaf area index profiles and photosynthesis curves at several heights in the canopy. We report fluxes and profiles for more than 500 VOCs. The deposition velocities of depositing compounds are compared to the maximum exchange velocity and the ozone deposition velocity. The sources and sinks location and magnitude are evaluated by inverse Lagrangian modelling assuming no reaction and simple reaction schemes in the canopy. The sources and sinks of VOC in the canopy are interpreted in terms crop phenology and the potential for reaction with ozone and NOx is evaluated. This study takes place in the ADEME CORTEA COV3ER French project (http://www6.inra.fr/cov3er).

  18. Personality profiles and problematic internet use in a sample of Italian adolescents

    OpenAIRE

    Fanny Guglielmucci; Antonella Granieri; Donato Munno; Giuseppina Zullo; Marta Saroldi

    2017-01-01

    Objective: The aim of the present study was to investigate the relationship between specific personality profiles and Internet use in a sample of Italian adolescents. Method: Four hundred thirty-two adolescents (58.3% males) with an average age of 14.41 years (SD=.95) were enrolled in the study. Participants were administered the Internet Addiction Test (IAT) and the Minnesota Multiphasic Inventory – Adolescent Form (MMPI-A). A two-step cluster analysis was relied according to IAT items’ ...

  19. The influence of snow grain size and impurities on the vertical profiles of actinic flux and associated NOx emissions on the Antarctic and Greenland ice sheets

    Directory of Open Access Journals (Sweden)

    M. C. Zatko

    2013-04-01

    Full Text Available We use observations of the absorption properties of black carbon and non-black carbon impurities in near-surface snow collected near the research stations at South Pole and Dome C, Antarctica, and Summit, Greenland, combined with a snowpack actinic flux parameterization to estimate the vertical profile and e-folding depth of ultraviolet/near-visible (UV/near-vis actinic flux in the snowpack at each location. We have developed a simple and broadly applicable parameterization to calculate depth and wavelength dependent snowpack actinic flux that can be easily integrated into large-scale (e.g., 3-D models of the atmosphere. The calculated e-folding depths of actinic flux at 305 nm, the peak wavelength of nitrate photolysis in the snowpack, are 8–12 cm near the stations and 15–31 cm away (>11 km from the stations. We find that the e-folding depth is strongly dependent on impurity content and wavelength in the UV/near-vis region, which explains the relatively shallow e-folding depths near stations where local activities lead to higher snow impurity levels. We calculate the lifetime of NOx in the snowpack interstitial air produced by photolysis of snowpack nitrate against wind pumping (τwind pumping from the snowpack, and compare this to the calculated lifetime of NOx against chemical conversion to HNO3 (τchemical to determine whether the NOx produced at a given depth can escape from the snowpack to the overlying atmosphere. Comparison of τwind pumping and τchemical suggests efficient escape of photoproduced NOx in the snowpack to the overlying atmosphere throughout most of the photochemically active zone. Calculated vertical actinic flux profiles and observed snowpack nitrate concentrations are used to estimate the potential flux of NOx from the snowpack. Calculated NOx fluxes of 4.4 × 108–3.8 × 109 molecules cm−2 s−1 in remote polar locations and 3.2–8.2 × 108 molecules cm−2 s−1 near polar stations for January at Dome C and

  20. Validation of refractivity profiles derived from GRAS raw-sampling data

    Directory of Open Access Journals (Sweden)

    F. Zus

    2011-07-01

    Full Text Available Results from GRAS (GNSS Receiver for Atmospheric Sounding RO (Radio Occultation data recorded in RS (Raw Sampling mode processed at the GFZ (German Research Centre for Geoscience Potsdam are presented. The experimental processing software POCS-X includes FSI (Full Spectrum Inversion in order to cope with multi-path regions and enables in connection with RS data to retrieve atmospheric refractivity profiles down to the Earths surface. Radio occultation events observed between 30 September and 30 October 2007 are processed and the retrievals are validated against co-located ECMWF (European Centre for Medium-Range Weather Forecasts profiles. The intercomparison indicates good quality of the retrieved profiles. In the altitude range 8 to 25 km the standard deviation is below 1 %. The mean deviation in this altitude range tends to be negative. At 30 km the negative bias reaches about −0.4 %. Below 8 km the standard deviation increases, reaching 2.5 % at 2 km. Below 2 km the mean deviation tends to be negative, reaching −1.9 % close to the ground. The negative bias mainly stems from the tropical lower troposphere; there, the negative bias reaches −3 %. The tropospheric penetration depth obtained from RS data shows a vast improvement compared to the tropospheric penetration depth typically obtained from CL (Closed Loop data; 50 % of all retrieved profiles reach 720 m.

  1. Language, reading, and math learning profiles in an epidemiological sample of school age children.

    Science.gov (United States)

    Archibald, Lisa M D; Oram Cardy, Janis; Joanisse, Marc F; Ansari, Daniel

    2013-01-01

    Dyscalculia, dyslexia, and specific language impairment (SLI) are relatively specific developmental learning disabilities in math, reading, and oral language, respectively, that occur in the context of average intellectual capacity and adequate environmental opportunities. Past research has been dominated by studies focused on single impairments despite the widespread recognition that overlapping and comorbid deficits are common. The present study took an epidemiological approach to study the learning profiles of a large school age sample in language, reading, and math. Both general learning profiles reflecting good or poor performance across measures and specific learning profiles involving either weak language, weak reading, weak math, or weak math and reading were observed. These latter four profiles characterized 70% of children with some evidence of a learning disability. Low scores in phonological short-term memory characterized clusters with a language-based weakness whereas low or variable phonological awareness was associated with the reading (but not language-based) weaknesses. The low math only group did not show these phonological deficits. These findings may suggest different etiologies for language-based deficits in language, reading, and math, reading-related impairments in reading and math, and isolated math disabilities.

  2. Language, Reading, and Math Learning Profiles in an Epidemiological Sample of School Age Children

    Science.gov (United States)

    Archibald, Lisa M. D.; Oram Cardy, Janis; Joanisse, Marc F.; Ansari, Daniel

    2013-01-01

    Dyscalculia, dyslexia, and specific language impairment (SLI) are relatively specific developmental learning disabilities in math, reading, and oral language, respectively, that occur in the context of average intellectual capacity and adequate environmental opportunities. Past research has been dominated by studies focused on single impairments despite the widespread recognition that overlapping and comorbid deficits are common. The present study took an epidemiological approach to study the learning profiles of a large school age sample in language, reading, and math. Both general learning profiles reflecting good or poor performance across measures and specific learning profiles involving either weak language, weak reading, weak math, or weak math and reading were observed. These latter four profiles characterized 70% of children with some evidence of a learning disability. Low scores in phonological short-term memory characterized clusters with a language-based weakness whereas low or variable phonological awareness was associated with the reading (but not language-based) weaknesses. The low math only group did not show these phonological deficits. These findings may suggest different etiologies for language-based deficits in language, reading, and math, reading-related impairments in reading and math, and isolated math disabilities. PMID:24155959

  3. Language, reading, and math learning profiles in an epidemiological sample of school age children.

    Directory of Open Access Journals (Sweden)

    Lisa M D Archibald

    Full Text Available Dyscalculia, dyslexia, and specific language impairment (SLI are relatively specific developmental learning disabilities in math, reading, and oral language, respectively, that occur in the context of average intellectual capacity and adequate environmental opportunities. Past research has been dominated by studies focused on single impairments despite the widespread recognition that overlapping and comorbid deficits are common. The present study took an epidemiological approach to study the learning profiles of a large school age sample in language, reading, and math. Both general learning profiles reflecting good or poor performance across measures and specific learning profiles involving either weak language, weak reading, weak math, or weak math and reading were observed. These latter four profiles characterized 70% of children with some evidence of a learning disability. Low scores in phonological short-term memory characterized clusters with a language-based weakness whereas low or variable phonological awareness was associated with the reading (but not language-based weaknesses. The low math only group did not show these phonological deficits. These findings may suggest different etiologies for language-based deficits in language, reading, and math, reading-related impairments in reading and math, and isolated math disabilities.

  4. Characterizing the optimal flux space of genome-scale metabolic reconstructions through modified latin-hypercube sampling

    NARCIS (Netherlands)

    Chaudhary, N.; Tøndel, K.; Bhatnagar, R.; Martins dos Santos, V.A.P.; Puchalka, J.

    2016-01-01

    Genome-Scale Metabolic Reconstructions (GSMRs), along with optimization-based methods, predominantly Flux Balance Analysis (FBA) and its derivatives, are widely applied for assessing and predicting the behavior of metabolic networks upon perturbation, thereby enabling identification of potential

  5. [Distribution and migration of heavy metals in soil profiles by high-resolution sampling].

    Science.gov (United States)

    Ruan, Xin-ling; Zhang, Gan-lin; Zhao, Yu-guo; Yuan, Da-gang; Wu, Yun-jin

    2006-05-01

    The vertical distribution of heavy metals in soils profiles is a result of heavy metals accumulation and migration under combining influence of edaphic factors and environmental conditions. It's an important basis for evaluation of heavy metals pollution and remediation of contaminated soils. By traditional sampling methods, i.e., soils were sampled according to pedogenetic horizons, only very general information about element migration can be learned. In the current study, three sites near a steel factory were selected to represent three types of land use, i.e. forest, dry land for vegetable cultivation and rice paddy field. Soils were sampled horizontally by high-resolution sampling method. In the top of 40 cm soils were sectioned in 2 cm intervals, then 5 cm intervals in next 40 cm, and 10 cm intervals in the last 20 cm of profile. Total content of Cu, Zn, Pb, Cr and Cd were determined, and the vertical distribution of Cu, Zn, Pb, Cr, Cd in every profile was analyzed. The results indicated that enrichment of heavy metals appeared in the upper most layer of the natural forest soil that without any anthropic disturbance, and this phenomenon proved that heavy metals were coming from atmospheric deposition. We found that Cu, Zn and Pb moved downward in a short distance, Cd migrated relatively faster than Cu, Zn and Pb, while Cr had no recognizable location of migration front. In the soil profiles of dry land and paddy field, there were influences of agricultural practice, the distribution and movement of metals were thus different form those of the forest soil. In cultivated layer heavy metals were evenly distributed because soils in the upper layer were mixed by cultivation, however, bellow the cultivated layer obvious migration took place again. It is concluded that different heavy metals have different mobility and there is such a relative order: Cd>Cu>Zn>Pb. The study shows that the distribution pattern can be obtained with the currently adopted high

  6. Whole-genome gene expression profiling of formalin-fixed, paraffin-embedded tissue samples.

    Directory of Open Access Journals (Sweden)

    Craig April

    2009-12-01

    Full Text Available We have developed a gene expression assay (Whole-Genome DASL, capable of generating whole-genome gene expression profiles from degraded samples such as formalin-fixed, paraffin-embedded (FFPE specimens.We demonstrated a similar level of sensitivity in gene detection between matched fresh-frozen (FF and FFPE samples, with the number and overlap of probes detected in the FFPE samples being approximately 88% and 95% of that in the corresponding FF samples, respectively; 74% of the differentially expressed probes overlapped between the FF and FFPE pairs. The WG-DASL assay is also able to detect 1.3-1.5 and 1.5-2 -fold changes in intact and FFPE samples, respectively. The dynamic range for the assay is approximately 3 logs. Comparing the WG-DASL assay with an in vitro transcription-based labeling method yielded fold-change correlations of R(2 approximately 0.83, while fold-change comparisons with quantitative RT-PCR assays yielded R(2 approximately 0.86 and R(2 approximately 0.55 for intact and FFPE samples, respectively. Additionally, the WG-DASL assay yielded high self-correlations (R(2>0.98 with low intact RNA inputs ranging from 1 ng to 100 ng; reproducible expression profiles were also obtained with 250 pg total RNA (R(2 approximately 0.92, with approximately 71% of the probes detected in 100 ng total RNA also detected at the 250 pg level. When FFPE samples were assayed, 1 ng total RNA yielded self-correlations of R(2 approximately 0.80, while still maintaining a correlation of R(2 approximately 0.75 with standard FFPE inputs (200 ng.Taken together, these results show that WG-DASL assay provides a reliable platform for genome-wide expression profiling in archived materials. It also possesses utility within clinical settings where only limited quantities of samples may be available (e.g. microdissected material or when minimally invasive procedures are performed (e.g. biopsied specimens.

  7. High Resolution Hydraulic Profiling and Groundwater Sampling using FLUTe™ System in a Fractured Limestone Setting

    DEFF Research Database (Denmark)

    Janniche, Gry Sander; Christensen, Anders G.; Grosen, Bernt

    innovative investi-gation methods for characterization of the source zone hydrogeology and contamination, including FLUTe system hydraulic profiling and Water-FLUTe multilevel groundwater sampling, in fractured bryo-zoan limestone bedrock. High resolution hydraulic profiling was conducted in three cored......Characterization of the contaminant source zone architecture and the hydraulics is essential to develop accurate site specific conceptual models, delineate and quantify contaminant mass, perform risk as-sessment, and select and design remediation alternatives. This characterization is particularly...... challeng-ing in deposit types as fractured limestone. The activities of a bulk distribution facility for perchloroe-thene (PCE) and trichloroethene (TCE) at the Naverland site near Copenhagen, Denmark, has resulted in PCE and TCE DNAPL impacts to a fractured clay till and an underlying fractured limestone...

  8. Sampling Modification Effects in the Subgingival Microbiome Profile of Healthy Children.

    Science.gov (United States)

    Santigli, Elisabeth; Trajanoski, Slave; Eberhard, Katharina; Klug, Barbara

    2016-01-01

    sampling modes ( p = 0.914 by R 2 = 0.09). Conclusion: A slight modification of sampling mode has minor effects corresponding to a natural variability in the microbiome profiles of healthy children. The inter-individual variability in subgingival microprints is greater than intra-individual differences. Statistical analyses of microbial populations should consider this baseline variability and move beyond mere quantification with input from visual analytics. Comparative results are difficult to summarize as methods for studying huge datasets are still evolving. Advanced approaches are needed for sample size calculations in clinical settings.

  9. Sampling Modification Effects in the Subgingival Microbiome Profile of Healthy Children

    Science.gov (United States)

    Santigli, Elisabeth; Trajanoski, Slave; Eberhard, Katharina; Klug, Barbara

    2017-01-01

    grouping by sampling modes (p = 0.914 by R2 = 0.09). Conclusion: A slight modification of sampling mode has minor effects corresponding to a natural variability in the microbiome profiles of healthy children. The inter-individual variability in subgingival microprints is greater than intra-individual differences. Statistical analyses of microbial populations should consider this baseline variability and move beyond mere quantification with input from visual analytics. Comparative results are difficult to summarize as methods for studying huge datasets are still evolving. Advanced approaches are needed for sample size calculations in clinical settings. PMID:28149291

  10. Effect of cerium addition on casting/chill interfacial heat flux and casting surface profile during solidification of Al-14%Si alloy

    Science.gov (United States)

    Vijeesh, V.; Prabhu, K. N.

    2016-03-01

    In the present investigation, Al-14 wt. % Si alloy was solidified against copper, brass and cast iron chills, to study the effect of Ce melt treatment on casting/chill interfacial heat flux transients and casting surface profile. The heat flux across the casting/chill interface was estimated using inverse modelling technique. On addition of 1.5% Ce, the peak heat flux increased by about 38%, 42% and 43% for copper, brass and cast iron chills respectively. The effect of Ce addition on casting surface texture was analyzed using a surface profilometer. The surface profile of the casting and the chill surfaces clearly indicated the formation of an air gap at the periphery of the casting. The arithmetic average value of the profile departure from the mean line (Ra) and arithmetical mean of the absolute departures of the waviness profile from the centre line (Wa) were found to decrease on Ce addition. The interfacial gap width formed for the unmodified and Ce treated casting surfaces at the periphery were found to be about 35µm and 13µm respectively. The enhancement in heat transfer on addition of Ce addition was attributed to the lowering of the surface tension of the liquid melt. The gap width at the interface was used to determine the variation of heat transfer coefficient (HTC) across the chill surface after the formation of stable solid shell. It was found that the HTC decreased along the radial direction for copper and brass chills and increased along radial direction for cast iron chills.

  11. Latent profile analysis and comorbidity in a sample of individuals with compulsive buying disorder.

    Science.gov (United States)

    Mueller, Astrid; Mitchell, James E; Black, Donald W; Crosby, Ross D; Berg, Kelly; de Zwaan, Martina

    2010-07-30

    The aims of this study were to perform a latent profile analysis in a sample of individuals with compulsive buying, to explore the psychiatric comorbidity, and to examine whether or not more severe compulsive buying is associated with greater comorbidity. Compulsive buying measures and SCID data obtained from 171 patients with compulsive buying behavior who had participated in treatment trials at different clinical centers in the U.S. and Germany were analyzed. Latent profile analysis produced two clusters. Overall, cluster 2, included subjects with more severe compulsive buying, and was characterized by higher lifetime as well as current prevalence rates for Axis I and impulse control disorders. Nearly 90% of the total sample reported at least one lifetime Axis I diagnosis, particularly mood (74%) and anxiety (57%) disorders. Twenty-one percent had a comorbid impulse control disorder, most commonly intermittent explosive disorder (11%). Half of the sample presented with at least one current Axis I disorder, most commonly anxiety disorders (44%). Given the substantial psychiatric comorbidity, it is reasonable to question whether or not compulsive buying represents a distinct psychiatric entity vs. an epiphenomenon of other psychiatric disorders. Copyright 2010 Elsevier Ltd. All rights reserved.

  12. Turbulent heat fluxes by profile and inertial dissipation methods: analysis of the atmospheric surface layer from shipboard measurements during the SOFIA/ASTEX and SEMAPHORE experiments

    Directory of Open Access Journals (Sweden)

    H. Dupuis

    Full Text Available Heat flux estimates obtained using the inertial dissipation method, and the profile method applied to radiosonde soundings, are assessed with emphasis on the parameterization of the roughness lengths for temperature and specific humidity. Results from the inertial dissipation method show a decrease of the temperature and humidity roughness lengths for increasing neutral wind speed, in agreement with previous studies. The sensible heat flux estimates were obtained using the temperature estimated from the speed of sound determined by a sonic anemometer. This method seems very attractive for estimating heat fluxes over the ocean. However allowance must be made in the inertial dissipation method for non-neutral stratification. The SOFIA/ASTEX and SEMAPHORE results show that, in unstable stratification, a term due to the transport terms in the turbulent kinetic energy budget, has to be included in order to determine the friction velocity with better accuracy. Using the profile method with radiosonde data, the roughness length values showed large scatter. A reliable estimate of the temperature roughness length could not be obtained. The humidity roughness length values were compatible with those found using the inertial dissipation method.

  13. Average profiles of the solar wind and outer radiation belt during the extreme flux enhancement of relativistic electrons at geosynchronous orbit

    Directory of Open Access Journals (Sweden)

    R. Kataoka

    2008-06-01

    Full Text Available We report average profiles of the solar wind and outer radiation belt during the extreme flux enhancement of relativistic electrons at geosynchronous orbit (GEO. It is found that seven of top ten extreme events at GEO during solar cycle 23 are associated with the magnetosphere inflation during the storm recovery phase as caused by the large-scale solar wind structure of very low dynamic pressure (<1.0 nPa during rapid speed decrease from very high (>650 km/s to typical (400–500 km/s in a few days. For the seven events, the solar wind parameters, geomagnetic activity indices, and relativistic electron flux and geomagnetic field at GEO are superposed at the local noon period of GOES satellites to investigate the physical cause. The average profiles support the "double inflation" mechanism that the rarefaction of the solar wind and subsequent magnetosphere inflation are one of the best conditions to produce the extreme flux enhancement at GEO because of the excellent magnetic confinement of relativistic electrons by reducing the drift loss of trapped electrons at dayside magnetopause.

  14. Impurity profiling/comparative analyses of samples of 1-phenyl-2-propanone.

    Science.gov (United States)

    Krawczyk, W; Kunda, T; Perkowska, I; Dudek, D

    2005-01-01

    1-Phenyl-2-propanone (P-2-P), also known as benzyl methyl ketone (BMK), is the main precursor used in amphetamine synthesis. In recent years, the number of seizures of P-2-P from both licit and illicit drug manufacture has increased. The present article comprises a discussion of some of the largest seizures of P-2-P diverted from regular production to the illicit market. It also presents the methods used in clandestine laboratories to synthesize P-2-P and a forensic approach to identify and differentiate between these methods. To that end, and to facilitate the monitoring of the P-2-P market, a method of P-2-P impurity profiling was designed for comparative purposes and for the identification of the synthesis route. P-2-P samples were analysed by means of gas chromatography/mass spectrometry (GC/MS). Out of 36 identified impurities, 14 were selected as markers for sample comparison. On the basis of the GC peak areas of those 14 markers, a cluster analysis was carried out, resulting in three clusters, each corresponding to a given P-2-P synthesis route. The results of P-2-P impurity profiling are stored in both a forensic database and a police database. The forensic database comprises chemical data, such as those on P-2-P purity, additives and specific impurities, as well as information on seized P-2-P samples having a similar impurity profile. Data stored in the police database, which is linked with the forensic database by case identification number, cover the circumstances of seizures and personal details of offenders. The databases enable the full use of forensic data in intelligence work and police investigative activities.

  15. Effects of tetracycline administration on the proteomic profile of pig muscle samples (L. dorsi)

    DEFF Research Database (Denmark)

    Gratacos-Cubarsi, M.; Castellari, M.; Hortos, M.

    2008-01-01

    Effect of tetracycline (TC) administration on the proteomic profile of pig muscle was evaluated by 2D electrophoresis and MALDI-TOF mass spectrometry. The TC content at slaughter was determined in L. dorsi samples by HPLC-DAD. Mean residual concentration of TC in the muscle of treated animals......, calculated as the sum of TC and epi-TC was 126.3 mu g/kg, indicating a rapid elimination of TC in this tissue. Several differential spots (n = 54, p match for 5 differential spots, that is...

  16. Assessing the British Isles CH4 flux using aircraft and ground-based sampling: a case study on 12 May 2015

    Science.gov (United States)

    Pitt, Joseph

    2017-04-01

    Aircraft and ground-based sampling of atmospheric greenhouse gas composition over the British Isles was conducted between 2014 and 2016 as part of the Greenhouse gAs UK and Global Emissions (GAUGE) project. We report a case study focussing on two research aircraft flights conducted on 12 May 2015 to sample inflow and outflow across the British Isles. We have employed the NAME Lagrangian dispersion model to simulate CH4 mole fraction enhancements corresponding to aircraft and ground-based sample times and locations, using CH4 surface fluxes derived from a composite flux inventory, which included both anthropogenic and natural sources. For each sampling location, variations in the baseline CH4 mole fraction were derived using the MOZART global chemical transport model, and added to the NAME enhancements to produce a dataset of modelled CH4 mole fractions which can be compared to the measurements. Using a multiple variable regression technique, we derive CH4 fluxes for the British Isles region from both aircraft and ground-based datasets. We discuss the applicability of our approach for both datasets, and conclude that in this case the assumptions inherent in our method are much better satisfied for the aircraft data than for the ground-based data. Using the aircraft data we derive a possible range of scale factors for the prior inventory flux of 0.53 - 0.97, with a central estimate of 0.82 based on our assessment of the most likely apportionment of model uncertainty. This leads to a posterior estimate of the British Isles CH4 flux of 67 kg s-1 - 121 kg s-1, with a central value of 103 kg s-1.

  17. Ex-Stream: A MATLAB program for calculating fluid flux through sediment-water interfaces based on steady and transient temperature profiles

    Science.gov (United States)

    Swanson, Travis E.; Cardenas, M. Bayani

    2011-10-01

    Temperature is a useful environmental tracer for quantifying movement and exchange of water and heat through and near sediment-water interfaces (SWI). Heat tracing involves analyzing temperature time series or profiles from temperature probes deployed in sediments. Ex-Stream is a MATLAB program that brings together two transient and two steady one-dimensional coupled heat and fluid flux analytical models. The program includes a graphical user interface, a detailed user manual, and postprocessing capabilities that enable users to extract fluid fluxes from time-series temperature observations. Program output is written to comma-separated values files, displayed within the MATLAB command window, and may be optionally plotted. The models that are integrated into Ex-Stream can be run collectively, allowing for direct comparison, or individually.

  18. Observations from a 4-Year Contamination Study of a Sample Depth Profile Through Martian Meteorite Nakhla

    Science.gov (United States)

    Toporski,Jan; Steele, Andrew

    2007-05-01

    Morphological, compositional, and biological evidence indicates the presence of numerous well-developed microbial hyphae structures distributed within four different sample splits of the Nakhla meteorite obtained from the British Museum (allocation BM1913,25). By examining depth profiles of the sample splits over time, morphological changes displayed by the structures were documented, as well as changes in their distribution on the samples, observations that indicate growth, decay, and reproduction of individual microorganisms. Biological staining with DNA-specific molecular dyes followed by epifluorescence microscopy showed that the hyphae structures contain DNA. Our observations demonstrate the potential of microbial interaction with extraterrestrial materials, emphasize the need for rapid investigation of Mars return samples as well as any other returned or impactor-delivered extraterrestrial materials, and suggest the identification of appropriate storage conditions that should be followed immediately after samples retrieved from the field are received by a handling/curation facility. The observations are further relevant in planetary protection considerations as they demonstrate that microorganisms may endure and reproduce in extraterrestrial materials over long (at least 4 years) time spans. The combination of microscopy images coupled with compositional and molecular staining techniques is proposed as a valid method for detection of life forms in martian materials as a first-order assessment. Time-resolved in situ observations further allow observation of possible (bio)dynamics within the system.

  19. Temperament and Character Profiles of Sasang Typology in an Adult Clinical Sample

    Directory of Open Access Journals (Sweden)

    Soo Hyun Park

    2011-01-01

    Full Text Available The purpose of this study was to examine the biopsychological personality profiles of traditional Korean Sasang typology based on the Temperament and Character Inventory (TCI in a Korean adult clinical sample. A total of 97 adults completed the Korean version of the TCI. The participants were classified as one of three traditional Korean Sasang types (31 So-Yang, 41 Tae-Eum, 25 So-Eum by three specialists in Sasang typology. The seven dimensions of TCI were compared between the different Sasang types using analysis of variance (ANOVA and profile analysis. There were no significant differences in age, gender and education across the Sasang types. The TCI profile for each of the Sasang types was significantly different (profile analysis, df = 5.038, F = 3.546, P = .004. There were significant differences in the temperament dimensions of Novelty Seeking (F = 3.43, P = .036 and Harm Avoidance (F = 5.43, P = .006 among the Sasang types. The Novelty Seeking score of the So-Yang type (31.90 ± 9.87 was higher than that of the So-Eum type (25.24 ± 9.21; P = .019 while the So-Eum type (44.64 ± 8.47 scored higher on the Harm Avoidance score compared to the So-Yang type (35.16 ± 11.50; P = .003. There were no significant differences in the temperament dimension of Reward Dependence and Persistence, and the three character dimensions of Self-Directedness, Cooperativeness and Self-Transcendence. Results demonstrated distinct temperament traits associated with traditional Korean Sasang types using an objective biopsychological personality inventory. With further study, the Sasang typology may lead to enhanced clinical safety and efficacy as part of personalized medicine with traditional medicine.

  20. Investigation of Pectenotoxin Profiles in the Yellow Sea (China Using a Passive Sampling Technique

    Directory of Open Access Journals (Sweden)

    Zhaoxin Li

    2010-04-01

    Full Text Available Pectenotoxins (PTXs are a group of lipophilic algal toxins. These toxins have been found in algae and shellfish from Japan, New Zealand, Ireland, Norway and Portugal. PTX profiles vary with geographic location of collection site. The aim of the present study was to investigate PTX profiles from the Yellow Sea, China. The sampling location was within an aquatic farm (N36°12.428´, E120°17.826´ near the coast of Qingdao, China, in the Yellow Sea from 28July to 29August 2006. PTXs in seawater were determined using a solid phase adsorption toxin tracking (SPATT method. PTXs were analyzed by HPLC-MSMS. PTX-2, PTX-2 sec acid (PTX-2 SA and 7-epi-PTX-2 SA were found in seawater samples. The highest levels of PTXs (107 ng/g of resin PTX-2, 50 ng/g of resin PTX-2 SA plus 7-epi-PTX-2 SA in seawater were found on 1 August, 2006. From 1 August to 29 August, the levels of PTX-2 and PTX-2 SA decreased. In the same area, the marine algae, Dinophysis acuminata was found in the seawater in the summer months of 2006. This indicated that Dinophysis acuumuta might be the original source of PTXs. PTX-11 and PTX-12a/b were not found in seawater.

  1. Efficient recovery of electrophoretic profiles of nucleoside metabolites from urine samples by multivariate curve resolution.

    Science.gov (United States)

    Szymańska, Ewa; Markuszewski, Michał J; Vander Heyden, Yvan; Kaliszan, Roman

    2009-10-01

    Chemometric techniques usually employed in purity assessment and resolution of multicomponent peaks have been applied to analytical data from complex biological samples obtained with CE-DAD. In the assessment of the purity of the electrophoretic peaks, the orthogonal projection approach, the orthogonal projection approach with Durbin-Watson criterion, and the simple-to-use interactive self-modeling mixture analysis method have been employed. Multivariate curve resolution with alternating least squares has been successfully implemented to resolve co-migrating peaks of metabolites in CE-DAD and to recover qualitative and quantitative information about co-migrating components of urine extract. The main challenge consisted of developing high-quality multivariate curve resolution with alternating least squares models of multicomponent peaks acquired during the CE analysis of nucleoside patterns in 18 urine samples. The recovered ultraviolet visible (UV-Vis) spectra have been employed to identify additional nucleosides, such as 1-methylinosine, 2-methylguanosine, and 1-methylguanosine, whose presence in the metabolic profile produced by the applied CE-DAD method has not yet been recognized. Concentration profiles of these compounds can be used in metabonomic studies.

  2. Comorbidity profiles and inpatient outcomes during hospitalization for heart failure: an analysis of the U.S. Nationwide inpatient sample

    OpenAIRE

    Lee, Christopher S.; Chien, Christopher V.; Bidwell, Julie T.; Gelow, Jill M.; Denfeld, Quin E.; Creber, Ruth Masterson; Buck, Harleah G.; Mudd, James O.

    2014-01-01

    Background Treatment of heart failure (HF) is particularly complex in the presence of comorbidities. We sought to identify and associate comorbidity profiles with inpatient outcomes during HF hospitalizations. Methods Latent mixture modeling was used to identify common profiles of comorbidities during adult hospitalizations for HF from the 2009 Nationwide Inpatient Sample (n = 192,327). Results Most discharges were characterized by "common" comorbidities. A "lifestyle" profile was characteriz...

  3. Establishment of a clinical pathway for home enteral nutrition prescription in Murcia. Profile and sample characteristics

    Science.gov (United States)

    Ferrer Gómez, Mercedes; Sánchez Romera, Juan Francisco; García Zafra, María Victoria; Cuenca Sánchez, José Ramón; Hernández Cascales, Ana Belén; Aranda García, Ana; Rausell Rausell, Víctor José; Hernández Martínez, Antonio Miguel

    2017-06-05

    Introduction: Before 2010, prescribed home enteral nutrition (HEN) in Murcia was characterized by the great variability of the receptor patients, in addition to a higher use compared with other geographical areas. Objectives: Developing and describing a clinical pathway for attending candidates for HEN, and analyzing their profi le and prescription characteristics. Methods: Establishment of a clinical pathway for HEN prescription. Bidirectional observational study of the samples of HEN in a specific area (Health Area I of the Region of Murcia) during 2010 (HEN1) and 2013-14 (HEN2). Results: An official management statement was established, generalizing the clinical pathway for the rest of the regional areas (Instruction no. 4/2012 of July 12 th). Although most prevalent diseases in both samples were neurological, followed, with a wide spread, by oncological and digestive cases, there was a signifi cant difference regarding distribution. The HEN1 sample showed a great number of no candidate patients according to the management statement. In both samples, the most prevalent route of administration was oral, but with a trend reversal to feeding tube and gastrostomy in HEN2, where the specifi c formulas were also reduced. Conclusions: The profile of HEN, before and after the deployment of the clinical pathway, changes signifi cantly concerning the main disease, the route of administration and the formula. It has been proved that there is a need for controlling HEN for an appropriate prescription.

  4. Depth profiling of the modification induced by high-flux deuterium plasma in tungsten and tungsten–tantalum alloys

    NARCIS (Netherlands)

    Zayachuk, Y.; Manhard, A.; Hoen, M. H. J. 't; Jacob, W.; van Emmichoven, P. A. Zeijlma; Van Oost, G.

    2014-01-01

    The present work reports the results of an experimental study of the depth distribution and fluence dependence of deuterium plasma-induced material modification of tungsten and tungsten–tantalum alloys. Plasma-induced damage was created by exposure to high-flux deuterium plasma in the plasma

  5. Comparison of tear lipid profile among basal, reflex, and flush tear samples.

    Science.gov (United States)

    Rohit, Athira; Stapleton, Fiona; Brown, Simon H J; Mitchell, Todd W; Willcox, Mark D P

    2014-12-01

    To determine whether tear collection by flushing the ocular surface with saline (flush tears) or collection by stimulation (reflex tears) can be used as an alternative to basal tear collection for the identification and quantification of lipids in the tear film. Tear samples were collected from 10 participants with no history of ocular surface disease or contact lens wear. Up to 10 μl of basal, reflex, and flush tear samples were collected from each eye using a microcapillary tube on three occasions with the order of methods randomized and allowing at least 24 hours between each collection method. Lipids were quantified from each tear sample using nano-electrospray ionization tandem mass spectrometry. Total lipids significantly differed in their concentration (pmol/μl) and mole % with each collection technique. Cholesterol esters [mean % (SE)] formed the major component of the total lipidome in basal [54.8% (3.1)], reflex [35.7% (6.4)], and flush [33.0% (3.1)] tear samples. However, the mole % of each lipid class substantially varied with each tear collection method. Nonpolar lipids, including cholesterol, wax esters, and triacylglycerols, dominated the tear lipidome in basal [92.8% (1.9)], reflex [71.8% (7.9)], and flush [83.6% (3.8)] tear samples. However, the mole % of phospholipids in reflex [27.5% (8.1)] and flush [15.8% (3.8)] tear samples was higher (p = 0.005) than that in basal tears [5.4% (2.0)]. Flush or reflex tears did not have similar lipid profiles in either concentration or in mole % to basal tears. It is recommended that basal tears are used for tear lipid analysis as the reflex or flush tears contain very low levels of most lipid components.

  6. miRNA expression profiling enables risk stratification in archived and fresh neuroblastoma tumor samples.

    Science.gov (United States)

    De Preter, Katleen; Mestdagh, Pieter; Vermeulen, Joëlle; Zeka, Fjoralba; Naranjo, Arlene; Bray, Isabella; Castel, Victoria; Chen, Caifu; Drozynska, Elzbieta; Eggert, Angelika; Hogarty, Michael D; Izycka-Swieszewska, Ewa; London, Wendy B; Noguera, Rosa; Piqueras, Marta; Bryan, Kenneth; Schowe, Benjamin; van Sluis, Peter; Molenaar, Jan J; Schramm, Alexander; Schulte, Johannes H; Stallings, Raymond L; Versteeg, Rogier; Laureys, Geneviève; Van Roy, Nadine; Speleman, Frank; Vandesompele, Jo

    2011-12-15

    More accurate assessment of prognosis is important to further improve the choice of risk-related therapy in neuroblastoma (NB) patients. In this study, we aimed to establish and validate a prognostic miRNA signature for children with NB and tested it in both fresh frozen and archived formalin-fixed paraffin-embedded (FFPE) samples. Four hundred-thirty human mature miRNAs were profiled in two patient subgroups with maximally divergent clinical courses. Univariate logistic regression analysis was used to select miRNAs correlating with NB patient survival. A 25-miRNA gene signature was built using 51 training samples, tested on 179 test samples, and validated on an independent set of 304 fresh frozen tumor samples and 75 archived FFPE samples. The 25-miRNA signature significantly discriminates the test patients with respect to progression-free and overall survival (P < 0.0001), both in the overall population and in the cohort of high-risk patients. Multivariate analysis indicates that the miRNA signature is an independent predictor of patient survival after controlling for current risk factors. The results were confirmed in an external validation set. In contrast to a previously published mRNA classifier, the 25-miRNA signature was found to be predictive for patient survival in a set of 75 FFPE neuroblastoma samples. In this study, we present the largest NB miRNA expression study so far, including more than 500 NB patients. We established and validated a robust miRNA classifier, able to identify a cohort of high-risk NB patients at greater risk for adverse outcome using both fresh frozen and archived material. ©2011 AACR.

  7. Microbial profiling of cpn60 universal target sequences in artificial mixtures of vaginal bacteria sampled by nylon swabs or self-sampling devices under different storage conditions.

    Science.gov (United States)

    Schellenberg, John J; Oh, Angela Yena; Hill, Janet E

    2017-05-01

    The vaginal microbiome is increasingly characterized by deep sequencing of universal genes. However, there are relatively few studies of how different specimen collection and sample storage and processing influence these molecular profiles. Here, we evaluate molecular microbial community profiles of samples collected using the HerSwab™ self-sampling device, compared to nylon swabs and under different storage conditions. In order to minimize technical variation, mixtures of 11 common vaginal bacteria in simulated vaginal fluid medium were sampled and DNA extracts prepared for massively parallel sequencing of the cpn60 universal target (UT). Three artificial mixtures imitating commonly observed vaginal microbiome profiles were easily distinguished and proportion of sequence reads correlated with the estimated proportion of the organism added to the artificial mixtures. Our results indicate that cpn60 UT amplicon sequencing quantifies the proportional abundance of member organisms in these artificial communities regardless of swab type or storage conditions, although some significant differences were observed between samples that were stored frozen and thawed prior to DNA extraction, compared to extractions from samples stored at room temperature for up to 7days. Our results indicate that an on-the-market device developed for infectious disease diagnostics may be appropriate for vaginal microbiome profiling, an approach that is increasingly facilitated by rapidly dropping deep sequencing costs. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. A high-resolution measurement technique for vertical CO2 and H2O profiles within and above crop canopies and its use for flux partitioning

    Science.gov (United States)

    Ney, Patrizia; Schmidt, Marius; Klosterhalfen, Anne; Graf, Alexander

    2017-04-01

    We present a portable elevator-based setup for measuring CO2, water vapor, temperature and wind profiles from the soil surface to the surface layer above crop canopies. The end of a tube connected to a closed-path gas analyzer is continuously moved up and down over the profile height (currently 2 m), while concentrations are logged at a frequency of 20 Hz. Temperature and wind speed are measured at the same frequency by a ventilated finewire thermocouple and a hotwire, respectively, and all measurements are duplicated as a continuous fixed-height measurement at the top of the profile. Test measurements were carried out at the TERENO research site of Selhausen (50°52'09"N, 06°27'01"E, 104.5 m MSL, Germany, ICOS site DE-RuS) in winter wheat, winter barley and a catch crop mixture during different stages of crop development and different times of the day (spring 2015 to autumn 2016). We demonstrate a simple approach to correct for time lags, and the resulting half-hourly mean profiles of CO2 and H2O over height increments of 2.5 cm. These results clearly show the effects of soil respiration and photosynthetic carbon assimilation, varying both during the daily cycle and during the growing season. Post-harvest measurements over bare soil and short intercrop canopy (theory to check the validity of the measurement and raw data processing approach. Derived CO2 and latent heat fluxes show a good agreement to eddy-covariance measurements. In a next step, we applied a dispersion matrix inversion (modified after Warland and Thurtell 2000, Santos et al. 2011) to the concentration profiles to estimate the vertical source and sink distribution of CO2 and H2O. First results showed reasonable values for evaporation, transpiration and aboveground net primary production, but a likely overestimation of soil respiration. We discuss possible causes associated with exchange processes near the soil surface below a dense canopy, and the potential use of the wind and temperature profiles

  9. Risk Profile in a Sample of Patients with Breast Cancer from the Public Health Perspective

    Directory of Open Access Journals (Sweden)

    Sorina IRIMIE

    2010-12-01

    Full Text Available Cancer represents a major public health and economical burden in developed countries and has emerged as a major public health problem in developing countries, matching its effect in industrialized nations. Although there have been recent declines in breast cancer mortality rates in some European Union countries, breast cancer remains of key importance to public health in Europe. Now days there is increasing recognition of the causative role of lifestyle factors, as smoking, diet, alcohol consumption, or lake of physical activity. The present study aimed to appreciate the presence and magnitude of modifiable risk factors for breast cancer in a sample of patients diagnosed with the disease, and to outline a risk profile liable to be changed in the intention of reducing the global risk. Risk factors have been investigated in 65 patients diagnosed with breast cancer using a questionnaire for breast cancer risk factors evaluation. The high risk profile was identified as taking shape for urban environment, modulated by the impact of overweight-obesity, smoking, reproductive factors and environmental exposure to different chemical substances. From the public health perspective, the control of overweight and obesity comes out in the foreground of preventive activities. Public health approaches emphasize on inexpensive, practical methods and in this perspective the approach of obesity should focus on the alteration of environmental context, promoting healthy eating and increased physical activity which could have a positive, independent impact on breast cancer risk

  10. Gene expression profiling of human whole blood samples with the Illumina WG-DASL assay

    Directory of Open Access Journals (Sweden)

    Klotzle Brandy

    2011-08-01

    Full Text Available Abstract Background Microarray-based gene expression analysis of peripheral whole blood is a common strategy in the development of clinically relevant biomarker panels for a variety of human diseases. However, the results of such an analysis are often plagued by decreased sensitivity and reliability due to the effects of relatively high levels of globin mRNA in whole blood. Globin reduction assays have been shown to overcome such effects, but they require large amounts of total RNA and may induce distinct gene expression profiles. The Illumina whole genome DASL assay can detect gene expression levels using partially degraded RNA samples and has the potential to detect rare transcripts present in highly heterogeneous whole blood samples without the need for globin reduction. We assessed the utility of the whole genome DASL assay in an analysis of peripheral whole blood gene expression profiles. Results We find that gene expression detection is significantly increased with the use of whole genome DASL compared to the standard IVT-based direct hybridization. Additionally, globin-probe negative whole genome DASL did not exhibit significant improvements over globin-probe positive whole genome DASL. Globin reduction further increases the detection sensitivity and reliability of both whole genome DASL and IVT-based direct hybridization with little effect on raw intensity correlations. Raw intensity correlations between total RNA and globin reduced RNA were 0.955 for IVT-based direct hybridization and 0.979 for whole genome DASL. Conclusions Overall, the detection sensitivity of the whole genome DASL assay is higher than the IVT-based direct hybridization assay, with or without globin reduction, and should be considered in conjunction with globin reduction methods for future blood-based gene expression studies.

  11. A simplified method for power-law modelling of metabolic pathways from time-course data and steady-state flux profiles

    Directory of Open Access Journals (Sweden)

    Sugimoto Masahiro

    2006-07-01

    Full Text Available Abstract Background In order to improve understanding of metabolic systems there have been attempts to construct S-system models from time courses. Conventionally, non-linear curve-fitting algorithms have been used for modelling, because of the non-linear properties of parameter estimation from time series. However, the huge iterative calculations required have hindered the development of large-scale metabolic pathway models. To solve this problem we propose a novel method involving power-law modelling of metabolic pathways from the Jacobian of the targeted system and the steady-state flux profiles by linearization of S-systems. Results The results of two case studies modelling a straight and a branched pathway, respectively, showed that our method reduced the number of unknown parameters needing to be estimated. The time-courses simulated by conventional kinetic models and those described by our method behaved similarly under a wide range of perturbations of metabolite concentrations. Conclusion The proposed method reduces calculation complexity and facilitates the construction of large-scale S-system models of metabolic pathways, realizing a practical application of reverse engineering of dynamic simulation models from the Jacobian of the targeted system and steady-state flux profiles.

  12. Metabolic profiling and flux analysis of MEL-2 human embryonic stem cells during exponential growth at physiological and atmospheric oxygen concentrations.

    Directory of Open Access Journals (Sweden)

    Jennifer Turner

    Full Text Available As human embryonic stem cells (hESCs steadily progress towards regenerative medicine applications there is an increasing emphasis on the development of bioreactor platforms that enable expansion of these cells to clinically relevant numbers. Surprisingly little is known about the metabolic requirements of hESCs, precluding the rational design and optimisation of such platforms. In this study, we undertook an in-depth characterisation of MEL-2 hESC metabolic behaviour during the exponential growth phase, combining metabolic profiling and flux analysis tools at physiological (hypoxic and atmospheric (normoxic oxygen concentrations. To overcome variability in growth profiles and the problem of closing mass balances in a complex environment, we developed protocols to accurately measure uptake and production rates of metabolites, cell density, growth rate and biomass composition, and designed a metabolic flux analysis model for estimating internal rates. hESCs are commonly considered to be highly glycolytic with inactive or immature mitochondria, however, whilst the results of this study confirmed that glycolysis is indeed highly active, we show that at least in MEL-2 hESC, it is supported by the use of oxidative phosphorylation within the mitochondria utilising carbon sources, such as glutamine to maximise ATP production. Under both conditions, glycolysis was disconnected from the mitochondria with all of the glucose being converted to lactate. No difference in the growth rates of cells cultured under physiological or atmospheric oxygen concentrations was observed nor did this cause differences in fluxes through the majority of the internal metabolic pathways associated with biogenesis. These results suggest that hESCs display the conventional Warburg effect, with high aerobic activity despite high lactate production, challenging the idea of an anaerobic metabolism with low mitochondrial activity. The results of this study provide new insight that

  13. An uncooked vegan diet shifts the profile of human fecal microflora: computerized analysis of direct stool sample gas-liquid chromatography profiles of bacterial cellular fatty acids.

    Science.gov (United States)

    Peltonen, R; Ling, W H; Hänninen, O; Eerola, E

    1992-01-01

    The effect of an uncooked extreme vegan diet on fecal microflora was studied by direct stool sample gas-liquid chromatography (GLC) of bacterial cellular fatty acids and by quantitative bacterial culture by using classical microbiological techniques of isolation, identification, and enumeration of different bacterial species. Eighteen volunteers were divided randomly into two groups. The test group received an uncooked vegan diet for 1 month and a conventional diet of mixed Western type for the other month of the study. The control group consumed a conventional diet throughout the study period. Stool samples were collected. Bacterial cellular fatty acids were extracted directly from the stool samples and measured by GLC. Computerized analysis of the resulting fatty acid profiles was performed. Such a profile represents all bacterial cellular fatty acids in a sample and thus reflects its microflora and can be used to detect changes, differences, or similarities of bacterial flora between individual samples or sample groups. GLC profiles changed significantly in the test group after the induction and discontinuation of the vegan diet but not in the control group at any time, whereas quantitative bacterial culture did not detect any significant change in fecal bacteriology in either of the groups. The results suggest that an uncooked extreme vegan diet alters the fecal bacterial flora significantly when it is measured by direct stool sample GLC of bacterial fatty acids. PMID:1482187

  14. Child abuse and neglect profiles and their psychosocial consequences in a large sample of incarcerated males.

    Science.gov (United States)

    Debowska, Agata; Boduszek, Daniel

    2017-03-01

    Research examining child abuse and neglect (CAN) profiles among adult offender populations is lacking. Therefore, the primary aim of the present study was to address this limitation by using latent class analysis (LCA) to identify meaningful classes of individuals who have experienced physical abuse, emotional abuse, sexual abuse, as well as neglect. Another aim was to estimate the association between CAN class membership and external criteria (psychopathy factors, self-esteem, attitudes towards male sexual violence in dating relationships, child sexual abuse myth acceptance, violent offending, and age). Data were collected among a large systematically selected sample of adult male inmates (N=1261). Based on LCA, three unique classes of CAN were distinguished, including a 'low abuse' group (43.4% of the sample), a 'high physical and emotional abuse' group (51.3%), and a 'poly-victimized' group (5.3%). The analysis revealed that the CAN classes were differentially associated with affective responsiveness, cognitive responsiveness, personal self-esteem, prison self-esteem, attitudes towards male sexual violence in dating relationships, and violent offending. Findings highlight the unique nature of CAN constellations among criminal justice involved participants. The significance of the present results is discussed in relation to past and future research. Potential contributions to treatment strategies are also presented. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Whole genome transcript profiling from fingerstick blood samples: a comparison and feasibility study

    Directory of Open Access Journals (Sweden)

    Williams Adam R

    2009-12-01

    Full Text Available Abstract Background Whole genome gene expression profiling has revolutionized research in the past decade especially with the advent of microarrays. Recently, there have been significant improvements in whole blood RNA isolation techniques which, through stabilization of RNA at the time of sample collection, avoid bias and artifacts introduced during sample handling. Despite these improvements, current human whole blood RNA stabilization/isolation kits are limited by the requirement of a venous blood sample of at least 2.5 mL. While fingerstick blood collection has been used for many different assays, there has yet to be a kit developed to isolate high quality RNA for use in gene expression studies from such small human samples. The clinical and field testing advantages of obtaining reliable and reproducible gene expression data from a fingerstick are many; it is less invasive, time saving, more mobile, and eliminates the need of a trained phlebotomist. Furthermore, this method could also be employed in small animal studies, i.e. mice, where larger sample collections often require sacrificing the animal. In this study, we offer a rapid and simple method to extract sufficient amounts of high quality total RNA from approximately 70 μl of whole blood collected via a fingerstick using a modified protocol of the commercially available Qiagen PAXgene RNA Blood Kit. Results From two sets of fingerstick collections, about 70 uL whole blood collected via finger lancet and capillary tube, we recovered an average of 252.6 ng total RNA with an average RIN of 9.3. The post-amplification yields for 50 ng of total RNA averaged at 7.0 ug cDNA. The cDNA hybridized to Affymetrix HG-U133 Plus 2.0 GeneChips had an average % Present call of 52.5%. Both fingerstick collections were highly correlated with r2 values ranging from 0.94 to 0.97. Similarly both fingerstick collections were highly correlated to the venous collection with r2 values ranging from 0.88 to 0

  16. Serum Protein Profile Study of Clinical Samples Using High Performance Liquid Chromatography-Laser Induced Fluorescence

    DEFF Research Database (Denmark)

    Karemore, Gopal Raghunath; Ukendt, Sujatha; Rai, Lavanya

    2009-01-01

    The serum protein profiles of normal subjects, patients diagnosed with cervical cancer, and oral cancer were recorded using High Performance Liquid Chromatography combined with Laser Induced Fluorescence detection (HPLC-LIF). Serum protein profiles of the above three classes were tested...... for establishing the ability of HPLC-LIF protein profiling technique for discrimination, using hard clustering and Fuzzy clustering methods. The clustering algorithms have quite successfully classified the profiles as belonging to normal, cancer of cervix, and oral cancer conditions....

  17. Inferring predominant pathways in cellular models of breast cancer using limited sample proteomic profiling

    Directory of Open Access Journals (Sweden)

    Klinke David J

    2010-06-01

    Full Text Available Abstract Background Molecularly targeted drugs inhibit aberrant signaling within oncogenic pathways. Identifying the predominant pathways at work within a tumor is a key step towards tailoring therapies to the patient. Clinical samples pose significant challenges for proteomic profiling, an attractive approach for identifying predominant pathways. The objective of this study was to determine if information obtained from a limited sample (i.e., a single gel replicate can provide insight into the predominant pathways in two well-characterized breast cancer models. Methods A comparative proteomic analysis of total cell lysates was obtained from two cellular models of breast cancer, BT474 (HER2+/ER+ and SKBR3 (HER2+/ER-, using two-dimensional electrophoresis and MALDI-TOF mass spectrometry. Protein interaction networks and canonical pathways were extracted from the Ingenuity Pathway Knowledgebase (IPK based on association with the observed pattern of differentially expressed proteins. Results Of the 304 spots that were picked, 167 protein spots were identified. A threshold of 1.5-fold was used to select 62 proteins used in the analysis. IPK analysis suggested that metabolic pathways were highly associated with protein expression in SKBR3 cells while cell motility pathways were highly associated with BT474 cells. Inferred protein networks were confirmed by observing an up-regulation of IGF-1R and profilin in BT474 and up-regulation of Ras and enolase in SKBR3 using western blot. Conclusion When interpreted in the context of prior information, our results suggest that the overall patterns of differential protein expression obtained from limited samples can still aid in clinical decision making by providing an estimate of the predominant pathways that underpin cellular phenotype.

  18. Contamination profiles of short-chain polychlorinated n-alkanes in foodstuff samples from Japan

    Energy Technology Data Exchange (ETDEWEB)

    Matsukami, Hidenori; Kurunthachalam, S.; Ohi, Etsumasa; Takasuga, Takumi [Shimadzu Techno Research, Inc., Kyoto (Japan); Iino, Fukuya; Nakanishi, Junko [National Inst. of Advanced Industrial Science and Technology, Tsukuba (Japan)

    2004-09-15

    Polychlorinated n-alkanes (PCAs) are group of chemicals manufactured by chlorination of liquid n-paraffin or paraffin wax that contain 30 to 70% chlorine by weight. Large amounts of PCAs are widely used as plasticizers for vinyl chloride, lubricants, paints, and flame retardants and number of other industrial applications. Annual global production of PCAs is approximately 300 kilo tones, with a majority having medium-carbon-chain (C14-C19) length. According to the investigation made by Kagaku Kogyo Nippon-Sha, the annual consumption of PCAs in Japan was about 83,000 tons in between 1986-2001. Short-carbon-chain (C10-C13) has been placed on the Priority Substance List under Canadian Environmental Protection Act and on the Environmental Protection Agency Toxic Release Inventory in the USA due to its potential to act as tumor promoters in mammals. Data on environment levels of PCAs is meager, nevertheless, PCAs have been measured at relatively high concentrations in biota from Sweden, biota, sediment from Canada and marine biota and human milk from the Canadian Arctic. In our earlier study, we reported concentrations of short-chain PCAs from sewage treatment plant (STP) collected from Tama River, Tokyo and river water and sediment from Tokyo and Osaka. STP influent water contained greater shortchain PCAs concentrations than STP effluent. In addition, some river water and sediment samples contained detectable concentrations of short-chain PCAs, which was similar to other industrial countries. However, there is no study conducted to explore the contamination profiles of short-chain PCAs in human foodstuff samples. In the present study, we analyzed eleven foodstuff samples that were purchased from various supermarkets in order to know the short-chain PCAs concentrations in the foodstuff and possible human total daily intake (TDI) amounts.

  19. Profiling the clinical presentation of diagnostic characteristics of a sample of symptomatic TMD patients

    Directory of Open Access Journals (Sweden)

    e Silva Machado Luciana

    2012-08-01

    Full Text Available Abstract Background Temporomandibular disorder (TMD patients might present a number of concurrent clinical diagnoses that may be clustered according to their similarity. Profiling patients’ clinical presentations can be useful for better understanding the behavior of TMD and for providing appropriate treatment planning. The aim of this study was to simultaneously classify symptomatic patients diagnosed with a variety of subtypes of TMD into homogenous groups based on their clinical presentation and occurrence of comorbidities. Methods Clinical records of 357 consecutive TMD patients seeking treatment in a private specialized clinic were included in the study sample. Patients presenting multiple subtypes of TMD diagnosed simultaneously were categorized according to the AAOP criteria. Descriptive statistics and two-step cluster analysis were used to characterize the clinical presentation of these patients based on the primary and secondary clinical diagnoses. Results The most common diagnoses were localized masticatory muscle pain (n = 125 and disc displacement without reduction (n = 104. Comorbidity was identified in 288 patients. The automatic selection of an optimal number of clusters included 100% of cases, generating an initial 6-cluster solution and a final 4-cluster solution. The interpretation of within-group ranking of the importance of variables in the clustering solutions resulted in the following characterization of clusters: chronic facial pain (n = 36, acute muscle pain (n = 125, acute articular pain (n = 75 and chronic articular impairment (n = 121. Conclusion Subgroups of acute and chronic TMD patients seeking treatment can be identified using clustering methods to provide a better understanding of the clinical presentation of TMD when multiple diagnosis are present. Classifying patients into identifiable symptomatic profiles would help clinicians to estimate how common a disorder is within a population of

  20. Observations of particle extinction, PM2.5 mass concentration profile and flux in north China based on mobile lidar technique

    Science.gov (United States)

    Lv, Lihui; Liu, Wenqing; Zhang, Tianshu; Chen, Zhenyi; Dong, Yunsheng; Fan, Guangqiang; Xiang, Yan; Yao, Yawei; Yang, Nan; Chu, Baolin; Teng, Man; Shu, Xiaowen

    2017-09-01

    Fine particle with diameter pollution levels in Beijing were presented to evaluate the contribution of regional transport. A vehicle-based mobile lidar system was used to obtain the spatial and temporal distributions of particle extinction in the measurement route. Fixed point lidar and a particulate matter sampler were operated next to each other at the University of Chinese Academy of Science (UCAS) in Beijing to determine the relationship between the particle extinction coefficient and PM2.5 mass concentration. The correlation coefficient (R2) between the particle extinction coefficient and PM2.5 mass concentration was found to be over 0.8 when relative humidity (RH) was less than 90%. A mesoscale meteorological model, the Weather Research and Forecasting (WRF) model, was used to obtain profiles of the horizontal wind speed, wind direction and relative humidity. A vehicle-based mobile lidar technique was applied to estimate transport flux based on the PM2.5 profile and vertical profile of wind data. This method was applicable when hygroscopic growth can be neglected (relatively humidityBeijing during the experiments.

  1. Relative power and sample size analysis on gene expression profiling data

    Directory of Open Access Journals (Sweden)

    den Dunnen JT

    2009-09-01

    Full Text Available Abstract Background With the increasing number of expression profiling technologies, researchers today are confronted with choosing the technology that has sufficient power with minimal sample size, in order to reduce cost and time. These depend on data variability, partly determined by sample type, preparation and processing. Objective measures that help experimental design, given own pilot data, are thus fundamental. Results Relative power and sample size analysis were performed on two distinct data sets. The first set consisted of Affymetrix array data derived from a nutrigenomics experiment in which weak, intermediate and strong PPARα agonists were administered to wild-type and PPARα-null mice. Our analysis confirms the hierarchy of PPARα-activating compounds previously reported and the general idea that larger effect sizes positively contribute to the average power of the experiment. A simulation experiment was performed that mimicked the effect sizes seen in the first data set. The relative power was predicted but the estimates were slightly conservative. The second, more challenging, data set describes a microarray platform comparison study using hippocampal δC-doublecortin-like kinase transgenic mice that were compared to wild-type mice, which was combined with results from Solexa/Illumina deep sequencing runs. As expected, the choice of technology greatly influences the performance of the experiment. Solexa/Illumina deep sequencing has the highest overall power followed by the microarray platforms Agilent and Affymetrix. Interestingly, Solexa/Illumina deep sequencing displays comparable power across all intensity ranges, in contrast with microarray platforms that have decreased power in the low intensity range due to background noise. This means that deep sequencing technology is especially more powerful in detecting differences in the low intensity range, compared to microarray platforms. Conclusion Power and sample size analysis

  2. Relative power and sample size analysis on gene expression profiling data

    Science.gov (United States)

    van Iterson, M; 't Hoen, PAC; Pedotti, P; Hooiveld, GJEJ; den Dunnen, JT; van Ommen, GJB; Boer, JM; Menezes, RX

    2009-01-01

    Background With the increasing number of expression profiling technologies, researchers today are confronted with choosing the technology that has sufficient power with minimal sample size, in order to reduce cost and time. These depend on data variability, partly determined by sample type, preparation and processing. Objective measures that help experimental design, given own pilot data, are thus fundamental. Results Relative power and sample size analysis were performed on two distinct data sets. The first set consisted of Affymetrix array data derived from a nutrigenomics experiment in which weak, intermediate and strong PPARα agonists were administered to wild-type and PPARα-null mice. Our analysis confirms the hierarchy of PPARα-activating compounds previously reported and the general idea that larger effect sizes positively contribute to the average power of the experiment. A simulation experiment was performed that mimicked the effect sizes seen in the first data set. The relative power was predicted but the estimates were slightly conservative. The second, more challenging, data set describes a microarray platform comparison study using hippocampal δC-doublecortin-like kinase transgenic mice that were compared to wild-type mice, which was combined with results from Solexa/Illumina deep sequencing runs. As expected, the choice of technology greatly influences the performance of the experiment. Solexa/Illumina deep sequencing has the highest overall power followed by the microarray platforms Agilent and Affymetrix. Interestingly, Solexa/Illumina deep sequencing displays comparable power across all intensity ranges, in contrast with microarray platforms that have decreased power in the low intensity range due to background noise. This means that deep sequencing technology is especially more powerful in detecting differences in the low intensity range, compared to microarray platforms. Conclusion Power and sample size analysis based on pilot data give

  3. Influence of stability on the flux-profile relationships for wind speed, Φm, and temperature, Φh, for the stable atmospheric boundary layer

    Directory of Open Access Journals (Sweden)

    C. Yagüe

    2006-01-01

    Full Text Available Data from SABLES98 experimental campaign have been used in order to study the influence of stability (from weak to strong stratification on the flux-profile relationships for momentum, Φm, and heat, Φh. Measurements from 14 thermocouples and 3 sonic anemometers at three levels (5.8, 13.5 and 32 m for the period from 10 to 28 September 1998 were analysed using the framework of the local-scaling approach (Nieuwstadt, 1984a; 1984b, which can be interpreted as an extension of the Monin-Obukhov similarity theory (Obukhov, 1946. The results show increasing values of Φm and Φh with increasing stability parameter ζ=z/Λ, up to a value of ζ≈1–2, above which the values remain constant. As a consequence of this levelling off in Φm and Φh for strong stability, the turbulent mixing is underestimated when linear similarity functions (Businger et al., 1971 are used to calculate surface fluxes of momentum and heat. On the other hand when Φm and Φh are related to the gradient Richardson number, Ri, a different behaviour is found, which could indicate that the transfer of momentum is greater than that of heat for high Ri. The range of validity of these linear functions is discussed in terms of the physical aspects of turbulent intermittent mixing.

  4. Influence of common preanalytical variations on the metabolic profile of serum samples in biobanks

    Energy Technology Data Exchange (ETDEWEB)

    Fliniaux, Ophelie [University of Picardie Jules Verne, Laboratoire de Phytotechnologie EA 3900-BioPI (France); Gaillard, Gwenaelle [Biobanque de Picardie (France); Lion, Antoine [University of Picardie Jules Verne, Laboratoire de Phytotechnologie EA 3900-BioPI (France); Cailleu, Dominique [Batiment Serres-Transfert, rue de Mai/rue Dallery, Plateforme Analytique (France); Mesnard, Francois, E-mail: francois.mesnard@u-picardie.fr [University of Picardie Jules Verne, Laboratoire de Phytotechnologie EA 3900-BioPI (France); Betsou, Fotini [Integrated Biobank of Luxembourg (Luxembourg)

    2011-12-15

    A blood pre-centrifugation delay of 24 h at room temperature influenced the proton NMR spectroscopic profiles of human serum. A blood pre-centrifugation delay of 24 h at 4 Degree-Sign C did not influence the spectroscopic profile as compared with 4 h delays at either room temperature or 4 Degree-Sign C. Five or ten serum freeze-thaw cycles also influenced the proton NMR spectroscopic profiles. Certain common in vitro preanalytical variations occurring in biobanks may impact the metabolic profile of human serum.

  5. Evaluation of spot and passive sampling for monitoring, flux estimation and risk assessment of pesticides within the constraints of a typical regulatory monitoring scheme.

    Science.gov (United States)

    Zhang, Zulin; Troldborg, Mads; Yates, Kyari; Osprey, Mark; Kerr, Christine; Hallett, Paul D; Baggaley, Nikki; Rhind, Stewart M; Dawson, Julian J C; Hough, Rupert L

    2016-11-01

    In many agricultural catchments of Europe and North America, pesticides occur at generally low concentrations with significant temporal variation. This poses several challenges for both monitoring and understanding ecological risks/impacts of these chemicals. This study aimed to compare the performance of passive and spot sampling strategies given the constraints of typical regulatory monitoring. Nine pesticides were investigated in a river currently undergoing regulatory monitoring (River Ugie, Scotland). Within this regulatory framework, spot and passive sampling were undertaken to understand spatiotemporal occurrence, mass loads and ecological risks. All the target pesticides were detected in water by both sampling strategies. Chlorotoluron was observed to be the dominant pesticide by both spot (maximum: 111.8ng/l, mean: 9.35ng/l) and passive sampling (maximum: 39.24ng/l, mean: 4.76ng/l). The annual pesticide loads were estimated to be 2735g and 1837g based on the spot and passive sampling data, respectively. The spatiotemporal trend suggested that agricultural activities were the primary source of the compounds with variability in loads explained in large by timing of pesticide applications and rainfall. The risk assessment showed chlorotoluron and chlorpyrifos posed the highest ecological risks with 23% of the chlorotoluron spot samples and 36% of the chlorpyrifos passive samples resulting in a Risk Quotient greater than 0.1. This suggests that mitigation measures might need to be taken to reduce the input of pesticides into the river. The overall comparison of the two sampling strategies supported the hypothesis that passive sampling tends to integrate the contaminants over a period of exposure and allows quantification of contamination at low concentration. The results suggested that within a regulatory monitoring context passive sampling was more suitable for flux estimation and risk assessment of trace contaminants which cannot be diagnosed by spot

  6. Determination of DNA profiling of siwak and toothbrush samples used in Kingdom of Saudi Arabia

    Directory of Open Access Journals (Sweden)

    Nagy Alfadaly

    2016-10-01

    Conclusion: Siwak contains enough quantity of DNA, and retained good DNA profiling; and when compared to toothbrushes, siwak is a reasonable source of DNA profiling when found at the scene of crime. In addition, time of storage up to 4 months had no or little effects on results.

  7. Distribution, diffusive fluxes, and toxicity of heavy metals and PAHs in pore water profiles from the northern bays of Taihu Lake.

    Science.gov (United States)

    Lei, Pei; Zhang, Hong; Shan, Baoqing; Zhang, Bozheng

    2016-11-01

    Pore water plays a more significant role than do sediments in pollutant cycling dynamics. Also, concentrations of pollutants in pore water provide important information about their bioavailability or eco-toxicity; however, very few studies have focused on this topic. In this study, four duplicate sediment cores from three typical northern bays as well as the central part of Taihu Lake were collected to investigate the distribution, diffusive fluxes, and toxicity of heavy metals and polycyclic aromatic hydrocarbons (PAHs) in pore water profiles, which will be good in understanding the mobility and toxicity of these toxic pollutants and achieving better environmental management. The diffusive fluxes of heavy metals across the sediment-water interface was estimated through Fick's First Law, and the toxicity of heavy metals and PAHs in pore water was assessed by applying a water quality index (interstitial water toxicity criteria unit, IWCTU) and a hazard index (HI), respectively. The average concentrations of Cr, Cu, Ni, Pb, and Zn in surface pore water were 18.8, 23.4, 12.0, 13.5, and 42.5 μg L-1, respectively. Also, concentrations of the selected heavy metals in both overlying water and pore water from Taihu Lake were all lower than the standard values of the environmental quality standards for surface water. The concentrations as the pore water depth increased, and the highest detected concentrations of heavy metals were recorded between 3 and 5 cm below the sediment surface. The average diffusive fluxes of these metals were 27.3, 24.8, 7.03, 7.81, and -3.32 μg (m2 day)-1, respectively, indicating export from sediment into overlying water, with the exception of Zn. There was a potential risk of toxicity, mainly from Pb and Cu, indicating that heavy metals in pore water had slight to moderate impact on sediment-dwelling organisms by values of the IWCTU and the Nemeraw index. The total PAH concentrations in pore water were higher than those in overlying water

  8. Sub-nano tesla magnetic imaging based on room-temperature magnetic flux sensors with vibrating sample magnetometry

    Science.gov (United States)

    Adachi, Yoshiaki; Oyama, Daisuke

    2017-05-01

    We developed a two-dimensional imaging method for weak magnetic charge distribution using a commercially available magnetic impedance sensor whose magnetic field resolution is 10 pT/Hz1/2 at 10 Hz. When we applied the vibrating sample magnetometry, giving a minute mechanical vibration to the sample and detecting magnetic signals modulated by the vibration frequency, the effects of 1/f noise and the environmental low-frequency band noise were suppressed, and a weak magnetic charge distribution was obtained without magnetic shielding. Furthermore, improvement in the spatial resolution was also expected when the signals were demodulated at the second harmonic frequency of the vibration. In this paper, a preliminary magnetic charge imaging using the vibrating sample magnetometry and its results are demonstrated.

  9. PERSONALITY PROFILES AND PROBLEMATIC INTERNET USE IN A SAMPLE OF ITALIAN ADOLESCENTS

    Directory of Open Access Journals (Sweden)

    Fanny Guglielmucci

    2017-02-01

    Full Text Available Objective: The aim of the present study was to investigate the relationship between specific personality profiles and Internet use in a sample of Italian adolescents. Method: Four hundred thirty-two adolescents (58.3% males with an average age of 14.41 years (SD=.95 were enrolled in the study. Participants were administered the Internet Addiction Test (IAT and the Minnesota Multiphasic Inventory – Adolescent Form (MMPI-A. A two-step cluster analysis was relied according to IAT items’ scores. Results: Participants were grouped into three clusters labeled “Regulated Internet users” (n=180, “Involved with Internet activities” (n=105, and “At risk for problematic Internet use” (n=147. Consistently, the group at-risk for problematic Internet use showed higher IAT score and MMPI-A scores than the other groups, while no differences emerged between the group of regulated Internet users and the group of those involved with Internet activities. For the group at risk for problematic Internet use, the MMPI-A Clinical Scales on Paranoia (Pa and Schizophrenia (Sc showed the highest elevation, indicating a MMPI-A codetype 6-8/8-6 which describes adolescents with ego immaturity, dysregulated affects and behaviors, and reduced reality testing. Conclusions: Adolescents at risk for developing a dysfunctional use of the Internet may have little insight, bizarre beliefs, grandiose thought, and a persecutory view of the external world that may limit their capacity to counteract feelings of hopelessness and anguish. They could perceive the Internet as safe environment where it is possible to express such dysregulated feelings and behaviors, and to cope with emotional distress.

  10. Microbial profile of a kefir sample preparations: grains in natura and lyophilized and fermented suspension

    Directory of Open Access Journals (Sweden)

    Rafaela Strada de Oliveira Bergmann

    2010-12-01

    Full Text Available Probiotics are supplementary foods developed by microbial strains that improve animal health beyond basic nutrition. Probiotics are consumed orally, regardless of being considered as normal inhabitants of the intestines, able to survive in enzimatic and biliary secretions. Kefir is a probiotic originated from the old continent, fermented by several bacteria and yeasts, encapsulated in a polyssacharide matrix, and resembles jelly grains. Kefir is also presented as its sourish product both in sugary or milky suspensions containing vitamins, aminoacids, peptides, carbohydrates, ethanol, and volatile compounds. Kefir is known to have a diverse microbial content depending on the country and fermentative substrates, which cause distinct probiotic effects. In this sense, the purpose of this work was to isolate, identify, and quantify the microbial content of a native sugary kefir sample (fermented suspension and lyophilized natural grains. Serial dilutions were plated on Rogosa agar (AR and De Man, Rogosa and Sharpe (MRS, for Lactobacillus; Brain Heart Infusion (BHI, for total bacteria; Sabouraud-Dextrose-Agar (SDA, for yeasts and filamentous fungi; Thioglycolate Agar (TA, for Streptococcus, Acetobacteria and Leuconostoc; and Coconut Water Agar (CWA, and CWA supplemented with yeast extract (CWAY, for various genera. Genera and species for all strains were identified through biochemical reactions and specific API systems. The microbial profile of kefir was different from other sources of grains despite the presence of similar microorganisms and others which have not been reported yet. The data obtained with the CWA and CWAE media suggest that both substrates are alternative and salutary media for culture of kefir strains.

  11. Dose-Response Analysis of RNA-Seq Profiles in Archival Formalin-Fixed Paraffin-Embedded (FFPE) Samples.

    Science.gov (United States)

    Use of archival resources has been limited to date by inconsistent methods for genomic profiling of degraded RNA from formalin-fixed paraffin-embedded (FFPE) samples. RNA-sequencing offers a promising way to address this problem. Here we evaluated transcriptomic dose responses us...

  12. Proteomic Profiling of Paraffin-Embedded Samples Identifies Metaplasia-Specific and Early-Stage Gastric Cancer Biomarkers

    Science.gov (United States)

    Sousa, Josane F.; Ham, Amy-Joan L.; Whitwell, Corbin; Nam, Ki Taek; Lee, Hyuk-Joon; Yang, Han-Kwang; Kim, Woo Ho; Zhang, Bing; Li, Ming; LaFleur, Bonnie; Liebler, Daniel C.; Goldenring, James R.

    2013-01-01

    Early diagnosis and curative resection are the predominant factors associated with increased survival in patients with gastric cancer. However, most gastric cancer cases are still diagnosed at later stages. Since most pathologic specimens are archived as FFPE samples, the ability to use them to generate expression profiles can greatly improve cancer biomarker discovery. We sought to uncover new biomarkers for stomach preneoplastic metaplasias and neoplastic lesions by generating proteome profiles using FFPE samples. We combined peptide isoelectric focusing and liquid chromatography–tandem mass spectrometry analysis to generate proteomic profiles from FFPE samples of intestinal-type gastric cancer, metaplasia, and normal mucosa. The expression patterns of selected proteins were analyzed by immunostaining first in single tissue sections from normal stomach, metaplasia, and gastric cancer and later in larger tissue array cohorts. We detected 60 proteins up-regulated and 87 proteins down-regulated during the progression from normal mucosa to metaplasia to gastric cancer. Two of the up-regulated proteins, LTF and DMBT1, were validated as specific markers for spasmolytic polypeptide–expressing metaplasia and intestinal metaplasia, respectively. In cancers, significantly lower levels of DMBT1 or LTF correlated with more advanced disease and worse prognosis. Thus, proteomic profiling using FFPE samples has led to the identification of two novel markers for stomach metaplasias and gastric cancer prognosis. PMID:22944598

  13. Bacterial community profiling of cryogenically ground samples from the apical and coronal root segments of teeth with apical periodontitis.

    Science.gov (United States)

    Alves, Flávio R F; Siqueira, José F; Carmo, Flávia L; Santos, Adriana L; Peixoto, Raquel S; Rôças, Isabela N; Rosado, Alexandre S

    2009-04-01

    Bacteria located at the apical part of infected root canals are arguably directly involved in the pathogenesis of apical periodontitis. This study was conducted to profile and further compare the bacterial communities established at the apical and middle/coronal segments of infected root canals. Extracted teeth with attached apical periodontitis lesions were sectioned so as to obtain two root fragments representing the apical third and the coronal two thirds. Root fragments were subjected to a cryogenic grinding approach. DNA was extracted from root powder samples and used as a template for bacterial community profiling using a 16S ribosomal RNA gene-based seminested polymerase chain reaction/denaturing gradient gel electrophoresis approach. The mean number of bands in apical samples from teeth with primary infections was 28, ranging from 18 to 48, whereas in the middle/coronal samples, it was also 28, ranging from 19 to 36. Findings showed that the profile of bacterial community colonizing the apical third of infected root canals is as diverse as that occurring at the middle/coronal thirds. A high variability was observed for both interindividual (samples from the same region but from different patients) and intraindividual (samples from different regions of the same tooth) comparisons. The methodology used to prepare and analyze samples was highly effective in disclosing a previously unanticipated broad diversity of endodontic bacterial communities, especially at the apical part of infected root canals.

  14. The Harter Self-Perception Profile for Adolescents: Psychometrics for an Early Adolescent, African American Sample.

    Science.gov (United States)

    Thomson, Nicole Renick; Zand, Debra H.

    2002-01-01

    Studied the factor structure and other psychometric properties of S. Harter's (1988) Self-Perception Profile for Adolescents for 174 African American early adolescents. Findings yielded six conceptually relevant factors and also indicated gender differences in several domains. (SLD)

  15. Comparison of DNA extraction methods for microbial community profiling with an application to pediatric bronchoalveolar lavage samples.

    Directory of Open Access Journals (Sweden)

    Dana Willner

    Full Text Available Barcoded amplicon sequencing is rapidly becoming a standard method for profiling microbial communities, including the human respiratory microbiome. While this approach has less bias than standard cultivation, several steps can introduce variation including the type of DNA extraction method used. Here we assessed five different extraction methods on pediatric bronchoalveolar lavage (BAL samples and a mock community comprised of nine bacterial genera to determine method reproducibility and detection limits for these typically low complexity communities. Additionally, using the mock community, we were able to evaluate contamination and select a relative abundance cut-off threshold based on the geometric distribution that optimizes the trade off between detecting bona fide operational taxonomic units and filtering out spurious ones. Using this threshold, the majority of genera in the mock community were predictably detected by all extraction methods including the hard-to-lyse Gram-positive genus Staphylococcus. Differences between extraction methods were significantly greater than between technical replicates for both the mock community and BAL samples emphasizing the importance of using a standardized methodology for microbiome studies. However, regardless of method used, individual patients retained unique diagnostic profiles. Furthermore, despite being stored as raw frozen samples for over five years, community profiles from BAL samples were consistent with historical culturing results. The culture-independent profiling of these samples also identified a number of anaerobic genera that are gaining acceptance as being part of the respiratory microbiome. This study should help guide researchers to formulate sampling, extraction and analysis strategies for respiratory and other human microbiome samples.

  16. A novel functional assay for simultaneous determination of total fatty acid beta-oxidation flux and acylcarnitine profiling in human skin fibroblasts using (2)H(31)-palmitate by isotope ratio mass spectrometry and electrospray tandem mass spectrometry

    NARCIS (Netherlands)

    Law, Lap-Kay; Tang, Nelson Leung-Sang; Hui, Joannie; Ho, Chung-Shun; Ruiter, Jos; Fok, Tai-Fai; Wanders, Ronald J. A.; Lam, Christopher Wai-Kei

    2007-01-01

    BACKGROUND: Two separate and complementary assays, total mitochondrial fatty acid beta-oxidation (FAO) flux rate and acylcarnitine profiling, have been used to establish a definitive diagnosis of FAO defects (FAOD) in cultured cells. We developed a novel functional assay for total FAO rate assay by

  17. Numerical simulation of vertical ground-water flux of the Rio Grande from ground-water temperature profiles, central New Mexico

    Science.gov (United States)

    Bartolino, James R.; Niswonger, Richard G.

    1999-01-01

    An important gap in the understanding of the hydrology of the Middle Rio Grande Basin, central New Mexico, is the rate at which water from the Rio Grande recharges the Santa Fe Group aquifer system. Several methodologies-including use of the Glover-Balmer equation, flood pulses, and channel permeameters- have been applied to this problem in the Middle Rio Grande Basin. In the work presented here, ground-water temperature profiles and ground-water levels beneath the Rio Grande were measured and numerically simulated at four sites. The direction and rate of vertical ground-water flux between the river and underlying aquifer was simulated and the effective vertical hydraulic conductivity of the sediments underlying the river was estimated through model calibration. Seven sets of nested piezometers were installed during July and August 1996 at four sites along the Rio Grande in the Albuquerque area, though only four of the piezometer nests were simulated. In downstream order, these four sites are (1) the Bernalillo site, upstream from the New Mexico State Highway 44 bridge in Bernalillo (piezometer nest BRN02); (2) the Corrales site, upstream from the Rio Rancho sewage treatment plant in Rio Rancho (COR01); (3) the Paseo del Norte site, upstream from the Paseo del Norte bridge in Albuquerque (PDN01); and (4) the Rio Bravo site, upstream from the Rio Bravo bridge in Albuquerque (RBR01). All piezometers were completed in the inner-valley alluvium of the Santa Fe Group aquifer system. Ground-water levels and temperatures were measured in the four piezometer nests a total of seven times in the 24-month period from September 1996 through August 1998. The flux between the surface- and ground-water systems at each of the field sites was quantified by one-dimensional numerical simulation of the water and heat exchange in the subsurface using the heat and water transport model VS2DH. Model calibration was aided by the use of PEST, a model-independent computer program that uses

  18. Fluxes of Ultrafine Particles Over and In a Deciduous Forest

    Science.gov (United States)

    Pryor, S. C.; Hornsby, K. E.

    2013-12-01

    Given the importance of forests to land surface cover and particle removal (due to the very high deposition velocities and well-developed turbulence) there is a specific need to understand removal to, and in, forests. Fluxes of size-resolved and total particle number fluxes over (at 46 m) and in (at 7 m) a deciduous forest over a 14 month period are presented based on data from two Gill 3-D WindMaster Pro sonic anemometers, an Ultrafine Condensation Particle Counter (UCPC) operated at 10 Hz and a Fast Mobility Particle Sizer (FMPS) operated at 1 Hz. Size-resolved particle profiles during the same period are measured using a separate FMPS scanning at three measurement heights across the canopy (top, middle and bottom). Three methods are being applied to derive the total number and size-resolved fluxes from the UCPC and FMPS respectively; eddy covariance, inertial dissipation and the co-spectral approach. The results are integrated with fluxes of sensible heat, momentum and carbon dioxide derived using a Licor LI-7200. Results for the total number flux concentrations and the size-resolved concentrations derived using the three different approaches applied to the above canopy sampling level show a high degree of accord, but that the eddy-covariance fluxes are generally of smaller magnitude than those derived using the spectral methods. In keeping with prior research our results show a considerable number of fluxes are characterized by upward fluxes. Further our results show distinctly different flux diurnal profiles for the nucleation versus Aitken mode particles indicating some differential control on fluxes of particles of different sizes (including a role for aerosol dynamics). This presentation will provide details regarding the experimental approach, flux and gradient estimation methodologies, diagnose the size dependence of the fluxes, and compare and contrast the canopy and ground partitioning of the particle fluxes during leaf-on and leaf-off periods.

  19. How Confocal Is Confocal Raman Microspectroscopy on the Skin? Impact of Microscope Configuration and Sample Preparation on Penetration Depth Profiles.

    Science.gov (United States)

    Lunter, Dominique Jasmin

    2016-01-01

    The aim of the study was to elucidate the effect of sample preparation and microscope configuration on the results of confocal Raman microspectroscopic evaluation of the penetration of a pharmaceutical active into the skin (depth profiling). Pig ear skin and a hydrophilic formulation containing procaine HCl were used as a model system. The formulation was either left on the skin during the measurement, or was wiped off or washed off prior to the analysis. The microscope configuration was varied with respect to objectives and pinholes used. Sample preparation and microscope configuration had a tremendous effect on the results of depth profiling. Regarding sample preparation, the best results could be observed when the formulation was washed off the skin prior to the analysis. Concerning microscope configuration, the use of a 40 × 0.6 numerical aperture (NA) objective in combination with a 25-µm pinhole or a 100 × 1.25 NA objective in combination with a 50-µm pinhole was found to be advantageous. Complete removal of the sample from the skin before the analysis was found to be crucial. A thorough analysis of the suitability of the chosen microscope configuration should be performed before acquiring concentration depth profiles. © 2016 S. Karger AG, Basel.

  20. Profiles of Emotional Intelligence and Learning Strategies in a Sample of Chilean Students

    Science.gov (United States)

    García-Fernández, José M.; Inglés, Cándido J.; Suriá, Raquel; Martín, Nelly Lagos-San; Gonzálvez-Maciá, Carolina; Aparisi, David; Martínez-Monteagudo, Mari C.

    2015-01-01

    In the last few years, one of the lines of research of great interest in the field of emotional intelligence (EI) has been the analysis of the role of emotions in the educational context and, in particular, their influence on learning strategies. The aims of this study are to identify the existence of different EI profiles and to determine…

  1. The importance of Guthrie cards and other medical samples for the direct matching of disaster victims using DNA profiling.

    Science.gov (United States)

    Hartman, D; Benton, L; Morenos, L; Beyer, J; Spiden, M; Stock, A

    2011-02-25

    The identification of disaster victims through the use of DNA analysis is an integral part of any Disaster Victim Identification (DVI) response, regardless of the scale and nature of the disaster. As part of the DVI response to the 2009 Victorian Bushfires Disaster, DNA analysis was performed to assist in the identification of victims through kinship (familial matching to relatives) or direct (self source sample) matching of DNA profiles. Although most of the DNA identifications achieved were to reference samples from relatives, there were a number of DNA identifications (12) made through direct matching. Guthrie cards, which have been collected in Australia over the past 30 years, were used to provide direct reference samples. Of the 236 ante-mortem (AM) samples received, 21 were Guthrie cards and one was a biopsy specimen; all yielding complete DNA profiles when genotyped. This publication describes the use of such Biobanks and medical specimens as a sample source for the recovery of good quality DNA for comparisons to post-mortem (PM) samples. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

  2. A simple and sensitive method for lipoprotein and lipids profiles analysis of individual micro-liter scale serum samples.

    Science.gov (United States)

    Yang, Liu; Fan, Baoyan; Yang, Kangmin; Zhu, Haibo

    2012-02-01

    A simple and sensitive method to determine lipoprotein and lipids profiles in micro-liter scale individual serum sample is not presently available. Traditional lipoprotein separation techniques either by ultra-centrifugation or by liquid chromatography methods have their disadvantages in both lipoprotein separation and lipids component quantification. In this study we used small volume needing size-exclusion fast protein liquid chromatography to separate different lipoprotein subclasses in 50μL serum. And lipids contents, such as cholesterol, cholesterol ester and triacylglycerol, were measured by using two different fluorescence-based lipid detection methods. With this method, very low density lipoprotein, low density lipoprotein and high density lipoprotein could be easily separated, and follow-up lipid detection was completed by simple kinds of reactions. Serum lipoprotein and lipids profiling from C57BL/6 mice (n=5) and human (n=5) were analyzed. The elution profiles of five individuals were highly reproducible, and there were lipoprotein and lipids distribution variations between C57BL/6 mice and human beings. In conclusion, this method which combined small volume needing size-exclusion fast protein liquid chromatography and fluorescence-based lipids measurement, provided a simple, efficient, integrity and reproducible procedure for determining serum lipoprotein and lipids profiles in micro-liter scale levels. It becomes possible that determination of lipoprotein profiles and gaining information of lipids in different lipoproteins can be accomplished simultaneously. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

  3. Sampling

    CERN Document Server

    Thompson, Steven K

    2012-01-01

    Praise for the Second Edition "This book has never had a competitor. It is the only book that takes a broad approach to sampling . . . any good personal statistics library should include a copy of this book." —Technometrics "Well-written . . . an excellent book on an important subject. Highly recommended." —Choice "An ideal reference for scientific researchers and other professionals who use sampling." —Zentralblatt Math Features new developments in the field combined with all aspects of obtaining, interpreting, and using sample data Sampling provides an up-to-date treat

  4. IHC Profiler: an open source plugin for the quantitative evaluation and automated scoring of immunohistochemistry images of human tissue samples.

    Directory of Open Access Journals (Sweden)

    Frency Varghese

    Full Text Available In anatomic pathology, immunohistochemistry (IHC serves as a diagnostic and prognostic method for identification of disease markers in tissue samples that directly influences classification and grading the disease, influencing patient management. However, till today over most of the world, pathological analysis of tissue samples remained a time-consuming and subjective procedure, wherein the intensity of antibody staining is manually judged and thus scoring decision is directly influenced by visual bias. This instigated us to design a simple method of automated digital IHC image analysis algorithm for an unbiased, quantitative assessment of antibody staining intensity in tissue sections. As a first step, we adopted the spectral deconvolution method of DAB/hematoxylin color spectra by using optimized optical density vectors of the color deconvolution plugin for proper separation of the DAB color spectra. Then the DAB stained image is displayed in a new window wherein it undergoes pixel-by-pixel analysis, and displays the full profile along with its scoring decision. Based on the mathematical formula conceptualized, the algorithm is thoroughly tested by analyzing scores assigned to thousands (n = 1703 of DAB stained IHC images including sample images taken from human protein atlas web resource. The IHC Profiler plugin developed is compatible with the open resource digital image analysis software, ImageJ, which creates a pixel-by-pixel analysis profile of a digital IHC image and further assigns a score in a four tier system. A comparison study between manual pathological analysis and IHC Profiler resolved in a match of 88.6% (P<0.0001, CI = 95%. This new tool developed for clinical histopathological sample analysis can be adopted globally for scoring most protein targets where the marker protein expression is of cytoplasmic and/or nuclear type. We foresee that this method will minimize the problem of inter-observer variations across labs and

  5. IHC Profiler: an open source plugin for the quantitative evaluation and automated scoring of immunohistochemistry images of human tissue samples.

    Science.gov (United States)

    Varghese, Frency; Bukhari, Amirali B; Malhotra, Renu; De, Abhijit

    2014-01-01

    In anatomic pathology, immunohistochemistry (IHC) serves as a diagnostic and prognostic method for identification of disease markers in tissue samples that directly influences classification and grading the disease, influencing patient management. However, till today over most of the world, pathological analysis of tissue samples remained a time-consuming and subjective procedure, wherein the intensity of antibody staining is manually judged and thus scoring decision is directly influenced by visual bias. This instigated us to design a simple method of automated digital IHC image analysis algorithm for an unbiased, quantitative assessment of antibody staining intensity in tissue sections. As a first step, we adopted the spectral deconvolution method of DAB/hematoxylin color spectra by using optimized optical density vectors of the color deconvolution plugin for proper separation of the DAB color spectra. Then the DAB stained image is displayed in a new window wherein it undergoes pixel-by-pixel analysis, and displays the full profile along with its scoring decision. Based on the mathematical formula conceptualized, the algorithm is thoroughly tested by analyzing scores assigned to thousands (n = 1703) of DAB stained IHC images including sample images taken from human protein atlas web resource. The IHC Profiler plugin developed is compatible with the open resource digital image analysis software, ImageJ, which creates a pixel-by-pixel analysis profile of a digital IHC image and further assigns a score in a four tier system. A comparison study between manual pathological analysis and IHC Profiler resolved in a match of 88.6% (P<0.0001, CI = 95%). This new tool developed for clinical histopathological sample analysis can be adopted globally for scoring most protein targets where the marker protein expression is of cytoplasmic and/or nuclear type. We foresee that this method will minimize the problem of inter-observer variations across labs and further help in

  6. Application of chemometric tools for automatic classification and profile extraction of DNA samples in forensic tasks.

    Science.gov (United States)

    Talavera Bustamante, Isneri; Silva Mata, Francisco; Hernández González, Noslen; González Gazapo, Ricardo; Palau, Juan; Ferreira, Marcia M Castro

    2007-07-09

    In this paper a method for the automatic DNA spots classification and extraction of profiles associated in DNA polyacrylamide gel electrophoresis is presented and it integrates the use of image processing techniques and chemometrics tools. A software which implements this method was developed; for feature extraction a combination of a PCA analysis and a C4.5 decision tree were used. To obtain good results in the profile extraction only DNA spots are useful; therefore, it was necessary to solve a two-class classification problem among DNA spots and no-DNA spots. In order to perform the classification process with high velocity, effectiveness and robustness, comparative classification studies among support vector machine (SVM), K-NN and PLS-DA classifiers were made. The best results obtained with the SVM classifier demonstrated the advantages attributed to it in the literature as a two-class classifier. A Sequential Cluster Leader Algorithm and another one developed for the restoration of pattern missing spots were needed to conclude the profiles extraction step. The experimental results show that this method has a very effective computational behavior and effectiveness, and provide a very useful tool to decrease the time and increase the quality of the specialist responses.

  7. Total Protein Profile and Drug Resistance in Candida albicans Isolated from Clinical Samples

    Directory of Open Access Journals (Sweden)

    Kamal Uddin Zaidi

    2016-01-01

    Full Text Available This study was done to assess the antifungal susceptibility of clinical isolates of Candida albicans and to evaluate its total protein profile based on morphological difference on drug resistance. Hundred and twenty clinical isolates of C. albicans from various clinical specimens were tested for susceptibility against four antifungal agents, namely, fluconazole, itraconazole, amphotericin B, and ketoconazole. A significant increase of drug resistance in clinical isolates of C. albicans was observed. The study showed 50% fluconazole and itraconazole resistance at 32 μg mL−1 with a MIC50 and MIC90 values at 34 and 47 and 36 and 49 μg mL−1, respectively. All isolates were sensitive to amphotericin B and ketoconazole. The SDS-PAGE protein profile showed a prevalent band of ~52.5 kDa, indicating overexpression of gene in 72% strains with fluconazole resistance. Since the opportunistic infections of Candida spp. are increasing along with drug resistance, the total protein profile will help in understanding the evolutionary changes in drug resistance and also to characterize them.

  8. Synthetic and non-synthetic anthropogenic fibers in a river under the impact of Paris Megacity: Sampling methodological aspects and flux estimations.

    Science.gov (United States)

    Dris, Rachid; Gasperi, Johnny; Rocher, Vincent; Tassin, Bruno

    2017-11-09

    Processed fibers are highly present in our daily life and can be either natural, artificial (regenerated cellulose) and synthetic (made with petrochemicals). Their widespread use lead inevitably to a high contamination of environment. Previous studies focus on plastic particles regardless of their type or shape as long as they are comprised between 330μm and 5mm. On the contrary, this study focuses exclusively on fibers using a smaller mesh size net (80μm) to sample freshwater. Moreover, all processed organic fibers are considered, irrespective to their nature. First, the short term temporal variability of the fibers in the environment was assessed. While exposing the sampling net during 1min a coefficient of variation of approx. 45% (with n=6) was determined. It was of only 26% (n=6) when the exposure was of 3min. The assessment of the distribution through the section showed a possible difference in concentrations between the middle of the water surface and the river banks which could be attributed to the intense river traffic within the Paris Megacity. The vertical variability seems negligible as turbulence and current conditions homogenize the distribution of the fibers. A monthly monitoring showed concentrations of 100.6±99.9fibers·m-3 in the Marne River and of: 48.5±98.5, 27.9±26.3, 27.9±40.3 and 22.1±25.3fibers·m-3 from the upstream to downstream points in the Seine River. Once these concentrations are converted into fluxes, it seems that the impact generated by the Paris Megacity cannot be distinguished. Investigations on the role of sedimentation and deposition on the banks are required. This study helped fill some major knowledge gaps regarding the fibers in rivers, their sampling, occurrence, spatial-temporal distribution and fluxes. It is encouraged that future studies include both synthetic and none synthetic fibers. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Sterile paper points as a bacterial DNA-contamination source in microbiome profiles of clinical samples

    NARCIS (Netherlands)

    van der Horst, J.; Buijs, M.J.; Laine, M.L.; Wismeijer, D.; Loos, B.G.; Crielaard, W.; Zaura, E.

    2013-01-01

    Objectives High throughput sequencing of bacterial DNA from clinical samples provides untargeted, open-ended information on the entire microbial community. The downside of this approach is the vulnerability to DNA contamination from other sources than the clinical sample. Here we describe

  10. The impact of in-canopy wind profile formulations on heat flux estimation using the remote sensing-based two-source model for an open orchard canopy in southern Italy

    Science.gov (United States)

    Cammalleri, C.; Anderson, M. C.; Ciraolo, G.; D'Urso, G.; Kustas, W. P.; La Loggia, G.; Minacapilli, M.

    2010-07-01

    For open orchard and vineyard canopies containing significant fractions of exposed soil (>50%), typical of Mediterranean agricultural regions, the energy balance of the vegetation elements is strongly influenced by heat exchange with the bare soil/substrate. For these agricultural systems a "two-source" approach, where radiation and turbulent exchange between the soil and canopy elements are explicitly modelled, appears to be the only suitable methodology for reliably assessing energy fluxes. In strongly clumped canopies, the effective wind speed profile inside and below the canopy layer can highly influence the partitioning of energy fluxes between the soil and vegetation components. To assess the impact of in-canopy wind profile on model flux estimates, an analysis of three different formulations is presented, including algorithms from Goudriaan (1977), Massman (1987) and Lalic et al. (2003). The in-canopy wind profile formulations are applied to the thermal-based Two-Source Energy Balance (TSEB) model developed by Norman et al. (1995) and modified by Kustas and Norman (1999). High resolution airborne remote sensing images, collected over an agricultural area located in the western part of Sicily (Italy) comprised primarily of vineyards, olive and citrus orchards, are used to derive all the input parameters need to apply the TSEB. The images were acquired from June to October 2008 and include a relatively wide range of meteorological and soil moisture conditions. A preliminary sensitivity analysis of the three wind profile algorithms highlight the dependence of wind speed just above the soil/substrate to leaf area index and canopy height over the typical canopy properties range of these agricultural area. It is found that differences in wind just above surface among the models is most significant under sparse and medium fractional cover conditions (20-60%). The TSEB model heat flux estimates are compared with micrometeorological measurements from a small aperture

  11. Somatic Coliphage Profiles of Produce and Environmental Samples from Farms in Northern México.

    Science.gov (United States)

    Bartz, Faith E; Hodge, Domonique Watson; Heredia, Norma; de Aceituno, Anna Fabiszewski; Solís, Luisa; Jaykus, Lee-Ann; Garcia, Santos; Leon, Juan S

    2016-09-01

    Somatic coliphages were quantified in 459 produce and environmental samples from 11 farms in Northern Mexico to compare amounts of somatic coliphages among different types of fresh produce and environmental samples across the production steps on farms. Rinsates from cantaloupe melons, jalapeño peppers, tomatoes, and the hands of workers, soil, and water were collected during 2011-2012 at four successive steps on each farm, from the field before harvest through the packing facility, and assayed by FastPhage MPN Quanti-tray method. Cantaloupe farm samples contained more coliphages than jalapeño or tomato (p range food safety during fruit and vegetable production.

  12. Assessing childhood maltreatment and mental health correlates of disordered eating profiles in a nationally representative sample of English females.

    Science.gov (United States)

    Armour, Cherie; Műllerová, Jana; Fletcher, Shelley; Lagdon, Susan; Burns, Carol Rhonda; Robinson, Martin; Robinson, Jake

    2016-03-01

    Previous research suggests that childhood maltreatment is associated with the onset of eating disorders (ED). In turn, EDs are associated with alternative psychopathologies such as depression and posttraumatic stress disorder (PTSD), and with suicidality. Moreover, it has been reported that various ED profiles may exist. The aim of the current study was to examine the profiles of disordered eating and the associations of these with childhood maltreatment and with mental health psychopathology. The current study utilised a representative sample of English females (N = 4206) and assessed for the presence of disordered eating profiles using Latent Class Analysis. Multinomial logistic regression was implemented to examine the associations of childhood sexual and physical abuse with the disordered eating profiles and the associations of these with PTSD, depression and suicidality. Results supported those of previous findings in that we found five latent classes of which three were regarded as disordered eating classes. Significant relationships were found between these and measures of childhood trauma and mental health outcomes. Childhood sexual and physical abuse increased the likelihood of membership in disordered eating classes and these in turn increased the likelihood of adverse mental health and suicidal outcomes.

  13. Methoxetamine: An early report on the motivations for use, effect profile and prevalence of use in a UK clubbing sample.

    Science.gov (United States)

    Winstock, Adam R; Lawn, Will; Deluca, Paolo; Borschmann, Rohan

    2016-03-01

    To assess the prevalence of use and subjective effect profile of methoxetamine among a group of polydrug users. Cross-sectional, anonymous, online survey of UK-based polydrug users was conducted. Prevalence of lifetime, last year and last month use, sourcing of the drugs, motivations for use, and subjective effect and risk profile compared with that of ketamine were measured. There were 7700 UK-based polydrug users, of whom 326 reported recent use of methoxetamine. Of the whole sample, 4.2% reported last 12 month use of methoxetamine compared with 24.5% for ketamine. The most common route of use was intranasal and the predominate effect described as psychedelic. Of the 15.5% of last year users of ketamine reporting last year use of methoxetamine, only 18.7% reported that they thought methoxetamine was less damaging to their kidneys or bladder than ketamine. Its broad effect profile, based on participants' first experience of use, was very similar to that of ketamine. Almost one-third of users reported that they did not intend to try the drug again. Methoxetamine appears to have a broadly similar effect profile to that of ketamine. Only a minority of participants were motivated to use it because they believed it was less damaging to their kidneys or bladder than ketamine. The impact of the recent temporary banning order on availability and use of both methoxetamine and ketamine should be monitored carefully. © 2015 Australasian Professional Society on Alcohol and other Drugs.

  14. A novel Whole Air Sample Profiler (WASP for the quantification of volatile organic compounds in the boundary layer

    Directory of Open Access Journals (Sweden)

    J. E. Mak

    2013-10-01

    Full Text Available The emission and fate of reactive volatile organic compounds (VOCs is of inherent interest to those studying chemical biosphere–atmosphere interactions. In-canopy VOC observations are obtainable using tower-based samplers, but the lack of suitable sampling systems for the full boundary layer has limited the availability of data characterizing the vertical structure of such gases above the canopy height and still in the boundary layer. This is an important region where many reactive VOCs are oxidized or otherwise removed. Here we describe an airborne sampling system designed to collect a vertical profile of air into a 3/8 in. OD (outer diameter tube 150 m in length. The inlet ram air pressure is used to flow sampled air through the tube, which results in a varying flow rate based on aircraft speed and altitude. Since aircraft velocity decreases during ascent, it is necessary to account for the variable flow rate into the tube. This is accomplished using a reference gas that is pulsed into the air stream so that the precise altitude of the collected air can be reconstructed post-collection. The pulsed injections are also used to determine any significant effect from diffusion/mixing within the sampling tube, either during collection or subsequent extraction for gas analysis. This system has been successfully deployed, and we show some measured vertical profiles of isoprene and its oxidation products methacrolein and methyl vinyl ketone from a mixed canopy near Columbia, Missouri.

  15. Sorption, desorption and mineralisation of the herbicides glyphosate and MCPA in samples from two Danish soil and subsurface profiles.

    Science.gov (United States)

    Sørensen, Sebastian R; Schultz, Anne; Jacobsen, Ole S; Aamand, Jens

    2006-05-01

    The vertical distribution of the sorption, desorption and mineralisation of glyphosate and MCPA was examined in samples from two contrasting soil and subsurface profiles, obtained from a sandy agricultural site and a non-agricultural clay rich site. The highest mineralisation of [14C-methylen]glyphosate, with 9.3-14.7% degraded to 14CO2 within 3 months was found in the deepest sample from the clay site. In the deeper parts of the sandy profile high sorption and low desorption of glyphosate coincided with no or minor mineralisation indicating a limited glyphosate bioavailability. MCPA was readily mineralised except in the deepest samples from both sites. The highest MCPA mineralisation was detected just below the surface layers with 72% or 44% degraded to 14CO2 at the sandy or the clay sites, respectively. MCPA sorped to a minor extent in all samples and no indications of sorption-controlled mineralisation was revealed. None of the herbicides were mineralised under anoxic conditions.

  16. Gene expression profiling of brain samples from patients with Lewy body dementia.

    Science.gov (United States)

    Pietrzak, Maciej; Papp, Audrey; Curtis, Amanda; Handelman, Samuel K; Kataki, Maria; Scharre, Douglas W; Rempala, Grzegorz; Sadee, Wolfgang

    2016-10-28

    Dementia with Lewy Bodies (DLB) is the second most common neurodegenerative disorder in the elderly. The development and progression of DLB remain unclear. In this study we used next generation sequencing to assess RNA expression profiles and cellular processes associated with DLB in the anterior cingulate cortex, a brain region affected by DLB pathology. The expression measurements were made in autopsy brain tissues from 8 DLB subjects and 10 age-matched controls using AmpliSeq technology with ion torrent sequencing. The analysis of RNA expression profiles revealed 490 differentially expressed genes, among which 367 genes were down-regulated and 123 were up-regulated. Functional enrichment analysis of genes differentially expressed in DLB indicated downregulation of genes associated with myelination, neurogenesis, and regulation of nervous system development. miRNA binding sites enriched in these mRNAs yielded a list of candidate miRNAs participating in DLB pathophysiology. Our study provides a comprehensive picture of gene expression landscape in DLB, identifying key cellular processes associated with DLB pathology. Copyright © 2016 Elsevier Inc. All rights reserved.

  17. Mutational profile of KIT and PDGFRA genes in gastrointestinal stromal tumors in Peruvian samples

    Directory of Open Access Journals (Sweden)

    José Buleje

    2015-02-01

    Full Text Available Introduction: Gastrointestinal stromal tumors (GISTs are mesenchymal neoplasms usually caused by somatic mutations in the genes KIT (c-KIT or PDGFRA. Mutation characterization has become an important exam for GIST patients because it is useful in predicting the response to the inhibitors of receptor tyrosine kinase (RTK. Objectives: The aim of this study was to determine the frequency of KIT and PDGFRA mutations in 25 GIST samples collected over two years at two national reference hospitals in Peru. There were 21 samples collected from the Instituto Nacional de Enfermedades Neoplásicas (INEN, national cancer center and 4 samples collected from Hospital A. Loayza. Methods and materials: In this retrospective study, we performed polymerase chain reaction (PCR amplification and deoxyribonucleic acid (DNA sequencing of KIT (exons 9, 11, 13, and 17 and PDGFRA (exons 12 and 18 genes in 20 FFPE (formalin-fixed, paraffin-embedded and 5 frozen GIST samples. Results: We report 21 mutations, including deletions, duplications, and missense, no mutations in 2 samples, and 2 samples with no useful DNA for further analysis. Eighty-six percent of these mutations were located in exon 11 of KIT, and 14 % were located in exon 18 of PDGFRA. Conclusions: Our study identified mutations in 21 out of 25 GIST samples from 2 referential national hospitals in Peru, and the mutation proportion follows a global tendency observed from previous studies (i.e., the majority of samples presented KIT mutations followed by a minor percentage of PDGFRA mutations. This study presents the first mutation data of the KIT and PDGFRA genes from Peruvian individuals with GIST.

  18. Application of a new vertical profiling tool (ESASS) for sampling groundwater quality during hollow-stem auger drilling

    Science.gov (United States)

    Harte, Philip T.; Flanagan, Sarah M.

    2011-01-01

    A new tool called ESASS (Enhanced Screen Auger Sampling System) was developed by the U.S. Geological Survey. The use of ESASS, because of its unique U.S. patent design (U.S. patent no. 7,631,705 B1), allows for the collection of representative, depth-specific groundwater samples (vertical profiling) in a quick and efficient manner using a 0.305-m long screen auger during hollow-stem auger drilling. With ESASS, the water column in the flights above the screen auger is separated from the water in the screen auger by a specially designed removable plug and collar. The tool fits inside an auger of standard inner diameter (82.55 mm). The novel design of the system constituted by the plug, collar, and A-rod allows the plug to be retrieved using conventional drilling A-rods. After retrieval, standard-diameter (50.8 mm) observation wells can be installed within the hollow-stem augers. Testing of ESASS was conducted at one waste-disposal site with tetrachloroethylene (PCE) contamination and at two reference sites with no known waste-disposal history. All three sites have similar geology and are underlain by glacial, stratified-drift deposits. For the applications tested, ESASS proved to be a useful tool in vertical profiling of groundwater quality. At the waste site, PCE concentrations measured with ESASS profiling at several depths were comparable (relative percent difference nitrate and nitrite) over short (0.61 m) distances.

  19. A Top-down soil moisture and sap flux sampling design to capture the effect of inter-annual climate variability on ecohydrology in mountain catchments

    Science.gov (United States)

    Son, K.; Tague, C.

    2010-12-01

    Soil moisture in mountain catchments is highly spatial heterogeneous due to steep topographic gradients, complex soil and vegetation patterns and seasonally varying energy and precipitation inputs. In an idealized setting, a randomized soil moisture sampling design with high spatial frequency can be used to resolve the spatial heterogeneity of soil moisture at catchment scales. However, this bottom-up approach is constrained by the feasibility of high frequency measurements particularly in mountain environments with limited accessibility. Thus, in these mountain environments, an alternative, top-down approach is often needed. In this study, we propose the top-down approach sampling design of soil moisture and sapflux measurement based on an ecohydrologic model and clustering analysis. The sampling strategy is explicitly designed to capture the effect of inter-annual climate variability on ecohydrolgy response of mountain catchments located in King River Experiment Watersheds, Sierra National Forest. The ecohydrolgic model (RHESSys model) is calibrated with existing collected data sets including snow depth, soil moisture, sapflux, evapotranspiration from a flux tower and streamflow. The model is used to generate spatial-temporal patterns of snow accumulation and melt, soil moisture and transpiration and compute inter-annual mean and coefficient of variation of five hydrologic similarity indices. Similarity indices are chosen to reflect seasonal trajectories of snowmelt, root-zone soil moisture storage and evapotranspiration. Clustering analysis, using Partitioning Around Medoid (PAM), is used to partition the watershed based on these similarity indices. For the Kings River Experimental Watersheds, clustering distinguished six clusters and a representative plot per cluster. These results were used to identify additional strategic sampling points within the watershed. For each of these points, we installed soil moisture sensors (5TE) at the two depths (30m and 90m

  20. DMD-based software-configurable spatially-offset Raman spectroscopy for spectral depth-profiling of optically turbid samples.

    Science.gov (United States)

    Liao, Zhiyu; Sinjab, Faris; Gibson, Graham; Padgett, Miles; Notingher, Ioan

    2016-06-13

    Spectral depth-profiling of optically turbid samples is of high interest to a broad range of applications. We present a method for measuring spatially-offset Raman spectroscopy (SORS) over a range of length scales by incorporating a digital micro-mirror device (DMD) into a sample-conjugate plane in the detection optical path. The DMD can be arbitrarily programmed to collect/reject light at spatial positions in the 2D sample-conjugate plane, allowing spatially offset Raman measurements. We demonstrate several detection geometries, including annular and simultaneous multi-offset modalities, for both macro- and micro-SORS measurements, all on the same instrument. Compared to other SORS modalities, DMD-based SORS provides more flexibility with only minimal additional experimental complexity for subsurface Raman collection.

  1. Untargeted metabolomic profiling plasma samples of patients with lung cancer for searching significant metabolites by HPLC-MS method

    Science.gov (United States)

    Dementeva, N.; Ivanova, K.; Kokova, D.; Kurzina, I.; Ponomaryova, A.; Kzhyshkowska, J.

    2017-09-01

    Lung cancer is one of the most common types of cancer leading to death. Consequently, the search and the identification of the metabolites associated with the risk of developing cancer are very valuable. For the purpose, untargeted metabolic profiling of the plasma samples collected from the patients with lung cancer (n = 100) and the control group (n = 100) was conducted. After sample preparation, the plasma samples were analyzed using LC-MS method. Biostatistics methods were applied to pre-process the data for elicitation of dominating metabolites which responded to the difference between the case and the control groups. At least seven significant metabolites were evaluated and annotated. The most part of identified metabolites are connected with lipid metabolism and their combination could be useful for follow-up studies of lung cancer pathogenesis.

  2. Identifying student profiles and their impact on academic performance in a Brazilian undergraduate student sample.

    Science.gov (United States)

    da Silva, E T; de Fátima Nunes, M; Santos, L B; Queiroz, M G; Leles, C R

    2012-02-01

    The recognition of the student profile provides strategic information for planning educational policies in the university environment. The aims of this study were to identify natural segmentation of freshman undergraduate dental students based on demographic, socioeconomic and educational variables, and to subsequently investigate their impact on academic performance of Brazilian undergraduate students. Cluster analysis (two-step algorithm) was used to segment students who entered dental school in the time period from 1999 to 2001 (n=158) into groups based on responses to a questionnaire completed by students at the time of the admission examination. Clustering analysis revealed three natural groups. Age, the parents' level of education, and performance on the first admission test were the most important variables for cluster segmentation. Cluster 1 (n=42; 26.6%) was characterized by female students with higher socioeconomic status and better previous educational indicators. Cluster 2 (n=62; 39.2%) represented disadvantaged socioeconomic profiles, with a predominance of females and older students. Cluster 3 (n=54; 34.2%) showed similar socioeconomic characteristics to cluster 1, except for male prevalence, higher age, and experiencing difficulty in the admission test. Clusters' academic performance was satisfactory in both overall course and course groups (grade point average of at least 7.0), with average ranging from 7.89 (SD=0.44) to 8.13 (SD=0.31) and 7.37 (SD=0.75) to 8.31(SD=0.26), respectively. Our findings provide encouraging evidence for the current context of equality of access to education and reveal the importance of financial support to maximize successful educational experiences of socioeconomically disadvantaged dental students. © 2010 John Wiley & Sons A/S.

  3. VizieR Online Data Catalog: REXCESS sample optical and X-ray profiles (Holland+, 2015)

    Science.gov (United States)

    Holland, J. G.; Bohringer, H.; Chon, G.; Pierini, D.

    2015-09-01

    The REXCESS sample has been compiled as a galaxy cluster sample, representative of clusters detected by their X-ray luminosity and independent of their morphology. The sample selection is described in Bohringer et al. (2007A&A...469..363B). The X-ray observations are described in Bohringer et al. (2007A&A...469..363B). Each cluster was observed using all three detectors (MOS1, MOS2 and PN). We used the Wide Field Imager (WFI) on the Max-Planck-Gesellschaft (MPG)/European Southern Observatory (ESO) 2.2m Telescope at La Silla, which is well suited to XMM-Newton follow-up as it has a similar field of view (34-arcminx33-arcmin). Each set of optical data cover the cluster and a region outside r200 which we use for the background assessment. (3 data files).

  4. IMPACT: a whole-exome sequencing analysis pipeline for integrating molecular profiles with actionable therapeutics in clinical samples.

    Science.gov (United States)

    Hintzsche, Jennifer; Kim, Jihye; Yadav, Vinod; Amato, Carol; Robinson, Steven E; Seelenfreund, Eric; Shellman, Yiqun; Wisell, Joshua; Applegate, Allison; McCarter, Martin; Box, Neil; Tentler, John; De, Subhajyoti; Robinson, William A; Tan, Aik Choon

    2016-07-01

    Currently, there is a disconnect between finding a patient's relevant molecular profile and predicting actionable therapeutics. Here we develop and implement the Integrating Molecular Profiles with Actionable Therapeutics (IMPACT) analysis pipeline, linking variants detected from whole-exome sequencing (WES) to actionable therapeutics. The IMPACT pipeline contains 4 analytical modules: detecting somatic variants, calling copy number alterations, predicting drugs against deleterious variants, and analyzing tumor heterogeneity. We tested the IMPACT pipeline on whole-exome sequencing data in The Cancer Genome Atlas (TCGA) lung adenocarcinoma samples with known EGFR mutations. We also used IMPACT to analyze melanoma patient tumor samples before treatment, after BRAF-inhibitor treatment, and after BRAF- and MEK-inhibitor treatment. IMPACT Food and Drug Administration (FDA) correctly identified known EGFR mutations in the TCGA lung adenocarcinoma samples. IMPACT linked these EGFR mutations to the appropriate FDA-approved EGFR inhibitors. For the melanoma patient samples, we identified NRAS p.Q61K as an acquired resistance mutation to BRAF-inhibitor treatment. We also identified CDKN2A deletion as a novel acquired resistance mutation to BRAFi/MEKi inhibition. The IMPACT analysis pipeline predicts these somatic variants to actionable therapeutics. We observed the clonal dynamic in the tumor samples after various treatments. We showed that IMPACT not only helped in successful prioritization of clinically relevant variants but also linked these variations to possible targeted therapies. IMPACT provides a new bioinformatics strategy to delineate candidate somatic variants and actionable therapies. This approach can be applied to other patient tumor samples to discover effective drug targets for personalized medicine.IMPACT is publicly available at http://tanlab.ucdenver.edu/IMPACT. © The Author 2016. Published by Oxford University Press on behalf of the American Medical

  5. Profiling quinones in ambient air samples collected from the Athabasca region (Canada).

    Science.gov (United States)

    Wnorowski, Andrzej; Charland, Jean-Pierre

    2017-12-01

    This paper presents new findings on polycyclic aromatic hydrocarbon oxidation products-quinones that were collected in ambient air samples in the proximity of oil sands exploration. Quinones were characterized for their diurnal concentration variability, phase partitioning, and molecular size distribution. Gas-phase (GP) and particle-phase (PM) ambient air samples were collected separately in the summer; a lower quinone content was observed in the PM samples from continuous 24-h sampling than from combined 12-h sampling (day and night). The daytime/nocturnal samples demonstrated that nighttime conditions led to lower concentrations and some quinones not being detected. The highest quinone levels were associated with wind directions originating from oil sands exploration sites. The statistical correlation with primary pollutants directly emitted from oil sands industrial activities indicated that the bulk of the detected quinones did not originate directly from primary emission sources and that quinone formation paralleled a reduction in primary source NOx levels. This suggests a secondary chemical transformation of primary pollutants as the origin of the determined quinones. Measurements of 19 quinones included five that have not previously been reported in ambient air or in Standard Reference Material 1649a/1649b and seven that have not been previously measured in ambient air in the underivatized form. This is the first paper to report on quinone characterization in secondary organic aerosols originating from oil sands activities, to distinguish chrysenequinone and anthraquinone positional isomers in ambient air, and to report the requirement of daylight conditions for benzo[a]pyrenequinone and naphthacenequinone to be present in ambient air. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

  6. Space charge profiles in low density polyethylene samples containing a permittivity/conductivity gradient

    DEFF Research Database (Denmark)

    Bambery, K.R.; Fleming, R.J.; Holbøll, Joachim

    2001-01-01

    Laser induced pressure pulse space charge measurements were made on 1.5 mm thick plaques of high purity low density polyethylene equipped with vacuum-evaporated aluminium electrodes. Temperature differences up to 20 °C were maintained across the samples, which were subjected to dc fields up to 1...

  7. RNA sample preparation applied to gene expression profiling for the horse biological passport.

    Science.gov (United States)

    Bailly-Chouriberry, Ludovic; Baudoin, Florent; Cormant, Florence; Glavieux, Yohan; Loup, Benoit; Garcia, Patrice; Popot, Marie-Agnès; Bonnaire, Yves

    2017-09-01

    The improvement of doping control is an ongoing race. Techniques to fight doping are usually based on the direct detection of drugs or their metabolites by analytical methods such as chromatography hyphenated to mass spectrometry after ad hoc sample preparation. Nowadays, omic methods constitute an attractive development and advances have been achieved particularly by application of molecular biology tools for detection of anabolic androgenic steroids (AAS), erythropoiesis-stimulating agent (ESA), or to control human growth hormone misuses. These interesting results across different animal species have suggested that modification of gene expression offers promising new methods of improving the window of detection of banned substances by targeting their effects on blood cell gene expression. In this context, the present study describes the possibility of using a modified version of the dedicated Human IVD (in vitro Diagnostics) PAXgene® Blood RNA Kit for horse gene expression analysis in blood collected on PAXgene® tubes applied to the horse biological passport. The commercial kit was only approved for human blood samples and has required an optimization of specific technical requirements for equine blood samples. Improvements and recommendations were achieved for sample collection, storage and RNA extraction procedure. Following these developments, RNA yield and quality were demonstrated to be suitable for downstream gene expression analysis by qPCR techniques. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

  8. Antibiotic resistance profile of bacteria isolated from raw milk samples of cattle and buffaloes

    Directory of Open Access Journals (Sweden)

    Tahlina Tanzin

    2016-03-01

    Conclusion: Two different species of bacteria i.e., S. aureus and E. coli are contaminating with milk samples. The pathogenic bacteria can be controlled effectively by using Ciprofloxacin and Levofloxacin in the case of mastitis in cattle and buffaloes in Bangladesh. [J Adv Vet Anim Res 2016; 3(1.000: 62-67

  9. A test for comparing two groups of samples when analyzing multiple omics profiles

    NARCIS (Netherlands)

    Chaturvedi, N.; Goeman, J.J.; Boer, J.M.A.; Wieringen, W.N. van; Menezes, R.X. de

    2014-01-01

    BACKGROUND: A number of statistical models has been proposed for studying the association between gene expression and copy number data in integrated analysis. The next step is to compare association patterns between different groups of samples. RESULTS: We propose a method, named dSIM, to find

  10. A test for comparing two groups of samples when analyzing multiple omics profiles

    NARCIS (Netherlands)

    N. Chaturvedi (Nimisha); J.J. Goeman (Jelle); J.M. Boer (Judith); W.N. Wieringen (Wessel); R.X. de Menezes (Renee)

    2014-01-01

    textabstractBackground: A number of statistical models has been proposed for studying the association between gene expression and copy number data in integrated analysis. The next step is to compare association patterns between different groups of samples.Results: We propose a method, named dSIM, to

  11. A test for comparing two groups of samples when analyzing multiple omics profiles

    NARCIS (Netherlands)

    Chaturvedi, N.; Goeman, J.J.; Boer, J.M.; van Wieringen, W.N.; Menezes, R.

    2014-01-01

    Background: A number of statistical models has been proposed for studying the association between gene expression and copy number data in integrated analysis. The next step is to compare association patterns between different groups of samples.Results: We propose a method, named dSIM, to find

  12. Mass-spectra-based peak alignment for automatic nontargeted metabolic profiling analysis for biomarker screening in plant samples.

    Science.gov (United States)

    Fu, Hai-Yan; Hu, Ou; Zhang, Yue-Ming; Zhang, Li; Song, Jing-Jing; Lu, Peang; Zheng, Qing-Xia; Liu, Ping-Ping; Chen, Qian-Si; Wang, Bing; Wang, Xiao-Yu; Han, Lu; Yu, Yong-Jie

    2017-09-01

    Nontargeted metabolic profiling analysis is a difficult task in a routine investigation because hundreds of chromatographic peaks are eluted within a short time, and the time shift problem is severe across samples. To address these problems, the present work developed an automatic nontargeted metabolic profiling analysis (anTMPA) method. First, peaks from the total ion chromatogram were extracted using modified multiscale Gaussian smoothing method. Then, a novel peak alignment strategy was employed based on the mass spectra and retention times of the peaks in which the maximum mass spectral correlation coefficient path was extracted using a modified dynamic programming method. Moreover, an automatic landmark peak-searching strategy was employed for self-adapting time shift modification. Missing peaks across samples were grouped and registered into the aligned peak list table for final refinement. Finally, the aligned peaks across samples were analyzed using statistical methods to identify potential biomarkers. Mass spectral information on the screened biomarkers could be directly imported into the National Institute of Standards and Technology library to select the candidate compounds. The performance of the anTMPA method was evaluated using a complicated plant gas chromatography-mass spectrometry dataset with the aim of identifying biomarkers between the growth and maturation stages of the tested plant. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Microbial Indicator Profiling of Fresh Produce and Environmental Samples from Farms and Packing Facilities in Northern Mexico.

    Science.gov (United States)

    Heredia, Norma; Caballero, Cindy; Cárdenas, Carmen; Molina, Karina; García, Rafael; Solís, Luisa; Burrowes, Vanessa; Bartz, Faith E; de Aceituno, Anna Fabiszewski; Jaykus, Lee-Ann; García, Santos; Leon, Juan

    2016-07-01

    To compare microbiological indicator and pathogen contamination among different types of fresh produce and environmental samples along the production chain, 636 samples of produce (rinsates from cantaloupe melons, jalapeño peppers, and tomatoes) and environmental samples (rinsates from hands of workers, soil, and water) were collected at four successive steps in the production process (from the field before harvest through the packing facility) on 11 farms in northern Mexico during 2011 and 2012. Samples were assayed for enteric pathogens (Escherichia coli O157:H7, other Shiga toxigenic E. coli, Salmonella, and Listeria monocytogenes) and microbial indicators (coliforms, other E. coli strains, and Enterococcus spp.). Salmonella was the only pathogen detected; it was found in one preharvest jalapeño sample (detection limits: 0.0033 CFU/ml in produce and hand samples, 0.0013 CFU/ml in water, and 0.04 CFU/g in soil). Microbial indicator profiles for produce, worker hands, and soil from jalapeño and tomato farms were similar, but cantaloupe farm samples had higher indicator levels (P coliforms, E. coli, and Enterococcus, respectively, and lower E. coli levels in soil (water from tomato farms, E. coli indicators were significantly more prevalent (70 to 89% of samples were positive; P = 0.01 to 0.02), and geometric mean levels were higher (0.3 to 0.6 log CFU/100 ml) than those in cantaloupe farm water (32 to 38% of samples were positive, geometric mean <1 CFU/100 ml). Microbial indicators were present during all production steps, but prevalence and levels were generally highest at the final on-farm production step (the packing facility) (P < 0.03 for significant comparisons). The finding that microbial contamination on produce farms is influenced by produce type and production step can inform the design of effective approaches to mitigate microbial contamination.

  14. Career anchor profiles of a sample of business and professional women

    Directory of Open Access Journals (Sweden)

    Ronel Erwee

    1990-06-01

    Full Text Available The career anchors of a sample of 95 business and professional woman were studied by means of the Career Orientations Inventory (DeLong, 1982. The hierarchy of career anchors of the sample was as follows: Service, Variety, Security (job tenure, Managerial competence. Autonomy, Identity, Technical/functional competence, Entrepreneurship and Security (geographical location. A few significant differences in career anchors did occur between various occupational groups. The implicatons of these findings in terms of career management in organisations are discussed. Opsomming Die loopbaanankers van 'n steekproef van 95 sake- en beroepsvroue is bestudeer deur middel van die "Career Orientations Inventory" (DeLong, 1982. Die steekproef het die volgende hierargie van loopbaanankers getoon: Diens, Verskeidenheid, Sekuriteit (organisatories, Bestuursbevoegdheid, Outonomie, Identiteit, Tegnies/funksionele bevoegdheid, Entrepreneurskap en Sekuriteit (geografies. 'n Paar beduidende verskille in loopbaanankerprofiele het tussen die onderskeie beroepsgroepe voorgekom. Die implikasies van die bevindings ten opsigte van loopbaanbeplanning in ondernemings word bespreek.

  15. Prevalence profile of odontogenic cysts and tumors on Brazilian sample after the reclassification of odontogenic keratocyst.

    Science.gov (United States)

    Jaeger, Filipe; de Noronha, Mariana Saturnino; Silva, Maiza Luiza Vieira; Amaral, Márcio Bruno Figueiredo; Grossmann, Soraya de Mattos Carmago; Horta, Martinho Campolina Rebello; de Souza, Paulo Eduardo Alencar; de Aguiar, Maria Cássia Ferreira; Mesquita, Ricardo Alves

    2017-02-01

    The aim of this study was to evaluate the impact of the reclassification of odontogenic keratocyst (OKC) as a tumor on the prevalence profile of odontogenic cysts (OCs) and odontogenic tumors (OTs). Two referral Oral and Maxillofacial Pathology services in Brazil were evaluated. All cases diagnosed as OCs or OTs were selected and classified according to the 1992 WHO-classification (cases before 2005 WHO classification of tumors excluding OKC) and the 2005 WHO classification of tumors, going forward including cases of odontogenic keratocyst tumor (KCOT). The frequency and prevalence of OCs and OTs were compared before and after the reclassification. Among 27,854 oral biopsies, 4920 (17.66%) were OCs and 992 (3.56%) were OTs. The prevalence of OTs before 2005 WHO classification of tumors was 2.04%, while the prevalence after 2005 WHO classification was 11.51% (p tumor diagnosed was odontoma with 194 cases (39.67%), and after 2005 WHO classification of tumors the KCOT was the most frequent with 207 cases (41.07%). The increase in the prevalence of OTs after 2005 WHO is related to the improvement of pathology services and to the inclusion of KCOT in the OTs group. Copyright © 2016 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.

  16. Sampling Modification Effects in the Subgingival Microbiome Profile of Healthy Children

    OpenAIRE

    Santigli, Elisabeth; Trajanoski, Slave; Eberhard, Katharina; Klug, Barbara

    2017-01-01

    Background: Oral microbiota are considered major players in the development of periodontal diseases. Thorough knowledge of intact subgingival microbiomes is required to elucidate microbial shifts from health to disease. Aims: This comparative study investigated the subgingival microbiome of healthy children, possible inter- and intra-individual effects of modified sampling, and basic comparability of subgingival microprints. Methods: In five 10-year-old children, biofilm was collected from th...

  17. Direct molecular diagnosis of aspergillosis and CYP51A profiling from respiratory samples of French patients

    Directory of Open Access Journals (Sweden)

    Yanan Zhao

    2016-07-01

    Full Text Available Background: Microbiological diagnosis of aspergillosis and triazole resistance is limited by poor culture yield. To better estimate this shortcoming, we compared culture and molecular detection of A. fumigatus in respiratory samples from French patients at risk for aspergillosis. Methods: A total of 97 respiratory samples including bronchoalveolar lavages (BAL, bronchial aspirates (BA, tracheal aspirates, sputa, pleural fluids, and lung biopsy were collected from 33 patients having invasive aspergillosis (n=12, chronic pulmonary aspergillosis (n=3, allergic bronchopulmonary aspergillosis (n=7 or colonization (n=11 and 28 controls. Each specimen was evaluated by culture, pan-Aspergillus qPCR, and CYP51A PCR and sequencing. Results: One A. flavus and 19 A. fumigatus with one multiazole resistant strain (5.3% were cultured from 20 samples. Culture positivity was 62.5%, 75%, 42.9%, and 15.8% in ABPA, CPA, IA and colonized patients, respectively. Aspergillus detection rate was significantly higher by pan-Aspergillus qPCR than by culture in IA (90.5% vs 42.9%; P<0.05 and colonization group (73.7% vs 15.8%; P<0.05. The CYP51A PCR found one TR34/L98H along with 5 novel cyp51A mutations (4 non-synonymous and 1 promoter mutations, yet no association can be established currently between these novel mutations and azole resistance. The analysis of 11 matched pairs of BA and BAL samples found that 9/11 BA carried greater fungal load than BAL and CYP51A detection was more sensitive in BA than in BAL. Conclusion: Direct molecular detection of Aspergillus spp. and azole resistance markers are useful adjunct tools for comprehensive aspergillosis diagnosis. The observed superior diagnostic value of BAs to BAL fluids warrants more in-depth study.

  18. Metabolite profiling on wheat grain to enable a distinction of samples from organic and conventional farming systems.

    Science.gov (United States)

    Bonte, Anja; Neuweger, Heiko; Goesmann, Alexander; Thonar, Cécile; Mäder, Paul; Langenkämper, Georg; Niehaus, Karsten

    2014-10-01

    Identification of biomarkers capable of distinguishing organic and conventional products would be highly welcome to improve the strength of food quality assurance. Metabolite profiling was used for biomarker search in organic and conventional wheat grain (Triticum aestivum L.) of 11 different old and new bread wheat cultivars grown in the DOK system comparison trial. Metabolites were extracted using methanol and analysed by gas chromatography-mass spectrometry. Altogether 48 metabolites and 245 non-identified metabolites (TAGs) were detected in the cultivar Runal. Principal component analysis showed a sample clustering according to farming systems and significant differences in peak areas between the farming systems for 10 Runal metabolites. Results obtained from all 11 cultivars indicated a greater influence of the cultivar than the farming system on metabolite concentrations. Nevertheless, a t-test on data of all cultivars still detected 5 metabolites and 11 TAGs with significant differences between the farming systems. Based on individual cultivars, metabolite profiling showed promising results for the categorization of organic and conventional wheat. Further investigations are necessary with wheat from more growing seasons and locations before definite conclusions can be drawn concerning the feasibility to evolve a combined set of biomarkers for organically grown wheat using metabolite profiles. © 2014 Society of Chemical Industry.

  19. Neuropsychological profile of pre-schoolers with metaphonological difficulties: results from a non-clinical sample.

    Science.gov (United States)

    Termine, C; Stella, G; Capsoni, C; Rosso, E; Binda, A; Pirola, A; Conti, C; Gruppi, E; Lanzi, G; Salini, S; Tognatti, C; Zoppello, M; Balottin, U

    2007-11-01

    The level of language development reached in pre-school age is considered the most reliable predictor of reading acquisition. In normally developing children, learning to read is strongly related to early language skills, and in particular to phonological processing abilities. In dyslexic children, reading abilities seem to show a correlation with phonological awareness. A group of 65 children (aged 5-6 years) were recruited and submitted to an in-depth neuropsychological assessment [i.e. metaphonological skills, intelligence, verbal short-term memory (VSTM) and other aspects of receptive and expressive language]. We were able to identify 14 children with significant metaphonological difficulties (MD): 11 children with exclusively MD, and the other three children with specific language impairment. This study compares the neuropsychological profile obtained from children with MD with that of a peer group without any language impairment (N). The performances of the MD were within the normal ability range in almost all the administered tests but significantly lower compared with those of their peers without language impairment (N) in some items of the intelligence scale (Wechsler Preschool and Primary Scale of Intelligence) and in the tests of VSTM and of receptive/expressive language. Nevertheless, there were not statistically significant differences between MD and N in output phonology. In pre-school age, in a group of non-clinical children, with a range of abilities, those with MD appear to be at the lower end of the normal range in many other verbal skills. These children could be considered at-risk for possible subsequent difficulties learning to read and thus need to be identified and to warrant prompt treatment.

  20. Biases during DNA extraction affect bacterial and archaeal community profile of anaerobic digestion samples.

    Science.gov (United States)

    Roopnarain, Ashira; Mukhuba, Mashudu; Adeleke, Rasheed; Moeletsi, Mokhele

    2017-12-01

    The anaerobic digestion (AD) of organic waste for biogas production has received much attention in recent years due to the increasing need for renewable energy and environmentally friendly waste management systems. Identification of the microbial community involved in AD aids in better understanding and optimising of the process. The choice of DNA extraction method is an integral step in any molecular biodiversity study. In the present study, potential biases introduced by DNA extraction methods were examined by comparing quality, quantity and representability of DNA extracted from AD samples using various extraction methods. In spite of the non-kit based method (cetyltrimethylammonium bromide) yielding the largest quantity of DNA (approximately 44 µg DNA per gram dry weight), the extracted DNA contained PCR inhibitors. Furthermore, the quantity of extracted DNA was not proportional to species diversity. Diversity, determined using denaturing gradient gel electrophoresis (DGGE), was strongly linked to the type of extraction method used. The spin-column filter-based kit that incorporated mechanical and chemical lysis (Macherey-Nagel kit) gave the best results in terms of bacterial and archaeal diversity (Shannon-Wiener indices: average 2.5 and 2.6, respectively). Furthermore, this kit was the most effective at lysing hard-to-lyse bacterial and archaeal cells. The choice of DNA extraction method significantly influences the reliability and comparability of results obtained during AD microbial ecology investigations. Moreover, the careful selection of the DNA extraction method is of particular importance when analysing AD samples since these samples are rich in PCR inhibitors and hard-to-lyse cells such as archaea and gram-positive bacteria.

  1. MPLEx: a method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling

    Energy Technology Data Exchange (ETDEWEB)

    Burnum-Johnson, Kristin E.; Kyle, Jennifer E.; Eisfeld, Amie J.; Casey, Cameron P.; Stratton, Kelly G.; Gonzalez, Juan F.; Habyarimana, Fabien; Negretti, Nicholas M.; Sims, Amy C.; Chauhan, Sadhana; Thackray, Larissa B.; Halfmann, Peter J.; Walters, Kevin B.; Kim, Young-Mo; Zink, Erika M.; Nicora, Carrie D.; Weitz, Karl K.; Webb-Robertson, Bobbie-Jo M.; Nakayasu, Ernesto S.; Ahmer, Brian; Konkel, Michael E.; Motin, Vladimir; Baric, Ralph S.; Diamond, Michael S.; Kawaoka, Yoshihiro; Waters, Katrina M.; Smith, Richard D.; Metz, Thomas O.

    2017-01-01

    The continued emergence and spread of infectious agents is of increasing concern due to increased population growth and the associated increased livestock production to meet food demands, increased urbanization and land-use changes, and greater travel. A systems biology approach to infectious disease research can significantly advance our understanding of host-pathogen relationships and facilitate the development of new therapies and vaccines. Molecular characterization of infectious samples outside of appropriate biosafety containment can only take place subsequent to pathogen inactivation. Herein, we describe a modified Folch extraction using chloroform/methanol that facilitates the molecular characterization of infectious samples by enabling simultaneous pathogen inactivation and extraction of proteins, metabolites, and lipids for subsequent mass spectrometry-based multi-omics measurements. This metabolite, protein and lipid extraction (MPLEx) method resulted in complete inactivation of bacterial and viral pathogens with exposed lipid membranes, including Yersinia pestis, Salmonella Typhimurium, and Campylobacter jejuni in pure culture, and Yersinia pestis, Campylobacter jejuni, West Nile, MERS-CoV, Ebola, and influenza H7N9 viruses in infection studies. Partial inactivation was observed for pathogens without exposed lipid membranes including 99.99% inactivation of community-associated methicillin-resistant Staphylococcus aureus, 99.6% and >99% inactivation of Clostridium difficile spores and vegetative cells, respectively, and 50% inactivation of adenovirus type 5. To demonstrate that MPLEx yields biomaterial of sufficient quality for subsequent multi-omics analyses, we highlight select proteomics, metabolomics and lipidomics data from human epithelial lung cells infected with wild-type and mutant forms of influenza H7N9. We believe that MPLEx will facilitate systems biology studies of infectious samples by enabling simultaneous pathogen inactivation and multi

  2. Comparison of Dilution, Filtration, and Microwave Digestion Sample Pretreatments in Elemental Profiling of Wine by ICP-MS

    Directory of Open Access Journals (Sweden)

    Joshua Godshaw

    2017-09-01

    Full Text Available Wine elemental composition varies by cultivar, geographic origin, viticultural and enological practices, and is often used for authenticity validation. Elemental analysis of wine by Inductively Coupled Plasma Mass Spectrometry (ICP-MS is challenging due to the potential for non-spectral interferences and plasma instability arising from organic matrix components. Sample preparation mitigates these interferences, however, conflicting recommendations of best practices in ICP-MS analysis of wine have been reported. This study compared direct dilution, microwave-assisted acid digestion, and two filtration sample pretreatments, acidification prior to filtration and filtration followed by acidification, in elemental profiling of one white and three red table wines by ICP-MS. Of 43 monitored isotopes, 37 varied by sample preparation method, with significantly higher results of 17 isotopes in the microwave-digested samples. Both filtration treatments resulted in lower results for 11 isotopes compared to the other methods. Finally, isotope dilution determination of copper based on natural abundances and the 63Cu:65Cu instrument response ratio agreed with external calibration and confirmed a significant sample preparation effect. Overall, microwave digestion did not compare favorably, and direct dilution was found to provide the best compromise between ease of use and result accuracy and precision, although all preparation strategies were able to differentiate the wines.

  3. Chemical characterization of a commercial Commiphora wightii resin sample and chemical profiling to assess for authenticity.

    Science.gov (United States)

    Ahmed, Rida; Ali, Zulfiqar; Wu, Yunshan; Kulkarni, Swapnil; Avery, Mitchell A; Choudhary, Muhammed Iqbal; Khan, Ikhlas A

    2011-06-01

    The gum resin of Commiphora wightii [(Hook. ex Stocks) Engl.] is an ayurvedic medicine for the treatment of arthritis, inflammation, obesity, lipid disorders, and cardiovascular diseases and is known as guggul. Morphologically, it is not easy to distinguish guggul from closely related gum resins of other plants. Reliability of the commercially available guggul is critical due to the high risk of adulteration. To check authenticity, a commercial guggul sample was investigated for its chemical markers and 17 metabolites were identified, including three new, 20(S),21-epoxy-3-oxocholest-4-ene (1), 8 β-hydroxy-3,20-dioxopregn-4,6-diene (2), and 5-(13' Z-nonadecenyl)resorcinol (17) from the ethyl acetate soluble part. During the current study, compounds 14- 17 were identified as constituents of Mangifera indica gum, as an adulterant in the commercial guggul sample. This discovery highlighted the common malpractices in the trade of medicinal raw material in the developing world. The structures of the compounds were deduced by the spectroscopic technique and chemical methods, as well as by comparison with the reported data. The structure of 20(S),21-epoxy-3-oxocholest-4-ene (1) was also unambiguously deduced by single-crystal X-ray diffraction technique. © Georg Thieme Verlag KG Stuttgart · New York.

  4. Depth profile of 236U/238U in soil samples in La Palma, Canary Islands

    Science.gov (United States)

    Srncik, M.; Steier, P.; Wallner, G.

    2011-01-01

    The vertical distribution of the 236U/238U isotopic ratio was investigated in soil samples from three different locations on La Palma (one of the seven Canary Islands, Spain). Additionally the 240Pu/239Pu atomic ratio, as it is a well establish tool for the source identification, was determined. The radiochemical procedure consisted of a U separation step by extraction chromatography using UTEVA® Resin (Eichrom Technologies, Inc.). Afterwards Pu was separated from Th and Np by anion exchange using Dowex 1x2 (Dow Chemical Co.). Furthermore a new chemical procedure with tandem columns to separate Pu and U from the matrix was tested. For the determination of the uranium and plutonium isotopes by alpha spectrometry thin sources were prepared by microprecipitation techniques. Additionally these fractions separated from the soil samples were measured by Accelerator Mass Spectrometry (AMS) to get information on the isotopic ratios 236U/238U, 240Pu/239Pu and 236U/239Pu, respectively. The 236U concentrations [atoms/g] in each surface layer (∼2 cm) were surprisingly high compared to deeper layers where values around two orders of magnitude smaller were found. Since the isotopic ratio 240Pu/239Pu indicated a global fallout signature we assume the same origin as the probable source for 236U. Our measured 236U/239Pu value of around 0.2 is within the expected range for this contamination source. PMID:21481502

  5. RNA Profiling for Biomarker Discovery: Practical Considerations for Limiting Sample Sizes

    Directory of Open Access Journals (Sweden)

    Danny J. Kelly

    2005-01-01

    Full Text Available We have compared microarray data generated on Affymetrix™ chips from standard (8 micrograms or low (100 nanograms amounts of total RNA. We evaluated the gene signals and gene fold-change estimates obtained from the two methods and validated a subset of the results by real time, polymerase chain reaction assays. The correlation of low RNA derived gene signals to gene signals obtained from standard RNA was poor for less to moderately abundant genes. Genes with high abundance showed better correlation in signals between the two methods. The signal correlation between the low RNA and standard RNA methods was improved by including a reference sample in the microarray analysis. In contrast, the fold-change estimates for genes were better correlated between the two methods regardless of the magnitude of gene signals. A reference sample based method is suggested for studies that would end up comparing gene signal data from a combination of low and standard RNA templates; no such referencing appears to be necessary when comparing fold-changes of gene expression between standard and low template reactions.

  6. Genealogy profiling through strain improvement by using metabolic network analysis: metabolic flux genealogy of several generations of lysine-producing corynebacteria.

    Science.gov (United States)

    Wittmann, Christoph; Heinzle, Elmar

    2002-12-01

    A comprehensive approach of metabolite balancing, (13)C tracer studies, gas chromatography-mass spectrometry, matrix-assisted laser desorption ionization-time of flight mass spectrometry, and isotopomer modeling was applied for comparative metabolic network analysis of a genealogy of five successive generations of lysine-producing Corynebacterium glutamicum. The five strains examined (C. glutamicum ATCC 13032, 13287, 21253, 21526, and 21543) were previously obtained by random mutagenesis and selection. Throughout the genealogy, the lysine yield in batch cultures increased markedly from 1.2 to 24.9% relative to the glucose uptake flux. Strain optimization was accompanied by significant changes in intracellular flux distributions. The relative pentose phosphate pathway (PPP) flux successively increased, clearly corresponding to the product yield. Moreover, the anaplerotic net flux increased almost twofold as a consequence of concerted regulation of C(3) carboxylation and C(4) decarboxylation fluxes to cover the increased demand for lysine formation; thus, the overall increase was a consequence of concerted regulation of C(3) carboxylation and C(4) decarboxylation fluxes. The relative flux through isocitrate dehydrogenase dropped from 82.7% in the wild type to 59.9% in the lysine-producing mutants. In contrast to the NADPH demand, which increased from 109 to 172% due to the increasing lysine yield, the overall NADPH supply remained constant between 185 and 196%, resulting in a decrease in the apparent NADPH excess through strain optimization. Extrapolated to industrial lysine producers, the NADPH supply might become a limiting factor. The relative contributions of PPP and the tricarboxylic acid cycle to NADPH generation changed markedly, indicating that C. glutamicum is able to maintain a constant supply of NADPH under completely different flux conditions. Statistical analysis by a Monte Carlo approach revealed high precision for the estimated fluxes, underlining the

  7. Metabolomics profiling of pre-and post-anesthesia plasma samples of colorectal patients obtained via Ficoll separation.

    Science.gov (United States)

    Ghini, Veronica; Unger, Florian T; Tenori, Leonardo; Turano, Paola; Juhl, Hartmut; David, Kerstin A

    2015-01-01

    (1)H NMR spectroscopy was used to investigate the metabolic consequences of general anesthesia in the plasma of two groups of patients with diagnosis for non-metastatic colorectal cancer and metastatic colorectal cancer with liver-metastasis, respectively. Patients were treated with etomidate or propofol, two frequently used sedation agents. Plasma samples were obtained via Ficoll separation. Here, we demonstrated that this procedure introduces a number of limitations for NMR-based metabolomics studies, due to the appearance of spurious signals. Nevertheless, the comparison of the (1)H NMR metabolomic profiles of patients treated with etomidate or propofol at equipotent dose ranges was still feasible and proved that both agents significantly decrease the plasma levels of several NMR-detectable metabolites. Consequently, samples collected during anesthesia are not suitable for metabolic profiling studies aimed at patient stratification, because interpersonal variability are reduced by the overall depression of metabolites levels. On the other hand, this study showed that plasma metabolomics could represent a valuable tool to monitor the effect of different sedation agents and/or the individual metabolic response to anesthesia, providing hints for an appropriate tuning of personalized sedation procedures. In our reference groups, the metabolomic signatures were slightly different in patients anesthetized with etomidate versus propofol. The importance of standardized collection procedures and availability of exhaustive metadata of the experimental design for the accurate evaluation of the significance of the observed changes in metabolites levels are critically discussed.

  8. Sensory profiles of bread made from paired samples of organic and conventionally grown wheat grain.

    Science.gov (United States)

    Annett, L E; Spaner, D; Wismer, W V

    2007-05-01

    The Canadian hard red spring wheat cultivar "Park" was grown in 2005 in Edmonton, AB, Canada on both conventionally and organically managed land, situated less than 1 km apart. Grains from the paired wheat samples were compared for cereal-grain-quality attributes. For sensory analysis, organically and conventionally produced wheat grains were milled into flour and baked into 60% whole wheat bread. Color, texture, taste, and aroma attributes of bread were compared using the sensory technique of descriptive analysis. Organic grain contained more wholemeal protein than conventional grain (P grain quality for yeast-leavened bread. Mixograph analysis revealed that conventional flour produced stronger bread dough than organic flour (P 0.05), but the panel perceived the organic bread to be more "dense" in texture (P < or = 0.05) with smaller air cells in the appearance of the crumb (P < or = 0.05) than conventional bread.

  9. Relationship between clinical parameters and cytokine profiles in inflamed gingival tissue and serum samples from patients with chronic periodontitis.

    Science.gov (United States)

    Górska, Renata; Gregorek, Hanna; Kowalski, Jan; Laskus-Perendyk, Agnieszka; Syczewska, Małgorzata; Madaliński, Kazimierz

    2003-12-01

    The purpose of the present study was to assess the relation between clinical parameters and concentrations of the key (IL-1beta, TNF-alpha, IL-2, IFN-gamma, IL-4, IL-10) cytokines, important in the initiation and progression of periodontal diseases, within inflamed gingival tissues and serum samples from patients with severe chronic periodontitis. Twenty-five patients with severe chronic periodontitis, who had sites with probing depths (PD) > 5 mm, and 25 periodontally healthy persons were included in the study. Clinical examinations including PD, clinical attachment loss, plaque index, and bleeding index were performed before periodontal treatment. Gingival tissue biopsies were collected from one active site of each patient and from healthy individuals, and blood samples were withdrawn on the day of tissue biopsy. The concentrations of cytokines were determined by an enzyme-linked immunosorbent assay, and the relationship between their profiles in situ and in circulation with clinical parameters was analysed. The concentrations of IL-1beta, TNF-alpha, IL-2, IFN-gamma were, on average, significantly higher in serum samples and gingival tissue biopsies from periodontitis patients than in healthy controls. However, serum samples from both groups showed high individual variability of cytokine profiles, and no association between cytokine concentrations and clinical parameters of periodontitis was found. On the contrary, the levels of IL-4 and IL-10 in both kinds of samples obtained from patients and controls were generally low or even undetectable, and remained, on average, on the same level. However, the frequency of IL-4 (88% positive samples) and IL-10 (72%) was much higher in healthy gingival tissues. High concentrations of TNF-alpha, IFN-gamma and IL-2 and, especially, a high ratio of IL-1beta/IL-10 and TNF-alpha/IL-4 found in tissue biopsies from periodontitis patients, strongly correlated with the severity of periodontitis. These results indicate that high

  10. Corrigendum to “Relative humidity effects on water vapour fluxes measured with closed-path eddy-covariance systems with short sampling lines” [Agric. Forest Meteorol. 165 (2012) 53–63

    DEFF Research Database (Denmark)

    Fratini, Gerardo; Ibrom, Andreas; Arriga, Nicola

    2012-01-01

    It has been formerly recognised that increasing relative humidity in the sampling line of closed-path eddy-covariance systems leads to increasing attenuation of water vapour turbulent fluctuations, resulting in strong latent heat flux losses. This occurrence has been analyzed for very long (50 m)...

  11. ) Mold Fluxes

    Science.gov (United States)

    Seo, Myung-Duk; Shi, Cheng-Bin; Cho, Jung-Wook; Kim, Seon-Hyo

    2014-10-01

    The effects of basicity (CaO/SiO2), B2O3, and Li2O addition on the crystallization behaviors of lime-silica-based mold fluxes have been investigated by non-isothermal differential scanning calorimetry (DSC), field emission scanning electron microscopy, X-ray diffraction (XRD), and single hot thermocouple technique. It was found that the crystallization temperature of cuspidine increased with increasing the basicity of mold fluxes. The crystallization of wollastonite was suppressed with increasing the mold flux basicity due to the enhancement of cuspidine crystallization. The addition of B2O3 suppresses the crystallization of mold flux. The crystallization temperature of mold flux decreases with Li2O addition. The size of cuspidine increases, while the number of cuspidine decreases with increasing mold flux basicity. The morphology of cuspidine in mold fluxes with lower basicity is largely dendritic. The dendritic cuspidine in mold fluxes is composed of many fine cuspidine crystals. On the contrary, in mold fluxes with higher basicity, the cuspidine crystals are larger in size with mainly faceted morphology. The crystalline phase evolution was also calculated using a thermodynamic database, and compared with the experimental results determined by DSC and XRD. The results of thermodynamic calculation of crystalline phase formation are in accordance with the results determined by DSC and XRD.

  12. Mycotoxin profiling of 1000 beer samples with a special focus on craft beer

    Science.gov (United States)

    van Dam, Ruud; van Doorn, Ronald; Katerere, David; Berthiller, Franz; Haasnoot, Willem; Nielen, Michel W. F.

    2017-01-01

    Currently beer is booming, mainly due to the steady rise of craft breweries worldwide. Previous surveys for occurrence of mycotoxins in beer, were mainly focussed on industrial produced beer. The present survey reports the presence of mycotoxins in craft beer and how this compares to industrial produced beer. More than 1000 beers were collected from 47 countries, of which 60% were craft beers. A selection of 1000 samples were screened for the presence of aflatoxin B1, ochratoxin A (OTA), zearalenone (ZEN), fumonisins (FBs), T-2 and HT-2 toxins (T-2 and HT-2) and deoxynivalenol (DON) using a mycotoxin 6-plex immunoassay. For confirmatory analysis, a liquid chromatography tandem mass spectrometry (LC-MS/MS) method was developed and applied. The 6-plex screening showed discrepancies with the LC-MS/MS analysis, possibly due to matrix interference and/or the presence of unknown mycotoxin metabolites. The major mycotoxins detected were DON and its plant metabolite deoxynivalenol-3-β-D-glucopyranoside (D3G). The 6-plex immunoassay reported the sum of DON and D3G (DON+D3G) contaminations ranging from 10 to 475 μg/L in 406 beers, of which 73% were craft beers. The popular craft beer style imperial stout, had the highest percentage of samples suspected positive (83%) with 29% of all imperial stout beers having DON+D3G contaminations above 100 μg/L. LC-MS/MS analysis showed that industrial pale lagers from Italy and Spain, predominantly contained FBs (3–69 μg/L). Besides FBs, African traditional beers also contained aflatoxins (0.1–1.2 μg/L). The presence of OTA, T-2, HT-2, ZEN, β-zearalenol, 3/15-acetyl-DON, nivalenol and the conjugated mycotoxin zearalenone 14-sulfate were confirmed in some beers. This study shows that in 27 craft beers, DON+D3G concentrations occurred above (or at) the Tolerable Daily Intake (TDI). Exceeding the TDI, may have a health impact. A better control of brewing malts for craft beer, should be put in place to circumvent this potential

  13. Mycotoxin profiling of 1000 beer samples with a special focus on craft beer.

    Directory of Open Access Journals (Sweden)

    Jeroen Peters

    Full Text Available Currently beer is booming, mainly due to the steady rise of craft breweries worldwide. Previous surveys for occurrence of mycotoxins in beer, were mainly focussed on industrial produced beer. The present survey reports the presence of mycotoxins in craft beer and how this compares to industrial produced beer. More than 1000 beers were collected from 47 countries, of which 60% were craft beers. A selection of 1000 samples were screened for the presence of aflatoxin B1, ochratoxin A (OTA, zearalenone (ZEN, fumonisins (FBs, T-2 and HT-2 toxins (T-2 and HT-2 and deoxynivalenol (DON using a mycotoxin 6-plex immunoassay. For confirmatory analysis, a liquid chromatography tandem mass spectrometry (LC-MS/MS method was developed and applied. The 6-plex screening showed discrepancies with the LC-MS/MS analysis, possibly due to matrix interference and/or the presence of unknown mycotoxin metabolites. The major mycotoxins detected were DON and its plant metabolite deoxynivalenol-3-β-D-glucopyranoside (D3G. The 6-plex immunoassay reported the sum of DON and D3G (DON+D3G contaminations ranging from 10 to 475 μg/L in 406 beers, of which 73% were craft beers. The popular craft beer style imperial stout, had the highest percentage of samples suspected positive (83% with 29% of all imperial stout beers having DON+D3G contaminations above 100 μg/L. LC-MS/MS analysis showed that industrial pale lagers from Italy and Spain, predominantly contained FBs (3-69 μg/L. Besides FBs, African traditional beers also contained aflatoxins (0.1-1.2 μg/L. The presence of OTA, T-2, HT-2, ZEN, β-zearalenol, 3/15-acetyl-DON, nivalenol and the conjugated mycotoxin zearalenone 14-sulfate were confirmed in some beers. This study shows that in 27 craft beers, DON+D3G concentrations occurred above (or at the Tolerable Daily Intake (TDI. Exceeding the TDI, may have a health impact. A better control of brewing malts for craft beer, should be put in place to circumvent this potential

  14. Mycotoxin profiling of 1000 beer samples with a special focus on craft beer.

    Science.gov (United States)

    Peters, Jeroen; van Dam, Ruud; van Doorn, Ronald; Katerere, David; Berthiller, Franz; Haasnoot, Willem; Nielen, Michel W F

    2017-01-01

    Currently beer is booming, mainly due to the steady rise of craft breweries worldwide. Previous surveys for occurrence of mycotoxins in beer, were mainly focussed on industrial produced beer. The present survey reports the presence of mycotoxins in craft beer and how this compares to industrial produced beer. More than 1000 beers were collected from 47 countries, of which 60% were craft beers. A selection of 1000 samples were screened for the presence of aflatoxin B1, ochratoxin A (OTA), zearalenone (ZEN), fumonisins (FBs), T-2 and HT-2 toxins (T-2 and HT-2) and deoxynivalenol (DON) using a mycotoxin 6-plex immunoassay. For confirmatory analysis, a liquid chromatography tandem mass spectrometry (LC-MS/MS) method was developed and applied. The 6-plex screening showed discrepancies with the LC-MS/MS analysis, possibly due to matrix interference and/or the presence of unknown mycotoxin metabolites. The major mycotoxins detected were DON and its plant metabolite deoxynivalenol-3-β-D-glucopyranoside (D3G). The 6-plex immunoassay reported the sum of DON and D3G (DON+D3G) contaminations ranging from 10 to 475 μg/L in 406 beers, of which 73% were craft beers. The popular craft beer style imperial stout, had the highest percentage of samples suspected positive (83%) with 29% of all imperial stout beers having DON+D3G contaminations above 100 μg/L. LC-MS/MS analysis showed that industrial pale lagers from Italy and Spain, predominantly contained FBs (3-69 μg/L). Besides FBs, African traditional beers also contained aflatoxins (0.1-1.2 μg/L). The presence of OTA, T-2, HT-2, ZEN, β-zearalenol, 3/15-acetyl-DON, nivalenol and the conjugated mycotoxin zearalenone 14-sulfate were confirmed in some beers. This study shows that in 27 craft beers, DON+D3G concentrations occurred above (or at) the Tolerable Daily Intake (TDI). Exceeding the TDI, may have a health impact. A better control of brewing malts for craft beer, should be put in place to circumvent this potential problem.

  15. Metabolic Profiling and Classification of Propolis Samples from Southern Brazil: An NMR-Based Platform Coupled with Machine Learning.

    Science.gov (United States)

    Maraschin, Marcelo; Somensi-Zeggio, Amélia; Oliveira, Simone K; Kuhnen, Shirley; Tomazzoli, Maíra M; Raguzzoni, Josiane C; Zeri, Ana C M; Carreira, Rafael; Correia, Sara; Costa, Christopher; Rocha, Miguel

    2016-01-22

    The chemical composition of propolis is affected by environmental factors and harvest season, making it difficult to standardize its extracts for medicinal usage. By detecting a typical chemical profile associated with propolis from a specific production region or season, certain types of propolis may be used to obtain a specific pharmacological activity. In this study, propolis from three agroecological regions (plain, plateau, and highlands) from southern Brazil, collected over the four seasons of 2010, were investigated through a novel NMR-based metabolomics data analysis workflow. Chemometrics and machine learning algorithms (PLS-DA and RF), including methods to estimate variable importance in classification, were used in this study. The machine learning and feature selection methods permitted construction of models for propolis sample classification with high accuracy (>75%, reaching ∼90% in the best case), better discriminating samples regarding their collection seasons comparatively to the harvest regions. PLS-DA and RF allowed the identification of biomarkers for sample discrimination, expanding the set of discriminating features and adding relevant information for the identification of the class-determining metabolites. The NMR-based metabolomics analytical platform, coupled to bioinformatic tools, allowed characterization and classification of Brazilian propolis samples regarding the metabolite signature of important compounds, i.e., chemical fingerprint, harvest seasons, and production regions.

  16. Gene expression profiling of human breast tissue samples using SAGE-Seq.

    Science.gov (United States)

    Wu, Zhenhua Jeremy; Meyer, Clifford A; Choudhury, Sibgat; Shipitsin, Michail; Maruyama, Reo; Bessarabova, Marina; Nikolskaya, Tatiana; Sukumar, Saraswati; Schwartzman, Armin; Liu, Jun S; Polyak, Kornelia; Liu, X Shirley

    2010-12-01

    We present a powerful application of ultra high-throughput sequencing, SAGE-Seq, for the accurate quantification of normal and neoplastic mammary epithelial cell transcriptomes. We develop data analysis pipelines that allow the mapping of sense and antisense strands of mitochondrial and RefSeq genes, the normalization between libraries, and the identification of differentially expressed genes. We find that the diversity of cancer transcriptomes is significantly higher than that of normal cells. Our analysis indicates that transcript discovery plateaus at 10 million reads/sample, and suggests a minimum desired sequencing depth around five million reads. Comparison of SAGE-Seq and traditional SAGE on normal and cancerous breast tissues reveals higher sensitivity of SAGE-Seq to detect less-abundant genes, including those encoding for known breast cancer-related transcription factors and G protein-coupled receptors (GPCRs). SAGE-Seq is able to identify genes and pathways abnormally activated in breast cancer that traditional SAGE failed to call. SAGE-Seq is a powerful method for the identification of biomarkers and therapeutic targets in human disease.

  17. Fast filtration sampling protocol for mammalian suspension cells tailored for phosphometabolome profiling by capillary ion chromatography - tandem mass spectrometry.

    Science.gov (United States)

    Kvitvang, Hans F N; Bruheim, Per

    2015-08-15

    Capillary ion chromatography (capIC) is the premium separation technology for low molecular phosphometabolites and nucleotides in biological extracts. Removal of excessive amounts of salt during sample preparation stages is a prerequisite to enable high quality capIC separation in combination with reproducible and sensitive MS detection. Existing sampling protocols for mammalian cells used for GC-MS and LC-MS metabolic profiling can therefore not be directly applied to capIC separations. Here, the development of a fast filtration sampling protocol for mammalian suspension cells tailored for quantitative profiling of the phosphometabolome on capIC-MS/MS is presented. The whole procedure from sampling the culture to transfer of filter to quenching and extraction solution takes less than 10s. To prevent leakage it is critical that a low vacuum pressure is applied, and satisfactorily reproducibility was only obtained by usage of a vacuum pressure controlling device. A vacuum of 60mbar was optimal for filtration of multiple myeloma Jjn-3 cell cultures through 5μm polyvinylidene (PVDF) filters. A quick deionized water (DI-water) rinse step prior to extraction was tested, and significantly higher metabolite yields were obtained during capIC-MS/MS analyses in this extract compared to extracts prepared by saline and reduced saline (25%) washing steps only. In addition, chromatographic performance was dramatically improved. Thus, it was verified that a quick DI-water rinse is tolerated by the cells and can be included as the final stage during filtration. Over 30 metabolites were quantitated in JJN-3 cell extracts by using the optimized sampling protocol with subsequent capIC-MS/MS analysis, and up to 2 million cells can be used in a single filtration step for the chosen filter and vacuum pressure. The technical set-up is also highly advantageous for microbial metabolome filtration protocols after optimization of vacuum pressure and washing solutions, and the reduced salt

  18. Measuring the oxygen profile and permeation flux across an ion transport KAUST Repository

    Hunt, Anton

    2014-10-01

    A novel ion transport membrane laboratory reactor is introduced which can sample gases at the La0.9Ca0.1FeO3 -δ membrane surface at high temperature flux conditions. Experimental data (spatial profiles and operating condition sensitivity) is presented and used to validate detailed 1D and 2D numerical models under inert (CO2 sweep) operating conditions; the numerical models account for mass transfer resistances to the membrane surface. Bypassing the mass transfer resistances experimentally allows for direct parameterization of a three resistance oxygen flux model; a unique solution method based on bespoke experimental datasets to find surface exchange reaction rate constants is demonstrated. Membrane operating regimes and oxygen off-stoichiometric coefficients can thus be determined highlighting the importance of surface exchange studies and the obvious requirement to reduce sweep surface P O2 through oxyfuel reaction integration and/or flow field adjustments. A more complex first-order flux model is also proposed and tested incorporating the surface oxygen ion concentrations in the surface exchange reactions; this is found to give similar material parameters to the simpler zero-order model studied in the literature for this particular case. © 2014 Elsevier B.V.

  19. Quantitative large scale gene expression profiling from human stem cell culture micro samples using multiplex pre-amplification.

    Science.gov (United States)

    Kibschull, Mark; Lye, Stephen J; Okino, Steven T; Sarras, Haya

    2016-01-01

    Transcriptional profiling is a powerful tool to study biological mechanisms during stem cell differentiation and reprogramming. Genome-wide methods like microarrays or next generation sequencing are expensive, time consuming, and require special equipment and bioinformatics expertise. Quantitative RT-PCR remains one of today's most widely accepted and used methods for analyzing gene expression in biological samples. However, limitations in the amount of starting materials often hinder the quantity and quality of information that could be obtained from a given sample. Here, we present a fast 4-step workflow allowing direct, column-free RNA isolation from limited human pluripotent stem cell (hPSC) cultures that is directly compatible with subsequent reverse transcription, target specific multiplex pre-amplification, and standard SYBR-Green quantitative PCR (qPCR) analysis. The workflow delivers excellent correlations in normalized gene-expression data obtained from different samples of hPSCs over a wide range of cell numbers (500-50,000 cells). We demonstrate accurate and unbiased target gene quantification in limiting stem cell cultures which allows for monitoring embryoid body differentiation and induced pluripotent stem cell (iPSC) reprogramming. This method highlights a rapid and cost effective screening process, allowing reduction of culture formats and increase of processing throughputs for various stem cell applications.

  20. A descriptive social and health profile of a community sample of adults and adolescents with Asperger syndrome.

    Science.gov (United States)

    Balfe, Myles; Tantam, Digby

    2010-11-12

    Little is known about the health and social profile of adolescents and adults with Asperger syndrome (AS) living in the community. We conducted a study to describe the living, employment and psycho-social situation of a community sample of forty two adults and adolescents with AS, and to describe these indivdiuals' experiences of accessing health services and taking medication. Most respondents (including those over eighteen years of age) lived at home with their parents. Most had trouble reading and responding to other people's feelings, and coping with unexpected changes. Difficulties with life skills, such as cleaning, washing and hygiene were prevalent. The majority of respondents were socially isolated and a large minority had been sexually or financially exploited. Almost all respondents had been bullied. Mental health problems such as anxiety or depression were common. 30% of respondents said that they regularly became violent and hit other people and 15% had attempted suicide. More positively, the majority of respondents felt that they could access health services if they had a health problem. The results of this study suggest a relatively poor social and health profile for many people with Asperger syndrome living in the community, with high levels of social problems and social exclusion, and difficulties managing day to day tasks such as washing and cleaning; these findings support the results of other studies that have examined psycho-social functioning in this group.

  1. A comparison of the Sensory Profile scores of children with autism and an age- and gender-matched sample.

    Science.gov (United States)

    Brockevelt, Barbara L; Nissen, Ranelle; Schweinle, William E; Kurtz, Eric; Larson, Kyle J

    2013-11-01

    The Centers for Disease Control and Prevention (CDC) reports that autism spectrum disorder (ASD) affects one in 88 children in the United States. The American Psychiatric Association's Diagnostic and Statistical Manual, Text Revision (DSM-IV-TR) defines ASD as a pervasive neurodevelopmental disorder characterized by qualitative impairment in communication and social interaction, and restricted, repetitive and stereotyped behavior patterns. The purpose of this study was to determine whether children with autism differ in their response to sensory input relative to typically developing age- and gender-matched peers. The Sensory Profile (SP) is a 125-item caregiver questionnaire designed to measure a child's ability to process sensory information and to profile the effect of sensory processing on daily life activity. The results of the SP of 21 participants with autism ages 3 to 9 years were compared with an age- and gender-matched sample of typically developing children. Significant differences were found across all four SP quadrants (Registration, Seeking, Sensitivity, and Avoiding) as well as eight of the nine SP factor scores. This study adds to the evidence indicating that children with autism process and respond to sensory input differently than typically-developing peers. The findings from this study support previous research findings that sensory processing differences exist between children with ASD and their typically-developing peers, as measured by the SP.

  2. A descriptive social and health profile of a community sample of adults and adolescents with Asperger syndrome

    Directory of Open Access Journals (Sweden)

    Tantam Digby

    2010-11-01

    Full Text Available Abstract Background Little is known about the health and social profile of adolescents and adults with Asperger syndrome (AS living in the community. We conducted a study to describe the living, employment and psycho-social situation of a community sample of forty two adults and adolescents with AS, and to describe these indivdiuals' experiences of accessing health services and taking medication. Findings Most respondents (including those over eighteen years of age lived at home with their parents. Most had trouble reading and responding to other people's feelings, and coping with unexpected changes. Difficulties with life skills, such as cleaning, washing and hygiene were prevalent. The majority of respondents were socially isolated and a large minority had been sexually or financially exploited. Almost all respondents had been bullied. Mental health problems such as anxiety or depression were common. 30% of respondents said that they regularly became violent and hit other people and 15% had attempted suicide. More positively, the majority of respondents felt that they could access health services if they had a health problem. Conclusions The results of this study suggest a relatively poor social and health profile for many people with Asperger syndrome living in the community, with high levels of social problems and social exclusion, and difficulties managing day to day tasks such as washing and cleaning; these findings support the results of other studies that have examined psycho-social functioning in this group.

  3. The reliability and factorial validity of the career decision profile for a sample of afrikaans-speaking students

    Directory of Open Access Journals (Sweden)

    G. P. De Bruin

    1997-06-01

    Full Text Available The purpose of this study was to examine the utility of the Career Decision Profile (CDP; Jones, 1989 for a sample of 133 Afrikaans-speaking students. The scores obtained on all six subscales showed acceptable reliability. The factor structure proposed by Jones for the Career Decision Needs dimension of the CDP was confirmed by means of a confirmatory factor analysis. In conclusion it appears that the CDP may be profitably used for the multidimensional assessment of career indecision with Afrikaans-speaking students. Opsomming Die doel van hierdie studie was om die bruikbaarheid van die Career Decision Profile (CDP; Jones, 1989 vir 'n steekproef van 133 Afrikaanssprekende studente te ondersoek. Al ses subskale het tellings met bevredigende betroubaarheidskoeffisiente opgelewer. Die faktorstruktuur wat deur Jones vir die Career Decision Needs-dimensie van die CDP gepostuleer is, is aan die hand van 'n bevestigende faktorontleding ondersteun. Ten slotte blyk dit dat die CDP nuttig aangewend kan word vir die multi-dimensionele taksering van loopbaanbesluiteloosheid by Afrikaanssprekende studente.

  4. A descriptive social and health profile of a community sample of adults and adolescents with Asperger syndrome

    Science.gov (United States)

    2010-01-01

    Background Little is known about the health and social profile of adolescents and adults with Asperger syndrome (AS) living in the community. We conducted a study to describe the living, employment and psycho-social situation of a community sample of forty two adults and adolescents with AS, and to describe these indivdiuals' experiences of accessing health services and taking medication. Findings Most respondents (including those over eighteen years of age) lived at home with their parents. Most had trouble reading and responding to other people's feelings, and coping with unexpected changes. Difficulties with life skills, such as cleaning, washing and hygiene were prevalent. The majority of respondents were socially isolated and a large minority had been sexually or financially exploited. Almost all respondents had been bullied. Mental health problems such as anxiety or depression were common. 30% of respondents said that they regularly became violent and hit other people and 15% had attempted suicide. More positively, the majority of respondents felt that they could access health services if they had a health problem. Conclusions The results of this study suggest a relatively poor social and health profile for many people with Asperger syndrome living in the community, with high levels of social problems and social exclusion, and difficulties managing day to day tasks such as washing and cleaning; these findings support the results of other studies that have examined psycho-social functioning in this group. PMID:21070680

  5. Protein profile study of clinical samples using laser induced fluorescence as the detection method: case of malignant and normal cervical tissues

    Science.gov (United States)

    Karemore, Gopal; Raja, Sujatha N.; Rai, Lavanya; Kartha, V. B.; Chidangil, Santhosh

    2009-02-01

    Protein profiles of tissue homogenates were recorded using HPLC separation and LIF detection method. The samples were collected from volunteers with clinically normal or cervical cancer conditions. It is shown that the protein profile can be classified as belonging to malignant or normal state by using hard and Fuzzy clustering methods. The study was performed to test the utility of the HPLC-LIF protein profiling method for classification of tissue samples as well as to establish a complementary method for histopathology for clinical diagnosis of the tissue as normal or malignant.

  6. A Self-Powered Fast-Sampling Profiling Float in support of a Mesoscale Ocean Observing System in the Western North Pacific

    Science.gov (United States)

    Valdez, T.; Chao, Y.; Davis, R. E.; Jones, J.

    2012-12-01

    This talk will describe a new self-powered profiling float that can perform fast sampling over the upper ocean for long durations in support of a mesoscale ocean observing system in the Western North Pacific. The current state-of-the-art profiling floats can provide several hundreds profiles for the upper ocean every ten days. To quantify the role of the upper ocean in modulating the development of Typhoons requires at least an order of magnitude reduction for the sampling interval. With today's profiling float and battery technology, a fast sampling of one day or even a few hours will reduce the typical lifetime of profiling floats from years to months. Interactions between the ocean and typhoons often involves mesoscale eddies and fronts, which require a dense array of floats to reveal the 3-dimensional structure. To measure the mesoscale ocean over a large area like the Western North Pacific therefore requires a new technology that enables fast sampling and long duration at the same time. Harvesting the ocean renewable energy associated with the vertical temperature differentials has the potential to power profiling floats with fast sampling over long durations. Results from the development and deployment of a prototype self-powered profiling float (known as SOLO-TREC) will be presented. With eight hours sampling in the upper 500 meters, the upper ocean temperature and salinity reveal pronounced high frequency variations. Plans to use the SOLO-TREC technology in support of a dense array of fast sampling profiling floats in the Western North Pacific will be discussed.

  7. Identification of sixteen peptides reflecting heat and/or storage induced processes by profiling of commercial milk samples.

    Science.gov (United States)

    Ebner, Jennifer; Baum, Florian; Pischetsrieder, Monika

    2016-09-16

    Peptide profiles of different drinking milk samples were examined to study how the peptide fingerprint of milk reflects processing conditions. The combination of a simple and fast method for peptide extraction using stage tips and MALDI-TOF-MS enabled the fast and easy generation and relative quantification of peptide fingerprints for high-temperature short-time (HTST), extended shelf life (ESL) and ultra-high temperature (UHT) milk of the same dairies. The relative quantity of 16 peptides changed as a function of increasing heat load. Additional heating experiments showed that among those, the intensity of peptide β-casein 196-209 (m/z 1460.9Da) was most heavily influenced by heat treatment indicating a putative marker peptide for milk processing conditions. Storage experiments with HTST- and UHT milk revealed that the differences between different types of milk samples were not only caused by the heating process. Relevant was also the proteolytic activity of enzymes during storage, which were differently influenced by the heat treatment. These results indicate that the peptide profile may be suitable to monitor processing as well as storage conditions of milk. In the present study, peptide profiling of different types of milk was carried out by MALDI-TOF-MS after stage-tip extraction and relative quantification using an internal reference peptide. Although MALDI-TOF-MS covers only part of the peptidome, the method is easy and quick and is, therefore, suited for routine analysis to address several aspects of food authenticity. Using this method, 16 native peptides were detected in milk that could be modulated by different industrial processes. Subsequent heating and storage experiments with pasteurized and UHT milk confirmed that these peptides are indeed related to the production or storage conditions of the respective products. Furthermore, the heating experiments revealed one peptide, namely the β-casein-derived sequence β-casein 196-209, which underwent

  8. The profile of Porphyromonas gingivalis kgp biotype and fimA genotype mosaic in subgingival plaque samples.

    Science.gov (United States)

    Nadkarni, Mangala A; Chhour, Kim-Ly; Chapple, Cheryl C; Nguyen, Ky-Anh; Hunter, Neil

    2014-12-01

    Combined analysis of allelic variation of the virulence-associated, strain-specific lys-gingipain gene (kgp) and major fimbrial gene (fimA) of Porphyromonas gingivalis was undertaken in 116 subgingival plaque samples to understand the kgp biotype and fimA genotype profile in a subject-specific manner. Allelic variation in the polyadhesin domain of kgp from P. gingivalis strains 381 (ATCC 33277), HG66 and W83 generated four isoforms corresponding to four biotypes of P. gingivalis. Similarly, variation in the fimA subunit of the fimA gene cluster of P. gingivalis resulted in six fimA genotypes. Strain-specific differential PCR was performed for kgp and fimA using DNA isolated from subgingival plaque samples. Our findings demonstrate that all of the P. gingivalis kgp biotypes detected in this study were predominantly associated with the fimA II genotype. Dominance of kgp biotypes 381 or HG66 combined with fimA II fimbriae could imply an adaptive strategy by P. gingivalis to generate the fittest strains for survival in the host environment. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  9. Diversity in the stellar velocity dispersion profiles of a large sample of Brightest Cluster Galaxies z ≤ 0.3

    Science.gov (United States)

    Loubser, S. I.; Hoekstra, H.; Babul, A.; O'Sullivan, E.

    2018-02-01

    We analyse spatially-resolved deep optical spectroscopy of Brightest Cluster Galaxies (BCGs) located in 32 massive clusters with redshifts of 0.05 ≤z ≤ 0.30, to investigate their velocity dispersion profiles. We compare these measurements to those of other massive early-type galaxies, as well as central group galaxies, where relevant. This unique, large sample extends to the most extreme of massive galaxies, spanning MK between -25.7 to -27.8 mag, and host cluster halo mass M500 up to 1.7 × 1015 M⊙. To compare the kinematic properties between brightest group and cluster members, we analyse similar spatially-resolved long-slit spectroscopy for 23 nearby Brightest Group Galaxies (BGGs) from the Complete Local-Volume Groups Sample (CLoGS). We find a surprisingly large variety in velocity dispersion slopes for BCGs, with a significantly larger fraction of positive slopes, unique compared to other (non-central) early-type galaxies as well as the majority of the brightest members of the groups. We find that the velocity dispersion slopes of the BCGs and BGGs correlate with the luminosity of the galaxies, and we quantify this correlation. It is not clear whether the full diversity in velocity dispersion slopes that we see is reproduced in simulations.

  10. Methane Flux

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — Methane (CH4) flux is the net rate of methane exchange between an ecosystem and the atmosphere. Data of this variable were generated by the USGS LandCarbon project...

  11. Aerodynamic Temperature Derived from Flux-Profile Measurements and Two-Source Model Predictions over a Cotton Row Crop in an Advective Environment

    Science.gov (United States)

    The surface aerodynamic temperature (SAT) is related to the atmospheric forcing conditions (radiation, wind speed and air temperature) and surface conditions. SAT is required in the bulk surface resistance equation to calculate the rate of sensible heat flux exchange. SAT cannot be measured directly...

  12. Human glioblastoma-associated microglia/monocytes express a distinct RNA profile compared to human control and murine samples.

    Science.gov (United States)

    Szulzewsky, Frank; Arora, Sonali; de Witte, Lot; Ulas, Thomas; Markovic, Darko; Schultze, Joachim L; Holland, Eric C; Synowitz, Michael; Wolf, Susanne A; Kettenmann, Helmut

    2016-08-01

    Glioblastoma (GBM) is the most aggressive brain tumor in adults. It is strongly infiltrated by microglia and peripheral monocytes that support tumor growth. In the present study we used RNA sequencing to compare the expression profile of CD11b(+) human glioblastoma-associated microglia/monocytes (hGAMs) to CD11b(+) microglia isolated from non-tumor samples. Hierarchical clustering and principal component analysis showed a clear separation of the two sample groups and we identified 334 significantly regulated genes in hGAMs. In comparison to human control microglia hGAMs upregulated genes associated with mitotic cell cycle, cell migration, cell adhesion, and extracellular matrix organization. We validated the expression of several genes associated with extracellular matrix organization in samples of human control microglia, hGAMs, and the hGAMs-depleted fraction via qPCR. The comparison to murine GAMs (mGAMs) showed that both cell populations share a significant fraction of upregulated transcripts compared with their respective controls. These genes were mostly related to mitotic cell cycle. However, in contrast to murine cells, human GAMs did not upregulate genes associated to immune activation. Comparison of human and murine GAMs expression data to several data sets of in vitro-activated human macrophages and murine microglia showed that, in contrast to mGAMs, hGAMs share a smaller overlap to these data sets in general and in particular to cells activated by proinflammatory stimulation with LPS + INFγ or TNFα. Our findings provide new insights into the biology of human glioblastoma-associated microglia/monocytes and give detailed information about the validity of murine experimental models. GLIA 2016 GLIA 2016;64:1416-1436. © 2016 Wiley Periodicals, Inc.

  13. Gemini NIFS survey of feeding and feedback processes in nearby active galaxies - II. The sample and surface mass density profiles

    Science.gov (United States)

    Riffel, R. A.; Storchi-Bergmann, T.; Riffel, R.; Davies, R.; Bianchin, M.; Diniz, M. R.; Schönell, A. J.; Burtscher, L.; Crenshaw, M.; Fischer, T. C.; Dahmer-Hahn, L. G.; Dametto, N. Z.; Rosario, D.

    2018-02-01

    We present and characterize a sample of 20 nearby Seyfert galaxies selected for having BAT 14-195 keV luminosities LX ≥ 1041.5 erg s-1, redshift z ≤ 0.015, being accessible for observations with the Gemini Near-Infrared Field Spectrograph (NIFS) and showing extended [O III]λ5007 emission. Our goal is to study Active Galactic Nucleus (AGN) feeding and feedback processes from near-infrared integral-field spectra, which include both ionized (H II) and hot molecular (H2) emission. This sample is complemented by other nine Seyfert galaxies previously observed with NIFS. We show that the host galaxy properties (absolute magnitudes MB, MH, central stellar velocity dispersion and axial ratio) show a similar distribution to those of the 69 BAT AGN. For the 20 galaxies already observed, we present surface mass density (Σ) profiles for H II and H2 in their inner ˜500 pc, showing that H II emission presents a steeper radial gradient than H2. This can be attributed to the different excitation mechanisms: ionization by AGN radiation for H II and heating by X-rays for H2. The mean surface mass densities are in the range (0.2 ≤ ΣH II ≤ 35.9) M⊙ pc-2, and (0.2 ≤ ΣH2 ≤ 13.9)× 10-3 M⊙ pc-2, while the ratios between the H II and H2 masses range between ˜200 and 8000. The sample presented here will be used in future papers to map AGN gas excitation and kinematics, providing a census of the mass inflow and outflow rates and power as well as their relation with the AGN luminosity.

  14. Neuropsychological profiles correlated with clinical and behavioral impairments in a sample of Brazilian children with Attention Deficit Hyperactivity Disorder (ADHD

    Directory of Open Access Journals (Sweden)

    Sueli eRizzutti

    2015-11-01

    Full Text Available ADHD is a complex neurodevelopmental disorder that implies several-step process and there is no single test to diagnose both ADHD and associated comorbidities such as oppositional defiant disorder, anxiety disorder, depression and certain types of learning disabilities. The purpose of the present study was to examine correlations between behavioral and clinical symptoms by administering an extensive neuropsychological battery to a sample of children and adolescents from a developing country. The sample was divided into three groups: non-ADHD; ADHD-non-comorbid; and ADHD+comorbidity. A full neuropsychological battery and clinical assessment found that 105 children met DSM-5 criteria, of whom 46.6% had the predominantly inattentive presentation, 37.3% had combined presentation and 16% were predominantly hyperactive/impulsive presentation. The internal correlation between neuropsychological tests did not reach statistical significance in the comparison between ADHD and non-ADHD cases (p<0.17. Clinical ADHD cases, including both +comorbidity and non-comorbid groups, performed substantially worse on CPT, working memory. Comparing ADHD-non-comorbid and ADHD+comorbidity groups, the latter did significantly worse on inhibitory control, time processing and the level of perseveration response on CPT indexes, as well as on working memory performance and CBCL tests particularly the CBCL-DESR (deficient emotional self-regulation test in the ADHD+comorbidity group. Children diagnosed as oppositional-defiant (ODD or with conduct disorder (CD showed close correlations between clinical CBCL profiles and externalized symptoms. Our findings suggest that ADHD+comorbidity and ADHD non-comorbid cases may be differentiated by a number of neuropsychological measures, such as processing speed, inhibitory control and working memory, that may reflect different levels of involvement of the hot and cool executive domains, which are more impaired in cases of severe

  15. Chemically-blocked Antibody Microarray for Multiplexed High-throughput Profiling of Specific Protein Glycosylation in Complex Samples

    Science.gov (United States)

    Lu, Chen; Wonsidler, Joshua L.; Li, Jianwei; Du, Yanming; Block, Timothy; Haab, Brian; Chen, Songming

    2012-01-01

    In this study, we describe an effective protocol for use in a multiplexed high-throughput antibody microarray with glycan binding protein detection that allows for the glycosylation profiling of specific proteins. Glycosylation of proteins is the most prevalent post-translational modification found on proteins, and leads diversified modifications of the physical, chemical, and biological properties of proteins. Because the glycosylation machinery is particularly susceptible to disease progression and malignant transformation, aberrant glycosylation has been recognized as early detection biomarkers for cancer and other diseases. However, current methods to study protein glycosylation typically are too complicated or expensive for use in most normal laboratory or clinical settings and a more practical method to study protein glycosylation is needed. The new protocol described in this study makes use of a chemically blocked antibody microarray with glycan-binding protein (GBP) detection and significantly reduces the time, cost, and lab equipment requirements needed to study protein glycosylation. In this method, multiple immobilized glycoprotein-specific antibodies are printed directly onto the microarray slides and the N-glycans on the antibodies are blocked. The blocked, immobilized glycoprotein-specific antibodies are able to capture and isolate glycoproteins from a complex sample that is applied directly onto the microarray slides. Glycan detection then can be performed by the application of biotinylated lectins and other GBPs to the microarray slide, while binding levels can be determined using Dylight 549-Streptavidin. Through the use of an antibody panel and probing with multiple biotinylated lectins, this method allows for an effective glycosylation profile of the different proteins found in a given human or animal sample to be developed. Introduction Glycosylation of protein, which is the most ubiquitous post-translational modification on proteins, modifies

  16. Stratigraphy of a proposed wind farm site southeast of Block Island: Utilization of borehole samples, downhole logging, and seismic profiles

    Science.gov (United States)

    Sheldon, Dane P. H.

    Seismic stratigraphy, sedimentology, lithostratigraphy, downhole geophysical logging, mineralogy, and palynology were used to study and interpret the upper 70 meters of the inner continental shelf sediments within a proposed wind farm site located approximately two to three nautical miles to the southeast of Block Island, Rhode Island. Core samples and downhole logging collected from borings drilled for geotechnical purposes at proposed wind turbine sites along with seismic surveys in the surrounding area provide the data for this study. Cretaceous coastal plain sediments that consist of non-marine to marine sand, silt, and clay are found overlying bedrock at a contact depth beyond the sampling depth of this study. The upper Cretaceous sediments sampled in borings are correlated with the Magothy/Matawan formations described regionally from New Jersey to Nantucket. An unconformity formed through sub-aerial, fluvial, marine, and glacial erosion marks the upper strata of the Cretaceous sediments separating them from the overlying deposits. The majority of Quaternary deposits overlying the unconformity represent the advance, pulsing, and retreat of the Laurentide ice sheet that reached its southern terminus in the area of Block Island approximately 25,000 to 21,000 years before present. The sequence consists of a basal glacial till overlain by sediments deposited by meltwater environments ranging from deltaic to proglacial lakefloor. A late Pleistocene to early Holocene unconformity marks the top of the glacial sequence and was formed after glacial retreat through fluvial and subaerial erosion/deposition. Overlying the glacial sequence are sediments deposited during the late Pleistocene and Holocene consisting of interbedded gravel, sand, silt, and clay. Sampling of these sediments was limited and surficial reflectors in seismic profiles were masked due to a hard bottom return. However, two depositional periods are interpreted as representing fluvial and estuarine

  17. Body Composition, Nutritional Profile and Muscular Fitness Affect Bone Health in a Sample of Schoolchildren from Colombia: The Fuprecol Study

    Science.gov (United States)

    Forero-Bogotá, Mónica Adriana; Ojeda-Pardo, Mónica Liliana; García-Hermoso, Antonio; Correa-Bautista, Jorge Enrique; González-Jiménez, Emilio; Schmidt-RíoValle, Jacqueline; Navarro-Pérez, Carmen Flores; Gracia-Marco, Luis; Vlachopoulos, Dimitris; Martínez-Torres, Javier; Ramírez-Vélez, Robinson

    2017-01-01

    The objective of the present study is to investigate the relationships between body composition, nutritional profile, muscular fitness (MF) and bone health in a sample of children and adolescents from Colombia. Participants included 1118 children and adolescents (54.6% girls). Calcaneal broadband ultrasound attenuation (c-BUA) was obtained as a marker of bone health. Body composition (fat mass and lean mass) was assessed using bioelectrical impedance analysis. Furthermore height, weight, waist circumference and Tanner stage were measured and body mass index (BMI) was calculated. Standing long-jump (SLJ) and isometric handgrip dynamometry were used respectively as indicators of lower and upper body muscular fitness. A muscular index score was also computed by summing up the standardised values of both SLJ and handgrip strength. Dietary intake and degree of adherence to the Mediterranean diet were assessed by a 7-day recall questionnaire for food frequency and the Kidmed questionnaire. Poor bone health was considered using a z-score cut off of ≤−1.5 standard deviation. Once the results were adjusted for age and Tanner stage, the predisposing factors of having a c-BUA z-score ≤−1.5 standard deviation included being underweight or obese, having an unhealthy lean mass, having an unhealthy fat mass, SLJ performance, handgrip performance, and unhealthy muscular index score. In conclusion, body composition (fat mass and lean body mass) and MF both influenced bone health in a sample of children and adolescents from Colombia. Thus promoting strength adaptation and preservation in Colombian youth will help to improve bone health, an important protective factor against osteoporosis in later life. PMID:28165360

  18. Body Composition, Nutritional Profile and Muscular Fitness Affect Bone Health in a Sample of Schoolchildren from Colombia: The Fuprecol Study

    Directory of Open Access Journals (Sweden)

    Mónica Adriana Forero-Bogotá

    2017-02-01

    Full Text Available The objective of the present study is to investigate the relationships between body composition, nutritional profile, muscular fitness (MF and bone health in a sample of children and adolescents from Colombia. Participants included 1118 children and adolescents (54.6% girls. Calcaneal broadband ultrasound attenuation (c-BUA was obtained as a marker of bone health. Body composition (fat mass and lean mass was assessed using bioelectrical impedance analysis. Furthermore height, weight, waist circumference and Tanner stage were measured and body mass index (BMI was calculated. Standing long-jump (SLJ and isometric handgrip dynamometry were used respectively as indicators of lower and upper body muscular fitness. A muscular index score was also computed by summing up the standardised values of both SLJ and handgrip strength. Dietary intake and degree of adherence to the Mediterranean diet were assessed by a 7-day recall questionnaire for food frequency and the Kidmed questionnaire. Poor bone health was considered using a z-score cut off of ≤−1.5 standard deviation. Once the results were adjusted for age and Tanner stage, the predisposing factors of having a c-BUA z-score ≤−1.5 standard deviation included being underweight or obese, having an unhealthy lean mass, having an unhealthy fat mass, SLJ performance, handgrip performance, and unhealthy muscular index score. In conclusion, body composition (fat mass and lean body mass and MF both influenced bone health in a sample of children and adolescents from Colombia. Thus promoting strength adaptation and preservation in Colombian youth will help to improve bone health, an important protective factor against osteoporosis in later life.

  19. Rapid and sensitive hormonal profiling of complex plant samples by liquid chromatography coupled to electrospray ionization tandem mass spectrometry

    Directory of Open Access Journals (Sweden)

    Müller Maren

    2011-11-01

    Full Text Available Abstract Background Plant hormones play a pivotal role in several physiological processes during a plant's life cycle, from germination to senescence, and the determination of endogenous concentrations of hormones is essential to elucidate the role of a particular hormone in any physiological process. Availability of a sensitive and rapid method to quantify multiple classes of hormones simultaneously will greatly facilitate the investigation of signaling networks in controlling specific developmental pathways and physiological responses. Due to the presence of hormones at very low concentrations in plant tissues (10-9 M to 10-6 M and their different chemistries, the development of a high-throughput and comprehensive method for the determination of hormones is challenging. Results The present work reports a rapid, specific and sensitive method using ultrahigh-performance liquid chromatography coupled to electrospray ionization tandem spectrometry (UPLC/ESI-MS/MS to analyze quantitatively the major hormones found in plant tissues within six minutes, including auxins, cytokinins, gibberellins, abscisic acid, 1-amino-cyclopropane-1-carboxyic acid (the ethylene precursor, jasmonic acid and salicylic acid. Sample preparation, extraction procedures and UPLC-MS/MS conditions were optimized for the determination of all plant hormones and are summarized in a schematic extraction diagram for the analysis of small amounts of plant material without time-consuming additional steps such as purification, sample drying or re-suspension. Conclusions This new method is applicable to the analysis of dynamic changes in endogenous concentrations of hormones to study plant developmental processes or plant responses to biotic and abiotic stresses in complex tissues. An example is shown in which a hormone profiling is obtained from leaves of plants exposed to salt stress in the aromatic plant, Rosmarinus officinalis.

  20. Bile acid profiling in human biological samples: comparison of extraction procedures and application to normal and cholestatic patients.

    Science.gov (United States)

    Humbert, Lydie; Maubert, Marie Anne; Wolf, Claude; Duboc, Henri; Mahé, Myriam; Farabos, Dominique; Seksik, Philippe; Mallet, Jean Maurice; Trugnan, Germain; Masliah, Joëlle; Rainteau, Dominique

    2012-06-15

    The role of bile acids in cell metabolism, membrane biology and cell signaling is increasingly recognized, thus making necessary a robust and versatile technique to extract, separate and quantify a large concentration range of these numerous molecular species. HPLC-MS/MS analysis provides the highest sensitivity to detect and identify bile acids. However, due to their large chemical diversity, extraction methods are critical and quite difficult to optimize, as shown by a survey of the literature. This paper compares the performances of four bile acid extraction protocols applied to either liquid (serum, urine, bile) or solid (stool) samples. Acetonitrile was found to be the best solvent for deproteinizing liquid samples and NaOH the best one for stool extraction. These optimized extraction procedures allowed us to quantitate as much as 27 distinct bile acids including sulfated species in a unique 30 min HPLC run, including both hydrophilic and hydrophobic species with a high efficiency. Tandem MS provided a non ambiguous identification of each metabolite with a good sensitivity (LOQ below 20 nmol/l except for THDCA and TLCA). After validation, these methods, successfully applied to a group of 39 control patients, detected 14 different species in serum in the range of 30-800 nmol/l, 11 species in urine in the range of 20-200 nmol/l and 25 species in stool in the range of 0.4-2000 nmol/g. The clinical interest of this method has been then validated on cholestatic patients. The proposed protocols seem suitable for profiling bile acids in routine analysis. Copyright © 2012 Elsevier B.V. All rights reserved.

  1. Flux Creep Investigation in Bi2Sr2CaCu2O8+d High-Temperature Superconductor

    Directory of Open Access Journals (Sweden)

    G. R. Blanca

    2004-12-01

    Full Text Available The flux creep process in a c-axis Bi2Sr2CaCu2O8+d thin film was investigated at different temperatures and applied fields using the Kim-Anderson (KA approach. The peaked behavior shown in the magnetoresistance profile was attributed to the competing mechanisms of flux motion and sample-intrinsic transition near Tc.Within the temperature range where the competition occurs, U increases with temperature and consequently a decrease in the superconducting volume corresponds to a decrease in the flux creep. Moreover, the flux creep potential barrier varies with applied current I at all temperatures consistent with the KA model.

  2. Detection of metabolites discriminating subtypes of thyroid cancer: Molecular profiling of FFPE samples using the GC/MS approach.

    Science.gov (United States)

    Wojakowska, Anna; Chekan, Mykola; Marczak, Łukasz; Polanski, Krzysztof; Lange, Dariusz; Pietrowska, Monika; Widlak, Piotr

    2015-12-05

    One of the critical issues in thyroid cancer diagnostic is differentiation between follicular adenoma, follicular carcinoma and the follicular variant of papillary carcinoma, which in some cases is not possible based on histopathological features only. In this paper we performed molecular profiling of thyroid tissue aiming to identify metabolites characteristic for different types of thyroid cancer. FFPE tissue specimens were analysed from 5 different types of thyroid malignancies (follicular, papillary/classical variant, papillary/follicular variant, medullary and anaplastic cancers), benign follicular adenoma and normal thyroid. Extracted metabolites were identified and semi-quantified using the GC/MS approach. There were 28 metabolites identified, whose abundances were significantly different among different types of thyroid tumours, including lipids, carboxylic acids, and saccharides. We concluded, that multi-component metabolome signature could be used for classification of different subtypes of follicular thyroid lesions. Moreover, potential applicability of the GC/MS-based analysis of FFPE tissue samples in diagnostics of thyroid cancer has been proved. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

  3. The profile of selected samples of Croatian athletes based on the items of sport jealousy scale (SJS

    Directory of Open Access Journals (Sweden)

    Sindik Joško

    2016-01-01

    Full Text Available The role of jealousy in sport, as a negative emotional reaction, accompanied by thoughts of inadequacy when compared to others, is the issue of this article. This study had a purpose to define the characteristic profiles of the Croatian athletes, based on single items of Sport Jealousy Scale (SJS II, labeled by several variables: gender, type of sport, age group. Purposive sample of 73 athletes competing at Croatian championships in different sports (football, bowling, volleyball and handball were examined with Croatian version of SJS-II. Three clusters obtained are similarly balanced, according to the number of cases in each cluster. The most simply explained, clusters clearly differentiate the most jealous, moderately jealous and slightly/low jealous athletes. Among the features of the athletes in each cluster, in the most jealous (first cluster are the athletes from team sports, women and older athletes. Females, bowling athletes, athletes from individual (coactive sports and the youngest athletes are the least jealous (grouped in third cluster.

  4. Dark Matter Profiles in Dwarf Galaxies: A Statistical Sample Using High-Resolution Hα Velocity Fields from PCWI

    Science.gov (United States)

    Relatores, Nicole C.; Newman, Andrew B.; Simon, Joshua D.; Ellis, Richard; Truong, Phuongmai N.; Blitz, Leo

    2018-01-01

    We present high quality Hα velocity fields for a sample of nearby dwarf galaxies (log M/M⊙ = 8.4-9.8) obtained as part of the Dark Matter in Dwarf Galaxies survey. The purpose of the survey is to investigate the cusp-core discrepancy by quantifying the variation of the inner slope of the dark matter distributions of 26 dwarf galaxies, which were selected as likely to have regular kinematics. The data were obtained with the Palomar Cosmic Web Imager, located on the Hale 5m telescope. We extract rotation curves from the velocity fields and use optical and infrared photometry to model the stellar mass distribution. We model the total mass distribution as the sum of a generalized Navarro-Frenk-White dark matter halo along with the stellar and gaseous components. We present the distribution of inner dark matter density profile slopes derived from this analysis. For a subset of galaxies, we compare our results to an independent analysis based on CO observations. In future work, we will compare the scatter in inner density slopes, as well as their correlations with galaxy properties, to theoretical predictions for dark matter core creation via supernovae feedback.

  5. Profile cytological tests, sensibility and specificity of fine needle puncture into skin and subcutaneous samples in dogs.

    Directory of Open Access Journals (Sweden)

    Arlinda Flores Coleto

    2016-09-01

    Full Text Available ABSTRACT. Coleto A.F., Moreira T. de A., Gundim L.F., Silva S. de A., de Castro M. de R., Bandarra M. de B. & Medeiros-Ronchi A.A. [Profile cytological tests, sensibility and specificity of fine needle puncture into skin and subcutaneous samples in dogs.] Perfil de exames citológicos, sensibilidade e especificidade da punção por agulha fina para amostras cutâneas e subcutâneas em cães. Revista Brasileira de Medicina Veterinária, 38(3:311-315, 2016. Programa de Pós-Graduação em Ciências Veterinárias, Universidade Federal de Uberlândia, Rua Ceará s/n - Bloco 2D, Sala 3, Campus Umuarama, Uberlândia, MG 38400- 902, Brasil. E-mail: arlindacoleto@hotmail.com The cytology has been routinely used in veterinary clinic and has a good correlation with histological examination. The objective was to conduct a retrospective study of cytological examinations in the period of six years and then calculate accuracy, sensitivity and specificity of cytology examination for neoplasms in cutaneous and subcutaneous samples collected by PAF (fine needle punction in dogs, using histology as golden pattern. The canine species was the most common in 92.2% (736/798. The PAF was the most used technique in 84.0% (814/968. The most frequent samples were from the Cutaneous System in 36.1% (344/951. There was 67.0% (36/53 agreement between the exams. The sensitivity of cytology in the diagnosis of neoplasms was 77% (moderate and specificity of 12.5% (low, and the PPV 83% and NPV 9.0%. Cytology is the most commonly test used in cutaneous and subcutaneous lesions in dogs and the PAF is the most used technique. The examination is recommended as a screening method because of its high sensitivity.

  6. Specific profiles of neurocognitive and reading functions in a sample of 42 Italian boys with Duchenne Muscular Dystrophy.

    Science.gov (United States)

    Lorusso, Maria Luisa; Civati, Federica; Molteni, Massimo; Turconi, Anna Carla; Bresolin, Nereo; D'Angelo, Maria Grazia

    2013-01-01

    A group of 42 Italian boys with Duchenne Muscular Dystrophy was compared with a control group of 10 boys with Spinal Muscular Atrophy and Osteogenesis Imperfecta on tests assessing general intellectual ability, language, neuropsychological functions, and reading skills with the aim of describing a comprehensive profile of the various functions and investigating their interrelationships. The influence of general intellectual level on performance was analyzed. Further, correlations between various neuropsychological measures and language performances were computed for the group with Duchenne Muscular Dystrophy, as well as the correlations between reading scores and other cognitive and linguistic measures. A general lowering in VIQ, PIQ, and FSIQ scores was found to characterize the group with Duchenne Muscular Dystrophy. Expressive language skills were within the normal range, while syntactic and grammatical comprehension were significantly impaired. The presence of below-average reading performances was further confirmed. However, unlike previous studies on irregular orthographies, the present results show that (a) the mild reading difficulties found in the sample essentially concern speed rather than accuracy; (b) they concern word rather than nonword reading; (c) lower reading performances are related to lower scores in general IQ; (d) no correlations emerge with phonological abilities, verbal short-term memory, or working memory, but rather with long-term memory and lexical skills. This may suggest that language-specific effects modulate the cognitive expressions of Duchenne Muscular Dystrophy and raises the possibility that the dysfunctions underlying the reading difficulties observed in affected readers of regular orthographies involve different neurocognitive systems than the cortico-cerebellar circuits usually invoked.

  7. Molecular identification and antifungal susceptibility profiles of Candida parapsilosis complex species isolated from culture collection of clinical samples

    Directory of Open Access Journals (Sweden)

    Fábio Silvestre Ataides

    2015-08-01

    Full Text Available AbstractINTRODUCTION:Candida parapsilosis is a common yeast species found in cases of onychomycosis and candidemia associated with infected intravascular devices. In this study, we differentiated Candida parapsilosis sensu stricto, Candida orthopsilosis , and Candida metapsilosis from a culture collection containing blood and subungual scraping samples. Furthermore, we assessed the in vitro antifungal susceptibility of these species to fluconazole, itraconazole, voriconazole, posaconazole, amphotericin B, and caspofungin.METHODS:Differentiation of C. parapsilosis complex species was performed by amplification of the secondary alcohol dehydrogenase (SADH gene and digestion by the restriction enzyme Ban I. All isolates were evaluated for the determination of minimal inhibitory concentrations using Etest, a method for antifungal susceptibility testing.RESULTS:Among the 87 isolates, 78 (89.7% were identified as C. parapsilosis sensu stricto , five (5.7% were identified as C. orthopsilosis , and four (4.6% were identified as C. metapsilosis . Analysis of antifungal susceptibility showed that C. parapsilosis sensu strictoisolates were less susceptible to amphotericin B and itraconazole. One C. parapsilosis sensu stricto isolate was resistant to amphotericin B and itraconazole. Moreover, 10.2% of C. parapsilosis sensu stricto isolates were resistant to caspofungin. Two C. parapsilosis sensu strictoisolates and one C. metapsilosis isolate were susceptible to fluconazole in a dose-dependent manner.CONCLUSIONS:We reported the first molecular identification of C. parapsilosiscomplex species in State of Goiás, Brazil. Additionally, we showed that although the three species exhibited differences in antifungal susceptibility profiles, the primary susceptibility of this species was to caspofungin.

  8. Microdialysis Sampling from Wound Fluids Enables Quantitative Assessment of Cytokines, Proteins, and Metabolites Reveals Bone Defect-Specific Molecular Profiles.

    Science.gov (United States)

    Förster, Yvonne; Schmidt, Johannes R; Wissenbach, Dirk K; Pfeiffer, Susanne E M; Baumann, Sven; Hofbauer, Lorenz C; von Bergen, Martin; Kalkhof, Stefan; Rammelt, Stefan

    2016-01-01

    Bone healing involves a variety of different cell types and biological processes. Although certain key molecules have been identified, the molecular interactions of the healing progress are not completely understood. Moreover, a clinical routine for predicting the quality of bone healing after a fracture in an early phase is missing. This is mainly due to a lack of techniques to comprehensively screen for cytokines, growth factors and metabolites at their local site of action. Since all soluble molecules of interest are present in the fracture hematoma, its in-depth assessment could reveal potential markers for the monitoring of bone healing. Here, we describe an approach for sampling and quantification of cytokines and metabolites by using microdialysis, combined with solid phase extractions of proteins from wound fluids. By using a control group with an isolated soft tissue wound, we could reveal several bone defect-specific molecular features. In bone defect dialysates the neutrophil chemoattractants CXCL1, CXCL2 and CXCL3 were quantified with either a higher or earlier response compared to dialysate from soft tissue wound. Moreover, by analyzing downstream adaptions of the cells on protein level and focusing on early immune response, several proteins involved in the immune cell migration and activity could be identified to be specific for the bone defect group, e.g. immune modulators, proteases and their corresponding inhibitors. Additionally, the metabolite screening revealed different profiles between the bone defect group and the control group. In summary, we identified potential biomarkers to indicate imbalanced healing progress on all levels of analysis.

  9. Microdialysis Sampling from Wound Fluids Enables Quantitative Assessment of Cytokines, Proteins, and Metabolites Reveals Bone Defect-Specific Molecular Profiles.

    Directory of Open Access Journals (Sweden)

    Yvonne Förster

    Full Text Available Bone healing involves a variety of different cell types and biological processes. Although certain key molecules have been identified, the molecular interactions of the healing progress are not completely understood. Moreover, a clinical routine for predicting the quality of bone healing after a fracture in an early phase is missing. This is mainly due to a lack of techniques to comprehensively screen for cytokines, growth factors and metabolites at their local site of action. Since all soluble molecules of interest are present in the fracture hematoma, its in-depth assessment could reveal potential markers for the monitoring of bone healing. Here, we describe an approach for sampling and quantification of cytokines and metabolites by using microdialysis, combined with solid phase extractions of proteins from wound fluids. By using a control group with an isolated soft tissue wound, we could reveal several bone defect-specific molecular features. In bone defect dialysates the neutrophil chemoattractants CXCL1, CXCL2 and CXCL3 were quantified with either a higher or earlier response compared to dialysate from soft tissue wound. Moreover, by analyzing downstream adaptions of the cells on protein level and focusing on early immune response, several proteins involved in the immune cell migration and activity could be identified to be specific for the bone defect group, e.g. immune modulators, proteases and their corresponding inhibitors. Additionally, the metabolite screening revealed different profiles between the bone defect group and the control group. In summary, we identified potential biomarkers to indicate imbalanced healing progress on all levels of analysis.

  10. Methane, Carbon Dioxide and Nitrous Oxide Fluxes in Soil Profile under a Winter Wheat-Summer Maize Rotation in the North China Plain

    NARCIS (Netherlands)

    Wang, Y.Y.; Hu, C.S.; Ming, H.; Oenema, O.; Schaefer, D.A.; Dong, W.X.; Zhang, Y.M.; Li, X.X.

    2014-01-01

    The production and consumption of the greenhouse gases (GHGs) methane (CH4), carbon dioxide (CO2) and nitrous oxide (N2O) in soil profile are poorly understood. This work sought to quantify the GHG production and consumption at seven depths (0-30, 30-60, 60-90, 90-150, 150-200, 200-250 and 250-300

  11. Interpretation of scrape-off layer profile evolution and first-wall ion flux statistics on JET using a stochastic framework based on fillamentary motion

    Science.gov (United States)

    Walkden, N. R.; Wynn, A.; Militello, F.; Lipschultz, B.; Matthews, G.; Guillemaut, C.; Harrison, J.; Moulton, D.; Contributors, JET

    2017-08-01

    This paper presents the use of a novel modelling technique based around intermittent transport due to filament motion, to interpret experimental profile and fluctuation data in the scrape-off layer (SOL) of JET during the onset and evolution of a density profile shoulder. A baseline case is established, prior to shoulder formation, and the stochastic model is shown to be capable of simultaneously matching the time averaged profile measurement as well as the PDF shape and autocorrelation function from the ion-saturation current time series at the outer wall. Aspects of the stochastic model are then varied with the aim of producing a profile shoulder with statistical measurements consistent with experiment. This is achieved through a strong localised reduction in the density sink acting on the filaments within the model. The required reduction of the density sink occurs over a highly localised region with the timescale of the density sink increased by a factor of 25. This alone is found to be insufficient to model the expansion and flattening of the shoulder region as the density increases, which requires additional changes within the stochastic model. An example is found which includes both a reduction in the density sink and filament acceleration and provides a consistent match to the experimental data as the shoulder expands, though the uniqueness of this solution can not be guaranteed. Within the context of the stochastic model, this implies that the localised reduction in the density sink can trigger shoulder formation, but additional physics is required to explain the subsequent evolution of the profile.

  12. Generating energy dependent neutron flux maps for effective ...

    African Journals Online (AJOL)

    For activation analysis and irradiation scheme of miniature neutron source reactor, designers or engineers usually require information on thermal neutron flux levels and other energy group flux levels (such as fast, resonance and epithermal). A methodology for readily generating such flux maps and flux profiles for any ...

  13. Passive Sampling and High Resolution Mass Spectrometry for Chemical Profiling of French Coastal Areas with a Focus on Marine Biotoxins.

    Science.gov (United States)

    Zendong, Zita; Bertrand, Samuel; Herrenknecht, Christine; Abadie, Eric; Jauzein, Cécile; Lemée, Rodolphe; Gouriou, Jérémie; Amzil, Zouher; Hess, Philipp

    2016-08-16

    Passive samplers (solid phase adsorption toxin tracking: SPATT) are able to accumulate biotoxins produced by microalgae directly from seawater, thus providing useful information for monitoring of the marine environment. SPATTs containing 0.3, 3, and 10 g of resin were deployed at four different coastal areas in France and analyzed using liquid chromatography coupled to high resolution mass spectrometry. Quantitative targeted screening provided insights into toxin profiles and showed that toxin concentrations and profiles in SPATTs were dependent on the amount of resin used. Between the three amounts of resin tested, SPATTs containing 3 g of resin appeared to be the best compromise, which is consistent with the use of 3 g of resin in SPATTs by previous studies. MassHunter and Mass Profiler Professional softwares were used for data reprocessing and statistical analyses. A differential profiling approach was developed to investigate and compare the overall chemical diversity of dissolved substances in different coastal water bodies. Principal component analysis (PCA) allowed for spatial differentiation between areas. Similarly, SPATTs retrieved from the same location at early, medium, and late deployment periods were also differentiated by PCA, reflecting seasonal variations in chemical profiles and in the microalgal community. This study used an untargeted metabolomic approach for spatial and temporal differentiation of marine environmental chemical profiles using SPATTs, and we propose this approach as a step forward in the discovery of chemical markers of short- or long-term changes in the microbial community structure.

  14. Primary health clinic toilet/bathroom surface swab sampling can indicate community profile of sexually transmitted infections.

    Science.gov (United States)

    Giffard, Philip M; Su, Jiunn-Yih; Andersson, Patiyan; Holt, Deborah C

    2017-01-01

    The microbiome of built environment surfaces is impacted by the presence of humans. In this study, we tested the hypothesis that analysis of surface swabs from clinic toilet/bathroom yields results correlated with sexually transmitted infection (STI) notifications from corresponding human populations. We extended a previously reported study in which surfaces in toilet/bathroom facilities in primary health clinics in the Australian Northern Territory (NT) were swabbed then tested for nucleic acid from the STI agents Chlamydia trachomatis, Neisseria gonorrhoeae and Trichomonas vaginalis. This was in the context of assessing the potential for such nucleic acid to contaminate specimens collected in such facilities. STIs are notifiable in the NT, thus allowing comparison of swab and notification data. An assumption in the design was that while absolute built environment loads of STI nucleic acids will be a function of patient traffic density and facility cleaning protocols, the relative loads of STI nucleic acids from different species will be largely unaffected by these processes. Another assumption was that the proportion of swabs testing positive for STIs provides a measure of surface contamination. Accordingly, "STI profiles" were calculated. These were the proportions that each of the three STIs of interest contributed to the summed STI positive swabs or notifications. Three comparisons were performed, using swab data from clinics in remote Indigenous communities, clinics in small-medium towns, and a single urban sexual health clinic. These data were compared with time and place-matched STI notifications. There were significant correlations between swab and notifications data for the both the remote Indigenous and regional data. For the remote Indigenous clinics the p values ranged from 0.041 to 0.0089, depending on data transformation and p value inference method. Further, the swab data appeared to strongly indicate known higher relative prevalence of gonorrhoeae

  15. Distributed Sensible Heat Flux Measurements for Wireless Sensor Networks

    Science.gov (United States)

    Huwald, H.; Brauchli, T.; Lehning, M.; Higgins, C. W.

    2015-12-01

    The sensible heat flux component of the surface energy balance is typically computed using eddy covariance or two point profile measurements while alternative approaches such as the flux variance method based on convective scaling has been much less explored and applied. Flux variance (FV) certainly has a few limitations and constraints but may be an interesting and competitive method in low-cost and power limited wireless sensor networks (WSN) with the advantage of providing spatio-temporal sensible heat flux over the domain of the network. In a first step, parameters such as sampling frequency, sensor response time, and averaging interval are investigated. Then we explore the applicability and the potential of the FV method for use in WSN in a field experiment. Low-cost sensor systems are tested and compared against reference instruments (3D sonic anemometers) to evaluate the performance and limitations of the sensors as well as the method with respect to the standard calculations. Comparison experiments were carried out at several sites to gauge the flux measurements over different surface types (gravel, grass, water) from the low-cost systems. This study should also serve as an example of spatially distributed sensible heat flux measurements.

  16. Determination of Energy Fluxes Over Agricultural Surfaces

    Directory of Open Access Journals (Sweden)

    Josefina Argete

    1994-12-01

    Full Text Available An energy budget was conducted over two kinds if surfaces: grass and corn canopy. The net radiative flux and the soil heat flux were directly measured while the latent and sensible heat flux were calculated from the vertical profiles if wet and dry-bulb temperature and wind speed. The crop storage flux was also estimated. Using the gradient or aerodynamic equations, the calculated fluxes when compared to the measured fluxes in the context of an energy budget gave an SEE = 63 Wm-2 over grass and SEE = 81 Wm-2 over corn canopy. The calculated fluxes compared reasonably well with those obtained using the Penman equations.For an energy budget research with limited instrumentation, the aerodynamic method performed satisfactorily in estimating the daytime fluxes, when atmospheric conditions are fully convective, but failed when conditions were stably stratified as during nighttime.

  17. Routine use of microarray-based gene expression profiling to identify patients with low cytogenetic risk acute myeloid leukemia: accurate results can be obtained even with suboptimal samples

    Directory of Open Access Journals (Sweden)

    de la Blétière Diane Raingeard

    2012-01-01

    Full Text Available Abstract Background Gene expression profiling has shown its ability to identify with high accuracy low cytogenetic risk acute myeloid leukemia such as acute promyelocytic leukemia and leukemias with t(8;21 or inv(16. The aim of this gene expression profiling study was to evaluate to what extent suboptimal samples with low leukemic blast load (range, 2-59% and/or poor quality control criteria could also be correctly identified. Methods Specific signatures were first defined so that all 71 acute promyelocytic leukemia, leukemia with t(8;21 or inv(16-AML as well as cytogenetically normal acute myeloid leukemia samples with at least 60% blasts and good quality control criteria were correctly classified (training set. The classifiers were then evaluated for their ability to assign to the expected class 111 samples considered as suboptimal because of a low leukemic blast load (n = 101 and/or poor quality control criteria (n = 10 (test set. Results With 10-marker classifiers, all training set samples as well as 97 of the 101 test samples with a low blast load, and all 10 samples with poor quality control criteria were correctly classified. Regarding test set samples, the overall error rate of the class prediction was below 4 percent, even though the leukemic blast load was as low as 2%. Sensitivity, specificity, negative and positive predictive values of the class assignments ranged from 91% to 100%. Of note, for acute promyelocytic leukemia and leukemias with t(8;21 or inv(16, the confidence level of the class assignment was influenced by the leukemic blast load. Conclusion Gene expression profiling and a supervised method requiring 10-marker classifiers enable the identification of favorable cytogenetic risk acute myeloid leukemia even when samples contain low leukemic blast loads or display poor quality control criterion.

  18. Characteristics of flux-time profiles, temporal evolution, and spatial distribution of radiation-belt electron precipitation bursts in the upper ionosphere before great and giant earthquakes

    Directory of Open Access Journals (Sweden)

    Sergey Pulinets

    2012-04-01

    Full Text Available

    The analysis of energetic electron observations made by the DEMETER satellite reveals that radiation belt electron precipitation (RBEP bursts are observed in general several (~1-6 days before a large (M > 6.5 earthquake (EQ in the presence of broad band (~1-20 kHz VLF waves. The EBs show in general a relative peak-to-background flux increase usually < 100, they have a time duration of ~0.5 – 3 min, and their energy spectrum reach up to energies <~500 keV. The RBEP activity is observed as one, two or three EBs throughout a semi-orbit, depended on the magnetic field structure above the EQ epicenter. A statistical analysis has been made for earthquakes in Japan, which reveals a standard temporal variation of the number of EBs, which begins with an incremental rate several days before major earthquakes, and after a maximum, decreases so that the electron precipitation ceases above the epicenter. Some earthquake induced EBs were observed not only in the nightside ionosphere, but also in the dayside ionosphere.

     

  19. Social Media Membership, Browsing, and Profile Updating in a Representative U.S. Sample: Independent and Interdependent Effects of Big Five Traits and Aging and Social Factors

    Science.gov (United States)

    Bogg, Tim

    2017-01-01

    Guided by cybernetic perspectives on personality, the present work used a representative sample of U.S. adults (N = 992) to examine Big Five personality traits and social and aging factors as predictors of social media network membership and past-month browsing/searching and profile updating among members. The results showed adults who were less extraverted and less neurotic and who reported greater physical limitations were less likely to be members. Moreover, extraverted adults without partners were more likely to be members than introverted adults without partners. Among members, the results showed extraverted and emotionally stable younger and older adults reported a similar frequency of profile updating. In contrast, older adults with all other combinations of extraversion and neuroticism showed a reduced frequency of profile updating compared to younger adults. The findings are discussed in terms of social media involvement as a response of a self-regulatory system of personality adaptation. PMID:28713320

  20. Social Media Membership, Browsing, and Profile Updating in a Representative U.S. Sample: Independent and Interdependent Effects of Big Five Traits and Aging and Social Factors.

    Science.gov (United States)

    Bogg, Tim

    2017-01-01

    Guided by cybernetic perspectives on personality, the present work used a representative sample of U.S. adults ( N = 992) to examine Big Five personality traits and social and aging factors as predictors of social media network membership and past-month browsing/searching and profile updating among members. The results showed adults who were less extraverted and less neurotic and who reported greater physical limitations were less likely to be members. Moreover, extraverted adults without partners were more likely to be members than introverted adults without partners. Among members, the results showed extraverted and emotionally stable younger and older adults reported a similar frequency of profile updating. In contrast, older adults with all other combinations of extraversion and neuroticism showed a reduced frequency of profile updating compared to younger adults. The findings are discussed in terms of social media involvement as a response of a self-regulatory system of personality adaptation.

  1. Optimized Estimation of Surface Layer Characteristics from Profiling Measurements

    Directory of Open Access Journals (Sweden)

    Doreene Kang

    2016-01-01

    Full Text Available New sampling techniques such as tethered-balloon-based measurements or small unmanned aerial vehicles are capable of providing multiple profiles of the Marine Atmospheric Surface Layer (MASL in a short time period. It is desirable to obtain surface fluxes from these measurements, especially when direct flux measurements are difficult to obtain. The profiling data is different from the traditional mean profiles obtained at two or more fixed levels in the surface layer from which surface fluxes of momentum, sensible heat, and latent heat are derived based on Monin-Obukhov Similarity Theory (MOST. This research develops an improved method to derive surface fluxes and the corresponding MASL mean profiles of wind, temperature, and humidity with a least-squares optimization method using the profiling measurements. This approach allows the use of all available independent data. We use a weighted cost function based on the framework of MOST with the cost being optimized using a quasi-Newton method. This approach was applied to seven sets of data collected from the Monterey Bay. The derived fluxes and mean profiles show reasonable results. An empirical bias analysis is conducted using 1000 synthetic datasets to evaluate the robustness of the method.

  2. Culture and Validity of the Symptom Checklist-90-Revised and Profile of Mood States in a New Zealand Student Sample.

    Science.gov (United States)

    Barker-Collo, Suzanne L.

    2003-01-01

    New Zealand students' performance was examined on assessments of psychopathology and mood as compared to normative data from the United States. New Zealand university students (N=137) completed the Symptom Checklist-90-Revised (SCL-90-R) and Profile of Mood States (POMS). Mean performances differed significantly from normative data for each…

  3. An LC-MS/MS method for steroid profiling during adrenal venous sampling for investigation of primary aldosteronism

    NARCIS (Netherlands)

    Peitzsch, M.; Dekkers, T.; Haase, M.; Sweep, F.C.; Quack, I.; Antoch, G.; Siegert, G.; Lenders, J.W.M.; Deinum, J.; Willenberg, H.S.; Eisenhofer, G.

    2015-01-01

    BACKGROUND: Steroid profiling for diagnosis of endocrine disorders featuring disordered production of steroid hormones is now possible from advances in liquid chromatography with tandem mass spectrometry (LC-MS/MS). Adrenal venous (AV) measurements of aldosterone and cortisol are a standard practice

  4. Somatoform symptoms profiles in relation to psychological disorders - A population classification analysis in a large sample of general adults.

    Science.gov (United States)

    Heidari, Zahra; Feizi, Awat; Roohafza, Hamidreza; Hassanzadeh Keshteli, Ammar; Adibi, Payman

    2017-08-01

    In order to identifying somatoform symptoms profiles, classifying study population and evaluating of psychological disorders in extracted classes, we carried out a cross-sectional study on 4762 Iranian adults. Somatoform symptoms were assessed using a comprehensive 30-items questionnaire and psychological disorders were evaluated by 12-item General Health Questionnaire (GHQ-12) and Hospital Anxiety and Depression Scale (HADS) questionnaires. Factor analysis and factor mixture modeling (FMM) were used for data analysis. Four somatoform symptoms profiles were extracted, including 'psycho-fatigue', 'gastrointestinal', 'neuro- skeletal' and 'pharyngeal-respiratory'. According to FMM results, a two-class four-factor structure, based somatoform symptoms, was identified in our study population. Two identified classes were labeled as "low psycho-fatigue complaints" and "high psycho-fatigue complaints". The scores of psychological disorders profile was significantly associated with four somatoform symptoms profiles in both classes; however the stronger relationship was observed in high psycho-fatigue complaints class. The prevalence of all the somatoform symptoms among participants assigned to the "high psycho-fatigue complaints" class was significantly higher than other class. We concluded that somatoform symptoms have a dimensional-categorical structure within our study population. Our study also provided informative pathways on the association of psychological disorders with somatoform symptoms. These findings could be useful for dealing with treatment's approaches. Copyright © 2017. Published by Elsevier B.V.

  5. Robust BRCA1-like classification of copy number profiles of samples repeated across different datasets and platforms

    NARCIS (Netherlands)

    Schouten, Philip C.; Grigoriadis, Anita; Kuilman, Thomas; Mirza, Hasan; Watkins, Johnathan A.; Cooke, Saskia A.; van Dyk, Ewald; Severson, Tesa M.; Rueda, Oscar M.; Hoogstraat, Marlous; Verhagen, Caroline V. M.; Natrajan, Rachael; Chin, Suet-Feung; Lips, Esther H.; Kruizinga, Janneke; Velds, Arno; Nieuwland, Marja; Kerkhoven, Ron M.; Krijgsman, Oscar; Vens, Conchita; Peeper, Daniel; Nederlof, Petra M.; Caldas, Carlos; Tutt, Andrew N.; Wessels, Lodewyk F.; Linn, Sabine C.

    Breast cancers with BRCA1 germline mutation have a characteristic DNA copy number (CN) pattern. We developed a test that assigns CN profiles to be 'BRCA1-like' or 'non-BRCA1-like', which refers to resembling a BRCA1-mutated tumor or resembling a tumor without a BRCA1 mutation, respectively.

  6. Role of the beam profile and sample geometry in the bonded-disk method on the shrinkage kinetics of two dental resins.

    Science.gov (United States)

    Kostylev, I; Winters, T; Labrie, D; Price, R B T

    2016-08-01

    To investigate the time evolution of the two dimensional axial shrinkage field for two dental resins in the bonded disk geometry and further test the bonded-disk method. An interferometric technique employing a camera was used to image the 2D axial shrinkage field when polymerizing dental resins in real time both during and after light exposure. Four different beam profiles from two light curing units and three sample geometries were utilized to investigate their roles on the 2D axial shrinkage field. The 2D axial shrinkage field correlates qualitatively with the beam profile shortly after the start of light exposure but takes on distinct shapes caused by the rigidity of the coverslip, beam profile, and the resin viscoelasticity. Using the conventional bonded disk geometry and uniform beam profile from a light curing unit, the axial 2D shrinkage field was uniform to within 4% in the central part of bonded disk samples. Copyright © 2016 The Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

  7. Partial pressure (or fugacity) of carbon dioxide, dissolved inorganic carbon, temperature, salinity and other variables collected from discrete sample, profile and time series profile observations using CTD, bottle and other instruments from ARNI FRIDRIKSSON and BJARNI SAEMUNDSSON in the North Greenland Sea from 1991-08-15 to 2006-10-02 (NODC Accession 0100063)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NCEI Accession 0100063 includes chemical, discrete sample, physical, profile and time series profile data collected from ARNI FRIDRIKSSON and BJARNI SAEMUNDSSON in...

  8. Partial pressure (or fugacity) of carbon dioxide, dissolved inorganic carbon, temperature, salinity and other variables collected from discrete sample, profile and time series profile observations using CTD, bottle and other instruments from ARNI FRIDRIKSSON and BJARNI SAEMUNDSSON in the North Atlantic Ocean from 1991-08-08 to 2006-02-02 (NODC Accession 0100114)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NCEI Accession 0100114 includes chemical, discrete sample, physical, profile and time series profile data collected from ARNI FRIDRIKSSON and BJARNI SAEMUNDSSON in...

  9. Dissolved inorganic carbon, alkalinity, temperature, salinity and other variables collected from discrete sample, profile and time series profile observations using CTD, bottle and other instruments from LA CURIEUSE in the Indian Ocean from 1990-01-27 to 1995-01-08 (NODC Accession 0112882)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NCEI Accession 0112882 includes biological, chemical, discrete sample, physical, profile and time series profile data collected from LA CURIEUSE in the Indian Ocean...

  10. Partial pressure (or fugacity) of carbon dioxide, dissolved inorganic carbon, pH, alkalinity, temperature, salinity and other variables collected from discrete sample, profile and time series profile observations using Alkalinity titrator, CTD and other instruments from HERMANO GINES in the Caribbean Sea from 1995-11-08 to 2015-07-29 (NODC Accession 0112926)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NCEI Accession 0112926 includes discrete sample, profile and time series profile data collected from HERMANO GINES in the Caribbean Sea from 1995-11-08 to...

  11. Dissolved inorganic carbon, alkalinity, temperature, salinity and other variables collected from discrete sample, profile and time series profile observations using Alkalinity titrator, CTD and other instruments from POLARFRONT in the Norwegian Sea from 2001-10-31 to 2007-11-29 (NODC Accession 0112884)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NCEI Accession 0112884 includes chemical, discrete sample, physical, profile and time series profile data collected from POLARFRONT in the Norwegian Sea from...

  12. A novel method for sampling the suspended sediment load in the tidal environment using bi-directional time-integrated mass-flux sediment (TIMS) samplers

    Science.gov (United States)

    Elliott, Emily A.; Monbureau, Elaine; Walters, Glenn W.; Elliott, Mark A.; McKee, Brent A.; Rodriguez, Antonio B.

    2017-12-01

    Identifying the source and abundance of sediment transported within tidal creeks is essential for studying the connectivity between coastal watersheds and estuaries. The fine-grained suspended sediment load (SSL) makes up a substantial portion of the total sediment load carried within an estuarine system and efficient sampling of the SSL is critical to our understanding of nutrient and contaminant transport, anthropogenic influence, and the effects of climate. Unfortunately, traditional methods of sampling the SSL, including instantaneous measurements and automatic samplers, can be labor intensive, expensive and often yield insufficient mass for comprehensive geochemical analysis. In estuaries this issue is even more pronounced due to bi-directional tidal flow. This study tests the efficacy of a time-integrated mass sediment sampler (TIMS) design, originally developed for uni-directional flow within the fluvial environment, modified in this work for implementation the tidal environment under bi-directional flow conditions. Our new TIMS design utilizes an 'L' shaped outflow tube to prevent backflow, and when deployed in mirrored pairs, each sampler collects sediment uniquely in one direction of tidal flow. Laboratory flume experiments using dye and particle image velocimetry (PIV) were used to characterize the flow within the sampler, specifically, to quantify the settling velocities and identify stagnation points. Further laboratory tests of sediment indicate that bidirectional TIMS capture up to 96% of incoming SSL across a range of flow velocities (0.3-0.6 m s-1). The modified TIMS design was tested in the field at two distinct sampling locations within the tidal zone. Single-time point suspended sediment samples were collected at high and low tide and compared to time-integrated suspended sediment samples collected by the bi-directional TIMS over the same four-day period. Particle-size composition from the bi-directional TIMS were representative of the array of

  13. Consumer-based product characterization using Pivot Profile, Projective Mapping and Check-all-that-apply (CATA): A comparative case with Greek yogurt samples.

    Science.gov (United States)

    Esmerino, Erick A; Tavares Filho, Elson R; Thomas Carr, B; Ferraz, Juliana P; Silva, Hugo L A; Pinto, Letícia P F; Freitas, Mônica Q; Cruz, Adriano G; Bolini, Helena M A

    2017-09-01

    Product characterization has been a primary concern for the food industry, and methodologies based on consumers' perceptions have become popular and widely used by industries to replace classical methods. Although there are several studies on other methods, the potential of reference-based one such as Pivot Profile is still little explored. Therefore, the aims of this study were to characterize Greek yogurt samples according to consumers' perceptions using three different methodologies: Pivot Profile (PP), Check-all-that-apply (CATA), and Projective Mapping (PM), and to assess which method is easier for consumers to describe products. The rapid methodologies assessed were equally effective in characterizing the different samples; however, some drawbacks evidenced in the study can help in targeting and choosing the best method to perform the sensory characterization. Pivot Profile showed some advantages, bypassing some limitations presented by the other methods. In addition, its experimental versatility also allows for broad applications evidencing the PP technique as a promising tool for routine use. Some implications of using it were also discussed. We suggest the supplemental use of Multidimensional Alignment (MDA) as it shows more accurately the correlations between attributes and samples, especially in the case of PP data. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Metabolite profiling on wheat grain to enable a distinction of samples from organic and conventional farming systems

    OpenAIRE

    Bonte, Anja; Neuweger, Heiko; Goesmann, Alexander; Thonar, Cécile; Mäder, Paul; Langenkämper, Georg; Niehaus, Karsten

    2014-01-01

    Identification of biomarkers capable of distinguishing organic and conventional products would be highly welcome to improve the strength of food quality assurance. Metabolite profiling was used for biomarker search in organic and conventional wheat grain (Triticum aestivum L.) of 11 different old and new bread wheat cultivars grown in the DOK system comparison trial. Metabolites were extracted usingmethanol and analysed by gas chromatography–mass spectrometry.

  15. Latent homeless risk profiles of a national sample of homeless veterans and their relation to program referral and admission patterns.

    Science.gov (United States)

    Tsai, Jack; Kasprow, Wesley J; Rosenheck, Robert A

    2013-12-01

    We identified risk and need profiles of homeless veterans and examined the relation between profiles and referrals and admissions to Department of Veterans Affairs (VA) homeless service programs. We examined data from the VA's new Homeless Operations Management and Evaluation System on 120,852 veterans from 142 sites nationally in 2011 and 2012 using latent class analyses based on 9 homeless risk factors. The final 4-class solution compared both referral and admission to VA homeless services. We identified 4 latent classes: relatively few problems, dual diagnosis, poverty-substance abuse-incarceration, and disabling medical problems. Homeless veterans in the first group were more likely to be admitted to the VA's permanent supportive housing program, whereas those in the second group were more likely to be admitted to more restrictive VA residential treatment. Homeless veterans in the third group were more likely to be admitted to the VA's prisoner re-entry program, and those in the fourth group were more likely to be directed to VA medical services. The heterogeneous risk and need profiles of homeless veterans supported the diversity of VA homeless services and encouraged the development of specialized services to meet their diverse needs.

  16. Assessing mental health in boys with Duchenne muscular dystrophy: Emotional, behavioural and neurodevelopmental profile in an Italian clinical sample.

    Science.gov (United States)

    Colombo, Paola; Nobile, Maria; Tesei, Alessandra; Civati, Federica; Gandossini, Sandra; Mani, Elisa; Molteni, Massimo; Bresolin, Nereo; D'Angelo, Grazia

    2017-07-01

    To evaluate through a comprehensive protocol, the psychopathological profile of DMD boys. The primary aim of this observational study was to describe the emotional and behavioural profile and the neurodevelopmental problems of Italian boys with Duchenne Muscular Dystrophy (DMD); the secondary aim was to explore the relation between psychopathological profile and DMD genotype. 47 DMD boys, aged 2-18, were included in the study and assessed through structured and validated tools including Wechsler scales or Griffiths for cognitive ability, Child Behavior Check List (CBCL), Youth Self Report (YSR) and Strengths and Difficulties Questionnaire (SDQ) for emotional and behavioural features. Patients "at risk" based on questionnaires scores were evaluated by a clinical structured interview using Development and Well Being Assessment (DAWBA) or Autism Diagnostic Observation Schedule (ADOS), as required. The 47 enrolled patients, defined with a Full Scale Intelligence Quotient (FSIQ) of 80.38 (one SD below average), and presenting a large and significant difference in FSIQ in relation to the site of mutation along the dystrophin gene (distal mutations associated with a more severe cognitive deficit), were showing Internalizing Problems (23.4%) and Autism Spectrum Disorders (14.8%). Interestingly, an association of internalizing problems with distal deletion of the DMD gene is documented. Even though preliminary, these data show that the use of validated clinical instruments, that focus on the impact of emotional/behaviour problems on everyday life, allows to carefully identify clinically significant psychopathology. Copyright © 2017 European Paediatric Neurology Society. Published by Elsevier Ltd. All rights reserved.

  17. Optimal protein extraction methods from diverse sample types for protein profiling by using Two-Dimensional Electrophoresis (2DE).

    Science.gov (United States)

    Tan, A A; Azman, S N; Abdul Rani, N R; Kua, B C; Sasidharan, S; Kiew, L V; Othman, N; Noordin, R; Chen, Y

    2011-12-01

    There is a great diversity of protein samples types and origins, therefore the optimal procedure for each sample type must be determined empirically. In order to obtain a reproducible and complete sample presentation which view as many proteins as possible on the desired 2DE gel, it is critical to perform additional sample preparation steps to improve the quality of the final results, yet without selectively losing the proteins. To address this, we developed a general method that is suitable for diverse sample types based on phenolchloroform extraction method (represented by TRI reagent). This method was found to yield good results when used to analyze human breast cancer cell line (MCF-7), Vibrio cholerae, Cryptocaryon irritans cyst and liver abscess fat tissue. These types represent cell line, bacteria, parasite cyst and pus respectively. For each type of samples, several attempts were made to methodically compare protein isolation methods using TRI-reagent Kit, EasyBlue Kit, PRO-PREP™ Protein Extraction Solution and lysis buffer. The most useful protocol allows the extraction and separation of a wide diversity of protein samples that is reproducible among repeated experiments. Our results demonstrated that the modified TRI-reagent Kit had the highest protein yield as well as the greatest number of total proteins spots count for all type of samples. Distinctive differences in spot patterns were also observed in the 2DE gel of different extraction methods used for each type of sample.

  18. The impact of freeze-drying infant fecal samples on measures of their bacterial community profiles and milk-derived oligosaccharide content.

    Science.gov (United States)

    Lewis, Zachery T; Davis, Jasmine C C; Smilowitz, Jennifer T; German, J Bruce; Lebrilla, Carlito B; Mills, David A

    2016-01-01

    Infant fecal samples are commonly studied to investigate the impacts of breastfeeding on the development of the microbiota and subsequent health effects. Comparisons of infants living in different geographic regions and environmental contexts are needed to aid our understanding of evolutionarily-selected milk adaptations. However, the preservation of fecal samples from individuals in remote locales until they can be processed can be a challenge. Freeze-drying (lyophilization) offers a cost-effective way to preserve some biological samples for transport and analysis at a later date. Currently, it is unknown what, if any, biases are introduced into various analyses by the freeze-drying process. Here, we investigated how freeze-drying affected analysis of two relevant and intertwined aspects of infant fecal samples, marker gene amplicon sequencing of the bacterial community and the fecal oligosaccharide profile (undigested human milk oligosaccharides). No differences were discovered between the fecal oligosaccharide profiles of wet and freeze-dried samples. The marker gene sequencing data showed an increase in proportional representation of Bacteriodes and a decrease in detection of bifidobacteria and members of class Bacilli after freeze-drying. This sample treatment bias may possibly be related to the cell morphology of these different taxa (Gram status). However, these effects did not overwhelm the natural variation among individuals, as the community data still strongly grouped by subject and not by freeze-drying status. We also found that compensating for sample concentration during freeze-drying, while not necessary, was also not detrimental. Freeze-drying may therefore be an acceptable method of sample preservation and mass reduction for some studies of microbial ecology and milk glycan analysis.

  19. The impact of freeze-drying infant fecal samples on measures of their bacterial community profiles and milk-derived oligosaccharide content

    Directory of Open Access Journals (Sweden)

    Zachery T. Lewis

    2016-01-01

    Full Text Available Infant fecal samples are commonly studied to investigate the impacts of breastfeeding on the development of the microbiota and subsequent health effects. Comparisons of infants living in different geographic regions and environmental contexts are needed to aid our understanding of evolutionarily-selected milk adaptations. However, the preservation of fecal samples from individuals in remote locales until they can be processed can be a challenge. Freeze-drying (lyophilization offers a cost-effective way to preserve some biological samples for transport and analysis at a later date. Currently, it is unknown what, if any, biases are introduced into various analyses by the freeze-drying process. Here, we investigated how freeze-drying affected analysis of two relevant and intertwined aspects of infant fecal samples, marker gene amplicon sequencing of the bacterial community and the fecal oligosaccharide profile (undigested human milk oligosaccharides. No differences were discovered between the fecal oligosaccharide profiles of wet and freeze-dried samples. The marker gene sequencing data showed an increase in proportional representation of Bacteriodes and a decrease in detection of bifidobacteria and members of class Bacilli after freeze-drying. This sample treatment bias may possibly be related to the cell morphology of these different taxa (Gram status. However, these effects did not overwhelm the natural variation among individuals, as the community data still strongly grouped by subject and not by freeze-drying status. We also found that compensating for sample concentration during freeze-drying, while not necessary, was also not detrimental. Freeze-drying may therefore be an acceptable method of sample preservation and mass reduction for some studies of microbial ecology and milk glycan analysis.

  20. Principal Metabolic Flux Mode Analysis.

    Science.gov (United States)

    Bhadra, Sahely; Blomberg, Peter; Castillo, Sandra; Rousu, Juho; Wren, Jonathan

    2018-02-06

    In the analysis of metabolism, two distinct and complementary approaches are frequently used: Principal component analysis (PCA) and stoichiometric flux analysis. PCA is able to capture the main modes of variability in a set of experiments and does not make many prior assumptions about the data, but does not inherently take into account the flux mode structure of metabolism. Stoichiometric flux analysis methods, such as Flux Balance Analysis (FBA) and Elementary Mode Analysis, on the other hand, are able to capture the metabolic flux modes, however, they are primarily designed for the analysis of single samples at a time, and not best suited for exploratory analysis on a large sets of samples. We propose a new methodology for the analysis of metabolism, called Principal Metabolic Flux Mode Analysis (PMFA), which marries the PCA and stoichiometric flux analysis approaches in an elegant regularized optimization framework. In short, the method incorporates a variance maximization objective form PCA coupled with a stoichiometric regularizer, which penalizes projections that are far from any flux modes of the network. For interpretability, we also introduce a sparse variant of PMFA that favours flux modes that contain a small number of reactions. Our experiments demonstrate the versatility and capabilities of our methodology. The proposed method can be applied to genome-scale metabolic network in efficient way as PMFA does not enumerate elementary modes. In addition, the method is more robust on out-of-steady steady-state experimental data than competing flux mode analysis approaches. Matlab software for PMFA and SPMFA and data set used for experiments are available in https://github.com/aalto-ics-kepaco/PMFA. sahely@iitpkd.ac.in, juho.rousu@aalto.fi, Peter.Blomberg@vtt.fi, Sandra.Castillo@vtt.fi. Detailed results are in Supplementary files. Supplementary data are available at https://github.com/aalto-ics-kepaco/PMFA/blob/master/Results.zip.

  1. Inorganic profile of some Brazilian medicinal plants obtained from ethanolic extract and ''in natura'' samples

    Energy Technology Data Exchange (ETDEWEB)

    Ferreira, M.O.M.; de Sousa, P.T.; Salvador, V.L.R.; Sato, I.M.

    2004-10-03

    The Anadenathera macrocarpa, Schinus molle, Hymenaea courbaril, Cariniana legalis, Solidago microglossa and Stryphnodendron barbatiman, were collected ''in natura'' samples (leaves, flowers, barks and seeds) from different commercial suppliers. The pharmaco-active compounds in ethanolic extracts had been made by the Mato Grosso Federal University (UFMT). The energy-dispersive x-ray fluorescence (ED-XRF) spectrometry was used for the elemental analysis in different parts of the plants and respective ethanolic extracts. The Ca, Cl, Cu, Fe, K, Mg, Mn, Na, Ni, P, Rb, S, Sr and Zn concentrations were determined by the fundamental parameters method. Some specimens showed a similar inorganic profile for ''in natura'' and ethanolic extract samples and some ones showed a distinct inorganic profile. For example, the Anadenathera macrocarpa showed a similar concentration in Mg, P, Cu, Zn and Rb elements in ''in natura'' and ethanolic extract samples; however very different concentration in Na, S, Cl, K , Ca, Mn, Fe and Sr was observed in distinctive samples. The Solidago microglossa showed the K, Ca, Cl, S, Mg, P and Fe elements as major constituents in both samples, suggesting that the extraction process did not affect in a considerable way the ''in natura'' inorganic composition. The elemental composition of the different parts of the plants (leaves, flowers, barks and seeds) has been also determined. For example, the Schinus molle specimen showed P, K, Cl and Ca elements as major constituents in the seeds, Mg, K and Sr in the barks and Mg, S, Cl and Mn in the leaves, demonstrating a differentiated elementary distribution. These inorganic profiles will contribute to evaluate the quality control of the Brazilian herbaceous trade and also will assist to identify which parts of the medicinal plants has greater therapeutic effect.

  2. Connecting extracellular metabolomic measurements to intracellular flux states in yeast

    Directory of Open Access Journals (Sweden)

    Herrgård Markus J

    2009-03-01

    Full Text Available Abstract Background Metabolomics has emerged as a powerful tool in the quantitative identification of physiological and disease-induced biological states. Extracellular metabolome or metabolic profiling data, in particular, can provide an insightful view of intracellular physiological states in a noninvasive manner. Results We used an updated genome-scale metabolic network model of Saccharomyces cerevisiae, iMM904, to investigate how changes in the extracellular metabolome can be used to study systemic changes in intracellular metabolic states. The iMM904 metabolic network was reconstructed based on an existing genome-scale network, iND750, and includes 904 genes and 1,412 reactions. The network model was first validated by comparing 2,888 in silico single-gene deletion strain growth phenotype predictions to published experimental data. Extracellular metabolome data measured in response to environmental and genetic perturbations of ammonium assimilation pathways was then integrated with the iMM904 network in the form of relative overflow secretion constraints and a flux sampling approach was used to characterize candidate flux distributions allowed by these constraints. Predicted intracellular flux changes were consistent with published measurements on intracellular metabolite levels and fluxes. Patterns of predicted intracellular flux changes could also be used to correctly identify the regions of the metabolic network that were perturbed. Conclusion Our results indicate that integrating quantitative extracellular metabolomic profiles in a constraint-based framework enables inferring changes in intracellular metabolic flux states. Similar methods could potentially be applied towards analyzing biofluid metabolome variations related to human physiological and disease states.

  3. Evaluation of volatile profiles obtained for minimally-processed pineapple fruit samples during storage by headspace-solid phase microextraction gas chromatography-mass spectrometry

    Directory of Open Access Journals (Sweden)

    Francielle Crocetta TURAZZI

    Full Text Available Abstract This paper describes the application of the solid-phase microextraction (SPME technique for the determination and monitoring of the volatile profile of minimally-processed pineapple fruit stored at various temperatures (-12 °C, 4 °C and 25 °C for different periods (1, 4 and 10 days. The SPME fiber coating composed of Car/PDMS presented the best performance. The optimal extraction conditions obtained through a Doehlert design were 60 min at 35 °C. The profiles for the volatile compounds content of the fruit at each stage of storage were determined by gas chromatography-mass spectrometry (GC-MS. The variation in the volatile profile over time was greater when the fruit samples were stored at 25 °C and at -12 °C compared to 4 °C. Thus, according to the volatile profiles associated with the storage conditions evaluated in this study, packaged pineapple retains best its fresh fruit aroma when stored at 4 °C.

  4. Chemical profile and anti-leishmanial activity of three Ecuadorian propolis samples from Quito, Guayaquil and Cotacachi regions.

    Science.gov (United States)

    Cuesta-Rubio, Osmany; Campo Fernández, Mercedes; Márquez Hernández, Ingrid; Jaramillo, Carmita Gladys Jaramillo; González, Victor Hugo; Montes De Oca Porto, Rodny; Marrero Delange, David; Monzote Fidalgo, Lianet; Piccinelli, Anna Lisa; Campone, Luca; Rastrelli, Luca

    2017-07-01

    Three propolis samples were collected from different regions of Ecuador (Quito, Guayaquil and Cotacachi) and their methanolic extracts were prepared. Preliminary information supplied by TLC and NMR data, allowed us to define two main types of propolis: Cotacachi propoli sample (CPS), rich in flavonoids and Quito and Guayaquil samples (QPS and GPS) containing triterpenic alcohols and acetyl triterpenes as the main constituents. Two different approaches based on RP-HPLC preparative procedure and NMR structural determination (CPS) and GC-MS analysis (QPS and GPS) were successfully used for the chemical characterization of their major compounds. All three propolis extracts were able to inhibit Leishmania amazonensis growth but propolis sample rich in flavonoids was the most active (IC50=17.1±1.7μg/mL). In the literature this is the first study on propolis from Ecuador. Copyright © 2017. Published by Elsevier B.V.

  5. Extensive surface protein profiles of extracellular vesicles from cancer cells may provide diagnostic signatures from blood samples

    Directory of Open Access Journals (Sweden)

    Larissa Belov

    2016-04-01

    Full Text Available Extracellular vesicles (EV are membranous particles (30–1,000 nm in diameter secreted by cells. Important biological functions have been attributed to 2 subsets of EV, the exosomes (bud from endosomal membranes and the microvesicles (MV; bud from plasma membranes. Since both types of particles contain surface proteins derived from their cell of origin, their detection in blood may enable diagnosis and prognosis of disease. We have used an antibody microarray (DotScan to compare the surface protein profiles of live cancer cells with those of their EV, based on their binding patterns to immobilized antibodies. Initially, EV derived from the cancer cell lines, LIM1215 (colorectal cancer and MEC1 (B-cell chronic lymphocytic leukaemia; CLL, were used for assay optimization. Biotinylated antibodies specific for EpCAM (CD326 and CD19, respectively, were used to detect captured particles by enhanced chemiluminescence. Subsequently, this approach was used to profile CD19+ EV from the plasma of CLL patients. These EV expressed a subset (~40% of the proteins detected on CLL cells from the same patients: moderate or high levels of CD5, CD19, CD31, CD44, CD55, CD62L, CD82, HLA-A,B,C, HLA-DR; low levels of CD21, CD49c, CD63. None of these proteins was detected on EV from the plasma of age- and gender-matched healthy individuals.

  6. Sample size estimation to substantiate freedom from disease for clustered binary data with a specific risk profile

    DEFF Research Database (Denmark)

    Kostoulas, P.; Nielsen, Søren Saxmose; Browne, W. J.

    2013-01-01

    SUMMARY Disease cases are often clustered within herds or generally groups that share common characteristics. Sample size formulae must adjust for the within-cluster correlation of the primary sampling units. Traditionally, the intra-cluster correlation coefficient (ICC), which is an average meas...... subsp. paratuberculosis infection, in Danish dairy cattle and a study on critical control points for Salmonella cross-contamination of pork, in Greek slaughterhouses....

  7. [Genetic profiling of Giardia intestinalis by polimerase chain in human and dogs samples of Colombian Caribean Coast].

    Science.gov (United States)

    Arroyo-Salgado, Bárbara; Buelvas-Montes, Yaleyvis; Villalba-Vizcaíno, Vivian; Salomón-Arzuza, Octavio

    2014-01-01

    Giardia intestinalis (G. Intestinalis) is a protozoan that causes diarrheal disease and malabsorption syndrome in humans and other mammals. It presents a high genetic diversity evidenced in the recognition of 7 genotypes (A-G). Genotypes A and B are commonly associated to humans and domestic animals such as dogs. The aim of this study was to conduct a preliminary genetic characterization of G. intestinalis in humans and dogs from two cities on the Caribbean coast of Colombia. Sampling areas were selected according to the highest numbers of acute diarrheal disease. Stool samples were collected from children under 7 years old, with positive medical tests for G. intestinalis. Cysts were purified by sucrose gradient and DNA samples were isolated by extraction with organic solvents. Molecular characterization was performed by amplifying the gene triose phosphate isomerase (tpi) by using a semi-nested PCR. A total of 202 samples of DNA were obtained; of these, 111 were positive in coproparasitological analysis (13 dogs and 98 children). Genotype distribution in positive samples was: 5.1% belonged to genotype A and 92.3% to genotype B. Genotype B was present in humans and animals. The most common genotype in both human and animal samples was genotype B, suggesting a zoonotic transmission cycle. Copyright © 2012 Elsevier España, S.L.U. y Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

  8. Expression profiling of blood samples from an SU5416 Phase III metastatic colorectal cancer clinical trial: a novel strategy for biomarker identification

    Directory of Open Access Journals (Sweden)

    Smolich Beverly D

    2003-02-01

    Full Text Available Abstract Background Microarray-based gene expression profiling is a powerful approach for the identification of molecular biomarkers of disease, particularly in human cancers. Utility of this approach to measure responses to therapy is less well established, in part due to challenges in obtaining serial biopsies. Identification of suitable surrogate tissues will help minimize limitations imposed by those challenges. This study describes an approach used to identify gene expression changes that might serve as surrogate biomarkers of drug activity. Methods Expression profiling using microarrays was applied to peripheral blood mononuclear cell (PBMC samples obtained from patients with advanced colorectal cancer participating in a Phase III clinical trial. The PBMC samples were harvested pre-treatment and at the end of the first 6-week cycle from patients receiving standard of care chemotherapy or standard of care plus SU5416, a vascular endothelial growth factor (VEGF receptor tyrosine kinase (RTK inhibitor. Results from matched pairs of PBMC samples from 23 patients were queried for expression changes that consistently correlated with SU5416 administration. Results Thirteen transcripts met this selection criterion; six were further tested by quantitative RT-PCR analysis of 62 additional samples from this trial and a second SU5416 Phase III trial of similar design. This method confirmed four of these transcripts (CD24, lactoferrin, lipocalin 2, and MMP-9 as potential biomarkers of drug treatment. Discriminant analysis showed that expression profiles of these 4 transcripts could be used to classify patients by treatment arm in a predictive fashion. Conclusions These results establish a foundation for the further exploration of peripheral blood cells as a surrogate system for biomarker analyses in clinical oncology studies.

  9. Aircraft trace gas measurements during the London 2012 Olympics: Air quality and emission fluxes derived from sampling upwind and downwind of a megacity

    Science.gov (United States)

    Allen, G.; O'Shea, S.; Muller, J.; Jones, B.; O'Sullivan, D.; Lee, J. D.; Bauguitte, S.; Gallagher, M. W.; Percival, C.; Barratt, B.; McQuaid, J. B.; Illingworth, S.

    2013-12-01

    This study presents airborne in situ and remote sensing measurements recorded during July and August 2012, across the period of the London 2012 Summer Olympics and simultaneous with the Clear air for London (ClearfLo) ground-based measurement and modelling campaign. Through long-term (2-year) and intensive observation periods (Winter 2011 and Summer 2012), the ClearfLo programme aims to better understand emissions, as well as the chemical, dynamical and micro-meteorological processes which modulate air quality in the London urban environment - an important risk factor for both acute and chronic health effects. The work presented here focuses on two contrasting case studies within the summer ClearfLo period: 30 July 2012 and 9 August 2012, representing relatively clean background and polluted background cases, respectively, and characterised by well-mixed Atlantic westerly maritime inflow in the former and stagnant air (high pressure) in the latter. Measurements of CO, CO2, CH4, N2O, O3, HCN, and other gases measured on board the UK Facility for Airborne Atmospheric Measurement (FAAM) BAe-146 aircraft will be presented and interpreted, with emphasis on observed concentration gradients and tracer-tracer correlations as well as airmass vertical structure and airmass history upwind and downwind of central London in each case. By applying a simple advective model and making use of vertically resolved thermodynamic and composition data, we are able to derive emission strengths for these gases that are representative of the total enclosed surface area. Example emissions for these two cases range between 6x105 kg(C)/hr and 9x105 kg(C)/hr for CO2, and ~0.6x105 kg(C)/hr for CH4. This airborne sampling methodology highlights the unique utility of aircraft measurements to routinely and climatologically characterise emissions from area sources such as cities, and points to future missions to target localised hotspots and distributed point sources.

  10. Not-so-clean fun: a profile of bath salt users among a college sample in the United States.

    Science.gov (United States)

    Miller, Bryan Lee; Stogner, John M

    2014-01-01

    This research examines the characteristics of users of synthetic stimulants marketed as "bath salts." Synthetic stimulants such as MDPV (3,4-Methylenedioxypyrovalerone), Mephedrone (4-Methylmethcathinone), and Methylone (3,4-Methylenedioxymethcathinone) are often contained in products sold at convenience stores and over the Internet in the United States. Despite the recent legal action banning these types of synthetic stimulants, little is known about the characteristics of the users of these substances. This research provides a profile of bath salt users in the United States among an emerging adult population. A self-report survey instrument was administered to 2,349 students at a large university in the southeastern United States. Respondents indicated whether they had used synthetic stimulants and reported demographic characteristics. Results indicated that users of bath salts were more likely to be male, Hispanic or Native American, student athletes, employed, identify as a members of the LGBT community, and users of other substances.

  11. SaVanT: a web-based tool for the sample-level visualization of molecular signatures in gene expression profiles.

    Science.gov (United States)

    Lopez, David; Montoya, Dennis; Ambrose, Michael; Lam, Larry; Briscoe, Leah; Adams, Claire; Modlin, Robert L; Pellegrini, Matteo

    2017-10-25

    Molecular signatures are collections of genes characteristic of a particular cell type, tissue, disease, or perturbation. Signatures can also be used to interpret expression profiles generated from heterogeneous samples. Large collections of gene signatures have been previously developed and catalogued in the MSigDB database. In addition, several consortia and large-scale projects have systematically profiled broad collections of purified primary cells, molecular perturbations of cell types, and tissues from specific diseases, and the specificity and breadth of these datasets can be leveraged to create additional molecular signatures. However, to date there are few tools that allow the visualization of individual signatures across large numbers of expression profiles. Signature visualization of individual samples allows, for example, the identification of patient subcategories a priori on the basis of well-defined molecular signatures. Here, we generate and compile 10,985 signatures (636 newly-generated and 10,349 previously available from MSigDB) and provide a web-based Signature Visualization Tool (SaVanT; http://newpathways.mcdb.ucla.edu/savant ), to visualize these signatures in user-generated expression data. We show that using SaVanT, immune activation signatures can distinguish patients with different types of acute infections (influenza A and bacterial pneumonia). Furthermore, SaVanT is able to identify the prominent signatures within each patient group, and identify the primary cell types underlying different leukemias (acute myeloid and acute lymphoblastic) and skin disorders. The development of SaVanT facilitates large-scale analysis of gene expression profiles on a patient-level basis to identify patient subphenotypes, or potential therapeutic target pathways.

  12. Meta-analysis of gene expression profiles associated with histological classification and survival in 829 ovarian cancer samples.

    Science.gov (United States)

    Fekete, Tibor; Rásó, Erzsébet; Pete, Imre; Tegze, Bálint; Liko, István; Munkácsy, Gyöngyi; Sipos, Norbert; Rigó, János; Györffy, Balázs

    2012-07-01

    Transcriptomic analysis of global gene expression in ovarian carcinoma can identify dysregulated genes capable to serve as molecular markers for histology subtypes and survival. The aim of our study was to validate previous candidate signatures in an independent setting and to identify single genes capable to serve as biomarkers for ovarian cancer progression. As several datasets are available in the GEO today, we were able to perform a true meta-analysis. First, 829 samples (11 datasets) were downloaded, and the predictive power of 16 previously published gene sets was assessed. Of these, eight were capable to discriminate histology subtypes, and none was capable to predict survival. To overcome the differences in previous studies, we used the 829 samples to identify new predictors. Then, we collected 64 ovarian cancer samples (median relapse-free survival 24.5 months) and performed TaqMan Real Time Polimerase Chain Reaction (RT-PCR) analysis for the best 40 genes associated with histology subtypes and survival. Over 90% of subtype-associated genes were confirmed. Overall survival was effectively predicted by hormone receptors (PGR and ESR2) and by TSPAN8. Relapse-free survival was predicted by MAPT and SNCG. In summary, we successfully validated several gene sets in a meta-analysis in large datasets of ovarian samples. Additionally, several individual genes identified were validated in a clinical cohort. Copyright © 2011 UICC.

  13. PARTICULATE ORGANIC CARBON and PARTICULATE ORGANIC NITROGEN profile, discrete sample and site samples data collected in the South Atlantic Ocean and South Pacific Ocean on the NATHANIEL B. PALMER cruises NBP0103, NBP0104 and others as part of the Southern Ocean GLOBEC project from 2001-04-29 to 2002-09-12 (NODC Accession 0112164)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0112164 includes profile, discrete sample, site samples and chemical data collected aboard the NATHANIEL B. PALMER during cruises NBP0103, NBP0104,...

  14. Cancer associated epigenetic transitions identified by genome-wide histone methylation binding profiles in human colorectal cancer samples and paired normal mucosa

    Directory of Open Access Journals (Sweden)

    Wallerman Ola

    2011-10-01

    Full Text Available Abstract Background Despite their well-established functional roles, histone modifications have received less attention than DNA methylation in the cancer field. In order to evaluate their importance in colorectal cancer (CRC, we generated the first genome-wide histone modification profiles in paired normal colon mucosa and tumor samples. Methods Chromatin immunoprecipitation and microarray hybridization (ChIP-chip was used to identify promoters enriched for histone H3 trimethylated on lysine 4 (H3K4me3 and lysine 27 (H3K27me3 in paired normal colon mucosa and tumor samples from two CRC patients and for the CRC cell line HT29. Results By comparing histone modification patterns in normal mucosa and tumors, we found that alterations predicted to have major functional consequences were quite rare. Furthermore, when normal or tumor tissue samples were compared to HT29, high similarities were observed for H3K4me3. However, the differences found for H3K27me3, which is important in determining cellular identity, indicates that cell lines do not represent optimal tissue models. Finally, using public expression data, we uncovered previously unknown changes in CRC expression patterns. Genes positive for H3K4me3 in normal and/or tumor samples, which are typically already active in normal mucosa, became hyperactivated in tumors, while genes with H3K27me3 in normal and/or tumor samples and which are expressed at low levels in normal mucosa, became hypersilenced in tumors. Conclusions Genome wide histone modification profiles can be used to find epigenetic aberrations in genes associated with cancer. This strategy gives further insights into the epigenetic contribution to the oncogenic process and may identify new biomarkers.

  15. Physicochemical characteristics and sensory profile of honey samples from stingless bees (Apidae: Meliponinae) submitted to a dehumidification process.

    Science.gov (United States)

    Carvalho, Carlos A L; Sodré, Geni S; Fonseca, Antonio A O; Alves, Rogério M O; Souza, Bruno A; Clarton, Lana

    2009-03-01

    This study was conducted to evaluate the effect of a dehumidification process on the physicochemical and sensory characteristics of stingless-bee honey. Melipona scutellaris and M. quadrifasciata honey samples were submitted to a dehumidification process and to physicochemical (reducing sugars, apparent sucrose, moisture, diastatic activity, hydroxymethylfurfural, ash, pH, acidity, and electric conductivity) and sensory evaluations (fluidity, color, aroma, crystallization,flavor,and acceptability). The results indicated that the dehumidification process does not interfere with honey quality and acceptability.

  16. Metabolomics profiling of pre-and post-anesthesia plasma samples of colorectal patients obtained via Ficoll separation

    OpenAIRE

    Ghini, Veronica; Unger, Florian T; Tenori, Leonardo; Turano, Paola; Juhl, Hartmut; David, Kerstin A.

    2015-01-01

    1H NMR spectroscopy was used to investigate the metabolic consequences of general anesthesia in the plasma of two groups of patients with diagnosis for non-metastatic colorectal cancer and metastatic colorectal cancer with liver-metastasis, respectively. Patients were treated with etomidate or propofol, two frequently used sedation agents. Plasma samples were obtained via Ficoll separation. Here, we demonstrated that this procedure introduces a number of limitations for NMR-based metabolomics...

  17. Diagnostic Role of MicroRNA Expression Profile in the Prenatal Amniotic Fluid Samples of Pregnant Women with Down Syndrome.

    Science.gov (United States)

    Karaca, Emin; Aykut, Ayça; Ertürk, Biray; Durmaz, Burak; Güler, Ahmet; Büke, Barış; Yeniel, Ahmet Özgür; Ergenoğlu, Ahmet Mete; Özkınay, Ferda; Özeren, Mehmet; Kazandı, Mert; Akercan, Fuat; Sağol, Sermet; Gündüz, Cumhur; Çoğulu, Özgür

    2017-12-08

    Down syndrome is the most common chromosomal anomaly in humans. Down syndrome is the most common chromosomal anomaly in humans affecting people from every race and age. Most of the cases are can be diagnosed by prenatal diagnostic methods in pregnancy. Due to the longtime of culture method applied for prenatal diagnosis, genetic analysis has been developed and developing for rapid diagnosis. For this reason, the effective use of miRNAs was investigated in the rapid analysis of prenatal samples with Down syndrome. We evaluated the expression levels of 14 miRNAs, located on chromosome 21 in prenatal samples and their utility for prenatal testing of Down syndrome. Case-control study. A total of 56 patients who underwent invasive prenatal testing, 23 carrying fetuses with DS; 33 control cases carrying fetuses with normal karyotype, were included. Indications for invasive prenatal testing were advanced maternal age and increased risk of Down syndrome in screening tests. Gestation weeks ranged between 17-18 in study and control groups. MicroRNA expression levels were measured by real-time-polymerase chain reaction. miR-125b-2, miR-155 and miR-3156 expression levels were significantly higher in prenatal samples. Significantly dysregulated miRNAs either may be associated with the phenotype or may be the result of abnormal development. Further large scale comparative studies carried out in a variety of conditions may bring novel insights in the field of abnormal conditions.

  18. MicroRNA profiling of dogs with transitional cell carcinoma of the bladder using blood and urine samples.

    Science.gov (United States)

    Kent, Michael S; Zwingenberger, Allison; Westropp, Jodi L; Barrett, Laura E; Durbin-Johnson, Blythe P; Ghosh, Paramita; Vinall, Ruth L

    2017-11-15

    Early signs of canine transitional cell carcinoma (TCC) are frequently assumed to be caused by other lower urinary tract diseases (LUTD) such as urinary tract infections, resulting in late diagnosis of TCC which could be fatal. The development of a non-invasive clinical test for TCC could dramatically reduce mortality. To determine whether microRNAs (miRNAs) can be used as non-invasive diagnostic biomarkers, we assessed miRNA expression in blood and/or urine from dogs with clinically normal bladders (n = 28), LUTD (n = 25), and TCC (n = 17). Expression levels of 5 miRNA associated with TCC pathophysiology (miR-34a, let-7c, miR-16, miR-103b, and miR-106b) were assessed by quantitative real-time PCR. Statistical analyses using ranked ANOVA identified significant differences in miR-103b and miR-16 levels between urine samples from LUTD and TCC patients (miR-103b, p = 0.002; and miR-16, p = 0.016). No statistically significant differences in miRNA levels were observed between blood samples from LUTD versus TCC patients. Expression levels of miR-34a trended with miR-16, let-7c, and miR-103b levels in individual normal urine samples, however, this coordination was completely lost in TCC urine samples. In contrast, co-ordination of miR-34a, miR-16, let-7c, and miR-103b expression levels was maintained in blood samples from TCC patients. Our combined data indicate a potential role for miR-103b and miR-16 as diagnostic urine biomarkers for TCC, and that further investigation of miR-103b and miR-16 in the dysregulation of coordinated miRNA expression in bladder carcinogenesis is warranted.

  19. Cross-reactivity profiles of hybrid capture II, cobas, and APTIMA human papillomavirus assays: split-sample study.

    Science.gov (United States)

    Preisler, Sarah; Rebolj, Matejka; Ejegod, Ditte Møller; Lynge, Elsebeth; Rygaard, Carsten; Bonde, Jesper

    2016-07-20

    High-risk Human Papillomavirus (HPV) testing is replacing cytology in cervical cancer screening as it is more sensitive for preinvasive cervical lesions. However, the bottleneck of HPV testing is the many false positive test results (positive tests without cervical lesions). Here, we evaluated to what extent these can be explained by cross-reactivity, i.e. positive test results without evidence of high-risk HPV genotypes. The patterns of cross-reactivity have been thoroughly studied for hybrid capture II (HC2) but not yet for newer HPV assays although the manufacturers claimed no or limited frequency of cross-reactivity. In this independent study we evaluated the frequency of cross-reactivity for HC2, cobas, and APTIMA assays. Consecutive routine cervical screening samples from 5022 Danish women, including 2859 from women attending primary screening, were tested with the three evaluated DNA and mRNA HPV assays. Genotyping was undertaken using CLART HPV2 assay, individually detecting 35 genotypes. The presence or absence of cervical lesions was determined with histological examinations; women with abnormal cytology were managed as per routine recommendations; those with normal cytology and positive high-risk HPV test results were invited for repeated testing in 18 months. Cross-reactivity to low-risk genotypes was detected in 109 (2.2 %) out of 5022 samples on HC2, 62 (1.2 %) on cobas, and 35 (0.7 %) on APTIMA with only 10 of the samples cross-reacting on all 3 assays. None of the 35 genotypes was detected in 49 (1.0 %), 162 (3.2 %), and 56 (1.1 %) samples, respectively. In primary screening at age 30 to 65 years (n = 2859), samples of 72 (25 %) out of 289 with high-risk infections on HC2 and < CIN2 histology were due to cross-reactivity. On cobas, this was 106 (26 %) out of 415, and on APTIMA 48 (21 %) out of 224. Despite manufacturer claims, all three assays showed cross-reactivity. In primary cervical screening at age ≥30 years, cross

  20. Critical flux determination by flux-stepping

    DEFF Research Database (Denmark)

    Beier, Søren; Jonsson, Gunnar Eigil

    2010-01-01

    In membrane filtration related scientific literature, often step-by-step determined critical fluxes are reported. Using a dynamic microfiltration device, it is shown that critical fluxes determined from two different flux-stepping methods are dependent upon operational parameters such as step...... length, step height, and.flux start level. Filtrating 8 kg/m(3) yeast cell suspensions by a vibrating 0.45 x 10(-6) m pore size microfiltration hollow fiber module, critical fluxes from 5.6 x 10(-6) to 1.2 x 10(-5) m/s have been measured using various step lengths from 300 to 1200 seconds. Thus...

  1. Techniques of Ozone Monitoring in a Mountain Forest Region: Passive and Continuous Sampling, Vertical and Canopy Profiles

    Directory of Open Access Journals (Sweden)

    Giacomo Gerosa

    2001-01-01

    Full Text Available Ozone is the most harmful air pollutant for plant ecosystems in the Mediterranean and Alpine areas due to its biological and economic damage to crops and forests. In order to evaluate the relation between ozone exposure and vegetation injury under on-field conditions, suitable ozone monitoring techniques were investi-gated. In the framework of a 5-year research project aimed at ozone risk assessment on forests, both continuous analysers and passive samplers were employed during the summer seasons (1994�1998 in different sites of a wide mountain region (80 x 40 km2 on the southern slope of the European Alps. Continuous analysers allowed the recording of ozone hourly concentration means necessary both to calculate specific exposure indexes (such as AOT, SUM, W126 and to record daily time-courses. Passive samplers, even though supplied only weekly mean concentration values, made it possible to estimate the altitude concentration gradient useful to correct the altitude dependence of ozone concentrations to be inserted into exposure indexes. In-canopy ozone profiles were also determined by placing passive samplers at different heights inside the forest canopy. Vertical ozone soundings by means of tethered balloons (kytoons allowed the measurement of the vertical concentration gradient above the forest canopy. They also revealed ozone reservoirs aloft and were useful to explain the ozone advection dynamic in mountain slopes where ground measurement proved to be inadequate. An intercomparison between passive (PASSAM, CH and continuous measurements highlighted the necessity to accurately standardize all the exposure operations, particularly the pre- and postexposure conservation at cold temperature to avoid dye (DPE activity. Advantages and disadvantages from each mentioned technique are discussed.

  2. Prevalence, Virulence Potential, and Antibiotic Susceptibility Profile of Listeria monocytogenes Isolated From Bovine Raw Milk Samples Obtained From Rajasthan, India.

    Science.gov (United States)

    Sharma, Sanjita; Sharma, Vishnu; Dahiya, Dinesh Kumar; Khan, Aarif; Mathur, Manisha; Sharma, Amit

    2017-03-01

    Listeriosis is a serious foodborne disease of a global concern, and can effectively be controlled by a continuous surveillance of the virulent and multidrug-resistant strains of Listeria monocytogenes. This study was planned to investigate prevalence of L. monocytogenes in bovine raw milk samples. A total of 457 raw milk samples collected from 15 major cities in Rajasthan, India, were analyzed for the presence of L. monocytogenes by using standard microbiological and molecular methods. Five of the 457 samples screen tested positive for L. monocytogenes. Multiplex serotyping showed that 3/5 strains belonged to serotype 4b followed by one strain each to 1/2a and to 1/2c. Further virulence potential assessment indicated that all strains possessed inlA and inlC internalins, and, in addition, two strains also possessed the gene for inlB. All strains were positive for Listeriolysin O (LLO) and showed phosphatidylinositol-specific phospholipase C (PI-PLC) activity on an in vitro agar medium with variations in production levels among the strains. A good correlation between the in vitro pathogenicity test and the chick embryo test was observed, as the strains showing higher LLO and PI-PLC activity were found to be lethal to fertilized chick embryos. All strains were resistant to the majority of antibiotics and were designated as multidrug-resistant strains. However, these strains were susceptible to 9 of the 22 tested antibiotics. The maximum zone of inhibition (mm) and acceptable minimum inhibitory concentration were observed with azithromycin, and thus it could be the first choice of a treatment. Overall, the presence of multidrug-resistant L. monocytogenes strains in the raw milk of Rajasthan region is an indicator of public health hazard and highlighting the need of consumer awareness in place and implementation of stricter food safety regulations at all levels of milk production.

  3. Sequential enzymatic derivatization coupled with online microdialysis sampling for simultaneous profiling of mouse tumor extracellular hydrogen peroxide, lactate, and glucose.

    Science.gov (United States)

    Su, Cheng-Kuan; Tseng, Po-Jen; Chiu, Hsien-Ting; Del Vall, Andrea; Huang, Yu-Fen; Sun, Yuh-Chang

    2017-03-01

    Probing tumor extracellular metabolites is a vitally important issue in current cancer biology. In this study an analytical system was constructed for the in vivo monitoring of mouse tumor extracellular hydrogen peroxide (H2O2), lactate, and glucose by means of microdialysis (MD) sampling and fluorescence determination in conjunction with a smart sequential enzymatic derivatization scheme-involving a loading sequence of fluorogenic reagent/horseradish peroxidase, microdialysate, lactate oxidase, pyruvate, and glucose oxidase-for step-by-step determination of sampled H2O2, lactate, and glucose in mouse tumor microdialysate. After optimization of the overall experimental parameters, the system's detection limit reached as low as 0.002 mM for H2O2, 0.058 mM for lactate, and 0.055 mM for glucose, based on 3 μL of microdialysate, suggesting great potential for determining tumor extracellular concentrations of lactate and glucose. Spike analyses of offline-collected mouse tumor microdialysate and monitoring of the basal concentrations of mouse tumor extracellular H2O2, lactate, and glucose, as well as those after imparting metabolic disturbance through intra-tumor administration of a glucose solution through a prior-implanted cannula, were conducted to demonstrate the system's applicability. Our results evidently indicate that hyphenation of an MD sampling device with an optimized sequential enzymatic derivatization scheme and a fluorescence spectrometer can be used successfully for multi-analyte monitoring of tumor extracellular metabolites in living animals. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. Comparative studies on polyphenolic profile and antimicrobial activity of propolis samples selected from distinctive geographical areas of Hungary.

    Science.gov (United States)

    Molnár, Szabolcs; Mikuska, Kata; Patonay, Katalin; Sisa, Krisztina; Daood, Hussein G; Némedi, Erzsébet; Kiss, Attila

    2017-06-01

    The present paper reports about a comparative survey on the chemical composition, antioxidant activity and in vitro antimicrobial activity of selected propolis samples collected in Hungary. The total levels of polyphenolic compounds including flavonoids in ethanolic extracts of propolis were assessed. The major constituents of ethanolic extracts of propolis were analysed by gas chromatography/mass spectrometry analysis. Total phenolic content was determined spectrophotometrically using a Folin-Ciocalteu reagent. Free radical scavenging activities were evaluated by means of 2,2-diphenyl-1-picrylhydrazyl assay. In vitro inhibitory activity was investigated against eight different bacterial strains by agar well diffusion assay. An extensive comparison was carried out regarding general parameters and specific polyphenolic components. The experimental data led to the observation that there is considerable variability in terms of the quality and the biological value of the distinctive propolis samples. These findings confirm the hypothesis of the study; versatile experimental results are required for proper, well-reasoned, balanced and standardised industrial applications. The major flavonoid components were found to be chrysin and pinocembrin; however, versatile minor components were also detected. The total polyphenol content of ethanolic extracts of propolis ranged between 104.6 mg/g and 286.9 mg/g (gallic acid equivalent). The radical scavenging activity of ethanolic extracts of propolis varied between 101.7 mg/g and 286.9 mg/g (ascorbic acid equivalent). As the quality of propolis depends on the season, vegetation and the area of collection, marked differences were found among the different products examined in terms of both composition and general characteristics. The studied samples exhibited significant differences in term of antimicrobial activities.

  5. Bacteriological Profile and Antimicrobial Susceptibility Patterns of Bacteria Isolated from Pus/Wound Swab Samples from Children Attending a Tertiary Care Hospital in Kathmandu, Nepal

    Directory of Open Access Journals (Sweden)

    Salu Rai

    2017-01-01

    Full Text Available In Nepal, little is known about the microbiological profile of wound infections in children and their antimicrobial susceptibility patterns. Total of 450 pus/wound swab samples collected were cultured using standard microbiological techniques and the colonies grown were identified with the help of biochemical tests. The antimicrobial susceptibility testing was performed by Kirby-Bauer disc diffusion technique. Methicillin-resistant Staphylococcus aureus isolates were detected by using cefoxitin disc and confirmed by determining minimum inhibitory concentrations (MIC of oxacillin. 264 (59% samples were culture positive. The highest incidence of bacterial infections was noted in the age group of less than 1 year (76%. Out of 264 growth positive samples, Gram-positive bacteria were isolated from 162 (61% samples and Gram-negative bacteria were found in 102 (39% samples. Staphylococcus aureus (99% was the predominant Gram-positive bacteria isolated and Pseudomonas aeruginosa (44% was predominant Gram-negative bacteria. About 19% of S. aureus isolates were found to be methicillin-resistant MIC of oxacillin ranging from 4 μg/mL to 128 μg/mL. Among the children of Nepal, those of age less than 1 year were at higher risk of wound infections by bacteria. Staphylococcus aureus followed by Pseudomonas aeruginosa were the most common bacteria causing wound infections in children.

  6. Potential bacterial core species associated with digital dermatitis in cattle herds identified by molecular profiling of interdigital skin samples

    DEFF Research Database (Denmark)

    Weiss Nielsen, Martin; Strube, Mikael Lenz; Isbrand, Anastasia

    2016-01-01

    of different molecular methods. Deep sequencing of the 16S rRNA gene variable regions V1–V2 showed that Treponema, Mycoplasma, Fusobacterium and Porphyromonas were the genera best differentiating the DD samples from the controls. Additional deep sequencing analysis of the most abundant genus, Treponema......, targeting another variable region of the 16S rRNA gene, V3–V4, identified 15 different phylotypes, among which Treponema phagedenis-like and Treponema refringens-like species were the most abundant. Although the presence of Treponema spp., Fusobacterium necrophorum and Porphyromonas levii was confirmed...

  7. Versatile pulsed laser setup for depth profiling analysis of multilayered samples in the field of cultural heritage

    Science.gov (United States)

    Mendes, N. F. C.; Osticioli, I.; Striova, J.; Sansonetti, A.; Becucci, M.; Castellucci, E.

    2009-04-01

    The present study considers the use of a nanosecond pulsed laser setup capable of performing laser induced breakdown spectroscopy (LIBS) and pulsed Raman spectroscopy for the study of multilayered objects in the field of cultural heritage. Controlled etching using the 4th harmonic 266 nm emission of a Nd:YAG laser source with a 8 ns pulse duration was performed on organic films and mineral strata meant to simulate different sequence of layers usually found in art objects such as in easel and mural paintings. The process of micro ablation coupled with powerful spectroscopic techniques operating with the same laser source, constitutes an interesting alternative to mechanical sampling especially when dealing with artworks such as ceramics and metal works which are problematic due to their hardness and brittleness. Another case is that of valuable pieces where sampling is not an option and the materials to analyse lie behind the surface. The capabilities and limitations of such instrumentation were assessed through several tests in order to characterize the trend of the laser ablation on different materials. Monitored ablation was performed on commercial sheets of polyethylene terephthalate (PET), a standard material of known thickness and mechanical stability, and rabbit glue, an adhesive often used in works of art. Measurements were finally carried out on a specimen with a stratigraphy similar to those found in real mural paintings.

  8. Comprehensive profiling of retroviral integration sites using target enrichment methods from historical koala samples without an assembled reference genome

    Directory of Open Access Journals (Sweden)

    Pin Cui

    2016-03-01

    Full Text Available Background. Retroviral integration into the host germline results in permanent viral colonization of vertebrate genomes. The koala retrovirus (KoRV is currently invading the germline of the koala (Phascolarctos cinereus and provides a unique opportunity for studying retroviral endogenization. Previous analysis of KoRV integration patterns in modern koalas demonstrate that they share integration sites primarily if they are related, indicating that the process is currently driven by vertical transmission rather than infection. However, due to methodological challenges, KoRV integrations have not been comprehensively characterized. Results. To overcome these challenges, we applied and compared three target enrichment techniques coupled with next generation sequencing (NGS and a newly customized sequence-clustering based computational pipeline to determine the integration sites for 10 museum Queensland and New South Wales (NSW koala samples collected between the 1870s and late 1980s. A secondary aim of this study sought to identify common integration sites across modern and historical specimens by comparing our dataset to previously published studies. Several million sequences were processed, and the KoRV integration sites in each koala were characterized. Conclusions. Although the three enrichment methods each exhibited bias in integration site retrieval, a combination of two methods, Primer Extension Capture and hybridization capture is recommended for future studies on historical samples. Moreover, identification of integration sites shows that the proportion of integration sites shared between any two koalas is quite small.

  9. Molecular characterization of Salmonella enterica serotype Enteritidis isolates from food and human samples by serotyping, antimicrobial resistance, plasmid profiling, (GTG5-PCR and ERIC-PCR

    Directory of Open Access Journals (Sweden)

    F. Fardsanei

    2016-11-01

    Full Text Available In recent years, Salmonella enterica serovar Enteritidis has been a primary cause of human salmonellosis in many countries. The major objective of this study was to investigate genetic diversity among Salmonella Enteritidis strains from different origins (food and human by Enterobacterial Repetitive Intergenic Consensus (ERIC -PCR, as well as to assess their plasmid profiling and antimicrobial resistance. A total of 30 Salmonella Enteritidis isolates, 15 from food samples (chicken, lamb, beef and duck meats and 15 from clinical samples were collected in Tehran. Identification of isolates as Salmonella was confirmed by using conventional standard biochemical and serological tests. Multiplex-PCR was used for serotyping of isolates to identify Salmonella Enteritidis. Antimicrobial susceptibility testing to 16 agents founds drug resistance patterns among Salmonella Enteritidis isolates. No resistance was observed to cephalexin, ceftriaxone, ceftazidime and cefotaxime, ciprofloxacin, imipenem or meropenem, chloramphenicol and gentamicin. The highest resistance (96.7% was observed to nitrofurantoin. Seven plasmid profiles (P1–P7 were detected, and a 68-kb plasmid was found in all isolates. Two different primers; ERIC and (GTG5 were used for genotyping, which each produced four profiles. The majority of clinical and food isolates fell into two separate common types (CTs with a similar percentage of 95% by ERIC-PCR. Using primer (GTG5, 29 isolates incorporated in three CTs with 70% of isolates showing a single banding pattern. Limited genetic diversity among human and food isolates of Salmonella Enteritidis may indicate that contaminated foods were possibly the source of human salmonellosis. These results confirmed that ERIC-PCR genotyping has limited discriminatory power for Salmonella Enteritidis of different origin.

  10. Highly sensitive and specific analysis of sterol profiles in biological samples by HPLC-ESI-MS/MS.

    Science.gov (United States)

    Honda, Akira; Miyazaki, Teruo; Ikegami, Tadashi; Iwamoto, Junichi; Yamashita, Kouwa; Numazawa, Mitsuteru; Matsuzaki, Yasushi

    2010-08-01

    High-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) is a powerful method for the microanalysis of compounds in biological samples. Compared with gas chromatography-mass spectrometry (GC-MS), this method is more broadly applicable to various compounds and usually does not require a derivatization step before analysis. However, when neutral sterols are analyzed, the sensitivities of usual HPLC-MS/MS method are not superior to those of GC-MS because the sterols are relatively resistant to ionization. In this review, we introduce the recent development of HPLC-MS/MS analysis for the quantification of non-cholesterol sterols. By adding an effective derivatization step to the conventional procedure, sterol analysis by HPLC-MS/MS surpassed that obtained by GC-MS in sensitivity. In addition, sufficient specificity of this method was achieved by selected reaction monitoring (SRM) and thorough chromatographic separation of each sterol. Copyright 2010 Elsevier Ltd. All rights reserved.

  11. Trace metal profiles in hair samples from children in urban and rural regions of the United Arab Emirates.

    Science.gov (United States)

    Hasan, M Y; Kosanovic, M; Fahim, M A; Adem, A; Petroianu, G

    2004-06-01

    Pollution has increased with industrialization and humans are subjected to exposure to heavy metals from different environmental sources. In oil-producing countries heavy metals are considered a major threat to the population. Metals such as lead, aluminum, manganese, nickel and cadmium may impact various organs of the body, and controlling their toxicity is crucial for individuals at risk. Previous studies utilized blood levels for monitoring metal toxicity. The current study was designed to investigate exposure to lead, aluminum, manganese, nickel and cadmium using scalp hair. Hair samples were randomly collected from 42 children (aged 6-18 y) representing rural and urban areas of the United Arab Emirates. The rural regions were defined as at least 50 km away from factories or traffic sites. Immediately after cutting, hairs were stored in plastic bags and attached to a questionnaire with the relevant background information. Samples were dried, weighed and sealed with polyethylene envelopes. Following extraction procedures with nitric acid, ICP-MS was utilized for metals determination. The analytical instrument showed a high degree of sensitivity and revealed significant differences between levels of some metals in hairs from rural and urban areas. Children from rural areas had mean hair lead levels (microg/g) of 0.79 + 0.10 whereas children from urban area had higher hair lead levels (3.47 + 0.47). Measuring metals concentration in scalp hair could be a useful method for studying exposure and assessing environmental pollution. Although the technique has the potential of being an effective tool for evaluating extent of pollution and identifying potentially toxic elements, it cannot yet replace the standard procedures of measuring air, water and soil metal content.

  12. Impact of delay to cryopreservation on RNA integrity and genome-wide expression profiles in resected tumor samples.

    Directory of Open Access Journals (Sweden)

    Elodie Caboux

    Full Text Available The quality of tissue samples and extracted mRNA is a major source of variability in tumor transcriptome analysis using genome-wide expression microarrays. During and immediately after surgical tumor resection, tissues are exposed to metabolic, biochemical and physical stresses characterized as "warm ischemia". Current practice advocates cryopreservation of biosamples within 30 minutes of resection, but this recommendation has not been systematically validated by measurements of mRNA decay over time. Using Illumina HumanHT-12 v3 Expression BeadChips, providing a genome-wide coverage of over 24,000 genes, we have analyzed gene expression variation in samples of 3 hepatocellular carcinomas (HCC and 3 lung carcinomas (LC cryopreserved at times up to 2 hours after resection. RNA Integrity Numbers (RIN revealed no significant deterioration of mRNA up to 2 hours after resection. Genome-wide transcriptome analysis detected non-significant gene expression variations of -3.5%/hr (95% CI: -7.0%/hr to 0.1%/hr; p = 0.054. In LC, no consistent gene expression pattern was detected in relation with warm ischemia. In HCC, a signature of 6 up-regulated genes (CYP2E1, IGLL1, CABYR, CLDN2, NQO1, SCL13A5 and 6 down-regulated genes (MT1G, MT1H, MT1E, MT1F, HABP2, SPINK1 was identified (FDR <0.05. Overall, our observations support current recommendation of time to cryopreservation of up to 30 minutes and emphasize the need for identifying tissue-specific genes deregulated following resection to avoid misinterpreting expression changes induced by warm ischemia as pathologically significant changes.

  13. Diffusion probe for gas sampling in undisturbed soil

    DEFF Research Database (Denmark)

    Petersen, Søren O

    2014-01-01

    Soil-atmosphere fluxes of trace gases such as methane (CH4) and nitrous oxide (N2O) are determined by complex interactions between biological activity and soil conditions. Soil gas concentration profiles may, in combination with other information about soil conditions, help to understand emission...... controls. This note describes a simple and robust diffusion probe for soil gas sampling as part of flux monitoring programs. It can be deployed with minimum disturbance of in-situ conditions, also at sites with a high or fluctuating water table. Separate probes are used for each sampling depth...

  14. High Throughput qPCR Expression Profiling of Circulating MicroRNAs Reveals Minimal Sex- and Sample Timing-Related Variation in Plasma of Healthy Volunteers.

    Science.gov (United States)

    Mooney, Catherine; Raoof, Rana; El-Naggar, Hany; Sanz-Rodriguez, Amaya; Jimenez-Mateos, Eva M; Henshall, David C

    2015-01-01

    MicroRNAs are a class of small non-coding RNA that regulate gene expression at a post-transcriptional level. MicroRNAs have been identified in various body fluids under normal conditions and their stability as well as their dysregulation in disease opens up a new field for biomarker study. However, diurnal and day-to-day variation in plasma microRNA levels, and differential regulation between males and females, may affect biomarker stability. A QuantStudio 12K Flex Real-Time PCR System was used to profile plasma microRNA levels using OpenArray in male and female healthy volunteers, in the morning and afternoon, and at four time points over a one month period. Using this system we were able to run four OpenArray plates in a single run, the equivalent of 32 traditional 384-well qPCR plates or 12,000 data points. Up to 754 microRNAs can be identified in a single plasma sample in under two hours. 108 individual microRNAs were identified in at least 80% of all our samples which compares favourably with other reports of microRNA profiles in serum or plasma in healthy adults. Many of these microRNAs, including miR-16-5p, miR-17-5p, miR-19a-3p, miR-24-3p, miR-30c-5p, miR-191-5p, miR-223-3p and miR-451a are highly expressed and consistent with previous studies using other platforms. Overall, microRNA levels were very consistent between individuals, males and females, and time points and we did not detect significant differences in levels of microRNAs. These results suggest the suitability of this platform for microRNA profiling and biomarker discovery and suggest minimal confounding influence of sex or sample timing. However, the platform has not been subjected to rigorous validation which must be demonstrated in future biomarker studies where large differences may exist between disease and control samples.

  15. High Throughput qPCR Expression Profiling of Circulating MicroRNAs Reveals Minimal Sex- and Sample Timing-Related Variation in Plasma of Healthy Volunteers.

    Directory of Open Access Journals (Sweden)

    Catherine Mooney

    Full Text Available MicroRNAs are a class of small non-coding RNA that regulate gene expression at a post-transcriptional level. MicroRNAs have been identified in various body fluids under normal conditions and their stability as well as their dysregulation in disease opens up a new field for biomarker study. However, diurnal and day-to-day variation in plasma microRNA levels, and differential regulation between males and females, may affect biomarker stability. A QuantStudio 12K Flex Real-Time PCR System was used to profile plasma microRNA levels using OpenArray in male and female healthy volunteers, in the morning and afternoon, and at four time points over a one month period. Using this system we were able to run four OpenArray plates in a single run, the equivalent of 32 traditional 384-well qPCR plates or 12,000 data points. Up to 754 microRNAs can be identified in a single plasma sample in under two hours. 108 individual microRNAs were identified in at least 80% of all our samples which compares favourably with other reports of microRNA profiles in serum or plasma in healthy adults. Many of these microRNAs, including miR-16-5p, miR-17-5p, miR-19a-3p, miR-24-3p, miR-30c-5p, miR-191-5p, miR-223-3p and miR-451a are highly expressed and consistent with previous studies using other platforms. Overall, microRNA levels were very consistent between individuals, males and females, and time points and we did not detect significant differences in levels of microRNAs. These results suggest the suitability of this platform for microRNA profiling and biomarker discovery and suggest minimal confounding influence of sex or sample timing. However, the platform has not been subjected to rigorous validation which must be demonstrated in future biomarker studies where large differences may exist between disease and control samples.

  16. Genome-wide association study on detailed profiles of smoking behavior and nicotine dependence in a twin sample.

    Science.gov (United States)

    Loukola, A; Wedenoja, J; Keskitalo-Vuokko, K; Broms, U; Korhonen, T; Ripatti, S; Sarin, A-P; Pitkäniemi, J; He, L; Häppölä, A; Heikkilä, K; Chou, Y-L; Pergadia, M L; Heath, A C; Montgomery, G W; Martin, N G; Madden, P A F; Kaprio, J

    2014-05-01

    Smoking is a major risk factor for several somatic diseases and is also emerging as a causal factor for neuropsychiatric disorders. Genome-wide association (GWA) and candidate gene studies for smoking behavior and nicotine dependence (ND) have disclosed too few predisposing variants to account for the high estimated heritability. Previous large-scale GWA studies have had very limited phenotypic definitions of relevance to smoking-related behavior, which has likely impeded the discovery of genetic effects. We performed GWA analyses on 1114 adult twins ascertained for ever smoking from the population-based Finnish Twin Cohort study. The availability of 17 smoking-related phenotypes allowed us to comprehensively portray the dimensions of smoking behavior, clustered into the domains of smoking initiation, amount smoked and ND. Our results highlight a locus on 16p12.3, with several single-nucleotide polymorphisms (SNPs) in the vicinity of CLEC19A showing association (Psmoking quantity. Interestingly, CLEC19A is located close to a previously reported attention-deficit hyperactivity disorder (ADHD) linkage locus and an evident link between ADHD and smoking has been established. Intriguing preliminary association (PMental Disorders, 4th edition) ND diagnosis and several SNPs in ERBB4, coding for a Neuregulin receptor, on 2q33. The association between ERBB4 and DSM-IV ND diagnosis was replicated in an independent Australian sample. Recently, a significant increase in ErbB4 and Neuregulin 3 (Nrg3) expression was revealed following chronic nicotine exposure and withdrawal in mice and an association between NRG3 SNPs and smoking cessation success was detected in a clinical trial. ERBB4 has previously been associated with schizophrenia; further, it is located within an established schizophrenia linkage locus and within a linkage locus for a smoker phenotype identified in this sample. In conclusion, we disclose novel tentative evidence for the involvement of ERBB4 in ND

  17. Slow Magic Angle Sample Spinning: A Non- or Minimally Invasive Method for High- Resolution 1H Nuclear Magnetic Resonance (NMR) Metabolic Profiling

    Energy Technology Data Exchange (ETDEWEB)

    Hu, Jian Z.

    2011-05-01

    High resolution 1H magic angle spinning nuclear magnetic resonance (NMR), using a sample spinning rate of several kHz or more (i.e., high resolution-magic angle spinning (hr-MAS)), is a well established method for metabolic profiling in intact tissues without the need for sample extraction. The only shortcoming with hr-MAS is that it is invasive and is thus unusable for non-destructive detections. Recently, a method called slow-MAS, using the concept of two dimensional NMR spectroscopy, has emerged as an alternative method for non- or minimal invasive metabolomics in intact tissues, including live animals, due to the slow or ultra-slow-sample spinning used. Although slow-MAS is a powerful method, its applications are hindered by experimental challenges. Correctly designing the experiment and choosing the appropriate slow-MAS method both require a fundamental understanding of the operation principles, in particular the details of line narrowing due to the presence of molecular diffusion. However, these fundamental principles have not yet been fully disclosed in previous publications. The goal of this chapter is to provide an in depth evaluation of the principles associated with slow-MAS techniques by emphasizing the challenges associated with a phantom sample consisting of glass beads and H2O, where an unusually large magnetic susceptibility field gradient is obtained.

  18. Sample-directed pseudotargeted method for the metabolic profiling analysis of rice seeds based on liquid chromatography with mass spectrometry.

    Science.gov (United States)

    Zhang, Junjie; Zhao, Chunxia; Zeng, Zhongda; Luo, Ping; Zhao, Yanni; Zhao, Jieyu; Li, Lili; Lu, Xin; Xu, Guowang

    2016-01-01

    Rice is one of the most important food crops in the world. Metabolite composition in rice seeds varies significantly depending on genetic variety, climatic alternation and agricultural practice. Metabolomics is a powerful tool to reveal the metabolic response of rice to various conditions. In this work, a rice seed sample-directed pseudotargeted metabolomics method was first established and validated based on ultra high performance liquid chromatography with triple quadrupole mass spectrometry in the multiple reaction monitoring mode. A total of 749 and 617 ion pairs in positive and negative modes were achieved, respectively. Among them, about 200 metabolites were identified or tentatively identified. The developed method showed better linearity and repeatability than those of non-targeted metabolomics method. Good intra-day and inter-day precisions, recoveries and wide linear range were also obtained. Furthermore, the method was applied for the investigation of metabolic variation of rice seeds with two wild cultivars and their transgenic lines that were grown in two locations. Principal component analysis indicated that the effects of cultivar and location on metabolic variations were far more than those of gene modification. The nonparametric Mann-Whitney U test revealed that most metabolites were influenced by cultivar, location and gene modifications together. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Physicochemical characteristics and sensory profile of honey samples from stingless bees (Apidae: Meliponinae submitted to a dehumidification process

    Directory of Open Access Journals (Sweden)

    Carlos A.L. Carvalho

    2009-03-01

    Full Text Available This study was conducted to evaluate the effect of a dehumidification process on the physicochemical and sensory characteristics of stingless-bee honey. Melipona scutellaris and M. quadrifasciata honey samples were submitted to a dehumidification process and to physicochemical (reducing sugars, apparent sucrose, moisture, diastatic activity, hydroxymethylfurfural, ash, pH, acidity, and electric conductivity and sensory evaluations (fluidity, color, aroma, crystallization,flavor,and acceptability. The results indicated that the dehumidification process does not interfere with honey quality and acceptability.Este estudo foi conduzido com o objetivo de avaliar o efeito do processo de desumidificação sobre as características físico-químicas e sensoriais do mel das abelhas sem ferrão. Amostras de méis de Melipona scutellaris e M. quadrifasciata foram submetidas ao processo de desumidificação, passando em seguida por avaliações físico-químicas (açúcares redutores, sacarose aparente, umidade, atividade diastásica, hidroximetilfurfural, cinzas, pH, acidez e condutividade elétrica e sensoriais (fluidez, cor, aroma, cristalização, sabor e aceitabilidade. Os resultados indicaram que o processo de desumidificação não interfere na qualidade e aceitabilidade do mel.

  20. Virome profiling of bats from Myanmar by metagenomic analysis of tissue samples reveals more novel Mammalian viruses.

    Directory of Open Access Journals (Sweden)

    Biao He

    Full Text Available Bats are reservoir animals harboring many important pathogenic viruses and with the capability of transmitting these to humans and other animals. To establish an effective surveillance to monitor transboundary spread of bat viruses between Myanmar and China, complete organs from the thorax and abdomen from 853 bats of six species from two Myanmar counties close to Yunnan province, China, were collected and tested for their virome through metagenomics by Solexa sequencing and bioinformatic analysis. In total, 3,742,314 reads of 114 bases were generated, and over 86% were assembled into 1,649,512 contigs with an average length of 114 bp, of which 26,698 (2% contigs were recognizable viral sequences belonging to 24 viral families. Of the viral contigs 45% (12,086/26,698 were related to vertebrate viruses, 28% (7,443/26,698 to insect viruses, 27% (7,074/26,698 to phages and 95 contigs to plant viruses. The metagenomic results were confirmed by PCR of selected viruses in all bat samples followed by phylogenetic analysis, which has led to the discovery of some novel bat viruses of the genera Mamastrovirus, Bocavirus, Circovirus, Iflavirus and Orthohepadnavirus and to their prevalence rates in two bat species. In conclusion, the present study aims to present the bat virome in Myanmar, and the results obtained further expand the spectrum of viruses harbored by bats.

  1. Isotope-coded ESI-enhancing derivatization reagents for differential analysis, quantification and profiling of metabolites in biological samples by LC/MS: A review.

    Science.gov (United States)

    Higashi, Tatsuya; Ogawa, Shoujiro

    2016-10-25

    The analysis of the qualitative and quantitative changes of metabolites in body fluids and tissues yields valuable information for the diagnosis, pathological analysis and treatment of many diseases. Recently, liquid chromatography/electrospray ionization-(tandem) mass spectrometry [LC/ESI-MS(/MS)] has been widely used for these purposes due to the high separation capability of LC, broad coverage of ESI for various compounds and high specificity of MS(/MS). However, there are still two major problems to be solved regarding the biological sample analysis; lack of sensitivity and limited availability of stable isotope-labeled analogues (internal standards, ISs) for most metabolites. Stable isotope-coded derivatization (ICD) can be the answer for these problems. By the ICD, different isotope-coded moieties are introduced to the metabolites and one of the resulting derivatives can serve as the IS, which minimize the matrix effects. Furthermore, the derivatization can improve the ESI efficiency, fragmentation property in the MS/MS and chromatographic behavior of the metabolites, which lead to a high sensitivity and specificity in the various detection modes. Based on this background, this article reviews the recently-reported isotope-coded ESI-enhancing derivatization (ICEED) reagents, which are key components for the ICD-based LC/MS(/MS) studies, and their applications to the detection, identification, quantification and profiling of metabolites in human and animal samples. The LC/MS(/MS) using the ICEED reagents is the powerful method especially for the differential analysis (relative quantification) of metabolites in two comparative samples, simultaneous quantification of multiple metabolites whose stable isotope-labeled ISs are not available, and submetabolome profiling. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. Cytokine and hormonal profile in serum samples of patients undergoing controlled ovarian stimulation: interleukin-1beta predicts ongoing pregnancy.

    Science.gov (United States)

    Bonetti, T C S; Salomao, R; Brunialti, M; Braga, D P A F; Borges, E; Silva, I D C G

    2010-08-01

    Changes in the endometrium are not regulated exclusively by ovarian hormones; the immune system has also been implicated in normal endometrial function, similar to processes taking place during inflammatory and reparative path. Many cytokines are crucially important for reproductive processes, and the role of cytokines in the female reproductive system function has been broadly investigated during controlled ovarian stimulation (COS) for IVF attempts. The aim of this study was to evaluate the levels of serum cytokines and hormones, and the clinical outcomes of women who underwent COS and ICSI procedures. The study prospectively included 96 patients (aged 22-43 years, unexplained or male infertility, n = 61; female infertility factors, n = 35) who underwent ICSI cycles. Serum levels of interleukin (IL-8, IL-6, IL-1beta, IL-10, IL-12), tumour necrosis factor and leukaemia-inhibitory factor (LIF) and the hormones FSH, estradiol, progesterone, anti-Mullerian hormone and Inhibin-B were measured on the day of oocyte retrieval. The ongoing pregnancy rate was 25.3%. The presence of serum IL-1beta positively affected the implantation rate (P = 0.004) and increased the chance of becoming pregnant by 15 fold. Furthermore, the percentage of patients with detectable serum IL-1beta levels who conceived (62.5%) was higher than those who failed to conceive (37.5%; P = 0.019). The LIF was undetectable in all serum samples, and no other factors influenced the clinical outcomes of patients undergoing ICSI cycles. Our findings revealed that detectable serum levels of IL-1beta on the day of oocyte retrieval in patients undergoing COS and ICSI are predictive of successful implantation and ongoing pregnancy.

  3. Temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the OCEANUS in the North Atlantic Ocean from 2008-05-10 to 2008-05-23 (NODC Accession 0117673)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0117673 includes chemical, discrete sample, physical and profile data collected from OCEANUS in the North Atlantic Ocean from 2008-05-10 to 2008-05-23...

  4. Temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from USCGC POLAR STAR in the Arctic Ocean from 2002-08-19 to 2002-09-23 (NODC Accession 0115588)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NCEI Accession 0115588 includes discrete sample and profile data collected from USCGC POLAR STAR in the Arctic Ocean from 2002-08-19 to 2002-09-23. These data...

  5. Temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the POLARSTERN in the South Atlantic Ocean from 1989-09-06 to 1989-10-30 (NODC Accession 0116645)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0116645 includes chemical, discrete sample, physical and profile data collected from POLARSTERN in the South Atlantic Ocean from 1989-09-06 to...

  6. Temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the SHOYO in the North Pacific Ocean from 1993-10-14 to 1993-11-27 (NODC Accession 0115607)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0115607 includes chemical, discrete sample, physical and profile data collected from SHOYO in the North Pacific Ocean from 1993-10-14 to 1993-11-27...

  7. Temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the JAN MAYEN in the Norwegian Sea from 1993-04-01 to 1995-11-01 (NODC Accession 0115677)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0115677 includes chemical, discrete sample, physical and profile data collected from JAN MAYEN in the Norwegian Sea from 1993-04-01 to 1995-11-01 and...

  8. Temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the KNORR in the North Atlantic Ocean from 1986-04-24 to 1986-05-18 (NODC Accession 0117678)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0117678 includes chemical, discrete sample, physical and profile data collected from KNORR in the North Atlantic Ocean from 1986-04-24 to 1986-05-18...

  9. Temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the KNORR in the South Pacific Ocean from 2006-01-30 to 2006-03-14 (NODC Accession 0115593)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0115593 includes chemical, discrete sample, physical and profile data collected from KNORR in the South Pacific Ocean from 2006-01-30 to 2006-03-14...

  10. Temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the AURORA AUSTRALIS in the Indian Ocean from 1991-09-25 to 1991-10-27 (NODC Accession 0116370)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0116370 includes chemical, discrete sample, physical and profile data collected from AURORA AUSTRALIS in the Indian Ocean from 1991-09-25 to...

  11. PH, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from DISCOVERY in the North Atlantic Ocean from 1998-04-23 to 1998-06-01 (NODC Accession 0113536)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NCEI Accession 0113536 includes biological, chemical, discrete sample, physical and profile data collected from DISCOVERY in the North Atlantic Ocean from 1998-04-23...

  12. Temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from CHARLES DARWIN in the Indian Ocean from 1987-11-12 to 1987-12-17 (NCEI Accession 0157468)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NCEI Accession 0157468 includes chemical, discrete sample, physical and profile data collected from CHARLES DARWIN in the Indian Ocean from 1987-11-12 to 1987-12-17....

  13. Temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the DISCOVERY in the North Atlantic Ocean from 1989-07-16 to 1989-08-10 (NODC Accession 0113532)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0113532 includes chemical, discrete sample, physical and profile data collected from DISCOVERY in the North Atlantic Ocean from 1989-07-16 to...

  14. Temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the METEOR in the North Atlantic Ocean from 2003-06-26 to 2003-07-21 (NODC Accession 0115682)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0115682 includes chemical, discrete sample, physical and profile data collected from METEOR in the North Atlantic Ocean from 2003-06-26 to 2003-07-21...

  15. Temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the Hakuho Maru in the North Pacific Ocean from 1993-05-13 to 1993-05-30 (NODC Accession 0115496)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0115496 includes chemical, discrete sample, physical and profile data collected from Hakuho Maru in the North Pacific Ocean from 1993-05-13 to...

  16. Temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from RYOFU MARU in the Philippine Sea from 1992-02-10 to 1992-02-17 (NCEI Accession 0143943)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NCEI Accession 0143943 includes discrete sample and profile data collected from RYOFU MARU in the Philippine Sea from 1992-02-10 to 1992-02-17. These data include...

  17. Temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the DARVIN in the North Atlantic Ocean from 1991-07-12 to 1991-07-24 (NODC Accession 0113526)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0113526 includes chemical, discrete sample, physical and profile data collected from DARVIN in the North Atlantic Ocean from 1991-07-12 to 1991-07-24...

  18. Temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the RYOFU MARU in the Philippine Sea from 1995-11-15 to 1995-11-30 (NODC Accession 0117669)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0117669 includes chemical, discrete sample, physical and profile data collected from RYOFU MARU in the Philippine Sea from 1995-11-15 to 1995-11-30...

  19. Temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from DISCOVERY in the Indian Ocean from 1995-01-06 to 1995-02-21 (NCEI Accession 0160543)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NCEI Accession 0160543 includes biological, chemical, discrete sample, physical and profile data collected from DISCOVERY in the Indian Ocean from 1995-01-06 to...

  20. PH, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from SHUMPU MARU in the Philippine Sea from 1992-02-25 to 1992-02-29 (NODC Accession 0115709)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NCEI Accession 0115709 includes chemical, discrete sample, physical and profile data collected from SHUMPU MARU in the Philippine Sea from 1992-02-25 to 1992-02-29....

  1. Temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from ATLANTIS in the North Atlantic Ocean from 2006-01-18 to 2006-01-31 (NCEI Accession 0157469)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NCEI Accession 0157469 includes chemical, discrete sample, physical and profile data collected from ATLANTIS in the North Atlantic Ocean from 2006-01-18 to...

  2. Temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the OCEAN RESEARCHER I in the Philippine Sea from 1991-06-26 to 1991-07-04 (NODC Accession 0115598)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0115598 includes chemical, discrete sample, physical and profile data collected from OCEAN RESEARCHER I in the Philippine Sea from 1991-06-26 to...

  3. Temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from Kaiyo in the Philippine Sea from 1994-02-12 to 1994-02-16 (NCEI Accession 0143635)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NCEI Accession 0143635 includes discrete sample and profile data collected from Kaiyo in the Philippine Sea from 1994-02-12 to 1994-02-16. These data include DELTA...

  4. Temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from DISCOVERY in the South Atlantic Ocean from 1992-12-22 to 1993-02-01 (NCEI Accession 0144287)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NCEI Accession 0144287 includes discrete sample and profile data collected from DISCOVERY in the South Atlantic Ocean from 1992-12-22 to 1993-02-01. These data...

  5. Temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from PROFESSOR MULTANOVSKIY in the North Atlantic Ocean from 1993-09-11 to 1993-11-21 (NCEI Accession 0143931)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NCEI Accession 0143931 includes discrete sample and profile data collected from PROFESSOR MULTANOVSKIY in the North Atlantic Ocean from 1993-09-11 to 1993-11-21....

  6. Temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the OCEAN RESEARCHER I in the Philippine Sea from 1990-10-11 to 1990-10-15 (NODC Accession 0115600)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0115600 includes chemical, discrete sample, physical and profile data collected from OCEAN RESEARCHER I in the Philippine Sea from 1990-10-11 to...

  7. PH, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from THALASSA in the North Atlantic Ocean from 2004-06-04 to 2004-07-06 (NODC Accession 0113918)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NCEI Accession 0113918 includes chemical, discrete sample, physical and profile data collected from THALASSA in the North Atlantic Ocean from 2004-06-04 to...

  8. Temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from THOMAS G. THOMPSON in the North Pacific Ocean from 1985-08-04 to 1985-09-07 (NCEI Accession 0143394)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NCEI Accession 0143394 includes discrete sample and profile data collected from THOMAS G. THOMPSON in the North Pacific Ocean from 1985-08-04 to 1985-09-07 and...

  9. Temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the METEOR in the North Atlantic Ocean from 1999-08-13 to 1999-08-31 (NODC Accession 0115603)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0115603 includes chemical, discrete sample, physical and profile data collected from METEOR in the North Atlantic Ocean from 1999-08-13 to 1999-08-31...

  10. Temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from DISCOVERY in the Indian Ocean and Southern Oceans from 1994-02-19 to 1994-03-30 (NCEI Accession 0144242)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NCEI Accession 0144242 includes discrete sample and profile data collected from DISCOVERY in the Indian Ocean and Southern Oceans (> 60 degrees South) from...

  11. Temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the NEW HORIZON in the North Pacific Ocean from 1980-08-10 to 1980-09-03 (NODC Accession 0116707)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0116707 includes chemical, discrete sample, physical and profile data collected from NEW HORIZON in the North Pacific Ocean from 1980-08-10 to...

  12. Temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from THOMAS G. THOMPSON in the South Pacific Ocean from 2013-10-25 to 2013-12-20 (NCEI Accession 0163186)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NCEI Accession 0163186 includes chemical, discrete sample, physical and profile data collected from THOMAS G. THOMPSON in the South Pacific Ocean from 2013-10-25 to...

  13. Temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the METEOR in the North Atlantic Ocean from 2001-06-20 to 2001-07-15 (NODC Accession 0115601)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0115601 includes chemical, discrete sample, physical and profile data collected from METEOR in the North Atlantic Ocean from 2001-06-20 to 2001-07-15...

  14. Temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the ENDEAVOR in the North Atlantic Ocean from 1991-03-28 to 1991-04-21 (NODC Accession 0113988)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0113988 includes chemical, discrete sample, physical and profile data collected from ENDEAVOR in the North Atlantic Ocean from 1991-03-28 to...

  15. Primary health clinic toilet/bathroom surface swab sampling can indicate community profile of sexually transmitted infections

    Science.gov (United States)

    Su, Jiunn-Yih; Andersson, Patiyan; Holt, Deborah C.

    2017-01-01

    relative prevalence of gonorrhoeae in central Australia than in northern Australia. Similarly, the regional clinics yielded p values from 0.0088–0.0022. In contrast, swab and notifications data from the sexual health clinic were not correlated. Discussion Strong correlations between swab and notifications were observed. However, there was evidence for limitations of this approach. Despite the correlation observed with the regional clinics data, one clinic yielded zero positive swabs for C. trachomatis, although this STI constituted 25.1% of the corresponding notifications. This could be ascribed to stochastic effects. The lack of correlation observed for sexual health clinic data was also likely due to stochastic effects. It was concluded that toilet/bathroom surface swab sampling has considerable potential for public health surveillance. The approach may be applicable in situations other than primary health clinics, and for targets other than STIs. PMID:28652937

  16. Primary health clinic toilet/bathroom surface swab sampling can indicate community profile of sexually transmitted infections

    Directory of Open Access Journals (Sweden)

    Philip M. Giffard

    2017-06-01

    known higher relative prevalence of gonorrhoeae in central Australia than in northern Australia. Similarly, the regional clinics yielded p values from 0.0088–0.0022. In contrast, swab and notifications data from the sexual health clinic were not correlated. Discussion Strong correlations between swab and notifications were observed. However, there was evidence for limitations of this approach. Despite the correlation observed with the regional clinics data, one clinic yielded zero positive swabs for C. trachomatis, although this STI constituted 25.1% of the corresponding notifications. This could be ascribed to stochastic effects. The lack of correlation observed for sexual health clinic data was also likely due to stochastic effects. It was concluded that toilet/bathroom surface swab sampling has considerable potential for public health surveillance. The approach may be applicable in situations other than primary health clinics, and for targets other than STIs.

  17. Profiles of organic food consumers in a large sample of French adults: results from the Nutrinet-Santé cohort study.

    Science.gov (United States)

    Kesse-Guyot, Emmanuelle; Péneau, Sandrine; Méjean, Caroline; Szabo de Edelenyi, Fabien; Galan, Pilar; Hercberg, Serge; Lairon, Denis

    2013-01-01

    Lifestyle, dietary patterns and nutritional status of organic food consumers have rarely been described, while interest for a sustainable diet is markedly increasing. Consumer attitude and frequency of use of 18 organic products were assessed in 54,311 adult participants in the Nutrinet-Santé cohort. Cluster analysis was performed to identify behaviors associated with organic product consumption. Socio-demographic characteristics, food consumption and nutrient intake across clusters are provided. Cross-sectional association with overweight/obesity was estimated using polytomous logistic regression. Five clusters were identified: 3 clusters of non-consumers whose reasons differed, occasional (OCOP, 51%) and regular (RCOP, 14%) organic product consumers. RCOP were more highly educated and physically active than other clusters. They also exhibited dietary patterns that included more plant foods and less sweet and alcoholic beverages, processed meat or milk. Their nutrient intake profiles (fatty acids, most minerals and vitamins, fibers) were healthier and they more closely adhered to dietary guidelines. In multivariate models (after accounting for confounders, including level of adherence to nutritional guidelines), compared to those not interested in organic products, RCOP participants showed a markedly lower probability of overweight (excluding obesity) (25 ≤ body mass indexorganic products, a sizeable group in our sample, exhibit specific socio-demographic characteristics, and an overall healthy profile which should be accounted for in further studies analyzing organic food intake and health markers.

  18. Profiles of Organic Food Consumers in a Large Sample of French Adults: Results from the Nutrinet-Santé Cohort Study

    Science.gov (United States)

    Kesse-Guyot, Emmanuelle; Péneau, Sandrine; Méjean, Caroline; Szabo de Edelenyi, Fabien; Galan, Pilar; Hercberg, Serge; Lairon, Denis

    2013-01-01

    Background Lifestyle, dietary patterns and nutritional status of organic food consumers have rarely been described, while interest for a sustainable diet is markedly increasing. Methods Consumer attitude and frequency of use of 18 organic products were assessed in 54,311 adult participants in the Nutrinet-Santé cohort. Cluster analysis was performed to identify behaviors associated with organic product consumption. Socio-demographic characteristics, food consumption and nutrient intake across clusters are provided. Cross-sectional association with overweight/obesity was estimated using polytomous logistic regression. Results Five clusters were identified: 3 clusters of non-consumers whose reasons differed, occasional (OCOP, 51%) and regular (RCOP, 14%) organic product consumers. RCOP were more highly educated and physically active than other clusters. They also exhibited dietary patterns that included more plant foods and less sweet and alcoholic beverages, processed meat or milk. Their nutrient intake profiles (fatty acids, most minerals and vitamins, fibers) were healthier and they more closely adhered to dietary guidelines. In multivariate models (after accounting for confounders, including level of adherence to nutritional guidelines), compared to those not interested in organic products, RCOP participants showed a markedly lower probability of overweight (excluding obesity) (25≤body mass indexorganic products, a sizeable group in our sample, exhibit specific socio-demographic characteristics, and an overall healthy profile which should be accounted for in further studies analyzing organic food intake and health markers. PMID:24204721

  19. Microextraction by Packed Sorbent (MEPS) and Solid-Phase Microextraction (SPME) as Sample Preparation Procedures for the Metabolomic Profiling of Urine

    Science.gov (United States)

    Silva, Catarina; Cavaco, Carina; Perestrelo, Rosa; Pereira, Jorge; Câmara, José S.

    2014-01-01

    For a long time, sample preparation was unrecognized as a critical issue in the analytical methodology, thus limiting the performance that could be achieved. However, the improvement of microextraction techniques, particularly microextraction by packed sorbent (MEPS) and solid-phase microextraction (SPME), completely modified this scenario by introducing unprecedented control over this process. Urine is a biological fluid that is very interesting for metabolomics studies, allowing human health and disease characterization in a minimally invasive form. In this manuscript, we will critically review the most relevant and promising works in this field, highlighting how the metabolomic profiling of urine can be an extremely valuable tool for the early diagnosis of highly prevalent diseases, such as cardiovascular, oncologic and neurodegenerative ones. PMID:24958388

  20. Flux-P: Automating Metabolic Flux Analysis

    Directory of Open Access Journals (Sweden)

    Birgitta E. Ebert

    2012-11-01

    Full Text Available Quantitative knowledge of intracellular fluxes in metabolic networks is invaluable for inferring metabolic system behavior and the design principles of biological systems. However, intracellular reaction rates can not often be calculated directly but have to be estimated; for instance, via 13C-based metabolic flux analysis, a model-based interpretation of stable carbon isotope patterns in intermediates of metabolism. Existing software such as FiatFlux, OpenFLUX or 13CFLUX supports experts in this complex analysis, but requires several steps that have to be carried out manually, hence restricting the use of this software for data interpretation to a rather small number of experiments. In this paper, we present Flux-P as an approach to automate and standardize 13C-based metabolic flux analysis, using the Bio-jETI workflow framework. Exemplarily based on the FiatFlux software, it demonstrates how services can be created that carry out the different analysis steps autonomously and how these can subsequently be assembled into software workflows that perform automated, high-throughput intracellular flux analysis of high quality and reproducibility. Besides significant acceleration and standardization of the data analysis, the agile workflow-based realization supports flexible changes of the analysis workflows on the user level, making it easy to perform custom analyses.

  1. In vivo cardiac glucose metabolism in the high-fat fed mouse: Comparison of euglycemic–hyperinsulinemic clamp derived measures of glucose uptake with a dynamic metabolomic flux profiling approach

    Energy Technology Data Exchange (ETDEWEB)

    Kowalski, Greg M., E-mail: greg.kowalski@deakin.edu.au [Centre for Physical Activity and Nutrition Research, School of Exercise and Nutrition Sciences, Deakin University, Burwood, Victoria 3125 (Australia); De Souza, David P. [Metabolomics Australia, Department of Biochemistry and Molecular Biology, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria 3010 (Australia); Risis, Steve [Cellular and Molecular Metabolism Laboratory, Baker IDI Heart and Diabetes Institute, Melbourne, Victoria 3004 (Australia); Burch, Micah L. [Brigham and Women' s Hospital, Department of Medicine, Boston, MA (United States); Hamley, Steven [Centre for Physical Activity and Nutrition Research, School of Exercise and Nutrition Sciences, Deakin University, Burwood, Victoria 3125 (Australia); Kloehn, Joachim [Metabolomics Australia, Department of Biochemistry and Molecular Biology, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria 3010 (Australia); Selathurai, Ahrathy [Centre for Physical Activity and Nutrition Research, School of Exercise and Nutrition Sciences, Deakin University, Burwood, Victoria 3125 (Australia); Lee-Young, Robert S. [Cellular and Molecular Metabolism Laboratory, Baker IDI Heart and Diabetes Institute, Melbourne, Victoria 3004 (Australia); Tull, Dedreia; O' Callaghan, Sean; McConville, Malcolm J. [Metabolomics Australia, Department of Biochemistry and Molecular Biology, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria 3010 (Australia); Bruce, Clinton R. [Centre for Physical Activity and Nutrition Research, School of Exercise and Nutrition Sciences, Deakin University, Burwood, Victoria 3125 (Australia)

    2015-08-07

    Rationale: Cardiac metabolism is thought to be altered in insulin resistance and type 2 diabetes (T2D). Our understanding of the regulation of cardiac substrate metabolism and insulin sensitivity has largely been derived from ex vivo preparations which are not subject to the same metabolic regulation as in the intact heart in vivo. Studies are therefore required to examine in vivo cardiac glucose metabolism under physiologically relevant conditions. Objective: To determine the temporal pattern of the development of cardiac insulin resistance and to compare with dynamic approaches to interrogate cardiac glucose and intermediary metabolism in vivo. Methods and results: Studies were conducted to determine the evolution of cardiac insulin resistance in C57Bl/6 mice fed a high-fat diet (HFD) for between 1 and 16 weeks. Dynamic in vivo cardiac glucose metabolism was determined following oral administration of [U-{sup 13}C] glucose. Hearts were collected after 15 and 60 min and flux profiling was determined by measuring {sup 13}C mass isotopomers in glycolytic and tricarboxylic acid (TCA) cycle intermediates. Cardiac insulin resistance, determined by euglycemic–hyperinsulinemic clamp, was evident after 3 weeks of HFD. Despite the presence of insulin resistance, in vivo cardiac glucose metabolism following oral glucose administration was not compromised in HFD mice. This contrasts our recent findings in skeletal muscle, where TCA cycle activity was reduced in mice fed a HFD. Similar to our report in muscle, glucose derived pyruvate entry into the TCA cycle in the heart was almost exclusively via pyruvate dehydrogenase, with pyruvate carboxylase mediated anaplerosis being negligible after oral glucose administration. Conclusions: Under experimental conditions which closely mimic the postprandial state, the insulin resistant mouse heart retains the ability to stimulate glucose metabolism. - Highlights: • Insulin clamp was used to determine the evolution of cardiac

  2. Polarized neutron imaging and three-dimensional calculation of magnetic flux trapping in bulk of superconductors

    Science.gov (United States)

    Treimer, Wolfgang; Ebrahimi, Omid; Karakas, Nursel; Prozorov, Ruslan

    2012-05-01

    Polarized neutron radiography was used to study the three-dimensional magnetic flux distribution inside of single-crystal and polycrystalline Pb cylinders with large (cm3) volume and virtually zero demagnetization. Experiments with single crystals being in the Meissner phase (Tsamples were exposed to the same homogeneous magnetic field (6.4 mT) and only a portion of the applied field was expelled. The trapped field in the sample (Tflux was nearly constant. The expelled field outside of the samples followed 1/R dependence. These measurements provided a unique and detailed picture of macroscopic superconducting samples, confirming the existence of both uniform bulk Meissner expulsion in single crystals and bulk flux trapping with nearly-Bean-model profiles due to flux pinning in polycrystalline samples.

  3. Clustering of Emerging Flux

    Science.gov (United States)

    Ruzmaikin, A.

    1997-01-01

    Observations show that newly emerging flux tends to appear on the Solar surface at sites where there is flux already. This results in clustering of solar activity. Standard dynamo theories do not predict this effect.

  4. Flavour mixings in flux compactifications

    Energy Technology Data Exchange (ETDEWEB)

    Buchmuller, Wilfried; Schweizer, Julian

    2017-01-15

    A multiplicity of quark-lepton families can naturally arise as zero-modes in flux compactifications. The flavour structure of quark and lepton mass matrices is then determined by the wave function profiles of the zero-modes. We consider a supersymmetric SO(10) x U(1) model in six dimensions compactified on the orbifold T{sup 2}=Z{sub 2} with Abelian magnetic flux. A bulk 16-plet charged under the U(1) provides the quark-lepton generations whereas two uncharged 10-plets yield two Higgs doublets. Bulk anomaly cancellation requires the presence of additional 16- and 10-plets. The corresponding zero-modes form vectorlike split multiplets that are needed to obtain a successful flavour phenomenology. We analyze the pattern of flavour mixings for the two heaviest families of the Standard Model and discuss possible generalizations to three and more generations.

  5. CycleFreeFlux: efficient removal of thermodynamically infeasible loops from flux distributions.

    Science.gov (United States)

    Desouki, Abdelmoneim Amer; Jarre, Florian; Gelius-Dietrich, Gabriel; Lercher, Martin J

    2015-07-01

    Constraint-based metabolic modeling methods such as Flux Balance Analysis (FBA) are routinely used to predict metabolic phenotypes, e.g. growth rates, ATP yield or the fitness of gene knockouts. One frequent difficulty of constraint-based solutions is the inclusion of thermodynamically infeasible loops (or internal cycles), which add nonbiological fluxes to the predictions. We propose a simple postprocessing of constraint-based solutions, which removes internal cycles from any given flux distribution [Formula: see text] without disturbing other fluxes not involved in the loops. This new algorithm, termed CycleFreeFlux, works by minimizing the sum of absolute fluxes [Formula: see text] while (i) conserving the exchange fluxes and (ii) using the fluxes of the original solution to bound the new flux distribution. This strategy reduces internal fluxes until at least one reaction of every possible internal cycle is inactive, a necessary and sufficient condition for the thermodynamic feasibility of a flux distribution. If alternative representations of the input flux distribution in terms of elementary flux modes exist that differ in their inclusion of internal cycles, then CycleFreeFlux is biased towards solutions that maintain the direction given by [Formula: see text] and towards solutions with lower total flux [Formula: see text]. Our method requires only one additional linear optimization, making it computationally very efficient compared to alternative strategies. We provide freely available R implementations for the enumeration of thermodynamically infeasible cycles as well as for cycle-free FBA solutions, flux variability calculations and random sampling of solution spaces. lercher@cs.uni-duesseldorf.de. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  6. 16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice.

    Science.gov (United States)

    Walker, Alan W; Martin, Jennifer C; Scott, Paul; Parkhill, Julian; Flint, Harry J; Scott, Karen P

    2015-01-01

    Characterisation of the bacterial composition of the gut microbiota is increasingly carried out with a view to establish the role of different bacterial species in causation or prevention of disease. It is thus essential that the methods used to determine the microbial composition are robust. Here, several widely used molecular techniques were compared to establish the optimal methods to assess the bacterial composition in faecal samples from babies, before weaning. The bacterial community profile detected in the faeces of infants is highly dependent on the methodology used. Bifidobacteria were the most abundant bacteria detected at 6 weeks in faeces from two initially breast-fed babies using fluorescent in situ hybridisation (FISH), in agreement with data from previous culture-based studies. Using the 16S rRNA gene sequencing approach, however, we found that the detection of bifidobacteria in particular crucially depended on the optimisation of the DNA extraction method, and the choice of primers used to amplify the V1-V3 regions of 16S rRNA genes prior to subsequent sequence analysis. Bifidobacteria were only well represented among amplified 16S rRNA gene sequences when mechanical disruption (bead-beating) procedures for DNA extraction were employed together with optimised "universal" PCR primers. These primers incorporate degenerate bases at positions where mismatches to bifidobacteria and other bacterial taxa occur. The use of a DNA extraction kit with no bead-beating step resulted in a complete absence of bifidobacteria in the sequence data, even when using the optimised primers. This work emphasises the importance of sample processing methodology to downstream sequencing results and illustrates the value of employing multiple approaches for determining microbiota composition.

  7. Physical profiling and IR spectroscopy: simple and effective methods to discriminate between genuine and counterfeit samples of Viagra® and Cialis®.

    Science.gov (United States)

    Custers, Deborah; Vandemoortele, Suzanne; Bothy, Jean-Luc; De Beer, Jacques O; Courselle, Patricia; Apers, Sandra; Deconinck, Eric

    2016-01-01

    Counterfeit medicines are a global threat to public health. High amounts enter the European market, enforcing the need for simple techniques to help customs detect these pharmaceuticals. This study focused on physical profiling and IR spectroscopy to obtain a prime discrimination between genuine and illegal Viagra® and Cialis® medicines. Five post-tableting characteristics were explored: colour, mass, long length, short length, and thickness. Hypothesis testing showed that most illegal samples (between 60 and 100%) significantly differ from the genuine medicines, in particular for mass and long length. Classification and Regression Trees (CART) analysis resulted in a good discrimination between genuine and illegal medicines (98.93% correct classification rate for Viagra®, 99.42% for Cialis®). Moreover, CART confirmed the observation that mass and long length are the key physical characteristics which determine the observed discrimination. IR analysis was performed on tablets without blister and on tablets in intact blister. These data were analyzed using Soft Independent Modelling of Class Analogy (SIMCA) and Partial Least Squares - Discriminant Analysis (PLS-DA). Supervised techniques needed to be applied since Principal Component Analysis (PCA) was not able to generate the desired discrimination. Our study shows that a perfect discrimination between genuine and illegal medicines can be made by both SIMCA and PLS-DA without removing the tablets from the blister. This approach has the advantage of keeping the blister intact. Our study demonstrates that these user friendly techniques are reliable methods to aid customs to obtain a prime distinction between genuine and illegal samples on the spot. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

  8. A profile of US-Mexico border mobility among a stratified random sample of Hispanics living in the El Paso-Juarez area.

    Science.gov (United States)

    Lapeyrouse, L M; Morera, O; Heyman, J M C; Amaya, M A; Pingitore, N E; Balcazar, H

    2012-04-01

    Examination of border-specific characteristics such as trans-border mobility and transborder health service illuminates the heterogeneity of border Hispanics and may provide greater insight toward understanding differential health behaviors and status among these populations. In this study, we create a descriptive profile of the concept of trans-border mobility by exploring the relationship between mobility status and a series of demographic, economic and socio-cultural characteristics among mobile and non-mobile Hispanics living in the El Paso-Juarez border region. Using a two-stage stratified random sampling design, bilingual interviewers collected survey data from border residents (n = 1,002). Findings show that significant economic, cultural, and behavioral differences exist between mobile and non-mobile respondents. While non-mobile respondents were found to have higher social economic status than their mobile counterparts, mobility across the border was found to offer less acculturated and poorer Hispanics access to alternative sources of health care and other services.

  9. Detecting regional patterns of changing CO2 flux in Alaska.

    Science.gov (United States)

    Parazoo, Nicholas C; Commane, Roisin; Wofsy, Steven C; Koven, Charles D; Sweeney, Colm; Lawrence, David M; Lindaas, Jakob; Chang, Rachel Y-W; Miller, Charles E

    2016-07-12

    With rapid changes in climate and the seasonal amplitude of carbon dioxide (CO2) in the Arctic, it is critical that we detect and quantify the underlying processes controlling the changing amplitude of CO2 to better predict carbon cycle feedbacks in the Arctic climate system. We use satellite and airborne observations of atmospheric CO2 with climatically forced CO2 flux simulations to assess the detectability of Alaskan carbon cycle signals as future warming evolves. We find that current satellite remote sensing technologies can detect changing uptake accurately during the growing season but lack sufficient cold season coverage and near-surface sensitivity to constrain annual carbon balance changes at regional scale. Airborne strategies that target regular vertical profile measurements within continental interiors are more sensitive to regional flux deeper into the cold season but currently lack sufficient spatial coverage throughout the entire cold season. Thus, the current CO2 observing network is unlikely to detect potentially large CO2 sources associated with deep permafrost thaw and cold season respiration expected over the next 50 y. Although continuity of current observations is vital, strategies and technologies focused on cold season measurements (active remote sensing, aircraft, and tall towers) and systematic sampling of vertical profiles across continental interiors over the full annual cycle are required to detect the onset of carbon release from thawing permafrost.

  10. Comparison of regional and ecosystem CO2 fluxes

    DEFF Research Database (Denmark)

    Gryning, Sven-Erik; Søgaard, Henrik; Batchvarova, Ekaterina

    2009-01-01

    A budget method to derive the regional surface flux of CO2 from the evolution of the boundary layer is presented and applied. The necessary input for the method can be deduced from a combination of vertical profile measurements of CO2 concentrations by i.e. an airplane, successive radio......-soundings and standard measurements of the CO2 concentration near the ground. The method was used to derive the regional flux of CO2 over an agricultural site at Zealand in Denmark during an experiment on 12–13 June 2006. The regional fluxes of CO2 represent a combination of agricultural and forest surface conditions....... It was found that the regional flux of CO2 in broad terms follows the behavior of the flux of CO2 at the agricultural (grassland) and the deciduous forest station. The regional flux is comparable not only in size but also in the diurnal (daytime) cycle of CO2 fluxes at the two stations....

  11. Benthic fluxes in San Francisco Bay

    Science.gov (United States)

    Hammond, Douglas E.; Fuller, C.; Harmon, D.; Hartman, Blayne; Korosec, M.; Miller, L.G.; Rea, R.; Warren, S.; Berelson, W.; Hager, S.W.

    1985-01-01

    variability is smaller, probably because the annual temperature range in San Francisco Bay is smaller. Budgets constructed for South San Francisco Bay show that large fractions of the net annual productivity of carbon (about 90%) and silica (about 65%) are recycled by the benthos. Substantial rates of simultaneous nitrification and denitrification must occur in shoal areas, apparently resulting in conversion to N2 of 55% of the particulate nitrogen reaching the sediments. In shoal areas, benthic fluxes can replace the water column standing stocks of ammonia in 2-6 days and silica in 17-34 days, indicating the importance of benthic fluxes in the maintenance of productivity. Pore water profiles of nutrients and Rn-222 show that macrofaunal irrigation is extremely important in transport of silica, ammonia, and alkalinity. Calculations of benthic fluxes from these profiles are less accurate, but yield results consistent with chamber measurements and indicate that most of the NH3, SiO2, and alkalinity fluxes are sustained by reactions occurring throughout the upper 20-40 cm of the sediment column. In contrast, O2, CO2, and N + N fluxes must be dominated by reactions occurring within the upper one cm of the sediment-water interface. While most data support the statements made above, a few flux measurements are contradictory and demonstrate the complexity of benthic exchange. ?? 1985 Dr W. Junk Publishers.

  12. Magnetic flux reconstruction methods for shaped tokamaks

    Energy Technology Data Exchange (ETDEWEB)

    Tsui, Chi-Wa [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)

    1993-12-01

    The use of a variational method permits the Grad-Shafranov (GS) equation to be solved by reducing the problem of solving the 2D non-linear partial differential equation to the problem of minimizing a function of several variables. This high speed algorithm approximately solves the GS equation given a parameterization of the plasma boundary and the current profile (p` and FF` functions). The author treats the current profile parameters as unknowns. The goal is to reconstruct the internal magnetic flux surfaces of a tokamak plasma and the toroidal current density profile from the external magnetic measurements. This is a classic problem of inverse equilibrium determination. The current profile parameters can be evaluated by several different matching procedures. Matching of magnetic flux and field at the probe locations using the Biot-Savart law and magnetic Green`s function provides a robust method of magnetic reconstruction. The matching of poloidal magnetic field on the plasma surface provides a unique method of identifying the plasma current profile. However, the power of this method is greatly compromised by the experimental errors of the magnetic signals. The Casing Principle provides a very fast way to evaluate the plasma contribution to the magnetic signals. It has the potential of being a fast matching method. The performance of this method is hindered by the accuracy of the poloidal magnetic field computed from the equilibrium solver. A flux reconstruction package has been implemented which integrates a vacuum field solver using a filament model for the plasma, a multi-layer perception neural network as an interface, and the volume integration of plasma current density using Green`s functions as a matching method for the current profile parameters. The flux reconstruction package is applied to compare with the ASEQ and EFIT data. The results are promising.

  13. Electron heat flux instability

    Science.gov (United States)

    Saeed, Sundas; Sarfraz, M.; Yoon, P. H.; Lazar, M.; Qureshi, M. N. S.

    2017-02-01

    The heat flux instability is an electromagnetic mode excited by a relative drift between the protons and two-component core-halo electrons. The most prominent application may be in association with the solar wind where drifting electron velocity distributions are observed. The heat flux instability is somewhat analogous to the electrostatic Buneman or ion-acoustic instability driven by the net drift between the protons and bulk electrons, except that the heat flux instability operates in magnetized plasmas and possesses transverse electromagnetic polarization. The heat flux instability is also distinct from the electrostatic counterpart in that it requires two electron species with relative drifts with each other. In the literature, the heat flux instability is often called the 'whistler' heat flux instability, but it is actually polarized in the opposite sense to the whistler wave. This paper elucidates all of these fundamental plasma physical properties associated with the heat flux instability starting from a simple model, and gradually building up more complexity towards a solar wind-like distribution functions. It is found that the essential properties of the instability are already present in the cold counter-streaming electron model, and that the instability is absent if the protons are ignored. These instability characteristics are highly reminiscent of the electron firehose instability driven by excessive parallel temperature anisotropy, propagating in parallel direction with respect to the ambient magnetic field, except that the free energy source for the heat flux instability resides in the effective parallel pressure provided by the counter-streaming electrons.

  14. Earth's surface heat flux

    Directory of Open Access Journals (Sweden)

    J. H. Davies

    2010-02-01

    Full Text Available We present a revised estimate of Earth's surface heat flux that is based upon a heat flow data-set with 38 347 measurements, which is 55% more than used in previous estimates. Our methodology, like others, accounts for hydrothermal circulation in young oceanic crust by utilising a half-space cooling approximation. For the rest of Earth's surface, we estimate the average heat flow for different geologic domains as defined by global digital geology maps; and then produce the global estimate by multiplying it by the total global area of that geologic domain. The averaging is done on a polygon set which results from an intersection of a 1 degree equal area grid with the original geology polygons; this minimises the adverse influence of clustering. These operations and estimates are derived accurately using methodologies from Geographical Information Science. We consider the virtually un-sampled Antarctica separately and also make a small correction for hot-spots in young oceanic lithosphere. A range of analyses is presented. These, combined with statistical estimates of the error, provide a measure of robustness. Our final preferred estimate is 47±2 TW, which is greater than previous estimates.

  15. Disjunct eddy covariance technique for trace gas flux measurements

    Science.gov (United States)

    Rinne, H. J. I.; Guenther, A. B.; Warneke, C.; de Gouw, J. A.; Luxembourg, S. L.

    A new approach for eddy covariance flux measurements is developed and applied for trace gas fluxes in the atmospheric surface layer. In disjunct eddy covariance technique, quick samples with a relatively long time interval between them are taken instead of continuously sampling air. This subset of the time series together with vertical wind velocity data at corresponding sampling times can be correlated to give a flux. The disjunct eddy sampling gives more time to analyze the trace gas concentrations and thus makes eddy covariance measurements possible using slower sensors. In this study a proton-transfer-reaction mass spectrometer with response time of about 1 second was used with a disjunct eddy sampler to measure fluxes of volatile organic compounds from an alfalfa field. The measured day-time maximum methanol fluxes ranged from 1 mg m-2 h-1 from uncut alfalfa to 8 mg m-2 h-1 from freshly cut alfalfa. Night-time fluxes were around zero.

  16. Quantitative high dynamic range beam profiling for fluorescence microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Mitchell, T. J., E-mail: t.j.mitchell@dur.ac.uk; Saunter, C. D.; O’Nions, W.; Girkin, J. M.; Love, G. D. [Centre for Advanced Instrumentation and Biophysical Sciences Institute, Department of Physics, Durham University, Durham DH1 3LE (United Kingdom)

    2014-10-15

    Modern developmental biology relies on optically sectioning fluorescence microscope techniques to produce non-destructive in vivo images of developing specimens at high resolution in three dimensions. As optimal performance of these techniques is reliant on the three-dimensional (3D) intensity profile of the illumination employed, the ability to directly record and analyze these profiles is of great use to the fluorescence microscopist or instrument builder. Though excitation beam profiles can be measured indirectly using a sample of fluorescent beads and recording the emission along the microscope detection path, we demonstrate an alternative approach where a miniature camera sensor is used directly within the illumination beam. Measurements taken using our approach are solely concerned with the illumination optics as the detection optics are not involved. We present a miniature beam profiling device and high dynamic range flux reconstruction algorithm that together are capable of accurately reproducing quantitative 3D flux maps over a large focal volume. Performance of this beam profiling system is verified within an optical test bench and demonstrated for fluorescence microscopy by profiling the low NA illumination beam of a single plane illumination microscope. The generality and success of this approach showcases a widely flexible beam amplitude diagnostic tool for use within the life sciences.

  17. Aeronet Solar Flux

    Data.gov (United States)

    National Aeronautics and Space Administration — SolRad-Net (Solar Radiation Network) is an established network of ground-based sensors providing high-frequency solar flux measurements in quasi-realtime to the...

  18. Net Ecosystem Carbon Flux

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — Net Ecosystem Carbon Flux is defined as the year-over-year change in Total Ecosystem Carbon Stock, or the net rate of carbon exchange between an ecosystem and the...

  19. Nitrous Oxide Flux

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — Nitrous Oxide (N20) flux is the net rate of nitrous oxide exchange between an ecosystem and the atmosphere. Data of this variable were generated by the USGS...

  20. Flux in Tallinn

    Index Scriptorium Estoniae

    2004-01-01

    Rahvusvahelise elektroonilise kunsti sümpoosioni ISEA2004 klubiõhtu "Flux in Tallinn" klubis Bon Bon. Eestit esindasid Ropotator, Ars Intel Inc., Urmas Puhkan, Joel Tammik, Taavi Tulev (pseud. Wochtzchee). Klubiõhtu koordinaator Andres Lõo

  1. Flux Emergence (Theory

    Directory of Open Access Journals (Sweden)

    Mark C. M. Cheung

    2014-07-01

    Full Text Available Magnetic flux emergence from the solar convection zone into the overlying atmosphere is the driver of a diverse range of phenomena associated with solar activity. In this article, we introduce theoretical concepts central to the study of flux emergence and discuss how the inclusion of different physical effects (e.g., magnetic buoyancy, magnetoconvection, reconnection, magnetic twist, interaction with ambient field in models impact the evolution of the emerging field and plasma.

  2. Generic flux coupling analysis

    OpenAIRE

    Reimers, Arne; Goldstein, Y.; Bockmayr, A.

    2015-01-01

    htmlabstractFlux coupling analysis (FCA) has become a useful tool for aiding metabolic reconstructions and guiding genetic manipulations. Originally, it was introduced for constraint-based models of metabolic networks that are based on the steady-state assumption. Recently, we have shown that the steady-state assumption can be replaced by a weaker lattice-theoretic property related to the supports of metabolic fluxes. In this paper, we further extend our approach and develop an efficient algo...

  3. Serial CSF sampling over a period of 30 h via an indwelling spinal catheter in healthy volunteers : headache, back pain, tolerability and measured acetylcholine profile

    NARCIS (Netherlands)

    den Daas, Izaak; Wemer, Johan; Abou Farha, Khalid; Tamminga, Wim; de Boer, Theo; Spanjersberg, Rob; Struys, Michel M. R. F.; Absalom, Anthony R.

    Timed interval cerebrospinal fluid (CSF) sampling by indwelling catheterization can be a valuable corroborative tool for the pharmacokinetic and pharmacodynamic assessment of drugs. CSF sampling in studies on drug candidates for Alzheimer's disease have been conducted in evaluations of the

  4. Cancer associated epigenetic transitions identified by genome-wide histone methylation binding profiles in human colorectal cancer samples and paired normal mucosa

    DEFF Research Database (Denmark)

    Enroth, Stefan; Rada-Iglesisas, Alvaro; Andersson, Robin

    2011-01-01

    Despite their well-established functional roles, histone modifications have received less attention than DNA methylation in the cancer field. In order to evaluate their importance in colorectal cancer (CRC), we generated the first genome-wide histone modification profiles in paired normal colon...

  5. Longitudinal Stability of Social Competence Indicators in a Portuguese Sample: Q-Sort Profiles of Social Competence, Measures of Social Engagement, and Peer Sociometric Acceptance

    Science.gov (United States)

    Santos, António J.; Vaughn, Brian E.; Peceguina, Inês; Daniel, João R.

    2014-01-01

    This study examines the temporal stability (over 3 years) of individual differences in 3 domains relevant to preschool children's social competence: social engagement/motivation, profiles of behavior and personality attributes characteristic of socially competent young children, and peer acceptance. Each domain was measured with multiple…

  6. Ultra-processed foods have the worst nutrient profile, yet they are the most available packaged products in a sample of New Zealand supermarkets

    NARCIS (Netherlands)

    Luiten, Claire M; Steenhuis, Ingrid Hm; Eyles, Helen; Ni Mhurchu, Cliona; Waterlander, Wilma E

    OBJECTIVE: To examine the availability of packaged food products in New Zealand supermarkets by level of industrial processing, nutrient profiling score (NPSC), price (energy, unit and serving costs) and brand variety. DESIGN: Secondary analysis of cross-sectional survey data on packaged supermarket

  7. Dynamic ignition regime of condensed system by radiate heat flux

    Science.gov (United States)

    Arkhipov, V. A.; Zolotorev, N. N.; Korotkikh, A. G.; Kuznetsov, V. T.

    2017-05-01

    The main ignition characteristics of high-energy materials are the ignition time and critical heat flux allowing evaluation of the critical conditions for ignition, fire and explosive safety for the test solid propellants. The ignition process is typically studied in stationary conditions of heat input at constant temperature of the heating surface, environment or the radiate heat flux on the sample surface. In real conditions, ignition is usually effected at variable time-dependent values of the heat flux. In this case, the heated layer is formed on the sample surface in dynamic conditions and significantly depends on the heat flux change, i.e. increasing or decreasing falling heat flux in the reaction period of the propellant sample. This paper presents a method for measuring the ignition characteristics of a high-energy material sample in initiation of the dynamic radiant heat flux, which includes the measurement of the ignition time when exposed to a sample time varying radiant heat flux given intensity. In case of pyroxyline containing 1 wt. % of soot, it is shown that the ignition times are reduced by 20-50 % depending on the initial value of the radiant flux density in initiation by increasing or decreasing radiant heat flux compared with the stationary conditions of heat supply in the same ambient conditions.

  8. Eddy covariance flux measurements of ozone: Three stations side-by-side

    Science.gov (United States)

    Song, G.; Voß, L.; Falge, E.; Mayer, J.-C.; Moravek, A.; Trebs, I.; Bruse, M.; Zhu, Z.; Andreae, M. O.; Meixner, F. X.

    2012-04-01

    Since about two decades, fast response ozone analyzers, based on gas-phase chemiluminescence ("Güsten type"), became more and more available and emerged to be operational in atmosphere-biosphere exchange studies using the eddy-covariance technique. While there are first preliminary reports about measurements of the vertical profile of ozone fluxes in forest canopies (addressing the question of vertical flux divergence), measurements by ozone flux stations distributed in a horizontally arranged array (addressing questions of horizontal divergence and/or footprint) might be feasible. For all these measurements, the precision of ozone flux stations is of particular interest, because it defines the vertical/horizontal resolution of expected flux divergence. As a first step in this direction, we performed a 9 week, side-by-side experiment of three ozone flux stations on a small airfield in Mainz-Finthen/Germany (49.969° N, 8.148° E, 227 m a.s.l.) in late summer/autumn 2011. Turbulent fluctuations of ozone concentration (in arbitrary units) have been measured by three identical gas-phase chemiluminescence anaylzers (enviscope GmbH/ Germany) with a sampling frequency of 20 Hz. Absolute ozone concentrations have been monitored by three slow-response UV-absorption based analyzers (model 205, 2BTechnologies/U.S.A.; model 49i, ThermoInstruments/U.S.A.) every 2 and 10 seconds, respectively. Three 3D sonic anemometers (model USA-1, METEK/Germany; model CSAT3, Campbell Scientific/U.K.) have been applied to obtain fluctuations of 3D wind vectors and temperature (20Hz). All fast response sensors were mounted at 3 m above ground, the three flux stations have been aligned in cross-wind direction in a distance of about 5.5 m to each other. Sensor separation (3D anemometer - ozone intake) was 0.3 m, the length of ozone intake tubes were about 3 m. Ozone monitors have routinely been calibrated every 15 days. For the calculation of turbulent fluxes of ozone, momentum, and sensible

  9. The flux-flux correlation function for anharmonic barriers

    NARCIS (Netherlands)

    Goussev, Arseni; Schubert, Roman; Waalkens, Holger; Wiggins, Stephen

    2010-01-01

    The flux-flux correlation function formalism is a standard and widely used approach for the computation of reaction rates. In this paper we introduce a method to compute the classical and quantum flux-flux correlation functions for anharmonic barriers essentially analytically through the use of the

  10. Perturbations in the Lipid Profile of Individuals with Newly Diagnosed Type 1 Diabetes Mellitus: Lipidomics Analysis of a Diabetes Antibody Standardization Program Sample Subset

    Energy Technology Data Exchange (ETDEWEB)

    Sorensen, Christina M.; Ding, Jie; Zhang, Qibin; Alquier, Thierry; Zhao, Rui; Mueller, Patricia W.; Smith, Richard D.; Metz, Thomas O.

    2010-08-01

    Objectives: To characterize the lipid profile of individuals with newly diagnosed type 1 diabetes mellitus using LC-MS-based lipidomics and the accurate mass and time (AMT) tag approach. Design and methods: Lipids were extracted from plasma and sera of 10 subjects from the Diabetes Antibody Standardization Program (years 2000-2005) and 10 non-diabetic subjects and analyzed by capillary liquid chromatography coupled with a hybrid ion-trap-Fourier transform ion cyclotron resonance mass spectrometer. Lipids were identified and quantified using the AMT tag approach. Results: Five hundred sixty lipid features differentiated (q < 0.05) diabetic from healthy individuals in a partial least-squares analysis, characterizing of individuals with recently diagnosed type 1 diabetes mellitus. Conclusions: A lipid profile associated with newly diagnosed type 1 diabetes may aid in further characterization of biochemical pathways involved in lipid regulation or mobilization and lipotoxicity of pancreatic beta-cells.

  11. Ultra-processed foods have the worst nutrient profile, yet they are the most available packaged products in a sample of New Zealand supermarkets.

    Science.gov (United States)

    Luiten, Claire M; Steenhuis, Ingrid Hm; Eyles, Helen; Ni Mhurchu, Cliona; Waterlander, Wilma E

    2016-02-01

    To examine the availability of packaged food products in New Zealand supermarkets by level of industrial processing, nutrient profiling score (NPSC), price (energy, unit and serving costs) and brand variety. Secondary analysis of cross-sectional survey data on packaged supermarket food and non-alcoholic beverages. Products were classified according to level of industrial processing (minimally, culinary and ultra-processed) and their NPSC. Packaged foods available in four major supermarkets in Auckland, New Zealand. Packaged supermarket food products for the years 2011 and 2013. The majority (84% in 2011 and 83% in 2013) of packaged foods were classified as ultra-processed. A significant positive association was found between the level of industrial processing and NPSC, i.e., ultra-processed foods had a worse nutrient profile (NPSC=11.63) than culinary processed foods (NPSC=7.95), which in turn had a worse nutrient profile than minimally processed foods (NPSC=3.27), Pprocessing. The study observed many variations of virtually the same product. The ten largest food manufacturers produced 35% of all packaged foods available. In New Zealand supermarkets, ultra-processed foods comprise the largest proportion of packaged foods and are less healthy than less processed foods. The lack of significant price difference between ultra- and less processed foods suggests ultra-processed foods might provide time-poor consumers with more value for money. These findings highlight the need to improve the supermarket food supply by reducing numbers of ultra-processed foods and by reformulating products to improve their nutritional profile.

  12. Flux Pinning in Superconductors

    CERN Document Server

    Matsushita, Teruo

    2007-01-01

    The book covers the flux pinning mechanisms and properties and the electromagnetic phenomena caused by the flux pinning common for metallic, high-Tc and MgB2 superconductors. The condensation energy interaction known for normal precipitates or grain boundaries and the kinetic energy interaction proposed for artificial Nb pins in Nb-Ti, etc., are introduced for the pinning mechanism. Summation theories to derive the critical current density are discussed in detail. Irreversible magnetization and AC loss caused by the flux pinning are also discussed. The loss originally stems from the ohmic dissipation of normal electrons in the normal core driven by the electric field induced by the flux motion. The readers will learn why the resultant loss is of hysteresis type in spite of such mechanism. The influence of the flux pinning on the vortex phase diagram in high Tc superconductors is discussed, and the dependencies of the irreversibility field are also described on other quantities such as anisotropy of supercondu...

  13. INNOVATIVE HEAT FLUX SENSOR

    Directory of Open Access Journals (Sweden)

    G. N. Lukyanov

    2017-02-01

    Full Text Available Subject of Study.We present a method for heat flux measuring with the use of polarization properties of ferroelectric ceramics. Heat flux innovative sensor is developed on the basis of the proposed method. Its experimental verification is carried out. Method. The measurements are based on maintaining a balance between the processes caused by thermal energy and the energy of the electric field in the ferroelectric ceramics. Main Results. The testing of the proposed heat flux sensor has been organized in two stages. At the first stage the primary calibration has been performed by calibrated sensors ITP MG4.03/x(y “Potok”. At the second stage the testing of heat flux sensor has been carried out for calculating the quantity of heat. The comparison of the results to the readings of serial heat meters VKT-7 and STK-15 has been performed. Experiments have shown that the polarization properties of the ferroelectric ceramics can be used to measure the heat flow. Practical Relevance. The proposed sensor can be recommended as an apartment-level heat meter. The calibration of the proposed heat flux sensor with more accurate measurement tools gives the possibility to include it on the State Register of Measuring Instruments.

  14. Flux pinning in superconductors

    CERN Document Server

    Matsushita, Teruo

    2014-01-01

    The book covers the flux pinning mechanisms and properties and the electromagnetic phenomena caused by the flux pinning common for metallic, high-Tc and MgB2 superconductors. The condensation energy interaction known for normal precipitates or grain boundaries and the kinetic energy interaction proposed for artificial Nb pins in Nb-Ti, etc., are introduced for the pinning mechanism. Summation theories to derive the critical current density are discussed in detail. Irreversible magnetization and AC loss caused by the flux pinning are also discussed. The loss originally stems from the ohmic dissipation of normal electrons in the normal core driven by the electric field induced by the flux motion. The readers will learn why the resultant loss is of hysteresis type in spite of such mechanism. The influence of the flux pinning on the vortex phase diagram in high Tc superconductors is discussed, and the dependencies of the irreversibility field are also described on other quantities such as anisotropy of supercondu...

  15. Deuterium retention in graphite exposed to high flux plasma at high temperatures

    Energy Technology Data Exchange (ETDEWEB)

    Rusinov, A., E-mail: rusinov.aleksandr@gmail.com [Moscow Engineering and Physics Institute, Kashirskoe sh. 31, 115409 Moscow (Russian Federation); Trifonov, N.; Gasparyan, Yu. [Moscow Engineering and Physics Institute, Kashirskoe sh. 31, 115409 Moscow (Russian Federation); Khripunov, B., E-mail: boris@nfi.kiae.ru [National Research Center Kurchatov Institute, Academic Kurchatov sq., 1, 123098 Moscow (Russian Federation); Mayer, M.; Roth, J. [Max-Planck-Institut fuer Plasmaphysik, EURATOM Association, Boltzmanstr.2, D-85748 Garching (Germany); Pisarev, A. [Moscow Engineering and Physics Institute, Kashirskoe sh. 31, 115409 Moscow (Russian Federation)

    2011-10-01

    Deuterium trapping in graphite under high flux plasma exposure at high temperatures was studied. A target of MPG-8 fine grain graphite was exposed to plasma beam in LENTA device at zero potential. The average ion flux was of about 10{sup 21} D/m{sup 2} s with a maximum in the center. The temperature was 1473 K in the center and 873 K outside the beam spot. After irradiation, the target was sectioned along and across the surface and studied by SEM, NRA, and TDS. Deuterium profiles measured by NRA showed a peak close to the surface and long tails in the bulk. TDS of samples taken for the front and back sides of the target were very similar. It is suggested, that D retention at the plasma irradiation is mainly controlled by trapping from the gas phase, locally created in the graphite pores by plasma ions injection and subsequent flow of gas to the back side through internal porosity.

  16. A benchmark analysis of radiation flux distribution for Boron Neutron Capture Therapy of canine brain tumors

    Energy Technology Data Exchange (ETDEWEB)

    Moran, J.M.

    1992-02-01

    Calculations of radiation flux and dose distributions for Boron Neutron Capture Therapy (BNCT) of brain tumors are typically performed using sophisticated three-dimensional analytical models based on either a homogeneous approximation or a simplified few-region approximation to the actual highly-heterogeneous geometry of the irradiation volume. Such models should be validated by comparison with calculations using detailed models in which all significant macroscopic tissue heterogeneities and geometric structures are explicitly represented as faithfully as possible. This work describes a validation exercise for BNCT of canine brain tumors. Geometric measurements of the canine anatomical structures of interest for this work were performed by dissecting and examining two essentially identical Labrador Retriever heads. Chemical analyses of various tissue samples taken during the dissections were conducted to obtain measurements of elemental compositions for tissues of interest. The resulting geometry and tissue composition data were then used to construct a detailed heterogeneous calculational model of the Labrador Retriever head. Calculations of three-dimensional radiation flux distributions pertinent to BNCT were performed for the model using the TORT discrete-ordinates radiation transport code. The calculations were repeated for a corresponding volume-weighted homogeneous tissue model. Comparison of the results showed that the peak neutron and photon flux magnitudes were quite similar for the two models (within 5%), but that the spatial flux profiles were shifted in the heterogeneous model such that the fluxes in some locations away from the peak differed from the corresponding fluxes in the homogeneous model by as much as 10-20%. Differences of this magnitude can be therapeutically significant, emphasizing the need for proper validation of simplified treatment planning models.

  17. Mold Flux Crystallization and Mold Thermal Behavior

    Science.gov (United States)

    Peterson, Elizabeth Irene

    Mold flux plays a small but critical role in the continuous casting of steel. The carbon-coated powder is added at the top of the water-cooled copper mold, over time it melts and infiltrates the gap between the copper mold and the solidifying steel strand. Mold powders serve five primary functions: (1) chemical insulation, (2) thermal insulation, (3) lubrication between the steel strand and mold, (4) absorption of inclusions, and (5) promotion of even heat flux. All five functions are critical to slab casting, but surface defect prevention is primarily controlled through even heat flux. Glassy fluxes have high heat transfer and result in a thicker steel shell. Steels with large volumetric shrinkage on cooling must have a crystalline flux to reduce the radiative heat transfer and avoid the formation of cracks in the shell. Crystallinity plays a critical role in steel shell formation, therefore it is important to study the thermal conditions that promote each phase and its morphology. Laboratory tests were performed to generate continuous cooling transformation (CCT) and time-temperature-transformation (TTT) diagrams. Continuous cooling transformation tests were performed in an instrumented eight cell step chill mold. Results showed that cuspidine was the only phase formed in conventional fluxes and all observed structures were dendritic. An isothermal tin bath quench method was also developed to isothermally age glassy samples. Isothermal tests yielded different microstructures and different phases than those observed by continuous cooling. Comparison of aged tests with industrial flux films indicates similar faceted structures along the mold wall, suggesting that mold flux first solidifies as a glass along the mold wall, but the elevated temperature devitrifies the glassy structure forming crystals that cannot form by continuous cooling.

  18. Recurrence Analysis of Eddy Covariance Fluxes

    Science.gov (United States)

    Lange, Holger; Flach, Milan; Foken, Thomas; Hauhs, Michael

    2015-04-01

    The eddy covariance (EC) method is one key method to quantify fluxes in biogeochemical cycles in general, and carbon and energy transport across the vegetation-atmosphere boundary layer in particular. EC data from the worldwide net of flux towers (Fluxnet) have also been used to validate biogeochemical models. The high resolution data are usually obtained at 20 Hz sampling rate but are affected by missing values and other restrictions. In this contribution, we investigate the nonlinear dynamics of EC fluxes using Recurrence Analysis (RA). High resolution data from the site DE-Bay (Waldstein-Weidenbrunnen) and fluxes calculated at half-hourly resolution from eight locations (part of the La Thuile dataset) provide a set of very long time series to analyze. After careful quality assessment and Fluxnet standard gapfilling pretreatment, we calculate properties and indicators of the recurrent structure based both on Recurrence Plots as well as Recurrence Networks. Time series of RA measures obtained from windows moving along the time axis are presented. Their interpretation is guided by three different questions: (1) Is RA able to discern periods where the (atmospheric) conditions are particularly suitable to obtain reliable EC fluxes? (2) Is RA capable to detect dynamical transitions (different behavior) beyond those obvious from visual inspection? (3) Does RA contribute to an understanding of the nonlinear synchronization between EC fluxes and atmospheric parameters, which is crucial for both improving carbon flux models as well for reliable interpolation of gaps? (4) Is RA able to recommend an optimal time resolution for measuring EC data and for analyzing EC fluxes? (5) Is it possible to detect non-trivial periodicities with a global RA? We will demonstrate that the answers to all five questions is affirmative, and that RA provides insights into EC dynamics not easily obtained otherwise.

  19. Enterotoxigenic profiling of emetic toxin- and enterotoxin-producing Bacillus cereus, Isolated from food, environmental, and clinical samples by multiplex PCR.

    Science.gov (United States)

    Forghani, Fereidoun; Kim, Jung-Beom; Oh, Deog-Hwan

    2014-11-01

    Bacillus cereus comprises the largest group of endospore-forming bacteria and can cause emetic and diarrheal food poisoning. A total of 496 B. cereus strains isolated from various sources (food, environmental, clinical) were assessed by a multiplex PCR for the presence of enterotoxin genes. The detection rate of nheA, entFM, hblC, and cytK enterotoxin genes among all B. cereus strains was 92.33%, 77.21%, 59.47%, and 47.58%, respectively. Enterotoxigenic profiles were determined in emetic toxin- (8 patterns) and enterotoxin-producing strains (12 patterns). The results provide important information on toxin prevalence and toxigenic profiles of B. cereus from various sources. Our findings revealed that B. cereus must be considered a serious health hazard and Bacillus thuringiensis should be considered of a greater potential concern to food safety among all B. cereus group members. Also, there is need for intensive and continuous monitoring of products embracing both emetic toxin and enterotoxin genes. © 2014 Institute of Food Technologists®

  20. Generic flux coupling analysis

    NARCIS (Netherlands)

    A.C. Reimers (Arne); Y. Goldstein; A. Bockmayr

    2015-01-01

    htmlabstractFlux coupling analysis (FCA) has become a useful tool for aiding metabolic reconstructions and guiding genetic manipulations. Originally, it was introduced for constraint-based models of metabolic networks that are based on the steady-state assumption. Recently, we have shown that the

  1. Flux Vacua and Supermanifolds

    CERN Document Server

    Grassi, P A

    2007-01-01

    As been recently pointed out, physically relevant models derived from string theory require the presence of non-vanishing form fluxes besides the usual geometrical constraints. In the case of NS-NS fluxes, the Generalized Complex Geometry encodes these informations in a beautiful geometrical structure. On the other hand, the R-R fluxes call for supergeometry as the underlying mathematical framework. In this context, we analyze the possibility of constructing interesting supermanifolds recasting the geometrical data and RR fluxes. To characterize these supermanifolds we have been guided by the fact topological strings on supermanifolds require the super-Ricci flatness of the target space. This can be achieved by adding to a given bosonic manifold enough anticommuting coordinates and new constraints on the bosonic sub-manifold. We study these constraints at the linear and non-linear level for a pure geometrical setting and in the presence of p-form field strengths. We find that certain spaces admit several supe...

  2. Soluble organic nutrient fluxes

    Science.gov (United States)

    Robert G. Qualls; Bruce L. Haines; Wayne Swank

    2014-01-01

    Our objectives in this study were (i) compare fluxes of the dissolved organic nutrients dissolved organic carbon (DOC), DON, and dissolved organic phosphorus (DOP) in a clearcut area and an adjacent mature reference area. (ii) determine whether concentrations of dissolved organic nutrients or inorganic nutrients were greater in clearcut areas than in reference areas,...

  3. Generic flux coupling analysis.

    Science.gov (United States)

    Reimers, Arne C; Goldstein, Yaron; Bockmayr, Alexander

    2015-04-01

    Flux coupling analysis (FCA) has become a useful tool for aiding metabolic reconstructions and guiding genetic manipulations. Originally, it was introduced for constraint-based models of metabolic networks that are based on the steady-state assumption. Recently, we have shown that the steady-state assumption can be replaced by a weaker lattice-theoretic property related to the supports of metabolic fluxes. In this paper, we further extend our approach and develop an efficient algorithm for generic flux coupling analysis that works with any kind of qualitative pathway model. We illustrate our method by thermodynamic flux coupling analysis (tFCA), which allows studying steady-state metabolic models with loop-law thermodynamic constraints. These models do not satisfy the lattice-theoretic properties required in our previous work. For a selection of genome-scale metabolic network reconstructions, we discuss both theoretically and practically, how thermodynamic constraints strengthen the coupling results that can be obtained with classical FCA. A prototype implementation of tFCA is available at http://hoverboard.io/L4FC. Copyright © 2015 Elsevier Inc. All rights reserved.

  4. Relative effectiveness of kinetic analysis vs single point readings for classifying environmental samples based on community-level physiological profiles (CLPP)

    Science.gov (United States)

    Garland, J. L.; Mills, A. L.; Young, J. S.

    2001-01-01

    The relative effectiveness of average-well-color-development-normalized single-point absorbance readings (AWCD) vs the kinetic parameters mu(m), lambda, A, and integral (AREA) of the modified Gompertz equation fit to the color development curve resulting from reduction of a redox sensitive dye from microbial respiration of 95 separate sole carbon sources in microplate wells was compared for a dilution series of rhizosphere samples from hydroponically grown wheat and potato ranging in inoculum densities of 1 x 10(4)-4 x 10(6) cells ml-1. Patterns generated with each parameter were analyzed using principal component analysis (PCA) and discriminant function analysis (DFA) to test relative resolving power. Samples of equivalent cell density (undiluted samples) were correctly classified by rhizosphere type for all parameters based on DFA analysis of the first five PC scores. Analysis of undiluted and 1:4 diluted samples resulted in misclassification of at least two of the wheat samples for all parameters except the AWCD normalized (0.50 abs. units) data, and analysis of undiluted, 1:4, and 1:16 diluted samples resulted in misclassification for all parameter types. Ordination of samples along the first principal component (PC) was correlated to inoculum density in analyses performed on all of the kinetic parameters, but no such influence was seen for AWCD-derived results. The carbon sources responsible for classification differed among the variable types with the exception of AREA and A, which were strongly correlated. These results indicate that the use of kinetic parameters for pattern analysis in CLPP may provide some additional information, but only if the influence of inoculum density is carefully considered. c2001 Elsevier Science Ltd. All rights reserved.

  5. Quantification of Regional and Continental Scale Surface Fluxes of Carbon Using Airborne Measurements in a Lagrangian Framework

    Science.gov (United States)

    Gerbig, C.; Lin, J. C.; Wofsy, S. C.

    2001-05-01

    In carbon cycle science a problem arises from linking local-scale observations (e.g. eddy flux) with the global-scale atmospheric constraint (e.g. latitudinal gradient and inversion modeling studies). Atmospheric budget methods involving airborne measurements of CO2 have the potential to fill the current gap on regional and continental scales. Optimizing the sampling strategy for such methods is one of the main objectives of the CO2 Budget and Rectification Airborne (COBRA) study. During the COBRA Summer campaign of 2000, 26 flights were conducted using the UND CITATION 2 over large parts of the U.S. during the month of August. First results of both, regional and continental scale experiments and their analysis using Lagrangian models will be presented. To quantify fluxes on the regional scale ( ~104 km2), diurnal vertical profiles within and above the PBL were made in an airmass-following framework. Combined with a simple transport model these measurements constrain regional scale fluxes and their spatial gradients. Conducted in the vicinity of long-term measurement sites (the WLEF tower in northern Wisconsin and the Howland forest site in Maine), such experiments allow for evaluation of methods for up-scaling. Continental scale fluxes ( ~106 km2) are derived from large-scale surveys conducted in COBRA-2000, with vertical soundings at ~200 km intervals across the U.S. The observed vertical and horizontal gradients show clear signatures of different biospheric activities upstream of the measurements. Influence of upstream exchange fluxes on the measured profiles is spatially and quantitatively resolved by an ensemble back-trajectory approach, the Time-Inverted Lagrangian Transport (TILT) model. A simple inversion is used to calculate photosynthetic and respiratory fluxes for a limited number of vegetation types.

  6. Triacylglycerol Analysis in Human Milk and Other Mammalian Species: Small-Scale Sample Preparation, Characterization, and Statistical Classification Using HPLC-ELSD Profiles.

    Science.gov (United States)

    Ten-Doménech, Isabel; Beltrán-Iturat, Eduardo; Herrero-Martínez, José Manuel; Sancho-Llopis, Juan Vicente; Simó-Alfonso, Ernesto Francisco

    2015-06-24

    In this work, a method for the separation of triacylglycerols (TAGs) present in human milk and from other mammalian species by reversed-phase high-performance liquid chromatography using a core-shell particle packed column with UV and evaporative light-scattering detectors is described. Under optimal conditions, a mobile phase containing acetonitrile/n-pentanol at 10 °C gave an excellent resolution among more than 50 TAG peaks. A small-scale method for fat extraction in these milks (particularly of interest for human milk samples) using minimal amounts of sample and reagents was also developed. The proposed extraction protocol and the traditional method were compared, giving similar results, with respect to the total fat and relative TAG contents. Finally, a statistical study based on linear discriminant analysis on the TAG composition of different types of milks (human, cow, sheep, and goat) was carried out to differentiate the samples according to their mammalian origin.

  7. First-order chemistry in the surface-flux layer

    DEFF Research Database (Denmark)

    Kristensen, L.; Andersen, C.E.; Ejsing Jørgensen, Hans

    1997-01-01

    We have discussed the behavior of a non-conserved scalar in the stationary, horizontally homogeneous, neutral surface-flux layer and, on the basis of conventional second-order closure, derived analytic expressions for flux and for mean concentration of a gas, subjected to a first-order removal pr...... on the validity of our predictions. The agreement seemed such that a falsification of our model was impossible. It is shown how the model can be used to predict the surface flux of Rn-220 from measured concentration profiles....

  8. Temporal and depth-related differences in prokaryotic communities in abyssal sediments associated with particulate organic carbon flux

    Science.gov (United States)

    Moeseneder, M. M.; Smith, K. L.; Ruhl, H. A.; Jones, D. O. B.; Witte, U.; Prosser, J. I.

    2012-12-01

    Particulate organic carbon (POC) flux is hypothesized to be the most important parameter influencing activity and biomass of prokaryotic and faunal communities in the abyssal seafloor, but there is little evidence of POC-related changes in community composition of prokaryotes. This hypothesis was tested by 16S rRNA-gene-based analysis of prokaryotic DNA and RNA extracted from abyssal seafloor sediments during periods of low and high POC flux. Fingerprint analysis of prokaryotic communities indicated that approximately 50% of the phylotypes were identical at each sediment horizon, regardless of the temporal variations in POC flux. However, phylotypes were also detected that represented a relatively dynamic component of these communities and were probably strongly influenced by the prevalent POC flux regime. These patterns were also detected in deeper sediment horizons. DNA- and RNA-based community profiles differed, although both approaches had similar community dynamics. Crenarchaeota showed the strongest shift in community composition in response to availability of labile POC, indicating that POC flux may have a more pronounced impact on crenarchaeal communities than on bacterial communities. The high number of phylotypes common to each sample time suggests that both standing stock and active prokaryotic communities are stable.

  9. Characterization of X-ray generator beam profiles.

    Energy Technology Data Exchange (ETDEWEB)

    Mitchell, Dean J; Harding, Lee T.; Thoreson, Gregory G.; Theisen, Lisa Anne; Parmeter, John Ethan; Thompson, Kyle Richard

    2013-07-01

    T to compute the radiography properties of various materials, the flux profiles of X-ray sources must be characterized. This report describes the characterization of X-ray beam profiles from a Kimtron industrial 450 kVp radiography system with a Comet MXC-45 HP/11 bipolar oil-cooled X-ray tube. The empirical method described here uses a detector response function to derive photon flux profiles based on data collected with a small cadmium telluride detector. The flux profiles are then reduced to a simple parametric form that enables computation of beam profiles for arbitrary accelerator energies.

  10. The role of the ejecta magnetic flux on the two-step Forbush decreases

    Science.gov (United States)

    Masías Meza, Jimmy; Dasso, Sergio

    A Forbush Decrease (FD) is a depression in the Galactic Cosmic Ray (GCR) background intensity, and are usually associated to the passage of an Interplanetary Coronal Mass Ejection (ICME). Magnetic Clouds (MCs) are a subset of ICMEs that are well studied, and are known to cause the deepest FDs. Usually, FDs present two steps in the depression profile, one associated to the shock arrival, and a steeper one restricted to the duration of the ejecta passage. There is a wide variety of processes responsible for the GCR depressions. For instance: the enhanced solar wind (SW) convection, reduced diffusion coefficients, enhanced adiabatic cooling, increase of the coherent magnetic field, etc. Our aim is to make a selection of FD events filtering those associated to well studied magnetic structures, such as Magnetic Clouds (MCs), in order to minimize the mixing processes involved in the ICME-GCR interactions in the resulting sample, and to study statistical properties. We determine the parameters of each FD profile and look for correlations with the associated MC parameters. We propose a method to decompose the FD profile into shock and ejecta components, and investigate correlations with the associated amplitudes of the ejecta components. We introduce the parameter, ``magnetic flux per unit length F/L'', and investigate its importance in the context of a simple ``diffusive barrier'' model. According to the correlations found, the two-step events are better represented by the ``diffusive barrier'' model, and the flux F/L is the parameter that better correlates with these events.

  11. Dependence of Core and Extended Flux on Core Dominance ...

    Indian Academy of Sciences (India)

    2016-01-27

    Jan 27, 2016 ... Based on two extragalactic radio source samples, the core dominance parameter is calculated, and the correlations between the core/extended flux density and core dominance parameter are investigated. When the core dominance parameter is lower than unity, it is linearly correlated with the core flux ...

  12. Dependence of Core and Extended Flux on Core Dominance ...

    Indian Academy of Sciences (India)

    Abstract. Based on two extragalactic radio source samples, the core dominance parameter is calculated, and the correlations between the core/extended flux density and core dominance parameter are investi- gated. When the core dominance parameter is lower than unity, it is linearly correlated with the core flux density, ...

  13. Depth-integrated suspended sediment and geochemical fluxes in large rivers: the Amazon River system

    Science.gov (United States)

    Bouchez, J.; Lupker, M.; Gaillardet, J.; Metivier, F.; France-Lanord, C.; Maurice, L.

    2010-12-01

    Erosion and weathering produce a wide range of residual solid products, in terms of size, density, mineralogy and chemical composition. These solid products are then transported by rivers from the continents to the oceans as suspended particulate matter (SPM) and bedload. Large rivers account for an important part of this transfer of sediments at the global scale. In those rivers, deep channels allow for vertical differentiation, or sorting, of suspended sediment, following their size and density. This hydrodynamic sorting results in vertically heterogeneous depth-profiles in terms of SPM concentration and size distribution (e.g. Garcia, 2008), which in turn likely result in an heterogeneous chemical composition of SPM throughout channel depth (e.g. Galy, 2007), which has to be evaluated. We sampled river water of the main tributaries of the Amazon River system (in the lowland basin), at two distinct water-stages, at various depths following depth-profiles, using a point depth-sampler. After filtration, and SPM recovery, SPM concentration, grain size distribution and chemical composition were determined. River discharge and water velocity throughout the sampled cross-sections were recorded using Acoustic Doppler Current Profiler (ADCP). The large increase in SPM concentration with depth observed at most of the sampled depth-profiles is well accounted for by the Rouse model (e.g. Rouse, 1950). This analysis allows us to reliably infer the SPM concentration and grain size distribution throughout the sampled river cross-section, and thus to estimate the spatially-integrated instantaneous SPM flux using ADCP data (Bouchez et al., 2010). The study also emphasizes the potential role of particle aggregation, within the river system, as a complicating factor regarding the prediction of these depth-integrated SPM fluxes from easily measurable hydrodynamic parameters (surface SPM concentration and grain size, and water velocity). Then, using the previous analysis, combined

  14. Metabolite profiling of small cerebrospinal fluid sample volumes with gas chromatography-mass spectrometry: application to a rat model of Multiple Sclerosis

    NARCIS (Netherlands)

    Coulier, L.; Muilwijk, B.; Bijlsma, S.; Noga, M.; Tienstra, M.; Attali, A.; Aken, H. van; Suidgeest, E.; Tuinstra, T.; Hankemeier, T.; Bobeldijk, I.

    2012-01-01

    Analysis of metabolites in biofluids by gas chromatography–mass spectrometry (GC–MS) after oximation and silylation is a key method in metabolomics. The GC–MS method was modified by a modified vial design and sample work-up procedure in order to make the method applicable to small volumes of

  15. Metabolite profiling of small cerebrospinal fluid sample volumes with gas chromatography-mass spectrometry: Application to a rat model of multiple sclerosis

    NARCIS (Netherlands)

    Coulier, L.; Muilwijk, B.; Bijlsma, S.; Noga, M.; Tienstra, M.; Attali, A.; Aken, H. van; Suidgeest, E.; Tuinstra, T.; Luider, T.M.; Hankemeier, T.; Bobeldijk, I.

    2013-01-01

    Analysis of metabolites in biofluids by gas chromatography-mass spectrometry (GC-MS) after oximation and silylation is a key method in metabolomics. The GC-MS method was modified by a modified vial design and sample work-up procedure in order to make the method applicable to small volumes of

  16. Effects of DNA Extraction Procedures on Bacteroides Profiles in Fecal Samples From Various Animals Determined by Terminal Restriction Fragment Length Polymorphism Analysis

    Science.gov (United States)

    A major assumption in microbial source tracking is that some fecal bacteria are specific to a host animal, and thus provide unique microbial fingerprints that can be used to differentiate hosts. However, the DNA information obtained from a particular sample may be biased dependi...

  17. A Novel Method for Profiling and Quantifying Short- and Medium-Chain Chlorinated Paraffins in Environmental Samples Using Comprehensive Two-Dimensional Gas Chromatography-Electron Capture Negative Ionization High-Resolution Time-of-Flight Mass Spectrometry.

    Science.gov (United States)

    Xia, Dan; Gao, Lirong; Zheng, Minghui; Tian, Qichang; Huang, Huiting; Qiao, Lin

    2016-07-19

    Chlorinated paraffins (CPs) are complex technical mixtures containing thousands of isomers. Analyzing CPs in environmental matrices is extremely challenging. CPs have broad, unresolved profiles when analyzed by one-dimensional gas chromatography (GC). Comprehensive two-dimensional GC (GC×GC) can separate CPs with a high degree of orthogonality. A novel method for simultaneously profiling and quantifying short- and medium-chain CPs, using GC×GC coupled with electron capture negative ionization high-resolution time-of-flight mass spectrometry, was developed. The method allowed 48 CP formula congener groups to be analyzed highly selectively in one injection through accurate mass measurements of the [M - Cl](-) ions in full scan mode. The correlation coefficients (R(2)) for the linear calibration curves for different chlorine contents were 0.982 for short-chain CPs and 0.945 for medium-chain CPs. The method was successfully used to determine CPs in sediment and fish samples. By using this method, with enhanced chromatographic separation and high mass resolution, interferences between CP congeners and other organohalogen compounds, such as toxaphene, are minimized. New compounds, with the formulas C9H14Cl6 and C9H13Cl7, were found in sediment and biological samples for the first time. The method was shown to be a powerful tool for the analysis of CPs in environmental samples.

  18. Methane Fluxes from Subtropical Wetlands

    Science.gov (United States)

    DeLucia, N.; Gomez-Casanovas, N.; Bernacchi, C.

    2013-12-01

    It is well documented that green house gas concentrations have risen at unequivocal rates since the industrial revolution but the disparity between anthropogenic sources and natural sources is uncertain. Wetlands are one example of a natural ecosystem that can be a substantial source or sink for methane (CH4) depending on climate conditions. Due to strict anaerobic conditions required for CH4-generating microorganisms, natural wetlands are one of the main sources for biogenic CH4. Although wetlands occupy less than 5% of total land surface area, they contribute approximately 20% of total CH4 emissions to the atmosphere. The processes regulating CH4 emissions are sensitive to land use and management practices of areas surrounding wetlands. Variation in adjacent vegetation or grazing intensity by livestock can, for example, alter CH4 fluxes from wetland soils by altering nutrient balance, carbon inputs and hydrology. Therefore, understanding how these changes will affect wetland source strength is essential to understand the impact of wetland management practices on the global climate system. In this study we quantify wetland methane fluxes from subtropical wetlands on a working cattle ranch in central Florida near Okeechobee Lake (27o10'52.04'N, 81o21'8.56'W). To determine differences in CH4 fluxes associated with land use and management, a replicated (n = 4) full factorial experiment was designed for wetlands where the surrounding vegetation was (1) grazed or un-grazed and (2) composed of native vegetation or improved pasture. Net exchange of CH4 and CO2 between the land surface and the atmosphere were sampled with a LICOR Li-7700 open path CH4 analyzer and Li-7500A open path CO2/H20 analyzer mounted in a 1-m3 static gas-exchange chamber. Our results showed and verified that CH4 emissions from subtropical wetlands were larger when high soil moisture was coupled with high temperatures. The presence of cattle only amplified these results. These results help quantify

  19. Integrated passive flux measurement in groundwater: design and performance of iFLUX samplers

    Science.gov (United States)

    Verreydt, Goedele; Razaei, Meisam; Meire, Patrick; Van Keer, Ilse; Bronders, Jan; Seuntjens, Piet

    2017-04-01

    monitor speed and direction of flow and 3 cartridges to monitor different sources of pollution - VOC's, heavy metals and nutrients. The modular design enables to sample several types of pollution at the same time. The principles and the design of the iFLUX technology will be presented, together with the results from performance and sensitivity analysis for different field scenarios and several field cases.

  20. Atmospheric lepton fluxes

    Directory of Open Access Journals (Sweden)

    Gaisser Thomas K.

    2015-01-01

    Full Text Available This review of atmospheric muons and neutrinos emphasizes the high energy range relevant for backgrounds to high-energy neutrinos of astrophysical origin. After a brief historical introduction, the main distinguishing features of atmospheric νμ and νe are discussed, along with the implications of the muon charge ratio for the νµ / ν̅µ ratio. Methods to account for effects of the knee in the primary cosmic-ray spectrum and the energy-dependence of hadronic interactions on the neutrino fluxes are discussed and illustrated in the context of recent results from IceCube. A simple numerical/analytic method is proposed for systematic investigation of uncertainties in neutrino fluxes arising from uncertainties in the primary cosmic-ray spectrum/composition and hadronic interactions.

  1. Culture conditions and sample preparation methods affect spectrum quality and reproducibility during profiling of Staphylococcus aureus with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

    Science.gov (United States)

    Goldstein, J E; Zhang, L; Borror, C M; Rago, J V; Sandrin, T R

    2013-08-01

    Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has emerged as a promising tool to rapidly characterize Staphylococcus aureus. Different protocols have been employed, but effects of experimental factors, such as culture condition and sample preparation, on spectrum quality and reproducibility have not been rigorously examined. We applied MALDI-TOF MS to characterize a model system consisting of five methicillin-sensitive (MSSA) and five methicillin-resistant S. aureus isolates (MRSA) under two culture conditions (agar and broth) and using two sample preparation methods [intact cell method and protein extraction method (PEM)]. The effects of these treatments on spectrum quality and reproducibility were quantified. PEM facilitated increases in the number of peaks and mass range width. Broth cultures further improved spectrum quality in terms of increasing the number of peaks. In addition, PEM increased reproducibility in samples prepared using identical culture conditions. MALDI imaging data suggested that the improvement in reproducibility may result from a more homogeneous distribution of sample associated with the broth/PEM treatment. Broth/PEM treatment also yielded the highest rate (96%) of correct classification for MRSA. Taken together, these results suggest that broth/PEM maximizes the performance of MALDI-TOF MS to characterize S. aureus. Two culture conditions (agar or broth) and two sample preparation methods (intact cell or protein extraction) were evaluated for their effects on profiling of Staphylococcus aureus using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Results indicated that MALDI-enabled profiling of S. aureus is most effective when cultures are grown in broth and processed using a protein extraction-based approach. These findings should enhance future efforts to maximize the performance of this approach to characterize strains of S. aureus. © 2013

  2. Profiling of adrenocorticotropic hormone and arginine vasopressin in human pituitary gland and tumor thin tissue sections using droplet-based liquid-microjunction surface-sampling-HPLC-ESI-MS-MS.

    Science.gov (United States)

    Kertesz, Vilmos; Calligaris, David; Feldman, Daniel R; Changelian, Armen; Laws, Edward R; Santagata, Sandro; Agar, Nathalie Y R; Van Berkel, Gary J

    2015-08-01

    Described here are the results from the profiling of the proteins arginine vasopressin (AVP) and adrenocorticotropic hormone (ACTH) from normal human pituitary gland and pituitary adenoma tissue sections, using a fully automated droplet-based liquid-microjunction surface-sampling-HPLC-ESI-MS-MS system for spatially resolved sampling, HPLC separation, and mass spectrometric detection. Excellent correlation was found between the protein distribution data obtained with this method and data obtained with matrix-assisted laser desorption/ionization (MALDI) chemical imaging analyses of serial sections of the same tissue. The protein distributions correlated with the visible anatomic pattern of the pituitary gland. AVP was most abundant in the posterior pituitary gland region (neurohypophysis), and ATCH was dominant in the anterior pituitary gland region (adenohypophysis). The relative amounts of AVP and ACTH sampled from a series of ACTH-secreting and non-secreting pituitary adenomas correlated with histopathological evaluation. ACTH was readily detected at significantly higher levels in regions of ACTH-secreting adenomas and in normal anterior adenohypophysis compared with non-secreting adenoma and neurohypophysis. AVP was mostly detected in normal neurohypophysis, as expected. This work reveals that a fully automated droplet-based liquid-microjunction surface-sampling system coupled to HPLC-ESI-MS-MS can be readily used for spatially resolved sampling, separation, detection, and semi-quantitation of physiologically-relevant peptide and protein hormones, including AVP and ACTH, directly from human tissue. In addition, the relative simplicity, rapidity, and specificity of this method support the potential of this basic technology, with further advancement, for assisting surgical decision-making. Graphical Abstract Mass spectrometry based profiling of hormones in human pituitary gland and tumor thin tissue sections.

  3. Effects of linseed and quercetin added to the diet of fattening lambs on the fatty acid profile and lipid antioxidant status of meat samples.

    Science.gov (United States)

    Andrés, S; Morán, L; Aldai, N; Tejido, M L; Prieto, N; Bodas, R; Giráldez, F J

    2014-06-01

    Thirty-two Merino lambs fed barley straw and a concentrate formulated either with palm oil (CTRL group) or with linseed (+LS group), both alone or supplemented with quercetin (+QCT group or +LS+QCT group) were used to assess the effects of these dietary supplements on meat quality attributes. After being slaughtered, the longissimus thoracis muscles were used to study the fatty acid (FA) profile in detail, whilst longissimus lumborum slices were stored under refrigerated conditions to determine the lipid stability. Linseed increased the content of highly unsaturated n-3 long-chain fatty acid (20:5n-3; 22:5n-3; 22:6n-3). Interestingly, a significant increment of rumenic acid content (9c,11t-18:2) was observed when this seed was administered together with dietary quercetin. Moreover, the feeding of quercetin resulted in a reduction in the proportion of saturated FA and a decrease in lipid peroxidation of meat when the lambs were fed linseed. In conclusion, from both a nutritional and a commercial (shelf-life) point of view, it may be useful to include a source of quercetin when lambs are fed linseed diets. Copyright © 2014 Elsevier Ltd. All rights reserved.

  4. 16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice

    OpenAIRE

    Walker, Alan W.; Martin, Jennifer C.; Scott, Paul; Parkhill, Julian; Flint, Harry J.; Scott, Karen P.

    2015-01-01

    Background Characterisation of the bacterial composition of the gut microbiota is increasingly carried out with a view to establish the role of different bacterial species in causation or prevention of disease. It is thus essential that the methods used to determine the microbial composition are robust. Here, several widely used molecular techniques were compared to establish the optimal methods to assess the bacterial composition in faecal samples from babies, before weaning. Results The bac...

  5. Microextraction by Packed Sorbent (MEPS) and Solid-Phase Microextraction (SPME) as Sample Preparation Procedures for the Metabolomic Profiling of Urine

    OpenAIRE

    Catarina Silva; Carina Cavaco; Rosa Perestrelo; Jorge Pereira; José S. Câmara

    2014-01-01

    For a long time, sample preparation was unrecognized as a critical issue in the analytical methodology, thus limiting the performance that could be achieved. However, the improvement of microextraction techniques, particularly microextraction by packed sorbent (MEPS) and solid-phase microextraction (SPME), completely modified this scenario by introducing unprecedented control over this process. Urine is a biological fluid that is very interesting for metabolomics studies, allowing human healt...

  6. The detection and antimicrobial susceptibility profile of Shigella isolates from meat and swab samples at butchers' shops in Gondar town, Northwest Ethiopia.

    Science.gov (United States)

    Garedew, Legesse; Hagos, Zenabu; Zegeye, Bidir; Addis, Zelalem

    2016-01-01

    Food borne pathogens are major causes of deaths, illnesses and billions of dollars of expenses. The burden of food borne illness is worsened by the ever increasing rate of antimicrobial resistance microbes. Shigella, a bacterial pathogen associated with food, is reported to account for higher prevalence rates of food borne illness in different settings. A cross-sectional study was conducted from February 10 to June 30, 2013, at the butcher houses of Gondar town in the Northwest of Ethiopia to assess the prevalence and antimicrobial susceptibility pattern of Shigella. Cattle raw meat and swab samples from selected critical control points, including knives, chopping boards, and the hands and noses of butchers, were collected and analyzed. The identification of Shigella was carried out using colony characteristics, the Gram reaction, and biochemical tests. Antimicrobial susceptibility testing was performed using the Kirby-Bauer disc diffusion method. The overall hygienic status of the butcher shops was also assessed using a checklist. An observational analysis revealed that the sanitary condition of the butcher shops and their premises was poor. Of 306 samples screened, 10.5% were positive for Shigella. Approximately 7.4% of meat samples and 10.2% of swab samples were contaminated with Shigella. Out of the total Shigella isolates, 90.6%, 46.9%, 18.8% and 9.4% were resistant to ampicillin, amoxicillin, ceftriaxone and tetracycline, respectively. A multidrug resistance pattern was recorded in 27.8% of the isolates. In conclusion, the safety of meat sold at Gondar butchers houses was poor. The identified Shigella isolates showed high levels of drug resistance and multidrug resistance patterns for commonly used antimicrobials in veterinary and human medicine. Practicing wise use of antimicrobials and strict sanitary interventions at different critical control points is strongly recommended, in addition to further in-depth studies to prevent unprecedented consequences from

  7. High flux diffractometers on reactor neutron sources

    Science.gov (United States)

    Hewat, Alan W.

    2006-11-01

    Continuous neutron sources such as reactors can deliver a very high time-averaged flux to the sample using a relatively wide band of wavelengths, while still retaining good resolution. For example, the D20 diffractometer at ILL Grenoble, the world's highest flux neutron powder machine, can collect complete patterns at 100 ms intervals, and this has been important for the real time study of explosive SHS reactions. New very large 2D detectors, such as those recently installed on D2B and D19 at ILL, are up to an order of magnitude larger than previous designs, and will provide unmatched speed of data collection from very small samples, opening up new scientific perspectives for powder and single crystal diffraction. We will discuss future reactor based diffractometers designed for rapid data collection from small samples in special environments.

  8. Characterization of the photosynthetic conditions and pigment profiles of the colour strains of Hypnea musciformis from field-collected and in vitro cultured samples

    Directory of Open Access Journals (Sweden)

    Daniela R. P. Fernandes

    2012-05-01

    Full Text Available Hypnea musciformis (Wulfen JV Lamour. is a species of great economic interest as it produces Κ-carrageenan and has shown biological activities against HIV and HSV viruses. This species displays different colour strains in its natural habitat, which may have implications for the biotechnological potential of the species. The aim of this study was to characterize the photosynthetic apparatus and pigment profile of three colour strains of H. musciformis (green, brown and red in their natural habitat and in culture. Chlorophyll a fluorescence of photosystem II was measured with a pulse-amplitude modulated fluorometer and pigments were quantified by spectrofluorimetry (chlorophyll a and spectrophotometry (phycobiliproteins. In the natural habitat, we detected significant differences between the colour strains for the following photochemical parameters: the green strain had a higher effective quantum yield (ΦPSII than the red strain and a higher maximum relative electron transport rate (rETRmax than the brown and red strains. Saturation irradiances were 1000 µE.m-2.s-1 (green and 500 µE.m-2.s-1 (brown and red. Concerning in vitro culture, the green strain presented the lowest ΦPSII, rETRmax, and α rETR, while the brown strain presented the highest values for these same parameters. The chlorophyll a content of the cultured green strain was the lowest. The phycoerythrin contents of the three colour strains were unchanged by either natural of in vitro conditions: lower in green, intermediate in brown and higher in the red strain, ensuring the chromatic identity of the strains. Our results suggest that the green strain has a better performance when exposed to high irradiance, but a lower efficiency under low irradiance compared to the brown and red strains.

  9. Characterization of the photosynthetic conditions and pigment profiles of the colour strains of Hypnea musciformis from field-collected and in vitro cultured samples

    Directory of Open Access Journals (Sweden)

    Daniela R. P. Fernandes

    2012-08-01

    Full Text Available Hypnea musciformis (Wulfen JV Lamour. is a species of great economic interest as it produces Κ-carrageenan and has shown biological activities against HIV and HSV viruses. This species displays different colour strains in its natural habitat, which may have implications for the biotechnological potential of the species. The aim of this study was to characterize the photosynthetic apparatus and pigment profile of three colour strains of H. musciformis (green, brown and red in their natural habitat and in culture. Chlorophyll a fluorescence of photosystem II was measured with a pulse-amplitude modulated fluorometer and pigments were quantified by spectrofluorimetry (chlorophyll a and spectrophotometry (phycobiliproteins. In the natural habitat, we detected significant differences between the colour strains for the following photochemical parameters: the green strain had a higher effective quantum yield (ΦPSII than the red strain and a higher maximum relative electron transport rate (rETRmax than the brown and red strains. Saturation irradiances were 1000 µE.m-2.s-1 (green and 500 µE.m-2.s-1 (brown and red. Concerning in vitro culture, the green strain presented the lowest ΦPSII, rETRmax, and α rETR, while the brown strain presented the highest values for these same parameters. The chlorophyll a content of the cultured green strain was the lowest. The phycoerythrin contents of the three colour strains were unchanged by either natural of in vitro conditions: lower in green, intermediate in brown and higher in the red strain, ensuring the chromatic identity of the strains. Our results suggest that the green strain has a better performance when exposed to high irradiance, but a lower efficiency under low irradiance compared to the brown and red strains.

  10. Development of a laser remote sensing instrument to measure sub-aerial volcanic CO2 fluxes

    Science.gov (United States)

    Queisser, Manuel; Burton, Mike

    2016-04-01

    A thorough quantification of volcanic CO2 fluxes would lead to an enhanced understanding of the role of volcanoes in the geological carbon cycle. This would enable a more subtle understanding of human impact on that cycle. Furthermore, variations in volcanic CO2 emissions are a key to understanding volcanic processes such as eruption phenomenology. However, measuring fluxes of volcanic CO2 is challenging as volcanic CO2 concentrations are modest compared with the ambient CO2 concentration (~400 ppm) . Volcanic CO2 quickly dilutes with the background air. For Mt. Etna (Italy), for instance, 1000 m downwind from the crater, dispersion modelling yields a signal of ~4 ppm only. It is for this reason that many magmatic CO2 concentration measurements focus on in situ techniques, such as direct sampling Giggenbach bottles, chemical sensors, IR absorption spectrometers or mass spectrometers. However, emission rates are highly variable in time and space. Point measurements fail to account for this variability. Inferring 1-D or 2-D gas concentration profiles, necessary to estimate gas fluxes, from point measurements may thus lead to erroneous flux estimations. Moreover, in situ probing is time consuming and, since many volcanoes emit toxic gases and are dangerous as mountains, may raise safety concerns. In addition, degassing is often diffuse and spatially extended, which makes a measurement approach with spatial coverage desirable. There are techniques that allow to indirectly retrieve CO2 fluxes from correlated SO2 concentrations and fluxes. However, they still rely on point measurements of CO2 and are prone to errors of SO2 fluxes due to light dilution and depend on blue sky conditions. Here, we present a new remote sensing instrument, developed with the ERC project CO2Volc, which measures 1-D column amounts of CO2 in the atmosphere with sufficient sensitivity to reveal the contribution of magmatic CO2. Based on differential absorption LIDAR (DIAL) the instrument measures

  11. Soil fertilization leads to a decline in between-samples variability of microbial community δ13C profiles in a grassland fertilization experiment.

    Directory of Open Access Journals (Sweden)

    Stavros D Veresoglou

    Full Text Available Gas chromatography combustion isotope ratio mass spectrometry (GC-C-IRMS was used to measure the (13C/(12C ratios of PLFAs at natural abundance levels from a temperate grassland nitrogen (N and phosphorus (P factorial fertilization experiment in northern Greece. In each plot two rhizosphere samples were derived centred around individual Agrostis capillaris and Prunella vulgaris plants. It was hypothesized that the isotopic signal of microbes that preferentially feed on recalcitrant litter such as fungi would be modified by fertilization more strongly than that of opportunistic microbes using labile C. Microbial community δ(13C was affected by both P and N fertilization regime and plant species identity. However, we have been unable to detect significant nutrient effects on individual groups of microbes when analyzed separately in contrast to our original hypothesis. Intra-treatment variability, as evaluated from Hartley's F(max tests in the five first PCA components axes as well as the size of the convex hulls in PCA scoreplots and Mahalanobis distances, was considerably higher in the non-fertilized controls. Moreover, a significant relationship was established between the change in PLFA abundances and their respective changes in δ(13C for the aggregate of samples and those simultaneously fertilized with N and P. We conclude that use of compound specific isotope analysis in the absence of labelling represents a valuable and overlooked tool in obtaining an insight of microbial community functioning.

  12. Phenolic Acid Profiling, Antioxidant, and Anti-Inflammatory Activities, and miRNA Regulation in the Polyphenols of 16 Blueberry Samples from China.

    Science.gov (United States)

    Su, Xianming; Zhang, Jian; Wang, Hongqing; Xu, Jing; He, Jiuming; Liu, Liying; Zhang, Ting; Chen, Ruoyun; Kang, Jie

    2017-02-18

    To investigate the anti-atherosclerosis related mechanism of blueberries, the phenolic acids (PAs) content, antioxidant and anti-inflammatory activities, as well as the microRNA (miRNA) regulation of polyphenol fractions in blueberry samples from China were studied. Sixteen batches of blueberries including 14 commercialized cultivars (Reka, Patriot, Brigitta, Bluecrop, Berkeley, Duke, Darrow, Northland, Northblue, Northcountry, Bluesource, Southgood, O'Neal, and Misty) were used in this study. Seven PAs in the polyphenol fractions from 16 blueberry samples in China were quantified by high performance liquid chromatography/tandem mass spectrometry (HPLC/MS²). The antioxidant activities of blueberry polyphenols were tested by (1,1-diphenyl-2-picrylhydrazyl [DPPH]) assay. The anti-inflammatory (tumor necrosis factor-α [TNF-α] and interleukin-6 [IL-6]) activities of the polyphenol fractions of the blueberries were investigated by using lipopolysaccharide (LPS) induced RAW 264.7 macrophages. The correlation analysis showed that the antioxidant (1,1-diphenyl-2-picrylhydrazyl [DPPH]) and anti-inflammatory (tumor necrosis factor-α [TNF-α] and interleukin-6 [IL-6]) activities of the polyphenol fractions of the blueberries were in accordance with their PA contents. Although the polyphenol-enriched fractions of blueberries could inhibit the microRNAs (miRNAs) (miR-21, miR-146a, and miR-125b) to different extents, no significant contribution from the PAs was observed. The inhibition of these miRNAs could mostly be attributed to the other compounds present in the polyphenol-enriched fraction of the blueberries. This is the first study to evaluate the PAs content, antioxidant and anti-inflammatory activities, and miRNA regulation of Chinese blueberries.

  13. Phenolic Acid Profiling, Antioxidant, and Anti-Inflammatory Activities, and miRNA Regulation in the Polyphenols of 16 Blueberry Samples from China

    Directory of Open Access Journals (Sweden)

    Xianming Su

    2017-02-01

    Full Text Available To investigate the anti-atherosclerosis related mechanism of blueberries, the phenolic acids (PAs content, antioxidant and anti-inflammatory activities, as well as the microRNA (miRNA regulation of polyphenol fractions in blueberry samples from China were studied. Sixteen batches of blueberries including 14 commercialized cultivars (Reka, Patriot, Brigitta, Bluecrop, Berkeley, Duke, Darrow, Northland, Northblue, Northcountry, Bluesource, Southgood, O’Neal, and Misty were used in this study. Seven PAs in the polyphenol fractions from 16 blueberry samples in China were quantified by high performance liquid chromatography/tandem mass spectrometry (HPLC/MS2. The antioxidant activities of blueberry polyphenols were tested by (1,1-diphenyl-2-picrylhydrazyl [DPPH] assay. The anti-inflammatory (tumor necrosis factor-α [TNF-α] and interleukin-6 [IL-6] activities of the polyphenol fractions of the blueberries were investigated by using lipopolysaccharide (LPS induced RAW 264.7 macrophages. The correlation analysis showed that the antioxidant (1,1-diphenyl-2-picrylhydrazyl [DPPH] and anti-inflammatory (tumor necrosis factor-α [TNF-α] and interleukin-6 [IL-6] activities of the polyphenol fractions of the blueberries were in accordance with their PA contents. Although the polyphenol-enriched fractions of blueberries could inhibit the microRNAs (miRNAs (miR-21, miR-146a, and miR-125b to different extents, no significant contribution from the PAs was observed. The inhibition of these miRNAs could mostly be attributed to the other compounds present in the polyphenol-enriched fraction of the blueberries. This is the first study to evaluate the PAs content, antioxidant and anti-inflammatory activities, and miRNA regulation of Chinese blueberries.

  14. The Study of Cardiovascular Risk in Adolescents--ERICA: rationale, design and sample characteristics of a national survey examining cardiovascular risk factor profile in Brazilian adolescents.

    Science.gov (United States)

    Bloch, Katia Vergetti; Szklo, Moyses; Kuschnir, Maria Cristina C; Abreu, Gabriela de Azevedo; Barufaldi, Laura Augusta; Klein, Carlos Henrique; de Vasconcelos, Maurício T L; da Veiga, Glória Valéria; Figueiredo, Valeska C; Dias, Adriano; Moraes, Ana Julia Pantoja; Souza, Ana Luiza Lima; de Oliveira, Ana Mayra Andrade; Schaan, Beatriz D'Argord; Tavares, Bruno Mendes; de Oliveira, Cecília Lacroix; Cunha, Cristiane de Freitas; Giannini, Denise Tavares; Belfort, Dilson Rodrigues; Ribas, Dulce Lopes Barboza; Santos, Eduardo Lima; de Leon, Elisa Brosina; Fujimori, Elizabeth; Oliveira, Elizabete Regina Araújo; Magliano, Erika da Silva; Vasconcelos, Francisco de Assis Guedes; Azevedo, George Dantas; Brunken, Gisela Soares; Dias, Glauber Monteiro; Filho, Heleno R Correa; Monteiro, Maria Inês; Guimarães, Isabel Cristina Britto; Faria Neto, José Rocha; Oliveira, Juliana Souza; de Carvalho, Kenia Mara B; Gonçalves, Luis Gonzaga de Oliveira; Santos, Marize M; Muniz, Pascoal Torres; Jardim, Paulo César B Veiga; Ferreira, Pedro Antônio Muniz; Montenegro, Renan Magalhães; Gurgel, Ricardo Queiroz; Vianna, Rodrigo Pinheiro; Vasconcelos, Sandra Mary; da Matta, Sandro Silva; Martins, Stella Maris Seixas; Goldberg, Tamara Beres Lederer; da Silva, Thiago Luiz Nogueira

    2015-02-07

    The Study of Cardiovascular Risk in Adolescents (Portuguese acronym, "ERICA") is a multicenter, school-based country-wide cross-sectional study funded by the Brazilian Ministry of Health, which aims at estimating the prevalence of cardiovascular risk factors, including those included in the definition of the metabolic syndrome, in a random sample of adolescents aged 12 to 17 years in Brazilian cities with more than 100,000 inhabitants. Approximately 85,000 students were assessed in public and private schools. Brazil is a continental country with a heterogeneous population of 190 million living in its five main geographic regions (North, Northeast, Midwest, South and Southeast). ERICA is a pioneering study that will assess the prevalence rates of cardiovascular risk factors in Brazilian adolescents using a sample with national and regional representativeness. This paper describes the rationale, design and procedures of ERICA. Participants answered a self-administered questionnaire using an electronic device, in order to obtain information on demographic and lifestyle characteristics, including physical activity, smoking, alcohol intake, sleeping hours, common mental disorders and reproductive and oral health. Dietary intake was assessed using a 24-hour dietary recall. Anthropometric measures (weight, height and waist circumference) and blood pressure were also be measured. Blood was collected from a subsample of approximately 44,000 adolescents for measurements of fasting glucose, total cholesterol, HDL-cholesterol, LDL-cholesterol, triglycerides, glycated hemoglobin and fasting insulin. The study findings will be instrumental to the development of public policies aiming at the prevention of obesity, atherosclerotic diseases and diabetes in an adolescent population.

  15. Reactor flux calculations

    Energy Technology Data Exchange (ETDEWEB)

    Lhuillier, D. [Commissariat à l' Énergie Atomique et aux Énergies Alternatives, Centre de Saclay, IRFU/SPhN, 91191 Gif-sur-Yvette (France)

    2013-02-15

    The status of the prediction of reactor anti-neutrino spectra is presented. The most accurate method is still the conversion of total β spectra of fissionning isotopes as measured at research reactors. Recent re-evaluations of the conversion process led to an increased predicted flux by few percent and were at the origin of the so-called reactor anomaly. The up to date predictions are presented with their main sources of error. Perspectives are given on the complementary ab-initio predictions and upcoming experimental cross-checks of the predicted spectrum shape.

  16. A profile of acute care in an aging America: snowball sample identification and characterization of United States geriatric emergency departments in 2013.

    Science.gov (United States)

    Hogan, Teresita M; Olade, Tolulope Oyeyemi; Carpenter, Christopher R

    2014-03-01

    The aging of America poses a challenge to emergency departments (EDs). Studies show that elderly patients have poor outcomes despite increased testing, prolonged periods of observation, and higher admission rates. In response, emergency medicine (EM) leaders have implemented strategies for improved ED elder care, enhancing expertise, equipment, policies, and protocols. One example is the development of geriatric EDs gaining in popularity nationwide. To the authors' knowledge, this is the first research to systematically identify and qualitatively characterize the existence, locations, and features of geriatric EDs across the United States. The primary objective was to determine the number, distribution, and characteristics of geriatric EDs in the United States in 2013. This was a survey with potential respondents identified via a snowball sampling of known geriatric EDs, EM professional organizations' geriatric interest groups, and a structured search of the Internet using multiple search engines. Sites were contacted by telephone, and those confirming geriatric EDs presence received the survey via e-mail. Category questions included date of opening, location, volumes, staffing, physical plant changes, screening tools, policies, and protocols. Categories were reported based on general interest to those seeking to understand components of a geriatric ED. Thirty-six hospitals confirmed geriatric ED existence and received surveys. Thirty (83%) responded to the survey and confirmed presence or plans for geriatric EDs: 24 (80%) had existing geriatric EDs, and six (20%) were planning to open geriatric EDs by 2014. The majority of geriatric EDs are located in the Midwest (46%) and Northeast (30%) regions of the United States. Eighty percent serve from 5,000 to 20,000 elder patients annually. Seventy percent of geriatric EDs are attached to the main ED, and 66% have from one to 10 geriatric beds. Physical plant changes include modifications to beds (96%), lighting (90

  17. Psychological and behavioral risk profiles as they relate to eating disorder diagnoses and symptomatology among a school-based sample of youth.

    Science.gov (United States)

    Ackard, Diann M; Fulkerson, Jayne A; Neumark-Sztainer, Dianne

    2011-07-01

    Examine substance use, depression, self-esteem, and suicidality by eating disorder (ED) classifications among nonclinical youth. A school-based sample of 4,746 youth completed anthropometric measures and Project EAT survey items matched to DSM-IV ED criteria. Logistic regression analyses and general linear models compared three threshold (AN, BN, or BED), two subthreshold (binge-eating and/or compensatory behaviors not meeting ED diagnosis, or body image disturbance without disordered eating) and one asymptomatic ED classifications. Subthreshold and threshold classifications reported lower self-esteem and greater substance use, depression, suicidal ideation/attempts than asymptomatic youth. The BED group had higher depressive mood, and BED and BN had lower self-esteem, than the subthreshold groups. Odds ratios for suicidality were highest among the BN group and lowest among the body image disturbance group. Subthreshold and threshold classifications are associated with compromised health, suggesting the importance of addressing the continuum of weight/shape concerns and disordered eating behaviors within prevention and treatment interventions. Copyright © 2010 Wiley Periodicals, Inc.

  18. Verifying agricultural emissions of methane. Air sampling from aircraft and mesoscale modelling.

    Energy Technology Data Exchange (ETDEWEB)

    Lassey, K.R.; Gimson, N.R.; Wratt, D.S.; Brailsford, G.W.; Bromley, A.M. [National Institute of Water and Atmospheric Research NIWA, Wellington (New Zealand)

    2000-07-01

    The most direct way to establish the level of surface emissions of greenhouse gases is to measure and interpret concentration gradients in the atmosphere. We have tested the efficacy of this approach for inferring average methane fluxes from regions of pastoral agriculture a few tens of km in extent. In its simplest form, vertical concentration profiles are measured upwind and downwind of the target region, based on air samples collected from light aircraft. Using simple mass balance models, the profile contrasts can be related to the mean surface flux over the intervening region. The inferred flux can then be compared with 'bottom-up' estimates based on livestock density and per-animal emissions. However, such simple models may poorly simulate air flows over the New Zealand terrain, and as an alternative, we deploy a state-of-the-art mesoscale meteorological model, RAMS, coupled to an atmospheric dispersion model. RAMS is used prognostically to guide the timing and siting of measurement campaigns, and diagnostically to simulate regional wind fields which are validated against local meteorological data. Source-oriented and receptor-oriented dispersion modelling techniques, in combination with aircraft-based sampling and laboratory gas analysis, provide 'top-down' methane flux estimates that compare favourably with 'bottom-up' estimates. These techniques thus enhance confidence in national emission inventories based on bottom-up estimation. However, the challenge for similar verification of nitrous oxide emission is more imposing. 5 refs.

  19. Profile of subjective quality of life and its correlates in a nation-wide sample of high school students in an Arab setting using the WHOQOL-Bref

    Directory of Open Access Journals (Sweden)

    Ohaeri Jude U

    2011-04-01

    Full Text Available Abstract Background The upsurge of interest in the quality of life (QOL of children is in line with the 1989 Convention on the Rights of the Child, which stressed the child's right to adequate circumstances for physical, mental, and social development. The study's objectives were to: (i highlight how satisfied Kuwaiti high school students were with life circumstances as in the WHOQOL-Bref; (ii assess the prevalence of at risk status for impaired QOL and establish the QOL domain normative values; and (iii examine the relationship of QOL with personal, parental, and socio-environmental factors. Method A nation-wide sample of students in senior classes in government high schools (N = 4467, 48.6% boys; aged 14-23 years completed questionnaires that included the WHOQOL-Bref. Results Using Cummins' norm of 70% - 80%, we found that, as a group, they barely achieved the well-being threshold score for physical health (70%, social relations (72.8%, environment (70.8% and general facet (70.2%, but not for psychological health (61.9%. These scores were lower than those reported from other countries. Using the recommended cut-off of SD of population mean, the prevalence of at risk status for impaired QOL was 12.9% - 18.8% (population age-adjusted: 15.9% - 21.1%. In all domains, boys had significantly higher QOL than girls, mediated by anxiety/depression; while the younger ones had significantly higher QOL (p Conclusion Poorer QOL seemed to reflect a circumstance of social disadvantage and poor psychosocial well-being in which girls fared worse than boys. The findings indicate that programs that address parental harmony and school programs that promote study-friendly atmospheres could help to improve psychosocial well-being. The application of QOL as a school population health measure may facilitate risk assessment and the tracking of health status.

  20. Profile of subjective quality of life and its correlates in a nation-wide sample of high school students in an Arab setting using the WHOQOL-Bref.

    Science.gov (United States)

    Al-Fayez, Ghenaim A; Ohaeri, Jude U

    2011-04-25

    The upsurge of interest in the quality of life (QOL) of children is in line with the 1989 Convention on the Rights of the Child, which stressed the child's right to adequate circumstances for physical, mental, and social development. The study's objectives were to: (i) highlight how satisfied Kuwaiti high school students were with life circumstances as in the WHOQOL-Bref; (ii) assess the prevalence of at risk status for impaired QOL and establish the QOL domain normative values; and (iii) examine the relationship of QOL with personal, parental, and socio-environmental factors. A nation-wide sample of students in senior classes in government high schools (N = 4467, 48.6% boys; aged 14-23 years) completed questionnaires that included the WHOQOL-Bref. Using Cummins' norm of 70% - 80%, we found that, as a group, they barely achieved the well-being threshold score for physical health (70%), social relations (72.8%), environment (70.8%) and general facet (70.2%), but not for psychological health (61.9%). These scores were lower than those reported from other countries. Using the recommended cut-off of divorce and father's low socio-economic status, the most important predictors of poorer QOL were perception of poor emotional relationship between the parents, poor self-esteem and difficulty with studies. Poorer QOL seemed to reflect a circumstance of social disadvantage and poor psychosocial well-being in which girls fared worse than boys. The findings indicate that programs that address parental harmony and school programs that promote study-friendly atmospheres could help to improve psychosocial well-being. The application of QOL as a school population health measure may facilitate risk assessment and the tracking of health status.

  1. Gene set enrichment analysis highlights different gene expression profiles in whole blood samples X-irradiated with low and high doses.

    Science.gov (United States)

    El-Saghire, Houssein; Thierens, Hubert; Monsieurs, Pieter; Michaux, Arlette; Vandevoorde, Charlot; Baatout, Sarah

    2013-08-01

    Health risks from exposure to low doses of ionizing radiation (IR) are becoming a concern due to the rapidly growing medical applications of X-rays. Using microarray techniques, this study aims for a better understanding of whole blood response to low and high doses of IR. Aliquots of peripheral blood samples were irradiated with 0, 0.05, and 1 Gy X-rays. RNA was isolated and prepared for microarray gene expression experiments. Bioinformatic approaches, i.e., univariate statistics and Gene Set Enrichment Analysis (GSEA) were used for analyzing the data generated. Seven differentially expressed genes were selected for further confirmation using quantitative real-time PCR (RT-PCR). Functional analysis of genes differentially expressed at 0.05 Gy showed the enrichment of chemokine and cytokine signaling. However, responsive genes to 1 Gy were mainly involved in tumor suppressor protein 53 (p53) pathways. In a second approach, GSEA showed a higher statistical ranking of inflammatory and immune-related gene sets that are involved in both responding and/or secretion of growth factors, chemokines, and cytokines. This indicates the activation of the immune response. Whereas, gene sets enriched at 1 Gy were 'classical' radiation pathways like p53 signaling, apoptosis, DNA damage and repair. Comparative RT-PCR studies showed the significant induction of chemokine-related genes (PF4, GNG11 and CCR4) at 0.05 Gy and DNA damage and repair genes at 1 Gy (DDB2, AEN and CDKN1A). This study moves a step forward in understanding the different cellular responses to low and high doses of X-rays. In addition to that, and in a broader context, it addresses the need for more attention to the risk assessment of health effects resulting from the exposure to low doses of IR.

  2. Dissolved inorganic carbon, pH, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using Alkalinity titrator, CTD and other instruments from the PELAGIA in the English Channel, North Atlantic Ocean and others from 2001-08-18 to 2002-05-25 (NODC Accession 0112844)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0112844 includes chemical, discrete sample, physical and profile data collected from PELAGIA in the English Channel, North Atlantic Ocean, North Sea,...

  3. Dissolved inorganic carbon, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using Alkalinity titrator, CTD and other instruments from the PELAGIA in the English Channel, North Atlantic Ocean and others from 2001-08-18 to 2002-05-25 (NODC Accession 0112843)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0112843 includes chemical, discrete sample, physical and profile data collected from PELAGIA in the English Channel, North Atlantic Ocean, North Sea,...

  4. Dissolved inorganic carbon, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the MARION DUFRESNE in the Indian Ocean and South Atlantic Ocean from 1985-02-27 to 1987-12-26 (NODC Accession 0117497)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0117497 includes chemical, discrete sample, physical and profile data collected from MARION DUFRESNE in the Indian Ocean and South Atlantic Ocean from...

  5. Dissolved inorganic carbon, pH, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using Alkalinity titrator, CTD and other instruments from POLARSTERN in the South Atlantic Ocean and Southern Oceans from 2014-12-02 to 2015-02-01 (NCEI Accession 0157620)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NCEI Accession 0157620 includes biological, chemical, discrete sample, optical, physical and profile data collected from POLARSTERN in the South Atlantic Ocean and...

  6. Dissolved inorganic carbon, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, PAR Sensor and other instruments from Investigator in the Indian Ocean from 2015-03-21 to 2015-03-30 (NCEI Accession 0157618)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NCEI Accession 0157618 includes biological, chemical, discrete sample, optical, physical and profile data collected from Investigator in the Indian Ocean from...

  7. pH, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the HESPERIDES in the South Atlantic Ocean from 1996-01-17 to 1996-02-05 (NODC Accession 0113755)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0113755 includes biological, chemical, discrete sample, physical and profile data collected from HESPERIDES in the South Atlantic Ocean from...

  8. pH, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the THALASSA in the North Atlantic Ocean from 2001-08-23 to 2001-09-13 (NODC Accession 0113600)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0113600 includes chemical, discrete sample, physical and profile data collected from THALASSA in the North Atlantic Ocean from 2001-08-23 to...

  9. Dissolved inorganic carbon, pH, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the HESPERIDES in the North Atlantic Ocean from 1992-06-14 to 1992-08-15 (NODC Accession 0115227)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0115227 includes chemical, discrete sample, physical and profile data collected from HESPERIDES in the North Atlantic Ocean from 1992-06-14 to...

  10. pH, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the L'ATALANTE in the North Atlantic Ocean from 2001-02-03 to 2001-02-24 (NODC Accession 0113520)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0113520 includes chemical, discrete sample, physical and profile data collected from L'ATALANTE in the North Atlantic Ocean from 2001-02-03 to...

  11. pH, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the L'ATALANTE in the North Atlantic Ocean from 2001-03-22 to 2001-04-13 (NODC Accession 0113521)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0113521 includes chemical, discrete sample, physical and profile data collected from L'ATALANTE in the North Atlantic Ocean from 2001-03-22 to...

  12. Dissolved inorganic carbon, pH, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using Alkalinity titrator, CTD and other instruments from the MARION DUFRESNE in the South Atlantic Ocean from 2008-02-07 to 2008-03-24 (NODC Accession 0112841)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0112841 includes chemical, discrete sample, physical and profile data collected from MARION DUFRESNE in the South Atlantic Ocean from 2008-02-07 to...

  13. pH, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the HESPERIDES in the South Atlantic Ocean from 1995-12-03 to 1996-01-05 (NODC Accession 0113549)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0113549 includes biological, chemical, discrete sample, physical and profile data collected from HESPERIDES in the South Atlantic Ocean from...

  14. Dissolved inorganic carbon, pH, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the RYOFU MARU in the North Pacific Ocean, Philippine Sea and South Pacific Ocean from 2010-07-06 to 2010-08-22 (NODC Accession 0109921)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0109921 includes biological, chemical, discrete sample, physical and profile data collected from RYOFU MARU in the North Pacific Ocean, Philippine Sea...

  15. Partial pressure (or fugacity) of carbon dioxide, dissolved inorganic carbon, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from ARNI FRIDRIKSSON and BJARNI SAEMUNDSSON in the North Greenland Sea from 1985-02-22 to 2013-11-26 (NCEI Accession 0157294)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NCEI Accession 0157294 includes chemical, discrete sample, physical and profile data collected from ARNI FRIDRIKSSON and BJARNI SAEMUNDSSON in the North Greenland...

  16. Partial pressure (or fugacity) of carbon dioxide, dissolved inorganic carbon, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from ARNI FRIDRIKSSON and BJARNI SAEMUNDSSON in the North Atlantic Ocean from 1983-03-05 to 2013-11-13 (NCEI Accession 0149098)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NCEI Accession 0149098 includes discrete sample and profile data collected from ARNI FRIDRIKSSON and BJARNI SAEMUNDSSON in the North Atlantic Ocean from 1983-03-05...

  17. Dissolved inorganic carbon, pH, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, Coulometer for DIC measurement and other instruments from the Ryofu Maru II in the North Pacific Ocean from 2004-06-08 to 2004-07-03 (NODC Accession 0112284)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0112284 includes biological, chemical, discrete sample, physical and profile data collected from Ryofu Maru II in the North Pacific Ocean from...

  18. Temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from AURORA AUSTRALIS in the Indian Ocean and Southern Oceans from 2003-01-03 to 2003-03-17 (NCEI Accession 0143930)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NCEI Accession 0143930 includes discrete sample and profile data collected from AURORA AUSTRALIS in the Indian Ocean and Southern Oceans (> 60 degrees South) from...

  19. Temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the Hakuho Maru in the North Pacific Ocean and South Pacific Ocean from 1991-09-17 to 1991-10-02 (NODC Accession 0115596)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0115596 includes chemical, discrete sample, physical and profile data collected from Hakuho Maru in the North Pacific Ocean and South Pacific Ocean...

  20. Partial pressure (or fugacity) of carbon dioxide, dissolved inorganic carbon, pH, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from NOAA Ship MALCOLM BALDRIGE in the Indian Ocean and Laccadive Sea from 1995-09-22 to 1995-10-25 (NODC Accession 0114478)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0114478 includes chemical, discrete sample, physical and profile data collected from NOAA Ship MALCOLM BALDRIGE in the Indian Ocean and Laccadive Sea...

  1. Partial pressure (or fugacity) of carbon dioxide, dissolved inorganic carbon, pH, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from NOAA Ship MALCOLM BALDRIGE in the North Atlantic Ocean and South Atlantic Ocean from 1991-07-11 to 1991-09-02 (NODC Accession 0115225)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0115225 includes chemical, discrete sample, physical and profile data collected from NOAA Ship MALCOLM BALDRIGE in the North Atlantic Ocean and South...

  2. Temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the METEOR in the North Atlantic Ocean and South Atlantic Ocean from 1981-03-28 to 1981-04-23 (NODC Accession 0116646)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0116646 includes chemical, discrete sample, physical and profile data collected from METEOR in the North Atlantic Ocean and South Atlantic Ocean from...

  3. Partial pressure (or fugacity) of carbon dioxide, dissolved inorganic carbon, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the JOHAN HJORT in the North Atlantic Ocean, North Greenland Sea and Norwegian Sea from 1994-07-23 to 1994-08-16 (NODC Accession 0113560)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0113560 includes chemical, discrete sample, physical and profile data collected from JOHAN HJORT in the North Atlantic Ocean, North Greenland Sea and...

  4. Species abundance profile and discrete sample data collected in the South Atlantic Ocean and South Pacific Ocean on the LAURENCE M. GOULD and NATHANIEL B. PALMER cruises LMG0104, LMG0203 and others as part of the Southern Ocean GLOBEC project from 2001-05-01 to 2002-09-11 (NODC Accession 0112189)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0112189 includes profile, discrete sample and biological data collected aboard the LAURENCE M. GOULD and NATHANIEL B. PALMER during cruises LMG0104,...

  5. Dissolved inorganic carbon, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the G.O. SARS in the Barents Sea, North Atlantic Ocean and others from 2009-05-28 to 2009-08-11 (NODC Accession 0114433)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0114433 includes biological, chemical, discrete sample, physical and profile data collected from G.O. SARS in the Barents Sea, North Atlantic Ocean,...

  6. Partial pressure (or fugacity) of carbon dioxide, dissolved inorganic carbon, pH, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using Alkalinity titrator, CTD and other instruments from NOAA Ship RONALD H. BROWN in the South Atlantic Ocean from 2011-09-26 to 2011-10-31 (NODC Accession 0109914)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NCEI Accession 0109914 includes discrete sample and profile data collected from NOAA Ship RONALD H. BROWN in the South Atlantic Ocean from 2011-09-26 to 2011-10-31....

  7. Dissolved inorganic carbon, pH, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, Coulometer for DIC measurement and other instruments from the HAKUREI MARU in the North Pacific Ocean and South Pacific Ocean from 1993-04-13 to 1993-06-11 (NODC Accession 0112228)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0112228 includes biological, chemical, discrete sample, physical and profile data collected from HAKUREI MARU in the North Pacific Ocean and South...

  8. Dissolved inorganic carbon, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using Alkalinity titrator, CTD and other instruments from the HUDSON in the Davis Strait, Gulf of St. Lawrence and others from 2006-05-24 to 2006-06-08 (NODC Accession 0108222)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0108222 includes chemical, discrete sample, physical and profile data collected from HUDSON in the Davis Strait, Gulf of St. Lawrence, Labrador Sea...

  9. Dissolved inorganic carbon, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, Coulometer for DIC measurement and other instruments from the WAKATAKA MARU in the North Pacific Ocean from 2006-03-01 to 2006-03-10 (NODC Accession 0112361)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0112361 includes chemical, discrete sample, physical and profile data collected from WAKATAKA MARU in the North Pacific Ocean from 2006-03-01 to...

  10. Dissolved inorganic carbon, pH, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, Coulometer for DIC measurement and other instruments from the HAKUREI MARU in the North Pacific Ocean from 2000-09-12 to 2000-11-21 (NODC Accession 0112345)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0112345 includes biological, chemical, discrete sample, physical and profile data collected from HAKUREI MARU in the North Pacific Ocean from...

  11. Dissolved inorganic carbon, pH, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, Coulometer for DIC measurement and other instruments from the ODEN in the Arctic Ocean, Beaufort Sea and Bering Sea from 2005-08-19 to 2005-09-25 (NODC Accession 0108129)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0108129 includes chemical, discrete sample, physical and profile data collected from ODEN in the Arctic Ocean, Beaufort Sea and Bering Sea from...

  12. Dissolved inorganic carbon, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, Coulometer for DIC measurement and other instruments from the MIRAI in the Arctic Ocean, Beaufort Sea and Bering Sea from 2000-08-03 to 2000-10-13 (NODC Accession 0112352)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0112352 includes chemical, discrete sample, physical and profile data collected from MIRAI in the Arctic Ocean, Beaufort Sea and Bering Sea from...

  13. Dissolved inorganic carbon, pH, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, Coulometer for DIC measurement and other instruments from the MIRAI in the North Pacific Ocean and South Pacific Ocean from 2002-12-17 to 2003-02-14 (NODC Accession 0113608)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0113608 includes chemical, discrete sample, physical and profile data collected from MIRAI in the North Pacific Ocean and South Pacific Ocean from...

  14. Dissolved inorganic carbon, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from DISCOVERY in the North Atlantic Ocean from 2011-07-15 to 2011-08-04 (NCEI Accession 0143389)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NCEI Accession 0143389 includes discrete sample and profile data collected from DISCOVERY in the North Atlantic Ocean from 2011-07-15 to 2011-08-04 and retrieved...

  15. Temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the L'ATALANTE in the North Atlantic Ocean and South Atlantic Ocean from 2008-02-23 to 2008-03-15 (NODC Accession 0117496)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0117496 includes chemical, discrete sample, physical and profile data collected from L'ATALANTE in the North Atlantic Ocean and South Atlantic Ocean...

  16. Dissolved inorganic carbon, pH, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, Coulometer for DIC measurement and other instruments from the Hokusei Maru in the North Pacific Ocean from 2001-06-04 to 2001-06-10 (NODC Accession 0112246)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0112246 includes chemical, discrete sample, physical and profile data collected from Hokusei Maru in the North Pacific Ocean from 2001-06-04 to...

  17. Dissolved inorganic carbon, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the STENA ARCTICA in the South Atlantic Ocean from 1989-02-14 to 1989-03-17 (NODC Accession 0113893)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0113893 includes chemical, discrete sample, physical and profile data collected from STENA ARCTICA in the South Atlantic Ocean from 1989-02-14 to...

  18. Dissolved inorganic carbon, pH, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, Coulometer for DIC measurement and other instruments from the Ryofu Maru II in the North Pacific Ocean and Philippine Sea from 2005-10-21 to 2005-11-08 (NODC Accession 0112289)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0112289 includes biological, chemical, discrete sample, physical and profile data collected from Ryofu Maru II in the North Pacific Ocean and...

  19. Dissolved inorganic carbon, pH, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, Coulometer for DIC measurement and other instruments from the HAKUREI MARU in the North Pacific Ocean and South Pacific Ocean from 1992-08-07 to 1992-10-05 (NODC Accession 0112227)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0112227 includes biological, chemical, discrete sample, physical and profile data collected from HAKUREI MARU in the North Pacific Ocean and South...

  20. Dissolved inorganic carbon, pH, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, Coulometer for DIC measurement and other instruments from the Hokusei Maru in the North Pacific Ocean from 1999-07-19 to 1999-08-19 (NODC Accession 0112242)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0112242 includes chemical, discrete sample, physical and profile data collected from Hokusei Maru in the North Pacific Ocean from 1999-07-19 to...

  1. Temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the POLARSTERN in the Arctic Ocean and North Greenland Sea from 1984-07-19 to 1984-08-07 (NODC Accession 0113894)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0113894 includes chemical, discrete sample, physical and profile data collected from POLARSTERN in the Arctic Ocean and North Greenland Sea from...

  2. Temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the USCGC POLAR STAR in the Arctic Ocean and Beaufort Sea from 2002-07-15 to 2002-08-13 (NODC Accession 0115609)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0115609 includes chemical, discrete sample, physical and profile data collected from USCGC POLAR STAR in the Arctic Ocean and Beaufort Sea from...

  3. Dissolved inorganic carbon, pH, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, Coulometer for DIC measurement and other instruments from the MIRAI in the Bering Sea and North Pacific Ocean from 2002-10-11 to 2002-11-06 (NODC Accession 0112258)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0112258 includes chemical, discrete sample, physical and profile data collected from MIRAI in the Bering Sea and North Pacific Ocean from 2002-10-11...

  4. Dissolved inorganic carbon, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, Coulometer for DIC measurement and other instruments from the TANKAI-MARU in the North Pacific Ocean from 2002-01-08 to 2002-01-22 (NODC Accession 0112319)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0112319 includes chemical, discrete sample, physical and profile data collected from TANKAI-MARU in the North Pacific Ocean from 2002-01-08 to...

  5. Dissolved inorganic carbon, pH, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, Coulometer for DIC measurement and other instruments from the HAKUREI MARU in the North Pacific Ocean from 1996-08-07 to 1996-10-03 (NODC Accession 0112232)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0112232 includes biological, chemical, discrete sample, physical and profile data collected from HAKUREI MARU in the North Pacific Ocean from...

  6. Dissolved inorganic carbon, pH, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, Coulometer for DIC measurement and other instruments from the Hokusei Maru in the North Pacific Ocean from 1998-07-18 to 1998-08-18 (NODC Accession 0112239)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0112239 includes chemical, discrete sample, physical and profile data collected from Hokusei Maru in the North Pacific Ocean from 1998-07-18 to...

  7. Partial pressure (or fugacity) of carbon dioxide, dissolved inorganic carbon, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the JOHAN HJORT in the North Atlantic Ocean, North Greenland Sea and Norwegian Sea from 1992-07-12 to 1992-07-28 (NODC Accession 0113558)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0113558 includes chemical, discrete sample, physical and profile data collected from JOHAN HJORT in the North Atlantic Ocean, North Greenland Sea and...

  8. Dissolved inorganic carbon, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the HEALY in the Arctic Ocean, Beaufort Sea and Bering Sea from 2004-07-18 to 2004-08-26 (NODC Accession 0115707)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0115707 includes biological, chemical, discrete sample, physical and profile data collected from HEALY in the Arctic Ocean, Beaufort Sea and Bering...

  9. Dissolved inorganic carbon, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, Coulometer for DIC measurement and other instruments from the TANKAI-MARU in the North Pacific Ocean from 1998-04-18 to 1998-04-20 (NODC Accession 0112316)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0112316 includes chemical, discrete sample, physical and profile data collected from TANKAI-MARU in the North Pacific Ocean from 1998-04-18 to...

  10. Temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the METEOR in the Caribbean Sea and North Atlantic Ocean from 2005-08-13 to 2005-09-19 (NODC Accession 0116566)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0116566 includes chemical, discrete sample, physical and profile data collected from METEOR in the Caribbean Sea and North Atlantic Ocean from...

  11. Temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the SONNE in the Caribbean Sea, North Atlantic Ocean and South Atlantic Ocean from 2003-05-25 to 2003-06-13 (NODC Accession 0116705)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0116705 includes chemical, discrete sample, physical and profile data collected from SONNE in the Caribbean Sea, North Atlantic Ocean and South...

  12. Dissolved inorganic carbon, alkalinity, temperature, salinity and SEA SURFACE TEMPERATURE collected from discrete sample and profile observations using CTD, bottle and other instruments from L'ASTROLABE in the Indian Ocean, South Pacific Ocean and others from 2002-10-16 to 2012-03-06 (NCEI Accession 0157351)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NCEI Accession 0157351 includes chemical, discrete sample, physical and profile data collected from L'ASTROLABE in the Indian Ocean, South Pacific Ocean, Southern...

  13. Dissolved inorganic carbon, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the HEALY in the Arctic Ocean, Beaufort Sea and Bering Sea from 2002-07-18 to 2002-08-21 (NODC Accession 0113953)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0113953 includes biological, chemical, discrete sample, physical and profile data collected from HEALY in the Arctic Ocean, Beaufort Sea and Bering...

  14. Dissolved inorganic carbon, pH, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the METEOR in the North Atlantic Ocean from 2001-07-17 to 2001-08-07 (NODC Accession 0113587)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0113587 includes biological, chemical, discrete sample, physical and profile data collected from METEOR in the North Atlantic Ocean from 2001-07-17 to...

  15. Partial pressure (or fugacity) of carbon dioxide, dissolved inorganic carbon, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the KNORR in the North Pacific Ocean and South Pacific Ocean from 1992-10-06 to 1993-04-13 (NODC Accession 0115156)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0115156 includes chemical, discrete sample, physical and profile data collected from KNORR in the North Pacific Ocean and South Pacific Ocean from...

  16. Dissolved inorganic carbon, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the AURORA AUSTRALIS in the Indian Ocean and South Pacific Ocean from 1994-12-13 to 1995-02-01 (NODC Accession 0115020)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0115020 includes chemical, discrete sample, physical and profile data collected from AURORA AUSTRALIS in the Indian Ocean and South Pacific Ocean from...

  17. Dissolved inorganic carbon, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from METEOR in the Aegean Sea, Mediterranean Sea and others from 2001-10-18 to 2001-11-11 (NODC Accession 0084620)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NCEI Accession 0084620 includes discrete sample and profile data collected from METEOR in the Aegean Sea, Mediterranean Sea, Mediterranean Sea - Eastern Basin,...

  18. Partial pressure (or fugacity) of carbon dioxide, dissolved inorganic carbon, pH, alkalinity, temperature, salinity and other variables collected from discrete sample, profile and underway - surface observations using CTD, Carbon dioxide (CO2) gas analyzer and other instruments from the METEOR in the South Atlantic Ocean from 1992-12-27 to 1993-01-31 (NODC Accession 0115173)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NODC Accession 0115173 includes chemical, discrete sample, meteorological, physical, profile and underway - surface data collected from METEOR in the South Atlantic...

  19. Dissolved inorganic carbon, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from POLARSTERN in the South Atlantic Ocean and Southern Oceans from 1998-03-28 to 1998-05-23 (NODC Accession 0113595)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NCEI Accession 0113595 includes discrete sample and profile data collected from POLARSTERN in the South Atlantic Ocean and Southern Oceans (> 60 degrees South)...

  20. Partial pressure (or fugacity) of carbon dioxide, dissolved inorganic carbon, pH, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using Alkalinity titrator, CTD and other instruments from ATLANTIS in the North Atlantic Ocean from 2012-04-19 to 2012-05-15 (NODC Accession 0108160)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NCEI Accession 0108160 includes discrete sample and profile data collected from ATLANTIS in the North Atlantic Ocean from 2012-04-19 to 2012-05-15. These data...