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Sample records for activity quantitative estimates

  1. Health Impacts of Increased Physical Activity from Changes in Transportation Infrastructure: Quantitative Estimates for Three Communities

    PubMed Central

    Mansfield, Theodore J.; MacDonald Gibson, Jacqueline

    2015-01-01

    Recently, two quantitative tools have emerged for predicting the health impacts of projects that change population physical activity: the Health Economic Assessment Tool (HEAT) and Dynamic Modeling for Health Impact Assessment (DYNAMO-HIA). HEAT has been used to support health impact assessments of transportation infrastructure projects, but DYNAMO-HIA has not been previously employed for this purpose nor have the two tools been compared. To demonstrate the use of DYNAMO-HIA for supporting health impact assessments of transportation infrastructure projects, we employed the model in three communities (urban, suburban, and rural) in North Carolina. We also compared DYNAMO-HIA and HEAT predictions in the urban community. Using DYNAMO-HIA, we estimated benefit-cost ratios of 20.2 (95% C.I.: 8.7–30.6), 0.6 (0.3–0.9), and 4.7 (2.1–7.1) for the urban, suburban, and rural projects, respectively. For a 40-year time period, the HEAT predictions of deaths avoided by the urban infrastructure project were three times as high as DYNAMO-HIA's predictions due to HEAT's inability to account for changing population health characteristics over time. Quantitative health impact assessment coupled with economic valuation is a powerful tool for integrating health considerations into transportation decision-making. However, to avoid overestimating benefits, such quantitative HIAs should use dynamic, rather than static, approaches. PMID:26504832

  2. Health Impacts of Increased Physical Activity from Changes in Transportation Infrastructure: Quantitative Estimates for Three Communities.

    PubMed

    Mansfield, Theodore J; MacDonald Gibson, Jacqueline

    2015-01-01

    Recently, two quantitative tools have emerged for predicting the health impacts of projects that change population physical activity: the Health Economic Assessment Tool (HEAT) and Dynamic Modeling for Health Impact Assessment (DYNAMO-HIA). HEAT has been used to support health impact assessments of transportation infrastructure projects, but DYNAMO-HIA has not been previously employed for this purpose nor have the two tools been compared. To demonstrate the use of DYNAMO-HIA for supporting health impact assessments of transportation infrastructure projects, we employed the model in three communities (urban, suburban, and rural) in North Carolina. We also compared DYNAMO-HIA and HEAT predictions in the urban community. Using DYNAMO-HIA, we estimated benefit-cost ratios of 20.2 (95% C.I.: 8.7-30.6), 0.6 (0.3-0.9), and 4.7 (2.1-7.1) for the urban, suburban, and rural projects, respectively. For a 40-year time period, the HEAT predictions of deaths avoided by the urban infrastructure project were three times as high as DYNAMO-HIA's predictions due to HEAT's inability to account for changing population health characteristics over time. Quantitative health impact assessment coupled with economic valuation is a powerful tool for integrating health considerations into transportation decision-making. However, to avoid overestimating benefits, such quantitative HIAs should use dynamic, rather than static, approaches.

  3. Health Impacts of Increased Physical Activity from Changes in Transportation Infrastructure: Quantitative Estimates for Three Communities.

    PubMed

    Mansfield, Theodore J; MacDonald Gibson, Jacqueline

    2015-01-01

    Recently, two quantitative tools have emerged for predicting the health impacts of projects that change population physical activity: the Health Economic Assessment Tool (HEAT) and Dynamic Modeling for Health Impact Assessment (DYNAMO-HIA). HEAT has been used to support health impact assessments of transportation infrastructure projects, but DYNAMO-HIA has not been previously employed for this purpose nor have the two tools been compared. To demonstrate the use of DYNAMO-HIA for supporting health impact assessments of transportation infrastructure projects, we employed the model in three communities (urban, suburban, and rural) in North Carolina. We also compared DYNAMO-HIA and HEAT predictions in the urban community. Using DYNAMO-HIA, we estimated benefit-cost ratios of 20.2 (95% C.I.: 8.7-30.6), 0.6 (0.3-0.9), and 4.7 (2.1-7.1) for the urban, suburban, and rural projects, respectively. For a 40-year time period, the HEAT predictions of deaths avoided by the urban infrastructure project were three times as high as DYNAMO-HIA's predictions due to HEAT's inability to account for changing population health characteristics over time. Quantitative health impact assessment coupled with economic valuation is a powerful tool for integrating health considerations into transportation decision-making. However, to avoid overestimating benefits, such quantitative HIAs should use dynamic, rather than static, approaches. PMID:26504832

  4. Estimating the Potential Toxicity of Chemicals Associated with Hydraulic Fracturing Operations Using Quantitative Structure-Activity Relationship Modeling.

    PubMed

    Yost, Erin E; Stanek, John; DeWoskin, Robert S; Burgoon, Lyle D

    2016-07-19

    The United States Environmental Protection Agency (EPA) identified 1173 chemicals associated with hydraulic fracturing fluids, flowback, or produced water, of which 1026 (87%) lack chronic oral toxicity values for human health assessments. To facilitate the ranking and prioritization of chemicals that lack toxicity values, it may be useful to employ toxicity estimates from quantitative structure-activity relationship (QSAR) models. Here we describe an approach for applying the results of a QSAR model from the TOPKAT program suite, which provides estimates of the rat chronic oral lowest-observed-adverse-effect level (LOAEL). Of the 1173 chemicals, TOPKAT was able to generate LOAEL estimates for 515 (44%). To address the uncertainty associated with these estimates, we assigned qualitative confidence scores (high, medium, or low) to each TOPKAT LOAEL estimate, and found 481 to be high-confidence. For 48 chemicals that had both a high-confidence TOPKAT LOAEL estimate and a chronic oral reference dose from EPA's Integrated Risk Information System (IRIS) database, Spearman rank correlation identified 68% agreement between the two values (permutation p-value =1 × 10(-11)). These results provide support for the use of TOPKAT LOAEL estimates in identifying and prioritizing potentially hazardous chemicals. High-confidence TOPKAT LOAEL estimates were available for 389 of 1026 hydraulic fracturing-related chemicals that lack chronic oral RfVs and OSFs from EPA-identified sources, including a subset of chemicals that are frequently used in hydraulic fracturing fluids. PMID:27172125

  5. Estimating the Potential Toxicity of Chemicals Associated with Hydraulic Fracturing Operations Using Quantitative Structure-Activity Relationship Modeling.

    PubMed

    Yost, Erin E; Stanek, John; DeWoskin, Robert S; Burgoon, Lyle D

    2016-07-19

    The United States Environmental Protection Agency (EPA) identified 1173 chemicals associated with hydraulic fracturing fluids, flowback, or produced water, of which 1026 (87%) lack chronic oral toxicity values for human health assessments. To facilitate the ranking and prioritization of chemicals that lack toxicity values, it may be useful to employ toxicity estimates from quantitative structure-activity relationship (QSAR) models. Here we describe an approach for applying the results of a QSAR model from the TOPKAT program suite, which provides estimates of the rat chronic oral lowest-observed-adverse-effect level (LOAEL). Of the 1173 chemicals, TOPKAT was able to generate LOAEL estimates for 515 (44%). To address the uncertainty associated with these estimates, we assigned qualitative confidence scores (high, medium, or low) to each TOPKAT LOAEL estimate, and found 481 to be high-confidence. For 48 chemicals that had both a high-confidence TOPKAT LOAEL estimate and a chronic oral reference dose from EPA's Integrated Risk Information System (IRIS) database, Spearman rank correlation identified 68% agreement between the two values (permutation p-value =1 × 10(-11)). These results provide support for the use of TOPKAT LOAEL estimates in identifying and prioritizing potentially hazardous chemicals. High-confidence TOPKAT LOAEL estimates were available for 389 of 1026 hydraulic fracturing-related chemicals that lack chronic oral RfVs and OSFs from EPA-identified sources, including a subset of chemicals that are frequently used in hydraulic fracturing fluids.

  6. Comparative evaluation of six quantitative lifting tools to estimate spine loads during static activities.

    PubMed

    Rajaee, Mohammad Ali; Arjmand, Navid; Shirazi-Adl, Aboulfazl; Plamondon, André; Schmidt, Hendrik

    2015-05-01

    Different lifting analysis tools are commonly used to assess spinal loads and risk of injury. Distinct musculoskeletal models with various degrees of accuracy are employed in these tools affecting thus their relative accuracy in practical applications. The present study aims to compare predictions of six tools (HCBCF, LSBM, 3DSSPP, AnyBody, simple polynomial, and regression models) for the L4-L5 and L5-S1 compression and shear loads in twenty-six static activities with and without hand load. Significantly different spinal loads but relatively similar patterns for the compression (R(2) > 0.87) were computed. Regression models and AnyBody predicted intradiscal pressures in closer agreement with available in vivo measurements (RMSE ≈ 0.12 MPa). Due to the differences in predicted spinal loads, the estimated risk of injury alters depending on the tool used. Each tool is evaluated to identify its shortcomings and preferred application domains.

  7. Quantitative estimation of minimum offset for multichannel surface-wave survey with actively exciting source

    USGS Publications Warehouse

    Xu, Y.; Xia, J.; Miller, R.D.

    2006-01-01

    Multichannel analysis of surface waves is a developing method widely used in shallow subsurface investigations. The field procedures and related parameters are very important for successful applications. Among these parameters, the source-receiver offset range is seldom discussed in theory and normally determined by empirical or semi-quantitative methods in current practice. This paper discusses the problem from a theoretical perspective. A formula for quantitatively evaluating a layered homogenous elastic model was developed. The analytical results based on simple models and experimental data demonstrate that the formula is correct for surface wave surveys for near-surface applications. ?? 2005 Elsevier B.V. All rights reserved.

  8. ESTIMATION OF MICROBIAL REDUCTIVE TRANSFORMATION RATES FOR CHLORINATED BENZENES AND PHENOLS USING A QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP APPROACH

    EPA Science Inventory

    A set of literature data was used to derive several quantitative structure-activity relationships (QSARs) to predict the rate constants for the microbial reductive dehalogenation of chlorinated aromatics. Dechlorination rate constants for 25 chloroaromatics were corrected for th...

  9. Evaluation of quantitative imaging methods for organ activity and residence time estimation using a population of phantoms having realistic variations in anatomy and uptake

    SciTech Connect

    He Bin; Du Yong; Segars, W. Paul; Wahl, Richard L.; Sgouros, George; Jacene, Heather; Frey, Eric C.

    2009-02-15

    Estimating organ residence times is an essential part of patient-specific dosimetry for radioimmunotherapy (RIT). Quantitative imaging methods for RIT are often evaluated using a single physical or simulated phantom but are intended to be applied clinically where there is variability in patient anatomy, biodistribution, and biokinetics. To provide a more relevant evaluation, the authors have thus developed a population of phantoms with realistic variations in these factors and applied it to the evaluation of quantitative imaging methods both to find the best method and to demonstrate the effects of these variations. Using whole body scans and SPECT/CT images, organ shapes and time-activity curves of 111In ibritumomab tiuxetan were measured in dosimetrically important organs in seven patients undergoing a high dose therapy regimen. Based on these measurements, we created a 3D NURBS-based cardiac-torso (NCAT)-based phantom population. SPECT and planar data at realistic count levels were then simulated using previously validated Monte Carlo simulation tools. The projections from the population were used to evaluate the accuracy and variation in accuracy of residence time estimation methods that used a time series of SPECT and planar scans. Quantitative SPECT (QSPECT) reconstruction methods were used that compensated for attenuation, scatter, and the collimator-detector response. Planar images were processed with a conventional (CPlanar) method that used geometric mean attenuation and triple-energy window scatter compensation and a quantitative planar (QPlanar) processing method that used model-based compensation for image degrading effects. Residence times were estimated from activity estimates made at each of five time points. The authors also evaluated hybrid methods that used CPlanar or QPlanar time-activity curves rescaled to the activity estimated from a single QSPECT image. The methods were evaluated in terms of mean relative error and standard deviation of the

  10. The impact of 3D volume of interest definition on accuracy and precision of activity estimation in quantitative SPECT and planar processing methods

    NASA Astrophysics Data System (ADS)

    He, Bin; Frey, Eric C.

    2010-06-01

    Accurate and precise estimation of organ activities is essential for treatment planning in targeted radionuclide therapy. We have previously evaluated the impact of processing methodology, statistical noise and variability in activity distribution and anatomy on the accuracy and precision of organ activity estimates obtained with quantitative SPECT (QSPECT) and planar (QPlanar) processing. Another important factor impacting the accuracy and precision of organ activity estimates is accuracy of and variability in the definition of organ regions of interest (ROI) or volumes of interest (VOI). The goal of this work was thus to systematically study the effects of VOI definition on the reliability of activity estimates. To this end, we performed Monte Carlo simulation studies using randomly perturbed and shifted VOIs to assess the impact on organ activity estimates. The 3D NCAT phantom was used with activities that modeled clinically observed 111In ibritumomab tiuxetan distributions. In order to study the errors resulting from misdefinitions due to manual segmentation errors, VOIs of the liver and left kidney were first manually defined. Each control point was then randomly perturbed to one of the nearest or next-nearest voxels in three ways: with no, inward or outward directional bias, resulting in random perturbation, erosion or dilation, respectively, of the VOIs. In order to study the errors resulting from the misregistration of VOIs, as would happen, e.g. in the case where the VOIs were defined using a misregistered anatomical image, the reconstructed SPECT images or projections were shifted by amounts ranging from -1 to 1 voxels in increments of with 0.1 voxels in both the transaxial and axial directions. The activity estimates from the shifted reconstructions or projections were compared to those from the originals, and average errors were computed for the QSPECT and QPlanar methods, respectively. For misregistration, errors in organ activity estimations were

  11. The impact of 3D volume of interest definition on accuracy and precision of activity estimation in quantitative SPECT and planar processing methods.

    PubMed

    He, Bin; Frey, Eric C

    2010-06-21

    Accurate and precise estimation of organ activities is essential for treatment planning in targeted radionuclide therapy. We have previously evaluated the impact of processing methodology, statistical noise and variability in activity distribution and anatomy on the accuracy and precision of organ activity estimates obtained with quantitative SPECT (QSPECT) and planar (QPlanar) processing. Another important factor impacting the accuracy and precision of organ activity estimates is accuracy of and variability in the definition of organ regions of interest (ROI) or volumes of interest (VOI). The goal of this work was thus to systematically study the effects of VOI definition on the reliability of activity estimates. To this end, we performed Monte Carlo simulation studies using randomly perturbed and shifted VOIs to assess the impact on organ activity estimates. The 3D NCAT phantom was used with activities that modeled clinically observed (111)In ibritumomab tiuxetan distributions. In order to study the errors resulting from misdefinitions due to manual segmentation errors, VOIs of the liver and left kidney were first manually defined. Each control point was then randomly perturbed to one of the nearest or next-nearest voxels in three ways: with no, inward or outward directional bias, resulting in random perturbation, erosion or dilation, respectively, of the VOIs. In order to study the errors resulting from the misregistration of VOIs, as would happen, e.g. in the case where the VOIs were defined using a misregistered anatomical image, the reconstructed SPECT images or projections were shifted by amounts ranging from -1 to 1 voxels in increments of with 0.1 voxels in both the transaxial and axial directions. The activity estimates from the shifted reconstructions or projections were compared to those from the originals, and average errors were computed for the QSPECT and QPlanar methods, respectively. For misregistration, errors in organ activity estimations were

  12. Rapid Quantitative Pharmacodynamic Imaging with Bayesian Estimation

    PubMed Central

    Koller, Jonathan M.; Vachon, M. Jonathan; Bretthorst, G. Larry; Black, Kevin J.

    2016-01-01

    We recently described rapid quantitative pharmacodynamic imaging, a novel method for estimating sensitivity of a biological system to a drug. We tested its accuracy in simulated biological signals with varying receptor sensitivity and varying levels of random noise, and presented initial proof-of-concept data from functional MRI (fMRI) studies in primate brain. However, the initial simulation testing used a simple iterative approach to estimate pharmacokinetic-pharmacodynamic (PKPD) parameters, an approach that was computationally efficient but returned parameters only from a small, discrete set of values chosen a priori. Here we revisit the simulation testing using a Bayesian method to estimate the PKPD parameters. This improved accuracy compared to our previous method, and noise without intentional signal was never interpreted as signal. We also reanalyze the fMRI proof-of-concept data. The success with the simulated data, and with the limited fMRI data, is a necessary first step toward further testing of rapid quantitative pharmacodynamic imaging. PMID:27092045

  13. Quantitative Estimation of Tissue Blood Flow Rate.

    PubMed

    Tozer, Gillian M; Prise, Vivien E; Cunningham, Vincent J

    2016-01-01

    The rate of blood flow through a tissue (F) is a critical parameter for assessing the functional efficiency of a blood vessel network following angiogenesis. This chapter aims to provide the principles behind the estimation of F, how F relates to other commonly used measures of tissue perfusion, and a practical approach for estimating F in laboratory animals, using small readily diffusible and metabolically inert radio-tracers. The methods described require relatively nonspecialized equipment. However, the analytical descriptions apply equally to complementary techniques involving more sophisticated noninvasive imaging.Two techniques are described for the quantitative estimation of F based on measuring the rate of tissue uptake following intravenous administration of radioactive iodo-antipyrine (or other suitable tracer). The Tissue Equilibration Technique is the classical approach and the Indicator Fractionation Technique, which is simpler to perform, is a practical alternative in many cases. The experimental procedures and analytical methods for both techniques are given, as well as guidelines for choosing the most appropriate method. PMID:27172960

  14. Radar Based Quantitative Precipitation Estimation in Taiwan

    NASA Astrophysics Data System (ADS)

    Wang, Y.; Zhang, J.; Chang, P.

    2012-12-01

    Accurate high-resolution radar quantitative precipitation estimation (QPE) has shown increasing values in hydrological predictions in the last decade. Such QPEs are especially valuable in complex terrain where rain gauge network is sparse and hard to maintain while flash floods and mudslides are common hazards. Taiwan Central Weather Bureau has deployed four S-band radars to support their flood warning operations in recent years, and a real-time multi-radar QPE system was developed. Evaluations of the real-time system over one-year revealed some underestimation issues in the radar QPE. The current work investigates these issues and develops a series of refinements to the system. The refinements include replacing the general R-Z relationships used in the old system with the local ones, mitigating non-standard beam blockage artifacts based on long-term accumulations, and applying vertical profile of reflectivity (VPR) corrections. The local R-Z relationships were derived from 2D video disdrometer observations of winter stratiform precipitation, meiyu fronts, local convective storms, and typhoons. The VPR correction was applied to reduce radar QPE errors in severely blocked area near the Central Mountain Range (CMR). The new radar QPE system was tested using different precipitation events and showed significant improvements over the old system especially along the CMR.

  15. Quantitative estimation in Health Impact Assessment: Opportunities and challenges

    SciTech Connect

    Bhatia, Rajiv; Seto, Edmund

    2011-04-15

    Health Impact Assessment (HIA) considers multiple effects on health of policies, programs, plans and projects and thus requires the use of diverse analytic tools and sources of evidence. Quantitative estimation has desirable properties for the purpose of HIA but adequate tools for quantification exist currently for a limited number of health impacts and decision settings; furthermore, quantitative estimation generates thorny questions about the precision of estimates and the validity of methodological assumptions. In the United States, HIA has only recently emerged as an independent practice apart from integrated EIA, and this article aims to synthesize the experience with quantitative health effects estimation within that practice. We use examples identified through a scan of available identified instances of quantitative estimation in the U.S. practice experience to illustrate methods applied in different policy settings along with their strengths and limitations. We then discuss opportunity areas and practical considerations for the use of quantitative estimation in HIA.

  16. Quantitative criteria for estimation of natural and artificial ecosystems functioning.

    PubMed

    Pechurkin, N S

    2005-01-01

    Using biotic turnover of substances in trophic chains, natural and artificial ecosystems are similar in functioning, but different in structure. It is necessary to have quantitative criteria to evaluate the efficiency of artificial ecosystems (AES). These criteria are dependent on the specific objectives for which the AES are designed. For example, if AES is considered for use in space, important criteria are efficiency in use of mass, power, volume (size) and human labor and reliability. Another task involves the determination of quantitative criteria for the functioning of natural ecosystems. To solve the problem, it is fruitful to use a hierarchical approach suitable for both individual links and the ecosystem as a whole. Energy flux criteria (principles) were developed to estimate the functional activities of biosystems at the population, community and ecosystem levels. A major feature of ecosystems as a whole is their biotic turnover of matter the rate of which is restricted by the lack of limiting substances. Obviously, the most generalized criterion is to take into account the energy flux used by the biosystem and the quantity of limiting substance included in its turnover. The use of energy flux by ecosystem, E(USED)--is determined from the photoassimilation of CO2 by plants (per time unit). It can be approximately estimated as the net primary production of photosynthesis (NPP). So, the ratio of CO2 photoassimilation rate (sometimes, measured as NPP) to the total mass of limiting substrate can serve as a main universal criterion (MUC). This MUC characterizes the specific cycling rate of limiting chemical elements in the system and effectiveness of every ecosystem including the global Biosphere. Comparative analysis and elaboration of quantitative criteria for estimation of natural and artificial ecosystems activities is of high importance both for theoretical considerations and for real applications.

  17. Quantitative estimation of infarct size by simultaneous dual radionuclide single photon emission computed tomography: comparison with peak serum creatine kinase activity

    SciTech Connect

    Kawaguchi, K.; Sone, T.; Tsuboi, H.; Sassa, H.; Okumura, K.; Hashimoto, H.; Ito, T.; Satake, T. )

    1991-05-01

    To test the hypothesis that simultaneous dual energy single photon emission computed tomography (SPECT) with technetium-99m (99mTc) pyrophosphate and thallium-201 (201TI) can provide an accurate estimate of the size of myocardial infarction and to assess the correlation between infarct size and peak serum creatine kinase activity, 165 patients with acute myocardial infarction underwent SPECT 3.2 +/- 1.3 (SD) days after the onset of acute myocardial infarction. In the present study, the difference in the intensity of 99mTc-pyrophosphate accumulation was assumed to be attributable to difference in the volume of infarcted myocardium, and the infarct volume was corrected by the ratio of the myocardial activity to the osseous activity to quantify the intensity of 99mTc-pyrophosphate accumulation. The correlation of measured infarct volume with peak serum creatine kinase activity was significant (r = 0.60, p less than 0.01). There was also a significant linear correlation between the corrected infarct volume and peak serum creatine kinase activity (r = 0.71, p less than 0.01). Subgroup analysis showed a high correlation between corrected volume and peak creatine kinase activity in patients with anterior infarctions (r = 0.75, p less than 0.01) but a poor correlation in patients with inferior or posterior infarctions (r = 0.50, p less than 0.01). In both the early reperfusion and the no reperfusion groups, a good correlation was found between corrected infarct volume and peak serum creatine kinase activity (r = 0.76 and r = 0.76, respectively; p less than 0.01).

  18. Estimation of Variance Components of Quantitative Traits in Inbred Populations

    PubMed Central

    Abney, Mark; McPeek, Mary Sara; Ober, Carole

    2000-01-01

    Summary Use of variance-component estimation for mapping of quantitative-trait loci in humans is a subject of great current interest. When only trait values, not genotypic information, are considered, variance-component estimation can also be used to estimate heritability of a quantitative trait. Inbred pedigrees present special challenges for variance-component estimation. First, there are more variance components to be estimated in the inbred case, even for a relatively simple model including additive, dominance, and environmental effects. Second, more identity coefficients need to be calculated from an inbred pedigree in order to perform the estimation, and these are computationally more difficult to obtain in the inbred than in the outbred case. As a result, inbreeding effects have generally been ignored in practice. We describe here the calculation of identity coefficients and estimation of variance components of quantitative traits in large inbred pedigrees, using the example of HDL in the Hutterites. We use a multivariate normal model for the genetic effects, extending the central-limit theorem of Lange to allow for both inbreeding and dominance under the assumptions of our variance-component model. We use simulated examples to give an indication of under what conditions one has the power to detect the additional variance components and to examine their impact on variance-component estimation. We discuss the implications for mapping and heritability estimation by use of variance components in inbred populations. PMID:10677322

  19. Quantitative estimation of urinary protein excretion by refractometry.

    PubMed

    Kumar, S; Visweswaran, K; Sobha, A; Sarasa, G; Nampoory, M R

    1992-09-01

    Quantitative estimation of proteinuria done by the refractometric method was compared with that done by the sulphosalycilic acid method and biuret method in 102 urine samples. The analysis of results by students' t test showed no statistically significant difference between the three methods. It is concluded that quantitative estimation of urinary protein excretion by refractometric method is a simple cheap and reliable method and can be performed easily in the outpatient clinic. The instrument is quite handy and can be carried in the pocket.

  20. Quantitative comparison of estimations for the density within pedestrian streams

    NASA Astrophysics Data System (ADS)

    Tordeux, Antoine; Zhang, Jun; Steffen, Bernhard; Seyfried, Armin

    2015-06-01

    In this work, the precision of estimators for the density within unidirectional pedestrian streams is evaluated. The analysis is done in controllable systems where the density is homogeneous and all the characteristics are known. The objectives are to estimate the global density with local measurements or density profile at high spatial resolution with no bias and low fluctuations. The classical estimation using discrete numbers of observed pedestrians is compared to continuous estimators using spacing distance, Voronoi diagram, Gaussian kernel as well as maximum likelihood. Mean squared error and bias of the estimators are calculated from empirical data and Monte Carlo experiments. The results show quantitatively how continuous approaches improve the precision of the estimations.

  1. Quantitative study of single molecule location estimation techniques.

    PubMed

    Abraham, Anish V; Ram, Sripad; Chao, Jerry; Ward, E S; Ober, Raimund J

    2009-12-21

    Estimating the location of single molecules from microscopy images is a key step in many quantitative single molecule data analysis techniques. Different algorithms have been advocated for the fitting of single molecule data, particularly the nonlinear least squares and maximum likelihood estimators. Comparisons were carried out to assess the performance of these two algorithms in different scenarios. Our results show that both estimators, on average, are able to recover the true location of the single molecule in all scenarios we examined. However, in the absence of modeling inaccuracies and low noise levels, the maximum likelihood estimator is more accurate than the nonlinear least squares estimator, as measured by the standard deviations of its estimates, and attains the best possible accuracy achievable for the sets of imaging and experimental conditions that were tested. Although neither algorithm is consistently superior to the other in the presence of modeling inaccuracies or misspecifications, the maximum likelihood algorithm emerges as a robust estimator producing results with consistent accuracy across various model mismatches and misspecifications. At high noise levels, relative to the signal from the point source, neither algorithm has a clear accuracy advantage over the other. Comparisons were also carried out for two localization accuracy measures derived previously. Software packages with user-friendly graphical interfaces developed for single molecule location estimation (EstimationTool) and limit of the localization accuracy calculations (FandPLimitTool) are also discussed.

  2. Bayesian parameter estimation in spectral quantitative photoacoustic tomography

    NASA Astrophysics Data System (ADS)

    Pulkkinen, Aki; Cox, Ben T.; Arridge, Simon R.; Kaipio, Jari P.; Tarvainen, Tanja

    2016-03-01

    Photoacoustic tomography (PAT) is an imaging technique combining strong contrast of optical imaging to high spatial resolution of ultrasound imaging. These strengths are achieved via photoacoustic effect, where a spatial absorption of light pulse is converted into a measurable propagating ultrasound wave. The method is seen as a potential tool for small animal imaging, pre-clinical investigations, study of blood vessels and vasculature, as well as for cancer imaging. The goal in PAT is to form an image of the absorbed optical energy density field via acoustic inverse problem approaches from the measured ultrasound data. Quantitative PAT (QPAT) proceeds from these images and forms quantitative estimates of the optical properties of the target. This optical inverse problem of QPAT is illposed. To alleviate the issue, spectral QPAT (SQPAT) utilizes PAT data formed at multiple optical wavelengths simultaneously with optical parameter models of tissue to form quantitative estimates of the parameters of interest. In this work, the inverse problem of SQPAT is investigated. Light propagation is modelled using the diffusion equation. Optical absorption is described with chromophore concentration weighted sum of known chromophore absorption spectra. Scattering is described by Mie scattering theory with an exponential power law. In the inverse problem, the spatially varying unknown parameters of interest are the chromophore concentrations, the Mie scattering parameters (power law factor and the exponent), and Gruneisen parameter. The inverse problem is approached with a Bayesian method. It is numerically demonstrated, that estimation of all parameters of interest is possible with the approach.

  3. Quantitative volumetric breast density estimation using phase contrast mammography

    NASA Astrophysics Data System (ADS)

    Wang, Zhentian; Hauser, Nik; Kubik-Huch, Rahel A.; D'Isidoro, Fabio; Stampanoni, Marco

    2015-05-01

    Phase contrast mammography using a grating interferometer is an emerging technology for breast imaging. It provides complementary information to the conventional absorption-based methods. Additional diagnostic values could be further obtained by retrieving quantitative information from the three physical signals (absorption, differential phase and small-angle scattering) yielded simultaneously. We report a non-parametric quantitative volumetric breast density estimation method by exploiting the ratio (dubbed the R value) of the absorption signal to the small-angle scattering signal. The R value is used to determine breast composition and the volumetric breast density (VBD) of the whole breast is obtained analytically by deducing the relationship between the R value and the pixel-wise breast density. The proposed method is tested by a phantom study and a group of 27 mastectomy samples. In the clinical evaluation, the estimated VBD values from both cranio-caudal (CC) and anterior-posterior (AP) views are compared with the ACR scores given by radiologists to the pre-surgical mammograms. The results show that the estimated VBD results using the proposed method are consistent with the pre-surgical ACR scores, indicating the effectiveness of this method in breast density estimation. A positive correlation is found between the estimated VBD and the diagnostic ACR score for both the CC view (p=0.033 ) and AP view (p=0.001 ). A linear regression between the results of the CC view and AP view showed a correlation coefficient γ = 0.77, which indicates the robustness of the proposed method and the quantitative character of the additional information obtained with our approach.

  4. Quantitative volumetric breast density estimation using phase contrast mammography.

    PubMed

    Wang, Zhentian; Hauser, Nik; Kubik-Huch, Rahel A; D'Isidoro, Fabio; Stampanoni, Marco

    2015-05-21

    Phase contrast mammography using a grating interferometer is an emerging technology for breast imaging. It provides complementary information to the conventional absorption-based methods. Additional diagnostic values could be further obtained by retrieving quantitative information from the three physical signals (absorption, differential phase and small-angle scattering) yielded simultaneously. We report a non-parametric quantitative volumetric breast density estimation method by exploiting the ratio (dubbed the R value) of the absorption signal to the small-angle scattering signal. The R value is used to determine breast composition and the volumetric breast density (VBD) of the whole breast is obtained analytically by deducing the relationship between the R value and the pixel-wise breast density. The proposed method is tested by a phantom study and a group of 27 mastectomy samples. In the clinical evaluation, the estimated VBD values from both cranio-caudal (CC) and anterior-posterior (AP) views are compared with the ACR scores given by radiologists to the pre-surgical mammograms. The results show that the estimated VBD results using the proposed method are consistent with the pre-surgical ACR scores, indicating the effectiveness of this method in breast density estimation. A positive correlation is found between the estimated VBD and the diagnostic ACR score for both the CC view (p = 0.033) and AP view (p = 0.001). A linear regression between the results of the CC view and AP view showed a correlation coefficient γ = 0.77, which indicates the robustness of the proposed method and the quantitative character of the additional information obtained with our approach.

  5. Computer Monte Carlo simulation in quantitative resource estimation

    USGS Publications Warehouse

    Root, D.H.; Menzie, W.D.; Scott, W.A.

    1992-01-01

    The method of making quantitative assessments of mineral resources sufficiently detailed for economic analysis is outlined in three steps. The steps are (1) determination of types of deposits that may be present in an area, (2) estimation of the numbers of deposits of the permissible deposit types, and (3) combination by Monte Carlo simulation of the estimated numbers of deposits with the historical grades and tonnages of these deposits to produce a probability distribution of the quantities of contained metal. Two examples of the estimation of the number of deposits (step 2) are given. The first example is for mercury deposits in southwestern Alaska and the second is for lode tin deposits in the Seward Peninsula. The flow of the Monte Carlo simulation program is presented with particular attention to the dependencies between grades and tonnages of deposits and between grades of different metals in the same deposit. ?? 1992 Oxford University Press.

  6. Quantitative estimation of time-variable earthquake hazard by using fuzzy set theory

    NASA Astrophysics Data System (ADS)

    Deyi, Feng; Ichikawa, M.

    1989-11-01

    In this paper, the various methods of fuzzy set theory, called fuzzy mathematics, have been applied to the quantitative estimation of the time-variable earthquake hazard. The results obtained consist of the following. (1) Quantitative estimation of the earthquake hazard on the basis of seismicity data. By using some methods of fuzzy mathematics, seismicity patterns before large earthquakes can be studied more clearly and more quantitatively, highly active periods in a given region and quiet periods of seismic activity before large earthquakes can be recognized, similarities in temporal variation of seismic activity and seismic gaps can be examined and, on the other hand, the time-variable earthquake hazard can be assessed directly on the basis of a series of statistical indices of seismicity. Two methods of fuzzy clustering analysis, the method of fuzzy similarity, and the direct method of fuzzy pattern recognition, have been studied is particular. One method of fuzzy clustering analysis is based on fuzzy netting, and another is based on the fuzzy equivalent relation. (2) Quantitative estimation of the earthquake hazard on the basis of observational data for different precursors. The direct method of fuzzy pattern recognition has been applied to research on earthquake precursors of different kinds. On the basis of the temporal and spatial characteristics of recognized precursors, earthquake hazards in different terms can be estimated. This paper mainly deals with medium-short-term precursors observed in Japan and China.

  7. Quantitative estimation of poikilocytosis by the coherent optical method

    NASA Astrophysics Data System (ADS)

    Safonova, Larisa P.; Samorodov, Andrey V.; Spiridonov, Igor N.

    2000-05-01

    The investigation upon the necessity and the reliability required of the determination of the poikilocytosis in hematology has shown that existing techniques suffer from grave shortcomings. To determine a deviation of the erythrocytes' form from the normal (rounded) one in blood smears it is expedient to use an integrative estimate. The algorithm which is based on the correlation between erythrocyte morphological parameters with properties of the spatial-frequency spectrum of blood smear is suggested. During analytical and experimental research an integrative form parameter (IFP) which characterizes the increase of the relative concentration of cells with the changed form over 5% and the predominating type of poikilocytes was suggested. An algorithm of statistically reliable estimation of the IFP on the standard stained blood smears has been developed. To provide the quantitative characterization of the morphological features of cells a form vector has been proposed, and its validity for poikilocytes differentiation was shown.

  8. Handling uncertainty in quantitative estimates in integrated resource planning

    SciTech Connect

    Tonn, B.E.; Wagner, C.G.

    1995-01-01

    This report addresses uncertainty in Integrated Resource Planning (IRP). IRP is a planning and decisionmaking process employed by utilities, usually at the behest of Public Utility Commissions (PUCs), to develop plans to ensure that utilities have resources necessary to meet consumer demand at reasonable cost. IRP has been used to assist utilities in developing plans that include not only traditional electricity supply options but also demand-side management (DSM) options. Uncertainty is a major issue for IRP. Future values for numerous important variables (e.g., future fuel prices, future electricity demand, stringency of future environmental regulations) cannot ever be known with certainty. Many economically significant decisions are so unique that statistically-based probabilities cannot even be calculated. The entire utility strategic planning process, including IRP, encompasses different types of decisions that are made with different time horizons and at different points in time. Because of fundamental pressures for change in the industry, including competition in generation, gone is the time when utilities could easily predict increases in demand, enjoy long lead times to bring on new capacity, and bank on steady profits. The purpose of this report is to address in detail one aspect of uncertainty in IRP: Dealing with Uncertainty in Quantitative Estimates, such as the future demand for electricity or the cost to produce a mega-watt (MW) of power. A theme which runs throughout the report is that every effort must be made to honestly represent what is known about a variable that can be used to estimate its value, what cannot be known, and what is not known due to operational constraints. Applying this philosophy to the representation of uncertainty in quantitative estimates, it is argued that imprecise probabilities are superior to classical probabilities for IRP.

  9. Study on the performance evaluation of quantitative precipitation estimation and quantitative precipitation forecast

    NASA Astrophysics Data System (ADS)

    Yang, H.; Chang, K.; Suk, M.; cha, J.; Choi, Y.

    2011-12-01

    Rainfall estimation and short-term (several hours) quantitative prediction of precipitation based on meteorological radar data is one of the intensely studied topics. The Korea Peninsula has the horizontally narrow land area and complex topography with many of mountains, and so it has the characteristics that the rainfall system changes in many cases. Quantitative precipitation estimation (QPE) and quantitative precipitation forecasts (QPF) are the crucial information for severe weather or water management. We have been conducted the performance evaluation of QPE/QPF of Korea Meteorological Administration (KMA), which is the first step for optimizing QPE/QPF system in South Korea. The real-time adjusted RAR (Radar-AWS-Rainrate) system gives better agreement with the observed rain-rate than that of the fixed Z-R relation, and the additional bias correction of RAR yields the slightly better results. A correlation coefficient of R2 = 0.84 is obtained between the daily accumulated observed and RAR estimated rainfall. The RAR will be available for the hydrological applications such as the water budget. The VSRF (Very Short Range Forecast) shows better performance than the MAPLE (McGill Algorithm for Precipitation Nowcasting by Lagrangian) within 40 minutes, but the MAPLE better than the VSRF after 40 minutes. In case of hourly forecast, MAPLE shows better performance than the VSRF. QPE and QPF are thought to be meaningful for the nowcasting (1~2 hours) except the model forecast. The long-term forecast longer than 3 hours by meteorological model is especially meaningful for such as water management.

  10. Quantitative Compactness Estimates for Hamilton-Jacobi Equations

    NASA Astrophysics Data System (ADS)

    Ancona, Fabio; Cannarsa, Piermarco; Nguyen, Khai T.

    2016-02-01

    We study quantitative compactness estimates in {W^{1,1}_{loc}} for the map {S_t}, {t > 0} that is associated with the given initial data {u_0in Lip (R^N)} for the corresponding solution {S_t u_0} of a Hamilton-Jacobi equation u_t+Hbig(nabla_{x} ubig)=0, qquad t≥ 0,quad xinR^N, with a uniformly convex Hamiltonian {H=H(p)}. We provide upper and lower estimates of order {1/\\varepsilon^N} on the Kolmogorov {\\varepsilon}-entropy in {W^{1,1}} of the image through the map S t of sets of bounded, compactly supported initial data. Estimates of this type are inspired by a question posed by Lax (Course on Hyperbolic Systems of Conservation Laws. XXVII Scuola Estiva di Fisica Matematica, Ravello, 2002) within the context of conservation laws, and could provide a measure of the order of "resolution" of a numerical method implemented for this equation.

  11. Estimation of methanogen biomass by quantitation of coenzyme M

    SciTech Connect

    Elias, D.A.; Krumholz, L.R.; Tanner, R.S.; Suflita, J.M.

    1999-12-01

    Determination of the role of methanogenic bacteria in an anaerobic ecosystem often requires quantitation of the organisms. Because of the extreme oxygen sensitivity of these organisms and the inherent limitations of cultural techniques, an accurate biomass value is very difficult to obtain. The authors standardized a simple method for estimating methanogen biomass in a variety of environmental matrices. In this procedure they used the thiol biomarker coenzyme M (CoM) (2-mercaptoethanesulfonic acid), which is known to be present in tall methanogenic bacteria. A high-performance liquid chromatography-based method for detecting thiols in pore water was modified in order to quantify CoM in pure cultures, sediments, and sewage water samples. The identity of the CoM derivative was verified by using liquid chromatography-mass spectroscopy. The assay was linear for CoM amounts ranging from 2 to 2,000 pmol, and the detection limit was 2 pmol of CoM/ml of sample. CoM was not adsorbed to sediments. The methanogens tested contained an average of 19.5 nmol of CoM/mg of protein and 0.39 {+-} 0.07 fmol of CoM/cell. Environmental samples contained an average of 0.41 {+-} 0.17 fmol/cell based on most-probable-number estimates. CoM was extracted by using 1% tri-(N)-butylphosphine in isopropanol. More than 90% of the CoM was recovered from pure cultures and environmental samples. The authors observed no interference from sediments in the CoM recovery process, and the method could be completed aerobically within 3 h. Freezing sediment samples resulted in 46 to 83% decreases in the amounts of detectable CoM, whereas freezing had no effect on the amounts of CoM determined in pure cultures. The method described here provides a quick and relatively simple way to estimate methanogenic biomass.

  12. Integrator for qualitative and quantitative unit activity.

    PubMed

    Woods, T E; Dafny, N

    1975-01-01

    A simple device constructed from inexpensive components enables spike activity to be integrated and displayed in a convenient scale (spikes/sec) on a pen recorder. An input voltage threshold detection circuit is employed to eliminate any random baseline noise from being integrated. A pulse output is provided to drive a counter or accumulator so that quantitative as well as qualitative results may be obtained. A monostable multivibrator is used to insure that the integrated output is a function of the frequency of spike activity and not the amplitude or pattern of the spikes. An output isolation and buffer stage is provided to eliminate any loading effect on the filter section and also provide a gain or scaling adjustment so that the integrator may be used with practically any pen recorder. PMID:1153530

  13. Quantitative estimates of the volatility of ambient organic aerosol

    NASA Astrophysics Data System (ADS)

    Cappa, C. D.; Jimenez, J. L.

    2010-01-01

    Measurements of the sensitivity of organic aerosol (OA, and its components) mass to changes in temperature were recently reported by Huffman et al. (2009) using a tandem thermodenuder-aerosol mass spectrometer (TD-AMS) system in Mexico City and the Los Angeles area. Here, we use these measurements to derive quantitative estimates of aerosol volatility within the framework of absorptive partitioning theory using a kinetic model of aerosol evaporation in the TD. OA volatility distributions (or "basis-sets") are determined using several assumptions as to the enthalpy of vaporization (ΔHvap). We present two definitions of "non-volatile OA," one being a global and one a local definition. Based on these definitions, our analysis indicates that a substantial fraction of the organic aerosol is comprised of non-volatile components that will not evaporate under any atmospheric conditions, on the order of 50-80% when the most realistic ΔHvap assumptions are considered. The sensitivity of the total OA mass to dilution and ambient changes in temperature has been assessed for the various ΔHvap assumptions. The temperature sensitivity is relatively independent of the particular ΔHvap assumptions whereas dilution sensitivity is found to be greatest for the low (ΔHvap = 50 kJ/mol) and lowest for the high (ΔHvap = 150 kJ/mol) assumptions. This difference arises from the high ΔHvap assumptions yielding volatility distributions with a greater fraction of non-volatile material than the low ΔHvap assumptions. If the observations are fit using a 1 or 2-component model the sensitivity of the OA to dilution is unrealistically high. An empirical method introduced by Faulhaber et al. (2009) has also been used to independently estimate a volatility distribution for the ambient OA and is found to give results consistent with the high and variable ΔHvap assumptions. Our results also show that the amount of semivolatile gas-phase organics in equilibrium with the OA could range from ~20

  14. Quantitative estimates of the volatility of ambient organic aerosol

    NASA Astrophysics Data System (ADS)

    Cappa, C. D.; Jimenez, J. L.

    2010-06-01

    Measurements of the sensitivity of organic aerosol (OA, and its components) mass to changes in temperature were recently reported by Huffman et al.~(2009) using a tandem thermodenuder-aerosol mass spectrometer (TD-AMS) system in Mexico City and the Los Angeles area. Here, we use these measurements to derive quantitative estimates of aerosol volatility within the framework of absorptive partitioning theory using a kinetic model of aerosol evaporation in the TD. OA volatility distributions (or "basis-sets") are determined using several assumptions as to the enthalpy of vaporization (ΔHvap). We present two definitions of "non-volatile OA," one being a global and one a local definition. Based on these definitions, our analysis indicates that a substantial fraction of the organic aerosol is comprised of non-volatile components that will not evaporate under any atmospheric conditions; on the order of 50-80% when the most realistic ΔHvap assumptions are considered. The sensitivity of the total OA mass to dilution and ambient changes in temperature has been assessed for the various ΔHvap assumptions. The temperature sensitivity is relatively independent of the particular ΔHvap assumptions whereas dilution sensitivity is found to be greatest for the low (ΔHvap = 50 kJ/mol) and lowest for the high (ΔHvap = 150 kJ/mol) assumptions. This difference arises from the high ΔHvap assumptions yielding volatility distributions with a greater fraction of non-volatile material than the low ΔHvap assumptions. If the observations are fit using a 1 or 2-component model the sensitivity of the OA to dilution is unrealistically high. An empirical method introduced by Faulhaber et al. (2009) has also been used to independently estimate a volatility distribution for the ambient OA and is found to give results consistent with the high and variable ΔHvap assumptions. Our results also show that the amount of semivolatile gas-phase organics in equilibrium with the OA could range from ~20

  15. Comparison of the scanning linear estimator (SLE) and ROI methods for quantitative SPECT imaging

    NASA Astrophysics Data System (ADS)

    Könik, Arda; Kupinski, Meredith; Hendrik Pretorius, P.; King, Michael A.; Barrett, Harrison H.

    2015-08-01

    In quantitative emission tomography, tumor activity is typically estimated from calculations on a region of interest (ROI) identified in the reconstructed slices. In these calculations, unpredictable bias arising from the null functions of the imaging system affects ROI estimates. The magnitude of this bias depends upon the tumor size and location. In prior work it has been shown that the scanning linear estimator (SLE), which operates on the raw projection data, is an unbiased estimator of activity when the size and location of the tumor are known. In this work, we performed analytic simulation of SPECT imaging with a parallel-hole medium-energy collimator. Distance-dependent system spatial resolution and non-uniform attenuation were included in the imaging simulation. We compared the task of activity estimation by the ROI and SLE methods for a range of tumor sizes (diameter: 1-3 cm) and activities (contrast ratio: 1-10) added to uniform and non-uniform liver backgrounds. Using the correct value for the tumor shape and location is an idealized approximation to how task estimation would occur clinically. Thus we determined how perturbing this idealized prior knowledge impacted the performance of both techniques. To implement the SLE for the non-uniform background, we used a novel iterative algorithm for pre-whitening stationary noise within a compact region. Estimation task performance was compared using the ensemble mean-squared error (EMSE) as the criterion. The SLE method performed substantially better than the ROI method (i.e. EMSE(SLE) was 23-174 times lower) when the background is uniform and tumor location and size are known accurately. The variance of the SLE increased when a non-uniform liver texture was introduced but the EMSE(SLE) continued to be 5-20 times lower than the ROI method. In summary, SLE outperformed ROI under almost all conditions that we tested.

  16. Transient stochastic downscaling of quantitative precipitation estimates for hydrological applications

    NASA Astrophysics Data System (ADS)

    Nogueira, M.; Barros, A. P.

    2015-10-01

    Rainfall fields are heavily thresholded and highly intermittent resulting in large areas of zero values. This deforms their stochastic spatial scale-invariant behavior, introducing scaling breaks and curvature in the spatial scale spectrum. To address this problem, spatial scaling analysis was performed inside continuous rainfall features (CRFs) delineated via cluster analysis. The results show that CRFs from single realizations of hourly rainfall display ubiquitous multifractal behavior that holds over a wide range of scales (from ≈1 km up to 100's km). The results further show that the aggregate scaling behavior of rainfall fields is intrinsically transient with the scaling parameters explicitly dependent on the atmospheric environment. These findings provide a framework for robust stochastic downscaling, bridging the gap between spatial scales of observed and simulated rainfall fields and the high-resolution requirements of hydrometeorological and hydrological studies. Here, a fractal downscaling algorithm adapted to CRFs is presented and applied to generate stochastically downscaled hourly rainfall products from radar derived Stage IV (∼4 km grid resolution) quantitative precipitation estimates (QPE) over the Integrated Precipitation and Hydrology Experiment (IPHEx) domain in the southeast USA. The methodology can produce large ensembles of statistically robust high-resolution fields without additional data or any calibration requirements, conserving the coarse resolution information and generating coherent small-scale variability and field statistics, hence adding value to the original fields. Moreover, it is computationally inexpensive enabling fast production of high-resolution rainfall realizations with latency adequate for forecasting applications. When the transient nature of the scaling behavior is considered, the results show a better ability to reproduce the statistical structure of observed rainfall compared to using fixed scaling parameters

  17. Models of quantitative estimations: rule-based and exemplar-based processes compared.

    PubMed

    von Helversen, Bettina; Rieskamp, Jörg

    2009-07-01

    The cognitive processes underlying quantitative estimations vary. Past research has identified task-contingent changes between rule-based and exemplar-based processes (P. Juslin, L. Karlsson, & H. Olsson, 2008). B. von Helversen and J. Rieskamp (2008), however, proposed a simple rule-based model-the mapping model-that outperformed the exemplar model in a task thought to promote exemplar-based processing. This raised questions about the assumptions of rule-based versus exemplar-based models that underlie the notion of task contingency of cognitive processes. Rule-based models, such as the mapping model, assume the abstraction of explicit task knowledge. In contrast, exemplar models should profit if storage and activation of the exemplars is facilitated. Two studies tested the importance of the two models' assumptions. When knowledge about cues existed, the rule-based mapping model predicted quantitative estimations best. In contrast, when knowledge about the cues was difficult to gain, participants' estimations were best described by an exemplar model. The results emphasize the task contingency of cognitive processes. PMID:19586258

  18. Quantitative estimation of sampling uncertainties for mycotoxins in cereal shipments.

    PubMed

    Bourgeois, F S; Lyman, G J

    2012-01-01

    Many countries receive shipments of bulk cereals from primary producers. There is a volume of work that is on-going that seeks to arrive at appropriate standards for the quality of the shipments and the means to assess the shipments as they are out-loaded. Of concern are mycotoxin and heavy metal levels, pesticide and herbicide residue levels, and contamination by genetically modified organisms (GMOs). As the ability to quantify these contaminants improves through improved analytical techniques, the sampling methodologies applied to the shipments must also keep pace to ensure that the uncertainties attached to the sampling procedures do not overwhelm the analytical uncertainties. There is a need to understand and quantify sampling uncertainties under varying conditions of contamination. The analysis required is statistical and is challenging as the nature of the distribution of contaminants within a shipment is not well understood; very limited data exist. Limited work has been undertaken to quantify the variability of the contaminant concentrations in the flow of grain coming from a ship and the impact that this has on the variance of sampling. Relatively recent work by Paoletti et al. in 2006 [Paoletti C, Heissenberger A, Mazzara M, Larcher S, Grazioli E, Corbisier P, Hess N, Berben G, Lübeck PS, De Loose M, et al. 2006. Kernel lot distribution assessment (KeLDA): a study on the distribution of GMO in large soybean shipments. Eur Food Res Tech. 224:129-139] provides some insight into the variation in GMO concentrations in soybeans on cargo out-turn. Paoletti et al. analysed the data using correlogram analysis with the objective of quantifying the sampling uncertainty (variance) that attaches to the final cargo analysis, but this is only one possible means of quantifying sampling uncertainty. It is possible that in many cases the levels of contamination passing the sampler on out-loading are essentially random, negating the value of variographic quantitation of

  19. Quantitative estimation of sampling uncertainties for mycotoxins in cereal shipments.

    PubMed

    Bourgeois, F S; Lyman, G J

    2012-01-01

    Many countries receive shipments of bulk cereals from primary producers. There is a volume of work that is on-going that seeks to arrive at appropriate standards for the quality of the shipments and the means to assess the shipments as they are out-loaded. Of concern are mycotoxin and heavy metal levels, pesticide and herbicide residue levels, and contamination by genetically modified organisms (GMOs). As the ability to quantify these contaminants improves through improved analytical techniques, the sampling methodologies applied to the shipments must also keep pace to ensure that the uncertainties attached to the sampling procedures do not overwhelm the analytical uncertainties. There is a need to understand and quantify sampling uncertainties under varying conditions of contamination. The analysis required is statistical and is challenging as the nature of the distribution of contaminants within a shipment is not well understood; very limited data exist. Limited work has been undertaken to quantify the variability of the contaminant concentrations in the flow of grain coming from a ship and the impact that this has on the variance of sampling. Relatively recent work by Paoletti et al. in 2006 [Paoletti C, Heissenberger A, Mazzara M, Larcher S, Grazioli E, Corbisier P, Hess N, Berben G, Lübeck PS, De Loose M, et al. 2006. Kernel lot distribution assessment (KeLDA): a study on the distribution of GMO in large soybean shipments. Eur Food Res Tech. 224:129-139] provides some insight into the variation in GMO concentrations in soybeans on cargo out-turn. Paoletti et al. analysed the data using correlogram analysis with the objective of quantifying the sampling uncertainty (variance) that attaches to the final cargo analysis, but this is only one possible means of quantifying sampling uncertainty. It is possible that in many cases the levels of contamination passing the sampler on out-loading are essentially random, negating the value of variographic quantitation of

  20. Methodology significantly affects genome size estimates: quantitative evidence using bryophytes.

    PubMed

    Bainard, Jillian D; Fazekas, Aron J; Newmaster, Steven G

    2010-08-01

    Flow cytometry (FCM) is commonly used to determine plant genome size estimates. Methodology has improved and changed during the past three decades, and researchers are encouraged to optimize protocols for their specific application. However, this step is typically omitted or undescribed in the current plant genome size literature, and this omission could have serious consequences for the genome size estimates obtained. Using four bryophyte species (Brachythecium velutinum, Fissidens taxifolius, Hedwigia ciliata, and Thuidium minutulum), three methodological approaches to the use of FCM in plant genome size estimation were tested. These included nine different buffers (Baranyi's, de Laat's, Galbraith's, General Purpose, LB01, MgSO(4), Otto's, Tris.MgCl(2), and Woody Plant), seven propidium iodide (PI) staining periods (5, 10, 15, 20, 45, 60, and 120 min), and six PI concentrations (10, 25, 50, 100, 150, and 200 microg ml(-1)). Buffer, staining period and staining concentration all had a statistically significant effect (P = 0.05) on the genome size estimates obtained for all four species. Buffer choice and PI concentration had the greatest effect, altering the 1C-values by as much as 8% and 14%, respectively. As well, the quality of the data varied with the different methodology used. Using the methodology determined to be the most accurate in this study (LB01 buffer and PI staining for 20 min at 150 microg ml(-1)), three new genome size estimates were obtained: B. velutinum: 0.46 pg, H. ciliata: 0.30 pg, and T. minutulum: 0.46 pg. While the peak quality of flow cytometry histograms is important, researchers must consider that changes in methodology can also affect the relative peak positions and therefore the genome size estimates obtained for plants using FCM.

  1. Improved dose-volume histogram estimates for radiopharmaceutical therapy by optimizing quantitative SPECT reconstruction parameters

    NASA Astrophysics Data System (ADS)

    Cheng, Lishui; Hobbs, Robert F.; Segars, Paul W.; Sgouros, George; Frey, Eric C.

    2013-06-01

    In radiopharmaceutical therapy, an understanding of the dose distribution in normal and target tissues is important for optimizing treatment. Three-dimensional (3D) dosimetry takes into account patient anatomy and the nonuniform uptake of radiopharmaceuticals in tissues. Dose-volume histograms (DVHs) provide a useful summary representation of the 3D dose distribution and have been widely used for external beam treatment planning. Reliable 3D dosimetry requires an accurate 3D radioactivity distribution as the input. However, activity distribution estimates from SPECT are corrupted by noise and partial volume effects (PVEs). In this work, we systematically investigated OS-EM based quantitative SPECT (QSPECT) image reconstruction in terms of its effect on DVHs estimates. A modified 3D NURBS-based Cardiac-Torso (NCAT) phantom that incorporated a non-uniform kidney model and clinically realistic organ activities and biokinetics was used. Projections were generated using a Monte Carlo (MC) simulation; noise effects were studied using 50 noise realizations with clinical count levels. Activity images were reconstructed using QSPECT with compensation for attenuation, scatter and collimator-detector response (CDR). Dose rate distributions were estimated by convolution of the activity image with a voxel S kernel. Cumulative DVHs were calculated from the phantom and QSPECT images and compared both qualitatively and quantitatively. We found that noise, PVEs, and ringing artifacts due to CDR compensation all degraded histogram estimates. Low-pass filtering and early termination of the iterative process were needed to reduce the effects of noise and ringing artifacts on DVHs, but resulted in increased degradations due to PVEs. Large objects with few features, such as the liver, had more accurate histogram estimates and required fewer iterations and more smoothing for optimal results. Smaller objects with fine details, such as the kidneys, required more iterations and less

  2. Quantitative Method of Measuring Metastatic Activity

    NASA Technical Reports Server (NTRS)

    Morrison, Dennis R. (Inventor)

    1999-01-01

    The metastatic potential of tumors can be evaluated by the quantitative detection of urokinase and DNA. The cell sample selected for examination is analyzed for the presence of high levels of urokinase and abnormal DNA using analytical flow cytometry and digital image analysis. Other factors such as membrane associated uroldnase, increased DNA synthesis rates and certain receptors can be used in the method for detection of potentially invasive tumors.

  3. Quantitative estimates of precision for molecular isotopic measurements.

    PubMed

    Jasper, J P

    2001-01-01

    At least three methods of calculating the random errors or variance of molecular isotopic data are presently in use. The major components of variance are differentiated and quantified here into least three to four individual components. The measurement of error of the analyte relative to a working (whether an internal or an external) standard is quantified via the statistical pooled estimate of error. A statistical method for calculating the total variance associated with the difference of two individual isotopic compositions from two isotope laboratories is given, including the variances of the laboratory (secondary) and working standards, as well as those of the analytes. An abbreviated method for estimation of of error typical for chromatographic/isotope mass spectrometric methods is also presented.

  4. Quantitative estimation of source complexity in tsunami-source inversion

    NASA Astrophysics Data System (ADS)

    Dettmer, Jan; Cummins, Phil R.; Hawkins, Rhys; Jakir Hossen, M.

    2016-04-01

    This work analyses tsunami waveforms to infer the spatiotemporal evolution of sea-surface displacement (the tsunami source) caused by earthquakes or other sources. Since the method considers sea-surface displacement directly, no assumptions about the fault or seafloor deformation are required. While this approach has no ability to study seismic aspects of rupture, it greatly simplifies the tsunami source estimation, making it much less dependent on subjective fault and deformation assumptions. This results in a more accurate sea-surface displacement evolution in the source region. The spatial discretization is by wavelet decomposition represented by a trans-D Bayesian tree structure. Wavelet coefficients are sampled by a reversible jump algorithm and additional coefficients are only included when required by the data. Therefore, source complexity is consistent with data information (parsimonious) and the method can adapt locally in both time and space. Since the source complexity is unknown and locally adapts, no regularization is required, resulting in more meaningful displacement magnitudes. By estimating displacement uncertainties in a Bayesian framework we can study the effect of parametrization choice on the source estimate. Uncertainty arises from observation errors and limitations in the parametrization to fully explain the observations. As a result, parametrization choice is closely related to uncertainty estimation and profoundly affects inversion results. Therefore, parametrization selection should be included in the inference process. Our inversion method is based on Bayesian model selection, a process which includes the choice of parametrization in the inference process and makes it data driven. A trans-dimensional (trans-D) model for the spatio-temporal discretization is applied here to include model selection naturally and efficiently in the inference by sampling probabilistically over parameterizations. The trans-D process results in better

  5. A Quantitative Method for Estimating Probable Public Costs of Hurricanes.

    PubMed

    BOSWELL; DEYLE; SMITH; BAKER

    1999-04-01

    / A method is presented for estimating probable public costs resulting from damage caused by hurricanes, measured as local government expenditures approved for reimbursement under the Stafford Act Section 406 Public Assistance Program. The method employs a multivariate model developed through multiple regression analysis of an array of independent variables that measure meteorological, socioeconomic, and physical conditions related to the landfall of hurricanes within a local government jurisdiction. From the regression analysis we chose a log-log (base 10) model that explains 74% of the variance in the expenditure data using population and wind speed as predictors. We illustrate application of the method for a local jurisdiction-Lee County, Florida, USA. The results show that potential public costs range from $4.7 million for a category 1 hurricane with winds of 137 kilometers per hour (85 miles per hour) to $130 million for a category 5 hurricane with winds of 265 kilometers per hour (165 miles per hour). Based on these figures, we estimate expected annual public costs of $2.3 million. These cost estimates: (1) provide useful guidance for anticipating the magnitude of the federal, state, and local expenditures that would be required for the array of possible hurricanes that could affect that jurisdiction; (2) allow policy makers to assess the implications of alternative federal and state policies for providing public assistance to jurisdictions that experience hurricane damage; and (3) provide information needed to develop a contingency fund or other financial mechanism for assuring that the community has sufficient funds available to meet its obligations. KEY WORDS: Hurricane; Public costs; Local government; Disaster recovery; Disaster response; Florida; Stafford Act

  6. Active contour approach for accurate quantitative airway analysis

    NASA Astrophysics Data System (ADS)

    Odry, Benjamin L.; Kiraly, Atilla P.; Slabaugh, Greg G.; Novak, Carol L.; Naidich, David P.; Lerallut, Jean-Francois

    2008-03-01

    Chronic airway disease causes structural changes in the lungs including peribronchial thickening and airway dilatation. Multi-detector computed tomography (CT) yields detailed near-isotropic images of the lungs, and thus the potential to obtain quantitative measurements of lumen diameter and airway wall thickness. Such measurements would allow standardized assessment, and physicians to diagnose and locate airway abnormalities, adapt treatment, and monitor progress over time. However, due to the sheer number of airways per patient, systematic analysis is infeasible in routine clinical practice without automation. We have developed an automated and real-time method based on active contours to estimate both airway lumen and wall dimensions; the method does not require manual contour initialization but only a starting point on the targeted airway. While the lumen contour segmentation is purely region-based, the estimation of the outer diameter considers the inner wall segmentation as well as local intensity variation, in order anticipate the presence of nearby arteries and exclude them. These properties make the method more robust than the Full-Width Half Maximum (FWHM) approach. Results are demonstrated on a phantom dataset with known dimensions and on a human dataset where the automated measurements are compared against two human operators. The average error on the phantom measurements was 0.10mm and 0.14mm for inner and outer diameters, showing sub-voxel accuracy. Similarly, the mean variation from the average manual measurement was 0.14mm and 0.18mm for inner and outer diameters respectively.

  7. Possibility of quantitative estimation of blood cell forms by the spatial-frequency spectrum analysis

    NASA Astrophysics Data System (ADS)

    Spiridonov, Igor N.; Safonova, Larisa P.; Samorodov, Andrey V.

    2000-05-01

    At present in hematology there are no quantitative estimates of such important for the cell classification parameters: cell form and nuclear form. Due to the absence of the correlation between morphological parameters and parameters measured by hemoanalyzers, both flow cytometers and computer recognition systems, do not provide the completeness of the clinical blood analysis. Analysis of the spatial-frequency spectra of blood samples (smears and liquid probes) permit the estimate the forms quantitatively. On the results of theoretical and experimental researches carried out an algorithm of the form quantitative estimation by means of SFS parameters has been created. The criteria of the quality of these estimates have been proposed. A test bench based on the coherent optical and digital processors. The received results could be applied for the automated classification of ether normal or pathological blood cells in the standard blood smears.

  8. "Help Wanted, Inquire Within": Estimation. Activities and Thoughts That Emphasize Dealing Sensibly with Numbers through the Processes of Estimation. (Grades 1-6). Title I Elementary Mathematics Program.

    ERIC Educational Resources Information Center

    Gronert, Joie; Marshall, Sally

    Developed for elementary teachers, this activity unit is designed to teach students the importance of estimation in developing quantitative thinking. Nine ways in which estimation is useful to students are listed, and five general guidelines are offered to the teacher for planning estimation activities. Specific guidelines are provided for…

  9. Comparison of blood flow models and acquisitions for quantitative myocardial perfusion estimation from dynamic CT.

    PubMed

    Bindschadler, Michael; Modgil, Dimple; Branch, Kelley R; La Riviere, Patrick J; Alessio, Adam M

    2014-04-01

    Myocardial blood flow (MBF) can be estimated from dynamic contrast enhanced (DCE) cardiac CT acquisitions, leading to quantitative assessment of regional perfusion. The need for low radiation dose and the lack of consensus on MBF estimation methods motivates this study to refine the selection of acquisition protocols and models for CT-derived MBF. DCE cardiac CT acquisitions were simulated for a range of flow states (MBF = 0.5, 1, 2, 3 ml (min g)(-1), cardiac output = 3, 5, 8 L min(-1)). Patient kinetics were generated by a mathematical model of iodine exchange incorporating numerous physiological features including heterogenenous microvascular flow, permeability and capillary contrast gradients. CT acquisitions were simulated for multiple realizations of realistic x-ray flux levels. CT acquisitions that reduce radiation exposure were implemented by varying both temporal sampling (1, 2, and 3 s sampling intervals) and tube currents (140, 70, and 25 mAs). For all acquisitions, we compared three quantitative MBF estimation methods (two-compartment model, an axially-distributed model, and the adiabatic approximation to the tissue homogeneous model) and a qualitative slope-based method. In total, over 11 000 time attenuation curves were used to evaluate MBF estimation in multiple patient and imaging scenarios. After iodine-based beam hardening correction, the slope method consistently underestimated flow by on average 47.5% and the quantitative models provided estimates with less than 6.5% average bias and increasing variance with increasing dose reductions. The three quantitative models performed equally well, offering estimates with essentially identical root mean squared error (RMSE) for matched acquisitions. MBF estimates using the qualitative slope method were inferior in terms of bias and RMSE compared to the quantitative methods. MBF estimate error was equal at matched dose reductions for all quantitative methods and range of techniques evaluated. This

  10. Comparison of blood flow models and acquisitions for quantitative myocardial perfusion estimation from dynamic CT

    NASA Astrophysics Data System (ADS)

    Bindschadler, Michael; Modgil, Dimple; Branch, Kelley R.; La Riviere, Patrick J.; Alessio, Adam M.

    2014-04-01

    Myocardial blood flow (MBF) can be estimated from dynamic contrast enhanced (DCE) cardiac CT acquisitions, leading to quantitative assessment of regional perfusion. The need for low radiation dose and the lack of consensus on MBF estimation methods motivates this study to refine the selection of acquisition protocols and models for CT-derived MBF. DCE cardiac CT acquisitions were simulated for a range of flow states (MBF = 0.5, 1, 2, 3 ml (min g)-1, cardiac output = 3, 5, 8 L min-1). Patient kinetics were generated by a mathematical model of iodine exchange incorporating numerous physiological features including heterogenenous microvascular flow, permeability and capillary contrast gradients. CT acquisitions were simulated for multiple realizations of realistic x-ray flux levels. CT acquisitions that reduce radiation exposure were implemented by varying both temporal sampling (1, 2, and 3 s sampling intervals) and tube currents (140, 70, and 25 mAs). For all acquisitions, we compared three quantitative MBF estimation methods (two-compartment model, an axially-distributed model, and the adiabatic approximation to the tissue homogeneous model) and a qualitative slope-based method. In total, over 11 000 time attenuation curves were used to evaluate MBF estimation in multiple patient and imaging scenarios. After iodine-based beam hardening correction, the slope method consistently underestimated flow by on average 47.5% and the quantitative models provided estimates with less than 6.5% average bias and increasing variance with increasing dose reductions. The three quantitative models performed equally well, offering estimates with essentially identical root mean squared error (RMSE) for matched acquisitions. MBF estimates using the qualitative slope method were inferior in terms of bias and RMSE compared to the quantitative methods. MBF estimate error was equal at matched dose reductions for all quantitative methods and range of techniques evaluated. This suggests that

  11. Accurate and quantitative polarization-sensitive OCT by unbiased birefringence estimator with noise-stochastic correction

    NASA Astrophysics Data System (ADS)

    Kasaragod, Deepa; Sugiyama, Satoshi; Ikuno, Yasushi; Alonso-Caneiro, David; Yamanari, Masahiro; Fukuda, Shinichi; Oshika, Tetsuro; Hong, Young-Joo; Li, En; Makita, Shuichi; Miura, Masahiro; Yasuno, Yoshiaki

    2016-03-01

    Polarization sensitive optical coherence tomography (PS-OCT) is a functional extension of OCT that contrasts the polarization properties of tissues. It has been applied to ophthalmology, cardiology, etc. Proper quantitative imaging is required for a widespread clinical utility. However, the conventional method of averaging to improve the signal to noise ratio (SNR) and the contrast of the phase retardation (or birefringence) images introduce a noise bias offset from the true value. This bias reduces the effectiveness of birefringence contrast for a quantitative study. Although coherent averaging of Jones matrix tomography has been widely utilized and has improved the image quality, the fundamental limitation of nonlinear dependency of phase retardation and birefringence to the SNR was not overcome. So the birefringence obtained by PS-OCT was still not accurate for a quantitative imaging. The nonlinear effect of SNR to phase retardation and birefringence measurement was previously formulated in detail for a Jones matrix OCT (JM-OCT) [1]. Based on this, we had developed a maximum a-posteriori (MAP) estimator and quantitative birefringence imaging was demonstrated [2]. However, this first version of estimator had a theoretical shortcoming. It did not take into account the stochastic nature of SNR of OCT signal. In this paper, we present an improved version of the MAP estimator which takes into account the stochastic property of SNR. This estimator uses a probability distribution function (PDF) of true local retardation, which is proportional to birefringence, under a specific set of measurements of the birefringence and SNR. The PDF was pre-computed by a Monte-Carlo (MC) simulation based on the mathematical model of JM-OCT before the measurement. A comparison between this new MAP estimator, our previous MAP estimator [2], and the standard mean estimator is presented. The comparisons are performed both by numerical simulation and in vivo measurements of anterior and

  12. Models of Quantitative Estimations: Rule-Based and Exemplar-Based Processes Compared

    ERIC Educational Resources Information Center

    von Helversen, Bettina; Rieskamp, Jorg

    2009-01-01

    The cognitive processes underlying quantitative estimations vary. Past research has identified task-contingent changes between rule-based and exemplar-based processes (P. Juslin, L. Karlsson, & H. Olsson, 2008). B. von Helversen and J. Rieskamp (2008), however, proposed a simple rule-based model--the mapping model--that outperformed the exemplar…

  13. A QUANTITATIVE APPROACH FOR ESTIMATING EXPOSURE TO PESTICIDES IN THE AGRICULTURAL HEALTH STUDY

    EPA Science Inventory

    We developed a quantitative method to estimate chemical-specific pesticide exposures in a large prospective cohort study of over 58,000 pesticide applicators in North Carolina and Iowa. An enrollment questionnaire was administered to applicators to collect basic time- and inten...

  14. Prediction of activated carbon adsorption capacities for organic vapors using quantitative structure-activity relationship methods

    SciTech Connect

    Nirmalakhandan, N.N. ); Speece, R.E. )

    1993-08-01

    Quantitative structure-activity relationship (QSAR) methods were used to develop models to estimate and predict activated carbon adsorption capacities for organic vapors. Literature isothermal data from two sources for 22 organic contaminants on six different carbons were merged to form a training set of 75 data points. Two different QSAR approaches were evaluated: the molecular connectivity approach and the linear solvation energy relationship approach. The QSAR model developed in this study using the molecular connectivity approach was able to fit the experimental data with r = 0.96 and standard error of 0.09. The utility of the model was demonstrated by using predicted k values to calculate adsorption capacities of 12 chemicals on two different carbons and comparing them with experimentally determined values. 9 refs., 1 fig., 3 tabs.

  15. Quantitative indices of autophagy activity from minimal models

    PubMed Central

    2014-01-01

    Background A number of cellular- and molecular-level studies of autophagy assessment have been carried out with the help of various biochemical and morphological indices. Still there exists ambiguity for the assessment of the autophagy status and of the causal relationship between autophagy and related cellular changes. To circumvent such difficulties, we probe new quantitative indices of autophagy which are important for defining autophagy activation and further assessing its roles associated with different physiopathological states. Methods Our approach is based on the minimal autophagy model that allows us to understand underlying dynamics of autophagy from biological experiments. Specifically, based on the model, we reconstruct the experimental context-specific autophagy profiles from the target autophagy system, and two quantitative indices are defined from the model-driven profiles. The indices are then applied to the simulation-based analysis, for the specific and quantitative interpretation of the system. Results Two quantitative indices measuring autophagy activities in the induction of sequestration fluxes and in the selective degradation are proposed, based on the model-driven autophagy profiles such as the time evolution of autophagy fluxes, levels of autophagosomes/autolysosomes, and corresponding cellular changes. Further, with the help of the indices, those biological experiments of the target autophagy system have been successfully analyzed, implying that the indices are useful not only for defining autophagy activation but also for assessing its role in a specific and quantitative manner. Conclusions Such quantitative autophagy indices in conjunction with the computer-aided analysis should provide new opportunities to characterize the causal relationship between autophagy activity and the corresponding cellular change, based on the system-level understanding of the autophagic process at good time resolution, complementing the current in vivo and in

  16. On sweat analysis for quantitative estimation of dehydration during physical exercise.

    PubMed

    Ring, Matthias; Lohmueller, Clemens; Rauh, Manfred; Eskofier, Bjoern M

    2015-08-01

    Quantitative estimation of water loss during physical exercise is of importance because dehydration can impair both muscular strength and aerobic endurance. A physiological indicator for deficit of total body water (TBW) might be the concentration of electrolytes in sweat. It has been shown that concentrations differ after physical exercise depending on whether water loss was replaced by fluid intake or not. However, to the best of our knowledge, this fact has not been examined for its potential to quantitatively estimate TBW loss. Therefore, we conducted a study in which sweat samples were collected continuously during two hours of physical exercise without fluid intake. A statistical analysis of these sweat samples revealed significant correlations between chloride concentration in sweat and TBW loss (r = 0.41, p <; 0.01), and between sweat osmolality and TBW loss (r = 0.43, p <; 0.01). A quantitative estimation of TBW loss resulted in a mean absolute error of 0.49 l per estimation. Although the precision has to be improved for practical applications, the present results suggest that TBW loss estimation could be realizable using sweat samples.

  17. A method for estimating and removing streaking artifacts in quantitative susceptibility mapping.

    PubMed

    Li, Wei; Wang, Nian; Yu, Fang; Han, Hui; Cao, Wei; Romero, Rebecca; Tantiwongkosi, Bundhit; Duong, Timothy Q; Liu, Chunlei

    2015-03-01

    Quantitative susceptibility mapping (QSM) is a novel MRI method for quantifying tissue magnetic property. In the brain, it reflects the molecular composition and microstructure of the local tissue. However, susceptibility maps reconstructed from single-orientation data still suffer from streaking artifacts which obscure structural details and small lesions. We propose and have developed a general method for estimating streaking artifacts and subtracting them from susceptibility maps. Specifically, this method uses a sparse linear equation and least-squares (LSQR)-algorithm-based method to derive an initial estimation of magnetic susceptibility, a fast quantitative susceptibility mapping method to estimate the susceptibility boundaries, and an iterative approach to estimate the susceptibility artifact from ill-conditioned k-space regions only. With a fixed set of parameters for the initial susceptibility estimation and subsequent streaking artifact estimation and removal, the method provides an unbiased estimate of tissue susceptibility with negligible streaking artifacts, as compared to multi-orientation QSM reconstruction. This method allows for improved delineation of white matter lesions in patients with multiple sclerosis and small structures of the human brain with excellent anatomical details. The proposed methodology can be extended to other existing QSM algorithms.

  18. Quantitative structure-activity relationships for fluoroelastomer/chlorofluorocarbon systems

    SciTech Connect

    Paciorek, K.J.L.; Masuda, S.R.; Nakahara, J.H. ); Snyder, C.E. Jr.; Warner, W.M. )

    1991-12-01

    This paper reports on swell, tensile, and modulus data that were determined for a fluoroelastomer after exposure to a series of chlorofluorocarbon model fluids. Quantitative structure-activity relationships (QSAR) were developed for the swell as a function of the number of carbons and chlorines and for tensile strength as a function of carbon number and chlorine positions in the chlorofluorocarbons.

  19. Quantitative Risk reduction estimation Tool For Control Systems, Suggested Approach and Research Needs

    SciTech Connect

    Miles McQueen; Wayne Boyer; Mark Flynn; Sam Alessi

    2006-03-01

    For the past year we have applied a variety of risk assessment technologies to evaluate the risk to critical infrastructure from cyber attacks on control systems. More recently, we identified the need for a stand alone control system risk reduction estimation tool to provide owners and operators of control systems with a more useable, reliable, and credible method for managing the risks from cyber attack. Risk is defined as the probability of a successful attack times the value of the resulting loss, typically measured in lives and dollars. Qualitative and ad hoc techniques for measuring risk do not provide sufficient support for cost benefit analyses associated with cyber security mitigation actions. To address the need for better quantitative risk reduction models we surveyed previous quantitative risk assessment research; evaluated currently available tools; developed new quantitative techniques [17] [18]; implemented a prototype analysis tool to demonstrate how such a tool might be used; used the prototype to test a variety of underlying risk calculational engines (e.g. attack tree, attack graph); and identified technical and research needs. We concluded that significant gaps still exist and difficult research problems remain for quantitatively assessing the risk to control system components and networks, but that a useable quantitative risk reduction estimation tool is not beyond reach.

  20. Estimation of avidin activity by two methods.

    PubMed

    Borza, B; Marcheş, F; Repanovici, R; Burducea, O; Popa, L M

    1991-01-01

    The biological activity of avidin was estimated by two different methods. The spectrophotometric method used the avidin titration with biotin in the presence of 4 hydroxiazobenzen-2'carboxilic acid as indicator. In the radioisotopic determination the titration with tritiated biotin was accomplished. Both methods led to the same results, but the spectrophotometric one is less avidin expensive and more rapid, being more convenient.

  1. New estimation method for highly sensitive quantitation of human immunodeficiency virus type 1 DNA and its application.

    PubMed

    Nagai, Hiromi; Wada, Kaoru; Morishita, Takayuki; Utsumi, Makoto; Nishiyama, Yukihiro; Kaneda, Tsuguhiro

    2005-03-01

    A new estimation method for quantitation of HIV-1 DNA was established by introducing a pre-quantitation polymerase chain reaction (PCR) before conventional real-time PCR. Two alternative methods for estimating the copy number can be used: the first method utilizes the rate of beta2-microglobulin (beta2M) gene amplification during the pre-quantitation PCR, and the second utilizes a calibration curve of the crossing point of real-time PCR versus the standard HIV-1-plasmid concentration. These methods could be used to reproducibly and accurately detect a provirus density down to five copies/10(6) cells (for methods 1 and 2, inter-assay CV=17 and 16% and accuracy=81 and 92%, respectively). The levels of HIV-1 DNA could be measurable using as little as 100 microl of whole blood or buffy coat cells. Using a combination of a conventional and highly sensitive methods, we found that the amount of HIV-1 DNA ranged from 2 to 5960 copies/10(6) cells (median of 830 copies/10(6) cells) in CD4-positive T lymphocytes isolated from 30 patients responding well to highly active antiretroviral therapy (HAART). Thus, the highly sensitive method developed in this study allows estimation of the HIV-1 reservoirs in peripheral CD4-positive T lymphocytes of patients responding well to HAART. PMID:15664064

  2. Estimating bioerosion rate on fossil corals: a quantitative approach from Oligocene reefs (NW Italy)

    NASA Astrophysics Data System (ADS)

    Silvestri, Giulia

    2010-05-01

    Bioerosion of coral reefs, especially when related to the activity of macroborers, is considered to be one of the major processes influencing framework development in present-day reefs. Macroboring communities affecting both living and dead corals are widely distributed also in the fossil record and their role is supposed to be analogously important in determining flourishing vs demise of coral bioconstructions. Nevertheless, many aspects concerning environmental factors controlling the incidence of bioerosion, shifting in composition of macroboring communities and estimation of bioerosion rate in different contexts are still poorly documented and understood. This study presents an attempt to quantify bioerosion rate on reef limestones characteristic of some Oligocene outcrops of the Tertiary Piedmont Basin (NW Italy) and deposited under terrigenous sedimentation within prodelta and delta fan systems. Branching coral rubble-dominated facies have been recognized as prevailing in this context. Depositional patterns, textures, and the generally low incidence of taphonomic features, such as fragmentation and abrasion, suggest relatively quiet waters where coral remains were deposited almost in situ. Thus taphonomic signatures occurring on corals can be reliably used to reconstruct environmental parameters affecting these particular branching coral assemblages during their life and to compare them with those typical of classical clear-water reefs. Bioerosion is sparsely distributed within coral facies and consists of a limited suite of traces, mostly referred to clionid sponges and polychaete and sipunculid worms. The incidence of boring bivalves seems to be generally lower. Together with semi-quantitative analysis of bioerosion rate along vertical logs and horizontal levels, two quantitative methods have been assessed and compared. These consist in the elaboration of high resolution scanned thin sections through software for image analysis (Photoshop CS3) and point

  3. A new method to estimate quantitatively seminal vesicle and prostate gland contributions to ejaculate

    PubMed Central

    Ndovi, Themba T; Parsons, Teresa; Choi, Leena; Caffo, Brian; Rohde, Charles; Hendrix, Craig W

    2007-01-01

    Aims We sought to optimize a quantitative noninvasive method to determine the concentration in their glands of origin of biochemical markers of compartments of the male genital tract as the first step towards validation of a novel method for estimation of drug concentrations in these male genital tract compartments. Methods Sixty-eight men participated. We compared four collection devices to split ejaculate into fractions. Fractions were assayed for fructose and prostate specific antigen (PSA) as unique markers of the seminal vesicle and prostate, respectively. Seminal vesicle fructose and prostatic PSA were estimated using a linear regression method, based on fructose-PSA axis intercepts, and compared with an older method which solves a simultaneous series of equations. Results A five-compartment collection device performed best with mean (95% confidence interval) PSA vs. fructose r2 of 0.84 (0.71, 0.98, P < 0.001). Using resampling simulations, glandular PSA and fructose estimates were highly variable and often implausible when using only two fractions. Using our method, the prostate contributed 37–44% to the whole ejaculate and the seminal vesicle contributed 55–61%. The novel regression method was highly correlated (r2 ≥ 0.98) with older methods. Conclusions We developed a noninvasive quantitative method of male genital tract biochemical marker estimation using a five-compartment tray to collect three to five ejaculate fractions. Our novel regression method is quantitative and more fully developed than older methods. This noninvasive method for determining glandular marker concentrations should be useful to provide quantitative estimates of drug concentrations in these glands. PMID:17076697

  4. Estimating quantitative genetic parameters in wild populations: a comparison of pedigree and genomic approaches

    PubMed Central

    Bérénos, Camillo; Ellis, Philip A; Pilkington, Jill G; Pemberton, Josephine M

    2014-01-01

    The estimation of quantitative genetic parameters in wild populations is generally limited by the accuracy and completeness of the available pedigree information. Using relatedness at genomewide markers can potentially remove this limitation and lead to less biased and more precise estimates. We estimated heritability, maternal genetic effects and genetic correlations for body size traits in an unmanaged long-term study population of Soay sheep on St Kilda using three increasingly complete and accurate estimates of relatedness: (i) Pedigree 1, using observation-derived maternal links and microsatellite-derived paternal links; (ii) Pedigree 2, using SNP-derived assignment of both maternity and paternity; and (iii) whole-genome relatedness at 37 037 autosomal SNPs. In initial analyses, heritability estimates were strikingly similar for all three methods, while standard errors were systematically lower in analyses based on Pedigree 2 and genomic relatedness. Genetic correlations were generally strong, differed little between the three estimates of relatedness and the standard errors declined only very slightly with improved relatedness information. When partitioning maternal effects into separate genetic and environmental components, maternal genetic effects found in juvenile traits increased substantially across the three relatedness estimates. Heritability declined compared to parallel models where only a maternal environment effect was fitted, suggesting that maternal genetic effects are confounded with direct genetic effects and that more accurate estimates of relatedness were better able to separate maternal genetic effects from direct genetic effects. We found that the heritability captured by SNP markers asymptoted at about half the SNPs available, suggesting that denser marker panels are not necessarily required for precise and unbiased heritability estimates. Finally, we present guidelines for the use of genomic relatedness in future quantitative genetics

  5. Estimation of glacial outburst floods in Himalayan watersheds by means of quantitative modelling

    NASA Astrophysics Data System (ADS)

    Brauner, M.; Agner, P.; Vogl, A.; Leber, D.; Haeusler, H.; Wangda, D.

    2003-04-01

    In the Himalayas intense glacier retreat rates and at quickly developing settlement activity in the downstream valleys, result in dramatically increasing Glacier Lake Outburst risk. As settlement activity concentrates on broad and productive valley areas, being typically 10 to 70 kilometres downstream of the flood source, hazard awareness and preparedness is limited. Therefore application of quantitative assessment methodology is crucial in order to delineate flood prone areas and develop hazard preparedness concepts by means of scenario modelling. For dam breach back-calculation the 1D-simulation tool BREACH is utilised. Generally the initiation by surge waves and the broad sediment size spectrum of tills are difficult to implement. Therefore a tool with long application history has been chosen. The flood propagation is simulated with the 2D-hydraulic simulation model FLO2D which enables water flood and sediment load routing. In three Himalayan watersheds (Pho Chhu valley, Bhutan; Tam Pokhari valley, Nepal) recent Glacier Lake Outbursts (each with more than 20 mill m3 volume) and consecutive floods are simulated and calibrated by means of multi-time morpho-logical information, high water marks, geomorphologic interpretation and eye witness consultation. These calculations show that for these events the dam breach process was slow (within 0.75 to 3 hours), with low flood hydrographs. The flood propagation was governed by a sequence of low-sloping, depositional channel sections, and steep channel section with intense lateral sediment mobilisation and temporary blockage. This resulted in a positive feedback and prolonged the flood. By means of sensitivity analysis the influence of morphological changes during the events and the imporance of the dam breach process to the whole is estimated. It can be shown, that the accuracy of the high water limit is governed by the following processes: sediment mobilisation, breaching process, water volume, morphological changes

  6. Estimating the effect of SNP genotype on quantitative traits from pooled DNA samples

    PubMed Central

    2012-01-01

    Background Studies to detect associations between DNA markers and traits of interest in humans and livestock benefit from increasing the number of individuals genotyped. Performing association studies on pooled DNA samples can provide greater power for a given cost. For quantitative traits, the effect of an SNP is measured in the units of the trait and here we propose and demonstrate a method to estimate SNP effects on quantitative traits from pooled DNA data. Methods To obtain estimates of SNP effects from pooled DNA samples, we used logistic regression of estimated allele frequencies in pools on phenotype. The method was tested on a simulated dataset, and a beef cattle dataset using a model that included principal components from a genomic correlation matrix derived from the allele frequencies estimated from the pooled samples. The performance of the obtained estimates was evaluated by comparison with estimates obtained using regression of phenotype on genotype from individual samples of DNA. Results For the simulated data, the estimates of SNP effects from pooled DNA are similar but asymptotically different to those from individual DNA data. Error in estimating allele frequencies had a large effect on the accuracy of estimated SNP effects. For the beef cattle dataset, the principal components of the genomic correlation matrix from pooled DNA were consistent with known breed groups, and could be used to account for population stratification. Correctly modeling the contemporary group structure was essential to achieve estimates similar to those from individual DNA data, and pooling DNA from individuals within groups was superior to pooling DNA across groups. For a fixed number of assays, pooled DNA samples produced results that were more correlated with results from individual genotyping data than were results from one random individual assayed from each pool. Conclusions Use of logistic regression of allele frequency on phenotype makes it possible to estimate SNP

  7. Estimation methods for monthly humidity from dynamical downscaling data for quantitative assessments of climate change impacts

    NASA Astrophysics Data System (ADS)

    Ueyama, Hideki

    2012-07-01

    Methods are proposed to estimate the monthly relative humidity and wet bulb temperature based on observations from a dynamical downscaling coupled general circulation model with a regional climate model (RCM) for a quantitative assessment of climate change impacts. The water vapor pressure estimation model developed was a regression model with a monthly saturated water vapor pressure that used minimum air temperature as a variable. The monthly minimum air temperature correction model for RCM bias was developed by stepwise multiple regression analysis using the difference in monthly minimum air temperatures between observations and RCM output as a dependent variable and geographic factors as independent variables. The wet bulb temperature was estimated using the estimated water vapor pressure, air temperature, and atmospheric pressure at ground level both corrected for RCM bias. Root mean square errors of the data decreased considerably in August.

  8. Quantitative Estimation of Trace Chemicals in Industrial Effluents with the Sticklet Transform Method

    SciTech Connect

    Mehta, N C; Scharlemann, E T; Stevens, C G

    2001-04-02

    Application of a novel transform operator, the Sticklet transform, to the quantitative estimation of trace chemicals in industrial effluent plumes is reported. The sticklet transform is a superset of the well-known derivative operator and the Haar wavelet, and is characterized by independently adjustable lobe width and separation. Computer simulations demonstrate that they can make accurate and robust concentration estimates of multiple chemical species in industrial effluent plumes in the presence of strong clutter background, interferent chemicals and random noise. In this paper they address the application of the sticklet transform in estimating chemical concentrations in effluent plumes in the presence of atmospheric transmission effects. They show that this transform retains the ability to yield accurate estimates using on-plume/off-plume measurements that represent atmospheric differentials up to 10% of the full atmospheric attenuation.

  9. A novel algorithm for QSAR (quantitative structure-activity relationships)

    SciTech Connect

    Carter, S. ); Nikolic, S.; Trinajstic, N. )

    1989-01-01

    A novel approach to quantitative structure-activity relationships (QSAR) is proposed. It is based on the molecular descriptor named the stereo-identification (SID) number. The applicability of this approach to QSAR studies is tested on aquatic toxicities of phenols against fathead minnows (Phimephales promelas). Our approach reproduced successfully the bioactivities of phenols and is superior to the Hall-Kier model based on Randic's connectivity index.

  10. (Quantitative structure-activity relationships in environmental toxicology)

    SciTech Connect

    Turner, J.E.

    1990-10-04

    The traveler attended the Fourth International Workshop on QSAR (Quantitative Structure-Activity Relationships) in Environmental Toxicology. He was an author or co-author on one platform and two poster presentations. The subject of the workshop offers a framework for analyzing and predicting the fate of chemical pollutants in organisms and the environment. QSAR is highly relevant to the ORNL program on the physicochemical characterization of chemical pollutants for health protection.

  11. Multi-voxel algorithm for quantitative bi-exponential MRI T1 estimation

    NASA Astrophysics Data System (ADS)

    Bladt, P.; Van Steenkiste, G.; Ramos-Llordén, G.; den Dekker, A. J.; Sijbers, J.

    2016-03-01

    Quantification of the spin-lattice relaxation time, T1, of tissues is important for characterization of tissues in clinical magnetic resonance imaging (MRI). In T1 mapping, T1 values are estimated from a set of T1-weighted MRI images. Due to the limited spatial resolution of the T1-weighted images, one voxel might consist of two tissues, causing partial volume effects (PVE). In conventional mono-exponential T1 estimation, these PVE result in systematic errors in the T1 map. To account for PVE, single-voxel bi-exponential estimators have been suggested. Unfortunately, in general, they suffer from low accuracy and precision. In this work, we propose a joint multi-voxel bi-exponential T1 estimator (JMBE) and compare its performance to a single-voxel bi-exponential T1 estimator (SBE). Results show that, in contrast to the SBE, and for clinically achievable single-voxel SNRs, the JMBE is accurate and efficient if four or more neighboring voxels are used in the joint estimation framework. This illustrates that, for clinically realistic SNRs, accurate results for quantitative biexponential T1 estimation are only achievable if information of neighboring voxels is incorporated.

  12. Estimators of annual probability of infection for quantitative microbial risk assessment.

    PubMed

    Karavarsamis, N; Hamilton, A J

    2010-06-01

    Four estimators of annual infection probability were compared pertinent to Quantitative Microbial Risk Analysis (QMRA). A stochastic model, the Gold Standard, was used as the benchmark. It is a product of independent daily infection probabilities which in turn are based on daily doses. An alternative and commonly-used estimator, here referred to as the Naïve, assumes a single daily infection probability from a single value of daily dose. The typical use of this estimator in stochastic QMRA involves the generation of a distribution of annual infection probabilities, but since each of these is based on a single realisation of the dose distribution, the resultant annual infection probability distribution simply represents a set of inaccurate estimates. While the medians of both distributions were within an order of magnitude for our test scenario, the 95th percentiles, which are sometimes used in QMRA as conservative estimates of risk, differed by around one order of magnitude. The other two estimators examined, the Geometric and Arithmetic, were closely related to the Naïve and use the same equation, and both proved to be poor estimators. Lastly, this paper proposes a simple adjustment to the Gold Standard equation accommodating periodic infection probabilities when the daily infection probabilities are unknown.

  13. Quantitative Structure-Antifungal Activity Relationships for cinnamate derivatives.

    PubMed

    Saavedra, Laura M; Ruiz, Diego; Romanelli, Gustavo P; Duchowicz, Pablo R

    2015-12-01

    Quantitative Structure-Activity Relationships (QSAR) are established with the aim of analyzing the fungicidal activities of a set of 27 active cinnamate derivatives. The exploration of more than a thousand of constitutional, topological, geometrical and electronic molecular descriptors, which are calculated with Dragon software, leads to predictions of the growth inhibition on Pythium sp and Corticium rolfsii fungi species, in close agreement to the experimental values extracted from the literature. A set containing 21 new structurally related cinnamate compounds is prepared. The developed QSAR models are applied to predict the unknown fungicidal activity of this set, showing that cinnamates like 38, 28 and 42 are expected to be highly active for Pythium sp, while this is also predicted for 28 and 34 in C. rolfsii. PMID:26410195

  14. Quantitative recording of physician clinical estimates, beyond a global estimate and formal joint count, in usual care: applying the scientific method, using a simple one-page worksheet.

    PubMed

    Pincus, Theodore; Bergman, Martin J

    2009-11-01

    Little attention has been directed to quantitation of clinical impressions and estimates of physicians. This article describes a one-page worksheet for completion by the physician at each patient visit. It includes a physician global estimate and estimate of change in status and four quantitative estimates for the degree of inflammation, degree of organ damage, and degree of fibromyalgia or somatization. An estimate of prognosis is recorded, with no therapy and with available therapies. All changes in medications are recorded. A template is available for a formal 42 joint count. The worksheet requires fewer than 15 seconds and has proven of considerable value in clinical care.

  15. Quantitative comparisons of in vitro assays for estrogenic activities.

    PubMed Central

    Fang, H; Tong, W; Perkins, R; Soto, A M; Prechtl, N V; Sheehan, D M

    2000-01-01

    Substances that may act as estrogens show a broad chemical structural diversity. To thoroughly address the question of possible adverse estrogenic effects, reliable methods are needed to detect and identify the chemicals of these diverse structural classes. We compared three assays--in vitro estrogen receptor competitive binding assays (ER binding assays), yeast-based reporter gene assays (yeast assays), and the MCF-7 cell proliferation assay (E-SCREEN assay)--to determine their quantitative agreement in identifying structurally diverse estrogens. We examined assay performance for relative sensitivity, detection of active/inactive chemicals, and estrogen/antiestrogen activities. In this examination, we combined individual data sets in a specific, quantitative data mining exercise. Data sets for at least 29 chemicals from five laboratories were analyzed pair-wise by X-Y plots. The ER binding assay was a good predictor for the other two assay results when the antiestrogens were excluded (r(2) is 0.78 for the yeast assays and 0.85 for the E-SCREEN assays). Additionally, the examination strongly suggests that biologic information that is not apparent from any of the individual assays can be discovered by quantitative pair-wise comparisons among assays. Antiestrogens are identified as outliers in the ER binding/yeast assay, while complete antagonists are identified in the ER binding and E-SCREEN assays. Furthermore, the presence of outliers may be explained by different mechanisms that induce an endocrine response, different impurities in different batches of chemicals, different species sensitivity, or limitations of the assay techniques. Although these assays involve different levels of biologic complexity, the major conclusion is that they generally provided consistent information in quantitatively determining estrogenic activity for the five data sets examined. The results should provide guidance for expanded data mining examinations and the selection of appropriate

  16. Quantitative estimation of the parameters for self-motion driven by difference in surface tension.

    PubMed

    Suematsu, Nobuhiko J; Sasaki, Tomohiro; Nakata, Satoshi; Kitahata, Hiroyuki

    2014-07-15

    Quantitative information on the parameters associated with self-propelled objects would enhance the potential of this research field; for example, finding a realistic way to develop a functional self-propelled object and quantitative understanding of the mechanism of self-motion. We therefore estimated five main parameters, including the driving force, of a camphor boat as a simple self-propelled object that spontaneously moves on water due to difference in surface tension. The experimental results and mathematical model indicated that the camphor boat generated a driving force of 4.2 μN, which corresponds to a difference in surface tension of 1.1 mN m(-1). The methods used in this study are not restricted to evaluate the parameters of self-motion of a camphor boat, but can be applied to other self-propelled objects driven by difference in surface tension. Thus, our investigation provides a novel method to quantitatively estimate the parameters for self-propelled objects driven by the interfacial tension difference.

  17. Estimation of undiscovered deposits in quantitative mineral resource assessments-examples from Venezuela and Puerto Rico

    USGS Publications Warehouse

    Cox, D.P.

    1993-01-01

    Quantitative mineral resource assessments used by the United States Geological Survey are based on deposit models. These assessments consist of three parts: (1) selecting appropriate deposit models and delineating on maps areas permissive for each type of deposit; (2) constructing a grade-tonnage model for each deposit model; and (3) estimating the number of undiscovered deposits of each type. In this article, I focus on the estimation of undiscovered deposits using two methods: the deposit density method and the target counting method. In the deposit density method, estimates are made by analogy with well-explored areas that are geologically similar to the study area and that contain a known density of deposits per unit area. The deposit density method is useful for regions where there is little or no data. This method was used to estimate undiscovered low-sulfide gold-quartz vein deposits in Venezuela. Estimates can also be made by counting targets such as mineral occurrences, geophysical or geochemical anomalies, or exploration "plays" and by assigning to each target a probability that it represents an undiscovered deposit that is a member of the grade-tonnage distribution. This method is useful in areas where detailed geological, geophysical, geochemical, and mineral occurrence data exist. Using this method, porphyry copper-gold deposits were estimated in Puerto Rico. ?? 1993 Oxford University Press.

  18. A quantitative structure-activity relationship model for radical scavenging activity of flavonoids.

    PubMed

    Om, A; Kim, J H

    2008-03-01

    A quantitative structure-activity relationship (QSAR) study has been carried out for a training set of 29 flavonoids to correlate and predict the 1,1-diphenyl-2-picrylhydrazyl radical scavenging activity (RSA) values obtained from published data. Genetic algorithm and multiple linear regression were employed to select the descriptors and to generate the best prediction model that relates the structural features to the RSA activities using (1) three-dimensional (3D) Dragon (TALETE srl, Milan, Italy) descriptors and (2) semi-empirical descriptor calculations. The predictivity of the models was estimated by cross-validation with the leave-one-out method. The result showed that a significant improvement of the statistical indices was obtained by deleting outliers. Based on the data for the compounds used in this study, our results suggest a QSAR model of RSA that is based on the following descriptors: 3D-Morse, WHIM, and GETAWAY. Therefore, satisfactory relationships between RSA and the semi-empirical descriptors were found, demonstrating that the energy of the highest occupied molecular orbital, total energy, and energy of heat of formation contributed more significantly than all other descriptors.

  19. The new approach of polarimetric attenuation correction for improving radar quantitative precipitation estimation(QPE)

    NASA Astrophysics Data System (ADS)

    Gu, Ji-Young; Suk, Mi-Kyung; Nam, Kyung-Yeub; Ko, Jeong-Seok; Ryzhkov, Alexander

    2016-04-01

    To obtain high-quality radar quantitative precipitation estimation data, reliable radar calibration and efficient attenuation correction are very important. Because microwave radiation at shorter wavelength experiences strong attenuation in precipitation, accounting for this attenuation is the essential work at shorter wavelength radar. In this study, the performance of different attenuation/differential attenuation correction schemes at C band is tested for two strong rain events which occurred in central Oklahoma. And also, a new attenuation correction scheme (combination of self-consistency and hot-spot concept methodology) that separates relative contributions of strong convective cells and the rest of the storm to the path-integrated total and differential attenuation is among the algorithms explored. A quantitative use of weather radar measurement such as rainfall estimation relies on the reliable attenuation correction. We examined the impact of attenuation correction on estimates of rainfall in heavy rain events by using cross-checking with S-band radar measurements which are much less affected by attenuation and compared the storm rain totals obtained from the corrected Z and KDP and rain gages in these cases. This new approach can be utilized at shorter wavelength radars efficiently. Therefore, it is very useful to Weather Radar Center of Korea Meteorological Administration preparing X-band research dual Pol radar network.

  20. Dansyl glutathione as a trapping agent for the quantitative estimation and identification of reactive metabolites.

    PubMed

    Gan, Jinping; Harper, Timothy W; Hsueh, Mei-Mann; Qu, Qinling; Humphreys, W Griffith

    2005-05-01

    A sensitive and quantitative method was developed for the estimation of reactive metabolite formation in vitro. The method utilizes reduced glutathione (GSH) labeled with a fluorescence tag as a trapping agent and fluorescent detection for quantitation. The derivatization of GSH was accomplished by reaction of oxidized glutathione (GSSG) with dansyl chloride to form dansylated GSSG. Subsequent reduction of the disulfide bond yielded dansylated GSH (dGSH). Test compounds were incubated with human liver microsomes in the presence of dGSH and NADPH, and the resulting mixtures were analyzed by HPLC coupled with a fluorescence detector and a mass spectrometer for the quantitation and mass determination of the resulting dGSH adducts. The comparative chemical reactivity of dGSH vs GSH was investigated by monitoring the reaction of each with 1-chloro-2,4-dinitrobenzene or R-(+)-pulegone after bioactivation. dGSH was found to be equivalent to GSH in chemical reactivity toward both thiol reactive molecules. dGSH did not serve as a cofactor for glutathione S-transferase (GST)-mediated conjugation of 3,4-dichloronitrobenzene in incubations with either human liver S9 fractions or a recombinant GST, GSTM1-1. Reference compounds were tested in this assay, including seven compounds that have been reported to form GSH adducts along with seven drugs that are among the most prescribed in the current U.S. market and have not been reported to form GSH adducts. dGSH adducts were detected and quantitated in incubations with all seven positive reference compounds; however, there were no dGSH adducts observed with any of the widely prescribed drugs. In comparison with existing methods, this method is sensitive, quantitative, cost effective, and easy to implement. PMID:15892584

  1. [Quantitative estimation of the dynamics of adventive flora (by the example of the Tula region)].

    PubMed

    Khorun, L V; Zakharov, V G; Sokolov, D D

    2006-01-01

    The rate of enrichment of the Tula region flora with adventive species was quantitatively estimated taking into account the changes of their degree of naturalization during the last 200 years. Numerical score of degree of the naturalization for each species was used to compile the initial database: "0", species absent from the territory; "1", ephemerophyte; "2", colonophyte; "3", epecophyte; "4", argiophyte; "?", lack of data. Non-interpolated integral index of the dynamics of adventive flora NI(t) was calculated from this database. This index displays the sum of the degrees of naturalization of all the adventive species in the flora in some particular year. The interpolation of the initial database, aimed at minimizing the influence of random factors (e.g., gaps in observations or different activity of the researchers in different years), was performed by substituting the "?" symbol by a series of intermediate values based on studies of the data for adjacent territories. Interpolated integral indices I(t) were calculated from the interpolated database. These indices were then leveled out with Morlet wavelets, in order to distinguish random spikes (lasting less than 50 years) from the analyzed signal, and thus approximate the index dynamics to the objective trend that represents the dynamics of the flora and not the rate of activity of the researchers. The dynamics of the adventive flora of the Tula region revealed with this method shows the following facts: 1) average rate of the enrichment of the adventive flora with strange species has been constant for these 200 years and amounted to 15 species per decade; 2) average rate of naturalization was relatively low and constant, amounting to 5 species per decade; 3) fluctuations of the composition and naturalization degree of the Tula region adventive flora species were not shown to be dependant directly on the changes in the territory's economic development during the last two centuries; 4) no periodicity was

  2. Background estimation methods for quantitative x-ray fluorescence analysis of gold nanoparticles in biomedical applications

    NASA Astrophysics Data System (ADS)

    Ren, Liqiang; Wu, Di; Li, Yuhua; Chen, Wei R.; Liu, Hong

    2014-02-01

    Accurate background estimation to isolate the fluorescence signals is an important issue for quantitative X-ray fluorescence (XRF) analysis of gold nanoparticles (GNPs). Though a good estimation can be obtained experimentally through acquiring the background spectrum of water solution, it inevitably leads to unnecessary second exposure in reality. Thus, several numerical methods such as trapezoidal shape estimation, interpolation by polynomial fitting and SNIP (Statistics sensitive Nonlinear Iterative Peak-Clipping) algorithm are proposed to achieve this goal. This paper aims to evaluate the estimation results calculated by these numerical methods through comparing with that acquired using the experimental way, in term of mean squared error (MSE). Four GNP/water solutions with various concentrations from 0.0% to 1.0% by weight are prepared. Then, ten spectra are acquired for each solution for further analysis, under the identical condition of using pencil beam x-ray and single spectrometer. Finally, the experimental and numerical methods are performed on these spectra within the optimally determined energy window and their statistical characteristics are analyzed and compared. These numerical background estimation methods as well as the evaluation methods can be easily extended to analyze the fluorescence signals of other nanoparticle biomarkers such as gadolinium, platinum and Barium in multiple biomedical applications.

  3. Estimation of intracellular [Ca2+] by nonlinear indicators. A quantitative analysis.

    PubMed Central

    Yue, D T; Wier, W G

    1985-01-01

    When spatial gradients of intracellular free [Ca2+] are present, intracellular calcium indicators that have a nonlinear response to [Ca2+] may yield an estimate of [Ca2+] that differs from the spatial average [Ca2+]. We present two rules that provide (a) general criteria to distinguish those classes of indicators that will yield an overestimate of spatial average [Ca2+] from those that will yield an underestimate, and (b) limits on the extent to which spatial average [Ca2+] might be over- or underestimated. These rules are used to interpret quantitatively the aequorin luminescence signals obtained from cardiac ventricular myocardium. PMID:4041543

  4. Quantitative genetic activity graphical profiles for use in chemical evaluation

    SciTech Connect

    Waters, M.D.; Stack, H.F.; Garrett, N.E.; Jackson, M.A.

    1990-12-31

    A graphic approach, terms a Genetic Activity Profile (GAP), was developed to display a matrix of data on the genetic and related effects of selected chemical agents. The profiles provide a visual overview of the quantitative (doses) and qualitative (test results) data for each chemical. Either the lowest effective dose or highest ineffective dose is recorded for each agent and bioassay. Up to 200 different test systems are represented across the GAP. Bioassay systems are organized according to the phylogeny of the test organisms and the end points of genetic activity. The methodology for producing and evaluating genetic activity profile was developed in collaboration with the International Agency for Research on Cancer (IARC). Data on individual chemicals were compiles by IARC and by the US Environmental Protection Agency (EPA). Data are available on 343 compounds selected from volumes 1-53 of the IARC Monographs and on 115 compounds identified as Superfund Priority Substances. Software to display the GAPs on an IBM-compatible personal computer is available from the authors. Structurally similar compounds frequently display qualitatively and quantitatively similar profiles of genetic activity. Through examination of the patterns of GAPs of pairs and groups of chemicals, it is possible to make more informed decisions regarding the selection of test batteries to be used in evaluation of chemical analogs. GAPs provided useful data for development of weight-of-evidence hazard ranking schemes. Also, some knowledge of the potential genetic activity of complex environmental mixtures may be gained from an assessment of the genetic activity profiles of component chemicals. The fundamental techniques and computer programs devised for the GAP database may be used to develop similar databases in other disciplines. 36 refs., 2 figs.

  5. Application of quantitative structure-property relationship analysis to estimate the vapor pressure of pesticides.

    PubMed

    Goodarzi, Mohammad; Coelho, Leandro dos Santos; Honarparvar, Bahareh; Ortiz, Erlinda V; Duchowicz, Pablo R

    2016-06-01

    The application of molecular descriptors in describing Quantitative Structure Property Relationships (QSPR) for the estimation of vapor pressure (VP) of pesticides is of ongoing interest. In this study, QSPR models were developed using multiple linear regression (MLR) methods to predict the vapor pressure values of 162 pesticides. Several feature selection methods, namely the replacement method (RM), genetic algorithms (GA), stepwise regression (SR) and forward selection (FS), were used to select the most relevant molecular descriptors from a pool of variables. The optimum subset of molecular descriptors was used to build a QSPR model to estimate the vapor pressures of the selected pesticides. The Replacement Method improved the predictive ability of vapor pressures and was more reliable for the feature selection of these selected pesticides. The results provided satisfactory MLR models that had a satisfactory predictive ability, and will be important for predicting vapor pressure values for compounds with unknown values. This study may open new opportunities for designing and developing new pesticide.

  6. Quantitative Cyber Risk Reduction Estimation Methodology for a Small Scada Control System

    SciTech Connect

    Miles A. McQueen; Wayne F. Boyer; Mark A. Flynn; George A. Beitel

    2006-01-01

    We propose a new methodology for obtaining a quick quantitative measurement of the risk reduction achieved when a control system is modified with the intent to improve cyber security defense against external attackers. The proposed methodology employs a directed graph called a compromise graph, where the nodes represent stages of a potential attack and the edges represent the expected time-to-compromise for differing attacker skill levels. Time-to-compromise is modeled as a function of known vulnerabilities and attacker skill level. The methodology was used to calculate risk reduction estimates for a specific SCADA system and for a specific set of control system security remedial actions. Despite an 86% reduction in the total number of vulnerabilities, the estimated time-to-compromise was increased only by about 3 to 30% depending on target and attacker skill level.

  7. Quantitative agent-based firm dynamics simulation with parameters estimated by financial and transaction data analysis

    NASA Astrophysics Data System (ADS)

    Ikeda, Yuichi; Souma, Wataru; Aoyama, Hideaki; Iyetomi, Hiroshi; Fujiwara, Yoshi; Kaizoji, Taisei

    2007-03-01

    Firm dynamics on a transaction network is considered from the standpoint of econophysics, agent-based simulations, and game theory. In this model, interacting firms rationally invest in a production facility to maximize net present value. We estimate parameters used in the model through empirical analysis of financial and transaction data. We propose two different methods ( analytical method and regression method) to obtain an interaction matrix of firms. On a subset of a real transaction network, we simulate firm's revenue, cost, and fixed asset, which is the accumulated investment for the production facility. The simulation reproduces the quantitative behavior of past revenues and costs within a standard error when we use the interaction matrix estimated by the regression method, in which only transaction pairs are taken into account. Furthermore, the simulation qualitatively reproduces past data of fixed assets.

  8. Uncertainty in Quantitative Precipitation Estimates and Forecasts in a Hydrologic Modeling Context (Invited)

    NASA Astrophysics Data System (ADS)

    Gourley, J. J.; Kirstetter, P.; Hong, Y.; Hardy, J.; Flamig, Z.

    2013-12-01

    This study presents a methodology to account for uncertainty in radar-based rainfall rate estimation using NOAA/NSSL's Multi-Radar Multisensor (MRMS) products. The focus of the study in on flood forecasting, including flash floods, in ungauged catchments throughout the conterminous US. An error model is used to derive probability distributions of rainfall rates that explicitly accounts for rain typology and uncertainty in the reflectivity-to-rainfall relationships. This approach preserves the fine space/time sampling properties (2 min/1 km) of the radar and conditions probabilistic quantitative precipitation estimates (PQPE) on the rain rate and rainfall type. Uncertainty in rainfall amplitude is the primary factor that is accounted for in the PQPE development. Additional uncertainties due to rainfall structures, locations, and timing must be considered when using quantitative precipitation forecast (QPF) products as forcing to a hydrologic model. A new method will be presented that shows how QPF ensembles are used in a hydrologic modeling context to derive probabilistic flood forecast products. This method considers the forecast rainfall intensity and morphology superimposed on pre-existing hydrologic conditions to identify basin scales that are most at risk.

  9. Quantitative estimation of carbonation and chloride penetration in reinforced concrete by laser-induced breakdown spectroscopy

    NASA Astrophysics Data System (ADS)

    Eto, Shuzo; Matsuo, Toyofumi; Matsumura, Takuro; Fujii, Takashi; Tanaka, Masayoshi Y.

    2014-11-01

    The penetration profile of chlorine in a reinforced concrete (RC) specimen was determined by laser-induced breakdown spectroscopy (LIBS). The concrete core was prepared from RC beams with cracking damage induced by bending load and salt water spraying. LIBS was performed using a specimen that was obtained by splitting the concrete core, and the line scan of laser pulses gave the two-dimensional emission intensity profiles of 100 × 80 mm2 within one hour. The two-dimensional profile of the emission intensity suggests that the presence of the crack had less effect on the emission intensity when the measurement interval was larger than the crack width. The chlorine emission spectrum was measured without using the buffer gas, which is usually used for chlorine measurement, by collinear double-pulse LIBS. The apparent diffusion coefficient, which is one of the most important parameters for chloride penetration in concrete, was estimated using the depth profile of chlorine emission intensity and Fick's law. The carbonation depth was estimated on the basis of the relationship between carbon and calcium emission intensities. When the carbon emission intensity was statistically higher than the calcium emission intensity at the measurement point, we determined that the point was carbonated. The estimation results were consistent with the spraying test results using phenolphthalein solution. These results suggest that the quantitative estimation by LIBS of carbonation depth and chloride penetration can be performed simultaneously.

  10. Estimation of Exercise Intensity in “Exercise and Physical Activity Reference for Health Promotion”

    NASA Astrophysics Data System (ADS)

    Ohkubo, Tomoyuki; Kurihara, Yosuke; Kobayashi, Kazuyuki; Watanabe, Kajiro

    To maintain or promote the health condition of elderly citizens is quite important for Japan. Given the circumstances, the Ministry of Health, Labour and Welfare has established the standards for the activities and exercises for promoting the health, and quantitatively determined the exercise intensity on 107 items of activities. This exercise intensity, however, requires recording the type and the duration of the activity to be calculated. In this paper, the exercise intensities are estimated using 3D accelerometer for 25 daily activities. As the result, the exercise intensities were estimated to be within the root mean square error of 0.83 METs for all 25 activities.

  11. Quantitative ultraviolet skin exposure in children during selected outdoor activities.

    PubMed

    Melville, S K; Rosenthal, F S; Luckmann, R; Lew, R A

    1991-06-01

    We determined the cumulative exposure of 3 body sites to ultraviolet radiation from sunlight for 126 children observed from 1-3 d during a variety of common recreational activities at a girl scout camp, baseball camp and community baseball field. Median arm exposure to children playing baseball at a camp ranged from 27.6% to 33.2% of the possible ambient exposure. These exposures are similar to adult exposures reported for comparable activities. Median exposure to the arm at the girl scout camp during mixed activities ranged from 9.0% to 26.5% of possible ambient exposure. At the girl scout camp, exposure both within and between activity groups varied substantially and were more variable than the baseball players' exposure. Arm exposure was greater than cheek and forehead exposure for all subject groups, with an arm-to-cheek exposure ratio ranging from 1.7 to 2.3. For organized sports, such as baseball, it may be possible to assign a single exposure estimate for use in epidemiologic studies or risk estimates. However, for less uniform outdoor activities, wide variability in exposure makes it more difficult to predict an individual's exposure.

  12. A Novel Method of Quantitative Anterior Chamber Depth Estimation Using Temporal Perpendicular Digital Photography

    PubMed Central

    Zamir, Ehud; Kong, George Y.X.; Kowalski, Tanya; Coote, Michael; Ang, Ghee Soon

    2016-01-01

    Purpose We hypothesize that: (1) Anterior chamber depth (ACD) is correlated with the relative anteroposterior position of the pupillary image, as viewed from the temporal side. (2) Such a correlation may be used as a simple quantitative tool for estimation of ACD. Methods Two hundred sixty-six phakic eyes had lateral digital photographs taken from the temporal side, perpendicular to the visual axis, and underwent optical biometry (Nidek AL scanner). The relative anteroposterior position of the pupillary image was expressed using the ratio between: (1) lateral photographic temporal limbus to pupil distance (“E”) and (2) lateral photographic temporal limbus to cornea distance (“Z”). In the first chronological half of patients (Correlation Series), E:Z ratio (EZR) was correlated with optical biometric ACD. The correlation equation was then used to predict ACD in the second half of patients (Prediction Series) and compared to their biometric ACD for agreement analysis. Results A strong linear correlation was found between EZR and ACD, R = −0.91, R2 = 0.81. Bland-Altman analysis showed good agreement between predicted ACD using this method and the optical biometric ACD. The mean error was −0.013 mm (range −0.377 to 0.336 mm), standard deviation 0.166 mm. The 95% limits of agreement were ±0.33 mm. Conclusions Lateral digital photography and EZR calculation is a novel method to quantitatively estimate ACD, requiring minimal equipment and training. Translational Relevance EZ ratio may be employed in screening for angle closure glaucoma. It may also be helpful in outpatient medical clinic settings, where doctors need to judge the safety of topical or systemic pupil-dilating medications versus their risk of triggering acute angle closure glaucoma. Similarly, non ophthalmologists may use it to estimate the likelihood of acute angle closure glaucoma in emergency presentations. PMID:27540496

  13. Quantitative determination of G6Pase activity in histochemically defined zones of the liver acinus.

    PubMed

    Teutsch, H F

    1978-12-13

    Qualitative histochemical G6Pase distribution patterns obtained with an improved method (Teutsch, 1978) served as the basis for a zonal microdissection of the liver acinus. G6Pase activity was determined quantitatively in tissue samples of zones 1 and 3 by a microfluorometric method (Burch et al., 1978). Using a correlation system it could be demonstrated that the histochemical distribution pattern obtained with the improved method was in better agreement with quantitatively estimated zonal differences of G6Pase activity, both in fed and starved female rats, than with the Wachstein and Meisel medium (1956). From a total of 50 tissue samples analyzed the following average G6Pase activities were calculated: in fed animals 15.36 +/- 3.48 U/g dry weight in zone 1, and 9.28 +/- 2.15 U/g dry weight in zone 3; in starved female rats 42.50 +/- 8.20 U/g dry weight in zone 1, and 29.25 +/- 5.68 U/g dry weight in zone 3. The qualitative histochemical as well as quantitative zonal differences of G6Pase activities are taken as further support for the hypothesis of metabolic zonation of liver parenchyma.

  14. Immunohistochemical quantitation of oestrogen receptors and proliferative activity in oestrogen receptor positive breast cancer.

    PubMed Central

    Jensen, V; Ladekarl, M

    1995-01-01

    AIM--To evaluate the effect of the duration of formalin fixation and of tumour heterogeneity on quantitative estimates of oestrogen receptor content (oestrogen receptor index) and proliferative activity (MIB-1 index) in breast cancer. METHODS--Two monoclonal antibodies, MIB-1 and oestrogen receptor, were applied to formalin fixed, paraffin wax embedded tissue from 25 prospectively collected oestrogen receptor positive breast carcinomas, using a microwave antigen retrieval method. Tumour tissue was allocated systematically to different periods of fixation to ensure minimal intraspecimen variation. The percentages of MIB-1 positive and oestrogen receptor positive nuclei were estimated in fields of vision sampled systematically from the entire specimen and from the whole tumour area of one "representative" cross-section. RESULTS--No correlation was found between the oestrogen receptor and MIB-1 indices and the duration of formalin fixation. The estimated MIB-1 and oestrogen receptor indices in tissue sampled systematically from the entire tumour were closely correlated with estimates obtained in a "representative" section. The intra- and interobserver correlation of the MIB-1 index was good, although a slight systematical error at the second assessment of the intraobserver study was noted. CONCLUSION--Quantitative estimates of oestrogen receptor content and proliferative activity are not significantly influenced by the period of fixation in formalin, varying from less than four hours to more than 48 hours. The MIB-1 and the oestrogen receptor indices obtained in a "representative" section do not deviate significantly from average indices determined in tissue samples from the entire tumour. Finally, the estimation of MIB-1 index is reproducible, justifying its routine use. PMID:7629289

  15. Quantitative precipitation estimation for an X-band weather radar network

    NASA Astrophysics Data System (ADS)

    Chen, Haonan

    Currently, the Next Generation (NEXRAD) radar network, a joint effort of the U.S. Department of Commerce (DOC), Defense (DOD), and Transportation (DOT), provides radar data with updates every five-six minutes across the United States. This network consists of about 160 S-band (2.7 to 3.0 GHz) radar sites. At the maximum NEXRAD range of 230 km, the 0.5 degree radar beam is about 5.4 km above ground level (AGL) because of the effect of earth curvature. Consequently, much of the lower atmosphere (1-3 km AGL) cannot be observed by the NEXRAD. To overcome the fundamental coverage limitations of today's weather surveillance radars, and improve the spatial and temporal resolution issues, the National Science Foundation Engineering Center (NSF-ERC) for Collaborative Adaptive Sensing of the Atmosphere (CASA) was founded to revolutionize weather sensing in the lower atmosphere by deploying a dense network of shorter-range, low-power X-band dual-polarization radars. The distributed CASA radars are operating collaboratively to adapt the changing atmospheric conditions. Accomplishments and breakthroughs after five years operation have demonstrated the success of CASA program. Accurate radar quantitative precipitation estimation (QPE) has been pursued since the beginning of weather radar. For certain disaster prevention applications such as flash flood and landslide forecasting, the rain rate must however be measured at a high spatial and temporal resolution. To this end, high-resolution radar QPE is one of the major research activities conducted by the CASA community. A radar specific differential propagation phase (Kdp)-based QPE methodology has been developed in CASA. Unlike the rainfall estimation based on the power terms such as radar reflectivity (Z) and differential reflectivity (Zdr), Kdp-based QPE is less sensitive to the path attenuation, drop size distribution (DSD), and radar calibration errors. The CASA Kdp-based QPE system is also immune to the partial beam

  16. Quantitative ultrasound characterization of locally advanced breast cancer by estimation of its scatterer properties

    SciTech Connect

    Tadayyon, Hadi; Sadeghi-Naini, Ali; Czarnota, Gregory; Wirtzfeld, Lauren; Wright, Frances C.

    2014-01-15

    Purpose: Tumor grading is an important part of breast cancer diagnosis and currently requires biopsy as its standard. Here, the authors investigate quantitative ultrasound parameters in locally advanced breast cancers that can potentially separate tumors from normal breast tissue and differentiate tumor grades. Methods: Ultrasound images and radiofrequency data from 42 locally advanced breast cancer patients were acquired and analyzed. Parameters related to the linear regression of the power spectrum—midband fit, slope, and 0-MHz-intercept—were determined from breast tumors and normal breast tissues. Mean scatterer spacing was estimated from the spectral autocorrelation, and the effective scatterer diameter and effective acoustic concentration were estimated from the Gaussian form factor. Parametric maps of each quantitative ultrasound parameter were constructed from the gated radiofrequency segments in tumor and normal tissue regions of interest. In addition to the mean values of the parametric maps, higher order statistical features, computed from gray-level co-occurrence matrices were also determined and used for characterization. Finally, linear and quadratic discriminant analyses were performed using combinations of quantitative ultrasound parameters to classify breast tissues. Results: Quantitative ultrasound parameters were found to be statistically different between tumor and normal tissue (p < 0.05). The combination of effective acoustic concentration and mean scatterer spacing could separate tumor from normal tissue with 82% accuracy, while the addition of effective scatterer diameter to the combination did not provide significant improvement (83% accuracy). Furthermore, the two advanced parameters, including effective scatterer diameter and mean scatterer spacing, were found to be statistically differentiating among grade I, II, and III tumors (p = 0.014 for scatterer spacing, p = 0.035 for effective scatterer diameter). The separation of the tumor

  17. Activation Likelihood Estimation meta-analysis revisited

    PubMed Central

    Eickhoff, Simon B.; Bzdok, Danilo; Laird, Angela R.; Kurth, Florian; Fox, Peter T.

    2011-01-01

    A widely used technique for coordinate-based meta-analysis of neuroimaging data is activation likelihood estimation (ALE), which determines the convergence of foci reported from different experiments. ALE analysis involves modelling these foci as probability distributions whose width is based on empirical estimates of the spatial uncertainty due to the between-subject and between-template variability of neuroimaging data. ALE results are assessed against a null-distribution of random spatial association between experiments, resulting in random-effects inference. In the present revision of this algorithm, we address two remaining drawbacks of the previous algorithm. First, the assessment of spatial association between experiments was based on a highly time-consuming permutation test, which nevertheless entailed the danger of underestimating the right tail of the null-distribution. In this report, we outline how this previous approach may be replaced by a faster and more precise analytical method. Second, the previously applied correction procedure, i.e. controlling the false discovery rate (FDR), is supplemented by new approaches for correcting the family-wise error rate and the cluster-level significance. The different alternatives for drawing inference on meta-analytic results are evaluated on an exemplary dataset on face perception as well as discussed with respect to their methodological limitations and advantages. In summary, we thus replaced the previous permutation algorithm with a faster and more rigorous analytical solution for the null-distribution and comprehensively address the issue of multiple-comparison corrections. The proposed revision of the ALE-algorithm should provide an improved tool for conducting coordinate-based meta-analyses on functional imaging data. PMID:21963913

  18. Developing Daily Quantitative Damage Estimates From Geospatial Layers To Support Post Event Recovery

    NASA Astrophysics Data System (ADS)

    Woods, B. K.; Wei, L. H.; Connor, T. C.

    2014-12-01

    With the growth of natural hazard data available in near real-time it is increasingly feasible to deliver damage estimates caused by natural disasters. These estimates can be used in disaster management setting or by commercial entities to optimize the deployment of resources and/or routing of goods and materials. This work outlines an end-to-end, modular process to generate estimates of damage caused by severe weather. The processing stream consists of five generic components: 1) Hazard modules that provide quantitate data layers for each peril. 2) Standardized methods to map the hazard data to an exposure layer based on atomic geospatial blocks. 3) Peril-specific damage functions that compute damage metrics at the atomic geospatial block level. 4) Standardized data aggregators, which map damage to user-specific geometries. 5) Data dissemination modules, which provide resulting damage estimates in a variety of output forms. This presentation provides a description of this generic tool set, and an illustrated example using HWRF-based hazard data for Hurricane Arthur (2014). In this example, the Python-based real-time processing ingests GRIB2 output from the HWRF numerical model, dynamically downscales it in conjunctions with a land cover database using a multiprocessing pool, and a just-in-time compiler (JIT). The resulting wind fields are contoured, and ingested into a PostGIS database using OGR. Finally, the damage estimates are calculated at the atomic block level and aggregated to user-defined regions using PostgreSQL queries to construct application specific tabular and graphics output.

  19. Spectral Feature Analysis for Quantitative Estimation of Cyanobacteria Chlorophyll-A

    NASA Astrophysics Data System (ADS)

    Lin, Yi; Ye, Zhanglin; Zhang, Yugan; Yu, Jie

    2016-06-01

    In recent years, lake eutrophication caused a large of Cyanobacteria bloom which not only brought serious ecological disaster but also restricted the sustainable development of regional economy in our country. Chlorophyll-a is a very important environmental factor to monitor water quality, especially for lake eutrophication. Remote sensed technique has been widely utilized in estimating the concentration of chlorophyll-a by different kind of vegetation indices and monitoring its distribution in lakes, rivers or along coastline. For each vegetation index, its quantitative estimation accuracy for different satellite data might change since there might be a discrepancy of spectral resolution and channel center between different satellites. The purpose this paper is to analyze the spectral feature of chlorophyll-a with hyperspectral data (totally 651 bands) and use the result to choose the optimal band combination for different satellites. The analysis method developed here in this study could be useful to recognize and monitor cyanobacteria bloom automatically and accrately. In our experiment, the reflectance (from 350nm to 1000nm) of wild cyanobacteria in different consistency (from 0 to 1362.11ug/L) and the corresponding chlorophyll-a concentration were measured simultaneously. Two kinds of hyperspectral vegetation indices were applied in this study: simple ratio (SR) and narrow band normalized difference vegetation index (NDVI), both of which consists of any two bands in the entire 651 narrow bands. Then multivariate statistical analysis was used to construct the linear, power and exponential models. After analyzing the correlation between chlorophyll-a and single band reflectance, SR, NDVI respetively, the optimal spectral index for quantitative estimation of cyanobacteria chlorophyll-a, as well corresponding central wavelength and band width were extracted. Results show that: Under the condition of water disturbance, SR and NDVI are both suitable for quantitative

  20. Reef-associated crustacean fauna: biodiversity estimates using semi-quantitative sampling and DNA barcoding

    NASA Astrophysics Data System (ADS)

    Plaisance, L.; Knowlton, N.; Paulay, G.; Meyer, C.

    2009-12-01

    The cryptofauna associated with coral reefs accounts for a major part of the biodiversity in these ecosystems but has been largely overlooked in biodiversity estimates because the organisms are hard to collect and identify. We combine a semi-quantitative sampling design and a DNA barcoding approach to provide metrics for the diversity of reef-associated crustacean. Twenty-two similar-sized dead heads of Pocillopora were sampled at 10 m depth from five central Pacific Ocean localities (four atolls in the Northern Line Islands and in Moorea, French Polynesia). All crustaceans were removed, and partial cytochrome oxidase subunit I was sequenced from 403 individuals, yielding 135 distinct taxa using a species-level criterion of 5% similarity. Most crustacean species were rare; 44% of the OTUs were represented by a single individual, and an additional 33% were represented by several specimens found only in one of the five localities. The Northern Line Islands and Moorea shared only 11 OTUs. Total numbers estimated by species richness statistics (Chao1 and ACE) suggest at least 90 species of crustaceans in Moorea and 150 in the Northern Line Islands for this habitat type. However, rarefaction curves for each region failed to approach an asymptote, and Chao1 and ACE estimators did not stabilize after sampling eight heads in Moorea, so even these diversity figures are underestimates. Nevertheless, even this modest sampling effort from a very limited habitat resulted in surprisingly high species numbers.

  1. A method for estimating the effective number of loci affecting a quantitative character.

    PubMed

    Slatkin, Montgomery

    2013-11-01

    A likelihood method is introduced that jointly estimates the number of loci and the additive effect of alleles that account for the genetic variance of a normally distributed quantitative character in a randomly mating population. The method assumes that measurements of the character are available from one or both parents and an arbitrary number of full siblings. The method uses the fact, first recognized by Karl Pearson in 1904, that the variance of a character among offspring depends on both the parental phenotypes and on the number of loci. Simulations show that the method performs well provided that data from a sufficient number of families (on the order of thousands) are available. This method assumes that the loci are in Hardy-Weinberg and linkage equilibrium but does not assume anything about the linkage relationships. It performs equally well if all loci are on the same non-recombining chromosome provided they are in linkage equilibrium. The method can be adapted to take account of loci already identified as being associated with the character of interest. In that case, the method estimates the number of loci not already known to affect the character. The method applied to measurements of crown-rump length in 281 family trios in a captive colony of African green monkeys (Chlorocebus aethiopus sabaeus) estimates the number of loci to be 112 and the additive effect to be 0.26 cm. A parametric bootstrap analysis shows that a rough confidence interval has a lower bound of 14 loci. PMID:23973416

  2. The overall impact of testing on medical student learning: quantitative estimation of consequential validity.

    PubMed

    Kreiter, Clarence D; Green, Joseph; Lenoch, Susan; Saiki, Takuya

    2013-10-01

    Given medical education's longstanding emphasis on assessment, it seems prudent to evaluate whether our current research and development focus on testing makes sense. Since any intervention within medical education must ultimately be evaluated based upon its impact on student learning, this report seeks to provide a quantitative accounting of the learning gains attained through educational assessments. To approach this question, we estimate achieved learning within a medical school environment that optimally utilizes educational assessments. We compare this estimate to learning that might be expected in a medical school that employs no educational assessments. Effect sizes are used to estimate testing's total impact on learning by summarizing three effects; the direct effect, the indirect effect, and the selection effect. The literature is far from complete, but the available evidence strongly suggests that each of these effects is large and the net cumulative impact on learning in medical education is over two standard deviations. While additional evidence is required, the current literature shows that testing within medical education makes a strong positive contribution to learning. PMID:22886140

  3. New service interface for River Forecasting Center derived quantitative precipitation estimates

    USGS Publications Warehouse

    Blodgett, David L.

    2013-01-01

    For more than a decade, the National Weather Service (NWS) River Forecast Centers (RFCs) have been estimating spatially distributed rainfall by applying quality-control procedures to radar-indicated rainfall estimates in the eastern United States and other best practices in the western United States to producea national Quantitative Precipitation Estimate (QPE) (National Weather Service, 2013). The availability of archives of QPE information for analytical purposes has been limited to manual requests for access to raw binary file formats that are difficult for scientists who are not in the climatic sciences to work with. The NWS provided the QPE archives to the U.S. Geological Survey (USGS), and the contents of the real-time feed from the RFCs are being saved by the USGS for incorporation into the archives. The USGS has applied time-series aggregation and added latitude-longitude coordinate variables to publish the RFC QPE data. Web services provide users with direct (index-based) data access, rendered visualizations of the data, and resampled raster representations of the source data in common geographic information formats.

  4. The overall impact of testing on medical student learning: quantitative estimation of consequential validity.

    PubMed

    Kreiter, Clarence D; Green, Joseph; Lenoch, Susan; Saiki, Takuya

    2013-10-01

    Given medical education's longstanding emphasis on assessment, it seems prudent to evaluate whether our current research and development focus on testing makes sense. Since any intervention within medical education must ultimately be evaluated based upon its impact on student learning, this report seeks to provide a quantitative accounting of the learning gains attained through educational assessments. To approach this question, we estimate achieved learning within a medical school environment that optimally utilizes educational assessments. We compare this estimate to learning that might be expected in a medical school that employs no educational assessments. Effect sizes are used to estimate testing's total impact on learning by summarizing three effects; the direct effect, the indirect effect, and the selection effect. The literature is far from complete, but the available evidence strongly suggests that each of these effects is large and the net cumulative impact on learning in medical education is over two standard deviations. While additional evidence is required, the current literature shows that testing within medical education makes a strong positive contribution to learning.

  5. The Effect of Quantitative Computed Tomography Acquisition Protocols on Bone Mineral Density Estimation.

    PubMed

    Giambini, Hugo; Dragomir-Daescu, Dan; Huddleston, Paul M; Camp, Jon J; An, Kai-Nan; Nassr, Ahmad

    2015-11-01

    Osteoporosis is characterized by bony material loss and decreased bone strength leading to a significant increase in fracture risk. Patient-specific quantitative computed tomography (QCT) finite element (FE) models may be used to predict fracture under physiological loading. Material properties for the FE models used to predict fracture are obtained by converting grayscale values from the CT into volumetric bone mineral density (vBMD) using calibration phantoms. If there are any variations arising from the CT acquisition protocol, vBMD estimation and material property assignment could be affected, thus, affecting fracture risk prediction. We hypothesized that material property assignments may be dependent on scanning and postprocessing settings including voltage, current, and reconstruction kernel, thus potentially having an effect in fracture risk prediction. A rabbit femur and a standard calibration phantom were imaged by QCT using different protocols. Cortical and cancellous regions were segmented, their average Hounsfield unit (HU) values obtained and converted to vBMD. Estimated vBMD for the cortical and cancellous regions were affected by voltage and kernel but not by current. Our study demonstrated that there exists a significant variation in the estimated vBMD values obtained with different scanning acquisitions. In addition, the large noise differences observed utilizing different scanning parameters could have an important negative effect on small subregions containing fewer voxels. PMID:26355694

  6. Heritability estimation of sex-specific effects on human quantitative traits.

    PubMed

    Pan, Lin; Ober, Carole; Abney, Mark

    2007-05-01

    Recent studies have suggested that sex-specific genetic architecture could be because of the effects of autosomal genes that are differentially expressed in males and females. Yet, few studies have explored the effects of X-linked genes on sex-specific genetic architecture. In this study, we extended the variance component, maximum likelihood method to evaluate the relative contributions of sex-specific effects on both autosomes and the X chromosome to estimates of heritability of 20 quantitative human phenotypes in the Hutterites. Seventeen of these traits were previously analyzed in this population under a model that did not include X chromosomal effects; three traits are analyzed for the first time (age at menarche, percent fat and fat-free mass [FFM]). Seven traits (systolic blood pressure (SBP), adult height, fasting insulin, triglycerides, lipoprotein (a) [Lp(a)], serotonin, and age at menarche) showed significant X-linked effects; three of these (SBP, adult height, and triglycerides) showed X-linked effects only in males. Four traits (Lp(a), low-density lipoprotein cholesterol, ratio of percent predicted forced expiratory volume at 1 s/forced vital capacity, and FFM) showed significant sex-environment interactions, and two traits (high-density lipoprotein cholesterol and FFM) showed significant sex-specific autosomal effects. Our analyses demonstrate that sex-specific genetic effects may not only be common in human quantitative traits, but also that the X chromosome both plays a large role in these effects and has a variable influence between the sexes.

  7. Accuracy in the estimation of quantitative minimal area from the diversity/area curve.

    PubMed

    Vives, Sergi; Salicrú, Miquel

    2005-05-01

    The problem of representativity is fundamental in ecological studies. A qualitative minimal area that gives a good representation of species pool [C.M. Bouderesque, Methodes d'etude qualitative et quantitative du benthos (en particulier du phytobenthos), Tethys 3(1) (1971) 79] can be discerned from a quantitative minimal area which reflects the structural complexity of community [F.X. Niell, Sobre la biologia de Ascophyllum nosodum (L.) Le Jolis en Galicia, Invest. Pesq. 43 (1979) 501]. This suggests that the populational diversity can be considered as the value of the horizontal asymptote corresponding to the curve sample diversity/biomass [F.X. Niell, Les applications de l'index de Shannon a l'etude de la vegetation interdidale, Soc. Phycol. Fr. Bull. 19 (1974) 238]. In this study we develop a expression to determine minimal areas and use it to obtain certain information about the community structure based on diversity/area curve graphs. This expression is based on the functional relationship between the expected value of the diversity and the sample size used to estimate it. In order to establish the quality of the estimation process, we obtained the confidence intervals as a particularization of the functional (h-phi)-entropies proposed in [M. Salicru, M.L. Menendez, D. Morales, L. Pardo, Asymptotic distribution of (h,phi)-entropies, Commun. Stat. (Theory Methods) 22 (7) (1993) 2015]. As an example used to demonstrate the possibilities of this method, and only for illustrative purposes, data about a study on the rocky intertidal seawed populations in the Ria of Vigo (N.W. Spain) are analyzed [F.X. Niell, Estudios sobre la estructura, dinamica y produccion del Fitobentos intermareal (Facies rocosa) de la Ria de Vigo. Ph.D. Mem. University of Barcelona, Barcelona, 1979]. PMID:15893337

  8. Accuracy in the estimation of quantitative minimal area from the diversity/area curve.

    PubMed

    Vives, Sergi; Salicrú, Miquel

    2005-05-01

    The problem of representativity is fundamental in ecological studies. A qualitative minimal area that gives a good representation of species pool [C.M. Bouderesque, Methodes d'etude qualitative et quantitative du benthos (en particulier du phytobenthos), Tethys 3(1) (1971) 79] can be discerned from a quantitative minimal area which reflects the structural complexity of community [F.X. Niell, Sobre la biologia de Ascophyllum nosodum (L.) Le Jolis en Galicia, Invest. Pesq. 43 (1979) 501]. This suggests that the populational diversity can be considered as the value of the horizontal asymptote corresponding to the curve sample diversity/biomass [F.X. Niell, Les applications de l'index de Shannon a l'etude de la vegetation interdidale, Soc. Phycol. Fr. Bull. 19 (1974) 238]. In this study we develop a expression to determine minimal areas and use it to obtain certain information about the community structure based on diversity/area curve graphs. This expression is based on the functional relationship between the expected value of the diversity and the sample size used to estimate it. In order to establish the quality of the estimation process, we obtained the confidence intervals as a particularization of the functional (h-phi)-entropies proposed in [M. Salicru, M.L. Menendez, D. Morales, L. Pardo, Asymptotic distribution of (h,phi)-entropies, Commun. Stat. (Theory Methods) 22 (7) (1993) 2015]. As an example used to demonstrate the possibilities of this method, and only for illustrative purposes, data about a study on the rocky intertidal seawed populations in the Ria of Vigo (N.W. Spain) are analyzed [F.X. Niell, Estudios sobre la estructura, dinamica y produccion del Fitobentos intermareal (Facies rocosa) de la Ria de Vigo. Ph.D. Mem. University of Barcelona, Barcelona, 1979].

  9. Estimation of multipath transmission parameters for quantitative ultrasound measurements of bone.

    PubMed

    Dencks, Stefanie; Schmitz, Georg

    2013-09-01

    When applying quantitative ultrasound (QUS) measurements to bone for predicting osteoporotic fracture risk, the multipath transmission of sound waves frequently occurs. In the last 10 years, the interest in separating multipath QUS signals for their analysis awoke, and led to the introduction of several approaches. Here, we compare the performances of the two fastest algorithms proposed for QUS measurements of bone: the modified least-squares Prony method (MLSP), and the space alternating generalized expectation maximization algorithm (SAGE) applied in the frequency domain. In both approaches, the parameters of the transfer functions of the sound propagation paths are estimated. To provide an objective measure, we also analytically derive the Cramér-Rao lower bound of variances for any estimator and arbitrary transmit signals. In comparison with results of Monte Carlo simulations, this measure is used to evaluate both approaches regarding their accuracy and precision. Additionally, with simulations using typical QUS measurement settings, we illustrate the limitations of separating two superimposed waves for varying parameters with focus on their temporal separation. It is shown that for good SNRs around 100 dB, MLSP yields better results when two waves are very close. Additionally, the parameters of the smaller wave are more reliably estimated. If the SNR decreases, the parameter estimation with MLSP becomes biased and inefficient. Then, the robustness to noise of the SAGE clearly prevails. Because a clear influence of the interrelation between the wavelength of the ultrasound signals and their temporal separation is observable on the results, these findings can be transferred to QUS measurements at other sites. The choice of the suitable algorithm thus depends on the measurement conditions.

  10. Apnea-hypopnea index estimation using quantitative analysis of sleep macrostructure.

    PubMed

    Jung, Da Woon; Hwang, Su Hwan; Lee, Yu Jin; Jeong, Do-Un; Park, Kwang Suk

    2016-04-01

    Obstructive sleep apnea, characterized by recurrent cessation or substantial reduction in breathing during sleep, is a prevalent and serious medical condition. Although a significant relationship between obstructive sleep apnea and sleep macrostructure has been revealed in several studies, useful applications of this relationship have been limited. The aim of this study was to suggest a novel approach using quantitative analysis of sleep macrostructure to estimate the apnea-hypopnea index, which is commonly used to assess obstructive sleep apnea. Without being bound by conventional sleep macrostructure parameters, various new sleep macrostructure parameters were extracted from the polysomnographic recordings of 132 subjects. These recordings were split into training and validation sets, each with 66 recordings including 48 recordings with an apnea-hypopnea index greater than 5 events h(-1). The nonlinear regression analysis, performed using the percentage transition probability from non-rapid eye movement sleep stage 2 to stage 1, was most effective in estimating the apnea-hypopnea index. Between the apnea-hypopnea index estimates and the reference values reported from polysomnography, a root mean square error of 7.30 events h(-1) was obtained in the validation set. At an apnea-hypopnea index cut-off of  ⩾30 events h(-1), the obstructive sleep apnea diagnostic performance was provided with a sensitivity of 90.0%, a specificity of 93.5%, and an accuracy of 92.4% by our method. The developed apnea-hypopnea index estimation model has the potential to be utilized in circumstances in which it is not possible to acquire or analyze respiration signal but it is possible to obtain information on sleep macrostructure. PMID:26999552

  11. Robust quantitative parameter estimation by advanced CMP measurements for vadose zone hydrological studies

    NASA Astrophysics Data System (ADS)

    Koyama, C.; Wang, H.; Khuut, T.; Kawai, T.; Sato, M.

    2015-12-01

    Soil moisture plays a crucial role in the understanding of processes in the vadose zone hydrology. In the last two decades ground penetrating radar (GPR) has been widely discussed has nondestructive measurement technique for soil moisture data. Especially the common mid-point (CMP) technique, which has been used in both seismic and GPR surveys to investigate the vertical velocity profiles, has a very high potential for quantitaive obervsations from the root zone to the ground water aquifer. However, the use is still rather limited today and algorithms for robust quantitative paramter estimation are lacking. In this study we develop an advanced processing scheme for operational soil moisture reetrieval at various depth. Using improved signal processing, together with a semblance - non-normalized cross-correlation sum combined stacking approach and the Dix formula, the interval velocities for multiple soil layers are obtained from the RMS velocities allowing for more accurate estimation of the permittivity at the reflecting point. Where the presence of a water saturated layer, like a groundwater aquifer, can be easily identified by its RMS velocity due to the high contrast compared to the unsaturated zone. By using a new semi-automated measurement technique the acquisition time for a full CMP gather with 1 cm intervals along a 10 m profile can be reduced significantly to under 2 minutes. The method is tested and validated under laboratory conditions in a sand-pit as well as on agricultural fields and beach sand in the Sendai city area. Comparison between CMP estimates and TDR measurements yield a very good agreement with RMSE of 1.5 Vol.-%. The accuracy of depth estimation is validated with errors smaller than 2%. Finally, we demonstrate application of the method in a test site in semi-arid Mongolia, namely the Orkhon River catchment in Bulgan, using commercial 100 MHz and 500 MHz RAMAC GPR antennas. The results demonstrate the suitability of the proposed method for

  12. Quantitative estimates of the impact of sensitivity and specificity in mammographic screening in Germany.

    PubMed Central

    Warmerdam, P G; de Koning, H J; Boer, R; Beemsterboer, P M; Dierks, M L; Swart, E; Robra, B P

    1997-01-01

    STUDY OBJECTIVE: To estimate quantitatively the impact of the quality of mammographic screening (in terms of sensitivity and specificity) on the effects and costs of nationwide breast cancer screening. DESIGN: Three plausible "quality" scenarios for a biennial breast cancer screening programme for women aged 50-69 in Germany were analysed in terms of costs and effects using the Microsimulation Screening Analysis model on breast cancer screening and the natural history of breast cancer. Firstly, sensitivity and specificity in the expected situation (or "baseline" scenario) were estimated from a model based analysis of empirical data from 35,000 screening examinations in two German pilot projects. In the second "high quality" scenario, these properties were based on the more favourable diagnostic results from breast cancer screening projects and the nationwide programme in The Netherlands. Thirdly, a worst case, "low quality" hypothetical scenario with a 25% lower sensitivity than that experienced in The Netherlands was analysed. SETTING: The epidemiological and social situation in Germany in relation to mass screening for breast cancer. RESULTS: In the "baseline" scenario, an 11% reduction in breast cancer mortality was expected in the total German female population, ie 2100 breast cancer deaths would be prevented per year. It was estimated that the "high quality" scenario, based on Dutch experience, would lead to the prevention of an additional 200 deaths per year and would also cut the number of false positive biopsy results by half. The cost per life year gained varied from Deutsche mark (DM) 15,000 on the "high quality" scenario to DM 21,000 in the "low quality" setting. CONCLUSIONS: Up to 20% of the total costs of a screening programme can be spent on quality improvement in order to achieve a substantially higher reduction in mortality and reduce undesirable side effects while retaining the same cost effectiveness ratio as that estimated from the German data

  13. Proficiency testing as a basis for estimating uncertainty of measurement: application to forensic alcohol and toxicology quantitations.

    PubMed

    Wallace, Jack

    2010-05-01

    While forensic laboratories will soon be required to estimate uncertainties of measurement for those quantitations reported to the end users of the information, the procedures for estimating this have been little discussed in the forensic literature. This article illustrates how proficiency test results provide the basis for estimating uncertainties in three instances: (i) For breath alcohol analyzers the interlaboratory precision is taken as a direct measure of uncertainty. This approach applies when the number of proficiency tests is small. (ii) For blood alcohol, the uncertainty is calculated from the differences between the laboratory's proficiency testing results and the mean quantitations determined by the participants; this approach applies when the laboratory has participated in a large number of tests. (iii) For toxicology, either of these approaches is useful for estimating comparability between laboratories, but not for estimating absolute accuracy. It is seen that data from proficiency tests enable estimates of uncertainty that are empirical, simple, thorough, and applicable to a wide range of concentrations.

  14. Lake number, a quantitative indicator of mixing used to estimate changes in dissolved oxygen

    USGS Publications Warehouse

    Robertson, Dale M.; Imberger, Jorg

    1994-01-01

    Lake Number, LN, values are shown to be quantitative indicators of deep mixing in lakes and reservoirs that can be used to estimate changes in deep water dissolved oxygen (DO) concentrations. LN is a dimensionless parameter defined as the ratio of the moments about the center of volume of the water body, of the stabilizing force of gravity associated with density stratification to the destabilizing forces supplied by wind, cooling, inflow, outflow, and other artificial mixing devices. To demonstrate the universality of this parameter, LN values are used to describe the extent of deep mixing and are compared with changes in DO concentrations in three reservoirs in Australia and four lakes in the U.S.A., which vary in productivity and mixing regimes. A simple model is developed which relates changes in LN values, i.e., the extent of mixing, to changes in near bottom DO concentrations. After calibrating the model for a specific system, it is possible to use real-time LN values, calculated using water temperature profiles and surface wind velocities, to estimate changes in DO concentrations (assuming unchanged trophic conditions).

  15. Improved radar data processing algorithms for quantitative rainfall estimation in real time.

    PubMed

    Krämer, S; Verworn, H R

    2009-01-01

    This paper describes a new methodology to process C-band radar data for direct use as rainfall input to hydrologic and hydrodynamic models and in real time control of urban drainage systems. In contrast to the adjustment of radar data with the help of rain gauges, the new approach accounts for the microphysical properties of current rainfall. In a first step radar data are corrected for attenuation. This phenomenon has been identified as the main cause for the general underestimation of radar rainfall. Systematic variation of the attenuation coefficients within predefined bounds allows robust reflectivity profiling. Secondly, event specific R-Z relations are applied to the corrected radar reflectivity data in order to generate quantitative reliable radar rainfall estimates. The results of the methodology are validated by a network of 37 rain gauges located in the Emscher and Lippe river basins. Finally, the relevance of the correction methodology for radar rainfall forecasts is demonstrated. It has become clearly obvious, that the new methodology significantly improves the radar rainfall estimation and rainfall forecasts. The algorithms are applicable in real time.

  16. The quantitative precipitation estimation system for Dallas-Fort Worth (DFW) urban remote sensing network

    NASA Astrophysics Data System (ADS)

    Chen, Haonan; Chandrasekar, V.

    2015-12-01

    The Dallas-Fort Worth (DFW) urban radar network consists of a combination of high resolution X band radars and a standard National Weather Service (NWS) Next-Generation Radar (NEXRAD) system operating at S band frequency. High spatiotemporal-resolution quantitative precipitation estimation (QPE) is one of the important applications of such a network. This paper presents a real-time QPE system developed by the Collaborative Adaptive Sensing of the Atmosphere (CASA) Engineering Research Center for the DFW urban region using both the high resolution X band radar network and the NWS S band radar observations. The specific dual-polarization radar rainfall algorithms at different frequencies (i.e., S- and X-band) and the fusion methodology combining observations at different temporal resolution are described. Radar and rain gauge observations from four rainfall events in 2013 that are characterized by different meteorological phenomena are used to compare the rainfall estimation products of the CASA DFW QPE system to conventional radar products from the national radar network provided by NWS. This high-resolution QPE system is used for urban flash flood mitigations when coupled with hydrological models.

  17. Quantitative estimation of transmembrane ion transport in rat renal collecting duct principal cells.

    PubMed

    Ilyaskin, Alexander V; Karpov, Denis I; Medvedev, Dmitriy A; Ershov, Alexander P; Baturina, Galina S; Katkova, Liubov E; Solenov, Evgeniy I

    2014-01-01

    Kidney collecting duct principal cells play a key role in regulated tubular reabsorption of water and sodium and secretion of potassium. The importance of this function for the maintenance of the osmotic homeostasis of the whole organism motivates extensive study of the ion transport properties of collecting duct principal cells. We performed experimental measurements of cell volume and intracellular sodium concentration in rat renal collecting duct principal cells from the outer medulla (OMCD) and used a mathematical model describing transmembrane ion fluxes to analyze the experimental data. The sodium and chloride concentrations ([Na+]in = 37.3 ± 3.3 mM, [Cl-]in = 32.2 ± 4.0 mM) in OMCD cells were quantitatively estimated. Correspondence between the experimentally measured cell physiological characteristics and the values of model permeability parameters was established. Plasma membrane permeabilities and the rates of transmembrane fluxes for sodium, potassium and chloride ions were estimated on the basis of ion substitution experiments and model predictions. In particular, calculated sodium (PNa), potassium (PK) and chloride (PCl) permeabilities were equal to 3.2 × 10-6 cm/s, 1.0 × 10-5 cm/s and 3.0 × 10-6 cm/s, respectively. This approach sets grounds for utilization of experimental measurements of intracellular sodium concentration and cell volume to quantify the ion permeabilities of OMCD principal cells and aids us in understanding the physiology of the adjustment of renal sodium and potassium excretion.

  18. Quantitative estimate of commercial fish enhancement by seagrass habitat in southern Australia

    NASA Astrophysics Data System (ADS)

    Blandon, Abigayil; zu Ermgassen, Philine S. E.

    2014-03-01

    Seagrass provides many ecosystem services that are of considerable value to humans, including the provision of nursery habitat for commercial fish stock. Yet few studies have sought to quantify these benefits. As seagrass habitat continues to suffer a high rate of loss globally and with the growing emphasis on compensatory restoration, valuation of the ecosystem services associated with seagrass habitat is increasingly important. We undertook a meta-analysis of juvenile fish abundance at seagrass and control sites to derive a quantitative estimate of the enhancement of juvenile fish by seagrass habitats in southern Australia. Thirteen fish of commercial importance were identified as being recruitment enhanced in seagrass habitat, twelve of which were associated with sufficient life history data to allow for estimation of total biomass enhancement. We applied von Bertalanffy growth models and species-specific mortality rates to the determined values of juvenile enhancement to estimate the contribution of seagrass to commercial fish biomass. The identified species were enhanced in seagrass by 0.98 kg m-2 y-1, equivalent to ˜$A230,000 ha-1 y-1. These values represent the stock enhancement where all fish species are present, as opposed to realized catches. Having accounted for the time lag between fish recruiting to a seagrass site and entering the fishery and for a 3% annual discount rate, we find that seagrass restoration efforts costing $A10,000 ha-1 have a potential payback time of less than five years, and that restoration costing $A629,000 ha-1 can be justified on the basis of enhanced commercial fish recruitment where these twelve fish species are present.

  19. Improved quantitative visualization of hypervelocity flow through wavefront estimation based on shadow casting of sinusoidal gratings.

    PubMed

    Medhi, Biswajit; Hegde, Gopalakrishna M; Gorthi, Sai Siva; Reddy, Kalidevapura Jagannath; Roy, Debasish; Vasu, Ram Mohan

    2016-08-01

    A simple noninterferometric optical probe is developed to estimate wavefront distortion suffered by a plane wave in its passage through density variations in a hypersonic flow obstructed by a test model in a typical shock tunnel. The probe has a plane light wave trans-illuminating the flow and casting a shadow of a continuous-tone sinusoidal grating. Through a geometrical optics, eikonal approximation to the distorted wavefront, a bilinear approximation to it is related to the location-dependent shift (distortion) suffered by the grating, which can be read out space-continuously from the projected grating image. The processing of the grating shadow is done through an efficient Fourier fringe analysis scheme, either with a windowed or global Fourier transform (WFT and FT). For comparison, wavefront slopes are also estimated from shadows of random-dot patterns, processed through cross correlation. The measured slopes are suitably unwrapped by using a discrete cosine transform (DCT)-based phase unwrapping procedure, and also through iterative procedures. The unwrapped phase information is used in an iterative scheme, for a full quantitative recovery of density distribution in the shock around the model, through refraction tomographic inversion. Hypersonic flow field parameters around a missile-shaped body at a free-stream Mach number of ∼8 measured using this technique are compared with the numerically estimated values. It is shown that, while processing a wavefront with small space-bandwidth product (SBP) the FT inversion gave accurate results with computational efficiency; computation-intensive WFT was needed for similar results when dealing with larger SBP wavefronts. PMID:27505389

  20. Improved quantitative visualization of hypervelocity flow through wavefront estimation based on shadow casting of sinusoidal gratings.

    PubMed

    Medhi, Biswajit; Hegde, Gopalakrishna M; Gorthi, Sai Siva; Reddy, Kalidevapura Jagannath; Roy, Debasish; Vasu, Ram Mohan

    2016-08-01

    A simple noninterferometric optical probe is developed to estimate wavefront distortion suffered by a plane wave in its passage through density variations in a hypersonic flow obstructed by a test model in a typical shock tunnel. The probe has a plane light wave trans-illuminating the flow and casting a shadow of a continuous-tone sinusoidal grating. Through a geometrical optics, eikonal approximation to the distorted wavefront, a bilinear approximation to it is related to the location-dependent shift (distortion) suffered by the grating, which can be read out space-continuously from the projected grating image. The processing of the grating shadow is done through an efficient Fourier fringe analysis scheme, either with a windowed or global Fourier transform (WFT and FT). For comparison, wavefront slopes are also estimated from shadows of random-dot patterns, processed through cross correlation. The measured slopes are suitably unwrapped by using a discrete cosine transform (DCT)-based phase unwrapping procedure, and also through iterative procedures. The unwrapped phase information is used in an iterative scheme, for a full quantitative recovery of density distribution in the shock around the model, through refraction tomographic inversion. Hypersonic flow field parameters around a missile-shaped body at a free-stream Mach number of ∼8 measured using this technique are compared with the numerically estimated values. It is shown that, while processing a wavefront with small space-bandwidth product (SBP) the FT inversion gave accurate results with computational efficiency; computation-intensive WFT was needed for similar results when dealing with larger SBP wavefronts.

  1. Quantitative structure-activity relationships for organophosphates binding to acetylcholinesterase.

    PubMed

    Ruark, Christopher D; Hack, C Eric; Robinson, Peter J; Anderson, Paul E; Gearhart, Jeffery M

    2013-02-01

    Organophosphates are a group of pesticides and chemical warfare nerve agents that inhibit acetylcholinesterase, the enzyme responsible for hydrolysis of the excitatory neurotransmitter acetylcholine. Numerous structural variants exist for this chemical class, and data regarding their toxicity can be difficult to obtain in a timely fashion. At the same time, their use as pesticides and military weapons is widespread, which presents a major concern and challenge in evaluating human toxicity. To address this concern, a quantitative structure-activity relationship (QSAR) was developed to predict pentavalent organophosphate oxon human acetylcholinesterase bimolecular rate constants. A database of 278 three-dimensional structures and their bimolecular rates was developed from 15 peer-reviewed publications. A database of simplified molecular input line entry notations and their respective acetylcholinesterase bimolecular rate constants are listed in Supplementary Material, Table I. The database was quite diverse, spanning 7 log units of activity. In order to describe their structure, 675 molecular descriptors were calculated using AMPAC 8.0 and CODESSA 2.7.10. Orthogonal projection to latent structures regression, bootstrap leave-random-many-out cross-validation and y-randomization were used to develop an externally validated consensus QSAR model. The domain of applicability was assessed by the William's plot. Six external compounds were outside the warning leverage indicating potential model extrapolation. A number of compounds had residuals >2 or <-2, indicating potential outliers or activity cliffs. The results show that the HOMO-LUMO energy gap contributed most significantly to the binding affinity. A mean training R (2) of 0.80, a mean test set R (2) of 0.76 and a consensus external test set R (2) of 0.66 were achieved using the QSAR. The training and external test set RMSE values were found to be 0.76 and 0.88. The results suggest that this QSAR model can be used in

  2. Improving satellite quantitative precipitation estimates by incorporating deep convective cloud optical depth

    NASA Astrophysics Data System (ADS)

    Stenz, Ronald D.

    As Deep Convective Systems (DCSs) are responsible for most severe weather events, increased understanding of these systems along with more accurate satellite precipitation estimates will improve NWS (National Weather Service) warnings and monitoring of hazardous weather conditions. A DCS can be classified into convective core (CC) regions (heavy rain), stratiform (SR) regions (moderate-light rain), and anvil (AC) regions (no rain). These regions share similar infrared (IR) brightness temperatures (BT), which can create large errors for many existing rain detection algorithms. This study assesses the performance of the National Mosaic and Multi-sensor Quantitative Precipitation Estimation System (NMQ) Q2, and a simplified version of the GOES-R Rainfall Rate algorithm (also known as the Self-Calibrating Multivariate Precipitation Retrieval, or SCaMPR), over the state of Oklahoma (OK) using OK MESONET observations as ground truth. While the average annual Q2 precipitation estimates were about 35% higher than MESONET observations, there were very strong correlations between these two data sets for multiple temporal and spatial scales. Additionally, the Q2 estimated precipitation distributions over the CC, SR, and AC regions of DCSs strongly resembled the MESONET observed ones, indicating that Q2 can accurately capture the precipitation characteristics of DCSs although it has a wet bias . SCaMPR retrievals were typically three to four times higher than the collocated MESONET observations, with relatively weak correlations during a year of comparisons in 2012. Overestimates from SCaMPR retrievals that produced a high false alarm rate were primarily caused by precipitation retrievals from the anvil regions of DCSs when collocated MESONET stations recorded no precipitation. A modified SCaMPR retrieval algorithm, employing both cloud optical depth and IR temperature, has the potential to make significant improvements to reduce the SCaMPR false alarm rate of retrieved

  3. Improving quantitative structure-activity relationships through multiobjective optimization.

    PubMed

    Nicolotti, Orazio; Giangreco, Ilenia; Miscioscia, Teresa Fabiola; Carotti, Angelo

    2009-10-01

    A multiobjective optimization algorithm was proposed for the automated integration of structure- and ligand-based molecular design. Driven by a genetic algorithm, the herein proposed approach enabled the detection of a number of trade-off QSAR models accounting simultaneously for two independent objectives. The first was biased toward best regressions among docking scores and biological affinities; the second minimized the atom displacements from a properly established crystal-based binding topology. Based on the concept of dominance, 3D QSAR equivalent models profiled the Pareto frontier and were, thus, designated as nondominated solutions of the search space. K-means clustering was, then, operated to select a representative subset of the available trade-off models. These were effectively subjected to GRID/GOLPE analyses for quantitatively featuring molecular determinants of ligand binding affinity. More specifically, it was demonstrated that a) diverse binding conformations occurred on the basis of the ligand ability to profitably contact different part of protein binding site; b) enzyme selectivity was better approached and interpreted by combining diverse equivalent models; and c) trade-off models were successful and even better than docking virtual screening, in retrieving at high sensitivity active hits from a large pool of chemically similar decoys. The approach was tested on a large series, very well-known to QSAR practitioners, of 3-amidinophenylalanine inhibitors of thrombin and trypsin, two serine proteases having rather different biological actions despite a high sequence similarity. PMID:19785453

  4. Determining cleanup levels in bioremediation: Quantitative structure activity relationship techniques

    SciTech Connect

    Arulgnanendran, V.R.J.; Nirmalakhandan, N.

    1995-12-31

    An important feature in the process of planning and initiating bioremediation is the quantification of the toxicity of either an individual chemical or a group of chemicals when multiple chemicals are involved. A laboratory protocol was developed to test the toxicity of single chemicals and mixtures of organic chemicals in a soil medium. Portions of these chemicals are used as a training set to develop Quantitative Structure Activity Relationship (QSAR) models. These predictive models are tested using the chemicals in the testing set, i.e., the remaining chemicals. Moreover mixtures with 10 contaminants in each mixture are tested experimentally to determine joint toxicity for mixtures of chemicals. Using the concepts of Toxic Units, Additivity Index, and Mixture Toxicity Index, the laboratory results are tested for additive, synergistic, or antagonistic effects of the contaminants. These concepts are further validated on mixtures containing eight chemicals that are tested in the laboratory. In addition to the use of the predictive models in evaluating cleanup levels for hazardous waste locations, they are useful to predict microbial toxicity in soils of new chemicals from a congeneric group acting by the same mode of toxicity. These models are applicable when the contaminants act singly or jointly in a mixture.

  5. Mycobactericidal activity of selected disinfectants using a quantitative suspension test.

    PubMed

    Griffiths, P A; Babb, J R; Fraise, A P

    1999-02-01

    In this study, a quantitative suspension test carried out under both clean and dirty conditions was used to assess the activity of various instrument and environmental disinfectants against the type strain NCTC 946 and an endoscope washer disinfector isolate of Mycobacterium chelonae, Mycobacterium fortuitum NCTC 10,394, Mycobacterium tuberculosis H37 Rv NCTC 7416 and a clinical isolate of Mycobacterium avium-intracellulare (MAI). The disinfectants tested were; a chlorine releasing agent, sodium dichloroisocyanurate (NaDCC) at 1000 ppm and 10,000 ppm av Cl; chlorine dioxide at 1100 ppm av ClO2 (Tristel, MediChem International Limited); 70% industrial methylated spirits (IMS); 2% alkaline glutaraldehyde (Asep, Galan); 10% succinedialdehyde and formaldehyde mixture (Gigasept, Schulke & Mayr); 0.35% peracetic acid (NuCidex, Johnson & Johnson); and a peroxygen compound at 1% and 3% (Virkon, Antec International). Results showed that the clinical isolate of MAI was much more resistant than M. tuberculosis to all the disinfectants, while the type strains of M. chelonae and M. fortuitum were far more sensitive. The washer disinfector isolate of M. chelonae was extremely resistant to 2% alkaline activated glutaraldehyde and appeared to be slightly more resistant than the type strain to Nu-Cidex, Gigasept, Virkon and the lower concentration of NaDCC. This study has shown peracetic acid (Nu-Cidex), chlorine dioxide (Tristel), alcohol (IMS) and high concentrations of a chlorine releasing agent (NaDCC) are rapidly mycobactericidal. Glutaraldehyde, although effective, is a slow mycobactericide. Gigasept and Virkon are poor mycobactericidal agents and are not therefore recommended for instruments or spillage if mycobacteria are likely to be present. PMID:10063473

  6. Quantitative coronary angiography using image recovery techniques for background estimation in unsubtracted images

    SciTech Connect

    Wong, Jerry T.; Kamyar, Farzad; Molloi, Sabee

    2007-10-15

    Densitometry measurements have been performed previously using subtracted images. However, digital subtraction angiography (DSA) in coronary angiography is highly susceptible to misregistration artifacts due to the temporal separation of background and target images. Misregistration artifacts due to respiration and patient motion occur frequently, and organ motion is unavoidable. Quantitative densitometric techniques would be more clinically feasible if they could be implemented using unsubtracted images. The goal of this study is to evaluate image recovery techniques for densitometry measurements using unsubtracted images. A humanoid phantom and eight swine (25-35 kg) were used to evaluate the accuracy and precision of the following image recovery techniques: Local averaging (LA), morphological filtering (MF), linear interpolation (LI), and curvature-driven diffusion image inpainting (CDD). Images of iodinated vessel phantoms placed over the heart of the humanoid phantom or swine were acquired. In addition, coronary angiograms were obtained after power injections of a nonionic iodinated contrast solution in an in vivo swine study. Background signals were estimated and removed with LA, MF, LI, and CDD. Iodine masses in the vessel phantoms were quantified and compared to known amounts. Moreover, the total iodine in left anterior descending arteries was measured and compared with DSA measurements. In the humanoid phantom study, the average root mean square errors associated with quantifying iodine mass using LA and MF were approximately 6% and 9%, respectively. The corresponding average root mean square errors associated with quantifying iodine mass using LI and CDD were both approximately 3%. In the in vivo swine study, the root mean square errors associated with quantifying iodine in the vessel phantoms with LA and MF were approximately 5% and 12%, respectively. The corresponding average root mean square errors using LI and CDD were both 3%. The standard deviations

  7. Improving high-resolution quantitative precipitation estimation via fusion of multiple radar-based precipitation products

    NASA Astrophysics Data System (ADS)

    Rafieeinasab, Arezoo; Norouzi, Amir; Seo, Dong-Jun; Nelson, Brian

    2015-12-01

    For monitoring and prediction of water-related hazards in urban areas such as flash flooding, high-resolution hydrologic and hydraulic modeling is necessary. Because of large sensitivity and scale dependence of rainfall-runoff models to errors in quantitative precipitation estimates (QPE), it is very important that the accuracy of QPE be improved in high-resolution hydrologic modeling to the greatest extent possible. With the availability of multiple radar-based precipitation products in many areas, one may now consider fusing them to produce more accurate high-resolution QPE for a wide spectrum of applications. In this work, we formulate and comparatively evaluate four relatively simple procedures for such fusion based on Fisher estimation and its conditional bias-penalized variant: Direct Estimation (DE), Bias Correction (BC), Reduced-Dimension Bias Correction (RBC) and Simple Estimation (SE). They are applied to fuse the Multisensor Precipitation Estimator (MPE) and radar-only Next Generation QPE (Q2) products at the 15-min 1-km resolution (Experiment 1), and the MPE and Collaborative Adaptive Sensing of the Atmosphere (CASA) QPE products at the 15-min 500-m resolution (Experiment 2). The resulting fused estimates are evaluated using the 15-min rain gauge observations from the City of Grand Prairie in the Dallas-Fort Worth Metroplex (DFW) in north Texas. The main criterion used for evaluation is that the fused QPE improves over the ingredient QPEs at their native spatial resolutions, and that, at the higher resolution, the fused QPE improves not only over the ingredient higher-resolution QPE but also over the ingredient lower-resolution QPE trivially disaggregated using the ingredient high-resolution QPE. All four procedures assume that the ingredient QPEs are unbiased, which is not likely to hold true in reality even if real-time bias correction is in operation. To test robustness under more realistic conditions, the fusion procedures were evaluated with and

  8. Quantitative estimation of groundwater recharge ratio along the riparian of the Yellow River.

    PubMed

    Yan, Zhang; Fadong, Li; Jing, Li; Qiang, Liu; Guangshuai, Zhao

    2013-01-01

    Quantitative estimation of groundwater recharge is crucial for limited water resources management. A combination of isotopic and chemical indicators has been used to evaluate the relationship between surface water, groundwater, and rainfall around the riparian of the Yellow River in the North China Plain (NCP). The ion molar ratio of sodium to chloride in surface- and groundwater is 0.6 and 0.9, respectively, indicating cation exchange of Ca(2+) and/or Mg(2+) for Na(+) in groundwater. The δD and δ(18)O values in rainfall varied from -64.4 to -33.4‰ and from -8.39 to -4.49‰. The groundwater samples have δD values in the range of -68.7 to -58.0‰ and δ(18)O from -9.29 to -6.85‰. The δ(18)O and δD in surface water varied from -8.51 to -7.23‰ and from -64.42 to -53.73‰. The average values of both δD and δ(18)O from surface water are 3.92‰ and 0.57‰, respectively, higher compared to groundwater. Isotopic composition indicated that the groundwater in the riparian area of the Yellow River was influenced by heavy rainfall events and seepage of surface water. The mass balance was applied for the first time to estimate the amount of recharge, which is probably 6% and 94% of the rainfall and surface water, respectively.

  9. Quantitative estimation of concentrations of dissolved rare earth elements using reflectance spectroscopy

    NASA Astrophysics Data System (ADS)

    Dai, Jingjing; Wang, Denghong; Wang, Runsheng; Chen, Zhenghui

    2013-01-01

    Characteristic spectral parameters such as the wavelength and depth of absorption bands are widely used to quantitatively estimate the composition of samples from hyperspectral reflectance data in soil science, mineralogy as well as vegetation study. However, little research has been conducted on the spectral characteristic of rare earth elements (REE) and their relationship with chemical composition of aqueous solutions. Reflectance spectra of ore leachate solutions and contaminated stream water from a few REE mines in the Jiangxi Province, China, are studied for the first time in this work. The results demonstrate that the six diagnostic absorption features of the rare earths are recognized in visible and near-infrared wavelengths at 574, 790, 736, 520, 861, and 443 nm. The intensity of each of these six absorption bands is linearly correlated with the abundance of total REE, with the r2 value >0.95 and the detection limit at ≥75,000 μg/L. It is suggested that reflectance spectroscopy provides an ideal routine analytical tool for characterizing leachate samples. The outcome of this study also has implications for monitoring the environmental effect of REE mining, in particular in stream water systems by hyperspectral remote sensing.

  10. Quantitative Simulations of MST Visual Receptive Field Properties Using a Template Model of Heading Estimation

    NASA Technical Reports Server (NTRS)

    Stone, Leland S.; Perrone, J. A.

    1997-01-01

    We previously developed a template model of primate visual self-motion processing that proposes a specific set of projections from MT-like local motion sensors onto output units to estimate heading and relative depth from optic flow. At the time, we showed that that the model output units have emergent properties similar to those of MSTd neurons, although there was little physiological evidence to test the model more directly. We have now systematically examined the properties of the model using stimulus paradigms used by others in recent single-unit studies of MST: 1) 2-D bell-shaped heading tuning. Most MSTd neurons and model output units show bell-shaped heading tuning. Furthermore, we found that most model output units and the finely-sampled example neuron in the Duffy-Wurtz study are well fit by a 2D gaussian (sigma approx. 35deg, r approx. 0.9). The bandwidth of model and real units can explain why Lappe et al. found apparent sigmoidal tuning using a restricted range of stimuli (+/-40deg). 2) Spiral Tuning and Invariance. Graziano et al. found that many MST neurons appear tuned to a specific combination of rotation and expansion (spiral flow) and that this tuning changes little for approx. 10deg shifts in stimulus placement. Simulations of model output units under the same conditions quantitatively replicate this result. We conclude that a template architecture may underlie MT inputs to MST.

  11. Quantitative Estimation of the Climatic Effects of Carbon Transferred by International Trade.

    PubMed

    Wei, Ting; Dong, Wenjie; Moore, John; Yan, Qing; Song, Yi; Yang, Zhiyong; Yuan, Wenping; Chou, Jieming; Cui, Xuefeng; Yan, Xiaodong; Wei, Zhigang; Guo, Yan; Yang, Shili; Tian, Di; Lin, Pengfei; Yang, Song; Wen, Zhiping; Lin, Hui; Chen, Min; Feng, Guolin; Jiang, Yundi; Zhu, Xian; Chen, Juan; Wei, Xin; Shi, Wen; Zhang, Zhiguo; Dong, Juan; Li, Yexin; Chen, Deliang

    2016-06-22

    Carbon transfer via international trade affects the spatial pattern of global carbon emissions by redistributing emissions related to production of goods and services. It has potential impacts on attribution of the responsibility of various countries for climate change and formulation of carbon-reduction policies. However, the effect of carbon transfer on climate change has not been quantified. Here, we present a quantitative estimate of climatic impacts of carbon transfer based on a simple CO2 Impulse Response Function and three Earth System Models. The results suggest that carbon transfer leads to a migration of CO2 by 0.1-3.9 ppm or 3-9% of the rise in the global atmospheric concentrations from developed countries to developing countries during 1990-2005 and potentially reduces the effectiveness of the Kyoto Protocol by up to 5.3%. However, the induced atmospheric CO2 concentration and climate changes (e.g., in temperature, ocean heat content, and sea-ice) are very small and lie within observed interannual variability. Given continuous growth of transferred carbon emissions and their proportion in global total carbon emissions, the climatic effect of traded carbon is likely to become more significant in the future, highlighting the need to consider carbon transfer in future climate negotiations.

  12. Quantitative Estimation of the Climatic Effects of Carbon Transferred by International Trade.

    PubMed

    Wei, Ting; Dong, Wenjie; Moore, John; Yan, Qing; Song, Yi; Yang, Zhiyong; Yuan, Wenping; Chou, Jieming; Cui, Xuefeng; Yan, Xiaodong; Wei, Zhigang; Guo, Yan; Yang, Shili; Tian, Di; Lin, Pengfei; Yang, Song; Wen, Zhiping; Lin, Hui; Chen, Min; Feng, Guolin; Jiang, Yundi; Zhu, Xian; Chen, Juan; Wei, Xin; Shi, Wen; Zhang, Zhiguo; Dong, Juan; Li, Yexin; Chen, Deliang

    2016-01-01

    Carbon transfer via international trade affects the spatial pattern of global carbon emissions by redistributing emissions related to production of goods and services. It has potential impacts on attribution of the responsibility of various countries for climate change and formulation of carbon-reduction policies. However, the effect of carbon transfer on climate change has not been quantified. Here, we present a quantitative estimate of climatic impacts of carbon transfer based on a simple CO2 Impulse Response Function and three Earth System Models. The results suggest that carbon transfer leads to a migration of CO2 by 0.1-3.9 ppm or 3-9% of the rise in the global atmospheric concentrations from developed countries to developing countries during 1990-2005 and potentially reduces the effectiveness of the Kyoto Protocol by up to 5.3%. However, the induced atmospheric CO2 concentration and climate changes (e.g., in temperature, ocean heat content, and sea-ice) are very small and lie within observed interannual variability. Given continuous growth of transferred carbon emissions and their proportion in global total carbon emissions, the climatic effect of traded carbon is likely to become more significant in the future, highlighting the need to consider carbon transfer in future climate negotiations. PMID:27329411

  13. Health risks in wastewater irrigation: comparing estimates from quantitative microbial risk analyses and epidemiological studies.

    PubMed

    Mara, D D; Sleigh, P A; Blumenthal, U J; Carr, R M

    2007-03-01

    The combination of standard quantitative microbial risk analysis (QMRA) techniques and 10,000-trial Monte Carlo risk simulations was used to estimate the human health risks associated with the use of wastewater for unrestricted and restricted crop irrigation. A risk of rotavirus infection of 10(-2) per person per year (pppy) was used as the reference level of acceptable risk. Using the model scenario of involuntary soil ingestion for restricted irrigation, the risk of rotavirus infection is approximately 10(-2) pppy when the wastewater contains < or =10(6) Escherichia coli per 100ml and when local agricultural practices are highly mechanised. For labour-intensive agriculture the risk of rotavirus infection is approximately 10(-2) pppy when the wastewater contains < or = 10(5) E. coli per 100ml; however, the wastewater quality should be < or = 10(4) E. coli per 100ml when children under 15 are exposed. With the model scenario of lettuce consumption for unrestricted irrigation, the use of wastewaters containing < or =10(4) E. coli per 100ml results in a rotavirus infection risk of approximately 10(-2) pppy; however, again based on epidemiological evidence from Mexico, the current WHO guideline level of < or =1,000 E. coli per 100ml should be retained for root crops eaten raw. PMID:17402278

  14. Quantitative Estimation of the Climatic Effects of Carbon Transferred by International Trade

    NASA Astrophysics Data System (ADS)

    Wei, Ting; Dong, Wenjie; Moore, John; Yan, Qing; Song, Yi; Yang, Zhiyong; Yuan, Wenping; Chou, Jieming; Cui, Xuefeng; Yan, Xiaodong; Wei, Zhigang; Guo, Yan; Yang, Shili; Tian, Di; Lin, Pengfei; Yang, Song; Wen, Zhiping; Lin, Hui; Chen, Min; Feng, Guolin; Jiang, Yundi; Zhu, Xian; Chen, Juan; Wei, Xin; Shi, Wen; Zhang, Zhiguo; Dong, Juan; Li, Yexin; Chen, Deliang

    2016-06-01

    Carbon transfer via international trade affects the spatial pattern of global carbon emissions by redistributing emissions related to production of goods and services. It has potential impacts on attribution of the responsibility of various countries for climate change and formulation of carbon-reduction policies. However, the effect of carbon transfer on climate change has not been quantified. Here, we present a quantitative estimate of climatic impacts of carbon transfer based on a simple CO2 Impulse Response Function and three Earth System Models. The results suggest that carbon transfer leads to a migration of CO2 by 0.1–3.9 ppm or 3–9% of the rise in the global atmospheric concentrations from developed countries to developing countries during 1990–2005 and potentially reduces the effectiveness of the Kyoto Protocol by up to 5.3%. However, the induced atmospheric CO2 concentration and climate changes (e.g., in temperature, ocean heat content, and sea-ice) are very small and lie within observed interannual variability. Given continuous growth of transferred carbon emissions and their proportion in global total carbon emissions, the climatic effect of traded carbon is likely to become more significant in the future, highlighting the need to consider carbon transfer in future climate negotiations.

  15. Quantitative Estimation of the Climatic Effects of Carbon Transferred by International Trade

    PubMed Central

    Wei, Ting; Dong, Wenjie; Moore, John; Yan, Qing; Song, Yi; Yang, Zhiyong; Yuan, Wenping; Chou, Jieming; Cui, Xuefeng; Yan, Xiaodong; Wei, Zhigang; Guo, Yan; Yang, Shili; Tian, Di; Lin, Pengfei; Yang, Song; Wen, Zhiping; Lin, Hui; Chen, Min; Feng, Guolin; Jiang, Yundi; Zhu, Xian; Chen, Juan; Wei, Xin; Shi, Wen; Zhang, Zhiguo; Dong, Juan; Li, Yexin; Chen, Deliang

    2016-01-01

    Carbon transfer via international trade affects the spatial pattern of global carbon emissions by redistributing emissions related to production of goods and services. It has potential impacts on attribution of the responsibility of various countries for climate change and formulation of carbon-reduction policies. However, the effect of carbon transfer on climate change has not been quantified. Here, we present a quantitative estimate of climatic impacts of carbon transfer based on a simple CO2 Impulse Response Function and three Earth System Models. The results suggest that carbon transfer leads to a migration of CO2 by 0.1–3.9 ppm or 3–9% of the rise in the global atmospheric concentrations from developed countries to developing countries during 1990–2005 and potentially reduces the effectiveness of the Kyoto Protocol by up to 5.3%. However, the induced atmospheric CO2 concentration and climate changes (e.g., in temperature, ocean heat content, and sea-ice) are very small and lie within observed interannual variability. Given continuous growth of transferred carbon emissions and their proportion in global total carbon emissions, the climatic effect of traded carbon is likely to become more significant in the future, highlighting the need to consider carbon transfer in future climate negotiations. PMID:27329411

  16. Quantitative analysis of wrist electrodermal activity during sleep

    PubMed Central

    Sano, Akane; Picard, Rosalind W.; Stickgold, Robert

    2015-01-01

    We present the first quantitative characterization of electrodermal activity (EDA) patterns on the wrists of healthy adults during sleep using dry electrodes. We compare the new results on the wrist to prior findings on palmar or finger EDA by characterizing data measured from 80 nights of sleep consisting of 9 nights of wrist and palm EDA from 9 healthy adults sleeping at home, 56 nights of wrist and palm EDA from one healthy adult sleeping at home, and 15 nights of wrist EDA from 15 healthy adults in a sleep laboratory, with the latter compared to concurrent polysomnography. While high frequency patterns of EDA called “storms” were identified by eye in the 1960’s, we systematically compare thresholds for automatically detecting EDA peaks and establish criteria for EDA storms. We found that more than 80% of EDA peaks occurred in non-REM sleep, specifically during slow-wave sleep (SWS) and non-REM stage 2 sleep (NREM2). Also, EDA amplitude is higher in SWS than in other sleep stages. Longer EDA storms were more likely in the first two quarters of sleep and during SWS and NREM2. We also found from the home studies (65 nights) that EDA levels were higher and the skin conductance peaks were larger and more frequent when measured on the wrist than when measured on the palm. These EDA high frequency peaks and high amplitude were sometimes associated with higher skin temperature, but more work is needed looking at neurological and other EDA elicitors in order to elucidate their complete behavior. PMID:25286449

  17. Evaluation of Quantitative Precipitation Estimations (QPE) and Hydrological Modelling in IFloodS Focal Basins

    NASA Astrophysics Data System (ADS)

    Wu, H.; Adler, R. F.; Huffman, G. J.; Tian, Y.

    2015-12-01

    A hydrology approach based on the intercomparisons of multiple-product-driven hydrological simulations was implemented for reliably evaluating both quantitative precipitation estimations (QPE) and hydrological modelling at river basin and subbasin scales in the IFloodS focal basin, Iowa-Cedar River Basin (ICRB), over a long-term (2002-2013) and a short-term period (Apr. 1-June 30, 2013). A reference precipitation dataset was created for the evaluation first by reversing the mean annual precipitation from independent observed streamflow and satellite-based ET product and then it was disaggregated to 3-hourly time steps based on NLDAS2. The intercomparisons from different perspectives consistently showed the QPE products with less bias leaded to better streamflow simulation. The reference dataset leaded to overall the best model performance, slightly better than original NLDAS2 (biased -4%) which derived better model performance than all other products in the long-term simulations with daily and monthly NSC of 0.81 and 0.88 respectively and MARE of -2% when compared to observed streamflow at the ICRB outlet, while having reasonable water budgets simulation. Other products (CPC-U, StageIV and TMPARP and satellite-only products) derived gradually decreased performance. All products with long-term records showed consistent merit over the IFloodS period, while the Q2 seemed to be the best estimation for the short-term period. Good correlation between the bias in precipitation and streamflow was found at all from annual to daily scales while the relation and the slope depended on seasons, river basin concentration (routing) time and antecedent river basin water storage condition. Precipitation products also showed significant impacts on streamflow and peak timing. Although satellite-only products could derive even better simulations (than conventional products) for some sub-basins from the short-term evaluation, it had less temporal-spatial quality consistency. While the

  18. A quantitative approach for estimating exposure to pesticides in the Agricultural Health Study.

    PubMed

    Dosemeci, Mustafa; Alavanja, Michael C R; Rowland, Andrew S; Mage, David; Zahm, Shelia Hoar; Rothman, Nathaniel; Lubin, Jay H; Hoppin, Jane A; Sandler, Dale P; Blair, Aaron

    2002-03-01

    We developed a quantitative method to estimate long-term chemical-specific pesticide exposures in a large prospective cohort study of more than 58000 pesticide applicators in North Carolina and Iowa. An enrollment questionnaire was administered to applicators to collect basic time- and intensity-related information on pesticide exposure such as mixing condition, duration and frequency of application, application methods and personal protective equipment used. In addition, a detailed take-home questionnaire was administered to collect further intensity-related exposure information such as maintenance or repair of mixing and application equipment, work practices and personal hygiene. More than 40% of the enrolled applicators responded to this detailed take-home questionnaire. Two algorithms were developed to identify applicators' exposure scenarios using information from the enrollment and take-home questionnaires separately in the calculation of subject-specific intensity of exposure score to individual pesticides. The 'general algorithm' used four basic variables (i.e. mixing status, application method, equipment repair status and personal protective equipment use) from the enrollment questionnaire and measurement data from the published pesticide exposure literature to calculate estimated intensity of exposure to individual pesticides for each applicator. The 'detailed' algorithm was based on variables in the general algorithm plus additional exposure information from the take-home questionnaire, including types of mixing system used (i.e. enclosed or open), having a tractor with enclosed cab and/or charcoal filter, frequency of washing equipment after application, frequency of replacing old gloves, personal hygiene and changing clothes after a spill. Weighting factors applied in both algorithms were estimated using measurement data from the published pesticide exposure literature and professional judgment. For each study subject, chemical-specific lifetime

  19. Improved quantitative precipitation estimation over complex terrain using cloud-to-ground lightning data

    NASA Astrophysics Data System (ADS)

    Minjarez-Sosa, Carlos Manuel

    Thunderstorms that occur in areas of complex terrain are a major severe weather hazard in the intermountain western U.S. Short-term quantitative estimation (QPE) of precipitation in complex terrain is a pressing need to better forecast flash flooding. Currently available techniques for QPE, that utilize a combination of rain gauge and weather radar information, may underestimate precipitation in areas where gauges do not exist or there is radar beam blockage. These are typically very mountainous and remote areas, that are quite vulnerable to flash flooding because of the steep topography. Lightning has been one of the novel ways suggested by the scientific community as an alternative to estimate precipitation over regions that experience convective precipitation, especially those continental areas with complex topography where the precipitation sensor measurements are scarce. This dissertation investigates the relationship between cloud-to-ground lightning and precipitation associated with convection with the purpose of estimating precipitation- mainly over areas of complex terrain which have precipitation sensor coverage problems (e.g. Southern Arizona). The results of this research are presented in two papers. The first, entitled Toward Development of Improved QPE in Complex Terrain Using Cloud-to-Ground Lighting Data: A case Study for the 2005 Monsoon in Southern Arizona, was published in the Journal of Hydrometeorology in December 2012. This initial study explores the relationship between cloud-to-ground lightning occurrences and multi-sensor gridded precipitation over southern Arizona. QPE is performed using a least squares approach for several time resolutions (seasonal---June, July and August---24 hourly and hourly) and for a 8 km grid size. The paper also presents problems that arise when the time resolution is increased, such as the spatial misplacing of discrete lightning events with gridded precipitation and the need to define a "diurnal day" that is

  20. Revised activation estimates for silicon carbide

    SciTech Connect

    Heinisch, H.L.; Cheng, E.T.; Mann, F.M.

    1996-10-01

    Recent progress in nuclear data development for fusion energy systems includes a reevaluation of neutron activation cross sections for silicon and aluminum. Activation calculations using the newly compiled Fusion Evaluated Nuclear Data Library result in calculated levels of {sup 26}Al in irradiated silicon that are about an order of magnitude lower than the earlier calculated values. Thus, according to the latest internationally accepted nuclear data, SiC is much more attractive as a low activation material, even in first wall applications.

  1. Quantitative structure-activity relationship models of chemical transformations from matched pairs analyses.

    PubMed

    Beck, Jeremy M; Springer, Clayton

    2014-04-28

    The concepts of activity cliffs and matched molecular pairs (MMP) are recent paradigms for analysis of data sets to identify structural changes that may be used to modify the potency of lead molecules in drug discovery projects. Analysis of MMPs was recently demonstrated as a feasible technique for quantitative structure-activity relationship (QSAR) modeling of prospective compounds. Although within a small data set, the lack of matched pairs, and the lack of knowledge about specific chemical transformations limit prospective applications. Here we present an alternative technique that determines pairwise descriptors for each matched pair and then uses a QSAR model to estimate the activity change associated with a chemical transformation. The descriptors effectively group similar transformations and incorporate information about the transformation and its local environment. Use of a transformation QSAR model allows one to estimate the activity change for novel transformations and therefore returns predictions for a larger fraction of test set compounds. Application of the proposed methodology to four public data sets results in increased model performance over a benchmark random forest and direct application of chemical transformations using QSAR-by-matched molecular pairs analysis (QSAR-by-MMPA).

  2. Comparative Application of PLS and PCR Methods to Simultaneous Quantitative Estimation and Simultaneous Dissolution Test of Zidovudine - Lamivudine Tablets.

    PubMed

    Üstündağ, Özgür; Dinç, Erdal; Özdemir, Nurten; Tilkan, M Günseli

    2015-01-01

    In the development strategies of new drug products and generic drug products, the simultaneous in-vitro dissolution behavior of oral dosage formulations is the most important indication for the quantitative estimation of efficiency and biopharmaceutical characteristics of drug substances. This is to force the related field's scientists to improve very powerful analytical methods to get more reliable, precise and accurate results in the quantitative analysis and dissolution testing of drug formulations. In this context, two new chemometric tools, partial least squares (PLS) and principal component regression (PCR) were improved for the simultaneous quantitative estimation and dissolution testing of zidovudine (ZID) and lamivudine (LAM) in a tablet dosage form. The results obtained in this study strongly encourage us to use them for the quality control, the routine analysis and the dissolution test of the marketing tablets containing ZID and LAM drugs.

  3. Synthesis, biological activity, and quantitative structure-activity relationship study of azanaphthalimide and arylnaphthalimide derivatives.

    PubMed

    Braña, Miguel F; Gradillas, Ana; Gómez, Angel; Acero, Nuria; Llinares, Francisco; Muñoz-Mingarro, Dolores; Abradelo, Cristina; Rey-Stolle, Fernanda; Yuste, Mercedes; Campos, Joaquín; Gallo, Miguel A; Espinosa, Antonio

    2004-04-22

    A series of quinoline derivatives as aza analogues of the naphthalene chromophore and a series of "nonfused" tricyclic aromatic systems, in particular 5-arylquinolines and 5- or 6-aryl and heteroaryl naphthalene systems, were synthesized and evaluated for growth-inhibitory properties in several human cell lines. The analysis of quantitative structure-antitumor activity relationships for the growth-inhibitory properties is also reported. Findings suggest that these compounds may not express their cytotoxicity via interaction on DNA. PMID:15084122

  4. Quantitative estimation of Newcastle disease virus antibody levels in chickens and turkeys by ELISA.

    PubMed

    Adair, B M; McNulty, M S; Todd, D; Connor, T J; Burns, K

    1989-01-01

    A quantitative single-well ELISA for estimation of Newcastle disease (ND) virus antibodies in chickens and turkeys was developed using purified antigen from PMV-1/Chicken/Ulster 2C/71. The test was standardised using sera from 20-week-old chickens or 20- 30-week-old turkeys. Absorbance values for negative sera in chickens increased with the age of the birds but overall was lower than the cut-off for the test. ND haemagglutination inhibition (HI) positive field sera were always positive by ELISA and the mean was significantly higher than that of the negative population. Standard antisera to four of seven of the other PMV serotypes (including PMV-3) gave positive reactions in ELISA and three were also positive at low level by PMV-1 HI test. Absorbance values remained negative in turkeys given two inoculations of PMV-3 vaccine in spite of good PMV-3 HI responses. Doubling dilutions of chicken and turkey sera were tested by ELISA and end-point titres calculated. Standard curves relating ELISA titre and absorbance of each sample at 1/100 dilution were constructed and used to determine titres of test samples from single well absorbance values. A significant positive correlation between ELISA titre and HI titre for chicken and turkey sera was demonstrated. Sensitivity of the test was investigated using birds experimentally infected with PMV-1/Chicken/Ulster 2C/71 or a pigeon PMV-1 isolate. Seroconversion was detected at the same time by ELISA and HI. In experiments to estimate the ELISA titre required to protect birds against virulent ND, five groups of chickens were vaccinated twice with one of four commercial ND vaccines (three inactivated; one live) on two occasions and challenged with a virulent ND strain (PMV-1/ Chicken/Antrim/73). Two of the groups vaccinated with inactivated vaccines were protected against challenge. In another group also given inactivated vaccine, clinical signs were seen in one bird and ELISA proved a better indicator of immune status than HI. In

  5. Revisiting borehole strain, typhoons, and slow earthquakes using quantitative estimates of precipitation-induced strain changes

    NASA Astrophysics Data System (ADS)

    Hsu, Ya-Ju; Chang, Yuan-Shu; Liu, Chi-Ching; Lee, Hsin-Ming; Linde, Alan T.; Sacks, Selwyn I.; Kitagawa, Genshio; Chen, Yue-Gau

    2015-06-01

    Taiwan experiences high deformation rates, particularly along its eastern margin where a shortening rate of about 30 mm/yr is experienced in the Longitudinal Valley and the Coastal Range. Four Sacks-Evertson borehole strainmeters have been installed in this area since 2003. Liu et al. (2009) proposed that a number of strain transient events, primarily coincident with low-barometric pressure during passages of typhoons, were due to deep-triggered slow slip. Here we extend that investigation with a quantitative analysis of the strain responses to precipitation as well as barometric pressure and the Earth tides in order to isolate tectonic source effects. Estimates of the strain responses to barometric pressure and groundwater level changes for the different stations vary over the ranges -1 to -3 nanostrain/millibar(hPa) and -0.3 to -1.0 nanostrain/hPa, respectively, consistent with theoretical values derived using Hooke's law. Liu et al. (2009) noted that during some typhoons, including at least one with very heavy rainfall, the observed strain changes were consistent with only barometric forcing. By considering a more extensive data set, we now find that the strain response to rainfall is about -5.1 nanostrain/hPa. A larger strain response to rainfall compared to that to air pressure and water level may be associated with an additional strain from fluid pressure changes that take place due to infiltration of precipitation. Using a state-space model, we remove the strain response to rainfall, in addition to those due to air pressure changes and the Earth tides, and investigate whether corrected strain changes are related to environmental disturbances or tectonic-original motions. The majority of strain changes attributed to slow earthquakes seem rather to be associated with environmental factors. However, some events show remaining strain changes after all corrections. These events include strain polarity changes during passages of typhoons (a characteristic that is

  6. Quantitative shape analysis with weighted covariance estimates for increased statistical efficiency

    PubMed Central

    2013-01-01

    Background The introduction and statistical formalisation of landmark-based methods for analysing biological shape has made a major impact on comparative morphometric analyses. However, a satisfactory solution for including information from 2D/3D shapes represented by ‘semi-landmarks’ alongside well-defined landmarks into the analyses is still missing. Also, there has not been an integration of a statistical treatment of measurement error in the current approaches. Results We propose a procedure based upon the description of landmarks with measurement covariance, which extends statistical linear modelling processes to semi-landmarks for further analysis. Our formulation is based upon a self consistent approach to the construction of likelihood-based parameter estimation and includes corrections for parameter bias, induced by the degrees of freedom within the linear model. The method has been implemented and tested on measurements from 2D fly wing, 2D mouse mandible and 3D mouse skull data. We use these data to explore possible advantages and disadvantages over the use of standard Procrustes/PCA analysis via a combination of Monte-Carlo studies and quantitative statistical tests. In the process we show how appropriate weighting provides not only greater stability but also more efficient use of the available landmark data. The set of new landmarks generated in our procedure (‘ghost points’) can then be used in any further downstream statistical analysis. Conclusions Our approach provides a consistent way of including different forms of landmarks into an analysis and reduces instabilities due to poorly defined points. Our results suggest that the method has the potential to be utilised for the analysis of 2D/3D data, and in particular, for the inclusion of information from surfaces represented by multiple landmark points. PMID:23548043

  7. Quantitative estimation of pulegone in Mentha longifolia growing in Saudi Arabia. Is it safe to use?

    PubMed

    Alam, Prawez; Saleh, Mahmoud Fayez; Abdel-Kader, Maged Saad

    2016-03-01

    Our TLC study of the volatile oil isolated from Mentha longifolia showed a major UV active spot with higher Rf value than menthol. Based on the fact that the components of the oil from same plant differ quantitatively due to environmental conditions, the major spot was isolated using different chromatographic techniques and identified by spectroscopic means as pulegone. The presence of pulegone in M. longifolia, a plant widely used in Saudi Arabia, raised a hot debate due to its known toxicity. The Scientific Committee on Food, Health & Consumer Protection Directorate General, European Commission set a limit for the presence of pulegone in foodstuffs and beverages. In this paper we attempted to determine the exact amount of pulegone in different extracts, volatile oil as well as tea flavoured with M. longifolia (Habak) by densitometric HPTLC validated methods using normal phase (Method I) and reverse phase (Method II) TLC plates. The study indicated that the style of use of Habak in Saudi Arabia resulted in much less amount of pulegone than the allowed limit. PMID:27087088

  8. Quantitative estimation of pulegone in Mentha longifolia growing in Saudi Arabia. Is it safe to use?

    PubMed

    Alam, Prawez; Saleh, Mahmoud Fayez; Abdel-Kader, Maged Saad

    2016-03-01

    Our TLC study of the volatile oil isolated from Mentha longifolia showed a major UV active spot with higher Rf value than menthol. Based on the fact that the components of the oil from same plant differ quantitatively due to environmental conditions, the major spot was isolated using different chromatographic techniques and identified by spectroscopic means as pulegone. The presence of pulegone in M. longifolia, a plant widely used in Saudi Arabia, raised a hot debate due to its known toxicity. The Scientific Committee on Food, Health & Consumer Protection Directorate General, European Commission set a limit for the presence of pulegone in foodstuffs and beverages. In this paper we attempted to determine the exact amount of pulegone in different extracts, volatile oil as well as tea flavoured with M. longifolia (Habak) by densitometric HPTLC validated methods using normal phase (Method I) and reverse phase (Method II) TLC plates. The study indicated that the style of use of Habak in Saudi Arabia resulted in much less amount of pulegone than the allowed limit.

  9. Tracking of EEG activity using motion estimation to understand brain wiring.

    PubMed

    Nisar, Humaira; Malik, Aamir Saeed; Ullah, Rafi; Shim, Seong-O; Bawakid, Abdullah; Khan, Muhammad Burhan; Subhani, Ahmad Rauf

    2015-01-01

    The fundamental step in brain research deals with recording electroencephalogram (EEG) signals and then investigating the recorded signals quantitatively. Topographic EEG (visual spatial representation of EEG signal) is commonly referred to as brain topomaps or brain EEG maps. In this chapter, full search full search block motion estimation algorithm has been employed to track the brain activity in brain topomaps to understand the mechanism of brain wiring. The behavior of EEG topomaps is examined throughout a particular brain activation with respect to time. Motion vectors are used to track the brain activation over the scalp during the activation period. Using motion estimation it is possible to track the path from the starting point of activation to the final point of activation. Thus it is possible to track the path of a signal across various lobes.

  10. Recapturing Quantitative Biology.

    ERIC Educational Resources Information Center

    Pernezny, Ken; And Others

    1996-01-01

    Presents a classroom activity on estimating animal populations. Uses shoe boxes and candies to emphasize the importance of mathematics in biology while introducing the methods of quantitative ecology. (JRH)

  11. Obscure phenomena in statistical analysis of quantitative structure-activity relationships. Part 1: Multicollinearity of physicochemical descriptors.

    PubMed

    Mager, P P; Rothe, H

    1990-10-01

    Multicollinearity of physicochemical descriptors leads to serious consequences in quantitative structure-activity relationship (QSAR) analysis, such as incorrect estimators and test statistics of regression coefficients of the ordinary least-squares (OLS) model applied usually to QSARs. Beside the diagnosis of the known simple collinearity, principal component regression analysis (PCRA) also allows the diagnosis of various types of multicollinearity. Only if the absolute values of PCRA estimators are order statistics that decrease monotonically, the effects of multicollinearity can be circumvented. Otherwise, obscure phenomena may be observed, such as good data recognition but low predictive model power of a QSAR model.

  12. Estimating phytoplankton photosynthesis by active fluorescence

    SciTech Connect

    Falkowski, P.G.; Kolber, Z.

    1992-01-01

    Photosynthesis can be described by target theory, At low photon flux densities, photosynthesis is a linear function of irradiance (I), The number of reaction centers (n), their effective absorption capture cross section {sigma}, and a quantum yield {phi}. As photosynthesis becomes increasingly light saturated, an increased fraction of reaction centers close. At light saturation the maximum photosynthetic rate is given as the product of the number of reaction centers (n) and their maximum electron transport rate (I/{tau}). Using active fluorometry it is possible to measure non-destructively and in real time the fraction of open or closed reaction centers under ambient irradiance conditions in situ, as well as {sigma} and {phi} {tau} can be readily, calculated from knowledge of the light saturation parameter, I{sub k} (which can be deduced by in situ by active fluorescence measurements) and {sigma}. We built a pump and probe fluorometer, which is interfaced with a CTD. The instrument measures the fluorescence yield of a weak probe flash preceding (f{sub 0}) and succeeding (f{sub 0}) a saturating pump flash. Profiles of the these fluorescence yields are used to derive the instantaneous rate of gross photosynthesis in natural phytoplankton communities without any incubation. Correlations with short-term simulated in situ radiocarbon measurements are extremely high. The average slope between photosynthesis derived from fluorescence and that measured by radiocarbon is 1.15 and corresponds to the average photosynthetic quotient. The intercept is about 15% of the maximum radiocarbon uptake and corresponds to the average net community respiration. Profiles of photosynthesis and sections showing the variability in its composite parameters reveal a significant effect of nutrient availability on biomass specific rates of photosynthesis in the ocean.

  13. Estimating phytoplankton photosynthesis by active fluorescence

    SciTech Connect

    Falkowski, P.G.; Kolber, Z.

    1992-10-01

    Photosynthesis can be described by target theory, At low photon flux densities, photosynthesis is a linear function of irradiance (I), The number of reaction centers (n), their effective absorption capture cross section {sigma}, and a quantum yield {phi}. As photosynthesis becomes increasingly light saturated, an increased fraction of reaction centers close. At light saturation the maximum photosynthetic rate is given as the product of the number of reaction centers (n) and their maximum electron transport rate (I/{tau}). Using active fluorometry it is possible to measure non-destructively and in real time the fraction of open or closed reaction centers under ambient irradiance conditions in situ, as well as {sigma} and {phi} {tau} can be readily, calculated from knowledge of the light saturation parameter, I{sub k} (which can be deduced by in situ by active fluorescence measurements) and {sigma}. We built a pump and probe fluorometer, which is interfaced with a CTD. The instrument measures the fluorescence yield of a weak probe flash preceding (f{sub 0}) and succeeding (f{sub 0}) a saturating pump flash. Profiles of the these fluorescence yields are used to derive the instantaneous rate of gross photosynthesis in natural phytoplankton communities without any incubation. Correlations with short-term simulated in situ radiocarbon measurements are extremely high. The average slope between photosynthesis derived from fluorescence and that measured by radiocarbon is 1.15 and corresponds to the average photosynthetic quotient. The intercept is about 15% of the maximum radiocarbon uptake and corresponds to the average net community respiration. Profiles of photosynthesis and sections showing the variability in its composite parameters reveal a significant effect of nutrient availability on biomass specific rates of photosynthesis in the ocean.

  14. Recovering the primary geochemistry of Jack Hills zircons through quantitative estimates of chemical alteration

    NASA Astrophysics Data System (ADS)

    Bell, Elizabeth A.; Boehnke, Patrick; Harrison, T. Mark

    2016-10-01

    Despite the robust nature of zircon in most crustal and surface environments, chemical alteration, especially associated with radiation damaged regions, can affect its geochemistry. This consideration is especially important when drawing inferences from the detrital record where the original rock context is missing. Typically, alteration is qualitatively diagnosed through inspection of zircon REE patterns and the style of zoning shown by cathodoluminescence imaging, since fluid-mediated alteration often causes a flat, high LREE pattern. Due to the much lower abundance of LREE in zircon relative both to other crustal materials and to the other REE, disturbance to the LREE pattern is the most likely first sign of disruption to zircon trace element contents. Using a database of 378 (148 new) trace element and 801 (201 new) oxygen isotope measurements on zircons from Jack Hills, Western Australia, we propose a quantitative framework for assessing chemical contamination and exchange with fluids in this population. The Light Rare Earth Element Index is scaled on the relative abundance of light to middle REE, or LREE-I = (Dy/Nd) + (Dy/Sm). LREE-I values vary systematically with other known contaminants (e.g., Fe, P) more faithfully than other suggested proxies for zircon alteration (Sm/La, various absolute concentrations of LREEs) and can be used to distinguish primary compositions when textural evidence for alteration is ambiguous. We find that zircon oxygen isotopes do not vary systematically with placement on or off cracks or with degree of LREE-related chemical alteration, suggesting an essentially primary signature. By omitting zircons affected by LREE-related alteration or contamination by mineral inclusions, we present the best estimate for the primary igneous geochemistry of the Jack Hills zircons. This approach increases the available dataset by allowing for discrimination of on-crack analyses (and analyses with ambiguous or no information on spot placement or

  15. Assimilation of radar quantitative precipitation estimations in the Canadian Precipitation Analysis (CaPA)

    NASA Astrophysics Data System (ADS)

    Fortin, Vincent; Roy, Guy; Donaldson, Norman; Mahidjiba, Ahmed

    2015-12-01

    The Canadian Precipitation Analysis (CaPA) is a data analysis system used operationally at the Canadian Meteorological Center (CMC) since April 2011 to produce gridded 6-h and 24-h precipitation accumulations in near real-time on a regular grid covering all of North America. The current resolution of the product is 10-km. Due to the low density of the observational network in most of Canada, the system relies on a background field provided by the Regional Deterministic Prediction System (RDPS) of Environment Canada, which is a short-term weather forecasting system for North America. For this reason, the North American configuration of CaPA is known as the Regional Deterministic Precipitation Analysis (RDPA). Early in the development of the CaPA system, weather radar reflectivity was identified as a very promising additional data source for the precipitation analysis, but necessary quality control procedures and bias-correction algorithms were lacking for the radar data. After three years of development and testing, a new version of CaPA-RDPA system was implemented in November 2014 at CMC. This version is able to assimilate radar quantitative precipitation estimates (QPEs) from all 31 operational Canadian weather radars. The radar QPE is used as an observation source and not as a background field, and is subject to a strict quality control procedure, like any other observation source. The November 2014 upgrade to CaPA-RDPA was implemented at the same time as an upgrade to the RDPS system, which brought minor changes to the skill and bias of CaPA-RDPA. This paper uses the frequency bias indicator (FBI), the equitable threat score (ETS) and the departure from the partial mean (DPM) in order to assess the improvements to CaPA-RDPA brought by the assimilation of radar QPE. Verification focuses on the 6-h accumulations, and is done against a network of 65 synoptic stations (approximately two stations per radar) that were withheld from the station data assimilated by Ca

  16. Automatic activity estimation based on object behaviour signature

    NASA Astrophysics Data System (ADS)

    Martínez-Pérez, F. E.; González-Fraga, J. A.; Tentori, M.

    2010-08-01

    Automatic estimation of human activities is a topic widely studied. However the process becomes difficult when we want to estimate activities from a video stream, because human activities are dynamic and complex. Furthermore, we have to take into account the amount of information that images provide, since it makes the modelling and estimation activities a hard work. In this paper we propose a method for activity estimation based on object behavior. Objects are located in a delimited observation area and their handling is recorded with a video camera. Activity estimation can be done automatically by analyzing the video sequences. The proposed method is called "signature recognition" because it considers a space-time signature of the behaviour of objects that are used in particular activities (e.g. patients' care in a healthcare environment for elder people with restricted mobility). A pulse is produced when an object appears in or disappears of the observation area. This means there is a change from zero to one or vice versa. These changes are produced by the identification of the objects with a bank of nonlinear correlation filters. Each object is processed independently and produces its own pulses; hence we are able to recognize several objects with different patterns at the same time. The method is applied to estimate three healthcare-related activities of elder people with restricted mobility.

  17. Immunologic methods for quantitative estimation of small peptides and their application to bradykinin.

    PubMed

    Anumula, K R; Schulz, R; Back, N

    1990-12-31

    A simple strategy was developed for the immunologic quantitative determination of small, biologically active peptides utilizing bradykinin (BK) as the model peptide prototype. Methods were developed for the preparation of a peptide-carrier complex suitable for immunization and for immobilization of peptides onto the plastic surface of enzyme-linked immunosorbent assay (ELISA) plates. An avidin-bound biotinylated peptide complex was used for raising peptide antibodies with high titers (1:4000) in the rabbit. The peptide BK was coupled to synthetic polymeric carriers poly-D-lysine (PL) and poly-D-lysine-succinylated (PLS) via the BK carboxy and amino terminus, respectively, with the aid of a water soluble carbodiimide. These carriers with antigen peptide side chains as well as avidin-biotinyl-peptide complexes were efficient surface immobilizing reagents for microwell plastic plates used in the detection of kinins by ELISA. Monoclonal antibodies reacted competitively with kinins in plates coated with either PL-BK or PLS-BK. In contrast, rabbit (polyclonal) antibodies reacted specifically in the plates coated with PLS-BK but only a non-specific reaction could be obtained with the PL-BK coated plates (i.e., could not be displaced with BK). Based on results using synthetic BK analogues, the carboxy terminal half of the BK molecule appears to be the stronger antigenic determinant in both mouse and rabbit systems. The polyclonal antibodies demonstrated a greater affinity to bradykinin compared to the monoclonal antibodies. Their use improved the sensitivity of the ELISA for kinin determination by one order of magnitude. Kinin levels determined in plasma tryptic digests by ELISA with the polyclonal antibodies and PLS-BK system were in agreement with published values.

  18. The ACCE method: an approach for obtaining quantitative or qualitative estimates of residual confounding that includes unmeasured confounding

    PubMed Central

    Smith, Eric G.

    2015-01-01

    Background:  Nonrandomized studies typically cannot account for confounding from unmeasured factors.  Method:  A method is presented that exploits the recently-identified phenomenon of  “confounding amplification” to produce, in principle, a quantitative estimate of total residual confounding resulting from both measured and unmeasured factors.  Two nested propensity score models are constructed that differ only in the deliberate introduction of an additional variable(s) that substantially predicts treatment exposure.  Residual confounding is then estimated by dividing the change in treatment effect estimate between models by the degree of confounding amplification estimated to occur, adjusting for any association between the additional variable(s) and outcome. Results:  Several hypothetical examples are provided to illustrate how the method produces a quantitative estimate of residual confounding if the method’s requirements and assumptions are met.  Previously published data is used to illustrate that, whether or not the method routinely provides precise quantitative estimates of residual confounding, the method appears to produce a valuable qualitative estimate of the likely direction and general size of residual confounding. Limitations:  Uncertainties exist, including identifying the best approaches for: 1) predicting the amount of confounding amplification, 2) minimizing changes between the nested models unrelated to confounding amplification, 3) adjusting for the association of the introduced variable(s) with outcome, and 4) deriving confidence intervals for the method’s estimates (although bootstrapping is one plausible approach). Conclusions:  To this author’s knowledge, it has not been previously suggested that the phenomenon of confounding amplification, if such amplification is as predictable as suggested by a recent simulation, provides a logical basis for estimating total residual confounding. The method's basic approach is

  19. Be the Volume: A Classroom Activity to Visualize Volume Estimation

    ERIC Educational Resources Information Center

    Mikhaylov, Jessica

    2011-01-01

    A hands-on activity can help multivariable calculus students visualize surfaces and understand volume estimation. This activity can be extended to include the concepts of Fubini's Theorem and the visualization of the curves resulting from cross-sections of the surface. This activity uses students as pillars and a sheet or tablecloth for the…

  20. Quantitative evaluation of hidden defects in cast iron components using ultrasound activated lock-in vibrothermography

    SciTech Connect

    Montanini, R.; Freni, F.; Rossi, G. L.

    2012-09-15

    This paper reports one of the first experimental results on the application of ultrasound activated lock-in vibrothermography for quantitative assessment of buried flaws in complex cast parts. The use of amplitude modulated ultrasonic heat generation allowed selective response of defective areas within the part, as the defect itself is turned into a local thermal wave emitter. Quantitative evaluation of hidden damages was accomplished by estimating independently both the area and the depth extension of the buried flaws, while x-ray 3D computed tomography was used as reference for sizing accuracy assessment. To retrieve flaw's area, a simple yet effective histogram-based phase image segmentation algorithm with automatic pixels classification has been developed. A clear correlation was found between the thermal (phase) signature measured by the infrared camera on the target surface and the actual mean cross-section area of the flaw. Due to the very fast cycle time (<30 s/part), the method could potentially be applied for 100% quality control of casting components.

  1. Validation of an ELISA for the quantitation of lanoteplase, a novel plasminogen activator.

    PubMed

    Stouffer, B; Habte, S; Vachharajani, N; Tay, L

    1999-11-01

    An ELISA was developed and validated for the quantitation of lanoteplase in human citrated plasma. The ELISA employed a monoclonal anti-lanoteplase antibody absorbed onto 96-well microtiter plates to capture lanoteplase in citrated human plasma samples containing PPACK, a protease inhibitor. The captured lanoteplase was detected using a biotinylated rabbit anti-lanoteplase polyclonal antibody. The standard curve range in human plasma for the ELISA was 7-100 ng/ml. Assessment of individual standard curve variability indicated reproducible responses with r2 values of > or = 0.985. The accuracy (% DEV) and precision (%RSD) estimates for the ELISA based on the predicted values from quality control (QC) samples were within 7.3% and 11%, respectively. Cross-reactivity with t-PA was determined to be less than 11% by ELISA. The stability of lanoteplase was established in human citrated PPACK plasma for 24 hours at 4 degrees C, for 2 months at -20 degrees C, for 22 months at -70 degrees C, three weeks at room temperature, and through four freeze/thaw cycles. To quantify lanoteplase plasminogen activator (PA) activity, a commercially available chromogenic activity assay was also validated. This method and its application is described briefly here. The lanoteplase ELISA as well as the commercial activity method were successfully employed to evaluate the pharmacokinetic parameters of lanoteplase in support of clinical Phase II/III studies. PMID:10595857

  2. The Impact of Acquisition Dose on Quantitative Breast Density Estimation with Digital Mammography: Results from ACRIN PA 4006.

    PubMed

    Chen, Lin; Ray, Shonket; Keller, Brad M; Pertuz, Said; McDonald, Elizabeth S; Conant, Emily F; Kontos, Despina

    2016-09-01

    Purpose To investigate the impact of radiation dose on breast density estimation in digital mammography. Materials and Methods With institutional review board approval and Health Insurance Portability and Accountability Act compliance under waiver of consent, a cohort of women from the American College of Radiology Imaging Network Pennsylvania 4006 trial was retrospectively analyzed. All patients underwent breast screening with a combination of dose protocols, including standard full-field digital mammography, low-dose digital mammography, and digital breast tomosynthesis. A total of 5832 images from 486 women were analyzed with previously validated, fully automated software for quantitative estimation of density. Clinical Breast Imaging Reporting and Data System (BI-RADS) density assessment results were also available from the trial reports. The influence of image acquisition radiation dose on quantitative breast density estimation was investigated with analysis of variance and linear regression. Pairwise comparisons of density estimations at different dose levels were performed with Student t test. Agreement of estimation was evaluated with quartile-weighted Cohen kappa values and Bland-Altman limits of agreement. Results Radiation dose of image acquisition did not significantly affect quantitative density measurements (analysis of variance, P = .37 to P = .75), with percent density demonstrating a high overall correlation between protocols (r = 0.88-0.95; weighted κ = 0.83-0.90). However, differences in breast percent density (1.04% and 3.84%, P < .05) were observed within high BI-RADS density categories, although they were significantly correlated across the different acquisition dose levels (r = 0.76-0.92, P < .05). Conclusion Precision and reproducibility of automated breast density measurements with digital mammography are not substantially affected by variations in radiation dose; thus, the use of low-dose techniques for the purpose of density estimation

  3. The Impact of Acquisition Dose on Quantitative Breast Density Estimation with Digital Mammography: Results from ACRIN PA 4006.

    PubMed

    Chen, Lin; Ray, Shonket; Keller, Brad M; Pertuz, Said; McDonald, Elizabeth S; Conant, Emily F; Kontos, Despina

    2016-09-01

    Purpose To investigate the impact of radiation dose on breast density estimation in digital mammography. Materials and Methods With institutional review board approval and Health Insurance Portability and Accountability Act compliance under waiver of consent, a cohort of women from the American College of Radiology Imaging Network Pennsylvania 4006 trial was retrospectively analyzed. All patients underwent breast screening with a combination of dose protocols, including standard full-field digital mammography, low-dose digital mammography, and digital breast tomosynthesis. A total of 5832 images from 486 women were analyzed with previously validated, fully automated software for quantitative estimation of density. Clinical Breast Imaging Reporting and Data System (BI-RADS) density assessment results were also available from the trial reports. The influence of image acquisition radiation dose on quantitative breast density estimation was investigated with analysis of variance and linear regression. Pairwise comparisons of density estimations at different dose levels were performed with Student t test. Agreement of estimation was evaluated with quartile-weighted Cohen kappa values and Bland-Altman limits of agreement. Results Radiation dose of image acquisition did not significantly affect quantitative density measurements (analysis of variance, P = .37 to P = .75), with percent density demonstrating a high overall correlation between protocols (r = 0.88-0.95; weighted κ = 0.83-0.90). However, differences in breast percent density (1.04% and 3.84%, P < .05) were observed within high BI-RADS density categories, although they were significantly correlated across the different acquisition dose levels (r = 0.76-0.92, P < .05). Conclusion Precision and reproducibility of automated breast density measurements with digital mammography are not substantially affected by variations in radiation dose; thus, the use of low-dose techniques for the purpose of density estimation

  4. Quantitative and cytotoxic activity determinations on Galanthus nivalis subsp. cilicicus.

    PubMed

    Kaya, G I; Gözler, B

    2005-06-01

    Aerial and underground parts of Galanthus nivalis subsp. cilicicus, a wild-growing species in Turkey, were collected during two different vegetation periods in flowering and fruiting seasons. Herba and bulbus Galanthi were prepared from each specimen. With the aim of collecting data for prospective monographs on this drug, contents of humidity, ash, sulphated ash and total alkaloids were determined according to DAB 10. The specimens were also analyzed quantitatively for two of the principal alkaloids of the genus, galanthamine and lycorine, by using a method based on spectrophotometry complemented with TLC. LC50 values were determined for the ethanolic and alkaloidal extracts of each of the specimens using brine shrimp lethality bioassay.

  5. NEXRAD quantitative precipitation estimates, data acquisition, and processing for the DuPage County, Illinois, streamflow-simulation modeling system

    USGS Publications Warehouse

    Ortel, Terry W.; Spies, Ryan R.

    2015-11-19

    Next-Generation Radar (NEXRAD) has become an integral component in the estimation of precipitation (Kitzmiller and others, 2013). The high spatial and temporal resolution of NEXRAD has revolutionized the ability to estimate precipitation across vast regions, which is especially beneficial in areas without a dense rain-gage network. With the improved precipitation estimates, hydrologic models can produce reliable streamflow forecasts for areas across the United States. NEXRAD data from the National Weather Service (NWS) has been an invaluable tool used by the U.S. Geological Survey (USGS) for numerous projects and studies; NEXRAD data processing techniques similar to those discussed in this Fact Sheet have been developed within the USGS, including the NWS Quantitative Precipitation Estimates archive developed by Blodgett (2013).

  6. NEXRAD quantitative precipitation estimates, data acquisition, and processing for the DuPage County, Illinois, streamflow-simulation modeling system

    USGS Publications Warehouse

    Ortel, Terry W.; Spies, Ryan R.

    2015-01-01

    Next-Generation Radar (NEXRAD) has become an integral component in the estimation of precipitation (Kitzmiller and others, 2013). The high spatial and temporal resolution of NEXRAD has revolutionized the ability to estimate precipitation across vast regions, which is especially beneficial in areas without a dense rain-gage network. With the improved precipitation estimates, hydrologic models can produce reliable streamflow forecasts for areas across the United States. NEXRAD data from the National Weather Service (NWS) has been an invaluable tool used by the U.S. Geological Survey (USGS) for numerous projects and studies; NEXRAD data processing techniques similar to those discussed in this Fact Sheet have been developed within the USGS, including the NWS Quantitative Precipitation Estimates archive developed by Blodgett (2013).

  7. [Quantitative estimation of vegetation cover and management factor in USLE and RUSLE models by using remote sensing data: a review].

    PubMed

    Wu, Chang-Guang; Li, Sheng; Ren, Hua-Dong; Yao, Xiao-Hua; Huang, Zi-Jie

    2012-06-01

    Soil loss prediction models such as universal soil loss equation (USLE) and its revised universal soil loss equation (RUSLE) are the useful tools for risk assessment of soil erosion and planning of soil conservation at regional scale. To make a rational estimation of vegetation cover and management factor, the most important parameters in USLE or RUSLE, is particularly important for the accurate prediction of soil erosion. The traditional estimation based on field survey and measurement is time-consuming, laborious, and costly, and cannot rapidly extract the vegetation cover and management factor at macro-scale. In recent years, the development of remote sensing technology has provided both data and methods for the estimation of vegetation cover and management factor over broad geographic areas. This paper summarized the research findings on the quantitative estimation of vegetation cover and management factor by using remote sensing data, and analyzed the advantages and the disadvantages of various methods, aimed to provide reference for the further research and quantitative estimation of vegetation cover and management factor at large scale.

  8. Reproducibility of CSF quantitative culture methods for estimating rate of clearance in cryptococcal meningitis.

    PubMed

    Dyal, Jonathan; Akampurira, Andrew; Rhein, Joshua; Morawski, Bozena M; Kiggundu, Reuben; Nabeta, Henry W; Musubire, Abdu K; Bahr, Nathan C; Williams, Darlisha A; Bicanic, Tihana; Larsen, Robert A; Meya, David B; Boulware, David R

    2016-05-01

    Quantitative cerebrospinal fluid (CSF) cultures provide a measure of disease severity in cryptococcal meningitis. The fungal clearance rate by quantitative cultures has become a primary endpoint for phase II clinical trials. This study determined the inter-assay accuracy of three different quantitative culture methodologies. Among 91 participants with meningitis symptoms in Kampala, Uganda, during August-November 2013, 305 CSF samples were prospectively collected from patients at multiple time points during treatment. Samples were simultaneously cultured by three methods: (1) St. George's 100 mcl input volume of CSF with five 1:10 serial dilutions, (2) AIDS Clinical Trials Group (ACTG) method using 1000, 100, 10 mcl input volumes, and two 1:100 dilutions with 100 and 10 mcl input volume per dilution on seven agar plates; and (3) 10 mcl calibrated loop of undiluted and 1:100 diluted CSF (loop). Quantitative culture values did not statistically differ between St. George-ACTG methods (P= .09) but did for St. George-10 mcl loop (P< .001). Repeated measures pairwise correlation between any of the methods was high (r≥0.88). For detecting sterility, the ACTG-method had the highest negative predictive value of 97% (91% St. George, 60% loop), but the ACTG-method had occasional (∼10%) difficulties in quantification due to colony clumping. For CSF clearance rate, St. George-ACTG methods did not differ overall (mean -0.05 ± 0.07 log10CFU/ml/day;P= .14) on a group level; however, individual-level clearance varied. The St. George and ACTG quantitative CSF culture methods produced comparable but not identical results. Quantitative cultures can inform treatment management strategies.

  9. Model-Based Estimation of Active Knee Stiffness

    PubMed Central

    Pfeifer, Serge; Hardegger, Michael; Vallery, Heike; List, Renate; Foresti, Mauro; Riener, Robert; Perreault, Eric J.

    2013-01-01

    Knee joint impedance varies substantially during physiological gait. Quantifying this modulation is critical for the design of transfemoral prostheses that aim to mimic physiological limb behavior. Conventional methods for quantifying joint impedance typically involve perturbing the joint in a controlled manner, and describing impedance as the dynamic relationship between applied perturbations and corresponding joint torques. These experimental techniques, however, are difficult to apply during locomotion without impeding natural movements. In this paper, we propose a method to estimate the elastic component of knee joint impedance that depends on muscle activation, often referred to as active knee stiffness. The method estimates stiffness using a musculoskeletal model of the leg and a model for activation-dependent short-range muscle stiffness. Muscle forces are estimated from measurements including limb kinematics, kinetics and muscle electromyograms. For isometric validation, we compare model estimates to measurements involving joint perturbations; measured stiffness is 17% lower than model estimates for extension, and 42% lower for flexion torques. We show that sensitivity of stiffness estimates to common approaches for estimating muscle force is small in isometric conditions. We also make initial estimates of how knee stiffness is modulated during gait, illustrating how this approach may be used to obtain parameters relevant to the design of transfemoral prostheses. PMID:22275672

  10. Using Active Learning to Teach Concepts and Methods in Quantitative Biology.

    PubMed

    Waldrop, Lindsay D; Adolph, Stephen C; Diniz Behn, Cecilia G; Braley, Emily; Drew, Joshua A; Full, Robert J; Gross, Louis J; Jungck, John A; Kohler, Brynja; Prairie, Jennifer C; Shtylla, Blerta; Miller, Laura A

    2015-11-01

    This article provides a summary of the ideas discussed at the 2015 Annual Meeting of the Society for Integrative and Comparative Biology society-wide symposium on Leading Students and Faculty to Quantitative Biology through Active Learning. It also includes a brief review of the recent advancements in incorporating active learning approaches into quantitative biology classrooms. We begin with an overview of recent literature that shows that active learning can improve students' outcomes in Science, Technology, Engineering and Math Education disciplines. We then discuss how this approach can be particularly useful when teaching topics in quantitative biology. Next, we describe some of the recent initiatives to develop hands-on activities in quantitative biology at both the graduate and the undergraduate levels. Throughout the article we provide resources for educators who wish to integrate active learning and technology into their classrooms.

  11. Quantitative Structure Activity Relationship Models for the Antioxidant Activity of Polysaccharides

    PubMed Central

    Nie, Kaiying; Wang, Zhaojing

    2016-01-01

    In this study, quantitative structure activity relationship (QSAR) models for the antioxidant activity of polysaccharides were developed with 50% effective concentration (EC50) as the dependent variable. To establish optimum QSAR models, multiple linear regressions (MLR), support vector machines (SVM) and artificial neural networks (ANN) were used, and 11 molecular descriptors were selected. The optimum QSAR model for predicting EC50 of DPPH-scavenging activity consisted of four major descriptors. MLR model gave EC50 = 0.033Ara-0.041GalA-0.03GlcA-0.025PC+0.484, and MLR fitted the training set with R = 0.807. ANN model gave the improvement of training set (R = 0.96, RMSE = 0.018) and test set (R = 0.933, RMSE = 0.055) which indicated that it was more accurately than SVM and MLR models for predicting the DPPH-scavenging activity of polysaccharides. 67 compounds were used for predicting EC50 of the hydroxyl radicals scavenging activity of polysaccharides. MLR model gave EC50 = 0.12PC+0.083Fuc+0.013Rha-0.02UA+0.372. A comparison of results from models indicated that ANN model (R = 0.944, RMSE = 0.119) was also the best one for predicting the hydroxyl radicals scavenging activity of polysaccharides. MLR and ANN models showed that Ara and GalA appeared critical in determining EC50 of DPPH-scavenging activity, and Fuc, Rha, uronic acid and protein content had a great effect on the hydroxyl radicals scavenging activity of polysaccharides. The antioxidant activity of polysaccharide usually was high in MW range of 4000–100000, and the antioxidant activity could be affected simultaneously by other polysaccharide properties, such as uronic acid and Ara. PMID:27685320

  12. Synthesis, biological activities, and quantitative structure-activity relationship (QSAR) study of novel camptothecin analogues.

    PubMed

    Wu, Dan; Zhang, Shao-Yong; Liu, Ying-Qian; Wu, Xiao-Bing; Zhu, Gao-Xiang; Zhang, Yan; Wei, Wei; Liu, Huan-Xiang; Chen, An-Liang

    2015-05-13

    In continuation of our program aimed at the development of natural product-based pesticidal agents, three series of novel camptothecin derivatives were designed, synthesized, and evaluated for their biological activities against T. Cinnabarinus, B. brassicae, and B. xylophilus. All of the derivatives showed good-to-excellent activity against three insect species tested, with LC50 values ranging from 0.00761 to 0.35496 mmol/L. Remarkably, all of the compounds were more potent than CPT against T. Cinnabarinus, and compounds 4d and 4c displayed superior activity (LC50 0.00761 mmol/L and 0.00942 mmol/L, respectively) compared with CPT (LC50 0.19719 mmol/L) against T. Cinnabarinus. Based on the observed bioactivities, preliminary structure-activity relationship (SAR) correlations were also discussed. Furthermore, a three-dimensional quantitative structure-activity relationship (3D-QSAR) model using comparative molecular field analysis (CoMFA) was built. The model gave statistically significant results with the cross-validated q2 values of 0.580 and correlation coefficient r2 of 0.991 and  of 0.993. The QSAR analysis indicated that the size of the substituents play an important in the activity of 7-modified camptothecin derivatives. These findings will pave the way for further design, structural optimization, and development of camptothecin-derived compounds as pesticidal agents.

  13. Quantitative Estimates of the Numbers of Casualties to be Expected due to Major Earthquakes Near Megacities

    NASA Astrophysics Data System (ADS)

    Wyss, M.; Wenzel, F.

    2004-12-01

    Defining casualties as the sum of the fatalities plus injured, we use their mean number, as calculated by QUAKELOSS (developed by Extreme Situations Research Center, Moscow) as a measure of the extent of possible disasters due to earthquakes. Examples of cities we examined include Algiers, Cairo, Istanbul, Mumbai and Teheran, with populations ranging from about 3 to 20 million. With the assumption that the properties of the building stock has not changed with time since 1950, we find that the number of expected casualties will have increased about 5 to 10 fold by the year 2015. This increase is directly proportional to the increase of the population. For the assumed magnitude, we used M7 and M6.5 because shallow earthquakes in this range can occur in the seismogenic layer, without rupturing the surface. This means, they could occur anywhere in a seismically active area, not only along known faults. As a function of epicentral distance the fraction of casualties of the population decrease from about 6% at 20 km, to 3% at 30 km and 0.5% at 50 km, for an earthquake of M7. At 30 km distance, the assumed variation of the properties of the building stock from country to country give rise to variations of 1% to 5% for the estimate of the percent of the population that become casualties. As a function of earthquake size, the expected number of casualties drop by approximately an order of magnitude for an M6.5, compared to an M7, at 30 km distance. Because the computer code and database in QUAKELOSS are calibrated based on about 1000 earthquakes with fatalities, and verified by real-time loss estimates for about 60 cases, these results are probably of the correct order of magnitude. However, the results should not be taken as overly reliable, because (1) the probability calculations of the losses result in uncertainties of about a factor of two, (2) the method has been tested for medium size cities, not for megacities, and (3) many assumptions were made. Nevertheless, it is

  14. Comparison of Estimated and Measured Muscle Activity During Inclined Walking.

    PubMed

    Alexander, Nathalie; Schwameder, Hermann

    2016-04-01

    While inclined walking is a frequent daily activity, muscle forces during this activity have rarely been examined. Musculoskeletal models are commonly used to estimate internal forces in healthy populations, but these require a priori validation. The aim of this study was to compare estimated muscle activity using a musculoskeletal model with measured EMG data during inclined walking. Ten healthy male participants walked at different inclinations of 0°, ± 6°, ± 12°, and ± 18° on a ramp equipped with 2 force plates. Kinematics, kinetics, and muscle activity of the musculus (m.) biceps femoris, m. rectus femoris, m. vastus lateralis, m. tibialis anterior, and m. gastrocnemius lateralis were recorded. Agreement between estimated and measured muscle activity was determined via correlation coefficients, mean absolute errors, and trend analysis. Correlation coefficients between estimated and measured muscle activity for approximately 69% of the conditions were above 0.7. Mean absolute errors were rather high with only approximately 38% being ≤ 30%. Trend analysis revealed similar estimated and measured muscle activities for all muscles and tasks (uphill and downhill walking), except m. tibialis anterior during uphill walking. This model can be used for further analysis in similar groups of participants.

  15. Quantitative structure-activity relationship (QSAR) for insecticides: development of predictive in vivo insecticide activity models.

    PubMed

    Naik, P K; Singh, T; Singh, H

    2009-07-01

    Quantitative structure-activity relationship (QSAR) analyses were performed independently on data sets belonging to two groups of insecticides, namely the organophosphates and carbamates. Several types of descriptors including topological, spatial, thermodynamic, information content, lead likeness and E-state indices were used to derive quantitative relationships between insecticide activities and structural properties of chemicals. A systematic search approach based on missing value, zero value, simple correlation and multi-collinearity tests as well as the use of a genetic algorithm allowed the optimal selection of the descriptors used to generate the models. The QSAR models developed for both organophosphate and carbamate groups revealed good predictability with r(2) values of 0.949 and 0.838 as well as [image omitted] values of 0.890 and 0.765, respectively. In addition, a linear correlation was observed between the predicted and experimental LD(50) values for the test set data with r(2) of 0.871 and 0.788 for both the organophosphate and carbamate groups, indicating that the prediction accuracy of the QSAR models was acceptable. The models were also tested successfully from external validation criteria. QSAR models developed in this study should help further design of novel potent insecticides.

  16. Quantitative analysis of cardiovascular modulation in respiratory neural activity.

    PubMed

    Dick, Thomas E; Morris, Kendall F

    2004-05-01

    We propose the 'delta(2)-statistic' for assessing the magnitude and statistical significance of arterial pulse-modulated activity of single neurones and present the results of applying this tool to medullary respiratory-modulated units. This analytical tool is a modification of the eta(2)-statistic and, consequently, based on the analysis of variance. The eta(2)-statistic reflects the consistency of respiratory-modulated activity on a cycle-by-cycle basis. However, directly applying this test to activity during the cardiac cycle proved ineffective because subjects-by-treatments matrices did not contain enough 'information'. We increased information by dividing the cardiac cycle into fewer bins, excluding cycles without activity and summing activity over multiple cycles. The analysed neuronal activity was an existing data set examining the neural control of respiration and cough. Neurones were recorded in the nuclei of the solitary tracts, and in the rostral and caudal ventral respiratory groups of decerebrate, neuromuscularly blocked, ventilated cats (n= 19). Two hundred of 246 spike trains were respiratory modulated; of these 53% were inspiratory (I), 36.5% expiratory (E), 6% IE phase spanning and 4.5% EI phase spanning and responsive to airway stimulation. Nearly half (n= 96/200) of the respiratory-modulated units were significantly pulse modulated and 13 were highly modulated with delta(2) values exceeding 0.3. In 10 of these highly modulated units, eta(2) values were greater than 0.3 and all 13 had, at least, a portion of their activity during expiration. We conclude that cardiorespiratory interaction is reciprocal; in addition to respiratory-modulated activity in a subset of neuronal activity patterns controlling the cardiovascular system, pulse-modulated activity exists in a subset of neuronal activity patterns controlling the respiratory system. Thus, cardio-ventilatory coupling apparent in respiratory motor output is evident and, perhaps, derived from the

  17. Quantitative structure-activity relationship of antifungal activity of rosin derivatives.

    PubMed

    Wang, Hui; Nguyen, Thi Thanh Hien; Li, Shujun; Liang, Tao; Zhang, Yuanyuan; Li, Jian

    2015-01-15

    To develop new rosin-based wood preservatives with good antifungal activity, 24 rosin derivatives were synthesized, bioassay tested with Trametes versicolor and Gloeophyllum trabeum, and subjected to analysis of their quantitative structure-activity relationships (QSAR). A QSAR analysis using Ampac 9.2.1 and Codessa 2.7.16 software built two QSAR models of antifungal ratio for T. versicolor and G. trabeum with values of R(2)=0.9740 and 0.9692, respectively. Based on the models, tri-N-(3-hydroabietoxy-2-hydroxy) propyl-triethyl ammonium chloride was designed and the bioassay test result proved its better inhibitory effect against the two selected fungi as expected.

  18. Quantitative structure-activity relationship of antifungal activity of rosin derivatives.

    PubMed

    Wang, Hui; Nguyen, Thi Thanh Hien; Li, Shujun; Liang, Tao; Zhang, Yuanyuan; Li, Jian

    2015-01-15

    To develop new rosin-based wood preservatives with good antifungal activity, 24 rosin derivatives were synthesized, bioassay tested with Trametes versicolor and Gloeophyllum trabeum, and subjected to analysis of their quantitative structure-activity relationships (QSAR). A QSAR analysis using Ampac 9.2.1 and Codessa 2.7.16 software built two QSAR models of antifungal ratio for T. versicolor and G. trabeum with values of R(2)=0.9740 and 0.9692, respectively. Based on the models, tri-N-(3-hydroabietoxy-2-hydroxy) propyl-triethyl ammonium chloride was designed and the bioassay test result proved its better inhibitory effect against the two selected fungi as expected. PMID:25466709

  19. Validation and Estimation of Additive Genetic Variation Associated with DNA Tests for Quantitative Beef Cattle Traits

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The U.S. National Beef Cattle Evaluation Consortium (NBCEC) has been involved in the validation of commercial DNA tests for quantitative beef quality traits since their first appearance on the U.S. market in the early 2000s. The NBCEC Advisory Council initially requested that the NBCEC set up a syst...

  20. The Overall Impact of Testing on Medical Student Learning: Quantitative Estimation of Consequential Validity

    ERIC Educational Resources Information Center

    Kreiter, Clarence D.; Green, Joseph; Lenoch, Susan; Saiki, Takuya

    2013-01-01

    Given medical education's longstanding emphasis on assessment, it seems prudent to evaluate whether our current research and development focus on testing makes sense. Since any intervention within medical education must ultimately be evaluated based upon its impact on student learning, this report seeks to provide a quantitative accounting of…

  1. Utilization of quantitative structure-activity relationships (QSARs) in risk assessment: Alkylphenols

    SciTech Connect

    Beck, B.D.; Toole, A.P.; Callahan, B.G.; Siddhanti, S.K. )

    1991-12-01

    Alkylphenols are a class of environmentally pervasive compounds, found both in natural (e.g., crude oils) and in anthropogenic (e.g., wood tar, coal gasification waste) materials. Despite the frequent environmental occurrence of these chemicals, there is a limited toxicity database on alkylphenols. The authors have therefore developed a 'toxicity equivalence approach' for alkylphenols which is based on their ability to inhibit, in a specific manner, the enzyme cyclooxygenase. Enzyme-inhibiting ability for individual alkylphenols can be estimated based on the quantitative structure-activity relationship developed by Dewhirst (1980) and is a function of the free hydroxyl group, electron-donating ring substituents, and hydrophobic aromatic ring substituents. The authors evaluated the toxicological significance of cyclooxygenase inhibition by comparison of the inhibitory capacity of alkylphenols with the inhibitory capacity of acetylsalicylic acid, or aspirin, a compound whose low-level effects are due to cyclooxygenase inhibition. Since nearly complete absorption for alkylphenols and aspirin is predicted, based on estimates of hydrophobicity and fraction of charged molecules at gastrointestinal pHs, risks from alkylphenols can be expressed directly in terms of 'milligram aspirin equivalence,' without correction for absorption differences. They recommend this method for assessing risks of mixtures of alkylphenols, especially for those compounds with no chronic toxicity data.38 references.

  2. 76 FR 27384 - Agency Information Collection Activity (Veteran Suicide Prevention Online Quantitative Surveys...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-11

    ... AFFAIRS Agency Information Collection Activity (Veteran Suicide Prevention Online Quantitative Surveys...). Type of Review: New collection. Abstract: VA's top priority is the prevention of Veterans suicide. It... better understand Veterans and their families' awareness of VA's suicide prevention and mental...

  3. PREDICTING TOXICOLOGICAL ENDPOINTS OF CHEMICALS USING QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIPS (QSARS)

    EPA Science Inventory

    Quantitative structure-activity relationships (QSARs) are being developed to predict the toxicological endpoints for untested chemicals similar in structure to chemicals that have known experimental toxicological data. Based on a very large number of predetermined descriptors, a...

  4. Quantitative Structure--Activity Relationship Modeling of Rat Acute Toxicity by Oral Exposure

    EPA Science Inventory

    Background: Few Quantitative Structure-Activity Relationship (QSAR) studies have successfully modeled large, diverse rodent toxicity endpoints. Objective: In this study, a combinatorial QSAR approach has been employed for the creation of robust and predictive models of acute toxi...

  5. A Bayesian quantitative nondestructive evaluation (QNDE) approach to estimating remaining life of aging pressure vessels and piping*

    NASA Astrophysics Data System (ADS)

    Fong, J. T.; Filliben, J. J.; Heckert, N. A.; Guthrie, W. F.

    2013-01-01

    In this paper, we use a Bayesian quantitative nondestructive evaluation (QNDE) approach to estimating the remaining life of aging structures and components. Our approach depends on in-situ NDE measurements of detectable crack lengths and crack growth rates in a multi-crack region of an aging component as a basis for estimating the mean and standard deviation of its remaining life. We introduce a general theory of crack growth involving multiple cracks such that the mean and standard deviation of the initial crack lengths can be directly estimated from NDEmeasured crack length data over a period of several inspection intervals. A numerical example using synthetic NDE data for high strength steels is presented to illustrate this new methodology.

  6. Methodologies for the quantitative estimation of toxicant dose to cigarette smokers using physical, chemical and bioanalytical data

    PubMed Central

    McAughey, John; Shepperd, Christopher J.

    2013-01-01

    Methodologies have been developed, described and demonstrated that convert mouth exposure estimates of cigarette smoke constituents to dose by accounting for smoke spilled from the mouth prior to inhalation (mouth-spill (MS)) and the respiratory retention (RR) during the inhalation cycle. The methodologies are applicable to just about any chemical compound in cigarette smoke that can be measured analytically and can be used with ambulatory population studies. Conversion of exposure to dose improves the relevancy for risk assessment paradigms. Except for urinary nicotine plus metabolites, biomarkers generally do not provide quantitative exposure or dose estimates. In addition, many smoke constituents have no reliable biomarkers. We describe methods to estimate the RR of chemical compounds in smoke based on their vapor pressure (VP) and to estimate the MS for a given subject. Data from two clinical studies were used to demonstrate dose estimation for 13 compounds, of which only 3 have urinary biomarkers. Compounds with VP > 10−5 Pa generally have RRs of 88% or greater, which do not vary appreciably with inhalation volume (IV). Compounds with VP < 10−7 Pa generally have RRs dependent on IV and lung exposure time. For MS, mean subject values from both studies were slightly greater than 30%. For constituents with urinary biomarkers, correlations with the calculated dose were significantly improved over correlations with mouth exposure. Of toxicological importance is that the dose correlations provide an estimate of the metabolic conversion of a constituent to its respective biomarker. PMID:23742081

  7. Using quantitative structure-activity relationship modeling to quantitatively predict the developmental toxicity of halogenated azole compounds.

    PubMed

    Craig, Evisabel A; Wang, Nina Ching; Zhao, Q Jay

    2014-07-01

    Developmental toxicity is a relevant endpoint for the comprehensive assessment of human health risk from chemical exposure. However, animal developmental toxicity data remain unavailable for many environmental contaminants due to the complexity and cost of these types of analyses. Here we describe an approach that uses quantitative structure-activity relationship modeling as an alternative methodology to fill data gaps in the developmental toxicity profile of certain halogenated compounds. Chemical information was obtained and curated using the OECD Quantitative Structure-Activity Relationship Toolbox, version 3.0. Data from 35 curated compounds were analyzed via linear regression to build the predictive model, which has an R(2) of 0.79 and a Q(2) of 0.77. The applicability domain (AD) was defined by chemical category and structural similarity. Seven halogenated chemicals that fit the AD but are not part of the training set were employed for external validation purposes. Our model predicted lowest observed adverse effect level values with a maximal threefold deviation from the observed experimental values for all chemicals that fit the AD. The good predictability of our model suggests that this method may be applicable to the analysis of qualifying compounds whenever developmental toxicity information is lacking or incomplete for risk assessment considerations.

  8. Commercial Activities in Primary Schools: A Quantitative Study

    ERIC Educational Resources Information Center

    Raine, Gary

    2007-01-01

    The commercialisation of schools is a controversial issue, but very little is known about the actual situation in UK schools. The aim of this study was to investigate, with particular reference to health education and health promotion, commercial activities and their regulation in primary schools in the Yorkshire and Humber region of the UK. A…

  9. Development and validation of a quantitative structure-activity relationship for chronic narcosis to fish.

    PubMed

    Claeys, Lieve; Iaccino, Federica; Janssen, Colin R; Van Sprang, Patrick; Verdonck, Frederik

    2013-10-01

    Vertebrate testing under the European Union's regulation on Registration, Evaluation, Authorisation and Restriction of Chemical substances (REACH) is discouraged, and the use of alternative nontesting approaches such as quantitative structure-activity relationships (QSARs) is encouraged. However, robust QSARs predicting chronic ecotoxicity of organic compounds to fish are not available. The Ecological Structure Activity Relationships (ECOSAR) Class Program is a computerized predictive system that estimates the acute and chronic toxicity of organic compounds for several chemical classes based on their log octanol-water partition coefficient (K(OW)). For those chemical classes for which chronic training data sets are lacking, acute to chronic ratios are used to predict chronic toxicity to aquatic organisms. Although ECOSAR reaches a high score against the Organisation for Economic Co-operation and Development (OECD) principles for QSAR validation, the chronic QSARs in ECOSAR are not fully compliant with OECD criteria in the framework of REACH or CLP (classification, labeling, and packaging) regulation. The objective of the present study was to develop a chronic ecotoxicity QSAR for fish for compounds acting via nonpolar and polar narcosis. These QSARs were built using a database of quality screened toxicity values, considering only chronic exposure durations and relevant end points. After statistical multivariate diagnostic analysis, literature-based, mechanistically relevant descriptors were selected to develop a multivariate regression model. Finally, these QSARs were tested for their acceptance for regulatory purposes and were found to be compliant with the OECD principles for the validation of a QSAR.

  10. Some methods of obtaining quantitative structure-activity relationships for quantities of environmental interest

    SciTech Connect

    Charton, M.

    1985-09-01

    Methods are described for obtaining quantitative structure-activity relationships (QSAR) for the estimation of quantities of environmental interest. Toxicities of alkylamines and of alkyl alkanoates are well correlated by the alkyl bioactivity branching equation (ABB). Narcotic activities of 1,1-disubstituted ethylenes are correlated by the intermolecular forces bioactivity (IMF) equation. When the data set has a limited number of substituents in equivalent positions the group number (GN) equation, derivable from the IMF equation, can be used for correlation. It has been successfully applied to aqueous solubilities, 1-octanol-water partition coefficients, and bioaccumulation factors and ecological magnifications for organochlorine compounds. A combination of the omega method for combining data sets for different organisms with the GN equation has been used to correlate toxicities of organochlorine insecticides in two species of fish. Toxicities of carbamates have been correlated by a combination of the zeta method and the IMFB equation. The ABB and the GN equations are particularly useful in that they generally do not require parameter tables, and that the parameters they use are error-free. The methods presented here, as shown by the examples given, should make it possible to establish a collection of QSAR for toxicities, bioaccumulation factors, aqueous solubilities, partition coefficients, and other properties of sets of compounds of environmental interest. 29 references.

  11. Matched-field depth estimation for active sonar.

    PubMed

    Hickman, Granger; Krolik, Jeffrey L

    2004-02-01

    This work concerns the problem of estimating the depth of a submerged scatterer in a shallow-water ocean by using an active sonar and a horizontal receiver array. As in passive matched-field processing (MFP) techniques, numerical modeling of multipath propagation is used to facilitate localization. However, unlike passive MFP methods where estimation of source range is critically dependent on relative modal phase modeling, in active sonar source range is approximately known from travel-time measurements. Thus the proposed matched-field depth estimation (MFDE) method does not require knowledge of the complex relative multipath amplitudes which also depend on the unknown scatterer characteristics. Depth localization is achieved by modeling depth-dependent relative delays and elevation angle spreads between multipaths. A maximum likelihood depth estimate is derived under the assumption that returns from a sequence of pings are uncorrelated and the scatterer is at constant depth. The Cramér-Rao lower bound on depth estimation mean-square-error is computed and compared with Monte Carlo simulation results for a typical range-dependent, shallow-water Mediterranean environment. Depth estimation performance to within 10% of the water column depth is predicted at signal-to-noise ratios of greater than 10 dB. Real data results are reported for depth estimation of an echo repeater to within 10-m accuracy in this same shallow water environment.

  12. Modeling real-time PCR kinetics: Richards reparametrized equation for quantitative estimation of European hake (Merluccius merluccius).

    PubMed

    Sánchez, Ana; Vázquez, José A; Quinteiro, Javier; Sotelo, Carmen G

    2013-04-10

    Real-time PCR is the most sensitive method for detection and precise quantification of specific DNA sequences, but it is not usually applied as a quantitative method in seafood. In general, benchmark techniques, mainly cycle threshold (Ct), are the routine method for quantitative estimations, but they are not the most precise approaches for a standard assay. In the present work, amplification data from European hake (Merluccius merluccius) DNA samples were accurately modeled by three sigmoid reparametrized equations, where the lag phase parameter (λc) from the Richards equation with four parameters was demonstrated to be the perfect substitute for Ct for PCR quantification. The concentrations of primers and probes were subsequently optimized by means of that selected kinetic parameter. Finally, the linear correlation among DNA concentration and λc was also confirmed.

  13. Quantitative measurements of active Ionian volcanoes in Galileo NIMS data

    NASA Astrophysics Data System (ADS)

    Saballett, Sebastian; Rathbun, Julie A.; Lopes, Rosaly M. C.; Spencer, John R.

    2016-10-01

    Io is the most volcanically active body in our solar system. The spatial distribution of volcanoes a planetary body's surface gives clues into its basic inner workings (i.e., plate tectonics on earth). Tidal heating is the major contributor to active surface geology in the outer solar system, and yet its mechanism is not completely understood. Io's volcanoes are the clearest signature of tidal heating and measurements of the total heat output and how it varies in space and time are useful constraints on tidal heating. Hamilton et al. (2013) showed through a nearest neighbor analysis that Io's hotspots are globally random, but regionally uniform near the equator. Lopes-Gautier et al. (1999) compared the locations of hotspots detected by NIMS to the spatial variation of heat flow predicted by two end-member tidal heating models. They found that the distribution of hotspots is more consistent with tidal heating occurring in asthenosphere rather than the mantle. Hamilton et al. (2013) demonstrate that clustering of hotspots also supports a dominant role for asthenosphere heating. These studies were unable to account for the relative brightness of the hotspots. Furthermore, studies of the temporal variability of Ionian volcanoes have yielded substantial insight into their nature. The Galileo Near Infrared Mapping Spectrometer (NIMS) gave us a large dataset from which to observe active volcanic activity. NIMS made well over 100 observations of Io over an approximately 10-year time frame. With wavelengths spanning from 0.7 to 5.2 microns, it is ideally suited to measure blackbody radiation from surfaces with temperatures over 300 K. Here, we report on our effort to determine the activity level of each hotspot observed in the NIMS data. We decide to use 3.5 micron brightness as a proxy for activity level because it will be easy to compare to, and incorporate, ground-based observations. We fit a 1-temperature blackbody to spectra in each grating position and averaged the

  14. Modeling Bone Surface Morphology: A Fully Quantitative Method for Age-at-Death Estimation Using the Pubic Symphysis.

    PubMed

    Slice, Dennis E; Algee-Hewitt, Bridget F B

    2015-07-01

    The pubic symphysis is widely used in age estimation for the adult skeleton. Standard practice requires the visual comparison of surface morphology against criteria representing predefined phases and the estimation of case-specific age from an age range associated with the chosen phase. Known problems of method and observer error necessitate alternative tools to quantify age-related change in pubic morphology. This paper presents an objective, fully quantitative method for estimating age-at-death from the skeleton, which exploits a variance-based score of surface complexity computed from vertices obtained from a scanner sampling the pubic symphysis. For laser scans from 41 modern American male skeletons, this method produces results that are significantly associated with known age-at-death (RMSE = 17.15 years). Chronological age is predicted, therefore, equally well, if not, better, with this robust, objective, and fully quantitative method than with prevailing phase-aging systems. This method contributes to forensic casework by responding to medico-legal expectations for evidence standards.

  15. Estimation of spatiotemporal neural activity using radial basis function networks.

    PubMed

    Anderson, R W; Das, S; Keller, E L

    1998-12-01

    We report a method using radial basis function (RBF) networks to estimate the time evolution of population activity in topologically organized neural structures from single-neuron recordings. This is an important problem in neuroscience research, as such estimates may provide insights into systems-level function of these structures. Since single-unit neural data tends to be unevenly sampled and highly variable under similar behavioral conditions, obtaining such estimates is a difficult task. In particular, a class of cells in the superior colliculus called buildup neurons can have very narrow regions of saccade vectors for which they discharge at high rates but very large surround regions over which they discharge at low, but not zero, levels. Estimating the dynamic movement fields for these cells for two spatial dimensions at closely spaced timed intervals is a difficult problem, and no general method has been described that can be applied to all buildup cells. Estimation of individual collicular cells' spatiotemporal movement fields is a prerequisite for obtaining reliable two-dimensional estimates of the population activity on the collicular motor map during saccades. Therefore, we have developed several computational-geometry-based algorithms that regularize the data before computing a surface estimation using RBF networks. The method is then expanded to the problem of estimating simultaneous spatiotemporal activity occurring across the superior colliculus during a single movement (the inverse problem). In principle, this methodology could be applied to any neural structure with a regular, two-dimensional organization, provided a sufficient spatial distribution of sampled neurons is available.

  16. Bottom-up modeling approach for the quantitative estimation of parameters in pathogen-host interactions

    PubMed Central

    Lehnert, Teresa; Timme, Sandra; Pollmächer, Johannes; Hünniger, Kerstin; Kurzai, Oliver; Figge, Marc Thilo

    2015-01-01

    Opportunistic fungal pathogens can cause bloodstream infection and severe sepsis upon entering the blood stream of the host. The early immune response in human blood comprises the elimination of pathogens by antimicrobial peptides and innate immune cells, such as neutrophils or monocytes. Mathematical modeling is a predictive method to examine these complex processes and to quantify the dynamics of pathogen-host interactions. Since model parameters are often not directly accessible from experiment, their estimation is required by calibrating model predictions with experimental data. Depending on the complexity of the mathematical model, parameter estimation can be associated with excessively high computational costs in terms of run time and memory. We apply a strategy for reliable parameter estimation where different modeling approaches with increasing complexity are used that build on one another. This bottom-up modeling approach is applied to an experimental human whole-blood infection assay for Candida albicans. Aiming for the quantification of the relative impact of different routes of the immune response against this human-pathogenic fungus, we start from a non-spatial state-based model (SBM), because this level of model complexity allows estimating a priori unknown transition rates between various system states by the global optimization method simulated annealing. Building on the non-spatial SBM, an agent-based model (ABM) is implemented that incorporates the migration of interacting cells in three-dimensional space. The ABM takes advantage of estimated parameters from the non-spatial SBM, leading to a decreased dimensionality of the parameter space. This space can be scanned using a local optimization approach, i.e., least-squares error estimation based on an adaptive regular grid search, to predict cell migration parameters that are not accessible in experiment. In the future, spatio-temporal simulations of whole-blood samples may enable timely

  17. Methods for the quantitative comparison of molecular estimates of clade age and the fossil record.

    PubMed

    Clarke, Julia A; Boyd, Clint A

    2015-01-01

    Approaches quantifying the relative congruence, or incongruence, of molecular divergence estimates and the fossil record have been limited. Previously proposed methods are largely node specific, assessing incongruence at particular nodes for which both fossil data and molecular divergence estimates are available. These existing metrics, and other methods that quantify incongruence across topologies including entirely extinct clades, have so far not taken into account uncertainty surrounding both the divergence estimates and the ages of fossils. They have also treated molecular divergence estimates younger than previously assessed fossil minimum estimates of clade age as if they were the same as cases in which they were older. However, these cases are not the same. Recovered divergence dates younger than compared oldest known occurrences require prior hypotheses regarding the phylogenetic position of the compared fossil record and standard assumptions about the relative timing of morphological and molecular change to be incorrect. Older molecular dates, by contrast, are consistent with an incomplete fossil record and do not require prior assessments of the fossil record to be unreliable in some way. Here, we compare previous approaches and introduce two new descriptive metrics. Both metrics explicitly incorporate information on uncertainty by utilizing the 95% confidence intervals on estimated divergence dates and data on stratigraphic uncertainty concerning the age of the compared fossils. Metric scores are maximized when these ranges are overlapping. MDI (minimum divergence incongruence) discriminates between situations where molecular estimates are younger or older than known fossils reporting both absolute fit values and a number score for incompatible nodes. DIG range (divergence implied gap range) allows quantification of the minimum increase in implied missing fossil record induced by enforcing a given set of molecular-based estimates. These metrics are used

  18. FPGA-Based Fused Smart-Sensor for Tool-Wear Area Quantitative Estimation in CNC Machine Inserts

    PubMed Central

    Trejo-Hernandez, Miguel; Osornio-Rios, Roque Alfredo; de Jesus Romero-Troncoso, Rene; Rodriguez-Donate, Carlos; Dominguez-Gonzalez, Aurelio; Herrera-Ruiz, Gilberto

    2010-01-01

    Manufacturing processes are of great relevance nowadays, when there is a constant claim for better productivity with high quality at low cost. The contribution of this work is the development of a fused smart-sensor, based on FPGA to improve the online quantitative estimation of flank-wear area in CNC machine inserts from the information provided by two primary sensors: the monitoring current output of a servoamplifier, and a 3-axis accelerometer. Results from experimentation show that the fusion of both parameters makes it possible to obtain three times better accuracy when compared with the accuracy obtained from current and vibration signals, individually used. PMID:22319304

  19. Quantitative evaluation of erythropoietic activity in dysmyelopoietic syndromes.

    PubMed

    Cazzola, M; Barosi, G; Berzuini, C; Dacco, M; Orlandi, E; Stefanelli, M; Ascari, E

    1982-01-01

    Based on the morphological appearances of the bone marrow and peripheral blood, 43 patients with dysmyelopoietic syndromes were categorized into four types: refractory anaemia with excess of blasts, chronic myelomonocytic leukaemia, primary acquired sideroblastic anaemia and refractory anaemia with cellular marrow, without excess of blasts and/or ring sideroblasts. Ferrokinetics allowed three distinct groups of patients to be defined. All cases of refractory anaemia with excess of blasts and chronic myelomonocytic leukaemia were classified in the same group. They were characterized by relative marrow failure and had a high likelihood of developing acute leukaemia. At the other end of the spectrum, individuals with primary acquired sideroblastic anaemia had high erythropoietic activity which was largely ineffective. They had a benign clinical course without evidence of leukaemic transformation. In the middle group, in terms of erythropoietic activity, lay patients with refractory anaemia with cellular marrow and a few individuals with primary acquired sideroblastic anaemia. Their clinical course and risk of developing acute leukaemia were intermediate between the other two groups. These findings indicate that separate entities may exist within the spectrum of dysmyelopoietic syndromes. In clinical practice, they may be recognized by morphological studies and other simple laboratory means.

  20. Quantitative analysis of phenol oxidase activity in insect hemolymph.

    PubMed

    Sorrentino, Richard Paul; Small, Chiyedza N; Govind, Shubha

    2002-04-01

    We describe a simple, inexpensive, and robust protocol for the quantification of phenol oxidase activity in insect hemolymph. Discrete volumes of hemolymph from Drosophila melanogaster larvae are applied to pieces of filter paper soaked in an L-3, 4-dihydroxyphenylalanine (L-DOPA) solution. Phenol oxidase present in the samples catalyzes melanin synthesis from the L-DOPA precursor, resulting in the appearance of a roughly circular melanized spot on the filter paper. The filter paper is then scanned and analyzed with image-processing software. Each pixel in an image is assigned a grayscale value. The mean of the grayscale values for a circular region of pixels at the center of the image of each spot is used to compute a melanization index (MI) value, the computation is based on a comparison to an external standard (India ink). Numerical MI values for control and experimental larvae can then be pooled and subjected to statistical analysis. This protocol was used to evaluate phenol oxidase activity in larvae of different backgrounds: wild-type, lozenge, hopscotch(Tumorous-lethal) (which induces the formation of large melanotic tumors), and body-color mutations ebony and yellow. Our results demonstrate that this assay is sensitive enough for use in genetic screens with D. melanogaster and could conceivably be used for evaluation of MI from hemolymph of other insects.

  1. Estimation of excitatory and inhibitory synaptic conductance variations in motoneurons during locomotor-like rhythmic activity.

    PubMed

    Kobayashi, Ryota; Nishimaru, Hiroshi; Nishijo, Hisao

    2016-10-29

    The rhythmic activity of motoneurons (MNs) that underlies locomotion in mammals is generated by synaptic inputs from the locomotor network in the spinal cord. Thus, the quantitative estimation of excitatory and inhibitory synaptic conductances is essential to understand the mechanism by which the network generates the functional motor output. Conductance estimation is obtained from the voltage-current relationship measured by voltage-clamp- or current-clamp-recording with knowledge of the leak parameters of the recorded neuron. However, it is often difficult to obtain sufficient data to estimate synaptic conductances due to technical difficulties in electrophysiological experiments using in vivo or in vitro preparations. To address this problem, we estimated the average variations in excitatory and inhibitory synaptic conductance during a locomotion cycle from a single voltage trace without measuring the leak parameters. We found that the conductance variations can be accurately reconstructed from a voltage trace of 10 cycles by analyzing synthetic data generated from a computational model. Next, the conductance variations were estimated from mouse spinal MNs in vitro during drug-induced-locomotor-like activity. We found that the peak of excitatory conductance occurred during the depolarizing phase of the locomotor cycle, whereas the peak of inhibitory conductance occurred during the hyperpolarizing phase. These results suggest that the locomotor-like activity is generated by push-pull modulation via excitatory and inhibitory synaptic inputs. PMID:27561702

  2. A quantitative framework for estimating risk of collision between marine mammals and boats

    USGS Publications Warehouse

    Martin, Julien; Sabatier, Quentin; Gowan, Timothy A.; Giraud, Christophe; Gurarie, Eliezer; Calleson, Scott; Ortega-Ortiz, Joel G.; Deutsch, Charles J.; Rycyk, Athena; Koslovsky, Stacie M.

    2016-01-01

    By applying encounter rate theory to the case of boat collisions with marine mammals, we gained new insights about encounter processes between wildlife and watercraft. Our work emphasizes the importance of considering uncertainty when estimating wildlife mortality. Finally, our findings are relevant to other systems and ecological processes involving the encounter between moving agents.

  3. Quantitative determination of activation energies in mechanochemical reactions.

    PubMed

    Fischer, Franziska; Wenzel, Klaus-Jürgen; Rademann, Klaus; Emmerling, Franziska

    2016-08-17

    Mechanochemical reactions often result in 100% yields of single products, making purifying procedures obsolete. Mechanochemistry is also a sustainable and eco-friendly method. The ever increasing interest in this method is contrasted by a lack in mechanistic understanding of the mechanochemical reactivity and selectivity. Recent in situ investigations provided direct insight into formation pathways. However, the currently available theories do not predict temperature T as an influential factor. Here, we report the first determination of an apparent activation energy for a mechanochemical reaction. In a temperature-dependent in situ study the cocrystallisation of ibuprofen and nicotinamide was investigated as a model system. These experiments provide a pivotal step towards a comprehensive understanding of milling reaction mechanisms.

  4. Human ECG signal parameters estimation during controlled physical activity

    NASA Astrophysics Data System (ADS)

    Maciejewski, Marcin; Surtel, Wojciech; Dzida, Grzegorz

    2015-09-01

    ECG signal parameters are commonly used indicators of human health condition. In most cases the patient should remain stationary during the examination to decrease the influence of muscle artifacts. During physical activity, the noise level increases significantly. The ECG signals were acquired during controlled physical activity on a stationary bicycle and during rest. Afterwards, the signals were processed using a method based on Pan-Tompkins algorithms to estimate their parameters and to test the method.

  5. Robust state estimation for neural networks with discontinuous activations.

    PubMed

    Liu, Xiaoyang; Cao, Jinde

    2010-12-01

    Discontinuous dynamical systems, particularly neural networks with discontinuous activation functions, arise in a number of applications and have received considerable research attention in recent years. In this paper, the robust state estimation problem is investigated for uncertain neural networks with discontinuous activations and time-varying delays, where the neuron-dependent nonlinear disturbance on the network outputs are only assumed to satisfy the local Lipschitz condition. Based on the theory of differential inclusions and nonsmooth analysis, several criteria are presented to guarantee the existence of the desired robust state estimator for the discontinuous neural networks. It is shown that the design of the state estimator for such networks can be achieved by solving some linear matrix inequalities, which are dependent on the size of the time derivative of the time-varying delays. Finally, numerical examples are given to illustrate the theoretical results.

  6. Predicting anti-androgenic activity of bisphenols using molecular docking and quantitative structure-activity relationships.

    PubMed

    Yang, Xianhai; Liu, Huihui; Yang, Qian; Liu, Jining; Chen, Jingwen; Shi, Lili

    2016-11-01

    Both in vivo and in vitro assay indicated that bisphenols can inhibit the androgen receptor. However, the underlying antagonistic mechanism is unclear. In this study, molecular docking was employed to probe the interaction mechanism between bisphenols and human androgen receptor (hAR). The binding pattern of ligands in hAR crystal structures was also analyzed. Results show that hydrogen bonding and hydrophobic interactions are the dominant interactions between the ligands and hAR. The critical amino acid residues involved in forming hydrogen bonding between bisphenols and hAR is Asn 705 and Gln 711. Furthermore, appropriate molecular structural descriptors were selected to characterize the non-bonded interactions. Stepwise multiple linear regressions (MLR) analysis was employed to develop quantitative structure-activity relationship (QSAR) models for predicting the anti-androgenic activity of bisphenols. Based on the QSAR development and validation guideline issued by OECD, the goodness-of-fit, robustness and predictive ability of constructed QSAR model were assessed. The model application domain was characterized by the Euclidean distance and Williams plot. The mechanisms of the constructed model were also interpreted based on the selected molecular descriptors i.e. the number of hydroxyl groups (nROH), the most positive values of the molecular surface potential (Vs,max) and the lowest unoccupied molecular orbital energy (ELUMO). Finally, based on the model developed, the data gap for other twenty-six bisphenols on their anti-androgenic activity was filled. The predicted results indicated that the anti-androgenic activity of seven bisphenols was higher than that of bisphenol A. PMID:27561732

  7. [Quantitative estimation of CaO content in surface rocks using hyperspectral thermal infrared emissivity].

    PubMed

    Zhang, Li-Fu; Zhang, Xue-Wen; Huang, Zhao-Qiang; Yang, Hang; Zhang, Fei-Zhou

    2011-11-01

    The objective of the present paper is to study the quantitative relationship between the CaO content and the thermal infrared emissivity spectra. The surface spectral emissivity of 23 solid rocks samples were measured in the field and the first derivative of the spectral emissivity was also calculated. Multiple linear regression (MLR), principal component analysis (PCR) and partial least squares regression (PLSR) were modeled and the regression results were compared. The results show that there is a good relationship between CaO content and thermal emissivity spectra features; emissivities become lower when CaO content increases in the 10.3-13 mm region; the first derivative spectra have a better predictive ability compared to the original emissivity spectra.

  8. Modeling elastic waves in coupled media: Estimate of soft tissue influence and application to quantitative ultrasound.

    PubMed

    Chen, Jiangang; Cheng, Li; Su, Zhongqing; Qin, Ling

    2013-02-01

    The effect of medium coupling on propagation of elastic waves is a general concern in a variety of engineering and bio-medical applications. Although some theories and analytical models are available for describing waves in multi-layered engineering structures, they do not focus on canvassing ultrasonic waves in human bones with coupled soft tissues, where the considerable differences in acoustic impedance between bone and soft tissue may pose a challenge in using these models (the soft tissues having an acoustic impedance around 80% less than that of a typical bone). Without proper treatment of this coupling effect, the precision of quantitative ultrasound (QUS) for clinical bone assessment can be compromised. The coupling effect of mimicked soft tissues on the first-arriving signal (FAS) and second-arriving signal (SAS) in a series of synthesized soft-tissue-bone phantoms was investigated experimentally and calibrated quantitatively. Understanding of the underlying mechanism of the coupling effect was supplemented by a dedicated finite element analysis. As revealed, the medium coupling impacts influence on different wave modes to different degrees: for FAS and SAS, the most significant changes take place when the soft tissues are initially introduced, and the decrease in signal peak energy continues with increase in the thickness or elastic modulus of the soft tissues, but the changes in propagation velocity fluctuate within 5% regardless of further increase in the thickness or elastic modulus of the soft tissues. As an application, the calibrated effects were employed to enhance the precision of SAS-based QUS when used for predicting the simulated healing status of a mimicked bone fracture, to find prediction of healing progress of bone fracture based on changes in velocity of the FAS or the SAS is inaccurate without taking into account the effect of soft tissue coupling, entailing appropriate compensation for the coupling effect.

  9. Skill Assessment of An Hybrid Technique To Estimate Quantitative Precipitation Forecast For Galicia (nw Spain)

    NASA Astrophysics Data System (ADS)

    Lage, A.; Taboada, J. J.

    Precipitation is the most obvious of the weather elements in its effects on normal life. Numerical weather prediction (NWP) is generally used to produce quantitative precip- itation forecast (QPF) beyond the 1-3 h time frame. These models often fail to predict small-scale variations of rain because of spin-up problems and their coarse spatial and temporal resolution (Antolik, 2000). Moreover, there are some uncertainties about the behaviour of the NWP models in extreme situations (de Bruijn and Brandsma, 2000). Hybrid techniques, combining the benefits of NWP and statistical approaches in a flexible way, are very useful to achieve a good QPF. In this work, a new technique of QPF for Galicia (NW of Spain) is presented. This region has a percentage of rainy days per year greater than 50% with quantities that may cause floods, with human and economical damages. The technique is composed of a NWP model (ARPS) and a statistical downscaling process based on an automated classification scheme of at- mospheric circulation patterns for the Iberian Peninsula (J. Ribalaygua and R. Boren, 1995). Results show that QPF for Galicia is improved using this hybrid technique. [1] Antolik, M.S. 2000 "An Overview of the National Weather Service's centralized statistical quantitative precipitation forecasts". Journal of Hydrology, 239, pp:306- 337. [2] de Bruijn, E.I.F and T. Brandsma "Rainfall prediction for a flooding event in Ireland caused by the remnants of Hurricane Charley". Journal of Hydrology, 239, pp:148-161. [3] Ribalaygua, J. and Boren R. "Clasificación de patrones espaciales de precipitación diaria sobre la España Peninsular". Informes N 3 y 4 del Servicio de Análisis e Investigación del Clima. Instituto Nacional de Meteorología. Madrid. 53 pp.

  10. Estimating Active Layer Thickness from Remotely Sensed Surface Deformation

    NASA Astrophysics Data System (ADS)

    Liu, L.; Schaefer, K. M.; Zhang, T.; Wahr, J. M.

    2010-12-01

    We estimate active layer thickness (ALT) from remotely sensed surface subsidence during thawing seasons derived from interferometric synthetic aperture radar (InSAR) measurements. Ground ice takes up more volume than ground water, so as the soil thaws in summer and the active layer deepens, the ground subsides. The volume of melted ground water during the summer thaw determines seasonal subsidence. ALT is defined as the maximum thaw depth at the end of a thawing season. By using InSAR to measure surface subsidence between the start and end of summer season, one can estimate the depth of thaw over a large area (typically 100 km by 100 km). We developed an ALT retrieval algorithm integrating InSAR-derived surface subsidence, observed soil texture, organic matter content, and moisture content. We validated this algorithm in the continuous permafrost area on the North Slope of Alaska. Based on InSAR measurements using ERS-1/2 SAR data, our estimated values match in situ measurements of ALT within 1--10 cm at Circumpolar Active Layer Monitoring (CALM) sites within the study area. The active layer plays a key role in land surface processes in cold regions. Current measurements of ALT using mechanical probing, frost/thaw tubes, or inferred from temperature measurements are of high quality, but limited in spatial coverage. Using InSAR to estimate ALT greatly expands the spatial coverage of ALT observations.

  11. EIA Corrects Errors in Its Drilling Activity Estimates Series

    EIA Publications

    1998-01-01

    The Energy Information Administration (EIA) has published monthly and annual estimates of oil and gas drilling activity since 1978. These data are key information for many industry analysts, serving as a leading indicator of trends in the industry and a barometer of general industry status.

  12. EIA Completes Corrections to Drilling Activity Estimates Series

    EIA Publications

    1999-01-01

    The Energy Information Administration (EIA) has published monthly and annual estimates of oil and gas drilling activity since 1978. These data are key information for many industry analysts, serving as a leading indicator of trends in the industry and a barometer of general industry status.

  13. Methane emission estimation from landfills in Korea (1978-2004): quantitative assessment of a new approach.

    PubMed

    Kim, Hyun-Sun; Yi, Seung-Muk

    2009-01-01

    Quantifying methane emission from landfills is important to evaluating measures for reduction of greenhouse gas (GHG) emissions. To quantify GHG emissions and identify sensitive parameters for their measurement, a new assessment approach consisting of six different scenarios was developed using Tier 1 (mass balance method) and Tier 2 (the first-order decay method) methodologies for GHG estimation from landfills, suggested by the Intergovernmental Panel on Climate Change (IPCC). Methane emissions using Tier 1 correspond to trends in disposed waste amount, whereas emissions from Tier 2 gradually increase as disposed waste decomposes over time. The results indicate that the amount of disposed waste and the decay rate for anaerobic decomposition were decisive parameters for emission estimation using Tier 1 and Tier 2. As for the different scenarios, methane emissions were highest under Scope 1 (scenarios I and II), in which all landfills in Korea were regarded as one landfill. Methane emissions under scenarios III, IV, and V, which separated the dissimilated fraction of degradable organic carbon (DOC(F)) by waste type and/or revised the methane correction factor (MCF) by waste layer, were underestimated compared with scenarios II and III. This indicates that the methodology of scenario I, which has been used in most previous studies, may lead to an overestimation of methane emissions. Additionally, separate DOC(F) and revised MCF were shown to be important parameters for methane emission estimation from landfills, and revised MCF by waste layer played an important role in emission variations. Therefore, more precise information on each landfill and careful determination of parameter values and characteristics of disposed waste in Korea should be used to accurately estimate methane emissions from landfills.

  14. Coupling radar and lightning data to improve the quantitative estimation of precipitation

    NASA Astrophysics Data System (ADS)

    François, B.; Molinié, G.; Betz, H. D.

    2009-09-01

    Forecasts in hydrology require rainfall intensity estimations at temporal scale of few tens of minutes and at spatial scales of few kilometer squares. Radars are the most efficient apparatus to provide such data. However, estimate the rainfall intensity (R) from the radar reflectivity (Z) is based on empirical Z-R relationships which are not robusts. Indeed, the Z-R relationships depend on hydrometeor types. The role of Lightning flashes in thunderclouds is to relax the electrical constraints. Generations of thundercloud electrical charges are due to thermodynamical and microphysical processes. Based on these physical considerations, Blyth et al. (2001) have derived a relationship between the product of ascending and descending hydrometeor fluxes and the lightning flash rate. Deierling et al. (2008) succesfully applied this relationship to data from the STERAO-A and STEPS field campains. We have applied the methodology described in Deierling et al. (2008) to operational radar (Météo-France network) and lightning (LINET) data. As these data don't allow to compute the ascending hydrometeor flux and as the descending mass flux is highly parameterized, thundercloud simulations (MésoNH) are used to assess the role of ascending fluxes and the estimated precipitating fluxes. In order to assess the budget of the Blyth et al. (2008) equation terms, the electrified version of MésoNH, including lightning, is run.

  15. Quantitative Estimate of the Relation Between Rolling Resistance on Fuel Consumption of Class 8 Tractor Trailers Using Both New and Retreaded Tires (SAE Paper 2014-01-2425)

    EPA Science Inventory

    Road tests of class 8 tractor trailers were conducted by the US Environmental Protection Agency on new and retreaded tires of varying rolling resistance in order to provide estimates of the quantitative relationship between rolling resistance and fuel consumption.

  16. Quantitative estimates of tropical temperature change in lowland Central America during the last 42 ka

    NASA Astrophysics Data System (ADS)

    Grauel, Anna-Lena; Hodell, David A.; Bernasconi, Stefano M.

    2016-03-01

    Determining the magnitude of tropical temperature change during the last glacial period is a fundamental problem in paleoclimate research. Large discrepancies exist in estimates of tropical cooling inferred from marine and terrestrial archives. Here we present a reconstruction of temperature for the last 42 ka from a lake sediment core from Lake Petén Itzá, Guatemala, located at 17°N in lowland Central America. We compared three independent methods of glacial temperature reconstruction: pollen-based temperature estimates, tandem measurements of δ18O in biogenic carbonate and gypsum hydration water, and clumped isotope thermometry. Pollen provides a near-continuous record of temperature change for most of the glacial period but the occurrence of a no-analog pollen assemblage during cold, dry stadials renders temperature estimates unreliable for these intervals. In contrast, the gypsum hydration and clumped isotope methods are limited mainly to the stadial periods when gypsum and biogenic carbonate co-occur. The combination of palynological and geochemical methods leads to a continuous record of tropical temperature change in lowland Central America over the last 42 ka. Furthermore, the gypsum hydration water method and clumped isotope thermometry provide independent estimates of not only temperature, but also the δ18O of lake water that is dependent on the hydrologic balance between evaporation and precipitation over the lake surface and its catchment. The results show that average glacial temperature was cooler in lowland Central America by 5-10 °C relative to the Holocene. The coldest and driest times occurred during North Atlantic stadial events, particularly Heinrich stadials (HSs), when temperature decreased by up to 6 to 10 °C relative to today. This magnitude of cooling is much greater than estimates derived from Caribbean marine records and model simulations. The extreme dry and cold conditions during HSs in the lowland Central America were associated

  17. Quantitative comparison of the convulsive activity of combinations of twelve fluoroquinolones with five nonsteroidal antiinflammatory agents.

    PubMed

    Kim, Jahye; Ohtani, Hisakazu; Tsujimoto, Masayuki; Sawada, Yasufumi

    2009-01-01

    Concomitant administration of certain fluoroquinolone antimicrobials and nonsteroidal antiinflammatory agents (NSAIDs) induces serious convulsion in humans. There are differences in convulsive activity among fluoroquinolones and in the potentiation of fluoroquinolone-induced convulsion among NSAIDs, but a comprehensive, quantitative comparison has not been carried out. This study evaluates the inhibitory effects of twelve fluoroquinolones (ciprofloxacin, enoxacin, fleroxacin, gatifloxacin, levofloxacin, lomefloxacin, norfloxacin, ofloxacin, pazufloxacin, prulifloxacin, sparfloxacin, and tosufloxacin) alone or in the presence of an NSAID (4-biphenylacetic acid, diclofenac sodium, loxoprofen, lornoxicam or zaltoprofen) on the GABA(A) receptor binding of [(3)H]muscimol in an in vitro study using mice synaptic plasma membrane. The rank order of inhibitory effects of the fluoroquinolones was prulifloxacin asymptotically equal to norfloxacin > ciprofloxacin > or = enoxacin > gatifloxacin > or = ofloxacin asymptotically equal to tosufloxacin asymptotically equal to lomefloxacin > levofloxacin > or = sparfloxacin > or = pazufloxacin asymptotically equal to fleroxacin. 4-Biphenylacetic acid most potently enhanced the inhibitory effects of the fluoroquinolones, while zaltoprofen, loxoprofen, lornoxicam and diclofenac had essentially no effect. The clinical risk of convulsion for each combination was estimated using a pharmacodynamic model based on receptor occupancy using the in vitro data set obtained and pharmacokinetic parameters in humans collected from the literature. The combinations of 4-biphenylacetic acid with prulifloxacin and enoxacin were concluded to be the most hazardous.

  18. Quantitative Structure--Activity Relationship (QSAR) for the Oxidation of Trace Organic Contaminants by Sulfate Radical.

    PubMed

    Xiao, Ruiyang; Ye, Tiantian; Wei, Zongsu; Luo, Shuang; Yang, Zhihui; Spinney, Richard

    2015-11-17

    The sulfate radical anion (SO4•–) based oxidation of trace organic contaminants (TrOCs) has recently received great attention due to its high reactivity and low selectivity. In this study, a meta-analysis was conducted to better understand the role of functional groups on the reactivity between SO4•– and TrOCs. The results indicate that compounds in which electron transfer and addition channels dominate tend to exhibit a faster second-order rate constants (kSO4•–) than that of H–atom abstraction, corroborating the SO4•– reactivity and mechanisms observed in the individual studies. Then, a quantitative structure activity relationship (QSAR) model was developed using a sequential approach with constitutional, geometrical, electrostatic, and quantum chemical descriptors. Two descriptors, ELUMO and EHOMO energy gap (ELUMO–EHOMO) and the ratio of oxygen atoms to carbon atoms (#O:C), were found to mechanistically and statistically affect kSO4•– to a great extent with the standardized QSAR model: ln kSO4•– = 26.8–3.97 × #O:C – 0.746 × (ELUMO–EHOMO). In addition, the correlation analysis indicates that there is no dominant reaction channel for SO4•– reactions with various structurally diverse compounds. Our QSAR model provides a robust predictive tool for estimating emerging micropollutants removal using SO4•– during wastewater treatment processes.

  19. Quantitative PCR-based genome size estimation of the astigmatid mites Sarcoptes scabiei, Psoroptes ovis and Dermatophagoides pteronyssinus

    PubMed Central

    2012-01-01

    Background The lack of genomic data available for mites limits our understanding of their biology. Evolving high-throughput sequencing technologies promise to deliver rapid advances in this area, however, estimates of genome size are initially required to ensure sufficient coverage. Methods Quantitative real-time PCR was used to estimate the genome sizes of the burrowing ectoparasitic mite Sarcoptes scabiei, the non-burrowing ectoparasitic mite Psoroptes ovis, and the free-living house dust mite Dermatophagoides pteronyssinus. Additionally, the chromosome number of S. scabiei was determined by chromosomal spreads of embryonic cells derived from single eggs. Results S. scabiei cells were shown to contain 17 or 18 small (< 2 μM) chromosomes, suggesting an XO sex-determination mechanism. The average estimated genome sizes of S. scabiei and P. ovis were 96 (± 7) Mb and 86 (± 2) Mb respectively, among the smallest arthropod genomes reported to date. The D. pteronyssinus genome was estimated to be larger than its parasitic counterparts, at 151 Mb in female mites and 218 Mb in male mites. Conclusions This data provides a starting point for understanding the genetic organisation and evolution of these astigmatid mites, informing future sequencing projects. A comparitive genomic approach including these three closely related mites is likely to reveal key insights on mite biology, parasitic adaptations and immune evasion. PMID:22214472

  20. Comparison of Myocardial Perfusion Estimates From Dynamic Contrast-Enhanced Magnetic Resonance Imaging With Four Quantitative Analysis Methods

    PubMed Central

    Pack, Nathan A.; DiBella, Edward V. R.

    2012-01-01

    Dynamic contrast-enhanced MRI has been used to quantify myocardial perfusion in recent years. Published results have varied widely, possibly depending on the method used to analyze the dynamic perfusion data. Here, four quantitative analysis methods (two-compartment modeling, Fermi function modeling, model-independent analysis, and Patlak plot analysis) were implemented and compared for quantifying myocardial perfusion. Dynamic contrast-enhanced MRI data were acquired in 20 human subjects at rest with low-dose (0.019 ± 0.005 mmol/kg) bolus injections of gadolinium. Fourteen of these subjects were also imaged at adenosine stress (0.021 ± 0.005 mmol/kg). Aggregate rest perfusion estimates were not significantly different between all four analysis methods. At stress, perfusion estimates were not significantly different between two-compartment modeling, model-independent analysis, and Patlak plot analysis. Stress estimates from the Fermi model were significantly higher (~20%) than the other three methods. Myocardial perfusion reserve values were not significantly different between all four methods. Model-independent analysis resulted in the lowest model curve-fit errors. When more than just the first pass of data was analyzed, perfusion estimates from two-compartment modeling and model-independent analysis did not change significantly, unlike results from Fermi function modeling. PMID:20577976

  1. Long-term accounting for raindrop size distribution variations improves quantitative precipitation estimation by weather radar

    NASA Astrophysics Data System (ADS)

    Hazenberg, Pieter; Leijnse, Hidde; Uijlenhoet, Remko

    2016-04-01

    Weather radars provide information on the characteristics of precipitation at high spatial and temporal resolution. Unfortunately, rainfall measurements by radar are affected by multiple error sources. The current study is focused on the impact of variations of the raindrop size distribution on radar rainfall estimates. Such variations lead to errors in the estimated rainfall intensity (R) and specific attenuation (k) when using fixed relations for the conversion of the observed reflectivity (Z) into R and k. For non-polarimetric radar, this error source has received relatively little attention compared to other error sources. We propose to link the parameters of the Z-R and Z-k relations directly to those of the normalized gamma DSD. The benefit of this procedure is that it reduces the number of unknown parameters. In this work, the DSD parameters are obtained using 1) surface observations from a Parsivel and Thies LPM disdrometer, and 2) a Monte Carlo optimization procedure using surface rain gauge observations. The impact of both approaches for a given precipitation type is assessed for 45 days of summertime precipitation observed in The Netherlands. Accounting for DSD variations using disdrometer observations leads to an improved radar QPE product as compared to applying climatological Z-R and Z-k relations. This especially holds for situations where widespread stratiform precipitation is observed. The best results are obtained when the DSD parameters are optimized. However, the optimized Z-R and Z-k relations show an unrealistic variability that arises from uncorrected error sources. As such, the optimization approach does not result in a realistic DSD shape but instead also accounts for uncorrected error sources resulting in the best radar rainfall adjustment. Therefore, to further improve the quality of preciptitation estimates by weather radar, usage should either be made of polarimetric radar or by extending the network of disdrometers.

  2. Estimating evaporative vapor generation from automobiles based on parking activities.

    PubMed

    Dong, Xinyi; Tschantz, Michael; Fu, Joshua S

    2015-07-01

    A new approach is proposed to quantify the evaporative vapor generation based on real parking activity data. As compared to the existing methods, two improvements are applied in this new approach to reduce the uncertainties: First, evaporative vapor generation from diurnal parking events is usually calculated based on estimated average parking duration for the whole fleet, while in this study, vapor generation rate is calculated based on parking activities distribution. Second, rather than using the daily temperature gradient, this study uses hourly temperature observations to derive the hourly incremental vapor generation rates. The parking distribution and hourly incremental vapor generation rates are then adopted with Wade-Reddy's equation to estimate the weighted average evaporative generation. We find that hourly incremental rates can better describe the temporal variations of vapor generation, and the weighted vapor generation rate is 5-8% less than calculation without considering parking activity.

  3. Total myrosinase activity estimates in brassica vegetable produce.

    PubMed

    Dosz, Edward B; Ku, Kang-Mo; Juvik, John A; Jeffery, Elizabeth H

    2014-08-13

    Isothiocyanates, generated from the hydrolysis of glucosinolates in plants of the Brassicaceae family, promote health, including anticancer bioactivity. Hydrolysis requires the plant enzyme myrosinase, giving myrosinase a key role in health promotion by brassica vegetables. Myrosinase measurement typically involves isolating crude protein, potentially underestimating activity in whole foods. Myrosinase activity was estimated using unextracted fresh tissues of five broccoli and three kale cultivars, measuring the formation of allyl isothiocyanate (AITC) and/or glucose from exogenous sinigrin. A correlation between AITC and glucose formation was found, although activity was substantially lower measured as glucose release. Using exogenous sinigrin or endogenous glucoraphanin, concentrations of the hydrolysis products AITC and sulforaphane correlated (r = 0.859; p = 0.006), suggesting that broccoli shows no myrosinase selectivity among sinigrin and glucoraphanin. Measurement of AITC formation provides a novel, reliable estimation of myrosinase-dependent isothiocyanate formation suitable for use with whole vegetable food samples. PMID:25051514

  4. Estimation of Evapotranspiration as a function of Photosynthetic Active Radiation

    NASA Astrophysics Data System (ADS)

    Wesley, E.; Migliaccio, K.; Judge, J.

    2012-12-01

    The purpose of this research project is to more accurately measure the water balance and energy movements to properly allocate water resources at the Snapper Creek Site in Miami-Dade County, FL, by quantifying and estimating evapotranspiration (ET). ET is generally estimated using weather based equations, this project focused on estimating ET as a function of Photosynthetic Active Radiation (PAR). The project objectives were first to compose a function of PAR and calculated coefficients that can accurately estimate daily ET values with the least amount of variables used in its estimation equation, and second, to compare the newly identified ET estimation PAR function to TURC estimations, in comparison to our actual Eddy Covariance (EC) ET data and determine the differences in ET values. PAR, volumetric water content (VWC), and temperature (T) data were quality checked and used in developing singular and multiple variable regression models fit with SigmaPlot software. Fifteen different ET estimation equations were evaluated against EC ET and TURC estimated ET using R2 and slope factors. The selected equation that best estimated EC ET was cross validated using a 5 month data set; its daily and monthly ET values and sums were compared against the commonly used TURC equation. Using a multiple variable regression model, an equation with three variables (i.e., VWC, T, and PAR) was identified that best fit EC ET daily data. However, a regression was also found that used only PAR and provided ET predictions of similar accuracy. The PAR based regression model predicted daily EC ET more accurately than the traditional TURC method. Using only PAR to estimate ET reduces the input variables as compared to using the TURC model which requires T and solar radiation. Thus, not only is the PAR approach more accurate but also more cost effective. The PAR-based ET estimation equation derived in this study may be over fit considering only 5 months of data were used to produce the PAR

  5. Raman spectroscopy of human skin: looking for a quantitative algorithm to reliably estimate human age

    NASA Astrophysics Data System (ADS)

    Pezzotti, Giuseppe; Boffelli, Marco; Miyamori, Daisuke; Uemura, Takeshi; Marunaka, Yoshinori; Zhu, Wenliang; Ikegaya, Hiroshi

    2015-06-01

    The possibility of examining soft tissues by Raman spectroscopy is challenged in an attempt to probe human age for the changes in biochemical composition of skin that accompany aging. We present a proof-of-concept report for explicating the biophysical links between vibrational characteristics and the specific compositional and chemical changes associated with aging. The actual existence of such links is then phenomenologically proved. In an attempt to foster the basics for a quantitative use of Raman spectroscopy in assessing aging from human skin samples, a precise spectral deconvolution is performed as a function of donors' ages on five cadaveric samples, which emphasizes the physical significance and the morphological modifications of the Raman bands. The outputs suggest the presence of spectral markers for age identification from skin samples. Some of them appeared as authentic "biological clocks" for the apparent exactness with which they are related to age. Our spectroscopic approach yields clear compositional information of protein folding and crystallization of lipid structures, which can lead to a precise identification of age from infants to adults. Once statistically validated, these parameters might be used to link vibrational aspects at the molecular scale for practical forensic purposes.

  6. Quantitative Estimation of Temperature Variations in Plantar Angiosomes: A Study Case for Diabetic Foot

    PubMed Central

    Peregrina-Barreto, H.; Morales-Hernandez, L. A.; Rangel-Magdaleno, J. J.; Avina-Cervantes, J. G.; Ramirez-Cortes, J. M.; Morales-Caporal, R.

    2014-01-01

    Thermography is a useful tool since it provides information that may help in the diagnostic of several diseases in a noninvasive and fast way. Particularly, thermography has been applied in the study of the diabetic foot. However, most of these studies report only qualitative information making it difficult to measure significant parameters such as temperature variations. These variations are important in the analysis of the diabetic foot since they could bring knowledge, for instance, regarding ulceration risks. The early detection of ulceration risks is considered an important research topic in the medicine field, as its objective is to avoid major complications that might lead to a limb amputation. The absence of symptoms in the early phase of the ulceration is conceived as the main disadvantage to provide an opportune diagnostic in subjects with neuropathy. Since the relation between temperature and ulceration risks is well established in the literature, a methodology that obtains quantitative temperature differences in the plantar area of the diabetic foot to detect ulceration risks is proposed in this work. Such methodology is based on the angiosome concept and image processing. PMID:24688595

  7. Raman spectroscopy of human skin: looking for a quantitative algorithm to reliably estimate human age.

    PubMed

    Pezzotti, Giuseppe; Boffelli, Marco; Miyamori, Daisuke; Uemura, Takeshi; Marunaka, Yoshinori; Zhu, Wenliang; Ikegaya, Hiroshi

    2015-06-01

    The possibility of examining soft tissues by Raman spectroscopy is challenged in an attempt to probe human age for the changes in biochemical composition of skin that accompany aging. We present a proof-of-concept report for explicating the biophysical links between vibrational characteristics and the specific compositional and chemical changes associated with aging. The actual existence of such links is then phenomenologically proved. In an attempt to foster the basics for a quantitative use of Raman spectroscopy in assessing aging from human skin samples, a precise spectral deconvolution is performed as a function of donors' ages on five cadaveric samples, which emphasizes the physical significance and the morphological modifications of the Raman bands. The outputs suggest the presence of spectral markers for age identification from skin samples. Some of them appeared as authentic "biological clocks" for the apparent exactness with which they are related to age. Our spectroscopic approach yields clear compositional information of protein folding and crystallization of lipid structures, which can lead to a precise identification of age from infants to adults. Once statistically validated, these parameters might be used to link vibrational aspects at the molecular scale for practical forensic purposes.

  8. Quantitatively estimating defects in graphene devices using discharge current analysis method

    PubMed Central

    Jung, Ukjin; Lee, Young Gon; Kang, Chang Goo; Lee, Sangchul; Kim, Jin Ju; Hwang, Hyeon June; Lim, Sung Kwan; Ham, Moon-Ho; Lee, Byoung Hun

    2014-01-01

    Defects of graphene are the most important concern for the successful applications of graphene since they affect device performance significantly. However, once the graphene is integrated in the device structures, the quality of graphene and surrounding environment could only be assessed using indirect information such as hysteresis, mobility and drive current. Here we develop a discharge current analysis method to measure the quality of graphene integrated in a field effect transistor structure by analyzing the discharge current and examine its validity using various device structures. The density of charging sites affecting the performance of graphene field effect transistor obtained using the discharge current analysis method was on the order of 1014/cm2, which closely correlates with the intensity ratio of the D to G bands in Raman spectroscopy. The graphene FETs fabricated on poly(ethylene naphthalate) (PEN) are found to have a lower density of charging sites than those on SiO2/Si substrate, mainly due to reduced interfacial interaction between the graphene and the PEN. This method can be an indispensable means to improve the stability of devices using a graphene as it provides an accurate and quantitative way to define the quality of graphene after the device fabrication. PMID:24811431

  9. Quantitative modelling to estimate the transfer of pharmaceuticals through the food production system.

    PubMed

    Chiţescu, Carmen Lidia; Nicolau, Anca Ioana; Römkens, Paul; Van Der Fels-Klerx, H J

    2014-01-01

    Use of pharmaceuticals in animal production may cause an indirect route of contamination of food products of animal origin. This study aimed to assess, through mathematical modelling, the transfer of pharmaceuticals from contaminated soil, through plant uptake, into the dairy food production chain. The scenarios, model parameters, and values refer to contaminants in emission slurry production, storage time, immission into soil, plant uptake, bioaccumulation in the animal's body, and transfer to meat and milk. Modelling results confirm the possibility of contamination of dairy cow's meat and milk due the ingestion of contaminated feed by the cattle. The estimated concentration of pharmaceutical residues obtained for meat ranged from 0 to 6 ng kg(-1) for oxytetracycline, from 0.011 to 0.181 μg kg(-1) for sulfamethoxazole, and from 4.70 to 11.86 μg kg(-1) for ketoconazole. The estimated concentrations for milk were: zero for oxytetracycline, lower than 40 ng L(-1) for sulfamethoxazole, and from 0.98 to 2.48 μg L(-1) for ketoconazole. Results obtained for the three selected pharmaceuticals indicate a minor risk for human health. This study showed that supply chain modelling could be an effective tool in assessing the indirect contamination of feedstuff and animal products by residues of pharmaceuticals. The model can easily be adjusted to other contaminants and supply chain and, in this way, present a valuable tool to underpin decision making. PMID:24813980

  10. Quantitative modelling to estimate the transfer of pharmaceuticals through the food production system.

    PubMed

    Chiţescu, Carmen Lidia; Nicolau, Anca Ioana; Römkens, Paul; Van Der Fels-Klerx, H J

    2014-01-01

    Use of pharmaceuticals in animal production may cause an indirect route of contamination of food products of animal origin. This study aimed to assess, through mathematical modelling, the transfer of pharmaceuticals from contaminated soil, through plant uptake, into the dairy food production chain. The scenarios, model parameters, and values refer to contaminants in emission slurry production, storage time, immission into soil, plant uptake, bioaccumulation in the animal's body, and transfer to meat and milk. Modelling results confirm the possibility of contamination of dairy cow's meat and milk due the ingestion of contaminated feed by the cattle. The estimated concentration of pharmaceutical residues obtained for meat ranged from 0 to 6 ng kg(-1) for oxytetracycline, from 0.011 to 0.181 μg kg(-1) for sulfamethoxazole, and from 4.70 to 11.86 μg kg(-1) for ketoconazole. The estimated concentrations for milk were: zero for oxytetracycline, lower than 40 ng L(-1) for sulfamethoxazole, and from 0.98 to 2.48 μg L(-1) for ketoconazole. Results obtained for the three selected pharmaceuticals indicate a minor risk for human health. This study showed that supply chain modelling could be an effective tool in assessing the indirect contamination of feedstuff and animal products by residues of pharmaceuticals. The model can easily be adjusted to other contaminants and supply chain and, in this way, present a valuable tool to underpin decision making.

  11. Estimates of the global electric circuit from global thunderstorm activity

    NASA Astrophysics Data System (ADS)

    Hutchins, M. L.; Holzworth, R. H.; Brundell, J. B.

    2013-12-01

    The World Wide Lightning Location Network (WWLLN) has a global detection efficiency around 10%, however the network has been shown to identify 99% of thunderstorms (Jacobson, et al 2006, using WWLLN data from 2005). To create an estimate of the global electric circuit activity a clustering algorithm is applied to the WWLLN dataset to identify global thunderstorms from 2009 - 2013. The annual, seasonal, and regional thunderstorm activity is investigated with this new WWLLN thunderstorm dataset in order to examine the source behavior of the global electric circuit. From the clustering algorithm the total number of active thunderstorms is found every 30 minutes to create a measure of the global electric circuit source function. The clustering algorithm used is shown to be robust over parameter ranges related to real physical storm sizes and times. The thunderstorm groupings are verified with case study comparisons using satellite and radar data. It is found that there are on average 714 × 81 thunderstorms active at any given time. Similarly the highest average number of thunderstorms occurs in July (783 × 69) with the lowest in January (599 × 76). The annual and diurnal thunderstorm activity seen with the WWLLN thunderstorms is in contrast with the bimodal stroke activity seen by WWLLN. Through utilizing the global coverage and high time resolution of WWLLN, it is shown that the total active thunderstorm count is less than previous estimates based on compiled climatologies.

  12. Antiproliferative Pt(IV) complexes: synthesis, biological activity, and quantitative structure-activity relationship modeling.

    PubMed

    Gramatica, Paola; Papa, Ester; Luini, Mara; Monti, Elena; Gariboldi, Marzia B; Ravera, Mauro; Gabano, Elisabetta; Gaviglio, Luca; Osella, Domenico

    2010-09-01

    Several Pt(IV) complexes of the general formula [Pt(L)2(L')2(L'')2] [axial ligands L are Cl-, RCOO-, or OH-; equatorial ligands L' are two am(m)ine or one diamine; and equatorial ligands L'' are Cl- or glycolato] were rationally designed and synthesized in the attempt to develop a predictive quantitative structure-activity relationship (QSAR) model. Numerous theoretical molecular descriptors were used alongside physicochemical data (i.e., reduction peak potential, Ep, and partition coefficient, log Po/w) to obtain a validated QSAR between in vitro cytotoxicity (half maximal inhibitory concentrations, IC50, on A2780 ovarian and HCT116 colon carcinoma cell lines) and some features of Pt(IV) complexes. In the resulting best models, a lipophilic descriptor (log Po/w or the number of secondary sp3 carbon atoms) plus an electronic descriptor (Ep, the number of oxygen atoms, or the topological polar surface area expressed as the N,O polar contribution) is necessary for modeling, supporting the general finding that the biological behavior of Pt(IV) complexes can be rationalized on the basis of their cellular uptake, the Pt(IV)-->Pt(II) reduction, and the structure of the corresponding Pt(II) metabolites. Novel compounds were synthesized on the basis of their predicted cytotoxicity in the preliminary QSAR model, and were experimentally tested. A final QSAR model, based solely on theoretical molecular descriptors to ensure its general applicability, is proposed.

  13. Validation of Quantitative Structure-Activity Relationship (QSAR) Model for Photosensitizer Activity Prediction

    PubMed Central

    Frimayanti, Neni; Yam, Mun Li; Lee, Hong Boon; Othman, Rozana; Zain, Sharifuddin M.; Rahman, Noorsaadah Abd.

    2011-01-01

    Photodynamic therapy is a relatively new treatment method for cancer which utilizes a combination of oxygen, a photosensitizer and light to generate reactive singlet oxygen that eradicates tumors via direct cell-killing, vasculature damage and engagement of the immune system. Most of photosensitizers that are in clinical and pre-clinical assessments, or those that are already approved for clinical use, are mainly based on cyclic tetrapyrroles. In an attempt to discover new effective photosensitizers, we report the use of the quantitative structure-activity relationship (QSAR) method to develop a model that could correlate the structural features of cyclic tetrapyrrole-based compounds with their photodynamic therapy (PDT) activity. In this study, a set of 36 porphyrin derivatives was used in the model development where 24 of these compounds were in the training set and the remaining 12 compounds were in the test set. The development of the QSAR model involved the use of the multiple linear regression analysis (MLRA) method. Based on the method, r2 value, r2 (CV) value and r2 prediction value of 0.87, 0.71 and 0.70 were obtained. The QSAR model was also employed to predict the experimental compounds in an external test set. This external test set comprises 20 porphyrin-based compounds with experimental IC50 values ranging from 0.39 μM to 7.04 μM. Thus the model showed good correlative and predictive ability, with a predictive correlation coefficient (r2 prediction for external test set) of 0.52. The developed QSAR model was used to discover some compounds as new lead photosensitizers from this external test set. PMID:22272096

  14. Estimation of whole body fat from appendicular soft tissue from peripheral quantitative computed tomography in adolescent girls

    PubMed Central

    Lee, Vinson R.; Blew, Rob M.; Farr, Josh N.; Tomas, Rita; Lohman, Timothy G.; Going, Scott B.

    2013-01-01

    Objective Assess the utility of peripheral quantitative computed tomography (pQCT) for estimating whole body fat in adolescent girls. Research Methods and Procedures Our sample included 458 girls (aged 10.7 ± 1.1y, mean BMI = 18.5 ± 3.3 kg/m2) who had DXA scans for whole body percent fat (DXA %Fat). Soft tissue analysis of pQCT scans provided thigh and calf subcutaneous percent fat and thigh and calf muscle density (muscle fat content surrogates). Anthropometric variables included weight, height and BMI. Indices of maturity included age and maturity offset. The total sample was split into validation (VS; n = 304) and cross-validation (CS; n = 154) samples. Linear regression was used to develop prediction equations for estimating DXA %Fat from anthropometric variables and pQCT-derived soft tissue components in VS and the best prediction equation was applied to CS. Results Thigh and calf SFA %Fat were positively correlated with DXA %Fat (r = 0.84 to 0.85; p <0.001) and thigh and calf muscle densities were inversely related to DXA %Fat (r = −0.30 to −0.44; p < 0.001). The best equation for estimating %Fat included thigh and calf SFA %Fat and thigh and calf muscle density (adj. R2 = 0.90; SEE = 2.7%). Bland-Altman analysis in CS showed accurate estimates of percent fat (adj. R2 = 0.89; SEE = 2.7%) with no bias. Discussion Peripheral QCT derived indices of adiposity can be used to accurately estimate whole body percent fat in adolescent girls. PMID:25147482

  15. THE EVOLUTION OF SOLAR FLUX FROM 0.1 nm TO 160 {mu}m: QUANTITATIVE ESTIMATES FOR PLANETARY STUDIES

    SciTech Connect

    Claire, Mark W.; Sheets, John; Meadows, Victoria S.; Cohen, Martin; Ribas, Ignasi; Catling, David C.

    2012-09-20

    Understanding changes in the solar flux over geologic time is vital for understanding the evolution of planetary atmospheres because it affects atmospheric escape and chemistry, as well as climate. We describe a numerical parameterization for wavelength-dependent changes to the non-attenuated solar flux appropriate for most times and places in the solar system. We combine data from the Sun and solar analogs to estimate enhanced UV and X-ray fluxes for the young Sun and use standard solar models to estimate changing visible and infrared fluxes. The parameterization, a series of multipliers relative to the modern top of the atmosphere flux at Earth, is valid from 0.1 nm through the infrared, and from 0.6 Gyr through 6.7 Gyr, and is extended from the solar zero-age main sequence to 8.0 Gyr subject to additional uncertainties. The parameterization is applied to a representative modern day flux, providing quantitative estimates of the wavelength dependence of solar flux for paleodates relevant to the evolution of atmospheres in the solar system (or around other G-type stars). We validate the code by Monte Carlo analysis of uncertainties in stellar age and flux, and with comparisons to the solar proxies {kappa}{sup 1} Cet and EK Dra. The model is applied to the computation of photolysis rates on the Archean Earth.

  16. Quantitative estimates of changes in marine and terrestrial primary productivity over the past 300 million years

    PubMed Central

    Beerling, D. J.

    1999-01-01

    Changes in marine primary production over geological time have influenced a network of global biogeochemical cycles with corresponding feedbacks on climate. However, these changes continue to remain largely unquantified because of uncertainties in calculating global estimates from sedimentary palaeoproductivity indicators. I therefore describe a new approach to the problem using a mass balance analysis of the stable isotopes (18O/16O) of oxygen with modelled O2 fluxes and isotopic exchanges by terrestrial vegetation for 300, 150, 100 and 50 million years before present, and the treatment of the Earth as a closed system, with respect to the cycling of O2. Calculated in this way, oceanic net primary productivity was low in the Carboniferous but high (up to four times that of modern oceans) during the Late Jurassic, mid-Cretaceous and early Eocene greenhouse eras with a greater requirement for key nutrients. Such a requirement would be compatible with accelerated rates of continental weathering under the greenhouse conditions of the Mesozoic and early Tertiary. These results indicate possible changes in the strength of a key component of the oceanic carbon (organic and carbonate) pump in the geological past, with a corresponding feedback on atmospheric CO2 and climate, and provide an improved framework for understanding the role of ocean biota in the evolution of the global biogeochemical cycles of C, N and P.

  17. Validation of quantitative IR thermography for estimating the U-value by a hot box apparatus

    NASA Astrophysics Data System (ADS)

    Nardi, I.; Paoletti, D.; Ambrosini, D.; de Rubeis, T.; Sfarra, S.

    2015-11-01

    Energy saving plays a key role in the reduction of energy consumption and carbon emission, and therefore it is essential for reaching the goal of the 20-20-2020 policy. In particular, buildings are responsible of about 30% of the total amount of Europe energy consumption; the increase of their energy efficiency with the reduction of the thermal transmittance of the envelope is a point of strength with the actions and strategies of the policy makers. Currently, the study of energy performance of buildings is based on international standards, in particular the Italian one allows to calculate the U-value according the ISO 6946 or by in-situ measurements, using a heat flow meter (HFM), following recommendations provided in ISO 9869. In the last few years, a new technique, based on Infrared Thermography (IRT) (also referred to as Infrared Thermovision Technique - ITT), has been proposed for in situ determination of the thermal transmittance of opaque building elements. Some case studies have been reported. This method has already been applied on existing buildings, providing reliable results, but also revealing some weaknesses. In order to overcome such weak points and to assess a systematic procedure for the application of IRT, a validation of the method has been performed in a monitored environment. Infrared camera, the heat flow meter sensors and a nearby meteorological station have been used for thermal transmittance measurement. Comparison between the U-values measured in a hot box with IRT as well as values calculated following international standards and HFM results has been effected. Results give a good description of the advantages, as well as of the open problems, of IR Thermography for estimating the U-value. Further studies will help to refine the technique, and to identify the best operative conditions.

  18. Quantitative estimates of metamorphic equilibria: Tallassee synform, Dadeville belt, Alabama's Inner Piedmont

    SciTech Connect

    Drummond, M.S.; Neilson, M.J. . Dept. of Geology)

    1993-03-01

    The Tallassee synform is the major structural feature in the western part of the Dadeville belt. This megascopic F2 structure folds amphibolite (Ropes Creek Amphibolite) and metasedimentary units (Agricola Schist, AS), as well as tonalitic (Camp Hill Gneiss, CHG), granitic (Chattasofka Creek Gneiss, CCG), and mafic-ultramafic plutons (Doss Mt. and Slaughters suites). Acadian-age prograde regional metamorphism preceded the F2 folding event, producing the pervasive S1 foliation and metamorphic recrystallization. Prograde mineralogy in the metapelites and metagraywackes of the AS includes garnet, biotite, muscovite, plagioclase, kyanite, sillimanite, and epidote. The intrusive rocks, both felsic and mafic-ultramafic, are occasionally garnetiferous and provide suitable mineral assemblages for P-T evaluation. The AS yields a range of T-P from 512--635C and 5.1--5.5 kb. Muscovite from the AS exhibits an increase in Ti content from 0.07 to 0.15 Ti/22 O formula unit with progressively increasing T's from 512 to 635C. This observation is consistent with other studies that show increasing Ti content with increasing grade. A CHG sample records an average metamorphic T-P of 604C and 5.79 kb. Hornblende-garnet pairs from a Doss Mt. amphibolite sample provides an average metamorphic T of 607C. These data are consistent with regional Barrovian-type middle to upper amphibolite facies metamorphism for the Tallassee synform. Peak metamorphism is represented by kyanite-sillimanite zone conditions and localized migmatization of the AS. The lithotectonic belts bounding the Dadeville belt to the NW and SE are the eastern Blue Ridge and Opelika belts. Studies have shown that these belts have also experienced Acadian-age amphibolite facies metamorphism with comparable P-T estimates to those presented here. These data suggest that the eastern Blue Ridge and Inner Piedmont of AL experienced the same pervasive dynamothermal Barrovian-type metamorphic episode during Acadian orogenesis.

  19. Lymphohaematopoietic malignancies and quantitative estimates of exposure to benzene in Canadian petroleum distribution workers.

    PubMed Central

    Schnatter, A R; Armstrong, T W; Nicolich, M J; Thompson, F S; Katz, A M; Huebner, W W; Pearlman, E D

    1996-01-01

    OBJECTIVE: To evaluate the relation between mortality from lymphohaematopoietic cancer and long term, low level exposures to benzene among male petroleum distribution workers. METHODS: This nested case control study identified all fatal cases of lymphohaematopoietic cancer among a previously studied cohort. Of the 29 cases, 14 had leukaemia, seven multiple myeloma, and eight non-Hodgkin's lymphoma. A four to one matching ratio was used to select a stratified sample of controls from the same cohort, controlling for year of birth and time at risk. Industrial hygienists estimated workplace exposures for benzene and total hydrocarbons, without knowledge of case or control status, for combinations of job, location, and era represented in all work histories. Average daily benzene concentrations ranged from 0.01 to 6.2 parts per million (ppm) for all jobs. Company medical records were used to abstract information on other potential confounders such as cigarette smoking, although the data were incomplete. Odds ratios (ORs) were calculated with conditional logistic regression techniques for several exposure variables. RESULTS: Risks of leukaemia, non-Hodgkin's lymphoma, and multiple myeloma were not associated with increasing cumulative exposure to benzene or total hydrocarbons. For leukaemia, the logistic regression model predicted an OR of 1.002 (P < 0.77) for each ppm-y of exposure to benzene. Duration of exposure to benzene was more closely associated with risk of leukaemia than other exposure variables. It was not possible to completely control for other risk factors, although there was suggestive evidence that smoking and a family history of cancer may have played a part in the risk of leukaemia. CONCLUSION: This study did not show a relation between lymphohaematopoietic cancer and long term, low level exposures to benzene. The power of the study to detect low-such as twofold-risks was limited. Thus, further study on exposures to benzene in this concentration range

  20. Quantitative assessment of the microbial risk of leafy greens from farm to consumption: preliminary framework, data, and risk estimates.

    PubMed

    Danyluk, Michelle D; Schaffner, Donald W

    2011-05-01

    This project was undertaken to relate what is known about the behavior of Escherichia coli O157:H7 under laboratory conditions and integrate this information to what is known regarding the 2006 E. coli O157:H7 spinach outbreak in the context of a quantitative microbial risk assessment. The risk model explicitly assumes that all contamination arises from exposure in the field. Extracted data, models, and user inputs were entered into an Excel spreadsheet, and the modeling software @RISK was used to perform Monte Carlo simulations. The model predicts that cut leafy greens that are temperature abused will support the growth of E. coli O157:H7, and populations of the organism may increase by as much a 1 log CFU/day under optimal temperature conditions. When the risk model used a starting level of -1 log CFU/g, with 0.1% of incoming servings contaminated, the predicted numbers of cells per serving were within the range of best available estimates of pathogen levels during the outbreak. The model predicts that levels in the field of -1 log CFU/g and 0.1% prevalence could have resulted in an outbreak approximately the size of the 2006 E. coli O157:H7 outbreak. This quantitative microbial risk assessment model represents a preliminary framework that identifies available data and provides initial risk estimates for pathogenic E. coli in leafy greens. Data gaps include retail storage times, correlations between storage time and temperature, determining the importance of E. coli O157:H7 in leafy greens lag time models, and validation of the importance of cross-contamination during the washing process.

  1. Contribution of Quantitative Methods of Estimating Mortality Dynamics to Explaining Mechanisms of Aging.

    PubMed

    Shilovsky, G A; Putyatina, T S; Markov, A V; Skulachev, V P

    2015-12-01

    . makes it possible to approximately divide animals and plants only by their levels of the Gompertz type of senescence (i.e. actuarial senescence), whereas susceptibility to biological senescence can be estimated only when principally different models are applied. PMID:26638679

  2. Merging Radar Quantitative Precipitation Estimates (QPEs) from the High-resolution NEXRAD Reanalysis over CONUS with Rain-gauge Observations

    NASA Astrophysics Data System (ADS)

    Prat, O. P.; Nelson, B. R.; Stevens, S. E.; Nickl, E.; Seo, D. J.; Kim, B.; Zhang, J.; Qi, Y.

    2015-12-01

    The processing of radar-only precipitation via the reanalysis from the National Mosaic and Multi-Sensor Quantitative (NMQ/Q2) based on the WSR-88D Next-generation Radar (Nexrad) network over the Continental United States (CONUS) is completed for the period covering from 2002 to 2011. While this constitutes a unique opportunity to study precipitation processes at higher resolution than conventionally possible (1-km, 5-min), the long-term radar-only product needs to be merged with in-situ information in order to be suitable for hydrological, meteorological and climatological applications. The radar-gauge merging is performed by using rain gauge information at daily (Global Historical Climatology Network-Daily: GHCN-D), hourly (Hydrometeorological Automated Data System: HADS), and 5-min (Automated Surface Observing Systems: ASOS; Climate Reference Network: CRN) resolution. The challenges related to incorporating differing resolution and quality networks to generate long-term large-scale gridded estimates of precipitation are enormous. In that perspective, we are implementing techniques for merging the rain gauge datasets and the radar-only estimates such as Inverse Distance Weighting (IDW), Simple Kriging (SK), Ordinary Kriging (OK), and Conditional Bias-Penalized Kriging (CBPK). An evaluation of the different radar-gauge merging techniques is presented and we provide an estimate of uncertainty for the gridded estimates. In addition, comparisons with a suite of lower resolution QPEs derived from ground based radar measurements (Stage IV) are provided in order to give a detailed picture of the improvements and remaining challenges.

  3. Estimating Active Transportation Behaviors to Support Health Impact Assessment in the United States

    PubMed Central

    Mansfield, Theodore J.; Gibson, Jacqueline MacDonald

    2016-01-01

    Health impact assessment (HIA) has been promoted as a means to encourage transportation and city planners to incorporate health considerations into their decision-making. Ideally, HIAs would include quantitative estimates of the population health effects of alternative planning scenarios, such as scenarios with and without infrastructure to support walking and cycling. However, the lack of baseline estimates of time spent walking or biking for transportation (together known as “active transportation”), which are critically related to health, often prevents planners from developing such quantitative estimates. To address this gap, we use data from the 2009 US National Household Travel Survey to develop a statistical model that estimates baseline time spent walking and biking as a function of the type of transportation used to commute to work along with demographic and built environment variables. We validate the model using survey data from the Raleigh–Durham–Chapel Hill, NC, USA, metropolitan area. We illustrate how the validated model could be used to support transportation-related HIAs by estimating the potential health benefits of built environment modifications that support walking and cycling. Our statistical model estimates that on average, individuals who commute on foot spend an additional 19.8 (95% CI 16.9–23.2) minutes per day walking compared to automobile commuters. Public transit riders walk an additional 5.0 (95% CI 3.5–6.4) minutes per day compared to automobile commuters. Bicycle commuters cycle for an additional 28.0 (95% CI 17.5–38.1) minutes per day compared to automobile commuters. The statistical model was able to predict observed transportation physical activity in the Raleigh–Durham–Chapel Hill region to within 0.5 MET-hours per day (equivalent to about 9 min of daily walking time) for 83% of observations. Across the Raleigh–Durham–Chapel Hill region, an estimated 38 (95% CI 15–59) premature deaths potentially could

  4. Estimating Active Transportation Behaviors to Support Health Impact Assessment in the United States.

    PubMed

    Mansfield, Theodore J; Gibson, Jacqueline MacDonald

    2016-01-01

    Health impact assessment (HIA) has been promoted as a means to encourage transportation and city planners to incorporate health considerations into their decision-making. Ideally, HIAs would include quantitative estimates of the population health effects of alternative planning scenarios, such as scenarios with and without infrastructure to support walking and cycling. However, the lack of baseline estimates of time spent walking or biking for transportation (together known as "active transportation"), which are critically related to health, often prevents planners from developing such quantitative estimates. To address this gap, we use data from the 2009 US National Household Travel Survey to develop a statistical model that estimates baseline time spent walking and biking as a function of the type of transportation used to commute to work along with demographic and built environment variables. We validate the model using survey data from the Raleigh-Durham-Chapel Hill, NC, USA, metropolitan area. We illustrate how the validated model could be used to support transportation-related HIAs by estimating the potential health benefits of built environment modifications that support walking and cycling. Our statistical model estimates that on average, individuals who commute on foot spend an additional 19.8 (95% CI 16.9-23.2) minutes per day walking compared to automobile commuters. Public transit riders walk an additional 5.0 (95% CI 3.5-6.4) minutes per day compared to automobile commuters. Bicycle commuters cycle for an additional 28.0 (95% CI 17.5-38.1) minutes per day compared to automobile commuters. The statistical model was able to predict observed transportation physical activity in the Raleigh-Durham-Chapel Hill region to within 0.5 MET-hours per day (equivalent to about 9 min of daily walking time) for 83% of observations. Across the Raleigh-Durham-Chapel Hill region, an estimated 38 (95% CI 15-59) premature deaths potentially could be avoided if the entire

  5. Simultaneous quantitative analysis of 12 methoxyflavones with melanogenesis inhibitory activity from the rhizomes of Kaempferia parviflora.

    PubMed

    Ninomiya, Kiyofumi; Matsumoto, Taku; Chaipech, Saowanee; Miyake, Sohachiro; Katsuyama, Yushi; Tsuboyama, Akihiro; Pongpiriyadacha, Yutana; Hayakawa, Takao; Muraoka, Osamu; Morikawa, Toshio

    2016-04-01

    A methanol extract from the rhizomes of Kaempferia parviflora Wall. ex Baker (Zingiberaceae) has shown inhibitory effects against melanogenesis in theophylline-stimulated murine B16 melanoma 4A5 cells (IC50 = 9.6 μg/mL). Among 25 flavonoids and three acetophenones isolated previously (1-28), several constituents including 5-hydroxy-7,3',4'-trimethoxyflavone (6, IC50 = 8.8 μM), 5,7,3',4'-tetramethoxyflavone (7, 8.6 μM), 5,3'-dihydroxy-3,7,4'-trimethoxyflavone (12, 2.9 μM), and 5-hydroxy-3,7,3',4'-tetramethoxyflavone (13, 3.5 μM) showed inhibitory effects without notable cytotoxicity at the effective concentrations. Compounds 6, 7, 12, and 13 inhibited the expression of tyrosinase, tyrosine-related protein (TRP)-1, and TRP-2 mRNA, which could be the mechanism of their melanogenesis inhibitory activity. In addition, a quantitative analytical method for 12 methoxyflavones (1, 2, 4-11, 13, and 14) in the extract was developed using HPLC. The optimal condition for separation and detection of these constituents were achieved on an ODS column (3 μm particle size, 2.1 mm i.d. × 100 mm) with MeOH-0.1 % aqueous acetic acid solvent systems as the mobile phase, and the detection and quantitation limits of the method were estimated to be 0.08-0.66 ng and 0.22-2.00ng, respectively. The relative standard deviation values of intra- and interday precision were lower than 0.95 and 1.08 %, respectively, overall mean recoveries of all flavonoids were 97.9-102.9 %, and the correlation coefficients of all the calibration curves showed good linearity within the test ranges. For validation of the protocol, extracts of three kinds of the plant's rhizomes collected from different regions in Thailand (Leoi, Phetchabun, and Chiang Mai provinces) were evaluated. The results indicated that the assay was reproducible, precise, and could be readily utilized for the quality evaluation of the plant materials. PMID:26711832

  6. 76 FR 9637 - Proposed Information Collection (Veteran Suicide Prevention Online Quantitative Surveys) Activity...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-02-18

    ... AFFAIRS Proposed Information Collection (Veteran Suicide Prevention Online Quantitative Surveys) Activity... outreach efforts on the prevention of suicide among Veterans and their families. DATES: Written comments...). Type of Review: New collection. Abstract: VA's top priority is the prevention of Veterans suicide....

  7. Genome-wide quantitative enhancer activity maps identified by STARR-seq.

    PubMed

    Arnold, Cosmas D; Gerlach, Daniel; Stelzer, Christoph; Boryń, Łukasz M; Rath, Martina; Stark, Alexander

    2013-03-01

    Genomic enhancers are important regulators of gene expression, but their identification is a challenge, and methods depend on indirect measures of activity. We developed a method termed STARR-seq to directly and quantitatively assess enhancer activity for millions of candidates from arbitrary sources of DNA, which enables screens across entire genomes. When applied to the Drosophila genome, STARR-seq identifies thousands of cell type-specific enhancers across a broad continuum of strengths, links differential gene expression to differences in enhancer activity, and creates a genome-wide quantitative enhancer map. This map reveals the highly complex regulation of transcription, with several independent enhancers for both developmental regulators and ubiquitously expressed genes. STARR-seq can be used to identify and quantify enhancer activity in other eukaryotes, including humans.

  8. Cdk1 activity acts as a quantitative platform for coordinating cell cycle progression with periodic transcription

    PubMed Central

    Banyai, Gabor; Baïdi, Feriel; Coudreuse, Damien; Szilagyi, Zsolt

    2016-01-01

    Cell proliferation is regulated by cyclin-dependent kinases (Cdks) and requires the periodic expression of particular gene clusters in different cell cycle phases. However, the interplay between the networks that generate these transcriptional oscillations and the core cell cycle machinery remains largely unexplored. In this work, we use a synthetic regulable Cdk1 module to demonstrate that periodic expression is governed by quantitative changes in Cdk1 activity, with different clusters directly responding to specific activity levels. We further establish that cell cycle events neither participate in nor interfere with the Cdk1-driven transcriptional program, provided that cells are exposed to the appropriate Cdk1 activities. These findings contrast with current models that propose self-sustained and Cdk1-independent transcriptional oscillations. Our work therefore supports a model in which Cdk1 activity serves as a quantitative platform for coordinating cell cycle transitions with the expression of critical genes to bring about proper cell cycle progression. PMID:27045731

  9. Quantitative structure-activity relationships for organophosphates binding to trypsin and chymotrypsin.

    PubMed

    Ruark, Christopher D; Hack, C Eric; Robinson, Peter J; Gearhart, Jeffery M

    2011-01-01

    Organophosphate (OP) nerve agents such as sarin, soman, tabun, and O-ethyl S-[2-(diisopropylamino) ethyl] methylphosphonothioate (VX) do not react solely with acetylcholinesterase (AChE). Evidence suggests that cholinergic-independent pathways over a wide range are also targeted, including serine proteases. These proteases comprise nearly one-third of all known proteases and play major roles in synaptic plasticity, learning, memory, neuroprotection, wound healing, cell signaling, inflammation, blood coagulation, and protein processing. Inhibition of these proteases by OP was found to exert a wide range of noncholinergic effects depending on the type of OP, the dose, and the duration of exposure. Consequently, in order to understand these differences, in silico biologically based dose-response and quantitative structure-activity relationship (QSAR) methodologies need to be integrated. Here, QSAR were used to predict OP bimolecular rate constants for trypsin and α-chymotrypsin. A heuristic regression of over 500 topological/constitutional, geometric, thermodynamic, electrostatic, and quantum mechanical descriptors, using the software Ampac 8.0 and Codessa 2.51 (SemiChem, Inc., Shawnee, KS), was developed to obtain statistically verified equations for the models. General models, using all data subsets, resulted in R(2) values of .94 and .92 and leave-one-out Q(2) values of 0.9 and 0.87 for trypsin and α-chymotrypsin. To validate the general model, training sets were split into independent subsets for test set evaluation. A y-randomization procedure, used to estimate chance correlation, was performed 10,000 times, resulting in mean R(2) values of .24 and .3 for trypsin and α-chymotrypsin. The results show that these models are highly predictive and capable of delineating the complex mechanism of action between OP and serine proteases, and ultimately, by applying this approach to other OP enzyme reactions such as AChE, facilitate the development of biologically based

  10. Quantitative structure-activity relationships (QSARs) for the transformation of organic micropollutants during oxidative water treatment.

    PubMed

    Lee, Yunho; von Gunten, Urs

    2012-12-01

    Various oxidants such as chlorine, chlorine dioxide, ferrate(VI), ozone, and hydroxyl radicals can be applied for eliminating organic micropollutant by oxidative transformation during water treatment in systems such as drinking water, wastewater, and water reuse. Over the last decades, many second-order rate constants (k) have been determined for the reaction of these oxidants with model compounds and micropollutants. Good correlations (quantitative structure-activity relationships or QSARs) are often found between the k-values for an oxidation reaction of closely related compounds (i.e. having a common organic functional group) and substituent descriptor variables such as Hammett or Taft sigma constants. In this study, we developed QSARs for the oxidation of organic and some inorganic compounds and organic micropollutants transformation during oxidative water treatment. A number of 18 QSARs were developed based on overall 412 k-values for the reaction of chlorine, chlorine dioxide, ferrate, and ozone with organic compounds containing electron-rich moieties such as phenols, anilines, olefins, and amines. On average, 303 out of 412 (74%) k-values were predicted by these QSARs within a factor of 1/3-3 compared to the measured values. For HO(·) reactions, some principles and estimation methods of k-values (e.g. the Group Contribution Method) are discussed. The developed QSARs and the Group Contribution Method could be used to predict the k-values for various emerging organic micropollutants. As a demonstration, 39 out of 45 (87%) predicted k-values were found within a factor 1/3-3 compared to the measured values for the selected emerging micropollutants. Finally, it is discussed how the uncertainty in the predicted k-values using the QSARs affects the accuracy of prediction for micropollutant elimination during oxidative water treatment. PMID:22939392

  11. Quantitative Structure--Activity Relationship (QSAR) for the Oxidation of Trace Organic Contaminants by Sulfate Radical.

    PubMed

    Xiao, Ruiyang; Ye, Tiantian; Wei, Zongsu; Luo, Shuang; Yang, Zhihui; Spinney, Richard

    2015-11-17

    The sulfate radical anion (SO4•–) based oxidation of trace organic contaminants (TrOCs) has recently received great attention due to its high reactivity and low selectivity. In this study, a meta-analysis was conducted to better understand the role of functional groups on the reactivity between SO4•– and TrOCs. The results indicate that compounds in which electron transfer and addition channels dominate tend to exhibit a faster second-order rate constants (kSO4•–) than that of H–atom abstraction, corroborating the SO4•– reactivity and mechanisms observed in the individual studies. Then, a quantitative structure activity relationship (QSAR) model was developed using a sequential approach with constitutional, geometrical, electrostatic, and quantum chemical descriptors. Two descriptors, ELUMO and EHOMO energy gap (ELUMO–EHOMO) and the ratio of oxygen atoms to carbon atoms (#O:C), were found to mechanistically and statistically affect kSO4•– to a great extent with the standardized QSAR model: ln kSO4•– = 26.8–3.97 × #O:C – 0.746 × (ELUMO–EHOMO). In addition, the correlation analysis indicates that there is no dominant reaction channel for SO4•– reactions with various structurally diverse compounds. Our QSAR model provides a robust predictive tool for estimating emerging micropollutants removal using SO4•– during wastewater treatment processes. PMID:26451961

  12. Quantitative estimation of foot-flat and stance phase of gait using foot-worn inertial sensors.

    PubMed

    Mariani, Benoit; Rouhani, Hossein; Crevoisier, Xavier; Aminian, Kamiar

    2013-02-01

    Time periods composing stance phase of gait can be clinically meaningful parameters to reveal differences between normal and pathological gait. This study aimed, first, to describe a novel method for detecting stance and inner-stance temporal events based on foot-worn inertial sensors; second, to extract and validate relevant metrics from those events; and third, to investigate their suitability as clinical outcome for gait evaluations. 42 subjects including healthy subjects and patients before and after surgical treatments for ankle osteoarthritis performed 50-m walking trials while wearing foot-worn inertial sensors and pressure insoles as a reference system. Several hypotheses were evaluated to detect heel-strike, toe-strike, heel-off, and toe-off based on kinematic features. Detected events were compared with the reference system on 3193 gait cycles and showed good accuracy and precision. Absolute and relative stance periods, namely loading response, foot-flat, and push-off were then estimated, validated, and compared statistically between populations. Besides significant differences observed in stance duration, the analysis revealed differing tendencies with notably a shorter foot-flat in healthy subjects. The result indicated which features in inertial sensors' signals should be preferred for detecting precisely and accurately temporal events against a reference standard. The system is suitable for clinical evaluations and provides temporal analysis of gait beyond the common swing/stance decomposition, through a quantitative estimation of inner-stance phases such as foot-flat.

  13. Estimating relative demand for wildlife: Conservation activity indicators

    NASA Astrophysics Data System (ADS)

    Gray, Gary G.; Larson, Joseph S.

    1982-09-01

    An alternative method of estimating relative demand among nonconsumptive uses of wildlife and among wildlife species is proposed. A demand intensity score (DIS), derived from the relative extent of an individual's involvement in outdoor recreation and conservation activities, is used as a weighting device to adjust the importance of preference rankings for wildlife uses and wildlife species relative to other members of a survey population. These adjusted preference rankings were considered to reflect relative demand levels (RDLs) for wildlife uses and for species by the survey population. This technique may be useful where it is not possible or desirable to estimate demand using traditional economic means. In one of the findings from a survey of municipal conservation commission members in Massachusetts, presented as an illustration of this methodology, poisonous snakes were ranked third in preference among five groups of reptiles. The relative demand level for poisonous snakes, however, was last among the five groups.

  14. On the precision of automated activation time estimation

    NASA Technical Reports Server (NTRS)

    Kaplan, D. T.; Smith, J. M.; Rosenbaum, D. S.; Cohen, R. J.

    1988-01-01

    We examined how the assignment of local activation times in epicardial and endocardial electrograms is affected by sampling rate, ambient signal-to-noise ratio, and sinx/x waveform interpolation. Algorithms used for the estimation of fiducial point locations included dV/dtmax, and a matched filter detection algorithm. Test signals included epicardial and endocardial electrograms overlying both normal and infarcted regions of dog myocardium. Signal-to-noise levels were adjusted by combining known data sets with white noise "colored" to match the spectral characteristics of experimentally recorded noise. For typical signal-to-noise ratios and sampling rates, the template-matching algorithm provided the greatest precision in reproducibly estimating fiducial point location, and sinx/x interpolation allowed for an additional significant improvement. With few restrictions, combining these two techniques may allow for use of digitization rates below the Nyquist rate without significant loss of precision.

  15. Quantitative contributions of CtBP-dependent and -independent repression activities of Knirps.

    PubMed

    Struffi, Paolo; Corado, Maria; Kulkarni, Meghana; Arnosti, David N

    2004-05-01

    The Drosophila Knirps protein is a short-range transcriptional repressor that locally inhibits activators by recruiting the CtBP co-repressor. Knirps also possesses CtBP-independent repression activity. The functional importance of multiple repression activities is not well understood, but the finding that Knirps does not repress some cis-regulatory elements in the absence of CtBP suggested that the co-factor may supply a unique function essential to repress certain types of activators. We assayed CtBP-dependent and -independent repression domains of Knirps in Drosophila embryos, and found that the CtBP-independent activity, when provided at higher than normal levels, can repress an eve regulatory element that normally requires CtBP. Dose response analysis revealed that the activity of Knirps containing both CtBP-dependent and -independent repression activities is higher than that of the CtBP-independent domain alone. The requirement for CtBP at certain enhancers appears to reflect the need for overall higher levels of repression, rather than a requirement for an activity unique to CtBP. Thus, CtBP contributes quantitatively, rather than qualitatively, to overall repression function. The finding that both repression activities are simultaneously deployed suggests that the multiple repression activities do not function as cryptic 'backup' systems, but that each contributes quantitatively to total repressor output.

  16. PEPIS: A Pipeline for Estimating Epistatic Effects in Quantitative Trait Locus Mapping and Genome-Wide Association Studies

    PubMed Central

    Dai, Xinbin; Wang, Qishan; Xu, Shizhong; Zhao, Patrick X.

    2016-01-01

    The term epistasis refers to interactions between multiple genetic loci. Genetic epistasis is important in regulating biological function and is considered to explain part of the ‘missing heritability,’ which involves marginal genetic effects that cannot be accounted for in genome-wide association studies. Thus, the study of epistasis is of great interest to geneticists. However, estimating epistatic effects for quantitative traits is challenging due to the large number of interaction effects that must be estimated, thus significantly increasing computing demands. Here, we present a new web server-based tool, the Pipeline for estimating EPIStatic genetic effects (PEPIS), for analyzing polygenic epistatic effects. The PEPIS software package is based on a new linear mixed model that has been used to predict the performance of hybrid rice. The PEPIS includes two main sub-pipelines: the first for kinship matrix calculation, and the second for polygenic component analyses and genome scanning for main and epistatic effects. To accommodate the demand for high-performance computation, the PEPIS utilizes C/C++ for mathematical matrix computing. In addition, the modules for kinship matrix calculations and main and epistatic-effect genome scanning employ parallel computing technology that effectively utilizes multiple computer nodes across our networked cluster, thus significantly improving the computational speed. For example, when analyzing the same immortalized F2 rice population genotypic data examined in a previous study, the PEPIS returned identical results at each analysis step with the original prototype R code, but the computational time was reduced from more than one month to about five minutes. These advances will help overcome the bottleneck frequently encountered in genome wide epistatic genetic effect analysis and enable accommodation of the high computational demand. The PEPIS is publically available at http://bioinfo.noble.org/PolyGenic_QTL/. PMID:27224861

  17. Quantitative observation and study on rhythmic abnormalities of activities in animals prior to earthquakes

    NASA Astrophysics Data System (ADS)

    Feng, Chungao; Jiang, Jinchang

    1992-11-01

    In this paper, the normal daily activities and abnormal activities related to earthquake premonitory information are given by a quantitative observation and analysis of activities in the sparrow (SR, Passer montanus), budgerigar (BG, Melopsittacus undulatus) and rat (RT, Rattus norvegicus). The results show that the quantitative observation of habitual abnormalities in animals may provide some cues for the short-term earthquake prediction. The normal activity rhythms for the SR and BG are similar, and both present M mode. The high activities occurs during 07h 10h and 15h 16h, respectively, the low activities occurs during 12h 13h, and at night both birds are basically silent. For the RT, the normal rhythmic activity has the middle magnitude during 07h 10h and 17h 18h, the low and high magnitudes occur during 11h 16h and from 19h to 06h at the next day. For the SR, BG and RT, observable abnormal changes of the normal activity rhythm were found before earthquakes. The night activities of the SR and BG were increased noticeably. For the RT the activities during the low magnitude of activities at the day time were also increased. They both are about 300 times greater than the normal activity value. Moreover, the total activity values per day were increased, and were about 2 times of the normal value. The x 2-test shows that the abnormalities of the daily activity rhythm and following increase of the daily activity events are significantly correlated with earthquakes of magnitude over 4.3 in Tangshan seismic area within the region of 200 km distance from the observation station.

  18. Toxicity Estimation Software Tool (TEST)

    EPA Science Inventory

    The Toxicity Estimation Software Tool (TEST) was developed to allow users to easily estimate the toxicity of chemicals using Quantitative Structure Activity Relationships (QSARs) methodologies. QSARs are mathematical models used to predict measures of toxicity from the physical c...

  19. Quantitative structure-antifungal activity relationships of some benzohydrazides against Botrytis cinerea.

    PubMed

    Reino, José L; Saiz-Urra, Liane; Hernandez-Galan, Rosario; Aran, Vicente J; Hitchcock, Peter B; Hanson, James R; Gonzalez, Maykel Perez; Collado, Isidro G

    2007-06-27

    Fourteen benzohydrazides have been synthesized and evaluated for their in vitro antifungal activity against the phytopathogenic fungus Botrytis cinerea. The best antifungal activity was observed for the N',N'-dibenzylbenzohydrazides 3b-d and for the N-aminoisoindoline-derived benzohydrazide 5. A quantitative structure-activity relationship (QSAR) study has been developed using a topological substructural molecular design (TOPS-MODE) approach to interpret the antifungal activity of these synthetic compounds. The model described 98.3% of the experimental variance, with a standard deviation of 4.02. The influence of an ortho substituent on the conformation of the benzohydrazides was investigated by X-ray crystallography and supported by QSAR study. Several aspects of the structure-activity relationships are discussed in terms of the contribution of different bonds to the antifungal activity, thereby making the relationships between structure and biological activity more transparent.

  20. A Quantitative Method for Comparing the Brightness of Antibody-dye Reagents and Estimating Antibodies Bound per Cell.

    PubMed

    Kantor, Aaron B; Moore, Wayne A; Meehan, Stephen; Parks, David R

    2016-01-01

    We present a quantitative method for comparing the brightness of antibody-dye reagents and estimating antibodies bound per cell. The method is based on complementary binding of test and fill reagents to antibody capture microspheres. Several aliquots of antibody capture beads are stained with varying amounts of the test conjugate. The remaining binding sites on the beads are then filled with a second conjugate containing a different fluorophore. Finally, the fluorescence of the test conjugate compared to the fill conjugate is used to measure the relative brightness of the test conjugate. The fundamental assumption of the test-fill method is that if it takes X molecules of one test antibody to lower the fill signal by Y units, it will take the same X molecules of any other test antibody to give the same effect. We apply a quadratic fit to evaluate the test-fill signal relationship across different amounts of test reagent. If the fit is close to linear, we consider the test reagent to be suitable for quantitative evaluation of antibody binding. To calibrate the antibodies bound per bead, a PE conjugate with 1 PE molecule per antibody is used as a test reagent and the fluorescence scale is calibrated with Quantibrite PE beads. When the fluorescence per antibody molecule has been determined for a particular conjugate, that conjugate can be used for measurement of antibodies bound per cell. This provides comparisons of the brightness of different conjugates when conducted on an instrument whose statistical photoelectron (Spe) scales are known. © 2016 by John Wiley & Sons, Inc.

  1. Cyclotide Structure–Activity Relationships: Qualitative and Quantitative Approaches Linking Cytotoxic and Anthelmintic Activity to the Clustering of Physicochemical Forces

    PubMed Central

    Park, Sungkyu; Strömstedt, Adam A.; Göransson, Ulf

    2014-01-01

    Cyclotides are a family of plant-derived proteins that are characterized by a cyclic backbone and a knotted disulfide topology. Their cyclic cystine knot (CCK) motif makes them exceptionally resistant to thermal, chemical, and enzymatic degradation. Cyclotides exert much of their biological activity via interactions with cell membranes. In this work, we qualitatively and quantitatively analyze the cytotoxic and anthelmintic membrane activities of cyclotides. The qualitative and quantitative models describe the potency of cyclotides using four simple physicochemical terms relevant to membrane contact. Specifically, surface areas of the cyclotides representing lipophilic and hydrogen bond donating properties were quantified and their distribution across the molecular surface was determined. The resulting quantitative structure-activity relation (QSAR) models suggest that the activity of the cyclotides is proportional to their lipophilic and positively charged surface areas, provided that the distribution of these surfaces is asymmetric. In addition, we qualitatively analyzed the physicochemical differences between the various cyclotide subfamilies and their effects on the cyclotides' orientation on the membrane and membrane activity. PMID:24682019

  2. A computational quantitative structure-activity relationship study of carbamate anticonvulsants using quantum pharmacological methods.

    PubMed

    Knight, J L; Weaver, D F

    1998-10-01

    A pattern recognition quantitative structure-activity relationship (QSAR) study has been performed to determine the molecular features of carbamate anticonvulsants which influence biological activity. Although carbamates, such as felbamate, have been used to treat epilepsy, their mechanisms of efficacy and toxicity are not completely understood. Quantum and classical mechanics calculations have been exploited to describe 46 carbamate drugs. Employing a principal component analysis and multiple linear regression calculations, five crucial structural descriptors were identified which directly relate to the bioactivity of the carbamate family. With the resulting mathematical model, the biological activity of carbamate analogues can be predicted with 85-90% accuracy.

  3. Quantitative structure-activity relationships and docking studies of calcitonin gene-related peptide antagonists.

    PubMed

    Kyani, Anahita; Mehrabian, Mohadeseh; Jenssen, Håvard

    2012-02-01

    Defining the role of calcitonin gene-related peptide in migraine pathogenesis could lead to the application of calcitonin gene-related peptide antagonists as novel migraine therapeutics. In this work, quantitative structure-activity relationship modeling of biological activities of a large range of calcitonin gene-related peptide antagonists was performed using a panel of physicochemical descriptors. The computational studies evaluated different variable selection techniques and demonstrated shuffling stepwise multiple linear regression to be superior over genetic algorithm-multiple linear regression. The linear quantitative structure-activity relationship model revealed better statistical parameters of cross-validation in comparison with the non-linear support vector regression technique. Implementing only five peptide descriptors into this linear quantitative structure-activity relationship model resulted in an extremely robust and highly predictive model with calibration, leave-one-out and leave-20-out validation R(2) of 0.9194, 0.9103, and 0.9214, respectively. We performed docking of the most potent calcitonin gene-related peptide antagonists with the calcitonin gene-related peptide receptor and demonstrated that peptide antagonists act by blocking access to the peptide-binding cleft. We also demonstrated the direct contact of residues 28-37 of the calcitonin gene-related peptide antagonists with the receptor. These results are in agreement with the conclusions drawn from the quantitative structure-activity relationship model, indicating that both electrostatic and steric factors should be taken into account when designing novel calcitonin gene-related peptide antagonists. PMID:21974743

  4. Quantitative end qualitative analysis of the electrical activity of rectus abdominis muscle portions.

    PubMed

    Negrão Filho, R de Faria; Bérzin, F; Souza, G da Cunha

    2003-01-01

    The purpose of this study was to investigate the electrical behavior pattern of the Rectus abdominis muscle by qualitative and quantitative analysis of the electromyographic signal obtained from its superior, medium and inferior portions during dynamic and static activities. Ten voluntaries (aged X = 17.8 years, SD = 1.6) athletic males were studied without history of muscle skeletal disfunction. For the quantitative analysis the RMS (Root Mean Square) values obtained in the electromyographic signal during the isometric exercises were normalized and expressed in maximum voluntary isometric contraction percentages. For the qualitative analysis of the dynamic activity the electromyographic signal was processed by full-wave rectification, linear envelope and normalization (amplitude and time), so that the resulting curve of the processed signal was submitted to descriptive graphic analysis. The results of the quantitative study show that there is not a statistically significant difference among the portions of the muscle. Qualitative analysis demonstrated two aspects: the presence of a common activation electric pattern in the portions of Rectus abdominis muscle and the absence of significant difference in the inclination angles in the electrical activity curve during the isotonic exercises. PMID:12964259

  5. Validation of a novel method for retrospectively estimating nutrient intake during pregnancy using a semi-quantitative food frequency questionnaire.

    PubMed

    Mejía-Rodríguez, Fabiola; Orjuela, Manuela A; García-Guerra, Armando; Quezada-Sanchez, Amado David; Neufeld, Lynnette M

    2012-10-01

    Case control studies evaluating the relationship between dietary intake of specific nutrients and risk of congenital, neonatal or early childhood disease require the ability to rank relative maternal dietary intake during pregnancy. Such studies are limited by the lack of validated instruments for assessing gestational dietary intake several years post-partum. This study aims to validate a semi-quantitative interview-administered food frequency questionnaire (FFQ) for retrospectively estimating nutrient intake at two critical time points during pregnancy. The FFQ was administered to women (N = 84), who 4-6 years earlier had participated in a prospective study to evaluate dietary intake during pregnancy. The FFQ queried participants about intake during the previous month (FFQ-month). This was then used as a reference point to estimate consumption by trimester (FFQ-pregnancy). The resulting data were compared to data collected during the original study from two 24-h recalls (24 h-original) using Spearman correlation and Wilcoxon sign-rank-test. Total energy intake as estimated by the retrospective and original instruments did not differ and was only weakly correlated in the trimesters (1st and 3rd) as a whole (r = 0.18-32), though more strongly correlated when restricted to the first half of the 1st trimester (r = 0.32) and later half of the 3rd trimester (r = 0.87). After energy adjustment, correlation between the 24hR-original and FFQ-pregnancy in the 3rd trimester were r = 0.25 (P < 0.05) for dietary intake of vitamin A, and r = 0.26 (P < 0.05) for folate, and r = 0.23-0.77 (P < 0.005) for folate, and vitamins A, B6 and B12 in the 1st and 3rd trimester after including vitamin supplement intake. The FFQ-pregnancy provides a consistent estimate of maternal intake of key micronutrients during pregnancy and permits accurate ranking of intake 4-6 years post-partum. PMID:22116778

  6. Quantitative assessment on soil enzyme activities of heavy metal contaminated soils with various soil properties.

    PubMed

    Xian, Yu; Wang, Meie; Chen, Weiping

    2015-11-01

    Soil enzyme activities are greatly influenced by soil properties and could be significant indicators of heavy metal toxicity in soil for bioavailability assessment. Two groups of experiments were conducted to determine the joint effects of heavy metals and soil properties on soil enzyme activities. Results showed that arylsulfatase was the most sensitive soil enzyme and could be used as an indicator to study the enzymatic toxicity of heavy metals under various soil properties. Soil organic matter (SOM) was the dominant factor affecting the activity of arylsulfatase in soil. A quantitative model was derived to predict the changes of arylsulfatase activity with SOM content. When the soil organic matter content was less than the critical point A (1.05% in our study), the arylsulfatase activity dropped rapidly. When the soil organic matter content was greater than the critical point A, the arylsulfatase activity gradually rose to higher levels showing that instead of harm the soil microbial activities were enhanced. The SOM content needs to be over the critical point B (2.42% in our study) to protect its microbial community from harm due to the severe Pb pollution (500mgkg(-1) in our study). The quantitative model revealed the pattern of variation of enzymatic toxicity due to heavy metals under various SOM contents. The applicability of the model under wider soil properties need to be tested. The model however may provide a methodological basis for ecological risk assessment of heavy metals in soil.

  7. Quantitative perturbation-based analysis of gene expression predicts enhancer activity in early Drosophila embryo.

    PubMed

    Sayal, Rupinder; Dresch, Jacqueline M; Pushel, Irina; Taylor, Benjamin R; Arnosti, David N

    2016-01-01

    Enhancers constitute one of the major components of regulatory machinery of metazoans. Although several genome-wide studies have focused on finding and locating enhancers in the genomes, the fundamental principles governing their internal architecture and cis-regulatory grammar remain elusive. Here, we describe an extensive, quantitative perturbation analysis targeting the dorsal-ventral patterning gene regulatory network (GRN) controlled by Drosophila NF-κB homolog Dorsal. To understand transcription factor interactions on enhancers, we employed an ensemble of mathematical models, testing effects of cooperativity, repression, and factor potency. Models trained on the dataset correctly predict activity of evolutionarily divergent regulatory regions, providing insights into spatial relationships between repressor and activator binding sites. Importantly, the collective predictions of sets of models were effective at novel enhancer identification and characterization. Our study demonstrates how experimental dataset and modeling can be effectively combined to provide quantitative insights into cis-regulatory information on a genome-wide scale. PMID:27152947

  8. Quantitative estimation of global patterns of surface ocean biological productivity and its seasonal variation on timescales from centuries to millennia

    NASA Astrophysics Data System (ADS)

    Loubere, Paul; Fariduddin, Mohammad

    1999-03-01

    We present a quantitative method, based on the relative abundances of benthic foraminifera in deep-sea sediments, for estimating surface ocean biological productivity over the timescale of centuries to millennia. We calibrate the method using a global data set composed of 207 samples from the Atlantic, Pacific, and Indian Oceans from a water depth range between 2300 and 3600 m. The sample set was developed so that other, potentially significant, environmental variables would be uncorrelated to overlying surface ocean productivity. A regression of assemblages against productivity yielded an r2 = 0.89 demonstrating a strong productivity signal in the faunal data. In addition, we examined assemblage response to annual variability in biological productivity (seasonality). Our data set included a range of seasonalities which we quantified into a seasonality index using the pigment color bands from the coastal zone color scanner (CZCS). The response of benthic foraminiferal assemblage composition to our seasonality index was tested with regression analysis. We obtained a statistically highly significant r2 = 0.75. Further, discriminant function analysis revealed a clear separation among sample groups based on surface ocean productivity and our seasonality index. Finally, we tested the response of benthic foraminiferal assemblages to three different modes of seasonality. We observed a distinct separation of our samples into groups representing low seasonal variability, strong seasonality with a single main productivity event in the year, and strong seasonality with multiple productivity events in the year. Reconstructing surface ocean biological productivity with benthic foraminifera will aid in modeling marine biogeochemical cycles. Also, estimating mode and range of annual seasonality will provide insight to changing oceanic processes, allowing the examination of the mechanisms causing changes in the marine biotic system over time. This article contains supplementary

  9. Towards a quantitative, measurement-based estimate of the uncertainty in photon mass attenuation coefficients at radiation therapy energies.

    PubMed

    Ali, E S M; Spencer, B; McEwen, M R; Rogers, D W O

    2015-02-21

    In this study, a quantitative estimate is derived for the uncertainty in the XCOM photon mass attenuation coefficients in the energy range of interest to external beam radiation therapy-i.e. 100 keV (orthovoltage) to 25 MeV-using direct comparisons of experimental data against Monte Carlo models and theoretical XCOM data. Two independent datasets are used. The first dataset is from our recent transmission measurements and the corresponding EGSnrc calculations (Ali et al 2012 Med. Phys. 39 5990-6003) for 10-30 MV photon beams from the research linac at the National Research Council Canada. The attenuators are graphite and lead, with a total of 140 data points and an experimental uncertainty of ∼0.5% (k = 1). An optimum energy-independent cross section scaling factor that minimizes the discrepancies between measurements and calculations is used to deduce cross section uncertainty. The second dataset is from the aggregate of cross section measurements in the literature for graphite and lead (49 experiments, 288 data points). The dataset is compared to the sum of the XCOM data plus the IAEA photonuclear data. Again, an optimum energy-independent cross section scaling factor is used to deduce the cross section uncertainty. Using the average result from the two datasets, the energy-independent cross section uncertainty estimate is 0.5% (68% confidence) and 0.7% (95% confidence). The potential for energy-dependent errors is discussed. Photon cross section uncertainty is shown to be smaller than the current qualitative 'envelope of uncertainty' of the order of 1-2%, as given by Hubbell (1999 Phys. Med. Biol 44 R1-22).

  10. Noise estimation in infrared image sequences: a tool for the quantitative evaluation of the effectiveness of registration algorithms.

    PubMed

    Agostini, Valentina; Delsanto, Silvia; Knaflitz, Marco; Molinari, Filippo

    2008-07-01

    Dynamic infrared imaging has been proposed in literature as an adjunctive technique to mammography in breast cancer diagnosis. It is based on the acquisition of hundreds of consecutive thermal images with a frame rate ranging from 50 to 200 frames/s, followed by the harmonic analysis of temperature time series at each image pixel. However, the temperature fluctuation due to blood perfusion, which is the signal of interest, is small compared to the signal fluctuation due to subject movements. Hence, before extracting the time series describing temperature fluctuations, it is fundamental to realign the thermal images to attenuate motion artifacts. In this paper, we describe a method for the quantitative evaluation of any kind of feature-based registration algorithm on thermal image sequences, provided that an estimation of local velocities of reference points on the skin is available. As an example of evaluation of a registration algorithm, we report the evaluation of the SNR improvement obtained by applying a nonrigid piecewise linear algorithm.

  11. Quantitative microbial risk assessment combined with hydrodynamic modelling to estimate the public health risk associated with bathing after rainfall events.

    PubMed

    Eregno, Fasil Ejigu; Tryland, Ingun; Tjomsland, Torulv; Myrmel, Mette; Robertson, Lucy; Heistad, Arve

    2016-04-01

    This study investigated the public health risk from exposure to infectious microorganisms at Sandvika recreational beaches, Norway and dose-response relationships by combining hydrodynamic modelling with Quantitative Microbial Risk Assessment (QMRA). Meteorological and hydrological data were collected to produce a calibrated hydrodynamic model using Escherichia coli as an indicator of faecal contamination. Based on average concentrations of reference pathogens (norovirus, Campylobacter, Salmonella, Giardia and Cryptosporidium) relative to E. coli in Norwegian sewage from previous studies, the hydrodynamic model was used for simulating the concentrations of pathogens at the local beaches during and after a heavy rainfall event, using three different decay rates. The simulated concentrations were used as input for QMRA and the public health risk was estimated as probability of infection from a single exposure of bathers during the three consecutive days after the rainfall event. The level of risk on the first day after the rainfall event was acceptable for the bacterial and parasitic reference pathogens, but high for the viral reference pathogen at all beaches, and severe at Kalvøya-small and Kalvøya-big beaches, supporting the advice of avoiding swimming in the day(s) after heavy rainfall. The study demonstrates the potential of combining discharge-based hydrodynamic modelling with QMRA in the context of bathing water as a tool to evaluate public health risk and support beach management decisions. PMID:26802355

  12. Topological study on the toxicity of ionic liquids on Vibrio fischeri by the quantitative structure-activity relationship method.

    PubMed

    Yan, Fangyou; Shang, Qiaoyan; Xia, Shuqian; Wang, Qiang; Ma, Peisheng

    2015-04-01

    As environmentally friendly solvents, ionic liquids (ILs) are unlikely to act as air contaminants or inhalation toxins resulting from their negligible vapor pressure and excellent thermal stability. However, they can be potential water contaminants because of their considerable solubility in water; therefore, a proper toxicological assessment of ILs is essential. The environmental fate of ILs is studied by quantitative structure-activity relationship (QSAR) method. A multiple linear regression (MLR) model is obtained by topological method using toxicity data of 157 ILs on Vibrio fischeri, which are composed of 74 cations and 22 anions. The topological index developed in our research group is used for predicting the V. fischeri toxicity for the first time. The MLR model is precise for estimating LogEC50 of ILs on V. fischeri with square of correlation coefficient (R(2)) = 0.908 and the average absolute error (AAE) = 0.278.

  13. Quantitative estimation of landslide risk from rapid debris slides on natural slopes in the Nilgiri hills, India

    NASA Astrophysics Data System (ADS)

    Jaiswal, P.; van Westen, C. J.; Jetten, V.

    2011-06-01

    A quantitative procedure for estimating landslide risk to life and property is presented and applied in a mountainous area in the Nilgiri hills of southern India. Risk is estimated for elements at risk located in both initiation zones and run-out paths of potential landslides. Loss of life is expressed as individual risk and as societal risk using F-N curves, whereas the direct loss of properties is expressed in monetary terms. An inventory of 1084 landslides was prepared from historical records available for the period between 1987 and 2009. A substantially complete inventory was obtained for landslides on cut slopes (1042 landslides), while for natural slopes information on only 42 landslides was available. Most landslides were shallow translational debris slides and debris flowslides triggered by rainfall. On natural slopes most landslides occurred as first-time failures. For landslide hazard assessment the following information was derived: (1) landslides on natural slopes grouped into three landslide magnitude classes, based on landslide volumes, (2) the number of future landslides on natural slopes, obtained by establishing a relationship between the number of landslides on natural slopes and cut slopes for different return periods using a Gumbel distribution model, (3) landslide susceptible zones, obtained using a logistic regression model, and (4) distribution of landslides in the susceptible zones, obtained from the model fitting performance (success rate curve). The run-out distance of landslides was assessed empirically using landslide volumes, and the vulnerability of elements at risk was subjectively assessed based on limited historic incidents. Direct specific risk was estimated individually for tea/coffee and horticulture plantations, transport infrastructures, buildings, and people both in initiation and run-out areas. Risks were calculated by considering the minimum, average, and maximum landslide volumes in each magnitude class and the

  14. Design, synthesis and exploring the quantitative structure-activity relationship of some antioxidant flavonoid analogues.

    PubMed

    Das, Sreeparna; Mitra, Indrani; Batuta, Shaikh; Niharul Alam, Md; Roy, Kunal; Begum, Naznin Ara

    2014-11-01

    A series of flavonoid analogues were synthesized and screened for the in vitro antioxidant activity through their ability to quench 1,1-diphenyl-2-picryl hydrazyl (DPPH) radical. The activity of these compounds, measured in comparison to the well-known standard antioxidants (29-32), their precursors (38-42) and other bioactive moieties (38-42) resembling partially the flavone skeleton was analyzed further to develop Quantitative Structure-Activity Relationship (QSAR) models using the Genetic Function Approximation (GFA) technique. Based on the essential structural requirements predicted by the QSAR models, some analogues were designed, synthesized and tested for activity. The predicted and experimental activities of these compounds were well correlated. Flavone analogue 20 was found to be the most potent antioxidant.

  15. Spectral estimators of absorbed photosynthetically active radiation in corn canopies

    NASA Technical Reports Server (NTRS)

    Gallo, K. P.; Daughtry, C. S. T.; Bauer, M. E.

    1984-01-01

    Most models of crop growth and yield require an estimate of canopy leaf area index (LAI) or absorption of radiation. Relationships between photosynthetically active radiation (PAR) absorbed by corn canopies and the spectral reflectance of the canopies were investigated. Reflectance factor data were acquired with a LANDSAT MSS band radiometer. From planting to silking, the three spectrally predicted vegetation indices examined were associated with more than 95% of the variability in absorbed PAR. The relationships developed between absorbed PAR and the three indices were evaluated with reflectance factor data acquired from corn canopies planted in 1979 through 1982. Seasonal cumulations of measured LAI and each of the three indices were associated with greater than 50% of the variation in final grain yields from the test years. Seasonal cumulations of daily absorbed PAR were associated with up to 73% of the variation in final grain yields. Absorbed PAR, cumulated through the growing season, is a better indicator of yield than cumulated leaf area index. Absorbed PAR may be estimated reliably from spectral reflectance data of crop canopies.

  16. Spectral estimators of absorbed photosynthetically active radiation in corn canopies

    NASA Technical Reports Server (NTRS)

    Gallo, K. P.; Daughtry, C. S. T.; Bauer, M. E.

    1985-01-01

    Most models of crop growth and yield require an estimate of canopy leaf area index (LAI) or absorption of radiation. Relationships between photosynthetically active radiation (PAR) absorbed by corn canopies and the spectral reflectance of the canopies were investigated. Reflectance factor data were acquired with a Landsat MSS band radiometer. From planting to silking, the three spectrally predicted vegetation indices examined were associated with more than 95 percent of the variability in absorbed PAR. The relationships developed between absorbed PAR and the three indices were evaluated with reflectance factor data acquired from corn canopies planted in 1979 through 1982. Seasonal cumulations of measured LAI and each of the three indices were associated with greater than 50 percent of the variation in final grain yields from the test years. Seasonal cumulations of daily absorbed PAR were associated with up to 73 percent of the variation in final grain yields. Absorbed PAR, cumulated through the growing season, is a better indicator of yield than cumulated leaf area index. Absorbed PAR may be estimated reliably from spectral reflectance data of crop canopies.

  17. Intercepted photosynthetically active radiation estimated by spectral reflectance

    NASA Technical Reports Server (NTRS)

    Hatfield, J. L.; Asrar, G.; Kanemasu, E. T.

    1984-01-01

    Interception of photosynthetically active radiation (PAR) was evaluated relative to greenness and normalized difference (MSS (7-5)/(7+5) for five planting dates of wheat for 1978-79 and 1979-80 at Phoenix, Arizona. Intercepted PAR was calculated from leaf area index and stage of growth. Linear relatinships were found with greeness and normalized difference with separate relatinships describing growth and senescence of the crop. Normalized difference was significantly better than greenness for all planting dates. For the leaf area growth portion of the season the relation between PAR interception and normalized difference was the same over years and planting dates. For the leaf senescence phase the relationships showed more variability due to the lack of data on light interception in sparse and senescing canopies. Normalized difference could be used to estimate PAR interception throughout a growing season.

  18. Warm dust and aromatic bands as quantitative probes of star-formation activity

    NASA Astrophysics Data System (ADS)

    Förster Schreiber, N. M.; Roussel, H.; Sauvage, M.; Charmandaris, V.

    2004-05-01

    We combine samples of spiral galaxies and starburst systems observed with ISOCAM on board ISO to investigate the reliability of mid-infrared dust emission as a quantitative tracer of star formation activity. The total sample covers very diverse galactic environments and probes a much wider dynamic range in star formation rate density than previous similar studies. We find that both the monochromatic 15 μm continuum and the 5-8.5 μm emission constitute excellent indicators of the star formation rate as quantified by the Lyman continuum luminosity LLyc, within specified validity limits which are different for the two tracers. Normalized to projected surface area, the 15 μm continuum luminosity Σ15 μm,ct is directly proportional to ΣLyc over several orders of magnitude. Two regimes are distinguished from the relative offsets in the observed relationship: the proportionality factor increases by a factor of ≈5 between quiescent disks in spiral galaxies, and moderate to extreme star-forming environments in circumnuclear regions of spirals and in starburst systems. The transition occurs near ΣLyc ˜ 102 L⊙ pc-2 and is interpreted as due to very small dust grains starting to dominate the emission at 15 μm over aromatic species above this threshold. The 5-8.5 μm luminosity per unit projected area is also directly proportional to the Lyman continuum luminosity, with a single conversion factor from the most quiescent objects included in the sample up to ΣLyc ˜ 104 L⊙ pc-2, where the relationship then flattens. The turnover is attributed to depletion of aromatic band carriers in the harsher conditions prevailing in extreme starburst environments. The observed relationships provide empirical calibrations useful for estimating star formation rates from mid-infrared observations, much less affected by extinction than optical and near-infrared tracers in deeply embedded H II regions and obscured starbursts, as well as for theoretical predictions from evolutionary

  19. Altered resting-state functional activity in posttraumatic stress disorder: A quantitative meta-analysis

    PubMed Central

    Wang, Ting; Liu, Jia; Zhang, Junran; Zhan, Wang; Li, Lei; Wu, Min; Huang, Hua; Zhu, Hongyan; Kemp, Graham J.; Gong, Qiyong

    2016-01-01

    Many functional neuroimaging studies have reported differential patterns of spontaneous brain activity in posttraumatic stress disorder (PTSD), but the findings are inconsistent and have not so far been quantitatively reviewed. The present study set out to determine consistent, specific regional brain activity alterations in PTSD, using the Effect Size Signed Differential Mapping technique to conduct a quantitative meta-analysis of resting-state functional neuroimaging studies of PTSD that used either a non-trauma (NTC) or a trauma-exposed (TEC) comparison control group. Fifteen functional neuroimaging studies were included, comparing 286 PTSDs, 203 TECs and 155 NTCs. Compared with NTC, PTSD patients showed hyperactivity in the right anterior insula and bilateral cerebellum, and hypoactivity in the dorsal medial prefrontal cortex (mPFC); compared with TEC, PTSD showed hyperactivity in the ventral mPFC. The pooled meta-analysis showed hypoactivity in the posterior insula, superior temporal, and Heschl’s gyrus in PTSD. Additionally, subgroup meta-analysis (non-medicated subjects vs. NTC) identified abnormal activation in the prefrontal-limbic system. In meta-regression analyses, mean illness duration was positively associated with activity in the right cerebellum (PTSD vs. NTC), and illness severity was negatively associated with activity in the right lingual gyrus (PTSD vs. TEC). PMID:27251865

  20. Rapid and quantitative measuring of telomerase activity using an electrochemiluminescent sensor

    NASA Astrophysics Data System (ADS)

    Zhou, Xiaoming; Xing, Da; Zhu, Debin; Jia, Li

    2007-11-01

    Telomerase, a ribonucleoprotein enzyme that adds telomeric repeats to the 3'end of chromosomal DNA for maintaining chromosomal integrity and stability. This strong association of telomerase activity with tumors establishing it is the most widespread cancer marker. A number of assays based on the polymerase chain reaction (PCR) have been developed for the evaluation of telomerase activity. However, those methods require gel electrophoresis and some staining procedures. We developed an electrochemiluminescent (ECL) sensor for the measuring of telomerase activity to overcome these problems such as troublesome post-PCR procedures and semi-quantitative assessment in the conventional method. In this assay 5'-biotinylated telomerase synthesis (TS) primer serve as the substrate for the extension of telomeric repeats under telomerase. The extension products were amplified with this TS primer and a tris-(2'2'-bipyridyl) ruthenium (TBR)-labeled reversed primer. The amplified products was separated and enriched in the surface of electrode by streptavidin-coated magnetic beads, and detected by measuring the ECL signals of the TBR labeled. Measuring telomerase activity use the sensor is easy, sensitive, rapid, and applicable to quantitative analysis, should be clinically useful for the detection and monitoring of telomerase activity.

  1. Impact of high 131I-activities on quantitative 124I-PET

    NASA Astrophysics Data System (ADS)

    Braad, P. E. N.; Hansen, S. B.; Høilund-Carlsen, P. F.

    2015-07-01

    Peri-therapeutic 124 I-PET/CT is of interest as guidance for radioiodine therapy. Unfortunately, image quality is complicated by dead time effects and increased random coincidence rates from high 131 I-activities. A series of phantom experiments with clinically relevant 124 I/131 I-activities were performed on a clinical PET/CT-system. Noise equivalent count rate (NECR) curves and quantitation accuracy were determined from repeated scans performed over several weeks on a decaying NEMA NU-2 1994 cylinder phantom initially filled with 25 MBq 124 I and 1250 MBq 131 I. Six spherical inserts with diameters 10-37 mm were filled with 124 I (0.45 MBq ml-1 ) and 131 I (22 MBq ml-1 ) and placed inside the background of the NEMA/IEC torso phantom. Contrast recovery, background variability and the accuracy of scatter and attenuation corrections were assessed at sphere-to-background activity ratios of 20, 10 and 5. Results were compared to pure 124 I-acquisitions. The quality of 124 I-PET images in the presence of high 131 I-activities was good and image quantification unaffected except at very high count rates. Quantitation accuracy and contrast recovery were uninfluenced at 131 I-activities below 1000 MBq, whereas image noise was slightly increased. The NECR peaked at 550 MBq of 131 I, where it was 2.8 times lower than without 131 I in the phantom. Quantitative peri-therapeutic 124 I-PET is feasible.

  2. Using Quantitative Skills in Introductory Geology Lab Activities at CSU Chico

    NASA Astrophysics Data System (ADS)

    Teasdale, R.; Karin, H.

    2006-12-01

    The "Rivers and Streams" activity for the introductory Geology course at CSU Chico has become an opportunity to engage students in hands-on data collection and synthesis of multiple data sets. Students collect stream flow data on campus from Big Chico Creek during week 1 of the semester as one activity in a "preview" lab. Measurements, unit conversions, and simple algebraic calculations are completed, along with discussions of the data. Students collect similar data sets approximately 5 miles upstream during a mid- semester fieldtrip and again during week 14 as part of the "Rivers and Streams" lab activity at the on-campus site. In each case stream velocity, width, depth, and discharge are determined. As part of the "Rivers and Streams" activity students also construct hydrographs and compare the measurements of all three sample sets. By collecting data three times during the semester students are able to observe and measure stream flow variations at different points along Big Chico Creek and consider seasonal variations. For some students the quantitative activities are a good opportunity to practice algebraic calculations as they learn geologic concepts, but other students are challenged by the quantitative operations and so benefit from multiple opportunities to learn and then improve their comprehension of the quantitative skills. Laboratory instructors (graduate teaching assistants) initially reported that review of simple calculations consumed excessive amounts of time in class so a "pre-work" was developed to give students a quick review of skills needed to complete lab work. Some students report completing the pre-work very quickly and others indicate that it provided a good opportunity for them to recall rusty skills or seek help from classmates or teaching assistants. Ongoing developments include a web based interface for data entry so that students can access data sets collected in previous semesters (new for Spring 2007).

  3. Behavior, sensitivity, and power of activation likelihood estimation characterized by massive empirical simulation.

    PubMed

    Eickhoff, Simon B; Nichols, Thomas E; Laird, Angela R; Hoffstaedter, Felix; Amunts, Katrin; Fox, Peter T; Bzdok, Danilo; Eickhoff, Claudia R

    2016-08-15

    Given the increasing number of neuroimaging publications, the automated knowledge extraction on brain-behavior associations by quantitative meta-analyses has become a highly important and rapidly growing field of research. Among several methods to perform coordinate-based neuroimaging meta-analyses, Activation Likelihood Estimation (ALE) has been widely adopted. In this paper, we addressed two pressing questions related to ALE meta-analysis: i) Which thresholding method is most appropriate to perform statistical inference? ii) Which sample size, i.e., number of experiments, is needed to perform robust meta-analyses? We provided quantitative answers to these questions by simulating more than 120,000 meta-analysis datasets using empirical parameters (i.e., number of subjects, number of reported foci, distribution of activation foci) derived from the BrainMap database. This allowed to characterize the behavior of ALE analyses, to derive first power estimates for neuroimaging meta-analyses, and to thus formulate recommendations for future ALE studies. We could show as a first consequence that cluster-level family-wise error (FWE) correction represents the most appropriate method for statistical inference, while voxel-level FWE correction is valid but more conservative. In contrast, uncorrected inference and false-discovery rate correction should be avoided. As a second consequence, researchers should aim to include at least 20 experiments into an ALE meta-analysis to achieve sufficient power for moderate effects. We would like to note, though, that these calculations and recommendations are specific to ALE and may not be extrapolated to other approaches for (neuroimaging) meta-analysis. PMID:27179606

  4. Quantitative assessment of olfactory receptors activity in immobilized nanosomes: a novel concept for bioelectronic nose.

    PubMed

    Vidic, Jasmina Minic; Grosclaude, Jeanne; Persuy, Marie-Annick; Aioun, Josiane; Salesse, Roland; Pajot-Augy, Edith

    2006-08-01

    We describe how mammalian olfactory receptors (ORs) could be used as sensing elements of highly specific and sensitive bioelectronic noses. An OR and an appropriate G(alpha) protein were co-expressed in Saccharomyces cerevisiae cells from which membrane nanosomes were prepared, and immobilized on a sensor chip. By Surface Plasmon Resonance, we were able to quantitatively evaluate OR stimulation by an odorant, and G protein activation. We demonstrate that ORs in nanosomes discriminate between odorant ligands and unrelated odorants, as in whole cells. This assay also provides the possibility for quantitative assessment of the coupling efficiency of the OR with different G(alpha) subunits, without the interference of the cellular transduction pathway. Our findings will be useful to develop a new generation of electronic noses for detection and discrimination of volatile compounds, particularly amenable to micro- and nano-sensor formats.

  5. Quantitative structure-activity relationships of antimicrobial fatty acids and derivatives against Staphylococcus aureus *

    PubMed Central

    Zhang, Hui; Zhang, Lu; Peng, Li-juan; Dong, Xiao-wu; Wu, Di; Wu, Vivian Chi-Hua; Feng, Feng-qin

    2012-01-01

    Fatty acids and derivatives (FADs) are resources for natural antimicrobials. In order to screen for additional potent antimicrobial agents, the antimicrobial activities of FADs against Staphylococcus aureus were examined using a microplate assay. Monoglycerides of fatty acids were the most potent class of fatty acids, among which monotridecanoin possessed the most potent antimicrobial activity. The conventional quantitative structure-activity relationship (QSAR) and comparative molecular field analysis (CoMFA) were performed to establish two statistically reliable models (conventional QSAR: R 2=0.942, Q 2 LOO=0.910; CoMFA: R 2=0.979, Q 2=0.588, respectively). Improved forecasting can be achieved by the combination of these two models that provide a good insight into the structure-activity relationships of the FADs and that may be useful to design new FADs as antimicrobial agents. PMID:22302421

  6. Quantitative Evaluation of Landsat 7 ETM+ SLC-off Images for Surface Velocity Estimation of Mountain Glaciers

    NASA Astrophysics Data System (ADS)

    Jiang, L.; Sun, Y.; Liu, L.; Wang, S.; Wang, H.

    2014-12-01

    In many cases the Landsat mission series (Landsat 1-5, 7 and 8) provide our only detailed and consistent data source for mapping the global glacier changes over the last 40 years. However, the scan-line corrector (SLC) of the ETM+ sensor on board Landsat 7 permanently failed, resulting in wedge-shaped data gaps in SLC-off images that caused roughly 22% of the pixels to be missed. The SLC failure has left a serious problem for the glacial applications of ETM+ data, particularly for monitoring long-term glacier dynamics in High Asian Mountain where has few available data due to the frequently cloudy covers. This study aims to evaluate the potential of the Landsat 7 SLC-off images in deriving surface velocities of mountain glaciers. A pair of SLC-off images over the Siachen glacier acquired in Aug 2009 and 2010 was used for this purpose. Firstly, two typical filling-gap methods, the localized linear histogram match (LLHM) and the weighted liner regression (WLR), were utilized to recover the mentioned SLC-off images. Subsequently these recovered pairs were applied for deriving glacier-surface velocities with the COSI-Corr feature tracking procedure. Finally, the glacier velocity results were quantitatively compared with that of a pair of Landsat-5 TM images acquired nearly at the same time with the SLC-off pair. Our results show that (1) the WLR method achieves a better performance of gap recovering than the LLHM method, (2) the surface velocities estimated with the recovered SLC-off images are highly agreement with those of the TM images, and (3) the annual mean velocity of the Siachen glacier is approximately 70 m/yr between 2009 and 2010 with a maximum of 280 m/yr close to the glacial equilibrium line that are similar with the results in previous studies. Therefore, if a suitable filling-gap method is adopted, e.g. the WLR method, it is highly feasible that the ETM+ SLC-off data can be utilized to estimate the surface velocities of mountain glaciers.

  7. Quantitative estimation of Tropical Rainfall Mapping Mission precipitation radar signals from ground-based polarimetric radar observations

    NASA Astrophysics Data System (ADS)

    Bolen, Steven M.; Chandrasekar, V.

    2003-06-01

    The Tropical Rainfall Mapping Mission (TRMM) is the first mission dedicated to measuring rainfall from space using radar. The precipitation radar (PR) is one of several instruments aboard the TRMM satellite that is operating in a nearly circular orbit with nominal altitude of 350 km, inclination of 35°, and period of 91.5 min. The PR is a single-frequency Ku-band instrument that is designed to yield information about the vertical storm structure so as to gain insight into the intensity and distribution of rainfall. Attenuation effects on PR measurements, however, can be significant and as high as 10-15 dB. This can seriously impair the accuracy of rain rate retrieval algorithms derived from PR signal returns. Quantitative estimation of PR attenuation is made along the PR beam via ground-based polarimetric observations to validate attenuation correction procedures used by the PR. The reflectivity (Zh) at horizontal polarization and specific differential phase (Kdp) are found along the beam from S-band ground radar measurements, and theoretical modeling is used to determine the expected specific attenuation (k) along the space-Earth path at Ku-band frequency from these measurements. A theoretical k-Kdp relationship is determined for rain when Kdp ≥ 0.5°/km, and a power law relationship, k = a Zhb, is determined for light rain and other types of hydrometers encountered along the path. After alignment and resolution volume matching is made between ground and PR measurements, the two-way path-integrated attenuation (PIA) is calculated along the PR propagation path by integrating the specific attenuation along the path. The PR reflectivity derived after removing the PIA is also compared against ground radar observations.

  8. Theoretical estimation of drag tag lengths for direct quantitative analysis of multiple miRNAs (DQAMmiR).

    PubMed

    Cherney, Leonid T; Krylov, Sergey N

    2013-01-21

    To better understand the regulatory roles of miRNA in biological functions and to use miRNA as molecular markers of diseases, we need to accurately measure amounts of multiple miRNAs in biological samples. Direct quantitative analysis of multiple miRNAs (DQAMmiR) has been recently developed by using a classical hybridization approach where miRNAs are hybridized with fluorescently labeled complementary DNA probes taken in excess, and the amounts of the hybrids and the unreacted probes are measured to calculate the amount of miRNAs. Capillary electrophoresis was used as an instrumental platform for analysis. The problem of separating the unreacted probes from the hybrids was solved by adding SSB to the run buffer. A more difficult problem of separating hybrids from each other was solved by attaching different drag tags to the probes. Biotin and a hairpin-forming extension on the probe were used as two drag tags in the proof-of-principle work. Making DQAMmiR a generic approach requires a generic solution for drag tags. Peptides have been suggested as drag tags for long oligonucleotides in DNA sequencing by electrophoresis. Here we theoretically consider short peptides of different lengths as drag tags for DQAMmiR. We find analytical equations that allow us to estimate mobilities of RNA-DNA hybrids with peptide drag tags of different lengths. Our calculations suggest that the mobility shifts required for DQAMmiR can be achieved with the length of peptide chains in the ranges of 5-20 residues for five miRNAs and 2-47 residues for nine miRNAs. Peptides of these lengths can be feasibly synthesized with good yield and purity. The results of this theoretical study will guide the design and production of hybridization probes for DQAMmiR.

  9. Quantitative gallium 67 lung scan to assess the inflammatory activity in the pneumoconioses

    SciTech Connect

    Bisson, G.; Lamoureux, G.; Begin, R.

    1987-01-01

    Gallium 67 lung scan has recently become increasingly used to evaluate the biological activity of alveolitis of interstitial lung diseases and to stage the disease process. In order to have a more precise and objective indicator of the inflammatory activity in the lung, we and others have developed computer-based quantitative techniques to process the /sup 67/Ga scan. In this report, we compare the results of three such computer-based methods of analysis of the scans of 38 normal humans and 60 patients suspected to have pneumoconiosis. Results of previous investigations on the mechanisms of /sup 67/Ga uptake in interstitial lung disease are reviewed. These data strengthen the view that quantitative /sup 67/Ga lung scan has become a standard technique to assess inflammatory activity in the interstitial lung diseases and that computer-based method of analysis of the scan provides an index of inflammatory activity of the lung disease that correlates with lung lavage and biopsy indices of inflammation in the lung tissue. 51 references.

  10. Quantitation of human MAO A and B in liver, intestine and placenta: Reassessment of activity

    SciTech Connect

    Riley, L.A.

    1989-01-01

    Monoamine oxidases (MAO) oxidize a variety of exogenous and endogenous amines including neurotransmitters such as serotonin, dopamine and norepinephrine as well as the potent dopaminergic neurotoxin 1-methyl-4-phenyl-1,2,5,6-tetrahydropyridine (MPTP). The two forms of MAO (A and B) differ in molecular weight and inhibitor selectivity, and are differentially expressed in the nervous system and many other tissues. Although some substrates are preferentially oxidized by one form of MAO, substrates that can be oxidized by only one MAO form have not been reported. How well each MAO oxidizes various substrates has not been thoroughly characterized because of difficulties in separating and quantitating MAO A and B active sites. By immunoblotting SDS-polyacrylamide gels of mitochondrial extracts with monoclonal antibodies specific for each form of MAO, MAO B protein was detected in intestine and placenta, tissues that have been reported to contain MAO A activity. An improved procedure was developed for quantitating the ratio and amounts of MAO A and B active sites, using the ligand ({sup 3}H)-pargyline to label MAO and specific monoclonal antibodies to separate MAO A from B. Data from liver, placenta and platelets were used to re-evaluate the molecular activity of both MAO A and B for six commonly studied substrates.

  11. Improvement of radar quantitative precipitation estimation based on real-time adjustments to Z-R relationships and inverse distance weighting correction schemes

    NASA Astrophysics Data System (ADS)

    Wang, Gaili; Liu, Liping; Ding, Yuanyuan

    2012-05-01

    The errors in radar quantitative precipitation estimations consist not only of systematic biases caused by random noises but also spatially nonuniform biases in radar rainfall at individual rain-gauge stations. In this study, a real-time adjustment to the radar reflectivity-rainfall rates ( Z-R) relationship scheme and the gauge-corrected, radar-based, estimation scheme with inverse distance weighting interpolation was developed. Based on the characteristics of the two schemes, the two-step correction technique of radar quantitative precipitation estimation is proposed. To minimize the errors between radar quantitative precipitation estimations and rain gauge observations, a real-time adjustment to the Z-R relationship scheme is used to remove systematic bias on the time-domain. The gauge-corrected, radar-based, estimation scheme is then used to eliminate non-uniform errors in space. Based on radar data and rain gauge observations near the Huaihe River, the two-step correction technique was evaluated using two heavy-precipitation events. The results show that the proposed scheme improved not only in the underestimation of rainfall but also reduced the root-mean-square error and the mean relative error of radar-rain gauge pairs.

  12. Quantitative Structure-Cytotoxic Activity Relationship 1-(Benzoyloxy)urea and Its Derivative.

    PubMed

    Hardjono, Suko; Siswodihardjo, Siswandono; Pramono, Purwanto; Darmanto, Win

    2016-01-01

    Drug development is originally carried out on a trial and error basis and it is cost-prohibitive. To minimize the trial and error risks, drug design is needed. One of the compound development processes to get a new drug is by designing a structure modification of the mother compound whose activities are recognized. A substitution of the mother compounds alters the physicochemical properties: lipophilic, electronic and steric properties. In Indonesia, one of medical treatments to cure cancer is through chemotherapy and hydroxyurea. Some derivatives, phenylthiourea, phenylurea, benzoylurea, thiourea and benzoylphenylurea, have been found to be anticancer drug candidates. To predict the activity of the drug compound before it is synthesized, the in-silico test is required. From the test, Rerank Score which is the energy of interaction between the receptor and the ligand molecule is then obtained. Hydroxyurea derivatives were synthesized by modifying Schotten-Baumann's method by the addition of benzoyl group and its homologs resulted in the increase of lipophilic, electronic and steric properties, and cytotoxic activity. Synthesized compounds were 1-(benzoyloxy)urea and its derivatives. Structure characterization was obtained by the spectrum of UV, IR, H NMR, C NMR and Mass Spectrometer. Anticancer activity was carried out using MTT method on HeLa cells. The Quantitative Structure-Cytotoxic Activity Relationships of 1-(benzoyloxy)urea compound and its derivatives was calculated using SPSS. The chemical structure was described, namely: ClogP, π, σ, RS, CMR and Es; while, the cytotoxic activity was indicated by log (1 / IC50). The results show that the best equation of Quantitative Structure-Cytotoxic Activity Relationships (QSAR) of 1- (benzoyloxy)urea compound and its derivatives is Log 1/IC50 = - 0.205 (+ 0.068) σ - 0.051 (+ 0.022) Es - 1.911 (+ 0.020). PMID:27222144

  13. Quantitative, directional measurement of electric field heterogeneity in the active site of ketosteroid isomerase.

    PubMed

    Fafarman, Aaron T; Sigala, Paul A; Schwans, Jason P; Fenn, Timothy D; Herschlag, Daniel; Boxer, Steven G

    2012-02-01

    Understanding the electrostatic forces and features within highly heterogeneous, anisotropic, and chemically complex enzyme active sites and their connection to biological catalysis remains a longstanding challenge, in part due to the paucity of incisive experimental probes of electrostatic properties within proteins. To quantitatively assess the landscape of electrostatic fields at discrete locations and orientations within an enzyme active site, we have incorporated site-specific thiocyanate vibrational probes into multiple positions within bacterial ketosteroid isomerase. A battery of X-ray crystallographic, vibrational Stark spectroscopy, and NMR studies revealed electrostatic field heterogeneity of 8 MV/cm between active site probe locations and widely differing sensitivities of discrete probes to common electrostatic perturbations from mutation, ligand binding, and pH changes. Electrostatic calculations based on active site ionization states assigned by literature precedent and computational pK(a) prediction were unable to quantitatively account for the observed vibrational band shifts. However, electrostatic models of the D40N mutant gave qualitative agreement with the observed vibrational effects when an unusual ionization of an active site tyrosine with a pK(a) near 7 was included. UV-absorbance and (13)C NMR experiments confirmed the presence of a tyrosinate in the active site, in agreement with electrostatic models. This work provides the most direct measure of the heterogeneous and anisotropic nature of the electrostatic environment within an enzyme active site, and these measurements provide incisive benchmarks for further developing accurate computational models and a foundation for future tests of electrostatics in enzymatic catalysis.

  14. The analysis of the trigger action exerted by electromagnetic fields on a geological medium: Quantitative estimates of the interaction

    NASA Astrophysics Data System (ADS)

    Avagimov, A. A.; Zeigarnik, V. A.

    2016-03-01

    By analyzing the threshold levels of the triggering action, we quantitatively substantiate the changes in the energy of the triggering impact for the cases of the initiation of the lowand high-energy earthquakes depending on the seismic activity of the medium. The analysis is based on the data on the seismicity caused by the high-power electric pulses and geomagnetic field of the magnetic storms with sudden commencement. The analysis of the threshold levels of the triggering action indicates that the energy level required for triggering grows with the increase in the energy class of the earthquake. This is inconsistent with the facts of initiation of strong earthquakes by physical fields in the absence of evident high-energy sources of triggering. The probable explanation suggests that if the source of a strong earthquake is adjoined by local potential sources, the rupturing of one of the local potential sources caused by an energetically weak pulsed impact of the physical fields by the triggering scenario leads to the initiation of a strong earthquake.

  15. The complexities of measuring access to parks and physical activity sites in New York City: a quantitative and qualitative approach

    PubMed Central

    Maroko, Andrew R; Maantay, Juliana A; Sohler, Nancy L; Grady, Kristen L; Arno, Peter S

    2009-01-01

    Background Proximity to parks and physical activity sites has been linked to an increase in active behaviors, and positive impacts on health outcomes such as lower rates of cardiovascular disease, diabetes, and obesity. Since populations with a low socio-economic status as well as racial and ethnic minorities tend to experience worse health outcomes in the USA, access to parks and physical activity sites may be an environmental justice issue. Geographic Information systems were used to conduct quantitative and qualitative analyses of park accessibility in New York City, which included kernel density estimation, ordinary least squares (global) regression, geographically weighted (local) regression, and longitudinal case studies, consisting of field work and archival research. Accessibility was measured by both density of park acreage and density of physical activity sites. Independent variables included percent non-Hispanic black, percent Hispanic, percent below poverty, percent of adults without high school diploma, percent with limited English-speaking ability, and population density. Results The ordinary least squares linear regression found weak relationships in both the park acreage density and the physical activity site density models (Ra2 = .11 and .23, respectively; AIC = 7162 and 3529, respectively). Geographically weighted regression, however, suggested spatial non-stationarity in both models, indicating disparities in accessibility that vary over space with respect to magnitude and directionality of the relationships (AIC = 2014 and -1241, respectively). The qualitative analysis supported the findings of the local regression, confirming that although there is a geographically inequitable distribution of park space and physical activity sites, it is not globally predicted by race, ethnicity, or socio-economic status. Conclusion The combination of quantitative and qualitative analyses demonstrated the complexity of the issues around racial and ethnic

  16. Mapping and Quantitation of the Interaction between the Recombination Activating Gene Proteins RAG1 and RAG2*♦

    PubMed Central

    Zhang, Yu-Hang; Shetty, Keerthi; Surleac, Marius D.; Petrescu, Andrei J.; Schatz, David G.

    2015-01-01

    The RAG endonuclease consists of RAG1, which contains the active site for DNA cleavage, and RAG2, an accessory factor whose interaction with RAG1 is critical for catalytic function. How RAG2 activates RAG1 is not understood. Here, we used biolayer interferometry and pulldown assays to identify regions of RAG1 necessary for interaction with RAG2 and to measure the RAG1-RAG2 binding affinity (KD ∼0.4 μm) (where RAG1 and RAG2 are recombination activating genes 1 or 2). Using the Hermes transposase as a guide, we constructed a 36-kDa “mini” RAG1 capable of interacting robustly with RAG2. Mini-RAG1 consists primarily of the catalytic center and the residues N-terminal to it, but it lacks a zinc finger region in RAG1 previously implicated in binding RAG2. The ability of Mini-RAG1 to interact with RAG2 depends on a predicted α-helix (amino acids 997–1008) near the RAG1 C terminus and a region of RAG1 from amino acids 479 to 559. Two adjacent acidic amino acids in this region (Asp-546 and Glu-547) are important for both the RAG1-RAG2 interaction and recombination activity, with Asp-546 of particular importance. Structural modeling of Mini-RAG1 suggests that Asp-546/Glu-547 lie near the predicted 997-1008 α-helix and components of the active site, raising the possibility that RAG2 binding alters the structure of the RAG1 active site. Quantitative Western blotting allowed us to estimate that mouse thymocytes contain on average ∼1,800 monomers of RAG1 and ∼15,000 molecules of RAG2, implying that nuclear concentrations of RAG1 and RAG2 are below the KD value for their interaction, which could help limit off-target RAG activity. PMID:25745109

  17. Relationship between N2O Fluxes from an Almond Soil and Denitrifying Bacterial Populations Estimated by Quantitative PCR

    NASA Astrophysics Data System (ADS)

    Matiasek, M.; Suddick, E. C.; Smart, D. R.; Scow, K. M.

    2008-12-01

    Cultivated soils emit substantial quantities of nitrous oxide (N2O), a greenhouse gas with almost 300 times the radiative forcing potential of CO2. Agriculture-related activities generate from 6 to 35 Tg N2O-N per year, or about 60 to 70% of global production. The microbial processes of nitrification, denitrification and nitrifier denitrification are major biogenic sources of N2O to the atmosphere from soils. Denitrification is considered the major source of N2O especially when soils are wet. The microbial N transformations that produce N2O depend primarily on nitrogen (N) fertilizer, with water content, available carbon and soil temperature being secondary controllers. Despite the fact that microbial processes are responsible for N2O emissions, very little is known about the numbers or types of populations involved. The objective of this study was to relate changes in denitrifying population densities, using quantitative PCR (qPCR) of functional genes, to N2O emissions in a fertilized almond orchard. Quantitative PCR targeted three specific genes involved in denitrification: nirS, nirK and nosZ. Copy numbers of the genes were related back to population densities and the portion of organisms likely to produce nitrous oxide. The study site, a 21.7 acre almond orchard fitted with micro-sprinklers, was fertigated (irrigated and fertilized simultaneously) with 50 lbs/acre sodium nitrate in late March 2008, then irrigated weekly. Immediately after the initial fertigation, fluxes of N2O and CO2, moisture content, inorganic N and denitrification gene copy numbers were measured 6 times over 24 days. Despite the fact that N2O emissions increased following fertigation, there was no consistent increase in any of the targeted genes. The genes nirK and nirS ranged from 0.4-1.4 × 107 and 0.4-1.4 × 108, whereas nosZ ranged from 2-8 × 106 copy numbers per g soil, respectively. Considerable variation, compounded by the small sample sizes used for DNA analysis, made it difficult

  18. Introduction of a method for quantitative evaluation of spontaneous motor activity development with age in infants.

    PubMed

    Disselhorst-Klug, Catherine; Heinze, Franziska; Breitbach-Faller, Nico; Schmitz-Rode, Thomas; Rau, Günter

    2012-04-01

    Coordination between perception and action is required to interact with the environment successfully. This is already trained by very young infants who perform spontaneous movements to learn how their body interacts with the environment. The strategies used by the infants for this purpose change with age. Therefore, very early progresses in action control made by the infants can be investigated by monitoring the development of spontaneous motor activity. In this paper, an objective method is introduced, which allows the quantitative evaluation of the development of spontaneous motor activity in newborns. The introduced methodology is based on the acquisition of spontaneous movement trajectories of the feet by 3D movement analysis and subsequent calculation of specific movement parameters from them. With these movement-based parameters, it was possible to provide an objective description of age-dependent developmental steps in healthy newborns younger than 6 months. Furthermore, it has been shown that pathologies like infantile cerebral palsy influence development of motor activity significantly. Since the introduced methodology is objective and quantitative, it is suitable to monitor how newborns train their cognitive processes, which will enable them to cope with their environment by motor interaction.

  19. Curating and Preparing High-Throughput Screening Data for Quantitative Structure-Activity Relationship Modeling.

    PubMed

    Kim, Marlene T; Wang, Wenyi; Sedykh, Alexander; Zhu, Hao

    2016-01-01

    Publicly available bioassay data often contains errors. Curating massive bioassay data, especially high-throughput screening (HTS) data, for Quantitative Structure-Activity Relationship (QSAR) modeling requires the assistance of automated data curation tools. Using automated data curation tools are beneficial to users, especially ones without prior computer skills, because many platforms have been developed and optimized based on standardized requirements. As a result, the users do not need to extensively configure the curation tool prior to the application procedure. In this chapter, a freely available automatic tool to curate and prepare HTS data for QSAR modeling purposes will be described.

  20. The current status and future applicability of quantitative structure-activity relationships (QSARs) in predicting toxicity.

    PubMed

    Cronin, Mark T D

    2002-12-01

    The current status of quantitative structure-activity relationships (QSARs) in predicting toxicity is assessed. Widespread use of these methods to predict toxicity from chemical structure is possible, both by industry to develop new compounds, and also by regulatory agencies. The current use of QSARs is restricted by the lack of suitable toxicity data available for modelling, the suitability of simplistic modelling approaches for the prediction of certain endpoints, and the poor definition and utilisation of the applicability domain of models. Suggestions to resolve these issues are made.

  1. Curating and Preparing High-Throughput Screening Data for Quantitative Structure-Activity Relationship Modeling.

    PubMed

    Kim, Marlene T; Wang, Wenyi; Sedykh, Alexander; Zhu, Hao

    2016-01-01

    Publicly available bioassay data often contains errors. Curating massive bioassay data, especially high-throughput screening (HTS) data, for Quantitative Structure-Activity Relationship (QSAR) modeling requires the assistance of automated data curation tools. Using automated data curation tools are beneficial to users, especially ones without prior computer skills, because many platforms have been developed and optimized based on standardized requirements. As a result, the users do not need to extensively configure the curation tool prior to the application procedure. In this chapter, a freely available automatic tool to curate and prepare HTS data for QSAR modeling purposes will be described. PMID:27518634

  2. Structure-activity relationships: quantitative techniques for predicting the behavior of chemicals in the ecosystem

    SciTech Connect

    Nirmalakhandan, N.; Speece, R.E.

    1988-06-01

    Quantitative Structure-Activity Relationships (QSARs) are used increasingly to screen and predict the toxicity and the fate of chemicals released into the environment. The impetus to use QSAR methods in this area has been the large number of synthetic chemicals introduced into the ecosystem via intensive agriculture and industrialization. Because of the costly and time-consuming nature of environmental fate testing, QSARs have been effectively used to screen large classes of chemical compounds and flag those that appear to warrant more thorough testing.

  3. Optimal stimulus scheduling for active estimation of evoked brain networks

    NASA Astrophysics Data System (ADS)

    Kafashan, MohammadMehdi; Ching, ShiNung

    2015-12-01

    Objective. We consider the problem of optimal probing to learn connections in an evoked dynamic network. Such a network, in which each edge measures an input-output relationship between sites in sensor/actuator-space, is relevant to emerging applications in neural mapping and neural connectivity estimation. Approach. We show that the problem of scheduling nodes to a probe (i.e., stimulate) amounts to a problem of optimal sensor scheduling. Main results. By formulating the evoked network in state-space, we show that the solution to the greedy probing strategy has a convenient form and, under certain conditions, is optimal over a finite horizon. We adopt an expectation maximization technique to update the state-space parameters in an online fashion and demonstrate the efficacy of the overall approach in a series of detailed numerical examples. Significance. The proposed method provides a principled means to actively probe time-varying connections in neuronal networks. The overall method can be implemented in real time and is particularly well-suited to applications in stimulation-based cortical mapping in which the underlying network dynamics are changing over time.

  4. Overview of data and conceptual approaches for derivation of quantitative structure-activity relationships for ecotoxicological effects of organic chemicals.

    PubMed

    Bradbury, Steven P; Russom, Christine L; Ankley, Gerald T; Schultz, T Wayne; Walker, John D

    2003-08-01

    The use of quantitative structure-activity relationships (QSARs) in assessing potential toxic effects of organic chemicals on aquatic organisms continues to evolve as computational efficiency and toxicological understanding advance. With the ever-increasing production of new chemicals, and the need to optimize resources to assess thousands of existing chemicals in commerce, regulatory agencies have turned to QSARs as essential tools to help prioritize tiered risk assessments when empirical data are not available to evaluate toxicological effects. Progress in designing scientifically credible QSARs is intimately associated with the development of empirically derived databases of well-defined and quantified toxicity endpoints, which are based on a strategic evaluation of diverse sets of chemical structures, modes of toxic action, and species. This review provides a brief overview of four databases created for the purpose of developing QSARs for estimating toxicity of chemicals to aquatic organisms. The evolution of QSARs based initially on general chemical classification schemes, to models founded on modes of toxic action that range from nonspecific partitioning into hydrophobic cellular membranes to receptor-mediated mechanisms is summarized. Finally, an overview of expert systems that integrate chemical-specific mode of action classification and associated QSAR selection for estimating potential toxicological effects of organic chemicals is presented. PMID:12924578

  5. Daphnia and fish toxicity of (benzo)triazoles: validated QSAR models, and interspecies quantitative activity-activity modelling.

    PubMed

    Cassani, Stefano; Kovarich, Simona; Papa, Ester; Roy, Partha Pratim; van der Wal, Leon; Gramatica, Paola

    2013-08-15

    Due to their chemical properties synthetic triazoles and benzo-triazoles ((B)TAZs) are mainly distributed to the water compartments in the environment, and because of their wide use the potential effects on aquatic organisms are cause of concern. Non testing approaches like those based on quantitative structure-activity relationships (QSARs) are valuable tools to maximize the information contained in existing experimental data and predict missing information while minimizing animal testing. In the present study, externally validated QSAR models for the prediction of acute (B)TAZs toxicity in Daphnia magna and Oncorhynchus mykiss have been developed according to the principles for the validation of QSARs and their acceptability for regulatory purposes, proposed by the Organization for Economic Co-operation and Development (OECD). These models are based on theoretical molecular descriptors, and are statistically robust, externally predictive and characterized by a verifiable structural applicability domain. They have been applied to predict acute toxicity for over 300 (B)TAZs without experimental data, many of which are in the pre-registration list of the REACH regulation. Additionally, a model based on quantitative activity-activity relationships (QAAR) has been developed, which allows for interspecies extrapolation from daphnids to fish. The importance of QSAR/QAAR, especially when dealing with specific chemical classes like (B)TAZs, for screening and prioritization of pollutants under REACH, has been highlighted.

  6. Effects of scatter modeling on time-activity curves estimated directly from dynamic SPECT projections

    SciTech Connect

    Reutter, Bryan W.; Gullberg, Grant T.; Huesman, Ronald H.

    2003-10-29

    Quantitative analysis of uptake and washout of cardiac single photon emission computed tomography (SPECT) radiopharmaceuticals has the potential to provide better contrast between healthy and diseased tissue, compared to conventional reconstruction of static images. Previously, we used B-splines to model time-activity curves (TACs) for segmented volumes of interest and developed fast least-squares algorithms to estimate spline TAC coefficients and their statistical uncertainties directly from dynamic SPECT projection data. This previous work incorporated physical effects of attenuation and depth-dependent collimator response. In the present work, we incorporate scatter and use a computer simulation to study how scatter modeling affects directly estimated TACs and subsequent estimates of compartmental model parameters. An idealized single-slice emission phantom was used to simulate a 15 min dynamic {sup 99m}Tc-teboroxime cardiac patient study in which 500,000 events containing scatter were detected from the slice. When scatter was modeled, unweighted least-squares estimates of TACs had root mean square (RMS) error that was less than 0.6% for normal left ventricular myocardium, blood pool, liver, and background tissue volumes and averaged 3% for two small myocardial defects. When scatter was not modeled, RMS error increased to average values of 16% for the four larger volumes and 35% for the small defects. Noise-to-signal ratios (NSRs) for TACs ranged between 1-18% for the larger volumes and averaged 110% for the small defects when scatter was modeled. When scatter was not modeled, NSR improved by average factors of 1.04 for the larger volumes and 1.25 for the small defects, as a result of the better-posed (though more biased) inverse problem. Weighted least-squares estimates of TACs had slightly better NSR and worse RMS error, compared to unweighted least-squares estimates. Compartmental model uptake and washout parameter estimates obtained from the TACs were less

  7. Synthesis and quantitative structure activity relationship (QSAR) of arylidene (benzimidazol-1-yl)acetohydrazones as potential antibacterial agents.

    PubMed

    El-Kilany, Yeldez; Nahas, Nariman M; Al-Ghamdi, Mariam A; Badawy, Mohamed E I; El Ashry, El Sayed H

    2015-01-01

    Ethyl (benzimidazol-1-yl)acetate was subjected to hydrazinolysis with hydrazine hydrate to give (benzimidazol-1-yl)acetohydrazide. The latter was reacted with various aromatic aldehydes to give the respective arylidene (1H-benzimidazol-1-yl)acetohydrazones. Solutions of the prepared hydrazones were found to contain two geometric isomers. Similarly (2-methyl-benzimidazol-1-yl)acetohydrazide was reacted with various aldehydes to give the corresponding hydrazones. The antibacterial activity was evaluated in vitro by minimum inhibitory concentration (MIC) against Agrobacterium tumefaciens (A. tumefaciens), Erwinia carotovora (E. carotovora), Corynebacterium fascians (C. fascians) and Pseudomonas solanacearum (P. solanacearum). MIC result demonstrated that salicylaldehyde(1H-benzimidazol-1-yl)acetohydrazone (4) was the most active compound (MIC = 20, 35, 25 and 30 mg/L against A. tumefaciens, C. fascians, E. carotovora and P. solanacearum, respectively). Quantitative structure activity relationship (QSAR) investigation using Hansch analysis was applied to find out the correlation between antibacterial activity and physicochemical properties. Various physicochemical descriptors and experimentally determined MIC values for different microorganisms were used as independent and dependent variables, respectively. pMICs of the compounds exhibited good correlation (r = 0.983, 0.914, 0.960 and 0.958 for A. tumefaciens, C. fascians, E. carotovora and P. solanacearum, respectively) with the prediction made by the model. QSAR study revealed that the hydrophobic parameter (ClogP), the aqueous solubility (LogS), calculated molar refractivity, topological polar surface area and hydrogen bond acceptor were found to have overall significant correlation with antibacterial activity. The statistical results of training set, correlation coefficient (r and r (2)), the ratio between regression and residual variances (f, Fisher's statistic), the standard error of estimates and

  8. Toxicity challenges in environmental chemicals: Prediction of human plasma protein binding through quantitative structure-activity relationship (QSAR) models

    EPA Science Inventory

    The present study explores the merit of utilizing available pharmaceutical data to construct a quantitative structure-activity relationship (QSAR) for prediction of the fraction of a chemical unbound to plasma protein (Fub) in environmentally relevant compounds. Independent model...

  9. Towards a Quantitative Use of Satellite Remote Sensing in Crop Growth Models for Large Scale Agricultural Production Estimate (Invited)

    NASA Astrophysics Data System (ADS)

    Defourny, P.

    2013-12-01

    such the Green Area Index (GAI), fAPAR and fcover usually retrieved from MODIS, MERIS, SPOT-Vegetation described the quality of the green vegetation development. The GLOBAM (Belgium) and EU FP-7 MOCCCASIN projects (Russia) improved the standard products and were demonstrated over large scale. The GAI retrieved from MODIS time series using a purity index criterion depicted successfully the inter-annual variability. Furthermore, the quantitative assimilation of these GAI time series into a crop growth model improved the yield estimate over years. These results showed that the GAI assimilation works best at the district or provincial level. In the context of the GEO Ag., the Joint Experiment of Crop Assessment and Monitoring (JECAM) was designed to enable the global agricultural monitoring community to compare such methods and results over a variety of regional cropping systems. For a network of test sites around the world, satellite and field measurements are currently collected and will be made available for collaborative effort. This experiment should facilitate international standards for data products and reporting, eventually supporting the development of a global system of systems for agricultural crop assessment and monitoring.

  10. Polar bear hepatic cytochrome P450: Immunochemical quantitation, EROD/PROD activity and organochlorines

    SciTech Connect

    Letcher, R.J.; Norstrom, R.J. |

    1994-12-31

    Polar bears (Ursus maritimus) are an ubiquitous mammal atop the arctic marine food chain and bioaccumulate lipophilic environmental contaminants. Antibodies prepared against purified rat liver cytochrome P450-1 Al, -1 A2, -2Bl and -3Al enzymes have been found to cross-react with structurally-related orthologues present in the hepatic microsomes of wild polar bears, immunochemically determined levels of P450-1 A and -2B proteins in polar bear liver relative to liver of untreated rats suggested enzyme induction, probably as a result of exposure to xenobiotic contaminants. Optical density quantitation of the most immunochemically responsive isozymes P450-I Al, -IA2 and -2Bi to polygonal rabbit anti-rat P450-IA/IA2 sera and -2BI antibodies in hepatic microsomes of 13 adult male polar bars from the Resolute Bay area of the Canadian Arctic is presented. Correlations with EROD and PROD catalytic activities and levels of organochlorines, such as polychlorinated biphenyls (PCBs), 1,1-dichloro-2,2-bis(4-chlorophenyl)ethene (p,p-DDE) and their methyl sulfone (MeSO2-) metabolites are made to determine if compound-specific enzyme induction linkages exist. Inter-species immunochemical quantitation of isozymic P450 cytochromes can serve as an indicator of exposure to biologically active contaminant.

  11. Quantitative perturbation-based analysis of gene expression predicts enhancer activity in early Drosophila embryo

    PubMed Central

    Sayal, Rupinder; Dresch, Jacqueline M; Pushel, Irina; Taylor, Benjamin R; Arnosti, David N

    2016-01-01

    Enhancers constitute one of the major components of regulatory machinery of metazoans. Although several genome-wide studies have focused on finding and locating enhancers in the genomes, the fundamental principles governing their internal architecture and cis-regulatory grammar remain elusive. Here, we describe an extensive, quantitative perturbation analysis targeting the dorsal-ventral patterning gene regulatory network (GRN) controlled by Drosophila NF-κB homolog Dorsal. To understand transcription factor interactions on enhancers, we employed an ensemble of mathematical models, testing effects of cooperativity, repression, and factor potency. Models trained on the dataset correctly predict activity of evolutionarily divergent regulatory regions, providing insights into spatial relationships between repressor and activator binding sites. Importantly, the collective predictions of sets of models were effective at novel enhancer identification and characterization. Our study demonstrates how experimental dataset and modeling can be effectively combined to provide quantitative insights into cis-regulatory information on a genome-wide scale. DOI: http://dx.doi.org/10.7554/eLife.08445.001 PMID:27152947

  12. Influence of drinking water composition on quantitation and biological activity of dissolved microcystin (cyanotoxin).

    PubMed

    Oliveira, Ana C P; Magalhães, Valéria F; Soares, Raquel M; Azevedo, Sandra M F O

    2005-04-01

    Toxic cyanobacteria in aquatic environments have been implicated in many poisoning incidents of livestock, wildlife, and domestic animals. Microcystins (MCYSTs) in water supplies represent a risk to public health. This work investigated the effect of water composition on the quantitation and biological activity of MCYSTs analyzed by different methods (HPLC, ELISA, and protein phosphatase 1 inhibition assay). Different MCYST concentrations were added to deionized water and quantified, confirming the efficiency of these analytical methods. MCYST concentrations diluted in drinking water had reduced detection by all methods tested. The drinking water used contained a free chlorine concentration of 2.5 mg/L and an Fe concentration of 0.45 mg/L, and the conductivity was 69.8 microS cm(-1), whereas in deionized water, free chlorine and Fe were not detectable, and the conductivity was 1.6 microS cm(-1). Drinking water also interfered with the biological activity of MYCSTs, as these toxins showed reduced protein phosphatase-1 inhibition. A free chlorine concentration of 2.5 mg/L in deionized water was completely effective in preventing any detection of 10 microg/L of added MCYSTs. Fe and Al ions also were very effective in reducing MCYST detection. The chemical composition of drinking water thus affected MCYST detection, indicating a significant reduction in quantitation of this molecule either because of its decomposition or through complexation with metal ions.

  13. Flavonoids promoting HaCaT migration: I. Hologram quantitative structure-activity relationships.

    PubMed

    Cho, Moonjae; Yoon, Hyuk; Park, Mijoo; Kim, Young Hwa; Lim, Yoongho

    2014-03-15

    Cell migration plays an important role in multicellular development and preservation. Because wound healing requires cell migration, compounds promoting cell migration can be used for wound repair therapy. Several plant-derived polyphenols are known to promote cell migration, which improves wound healing. Previous studies of flavonoids on cell lines have focused on their inhibitory effects and not on wound healing. In addition, studies of flavonoids on wound healing have been performed using mixtures. In this study, individual flavonoids were used for cellular migration measurements. Relationships between the cell migration effects of flavonoids and their structural properties have never been reported. Here, we investigated the migration of keratinocytes caused by 100 flavonoids and examined their relationships using hologram quantitative structure-activity relationships. The structural conditions responsible for efficient cell migration on keratinocyte cell lines determined from the current study will facilitate the design of flavonoids with improved activity.

  14. A Rapid and Quantitative Flow Cytometry Method for the Analysis of Membrane Disruptive Antimicrobial Activity

    PubMed Central

    O’Brien-Simpson, Neil M.; Pantarat, Namfon; Attard, Troy J.; Walsh, Katrina A.; Reynolds, Eric C.

    2016-01-01

    We describe a microbial flow cytometry method that quantifies within 3 hours antimicrobial peptide (AMP) activity, termed Minimum Membrane Disruptive Concentration (MDC). Increasing peptide concentration positively correlates with the extent of bacterial membrane disruption and the calculated MDC is equivalent to its MBC. The activity of AMPs representing three different membranolytic modes of action could be determined for a range of Gram positive and negative bacteria, including the ESKAPE pathogens, E. coli and MRSA. By using the MDC50 concentration of the parent AMP, the method provides high-throughput, quantitative screening of AMP analogues. A unique feature of the MDC assay is that it directly measures peptide/bacteria interactions and lysed cell numbers rather than bacteria survival as with MIC and MBC assays. With the threat of multi-drug resistant bacteria, this high-throughput MDC assay has the potential to aid in the development of novel antimicrobials that target bacteria with improved efficacy. PMID:26986223

  15. Introduction to the Symposium "Leading Students and Faculty to Quantitative Biology through Active Learning".

    PubMed

    Waldrop, Lindsay D; Miller, Laura A

    2015-11-01

    The broad aim of this symposium and set of associated papers is to motivate the use of inquiry-based, active-learning teaching techniques in undergraduate quantitative biology courses. Practical information, resources, and ready-to-use classroom exercises relevant to physicists, mathematicians, biologists, and engineers are presented. These resources can be used to address the lack of preparation of college students in STEM fields entering the workforce by providing experience working on interdisciplinary and multidisciplinary problems in mathematical biology in a group setting. Such approaches can also indirectly help attract and retain under-represented students who benefit the most from "non-traditional" learning styles and strategies, including inquiry-based, collaborative, and active learning.

  16. A Quantitative High-Throughput Screening Data Analysis Pipeline for Activity Profiling.

    PubMed

    Huang, Ruili

    2016-01-01

    The US Tox21 program has developed in vitro assays to test large collections of environmental chemicals in a quantitative high-throughput screening (qHTS) format, using triplicate 15-dose titrations to generate over 50 million data points to date. Counter screens are also employed to minimize interferences from non-target-specific assay artifacts, such as compound auto fluorescence and cytotoxicity. New data analysis approaches are needed to integrate these data and characterize the activities observed from these assays. Here, we describe a complete analysis pipeline that evaluates these qHTS data for technical quality in terms of signal reproducibility. We integrate signals from repeated assay runs, primary readouts, and counter screens to produce a final call on on-target compound activity. PMID:27518629

  17. Quantitative structure-activity relationships of imidazolium oximes as nerve agent antidotes

    SciTech Connect

    Musallam, H.A.; Foye, W.O.; Hansch, C.; Harris, R.N.; Engle, R.R.

    1993-05-13

    Organophosphorus-containing pesticides and chemical warfare agents are potent inhibitors of synaptic acetylcholinesterase, a key regulator of cholinergic neurotransmission. These nerve agents have for many years constituted a serious threat to military personnel. These threats stimulated considerable efforts to develop effective medical countermeasures. Several potential drugs have been found recently which are capable of protecting animals from lethal levels of nerve agents. A recent U. S. Army Medical Research and Development Command drug development project synthesized a large number of imidazolium oximes. These compounds were found to possess strong antidotal activity against one of the most lethal nerve agents, soman. The Army's approach, like most conventional drug discovery approaches, depended primarily on the trial and error method. This research was carried out to determine if these potential nerve agent antidotes could have been discovered through the use of Quantitative Structure Activity-Relationships (QSAR) technique.

  18. Quantitative structure-activity relationships of selective antagonists of glucagon receptor using QuaSAR descriptors.

    PubMed

    Manoj Kumar, Palanivelu; Karthikeyan, Chandrabose; Hari Narayana Moorthy, Narayana Subbiah; Trivedi, Piyush

    2006-11-01

    In the present paper, quantitative structure activity relationship (QSAR) approach was applied to understand the affinity and selectivity of a novel series of triaryl imidazole derivatives towards glucagon receptor. Statistically significant and highly predictive QSARs were derived for glucagon receptor inhibition by triaryl imidazoles using QuaSAR descriptors of molecular operating environment (MOE) employing computer-assisted multiple regression procedure. The generated QSAR models revealed that factors related to hydrophobicity, molecular shape and geometry predominantly influences glucagon receptor binding affinity of the triaryl imidazoles indicating the relevance of shape specific steric interactions between the molecule and the receptor. Further, QSAR models formulated for selective inhibition of glucagon receptor over p38 mitogen activated protein (MAP) kinase of the compounds in the series highlights that the same structural features, which influence the glucagon receptor affinity, also contribute to their selective inhibition.

  19. A Quantitative High-Throughput Screening Data Analysis Pipeline for Activity Profiling.

    PubMed

    Huang, Ruili

    2016-01-01

    The US Tox21 program has developed in vitro assays to test large collections of environmental chemicals in a quantitative high-throughput screening (qHTS) format, using triplicate 15-dose titrations to generate over 50 million data points to date. Counter screens are also employed to minimize interferences from non-target-specific assay artifacts, such as compound auto fluorescence and cytotoxicity. New data analysis approaches are needed to integrate these data and characterize the activities observed from these assays. Here, we describe a complete analysis pipeline that evaluates these qHTS data for technical quality in terms of signal reproducibility. We integrate signals from repeated assay runs, primary readouts, and counter screens to produce a final call on on-target compound activity.

  20. A Rapid and Quantitative Flow Cytometry Method for the Analysis of Membrane Disruptive Antimicrobial Activity.

    PubMed

    O'Brien-Simpson, Neil M; Pantarat, Namfon; Attard, Troy J; Walsh, Katrina A; Reynolds, Eric C

    2016-01-01

    We describe a microbial flow cytometry method that quantifies within 3 hours antimicrobial peptide (AMP) activity, termed Minimum Membrane Disruptive Concentration (MDC). Increasing peptide concentration positively correlates with the extent of bacterial membrane disruption and the calculated MDC is equivalent to its MBC. The activity of AMPs representing three different membranolytic modes of action could be determined for a range of Gram positive and negative bacteria, including the ESKAPE pathogens, E. coli and MRSA. By using the MDC50 concentration of the parent AMP, the method provides high-throughput, quantitative screening of AMP analogues. A unique feature of the MDC assay is that it directly measures peptide/bacteria interactions and lysed cell numbers rather than bacteria survival as with MIC and MBC assays. With the threat of multi-drug resistant bacteria, this high-throughput MDC assay has the potential to aid in the development of novel antimicrobials that target bacteria with improved efficacy. PMID:26986223

  1. Quantitative Evaluation of Stomatal Cytoskeletal Patterns during the Activation of Immune Signaling in Arabidopsis thaliana

    PubMed Central

    Shimono, Masaki; Higaki, Takumi; Kaku, Hanae; Shibuya, Naoto; Hasezawa, Seiichiro

    2016-01-01

    Historically viewed as primarily functioning in the regulation of gas and water vapor exchange, it is now evident that stomata serve an important role in plant immunity. Indeed, in addition to classically defined functions related to cell architecture and movement, the actin cytoskeleton has emerged as a central component of the plant immune system, underpinning not only processes related to cell shape and movement, but also receptor activation and signaling. Using high resolution quantitative imaging techniques, the temporal and spatial changes in the actin microfilament array during diurnal cycling of stomatal guard cells has revealed a highly orchestrated transition from random arrays to ordered bundled filaments. While recent studies have demonstrated that plant stomata close in response to pathogen infection, an evaluation of stimulus-induced changes in actin cytoskeletal dynamics during immune activation in the guard cell, as well as the relationship of these changes to the function of the actin cytoskeleton and stomatal aperture, remains undefined. In the current study, we employed quantitative cell imaging and hierarchical clustering analyses to define the response of the guard cell actin cytoskeleton to pathogen infection and the elicitation of immune signaling. Using this approach, we demonstrate that stomatal-localized actin filaments respond rapidly, and specifically, to both bacterial phytopathogens and purified pathogen elicitors. Notably, we demonstrate that higher order temporal and spatial changes in the filament array show distinct patterns of organization during immune activation, and that changes in the naïve diurnal oscillations of guard cell actin filaments are perturbed by pathogens, and that these changes parallel pathogen-induced stomatal gating. The data presented herein demonstrate the application of a highly tractable and quantifiable method to assign transitions in actin filament organization to the activation of immune signaling in

  2. Quantitative Evaluation of Stomatal Cytoskeletal Patterns during the Activation of Immune Signaling in Arabidopsis thaliana.

    PubMed

    Shimono, Masaki; Higaki, Takumi; Kaku, Hanae; Shibuya, Naoto; Hasezawa, Seiichiro; Day, Brad

    2016-01-01

    Historically viewed as primarily functioning in the regulation of gas and water vapor exchange, it is now evident that stomata serve an important role in plant immunity. Indeed, in addition to classically defined functions related to cell architecture and movement, the actin cytoskeleton has emerged as a central component of the plant immune system, underpinning not only processes related to cell shape and movement, but also receptor activation and signaling. Using high resolution quantitative imaging techniques, the temporal and spatial changes in the actin microfilament array during diurnal cycling of stomatal guard cells has revealed a highly orchestrated transition from random arrays to ordered bundled filaments. While recent studies have demonstrated that plant stomata close in response to pathogen infection, an evaluation of stimulus-induced changes in actin cytoskeletal dynamics during immune activation in the guard cell, as well as the relationship of these changes to the function of the actin cytoskeleton and stomatal aperture, remains undefined. In the current study, we employed quantitative cell imaging and hierarchical clustering analyses to define the response of the guard cell actin cytoskeleton to pathogen infection and the elicitation of immune signaling. Using this approach, we demonstrate that stomatal-localized actin filaments respond rapidly, and specifically, to both bacterial phytopathogens and purified pathogen elicitors. Notably, we demonstrate that higher order temporal and spatial changes in the filament array show distinct patterns of organization during immune activation, and that changes in the naïve diurnal oscillations of guard cell actin filaments are perturbed by pathogens, and that these changes parallel pathogen-induced stomatal gating. The data presented herein demonstrate the application of a highly tractable and quantifiable method to assign transitions in actin filament organization to the activation of immune signaling in

  3. Identifying hazard parameter to develop quantitative and dynamic hazard map of an active volcano in Indonesia

    NASA Astrophysics Data System (ADS)

    Suminar, Wulan; Saepuloh, Asep; Meilano, Irwan

    2016-05-01

    Analysis of hazard assessment to active volcanoes is crucial for risk management. The hazard map of volcano provides information to decision makers and communities before, during, and after volcanic crisis. The rapid and accurate hazard assessment, especially to an active volcano is necessary to be developed for better mitigation on the time of volcanic crises in Indonesia. In this paper, we identified the hazard parameters to develop quantitative and dynamic hazard map of an active volcano. The Guntur volcano in Garut Region, West Java, Indonesia was selected as study area due population are resided adjacent to active volcanoes. The development of infrastructures, especially related to tourism at the eastern flank from the Summit, are growing rapidly. The remote sensing and field investigation approaches were used to obtain hazard parameters spatially. We developed a quantitative and dynamic algorithm to map spatially hazard potential of volcano based on index overlay technique. There were identified five volcano hazard parameters based on Landsat 8 and ASTER imageries: volcanic products including pyroclastic fallout, pyroclastic flows, lava and lahar, slope topography, surface brightness temperature, and vegetation density. Following this proposed technique, the hazard parameters were extracted, indexed, and calculated to produce spatial hazard values at and around Guntur Volcano. Based on this method, the hazard potential of low vegetation density is higher than high vegetation density. Furthermore, the slope topography, surface brightness temperature, and fragmental volcanic product such as pyroclastics influenced to the spatial hazard value significantly. Further study to this proposed approach will be aimed for effective and efficient analyses of volcano risk assessment.

  4. Estimation of genetic parameters and their sampling variances of quantitative traits in the type 2 modified augmented design

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We proposed a method to estimate the error variance among non-replicated genotypes, thus to estimate the genetic parameters by using replicated controls. We derived formulas to estimate sampling variances of the genetic parameters. Computer simulation indicated that the proposed methods of estimatin...

  5. Docking and quantitative structure-activity relationship of oxadiazole derivates as inhibitors of GSK3β.

    PubMed

    Quesada-Romero, Luisa; Caballero, Julio

    2014-02-01

    The binding modes of 42 oxadiazole derivates inside glycogen synthase kinase 3 beta (GSK3β were determined using docking experiments; thus, the preferred active conformations of these inhibitors are proposed. We found that these compounds adopt a scorpion-shaped conformation and they accept a hydrogen bond (HB) from the residue Val135 of the GSK3β ATP-binding site hinge region. In addition, quantitative structure-activity relationship (QSAR) models were constructed to explain the trend of the GSK3β inhibitory activities for the studied compounds. In a first approach, three-dimensional (3D) vectors were calculated using docking conformations and, by using multiple-linear regression, we assessed that GETAWAY vectors were able to describe the reported biological activities. In other QSAR approach, SMILES-based optimal descriptors were calculated. The best model included three-SMILES elements SSSβ leading to the identification of key molecular features that contribute to a high GSK3β inhibitory activity.

  6. Docking and quantitative structure-activity relationship of oxadiazole derivates as inhibitors of GSK3β.

    PubMed

    Quesada-Romero, Luisa; Caballero, Julio

    2014-02-01

    The binding modes of 42 oxadiazole derivates inside glycogen synthase kinase 3 beta (GSK3β were determined using docking experiments; thus, the preferred active conformations of these inhibitors are proposed. We found that these compounds adopt a scorpion-shaped conformation and they accept a hydrogen bond (HB) from the residue Val135 of the GSK3β ATP-binding site hinge region. In addition, quantitative structure-activity relationship (QSAR) models were constructed to explain the trend of the GSK3β inhibitory activities for the studied compounds. In a first approach, three-dimensional (3D) vectors were calculated using docking conformations and, by using multiple-linear regression, we assessed that GETAWAY vectors were able to describe the reported biological activities. In other QSAR approach, SMILES-based optimal descriptors were calculated. The best model included three-SMILES elements SSSβ leading to the identification of key molecular features that contribute to a high GSK3β inhibitory activity. PMID:24081608

  7. A new quantitative method to measure activity of ice structuring proteins using differential scanning calorimetry.

    PubMed

    Hassa-Roudsari, Majid; Goff, H Douglas

    2012-01-01

    There are very few quantitative assays to measure the activity of antifreeze proteins (AFPs, or Ice Structuring Proteins, ISPs) and these can be prone to various inaccuracies and inconsistencies. Some methods rely only on unassisted visual assessment. When microscopy is used to measure ice crystal size, it is critical that standardized procedures be adopted, especially when image analysis software is used to quantify sizes. Differential Scanning Calorimetry (DSC) has been used to measure the thermal hysteresis activity (TH) of AFPs. In this study, DSC was used isothermally to measure enthalpic changes associated with structural rearrangements as a function of time. Differences in slopes of isothermal heat flow vs. time between winter wheat ISP or AFP type I containing samples, and those without ISP or AFP type I were demonstrated. ISP or AFP type I containing samples had significantly higher slopes compared to those without ISP or AFP type I. Samples with higher concentration of ISP or AFP type I showed higher slope values during the first hour and took up to 3 hr to attain equilibrium. Differences were attributed to activity of the proteins at the ice interface. Proteinaceous activity of ISPs or AFP type I was confirmed by loss of activity after treatment with protease.

  8. Application of (13)C ramp CPMAS NMR with phase-adjusted spinning sidebands (PASS) for the quantitative estimation of carbon functional groups in natural organic matter.

    PubMed

    Ikeya, Kosuke; Watanabe, Akira

    2016-01-01

    The composition of carbon (C) functional groups in natural organic matter (NOM), such as dissolved organic matter, soil organic matter, and humic substances, is frequently estimated using solid-state (13)C NMR techniques. A problem associated with quantitative analysis using general cross polarization/magic angle spinning (CPMAS) spectra is the appearance of spinning side bands (SSBs) split from the original center peaks of sp (2) hybridized C species (i.e., aromatic and carbonyl C). Ramp CP/phase-adjusted side band suppressing (PASS) is a pulse sequence that integrates SSBs separately and quantitatively recovers them into their inherent center peaks. In the present study, the applicability of ramp CP/PASS to NOM analysis was compared with direct polarization (DPMAS), another quantitative method but one that requires a long operation time, and/or a ramp CP/total suppression side band (ramp CP/TOSS) technique, a popular but non-quantitative method for deleting SSBs. The test materials were six soil humic acid samples with various known degrees of aromaticity and two fulvic acids. There were no significant differences in the relative abundance of alkyl C, O-alkyl C, and aromatic C between the ramp CP/PASS and DPMAS methods, while the signal intensities corresponding to aromatic C in the ramp CP/TOSS spectra were consistently less than the values obtained in the ramp CP/PASS spectra. These results indicate that ramp CP/PASS can be used to accurately estimate the C composition of NOM samples.

  9. Estimation of the measurement uncertainty in quantitative determination of ketamine and norketamine in urine using a one-point calibration method.

    PubMed

    Ma, Yi-Chun; Wang, Che-Wei; Hung, Sih-Hua; Chang, Yan-Zin; Liu, Chia-Reiy; Her, Guor-Rong

    2012-09-01

    An approach was proposed for the estimation of measurement uncertainty for analytical methods based on one-point calibration. The proposed approach is similar to the popular multiple-point calibration approach. However, the standard deviation of calibration was estimated externally. The approach was applied to the estimation of measurement uncertainty for the quantitative determination of ketamine (K) and norketamine (NK) at a 100 ng/mL threshold concentration in urine. In addition to uncertainty due to calibration, sample analysis was the other major source of uncertainty. To include the variation due to matrix effect and temporal effect in sample analysis, different blank urines were spiked with K and NK and analyzed at equal time intervals within and between batches. The expanded uncertainties (k = 2) were estimated to be 10 and 8 ng/mL for K and NK, respectively.

  10. Effects of geomagnetic activity and atmospheric power variations on quantitative measures of brain activity: Replication of the Azerbaijani studies

    NASA Astrophysics Data System (ADS)

    Mulligan, Bryce P.; Hunter, Mathew D.; Persinger, Michael A.

    2010-04-01

    This study replicates and extends the observations by Babayev and Allahveriyeva that changes in right hemispheric electroencephalographic activity are correlated with increases in geomagnetic activity. During the geomagnetically quiet interface between solar cycle 23 and 24 quantitative electroencephalographic (QEEG) measurements were completed for normal young adults in three separate experiments involving about 120 samples over 1.5 years. The most consistent, moderate strength correlations occurred for the changes in power within the gamma and theta ranges over the right frontal lobe. Real-time measures of atmospheric power obtained from polar orbiting satellites showed similar effects. The preferential involvement of the right frontal lobe and the regions subject to its inhibition with environmental energetic changes are consistent with the behavioural correlations historically associated with these conditions. They include increased incidence of emotional lability, erroneous reconstruction of experiences, social confrontations, and unusual perceptions.

  11. Quantitative comparison of cis-regulatory element (CRE) activities in transgenic Drosophila melanogaster.

    PubMed

    Rogers, William A; Williams, Thomas M

    2011-01-01

    Gene expression patterns are specified by cis-regulatory element (CRE) sequences, which are also called enhancers or cis-regulatory modules. A typical CRE possesses an arrangement of binding sites for several transcription factor proteins that confer a regulatory logic specifying when, where, and at what level the regulated gene(s) is expressed. The full set of CREs within an animal genome encodes the organism's program for development, and empirical as well as theoretical studies indicate that mutations in CREs played a prominent role in morphological evolution. Moreover, human genome wide association studies indicate that genetic variation in CREs contribute substantially to phenotypic variation. Thus, understanding regulatory logic and how mutations affect such logic is a central goal of genetics. Reporter transgenes provide a powerful method to study the in vivo function of CREs. Here a known or suspected CRE sequence is coupled to heterologous promoter and coding sequences for a reporter gene encoding an easily observable protein product. When a reporter transgene is inserted into a host organism, the CRE's activity becomes visible in the form of the encoded reporter protein. P-element mediated transgenesis in the fruit fly species Drosophila (D.) melanogaster has been used for decades to introduce reporter transgenes into this model organism, though the genomic placement of transgenes is random. Hence, reporter gene activity is strongly influenced by the local chromatin and gene environment, limiting CRE comparisons to being qualitative. In recent years, the phiC31 based integration system was adapted for use in D. melanogaster to insert transgenes into specific genome landing sites. This capability has made the quantitative measurement of gene and, relevant here, CRE activity feasible. The production of transgenic fruit flies can be outsourced, including phiC31-based integration, eliminating the need to purchase expensive equipment and/or have proficiency at

  12. An Improved Flow Cytometry Method For Precise Quantitation Of Natural-Killer Cell Activity

    NASA Technical Reports Server (NTRS)

    Crucian, Brian; Nehlsen-Cannarella, Sandra; Sams, Clarence

    2006-01-01

    The ability to assess NK cell cytotoxicity using flow cytometry has been previously described and can serve as a powerful tool to evaluate effector immune function in the clinical setting. Previous methods used membrane permeable dyes to identify target cells. The use of these dyes requires great care to achieve optimal staining and results in a broad spectral emission that can make multicolor cytometry difficult. Previous methods have also used negative staining (the elimination of target cells) to identify effector cells. This makes a precise quantitation of effector NK cells impossible due to the interfering presence of T and B lymphocytes, and the data highly subjective to the variable levels of NK cells normally found in human peripheral blood. In this study an improved version of the standard flow cytometry assay for NK activity is described that has several advantages of previous methods. Fluorescent antibody staining (CD45FITC) is used to positively identify target cells in place of membranepermeable dyes. Fluorescent antibody staining of target cells is less labor intensive and more easily reproducible than membrane dyes. NK cells (true effector lymphocytes) are also positively identified by fluorescent antibody staining (CD56PE) allowing a simultaneous absolute count assessment of both NK cells and target cells. Dead cells are identified by membrane disruption using the DNA intercalating dye PI. Using this method, an exact NK:target ratio may be determined for each assessment, including quantitation of NK target complexes. Backimmunoscatter gating may be used to track live vs. dead Target cells via scatter properties. If desired, NK activity may then be normalized to standardized ratios for clinical comparisons between patients, making the determination of PBMC counts or NK cell percentages prior to testing unnecessary. This method provides an exact cytometric determination of NK activity that highly reproducible and may be suitable for routine use in the

  13. Lower reference limits of quantitative cord glucose-6-phosphate dehydrogenase estimated from healthy term neonates according to the clinical and laboratory standards institute guidelines: a cross sectional retrospective study

    PubMed Central

    2013-01-01

    Background Previous studies have reported the lower reference limit (LRL) of quantitative cord glucose-6-phosphate dehydrogenase (G6PD), but they have not used approved international statistical methodology. Using common standards is expecting to yield more true findings. Therefore, we aimed to estimate LRL of quantitative G6PD detection in healthy term neonates by using statistical analyses endorsed by the International Federation of Clinical Chemistry (IFCC) and the Clinical and Laboratory Standards Institute (CLSI) for reference interval estimation. Methods This cross sectional retrospective study was performed at King Abdulaziz Hospital, Saudi Arabia, between March 2010 and June 2012. The study monitored consecutive neonates born to mothers from one Arab Muslim tribe that was assumed to have a low prevalence of G6PD-deficiency. Neonates that satisfied the following criteria were included: full-term birth (37 weeks); no admission to the special care nursery; no phototherapy treatment; negative direct antiglobulin test; and fathers of female neonates were from the same mothers’ tribe. The G6PD activity (Units/gram Hemoglobin) was measured spectrophotometrically by an automated kit. This study used statistical analyses endorsed by IFCC and CLSI for reference interval estimation. The 2.5th percentiles and the corresponding 95% confidence intervals (CI) were estimated as LRLs, both in presence and absence of outliers. Results 207 males and 188 females term neonates who had cord blood quantitative G6PD testing met the inclusion criteria. Method of Horn detected 20 G6PD values as outliers (8 males and 12 females). Distributions of quantitative cord G6PD values exhibited a normal distribution in absence of the outliers only. The Harris-Boyd method and proportion criteria revealed that combined gender LRLs were reliable. The combined bootstrap LRL in presence of the outliers was 10.0 (95% CI: 7.5-10.7) and the combined parametric LRL in absence of the outliers was 11

  14. Applying quantitative structure-activity relationship approaches to nanotoxicology: current status and future potential.

    PubMed

    Winkler, David A; Mombelli, Enrico; Pietroiusti, Antonio; Tran, Lang; Worth, Andrew; Fadeel, Bengt; McCall, Maxine J

    2013-11-01

    The potential (eco)toxicological hazard posed by engineered nanoparticles is a major scientific and societal concern since several industrial sectors (e.g. electronics, biomedicine, and cosmetics) are exploiting the innovative properties of nanostructures resulting in their large-scale production. Many consumer products contain nanomaterials and, given their complex life-cycle, it is essential to anticipate their (eco)toxicological properties in a fast and inexpensive way in order to mitigate adverse effects on human health and the environment. In this context, the application of the structure-toxicity paradigm to nanomaterials represents a promising approach. Indeed, according to this paradigm, it is possible to predict toxicological effects induced by chemicals on the basis of their structural similarity with chemicals for which toxicological endpoints have been previously measured. These structure-toxicity relationships can be quantitative or qualitative in nature and they can predict toxicological effects directly from the physicochemical properties of the entities (e.g. nanoparticles) of interest. Therefore, this approach can aid in prioritizing resources in toxicological investigations while reducing the ethical and monetary costs that are related to animal testing. The purpose of this review is to provide a summary of recent key advances in the field of QSAR modelling of nanomaterial toxicity, to identify the major gaps in research required to accelerate the use of quantitative structure-activity relationship (QSAR) methods, and to provide a roadmap for future research needed to achieve QSAR models useful for regulatory purposes. PMID:23165187

  15. Quantitative structure-activity relationship for toxicity of ionic liquids to Daphnia magna: aromaticity vs. lipophilicity.

    PubMed

    Roy, Kunal; Das, Rudra Narayan; Popelier, Paul L A

    2014-10-01

    Water solubility of ionic liquids (ILs) allows their dispersion into aquatic systems and raises concerns on their pollutant potential. Again, lipophilicity can contribute to the toxicity of ILs due to increased ability of the compounds to cross lipoidal bio-membranes. In the present work, we have performed statistical model development for toxicity of a set of ionic liquids to Daphnia magna, a widely accepted model organism for toxicity testing, using computed lipophilicity, atom-type fragment, quantum topological molecular similarity (QTMS) and extended topochemical atom (ETA) descriptors. The models have been developed and validated in accordance with the Organization for Economic Co-operation and Development (OECD) guidelines for quantitative structure-activity relationships (QSARs). The best partial least squares (PLS) model outperforms the previously reported multiple linear regression (MLR) model in statistical quality and predictive ability (R(2)=0.955, Q(2)=0.917, Rpred(2)=0.848). In this work, the ETA descriptors show importance of branching and aromaticity while the QTMS descriptor ellipticity efficiently shows which compounds are influential in the data set, with reference to the model. While obvious importance of lipophilicity is evident from the models, the best model clearly shows the importance of aromaticity suggesting that more lipophilic ILs with less toxicity may be designed by avoiding aromaticity, nitrogen atoms and increasing branching in the cationic structure. The developed quantitative models are in consonance with the recent hypothesis of importance of aromaticity for toxicity of ILs.

  16. Applying quantitative structure-activity relationship approaches to nanotoxicology: current status and future potential.

    PubMed

    Winkler, David A; Mombelli, Enrico; Pietroiusti, Antonio; Tran, Lang; Worth, Andrew; Fadeel, Bengt; McCall, Maxine J

    2013-11-01

    The potential (eco)toxicological hazard posed by engineered nanoparticles is a major scientific and societal concern since several industrial sectors (e.g. electronics, biomedicine, and cosmetics) are exploiting the innovative properties of nanostructures resulting in their large-scale production. Many consumer products contain nanomaterials and, given their complex life-cycle, it is essential to anticipate their (eco)toxicological properties in a fast and inexpensive way in order to mitigate adverse effects on human health and the environment. In this context, the application of the structure-toxicity paradigm to nanomaterials represents a promising approach. Indeed, according to this paradigm, it is possible to predict toxicological effects induced by chemicals on the basis of their structural similarity with chemicals for which toxicological endpoints have been previously measured. These structure-toxicity relationships can be quantitative or qualitative in nature and they can predict toxicological effects directly from the physicochemical properties of the entities (e.g. nanoparticles) of interest. Therefore, this approach can aid in prioritizing resources in toxicological investigations while reducing the ethical and monetary costs that are related to animal testing. The purpose of this review is to provide a summary of recent key advances in the field of QSAR modelling of nanomaterial toxicity, to identify the major gaps in research required to accelerate the use of quantitative structure-activity relationship (QSAR) methods, and to provide a roadmap for future research needed to achieve QSAR models useful for regulatory purposes.

  17. Quantitative mechanistically based dose-response modeling with endocrine-active compounds.

    PubMed Central

    Andersen, M E; Conolly, R B; Faustman, E M; Kavlock, R J; Portier, C J; Sheehan, D M; Wier, P J; Ziese, L

    1999-01-01

    A wide range of toxicity test methods is used or is being developed for assessing the impact of endocrine-active compounds (EACs) on human health. Interpretation of these data and their quantitative use in human and ecologic risk assessment will be enhanced by the availability of mechanistically based dose-response (MBDR) models to assist low-dose, interspecies, and (italic)in vitro(/italic) to (italic)in vivo(/italic) extrapolations. A quantitative dose-response modeling work group examined the state of the art for developing MBDR models for EACs and the near-term needs to develop, validate, and apply these models for risk assessments. Major aspects of this report relate to current status of these models, the objectives/goals in MBDR model development for EACs, low-dose extrapolation issues, regulatory inertia impeding acceptance of these approaches, and resource/data needs to accelerate model development and model acceptance by the research and the regulatory community. PMID:10421774

  18. Quantitative Estimation of the Amount of Fibrosis in the Rat Liver Using Fractal Dimension of the Shape of Power Spectrum

    NASA Astrophysics Data System (ADS)

    Kikuchi, Tsuneo; Nakazawa, Toshihiro; Furukawa, Tetsuo; Higuchi, Toshiyuki; Maruyama, Yukio; Sato, Sojun

    1995-05-01

    This paper describes the quantitative measurement of the amount of fibrosis in the rat liver using the fractal dimension of the shape of power spectrum. The shape of the power spectrum of the scattered echo from biotissues is strongly affected by its internal structure. The fractal dimension, which is one of the important parameters of the fractal theory, is useful to express the complexity of shape of figures such as the power spectrum. From in vitro experiments using rat liver, it was found that this method can be used to quantitatively measure the amount of fibrosis in the liver, and has the possibility for use in the diagnosis of human liver cirrhosis.

  19. Technology Efficacy in Active Prosthetic Knees for Transfemoral Amputees: A Quantitative Evaluation

    PubMed Central

    El-Sayed, Amr M.; Abu Osman, Noor Azuan

    2014-01-01

    Several studies have presented technological ensembles of active knee systems for transfemoral prosthesis. Other studies have examined the amputees' gait performance while wearing a specific active prosthesis. This paper combined both insights, that is, a technical examination of the components used, with an evaluation of how these improved the gait of respective users. This study aims to offer a quantitative understanding of the potential enhancement derived from strategic integration of core elements in developing an effective device. The study systematically discussed the current technology in active transfemoral prosthesis with respect to its functional walking performance amongst above-knee amputee users, to evaluate the system's efficacy in producing close-to-normal user performance. The performances of its actuator, sensory system, and control technique that are incorporated in each reported system were evaluated separately and numerical comparisons were conducted based on the percentage of amputees' gait deviation from normal gait profile points. The results identified particular components that contributed closest to normal gait parameters. However, the conclusion is limitedly extendable due to the small number of studies. Thus, more clinical validation of the active prosthetic knee technology is needed to better understand the extent of contribution of each component to the most functional development. PMID:25110727

  20. Interpretable, probability-based confidence metric for continuous quantitative structure-activity relationship models.

    PubMed

    Keefer, Christopher E; Kauffman, Gregory W; Gupta, Rishi Raj

    2013-02-25

    A great deal of research has gone into the development of robust confidence in prediction and applicability domain (AD) measures for quantitative structure-activity relationship (QSAR) models in recent years. Much of the attention has historically focused on structural similarity, which can be defined in many forms and flavors. A concept that is frequently overlooked in the realm of the QSAR applicability domain is how the local activity landscape plays a role in how accurate a prediction is or is not. In this work, we describe an approach that pairs information about both the chemical similarity and activity landscape of a test compound's neighborhood into a single calculated confidence value. We also present an approach for converting this value into an interpretable confidence metric that has a simple and informative meaning across data sets. The approach will be introduced to the reader in the context of models built upon four diverse literature data sets. The steps we will outline include the definition of similarity used to determine nearest neighbors (NN), how we incorporate the NN activity landscape with a similarity-weighted root-mean-square distance (wRMSD) value, and how that value is then calibrated to generate an intuitive confidence metric for prospective application. Finally, we will illustrate the prospective performance of the approach on five proprietary models whose predictions and confidence metrics have been tracked for more than a year.

  1. The roadmap for estimation of cell-type-specific neuronal activity from non-invasive measurements.

    PubMed

    Uhlirova, Hana; Kılıç, Kıvılcım; Tian, Peifang; Sakadžić, Sava; Gagnon, Louis; Thunemann, Martin; Desjardins, Michèle; Saisan, Payam A; Nizar, Krystal; Yaseen, Mohammad A; Hagler, Donald J; Vandenberghe, Matthieu; Djurovic, Srdjan; Andreassen, Ole A; Silva, Gabriel A; Masliah, Eliezer; Kleinfeld, David; Vinogradov, Sergei; Buxton, Richard B; Einevoll, Gaute T; Boas, David A; Dale, Anders M; Devor, Anna

    2016-10-01

    The computational properties of the human brain arise from an intricate interplay between billions of neurons connected in complex networks. However, our ability to study these networks in healthy human brain is limited by the necessity to use non-invasive technologies. This is in contrast to animal models where a rich, detailed view of cellular-level brain function with cell-type-specific molecular identity has become available due to recent advances in microscopic optical imaging and genetics. Thus, a central challenge facing neuroscience today is leveraging these mechanistic insights from animal studies to accurately draw physiological inferences from non-invasive signals in humans. On the essential path towards this goal is the development of a detailed 'bottom-up' forward model bridging neuronal activity at the level of cell-type-specific populations to non-invasive imaging signals. The general idea is that specific neuronal cell types have identifiable signatures in the way they drive changes in cerebral blood flow, cerebral metabolic rate of O2 (measurable with quantitative functional Magnetic Resonance Imaging), and electrical currents/potentials (measurable with magneto/electroencephalography). This forward model would then provide the 'ground truth' for the development of new tools for tackling the inverse problem-estimation of neuronal activity from multimodal non-invasive imaging data.This article is part of the themed issue 'Interpreting BOLD: a dialogue between cognitive and cellular neuroscience'. PMID:27574309

  2. Assessing the activity of sarcoidosis: quantitative /sup 67/Ga-citrate imaging

    SciTech Connect

    Fajman, W.A.; Greenwald, L.V.; Staton, G.; Check, I.J.; Pine, J.; Gilman, M.; Scheidt, K.A.; McClees, E.C.

    1984-04-01

    Three different methods of quantitating /sup 67/Ga-citrate lung images - a visual index, a computer-assisted index, and the total-lung-to-background ratio - were compared in 71 studies of patients with biopsy-proven sarcoidosis. Fifty consecutive cases were analyzed independently by two different observers using all three methods. In these studies, each index was correlated with the cell differential in the bronchoalveolar lavage fluid. The total-lung-to-background ratio proved to be the simplest to perform; correlated best with the original visual index and the percentage of lymphocytes obtained in bronchoalveolar lavage fluid. Sensitivity for detecting active disease was 84% compared with 64% and 58% for the visual and computer-assisted indices, respectively, with no sacrifice in specificity.

  3. New Quantitative Structure-Activity Relationship Models Improve Predictability of Ames Mutagenicity for Aromatic Azo Compounds.

    PubMed

    Manganelli, Serena; Benfenati, Emilio; Manganaro, Alberto; Kulkarni, Sunil; Barton-Maclaren, Tara S; Honma, Masamitsu

    2016-10-01

    Existing Quantitative Structure-Activity Relationship (QSAR) models have limited predictive capabilities for aromatic azo compounds. In this study, 2 new models were built to predict Ames mutagenicity of this class of compounds. The first one made use of descriptors based on simplified molecular input-line entry system (SMILES), calculated with the CORAL software. The second model was based on the k-nearest neighbors algorithm. The statistical quality of the predictions from single models was satisfactory. The performance further improved when the predictions from these models were combined. The prediction results from other QSAR models for mutagenicity were also evaluated. Most of the existing models were found to be good at finding toxic compounds but resulted in many false positive predictions. The 2 new models specific for this class of compounds avoid this problem thanks to a larger set of related compounds as training set and improved algorithms.

  4. Quantitative super-resolution imaging of Bruchpilot distinguishes active zone states

    NASA Astrophysics Data System (ADS)

    Ehmann, Nadine; van de Linde, Sebastian; Alon, Amit; Ljaschenko, Dmitrij; Keung, Xi Zhen; Holm, Thorge; Rings, Annika; Diantonio, Aaron; Hallermann, Stefan; Ashery, Uri; Heckmann, Manfred; Sauer, Markus; Kittel, Robert J.

    2014-08-01

    The precise molecular architecture of synaptic active zones (AZs) gives rise to different structural and functional AZ states that fundamentally shape chemical neurotransmission. However, elucidating the nanoscopic protein arrangement at AZs is impeded by the diffraction-limited resolution of conventional light microscopy. Here we introduce new approaches to quantify endogenous protein organization at single-molecule resolution in situ with super-resolution imaging by direct stochastic optical reconstruction microscopy (dSTORM). Focusing on the Drosophila neuromuscular junction (NMJ), we find that the AZ cytomatrix (CAZ) is composed of units containing ~137 Bruchpilot (Brp) proteins, three quarters of which are organized into about 15 heptameric clusters. We test for a quantitative relationship between CAZ ultrastructure and neurotransmitter release properties by engaging Drosophila mutants and electrophysiology. Our results indicate that the precise nanoscopic organization of Brp distinguishes different physiological AZ states and link functional diversification to a heretofore unrecognized neuronal gradient of the CAZ ultrastructure.

  5. Simplifying complex QSAR's (quantitative structure-activity relationships) in toxicity studies with multivariate statistics

    SciTech Connect

    Niemi, G.J.; McKim, J.M.

    1988-07-01

    During the past several decades many quantitative structure-activity relationships (QSAR's) have been derived from relatively small data sets of chemicals in a homologous series and selected empirical observations. An alternative approach is to analyze large data sets consisting of heterogeneous groups of chemicals and to explore QSAR's among these chemicals for generalized patterns of chemical behavior. The use of exploratory multivariate statistical techniques for simplifying complex QSAR problems is demonstrated through the use of research data on biodegradation and mode of toxic action. In these examples, a large number of explanatory variables were examined to explore which variables might best explain whether a chemical biodegrades or whether a toxic response by an organism can be used to identify a mode of toxic action. In both cases, the procedures reduced the number of potential explanatory variables and generated hypotheses about biodegradation and mode of toxic action for future research without explicitly testing an existing hypothesis.

  6. A quantitative structure-activity relationship approach for assessing toxicity of mixture of organic compounds.

    PubMed

    Chang, C M; Ou, Y H; Liu, T-C; Lu, S-Y; Wang, M-K

    2016-06-01

    Four types of reactivity indices were employed to construct quantitative structure-activity relationships for the assessment of toxicity of organic chemical mixtures. Results of analysis indicated that the maximum positive charge of the hydrogen atom and the inverse of the apolar surface area are the most important descriptors for the toxicity of mixture of benzene and its derivatives to Vibrio fischeri. The toxicity of mixture of aromatic compounds to green alga Scenedesmus obliquus is mainly affected by the electron flow and electrostatic interactions. The electron-acceptance chemical potential and the maximum positive charge of the hydrogen atom are found to be the most important descriptors for the joint toxicity of aromatic compounds.

  7. Quantitative super-resolution imaging of Bruchpilot distinguishes active zone states.

    PubMed

    Ehmann, Nadine; van de Linde, Sebastian; Alon, Amit; Ljaschenko, Dmitrij; Keung, Xi Zhen; Holm, Thorge; Rings, Annika; DiAntonio, Aaron; Hallermann, Stefan; Ashery, Uri; Heckmann, Manfred; Sauer, Markus; Kittel, Robert J

    2014-08-18

    The precise molecular architecture of synaptic active zones (AZs) gives rise to different structural and functional AZ states that fundamentally shape chemical neurotransmission. However, elucidating the nanoscopic protein arrangement at AZs is impeded by the diffraction-limited resolution of conventional light microscopy. Here we introduce new approaches to quantify endogenous protein organization at single-molecule resolution in situ with super-resolution imaging by direct stochastic optical reconstruction microscopy (dSTORM). Focusing on the Drosophila neuromuscular junction (NMJ), we find that the AZ cytomatrix (CAZ) is composed of units containing ~137 Bruchpilot (Brp) proteins, three quarters of which are organized into about 15 heptameric clusters. We test for a quantitative relationship between CAZ ultrastructure and neurotransmitter release properties by engaging Drosophila mutants and electrophysiology. Our results indicate that the precise nanoscopic organization of Brp distinguishes different physiological AZ states and link functional diversification to a heretofore unrecognized neuronal gradient of the CAZ ultrastructure.

  8. Quantitative super-resolution imaging of Bruchpilot distinguishes active zone states

    PubMed Central

    Ehmann, Nadine; van de Linde, Sebastian; Alon, Amit; Ljaschenko, Dmitrij; Keung, Xi Zhen; Holm, Thorge; Rings, Annika; DiAntonio, Aaron; Hallermann, Stefan; Ashery, Uri; Heckmann, Manfred; Sauer, Markus; Kittel, Robert J.

    2014-01-01

    The precise molecular architecture of synaptic active zones (AZs) gives rise to different structural and functional AZ states that fundamentally shape chemical neurotransmission. However, elucidating the nanoscopic protein arrangement at AZs is impeded by the diffraction-limited resolution of conventional light microscopy. Here we introduce new approaches to quantify endogenous protein organization at single-molecule resolution in situ with super-resolution imaging by direct stochastic optical reconstruction microscopy (dSTORM). Focusing on the Drosophila neuromuscular junction (NMJ), we find that the AZ cytomatrix (CAZ) is composed of units containing ~137 Bruchpilot (Brp) proteins, three quarters of which are organized into about 15 heptameric clusters. We test for a quantitative relationship between CAZ ultrastructure and neurotransmitter release properties by engaging Drosophila mutants and electrophysiology. Our results indicate that the precise nanoscopic organization of Brp distinguishes different physiological AZ states and link functional diversification to a heretofore unrecognized neuronal gradient of the CAZ ultrastructure. PMID:25130366

  9. New Quantitative Structure-Activity Relationship Models Improve Predictability of Ames Mutagenicity for Aromatic Azo Compounds.

    PubMed

    Manganelli, Serena; Benfenati, Emilio; Manganaro, Alberto; Kulkarni, Sunil; Barton-Maclaren, Tara S; Honma, Masamitsu

    2016-10-01

    Existing Quantitative Structure-Activity Relationship (QSAR) models have limited predictive capabilities for aromatic azo compounds. In this study, 2 new models were built to predict Ames mutagenicity of this class of compounds. The first one made use of descriptors based on simplified molecular input-line entry system (SMILES), calculated with the CORAL software. The second model was based on the k-nearest neighbors algorithm. The statistical quality of the predictions from single models was satisfactory. The performance further improved when the predictions from these models were combined. The prediction results from other QSAR models for mutagenicity were also evaluated. Most of the existing models were found to be good at finding toxic compounds but resulted in many false positive predictions. The 2 new models specific for this class of compounds avoid this problem thanks to a larger set of related compounds as training set and improved algorithms. PMID:27413112

  10. The 18th European symposium on quantitative structure-activity relationships.

    PubMed

    Tsantili-Kakoulidou, Anna; Agrafiotis, Dimitris K

    2011-04-01

    The 18th European Symposium on Quantitative Structure-Activity Relationships (QSAR) took place in Rhodes, Greece, on 19 - 24 September 2010. It was organized by the Hellenic Society of Medicinal Chemistry and the Cheminformatics and QSAR Society, and co-sponsored by the European Federation of Medicinal Chemistry. The conference was thematically dedicated to discovery informatics and drug design and addressed the impact of informatics in all its variants (chemoinformatics, bioinformatics, pharmacoinformatics) on drug discovery in the broader context of biological complexity. The latest scientific and technological advances in QSAR as tools for the discovery of new, safer and more efficacious drugs were discussed during the meeting. This paper highlights the most important outcomes of the symposium, commenting briefly on some of the key presentations.

  11. Estimation of the genome sizes of the chigger mites Leptotrombidium pallidum and Leptotrombidium scutellare based on quantitative PCR and k-mer analysis

    PubMed Central

    2014-01-01

    Background Leptotrombidium pallidum and Leptotrombidium scutellare are the major vector mites for Orientia tsutsugamushi, the causative agent of scrub typhus. Before these organisms can be subjected to whole-genome sequencing, it is necessary to estimate their genome sizes to obtain basic information for establishing the strategies that should be used for genome sequencing and assembly. Method The genome sizes of L. pallidum and L. scutellare were estimated by a method based on quantitative real-time PCR. In addition, a k-mer analysis of the whole-genome sequences obtained through Illumina sequencing was conducted to verify the mutual compatibility and reliability of the results. Results The genome sizes estimated using qPCR were 191 ± 7 Mb for L. pallidum and 262 ± 13 Mb for L. scutellare. The k-mer analysis-based genome lengths were estimated to be 175 Mb for L. pallidum and 286 Mb for L. scutellare. The estimates from these two independent methods were mutually complementary and within a similar range to those of other Acariform mites. Conclusions The estimation method based on qPCR appears to be a useful alternative when the standard methods, such as flow cytometry, are impractical. The relatively small estimated genome sizes should facilitate whole-genome analysis, which could contribute to our understanding of Arachnida genome evolution and provide key information for scrub typhus prevention and mite vector competence. PMID:24947244

  12. Quantitative impedimetric NPY-receptor activation monitoring and signal pathway profiling in living cells.

    PubMed

    te Kamp, Verena; Lindner, Ricco; Jahnke, Heinz-Georg; Krinke, Dana; Kostelnik, Katja B; Beck-Sickinger, Annette G; Robitzki, Andrea A

    2015-05-15

    Label-free and non-invasive monitoring of receptor activation and identification of the involved signal pathways in living cells is an ongoing analytic challenge and a great opportunity for biosensoric systems. In this context, we developed an impedance spectroscopy-based system for the activation monitoring of NPY-receptors in living cells. Using an optimized interdigital electrode array for sensitive detection of cellular alterations, we were able for the first time to quantitatively detect the NPY-receptor activation directly without a secondary or enhancer reaction like cAMP-stimulation by forskolin. More strikingly, we could show that the impedimetric based NPY-receptor activation monitoring is not restricted to the Y1-receptor but also possible for the Y2- and Y5-receptor. Furthermore, we could monitor the NPY-receptor activation in different cell lines that natively express NPY-receptors and proof the specificity of the observed impedimetric effect by agonist/antagonist studies in recombinant NPY-receptor expressing cell lines. To clarify the nature of the observed impedimetric effect we performed an equivalent circuit analysis as well as analyzed the role of cell morphology and receptor internalization. Finally, an antagonist based extensive molecular signal pathway analysis revealed small alterations of the actin cytoskeleton as well as the inhibition of at least L-type calcium channels as major reasons for the observed NPY-induced impedance increase. Taken together, our novel impedance spectroscopy based NPY-receptor activation monitoring system offers the opportunity to identify signal pathways as well as for novel versatile agonist/antagonist screening systems for identification of novel therapeutics in the field of obesity and cancer.

  13. Quantitative detection of powdered activated carbon in wastewater treatment plant effluent by thermogravimetric analysis (TGA).

    PubMed

    Krahnstöver, Therese; Plattner, Julia; Wintgens, Thomas

    2016-09-15

    For the elimination of potentially harmful micropollutants, powdered activated carbon (PAC) adsorption is applied in many wastewater treatment plants (WWTP). This holds the risk of PAC leakage into the WWTP effluent and desorption of contaminants into natural water bodies. In order to assess a potential PAC leakage, PAC concentrations below several mg/L have to be detected in the WWTP effluent. None of the methods that are used for water analysis today are able to differentiate between activated carbon and solid background matrix. Thus, a selective, quantitative and easily applicable method is still needed for the detection of PAC residues in wastewater. In the present study, a method was developed to quantitatively measure the PAC content in wastewater by using filtration and thermogravimetric analysis (TGA), which is a well-established technique for the distinction between different solid materials. For the sample filtration, quartz filters with a temperature stability up to 950 °C were used. This allowed for sensitive and well reproducible measurements, as the TGA was not affected by the presence of the filter. The sample's mass fractions were calculated by integrating the mass decrease rate obtained by TGA in specific, clearly identifiable peak areas. A two-step TGA heating method consisting of N2 and O2 atmospheres led to a good differentiation between PAC and biological background matrix, thanks to the reduction of peak overlapping. A linear correlation was found between a sample's PAC content and the corresponding peak areas under N2 and O2, the sample volume and the solid mass separated by filtration. Based on these findings, various wastewater samples from different WWTPs were then analyzed by TGA with regard to their PAC content. It was found that, compared to alternative techniques such as measurement of turbidity or total suspended solids, the newly developed TGA method allows for a quantitative and selective detection of PAC concentrations down to 0

  14. Quantitative detection of powdered activated carbon in wastewater treatment plant effluent by thermogravimetric analysis (TGA).

    PubMed

    Krahnstöver, Therese; Plattner, Julia; Wintgens, Thomas

    2016-09-15

    For the elimination of potentially harmful micropollutants, powdered activated carbon (PAC) adsorption is applied in many wastewater treatment plants (WWTP). This holds the risk of PAC leakage into the WWTP effluent and desorption of contaminants into natural water bodies. In order to assess a potential PAC leakage, PAC concentrations below several mg/L have to be detected in the WWTP effluent. None of the methods that are used for water analysis today are able to differentiate between activated carbon and solid background matrix. Thus, a selective, quantitative and easily applicable method is still needed for the detection of PAC residues in wastewater. In the present study, a method was developed to quantitatively measure the PAC content in wastewater by using filtration and thermogravimetric analysis (TGA), which is a well-established technique for the distinction between different solid materials. For the sample filtration, quartz filters with a temperature stability up to 950 °C were used. This allowed for sensitive and well reproducible measurements, as the TGA was not affected by the presence of the filter. The sample's mass fractions were calculated by integrating the mass decrease rate obtained by TGA in specific, clearly identifiable peak areas. A two-step TGA heating method consisting of N2 and O2 atmospheres led to a good differentiation between PAC and biological background matrix, thanks to the reduction of peak overlapping. A linear correlation was found between a sample's PAC content and the corresponding peak areas under N2 and O2, the sample volume and the solid mass separated by filtration. Based on these findings, various wastewater samples from different WWTPs were then analyzed by TGA with regard to their PAC content. It was found that, compared to alternative techniques such as measurement of turbidity or total suspended solids, the newly developed TGA method allows for a quantitative and selective detection of PAC concentrations down to 0

  15. High sensitivity detection of active botulinum neurotoxin by glyco-quantitative polymerase chain-reaction.

    PubMed

    Kwon, Seok Joon; Jeong, Eun Ji; Yoo, Yung Choon; Cai, Chao; Yang, Gi-Hyeok; Lee, Jae Chul; Dordick, Jonathan S; Linhardt, Robert J; Lee, Kyung Bok

    2014-03-01

    The sensitive detection of highly toxic botulinum neurotoxin (BoNT) from Clostridium botulinum is of critical importance because it causes human illnesses if foodborne or introduced in wounds and as an iatrogenic substance. Moreover, it has been recently considered a possible biological warfare agent. Over the past decade, significant progress has been made in BoNT detection technologies, including mouse lethality assays, enzyme-linked immunosorbent assays, and endopeptidase assays and by mass spectrometry. Critical assay requirements, including rapid assay, active toxin detection, sensitive and accurate detection, still remain challenging. Here, we present a novel method to detect active BoNTs using a Glyco-quantitative polymerase chain-reaction (qPCR) approach. Sialyllactose, which interacts with the binding-domain of BoNTs, is incorporated into a sialyllactose-DNA conjugate as a binding-probe for active BoNT and recovered through BoNT-immunoprecipitation. Glyco-qPCR analysis of the bound sialyllactose-DNA is then used to detect low attomolar concentrations of BoNT and attomolar to femtomolar concentrations of BoNT in honey, the most common foodborne source of infant botulism.

  16. Quantitative imaging of transcription in living Drosophila embryos links polymerase activity to patterning.

    PubMed

    Garcia, Hernan G; Tikhonov, Mikhail; Lin, Albert; Gregor, Thomas

    2013-11-01

    Spatiotemporal patterns of gene expression are fundamental to every developmental program. The resulting macroscopic domains have been mainly characterized by their levels of gene products. However, the establishment of such patterns results from differences in the dynamics of microscopic events in individual cells such as transcription. It is unclear how these microscopic decisions lead to macroscopic patterns, as measurements in fixed tissue cannot access the underlying transcriptional dynamics. In vivo transcriptional dynamics have long been approached in single-celled organisms, but never in a multicellular developmental context. Here, we directly address how boundaries of gene expression emerge in the Drosophila embryo by measuring the absolute number of actively transcribing polymerases in real time in individual nuclei. Specifically, we show that the formation of a boundary cannot be quantitatively explained by the rate of mRNA production in each cell, but instead requires amplification of the dynamic range of the expression boundary. This amplification is accomplished by nuclei randomly adopting active or inactive states of transcription, leading to a collective effect where the fraction of active nuclei is modulated in space. Thus, developmental patterns are not just the consequence of reproducible transcriptional dynamics in individual nuclei, but are the result of averaging expression over space and time.

  17. Improving quantitative structure-activity relationship models using Artificial Neural Networks trained with dropout.

    PubMed

    Mendenhall, Jeffrey; Meiler, Jens

    2016-02-01

    Dropout is an Artificial Neural Network (ANN) training technique that has been shown to improve ANN performance across canonical machine learning (ML) datasets. Quantitative Structure Activity Relationship (QSAR) datasets used to relate chemical structure to biological activity in Ligand-Based Computer-Aided Drug Discovery pose unique challenges for ML techniques, such as heavily biased dataset composition, and relatively large number of descriptors relative to the number of actives. To test the hypothesis that dropout also improves QSAR ANNs, we conduct a benchmark on nine large QSAR datasets. Use of dropout improved both enrichment false positive rate and log-scaled area under the receiver-operating characteristic curve (logAUC) by 22-46 % over conventional ANN implementations. Optimal dropout rates are found to be a function of the signal-to-noise ratio of the descriptor set, and relatively independent of the dataset. Dropout ANNs with 2D and 3D autocorrelation descriptors outperform conventional ANNs as well as optimized fingerprint similarity search methods.

  18. Quantitation of Na+, K+-atpase Enzymatic Activity in Tissues of the Mammalian Vestibular System

    NASA Technical Reports Server (NTRS)

    Kerr, T. P.

    1985-01-01

    In order to quantify vestibular Na(+), K(+)-ATPase, a microassay technique was developed which is sufficiently sensitive to measure the enzymatic activity in tissue from a single animal. The assay was used to characterize ATPase in he vestibular apparatus of the Mongolian gerbil. The quantitative procedure employs NPP (5 mM) as synthetic enzyme substrate. The assay relies upon spectrophotometric measurement (410 nm) of nitrophenol (NP) released by enzymatic hydrolysis of the substrate. Product formation in the absence of ouabain reflects both specific (Na(+), K(+)-ATPase) and non-specific (Mg(++)-ATPase) enzymatic activity. By measuring the accumulation of reaction product (NP) at three-minute intervals during the course of incubation, it is found that the overall enzymatic reaction proceeds linearly for at least 45 minutes. It is therefore possible to determine two separate reaction rates from a single set of tissues. Initial results indicate that total activity amounts to 53.3 + or - 11.2 (S.E.M.) nmol/hr/mg dry tissue, of which approximately 20% is ouabain-sensitive.

  19. Quantitation of Alpha-Glucosidase Activity Using Fluorinated Carbohydrate Array and MALDI-TOF-MS.

    PubMed

    Yang, Hyojik; Chan, Allen L; LaVallo, Vincent; Cheng, Quan

    2016-02-01

    Quantitation of alpha-glucosidase (α-GD) activity is of significance to diagnosis of many diseases including Pompe disease and type II diabetes. We report here a new method to determine α-GD activity using matrix-assisted laser desorption/ionization (MALDI)-time-of-flight (TOF) mass spectrometry (MS) in combination with carbohydrate microarray and affinity surface chemistry. Carbohydrate probes are synthesized for capture of the enzymatic reaction products and the adducts are loaded onto a fluorinated gold surface to generate an array, which is followed by characterization by MALDI-TOF-MS. The ratio of intensities is used to determine the level of activity of several enzymes. In addition, half maximal inhibitory concentration (IC50) of acarbose and epigallocatechin gallate are also determined using this approach, and the results agree well with the reported values. This method is advantageous as compared to conventional colorimetric techniques that typically suffer matrix interference problems from samples. The use of the polyfluorinated surface has effectively suppressed the interference. PMID:26760440

  20. Monocular distance estimation from optic flow during active landing maneuvers.

    PubMed

    van Breugel, Floris; Morgansen, Kristi; Dickinson, Michael H

    2014-06-01

    Vision is arguably the most widely used sensor for position and velocity estimation in animals, and it is increasingly used in robotic systems as well. Many animals use stereopsis and object recognition in order to make a true estimate of distance. For a tiny insect such as a fruit fly or honeybee, however, these methods fall short. Instead, an insect must rely on calculations of optic flow, which can provide a measure of the ratio of velocity to distance, but not either parameter independently. Nevertheless, flies and other insects are adept at landing on a variety of substrates, a behavior that inherently requires some form of distance estimation in order to trigger distance-appropriate motor actions such as deceleration or leg extension. Previous studies have shown that these behaviors are indeed under visual control, raising the question: how does an insect estimate distance solely using optic flow? In this paper we use a nonlinear control theoretic approach to propose a solution for this problem. Our algorithm takes advantage of visually controlled landing trajectories that have been observed in flies and honeybees. Finally, we implement our algorithm, which we term dynamic peering, using a camera mounted to a linear stage to demonstrate its real-world feasibility.

  1. Design and prediction of new acetylcholinesterase inhibitor via quantitative structure activity relationship of huprines derivatives.

    PubMed

    Zhang, Shuqun; Hou, Bo; Yang, Huaiyu; Zuo, Zhili

    2016-05-01

    Acetylcholinesterase (AChE) is an important enzyme in the pathogenesis of Alzheimer's disease (AD). Comparative quantitative structure-activity relationship (QSAR) analyses on some huprines inhibitors against AChE were carried out using comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA), and hologram QSAR (HQSAR) methods. Three highly predictive QSAR models were constructed successfully based on the training set. The CoMFA, CoMSIA, and HQSAR models have values of r (2) = 0.988, q (2) = 0.757, ONC = 6; r (2) = 0.966, q (2) = 0.645, ONC = 5; and r (2) = 0.957, q (2) = 0.736, ONC = 6. The predictabilities were validated using an external test sets, and the predictive r (2) values obtained by the three models were 0.984, 0.973, and 0.783, respectively. The analysis was performed by combining the CoMFA and CoMSIA field distributions with the active sites of the AChE to further understand the vital interactions between huprines and the protease. On the basis of the QSAR study, 14 new potent molecules have been designed and six of them are predicted to be more active than the best active compound 24 described in the literature. The final QSAR models could be helpful in design and development of novel active AChE inhibitors.

  2. Application of MassSQUIRM for quantitative measurements of lysine demethylase activity.

    PubMed

    Blair, Lauren P; Avaritt, Nathan L; Tackett, Alan J

    2012-03-11

    Recently, epigenetic regulators have been discovered as key players in many different diseases (1-3). As a result, these enzymes are prime targets for small molecule studies and drug development( 4). Many epigenetic regulators have only recently been discovered and are still in the process of being classified. Among these enzymes are lysine demethylases which remove methyl groups from lysines on histones and other proteins. Due to the novel nature of this class of enzymes, few assays have been developed to study their activity. This has been a road block to both the classification and high throughput study of histone demethylases. Currently, very few demethylase assays exist. Those that do exist tend to be qualitative in nature and cannot simultaneously discern between the different lysine methylation states (un-, mono-, di- and tri-). Mass spectrometry is commonly used to determine demethylase activity but current mass spectrometric assays do not address whether differentially methylated peptides ionize differently. Differential ionization of methylated peptides makes comparing methylation states difficult and certainly not quantitative (Figure 1A). Thus available assays are not optimized for the comprehensive analysis of demethylase activity. Here we describe a method called MassSQUIRM (mass spectrometric quantitation using isotopic reductive methylation) that is based on reductive methylation of amine groups with deuterated formaldehyde to force all lysines to be di-methylated, thus making them essentially the same chemical species and therefore ionize the same (Figure 1B). The only chemical difference following the reductive methylation is hydrogen and deuterium, which does not affect MALDI ionization efficiencies. The MassSQUIRM assay is specific for demethylase reaction products with un-, mono- or di-methylated lysines. The assay is also applicable to lysine methyltransferases giving the same reaction products. Here, we use a combination of reductive

  3. Quantitative estimation of bioclimatic parameters from presence/absence vegetation data in North America by the modern analog technique

    USGS Publications Warehouse

    Thompson, R.S.; Anderson, K.H.; Bartlein, P.J.

    2008-01-01

    The method of modern analogs is widely used to obtain estimates of past climatic conditions from paleobiological assemblages, and despite its frequent use, this method involved so-far untested assumptions. We applied four analog approaches to a continental-scale set of bioclimatic and plant-distribution presence/absence data for North America to assess how well this method works under near-optimal modern conditions. For each point on the grid, we calculated the similarity between its vegetation assemblage and those of all other points on the grid (excluding nearby points). The climate of the points with the most similar vegetation was used to estimate the climate at the target grid point. Estimates based the use of the Jaccard similarity coefficient had smaller errors than those based on the use of a new similarity coefficient, although the latter may be more robust because it does not assume that the "fossil" assemblage is complete. The results of these analyses indicate that presence/absence vegetation assemblages provide a valid basis for estimating bioclimates on the continental scale. However, the accuracy of the estimates is strongly tied to the number of species in the target assemblage, and the analog method is necessarily constrained to produce estimates that fall within the range of observed values. We applied the four modern analog approaches and the mutual overlap (or "mutual climatic range") method to estimate bioclimatic conditions represented by the plant macrofossil assemblage from a packrat midden of Last Glacial Maximum age from southern Nevada. In general, the estimation approaches produced similar results in regard to moisture conditions, but there was a greater range of estimates for growing-degree days. Despite its limitations, the modern analog technique can provide paleoclimatic reconstructions that serve as the starting point to the interpretation of past climatic conditions.

  4. A Quantitative Structure Activity Relationship for acute oral toxicity of pesticides on rats: Validation, domain of application and prediction.

    PubMed

    Hamadache, Mabrouk; Benkortbi, Othmane; Hanini, Salah; Amrane, Abdeltif; Khaouane, Latifa; Si Moussa, Cherif

    2016-02-13

    Quantitative Structure Activity Relationship (QSAR) models are expected to play an important role in the risk assessment of chemicals on humans and the environment. In this study, we developed a validated QSAR model to predict acute oral toxicity of 329 pesticides to rats because a few QSAR models have been devoted to predict the Lethal Dose 50 (LD50) of pesticides on rats. This QSAR model is based on 17 molecular descriptors, and is robust, externally predictive and characterized by a good applicability domain. The best results were obtained with a 17/9/1 Artificial Neural Network model trained with the Quasi Newton back propagation (BFGS) algorithm. The prediction accuracy for the external validation set was estimated by the Q(2)ext and the root mean square error (RMS) which are equal to 0.948 and 0.201, respectively. 98.6% of external validation set is correctly predicted and the present model proved to be superior to models previously published. Accordingly, the model developed in this study provides excellent predictions and can be used to predict the acute oral toxicity of pesticides, particularly for those that have not been tested as well as new pesticides.

  5. Quantitative structure-activity relationships and mixture toxicity of organic chemicals in Photobacterium phosphoreum: the Microtox test

    SciTech Connect

    Hermens, J.; Busser, F.; Leeuwangh, P.; Musch, A.

    1985-02-01

    Quantitative structure-activity relationships were calculated for the inhibition of bioluminescence of Photobacterium phosphoreum by 22 nonreactive organic chemicals. The inhibition was measured using the Microtox test and correlated with the partition coefficient between n-octanol and water (Poct), molar refractivity (MR), and molar volume (MW/d). At log Poct less than 1 and greater than 3, deviations from linearity were observed. Introduction of MR and MW/d improved the quality of the relationships. The influences of MR or MW/d may be related with an interaction of the tested chemicals to the enzyme system which produces the light emission. The sensitivity of the Microtox test to the 22 tested compounds is comparable to a 14-day acute mortality test with guppies for chemicals with log Poct less than 4. The inhibition of bioluminescence by a mixture of the tested compounds was slightly less than was expected in case of concentration addition. The Microtox test can give a good estimate of the total aspecific minimum toxicity of polluted waters. When rather lipophilic compounds or pollutants with more specific modes of action are present, this test will underestimate the toxicity to other aquatic life.

  6. Quantitative Estimation of the Number of Contaminated Hatching Eggs Released from an Infected, Undetected Turkey Breeder Hen Flock During a Highly Pathogenic Avian Influenza Outbreak.

    PubMed

    Malladi, Sasidhar; Weaver, J Todd; Alexander, Catherine Y; Middleton, Jamie L; Goldsmith, Timothy J; Snider, Timothy; Tilley, Becky J; Gonder, Eric; Hermes, David R; Halvorson, David A

    2015-09-01

    The regulatory response to an outbreak of highly pathogenic avian influenza (HPAI) in the United States may involve quarantine and stop movement orders that have the potential to disrupt continuity of operations in the U.S. turkey industry--particularly in the event that an uninfected breeder flock is located within an HPAI Control Area. A group of government-academic-industry leaders developed an approach to minimize the unintended consequences associated with outbreak response, which incorporates HPAI control measures to be implemented prior to moving hatching eggs off of the farm. Quantitative simulation models were used to evaluate the movement of potentially contaminated hatching eggs from a breeder henhouse located in an HPAI Control Area, given that active surveillance testing, elevated biosecurity, and a 2-day on-farm holding period were employed. The risk analysis included scenarios of HPAI viruses differing in characteristics as well as scenarios in which infection resulted from artificial insemination. The mean model-predicted number of internally contaminated hatching eggs released per movement from an HPAI-infected turkey breeder henhouse ranged from 0 to 0.008 under the four scenarios evaluated. The results indicate a 95% chance of no internally contaminated eggs being present per movement from an infected house before detection. Sensitivity analysis indicates that these results are robust to variation in key transmission model parameters within the range of their estimates from available literature. Infectious birds at the time of egg collection are a potential pathway of external contamination for eggs stored and then moved off of the farm; the predicted number of such infectious birds was estimated to be low. To date, there has been no evidence of vertical transmission of HPAI virus or low pathogenic avian influenza virus to day-old poults from hatching eggs originating from infected breeders. The application of risk analysis methods was beneficial

  7. Quantitative Estimation of the Number of Contaminated Hatching Eggs Released from an Infected, Undetected Turkey Breeder Hen Flock During a Highly Pathogenic Avian Influenza Outbreak.

    PubMed

    Malladi, Sasidhar; Weaver, J Todd; Alexander, Catherine Y; Middleton, Jamie L; Goldsmith, Timothy J; Snider, Timothy; Tilley, Becky J; Gonder, Eric; Hermes, David R; Halvorson, David A

    2015-09-01

    The regulatory response to an outbreak of highly pathogenic avian influenza (HPAI) in the United States may involve quarantine and stop movement orders that have the potential to disrupt continuity of operations in the U.S. turkey industry--particularly in the event that an uninfected breeder flock is located within an HPAI Control Area. A group of government-academic-industry leaders developed an approach to minimize the unintended consequences associated with outbreak response, which incorporates HPAI control measures to be implemented prior to moving hatching eggs off of the farm. Quantitative simulation models were used to evaluate the movement of potentially contaminated hatching eggs from a breeder henhouse located in an HPAI Control Area, given that active surveillance testing, elevated biosecurity, and a 2-day on-farm holding period were employed. The risk analysis included scenarios of HPAI viruses differing in characteristics as well as scenarios in which infection resulted from artificial insemination. The mean model-predicted number of internally contaminated hatching eggs released per movement from an HPAI-infected turkey breeder henhouse ranged from 0 to 0.008 under the four scenarios evaluated. The results indicate a 95% chance of no internally contaminated eggs being present per movement from an infected house before detection. Sensitivity analysis indicates that these results are robust to variation in key transmission model parameters within the range of their estimates from available literature. Infectious birds at the time of egg collection are a potential pathway of external contamination for eggs stored and then moved off of the farm; the predicted number of such infectious birds was estimated to be low. To date, there has been no evidence of vertical transmission of HPAI virus or low pathogenic avian influenza virus to day-old poults from hatching eggs originating from infected breeders. The application of risk analysis methods was beneficial

  8. Assessment of a rapid method for quantitative reach-scale estimates of deposited fine sediment in rivers

    NASA Astrophysics Data System (ADS)

    Duerdoth, C. P.; Arnold, A.; Murphy, J. F.; Naden, P. S.; Scarlett, P.; Collins, A. L.; Sear, D. A.; Jones, J. I.

    2015-02-01

    Despite increasing concerns about the negative effects that increased loads of fine-grained sediment are having on freshwaters, the need is clear for a rapid and cost-effective methodology that gives precise estimates of deposited sediment across all river types and that are relevant to morphological and ecological impact. To date few attempts have been made to assess the precision of techniques used to assemble data on fine sediment storage in river channels. Accordingly, we present an investigation into the sources of uncertainty associated with estimates of deposited fine-grained sediment in rivers using a sediment resuspension technique, an approach that provides an instantaneous measure of deposited fine sediment (surface and subsurface) in terms of quantity and quality. We investigated how variation associated with river type, spatial patchiness within rivers, sampling, and individual operators influenced estimates of deposited fine sediment using this approach and compared the precision with that of visual estimates of river bed composition - a commonly applied technique in rapid river surveys. We have used this information to develop an effective methodology for producing reach-scale estimates with known confidence intervals. By using a spatially-focussed sampling strategy that captured areas of visually high and low deposition of fine-grained sediment, the dominant aspects of small-scale spatial variability were controlled and a more precise instantaneous estimate of deposited fine sediment derived. The majority of the remaining within-site variance was attributable to spatial and sampling variability at the smallest (patch) scale. The method performed as well as visual estimates of percentage of the river bed comprising fines in its ability to discriminate between rivers but, unlike visual estimates, was not affected by operator bias. Confidence intervals for reach-scale measures of deposited fine-grained sediment were derived for the technique, and these

  9. Chemical graphs, molecular matrices and topological indices in chemoinformatics and quantitative structure-activity relationships.

    PubMed

    Ivanciuc, Ovidiu

    2013-06-01

    Chemical and molecular graphs have fundamental applications in chemoinformatics, quantitative structureproperty relationships (QSPR), quantitative structure-activity relationships (QSAR), virtual screening of chemical libraries, and computational drug design. Chemoinformatics applications of graphs include chemical structure representation and coding, database search and retrieval, and physicochemical property prediction. QSPR, QSAR and virtual screening are based on the structure-property principle, which states that the physicochemical and biological properties of chemical compounds can be predicted from their chemical structure. Such structure-property correlations are usually developed from topological indices and fingerprints computed from the molecular graph and from molecular descriptors computed from the three-dimensional chemical structure. We present here a selection of the most important graph descriptors and topological indices, including molecular matrices, graph spectra, spectral moments, graph polynomials, and vertex topological indices. These graph descriptors are used to define several topological indices based on molecular connectivity, graph distance, reciprocal distance, distance-degree, distance-valency, spectra, polynomials, and information theory concepts. The molecular descriptors and topological indices can be developed with a more general approach, based on molecular graph operators, which define a family of graph indices related by a common formula. Graph descriptors and topological indices for molecules containing heteroatoms and multiple bonds are computed with weighting schemes based on atomic properties, such as the atomic number, covalent radius, or electronegativity. The correlation in QSPR and QSAR models can be improved by optimizing some parameters in the formula of topological indices, as demonstrated for structural descriptors based on atomic connectivity and graph distance. PMID:23701000

  10. Quantitative Structure Activity Relationship for Inhibition of Human Organic Cation/Carnitine Transporter (OCTN2)

    PubMed Central

    Diao, Lei; Ekins, Sean; Polli, James E.

    2010-01-01

    Organic cation/carnitine transporter (OCTN2; SLC22A5) is an important transporter for L-carnitine homeostasis, but can be inhibited by drugs, which may cause L-carnitine deficiency and possibly other OCTN2-mediated drug-drug interactions. One objective was to develop a quantitative structure–activity relationship (QSAR) of OCTN2 inhibitors, in order to predict and identify other potential OCTN2 inhibitors and infer potential clinical interactions. A second objective was to assess two high renal clearance drugs that interact with OCTN2 in vitro (cetirizine and cephaloridine) for possible OCTN2-mediated drug-drug interactions. Using previously generated in vitro data of 22 drugs, a 3D quantitative pharmacophore model and a Bayesian machine learning model were developed. The four pharmacophore features include two hydrophobic groups, one hydrogen-bond acceptor, and one positive ionizable center. The Bayesian machine learning model was developed using simple interpretable descriptors and function class fingerprints of maximum diameter 6 (FCFP_6). An external test set of 27 molecules, including 15 newly identified OCTN2 inhibitors, and a literature test set of 22 molecules were used to validate both models. The computational models afforded good capability to identify structurally diverse OCTN2 inhibitors, providing a valuable tool to predict new inhibitors efficiently. Inhibition results confirmed our previously observed association between rhabdomyolysis and Cmax/Ki ratio. The two high renal clearance drugs cetirizine and cephaloridine were found not to be OCTN2 substrates and their diminished elimination by other drugs is concluded not to be mediated by OCTN2. PMID:20831193

  11. Quantitative monitoring of pluripotency gene activation after somatic cloning in cattle.

    PubMed

    Wuensch, Annegret; Habermann, Felix A; Kurosaka, Satoshi; Klose, Regina; Zakhartchenko, Valeri; Reichenbach, Horst-Dieter; Sinowatz, Fred; McLaughlin, K John; Wolf, Eckhard

    2007-06-01

    The development of somatic cell nuclear transfer (SCNT) embryos critically depends on appropriate reprogramming and expression of pluripotency genes, such as Pou5f1/POU5F1 (previously known as Oct4/OCT4). To study POU5F1 transcription activation in living bovine SCNT embryos without interference by maternal POU5F1 mRNA, we generated chromosomally normal fetal fibroblast donor cells stably carrying a mouse Pou5f1 promoter-driven enhanced green fluorescent protein (EGFP) reporter gene at a single integration site without detectable EGFP expression. Morphologic and quantitative analyses of whole-mount SCNT embryos by confocal microscopy revealed robust initial activation of the Pou5f1 reporter gene during the fourth cell cycle. In Day 6 SCNT embryos EGFP expression levels were markedly higher than in Day 4 embryos but varied substantially between individual embryos, even at comparable cell numbers. Embryos with low EGFP levels had far more morphologically abnormal cell nuclei than those with high EGFP levels. Our data strongly suggest that bovine SCNT embryos consistently start activation of the POU5F1 promoter during the fourth cell cycle, whereas later in development the expression level substantially differs between individual embryos, which may be associated with developmental potential. In fibroblasts from phenotypically normal SCNT fetuses recovered on Day 34, the Pou5f1 reporter promoter was silent but was activated by a second round of SCNT. The restoration of pluripotency can be directly observed in living cells or SCNT embryos from such Pou5f1-EGFP transgenic fetuses, providing an attractive model for systematic investigation of epigenetic reprogramming in large mammals.

  12. Measurement of ice nucleation-active bacteria on plants and in precipitation by quantitative PCR.

    PubMed

    Hill, Thomas C J; Moffett, Bruce F; Demott, Paul J; Georgakopoulos, Dimitrios G; Stump, William L; Franc, Gary D

    2014-02-01

    Ice nucleation-active (INA) bacteria may function as high-temperature ice-nucleating particles (INP) in clouds, but their effective contribution to atmospheric processes, i.e., their potential to trigger glaciation and precipitation, remains uncertain. We know little about their abundance on natural vegetation, factors that trigger their release, or persistence of their ice nucleation activity once airborne. To facilitate these investigations, we developed two quantitative PCR (qPCR) tests of the ina gene to directly count INA bacteria in environmental samples. Each of two primer pairs amplified most alleles of the ina gene and, taken together, they should amplify all known alleles. To aid primer design, we collected many new INA isolates. Alignment of their partial ina sequences revealed new and deeply branching clades, including sequences from Pseudomonas syringae pv. atropurpurea, Ps. viridiflava, Pantoea agglomerans, Xanthomonas campestris, and possibly Ps. putida, Ps. auricularis, and Ps. poae. qPCR of leaf washings recorded ∼10(8) ina genes g(-1) fresh weight of foliage on cereals and 10(5) to 10(7) g(-1) on broadleaf crops. Much lower populations were found on most naturally occurring vegetation. In fresh snow, ina genes from various INA bacteria were detected in about half the samples but at abundances that could have accounted for only a minor proportion of INP at -10°C (assuming one ina gene per INA bacterium). Despite this, an apparent biological source contributed an average of ∼85% of INP active at -10°C in snow samples. In contrast, a thunderstorm hail sample contained 0.3 INA bacteria per INP active at -10°C, suggesting a significant contribution to this sample. PMID:24317082

  13. Measurement of ice nucleation-active bacteria on plants and in precipitation by quantitative PCR.

    PubMed

    Hill, Thomas C J; Moffett, Bruce F; Demott, Paul J; Georgakopoulos, Dimitrios G; Stump, William L; Franc, Gary D

    2014-02-01

    Ice nucleation-active (INA) bacteria may function as high-temperature ice-nucleating particles (INP) in clouds, but their effective contribution to atmospheric processes, i.e., their potential to trigger glaciation and precipitation, remains uncertain. We know little about their abundance on natural vegetation, factors that trigger their release, or persistence of their ice nucleation activity once airborne. To facilitate these investigations, we developed two quantitative PCR (qPCR) tests of the ina gene to directly count INA bacteria in environmental samples. Each of two primer pairs amplified most alleles of the ina gene and, taken together, they should amplify all known alleles. To aid primer design, we collected many new INA isolates. Alignment of their partial ina sequences revealed new and deeply branching clades, including sequences from Pseudomonas syringae pv. atropurpurea, Ps. viridiflava, Pantoea agglomerans, Xanthomonas campestris, and possibly Ps. putida, Ps. auricularis, and Ps. poae. qPCR of leaf washings recorded ∼10(8) ina genes g(-1) fresh weight of foliage on cereals and 10(5) to 10(7) g(-1) on broadleaf crops. Much lower populations were found on most naturally occurring vegetation. In fresh snow, ina genes from various INA bacteria were detected in about half the samples but at abundances that could have accounted for only a minor proportion of INP at -10°C (assuming one ina gene per INA bacterium). Despite this, an apparent biological source contributed an average of ∼85% of INP active at -10°C in snow samples. In contrast, a thunderstorm hail sample contained 0.3 INA bacteria per INP active at -10°C, suggesting a significant contribution to this sample.

  14. Measurement of Ice Nucleation-Active Bacteria on Plants and in Precipitation by Quantitative PCR

    PubMed Central

    Moffett, Bruce F.; DeMott, Paul J.; Georgakopoulos, Dimitrios G.; Stump, William L.; Franc, Gary D.

    2014-01-01

    Ice nucleation-active (INA) bacteria may function as high-temperature ice-nucleating particles (INP) in clouds, but their effective contribution to atmospheric processes, i.e., their potential to trigger glaciation and precipitation, remains uncertain. We know little about their abundance on natural vegetation, factors that trigger their release, or persistence of their ice nucleation activity once airborne. To facilitate these investigations, we developed two quantitative PCR (qPCR) tests of the ina gene to directly count INA bacteria in environmental samples. Each of two primer pairs amplified most alleles of the ina gene and, taken together, they should amplify all known alleles. To aid primer design, we collected many new INA isolates. Alignment of their partial ina sequences revealed new and deeply branching clades, including sequences from Pseudomonas syringae pv. atropurpurea, Ps. viridiflava, Pantoea agglomerans, Xanthomonas campestris, and possibly Ps. putida, Ps. auricularis, and Ps. poae. qPCR of leaf washings recorded ∼108 ina genes g−1 fresh weight of foliage on cereals and 105 to 107 g−1 on broadleaf crops. Much lower populations were found on most naturally occurring vegetation. In fresh snow, ina genes from various INA bacteria were detected in about half the samples but at abundances that could have accounted for only a minor proportion of INP at −10°C (assuming one ina gene per INA bacterium). Despite this, an apparent biological source contributed an average of ∼85% of INP active at −10°C in snow samples. In contrast, a thunderstorm hail sample contained 0.3 INA bacteria per INP active at −10°C, suggesting a significant contribution to this sample. PMID:24317082

  15. A Caco-2 cell-based quantitative antioxidant activity assay for antioxidants.

    PubMed

    Wan, Hongxia; Liu, Dong; Yu, Xiangying; Sun, Haiyan; Li, Yan

    2015-05-15

    A Caco-2 cell-based antioxidant activity (CAA) assay for quantitative evaluation of antioxidants was developed by optimizing seeding density and culture time of Caco-2 cells, incubation time and concentration of fluorescent probe (2',7'-dichlorofluorescin diacetate, DCFH-DA), incubation way and incubation time of antioxidants (pure phytochemicals) and DCFH-DA with cells, and detection time of fluorescence. Results showed that the CAA assay was of good reproducibility and could be used to evaluate the antioxidant activity of antioxidants at the following conditions: seeding density of 5 × 10(4)/well, cell culture time of 24h, co-incubation of 60 μM DCFH-DA and pure phytochemicals with Caco-2 cells for 20 min and fluorescence recorded for 90 min. Additionally, a significant correlation was observed between CAA values and rat plasma ORAC values following the intake of antioxidants for selected pure phytochemicals (R(2) = 0.815, p < 0.01), demonstrating the good biological relevance of CAA assay.

  16. Quantitative Proteomics Reveals the Induction of Mitophagy in Tumor Necrosis Factor-α-activated (TNFα) Macrophages*

    PubMed Central

    Bell, Christina; English, Luc; Boulais, Jonathan; Chemali, Magali; Caron-Lizotte, Olivier; Desjardins, Michel; Thibault, Pierre

    2013-01-01

    Macrophages play an important role in innate and adaptive immunity as professional phagocytes capable of internalizing and degrading pathogens to derive antigens for presentation to T cells. They also produce pro-inflammatory cytokines such as tumor necrosis factor alpha (TNF-α) that mediate local and systemic responses and direct the development of adaptive immunity. The present work describes the use of label-free quantitative proteomics to profile the dynamic changes of proteins from resting and TNF-α-activated mouse macrophages. These analyses revealed that TNF-α activation of macrophages led to the down-regulation of mitochondrial proteins and the differential regulation of several proteins involved in vesicle trafficking and immune response. Importantly, we found that the down-regulation of mitochondria proteins occurred through mitophagy and was specific to TNF-α, as other cytokines such as IL-1β and IFN-γ had no effect on mitochondria degradation. Furthermore, using a novel antigen presentation system, we observed that the induction of mitophagy by TNF-α enabled the processing and presentation of mitochondrial antigens at the cell surface by MHC class I molecules. These findings highlight an unsuspected role of TNF-α in mitophagy and expanded our understanding of the mechanisms responsible for MHC presentation of self-antigens. PMID:23674617

  17. Quantitative structure-activity relationships for toxicity of nonpolar narcotic chemicals to Pseudokirchneriella subcapitata.

    PubMed

    Hsieh, Shih-Hung; Hsu, Chih-Hsiung; Tsai, Din-Yu; Chen, Chung-Yuan

    2006-11-01

    This study presents data for 27 nonpolar narcotic compounds regarding toxicity to Pseudokirchneriella subcapitata as evaluated using a closed-system algal toxicity test with an exposure time of 48 h. Two test endpoints, dissolved oxygen production and algal growth rate, were used to assess the toxicity of nonpolar narcotic chemicals on algae. Hydrophobicity (1-octanol-water partition coefficient [K(OW)]) provided satisfactory descriptions for the toxicity of nonpolar narcotic compounds, and quantitative structure-activity relationships based on log K(OW) were established. The relative sensitivity of various aquatic organisms to nonpolar chemicals was as follows: P. subcapitata > Vibriofischeri > or = Nitrosomonas sp. > fathead minnow > Daphnia magna > polytox > activated sludge. In addition, linear relationships were found between the toxicity observed in P. subcapitata and other aquatic organisms, except in the case of Nitrosomonas sp. Therefore, for nonpolar toxicants, the closed-system technique applied in the present study can be an ideal surrogate for other tests, such as fathead minnow and D. magna, that are either time-consuming or labor-intensive. However, because the current toxicity database is based primarily on the conventional batch tests, it cannot provide adequate assessment regarding the effects of various organic toxicants. Therefore, more extensive research is needed to revise the database for the toxicity of organic compounds on phytoplankton using the closed-system technique.

  18. Quantitation of lysolipids, fatty acids, and phospholipase A2 activity and correlation with membrane polarity

    PubMed Central

    Singh, Jasmeet; Ranganathan, Radha

    2012-01-01

    Acrylodan-labeled rat-intestinal fatty acid binding protein, ADIFAB, binds both of lysophosphatidylcholines (LPC) and FA. Binding displaces Acrylodan and its fluorescence peak shifts from 432 to 505 nm. A fluorescence assay that relies on this shift is presented for quantitating LPC, FA, and phospholipase A2 (PLA2) activity in phospholipid bilayers in absolute units of μM/min/mg of enzyme. This is a development over an earlier assay that took into account only FA binding. Activities of bee venom PLA2 on dipalmitoylphosphatidylcholine (DPPC) and dioleylphosphatidylcholine (DOPC) bilayers were measured. Standard pH-Stat assays validated the present assay. Products increase linearly with time for about one minute in DOPC and five minutes in DPPC corresponding to completion of 5 to 8% hydrolysis in DOPC and 20% in DPPC. Membrane polarity and microviscosity measured using electron spin resonance (ESR) exhibited discontinuities at compositions that mimicked similar percentages of hydrolysis products in the respective bilayers. The observed hydrolysis rate decrease following the initial linear period thus correlates to changes in membrane polarity. The ability of the assay to yield actual product concentrations, reveal structure in the reaction progress curves, and interpretation in light of the ESR data bring insight into the shape of the reaction curve. PMID:22773689

  19. Quantitative structure-activity relationships and the prediction of MHC supermotifs.

    PubMed

    Doytchinova, Irini A; Guan, Pingping; Flower, Darren R

    2004-12-01

    The underlying assumption in quantitative structure-activity relationship (QSAR) methodology is that related chemical structures exhibit related biological activities. We review here two QSAR methods in terms of their applicability for human MHC supermotif definition. Supermotifs are motifs that characterise binding to more than one allele. Supermotif definition is the initial in silico step of epitope-based vaccine design. The first QSAR method we review here--the additive method--is based on the assumption that the binding affinity of a peptide depends on contributions from both amino acids and the interactions between them. The second method is a 3D-QSAR method: comparative molecular similarity indices analysis (CoMSIA). Both methods were applied to 771 peptides binding to 9 HLA alleles. Five of the alleles (A*0201, A*0202, A*0203, A*0206 and A*6802) belong to the HLA-A2 superfamily and the other four (A*0301, A*1101, A*3101 and A*6801) to the HLA-A3 superfamily. For each superfamily, supermotifs defined by the two QSAR methods agree closely and are supported by many experimental data. PMID:15542370

  20. Quantitative genetic analysis of copia retrotransposon activity in inbred Drosophila melanogaster lines.

    PubMed Central

    Nuzhdin, S V; Pasyukova, E G; Morozova, E A; Flavell, A J

    1998-01-01

    The rates of transcription and transposition of retrotransposons vary between lines of Drosophila melanogaster. We have studied the genetics of differences in copia retrotransposon activity by quantitative trait loci (QTL) mapping. Ninety-eight recombinant inbred lines were constructed from two parental lines exhibiting a 10-fold difference in copia transcript level and a 100-fold difference in transposition rate. The lines were scored for 126 molecular markers, copia transcript level, and rate of copia transposition. Transcript level correlated with copia copy number, and the difference in copia copy number between parental lines accounted for 45.1% of copia transcript-level difference. Most of the remaining difference was accounted for by two transcript-level QTL mapping to cytological positions 27B-30D and 50F-57C on the second chromosome, which accounted for 11.5 and 30.4%, respectively. copia transposition rate was controlled by interacting QTL mapping to the region 27B-48D on the second and 61A-65A and 97D-100A on the third chromosome. The genes controlling copia transcript level are thus not necessarily those involved in controlling copia transposition rate. Segregation of modifying genes, rather than mutations, might explain the variability in copia retrotransposon activity between lines. PMID:9755206

  1. Odor-active constituents in fresh pineapple (Ananas comosus [L.] Merr.) by quantitative and sensory evaluation.

    PubMed

    Tokitomo, Yukiko; Steinhaus, Martin; Büttner, Andrea; Schieberle, Peter

    2005-07-01

    By application of aroma extract dilution analysis (AEDA) to an aroma distillate prepared from fresh pineapple using solvent-assisted flavor evaporation (SAFE), 29 odor-active compounds were detected in the flavor dilution (FD) factor range of 2 to 4,096. Quantitative measurements performed by stable isotope dilution assays (SIDA) and a calculation of odor activity values (OAVs) of 12 selected odorants revealed the following compounds as key odorants in fresh pineapple flavor: 4-hydroxy-2,5-dimethyl-3(2H)-furanone (HDF; sweet, pineapple-like, caramel-like), ethyl 2-methylpropanoate (fruity), ethyl 2-methylbutanoate (fruity) followed by methyl 2-methylbutanoate (fruity, apple-like) and 1-(E,Z)-3,5-undecatriene (fresh, pineapple-like). A mixture of these 12 odorants in concentrations equal to those in the fresh pineapple resulted in an odor profile similar to that of the fresh juice. Furthermore, the results of omission tests using the model mixture showed that HDF and ethyl 2-methylbutanoate are character impact odorants in fresh pineapple.

  2. Proceedings of the third international workshop on quantitative structure-activity relationships in environmental toxicology

    SciTech Connect

    Turner, J.E.; England, M.W.; Schultz, T.W.; Kwaak, N.J.

    1988-06-01

    The 3rd International Workshop on Quantitative Structure-Activity Relationships (QSAR) in Environmental Toxicology (QSAR-88) was organized to facilitate the exchange of ideas between experts in different areas working in QSAR. Invited participants were selected to provide a mixture of representatives from biology, chemistry, and statistics as well as industry, government, and academia. The theme for QSAR-88 was ''Interrelationships of QSAR and Mechanisms of Toxic Actions.'' The program was divided into four sessions of invited talks on statistics, molecular descriptors, fish QSARs, and non-fish QSARs and a poster session. These Proceedings contain the text of the 16 invited technical papers and descriptions of the 16 contributed poster presentations. In addition, we include a summary of the Workshop prepared by Dr. Kaiser. The use of structure-activity relationships to elucidate trends in toxicology has been documented for more than a century. However, it is only over the past fifteen years that the modern tools, initially developed for experimental drug design, have been brought to bear on the problem of environmental contamination. The very nature of the field has, from the start, required the collaboration of experts from several scientific disciplines.

  3. Quantitative structure-activity relationship correlation between molecular structure and the Rayleigh enantiomeric enrichment factor.

    PubMed

    Jammer, S; Rizkov, D; Gelman, F; Lev, O

    2015-08-01

    It was recently demonstrated that under environmentally relevant conditions the Rayleigh equation is valid to describe the enantiomeric enrichment - conversion relationship, yielding a proportional constant called the enantiomeric enrichment factor, εER. In the present study we demonstrate a quantitative structure-activity relationship model (QSAR) that describes well the dependence of εER on molecular structure. The enantiomeric enrichment factor can be predicted by the linear Hansch model, which correlates biological activity with physicochemical properties. Enantioselective hydrolysis of sixteen derivatives of 2-(phenoxy)propionate (PPMs) have been analyzed during enzymatic degradation by lipases from Pseudomonas fluorescens (PFL), Pseudomonas cepacia (PCL), and Candida rugosa (CRL). In all cases the QSAR relationships were significant with R(2) values of 0.90-0.93, and showed high predictive abilities with internal and external validations providing QLOO(2) values of 0.85-0.87 and QExt(2) values of 0.8-0.91. Moreover, it is demonstrated that this model enables differentiation between enzymes with different binding site shapes. The enantioselectivity of PFL and PCL was dictated by electronic properties, whereas the enantioselectivity of CRL was determined by lipophilicity and steric factors. The predictive ability of the QSAR model demonstrated in the present study may serve as a helpful tool in environmental studies, assisting in source tracking of unstudied chiral compounds belonging to a well-studied homologous series.

  4. Quantitative trait locus analysis of symbiotic nitrogen fixation activity in the model legume Lotus japonicus.

    PubMed

    Tominaga, Akiyoshi; Gondo, Takahiro; Akashi, Ryo; Zheng, Shao-Hui; Arima, Susumu; Suzuki, Akihiro

    2012-05-01

    Many legumes form nitrogen-fixing root nodules. An elevation of nitrogen fixation in such legumes would have significant implications for plant growth and biomass production in agriculture. To identify the genetic basis for the regulation of nitrogen fixation, quantitative trait locus (QTL) analysis was conducted with recombinant inbred lines derived from the cross Miyakojima MG-20 × Gifu B-129 in the model legume Lotus japonicus. This population was inoculated with Mesorhizobium loti MAFF303099 and grown for 14 days in pods containing vermiculite. Phenotypic data were collected for acetylene reduction activity (ARA) per plant (ARA/P), ARA per nodule weight (ARA/NW), ARA per nodule number (ARA/NN), NN per plant, NW per plant, stem length (SL), SL without inoculation (SLbac-), shoot dry weight without inoculation (SWbac-), root length without inoculation (RLbac-), and root dry weight (RWbac-), and finally 34 QTLs were identified. ARA/P, ARA/NN, NW, and SL showed strong correlations and QTL co-localization, suggesting that several plant characteristics important for symbiotic nitrogen fixation are controlled by the same locus. QTLs for ARA/P, ARA/NN, NW, and SL, co-localized around marker TM0832 on chromosome 4, were also co-localized with previously reported QTLs for seed mass. This is the first report of QTL analysis for symbiotic nitrogen fixation activity traits.

  5. The influence of the design matrix on treatment effect estimates in the quantitative analyses of single-subject experimental design research.

    PubMed

    Moeyaert, Mariola; Ugille, Maaike; Ferron, John M; Beretvas, S Natasha; Van den Noortgate, Wim

    2014-09-01

    The quantitative methods for analyzing single-subject experimental data have expanded during the last decade, including the use of regression models to statistically analyze the data, but still a lot of questions remain. One question is how to specify predictors in a regression model to account for the specifics of the design and estimate the effect size of interest. These quantitative effect sizes are used in retrospective analyses and allow synthesis of single-subject experimental study results which is informative for evidence-based decision making, research and theory building, and policy discussions. We discuss different design matrices that can be used for the most common single-subject experimental designs (SSEDs), namely, the multiple-baseline designs, reversal designs, and alternating treatment designs, and provide empirical illustrations. The purpose of this article is to guide single-subject experimental data analysts interested in analyzing and meta-analyzing SSED data.

  6. Quantitation of CYP24A1 Enzymatic Activity With a Simple Two-Hybrid System

    PubMed Central

    Mugg, Amy; Legeza, Balazs; Tee, Meng Kian; Damm, Izabella; Long, Roger K.

    2015-01-01

    Context: Mutations of the CYP24A1 gene encoding the 24-hydroxylase (24OHase) that inactivates metabolites of vitamin D can cause hypercalcemia in infants and adults; in vitro assays of 24OHase activity have been difficult. Objective: We sought an alternative assay to characterize a CYP24A1 mutation in a young adult with bilateral nephrolithiasis and hypercalcemia associated with ingestion of excess vitamin D supplements and robust dairy intake for 5 years. Methods: CYP24A1 exons were sequenced from leukocyte DNA. Wild-type and mutant CYP24A1 cDNAs were expressed in JEG-3 cells, and 24OHase activity was assayed by a two-hybrid system. Results: The CYP24A1 missense mutation L409S was found on only one allele; no other mutation was found in exons or in at least 30 bp of each intron/exon junction. Based on assays of endogenous 24OHase activity and of activity from a transiently transfected CYP24A1 cDNA expression vector, JEG-3 cells were chosen over HepG2, Y1, MA10, and NCI-H295A cells for two-hybrid assays of 24OHase activity. The apparent Michaelis constant, Km(app), was 9.0 ± 2.0 nm for CYP24A1 and 8.6 ± 2.2 nm for its mutant; the apparent maximum velocity, Vmax(app), was 0.71 ± 0.055 d−1 for the wild type and 0.22 ± 0.026 d−1 for the mutant. As assessed by Vmax/Km, the L409S mutant has 32% of wild-type activity (P = .0012). Conclusions: The two-hybrid system in JEG-3 cells provides a simple, sensitive, quantitative assay of 24OHase activity. Heterozygous mutation of CYP24A1 may cause hypercalcemia in the setting of excessive vitamin D intake, but it is also possible that the patient had another, unidentified CYP24A1 mutation on the other allele. PMID:25375986

  7. Shared spatial effects on quantitative genetic parameters: accounting for spatial autocorrelation and home range overlap reduces estimates of heritability in wild red deer.

    PubMed

    Stopher, Katie V; Walling, Craig A; Morris, Alison; Guinness, Fiona E; Clutton-Brock, Tim H; Pemberton, Josephine M; Nussey, Daniel H

    2012-08-01

    Social structure, limited dispersal, and spatial heterogeneity in resources are ubiquitous in wild vertebrate populations. As a result, relatives share environments as well as genes, and environmental and genetic sources of similarity between individuals are potentially confounded. Quantitative genetic studies in the wild therefore typically account for easily captured shared environmental effects (e.g., parent, nest, or region). Fine-scale spatial effects are likely to be just as important in wild vertebrates, but have been largely ignored. We used data from wild red deer to build "animal models" to estimate additive genetic variance and heritability in four female traits (spring and rut home range size, offspring birth weight, and lifetime breeding success). We then, separately, incorporated spatial autocorrelation and a matrix of home range overlap into these models to estimate the effect of location or shared habitat on phenotypic variation. These terms explained a substantial amount of variation in all traits and their inclusion resulted in reductions in heritability estimates, up to an order of magnitude up for home range size. Our results highlight the potential of multiple covariance matrices to dissect environmental, social, and genetic contributions to phenotypic variation, and the importance of considering fine-scale spatial processes in quantitative genetic studies.

  8. Secular trends of infectious disease mortality in The Netherlands, 1911-1978: quantitative estimates of changes coinciding with the introduction of antibiotics.

    PubMed

    Mackenbach, J P; Looman, C W

    1988-09-01

    Secular trends of mortality from 21 infectious diseases in the Netherlands were studied by inspection of age/sex-standardized mortality curves and by log-linear regression analysis. An attempt was made to obtain quantitative estimates for changes coinciding with the introduction of antibiotics. Two possible types of effect were considered: a sharp reduction of mortality at the moment of the introduction of antibiotics, and a longer lasting (acceleration of) mortality decline after the introduction. Changes resembling the first type of effect were possibly present for many infectious diseases, but were difficult to measure exactly, due to late effects on mortality of World War II. Changes resembling the second type of effect were present in 16 infectious diseases and were sometimes quite large. For example, estimated differences in per cent per annum mortality change were 10% or larger for puerperal fever, scarlet fever, rheumatic fever, erysipelas, otitis media, tuberculosis, and bacillary dysentery. No acceleration of mortality decline after the introduction of antibiotics was present in mortality from 'all other diseases'. Although the exact contribution of antibiotics to the observed changes cannot be inferred from this time trend analysis, the quantitative estimates of the changes show that even a partial contribution would represent a substantial effect of antibiotics on mortality from infectious diseases in the Netherlands.

  9. Quantitative model of calcium/calmodulin-dependent protein kinase II activation

    NASA Astrophysics Data System (ADS)

    Mihalas, Stefan

    Calcium/calmodulin-dependent protein kinase II (CaMKII) is a key element in the calcium second messenger cascades that lead to long term potentiation (LTP) of synaptic strength. In this thesis, I have constructed kinetic models of activation of CaMKII and measured some of the unknown parameters of the model. I used the models to elucidate mechanisms of activation of CaMKII and to study the kinetics of its activation under conditions similar to those in dendritic spines.In chapter 2, I developed a new experimental method to rapidly stop the autophosphorylation reaction. I used this method to measure the catalytic turnover number of CaMKII. To quantitatively characterize CaMKII atophosphorylation in nonsaturating calcium, I also measured the autophosphorylation turnover number when CaMKII is activated by calmodulin mutants that can bind calcium ions only in either the amino or the carboxyl lobes.Previous models of CaMKII activation assumed that binding of calmodulins to individual CaMKII subunits is independent and that autophosphorylation occurs within a ring of 6 subunits. However, a recent structure of CaMKII suggests that pairs of subunits cooperate in binding calmodulin and raises the possibility that the autophosphorylation occurs within pairs of subunits. In chapter 3, I constructed a model in which CaMKII subunits cooperate in binding calmodulin. This model reconciled previous experimental results from the literature that appeared contradictory. In chapter 4, I constructed two models for CaMKII autophosphorylation, in which autophosphorylation can occur either in rings or pairs, and used them to design experiments aimed at differentiating between these possibilities. Previously published measurements and the measurements that I performed are more consistent with autophosphorylation occurring within pairs.In chapter 5, I constructed a model for simultaneous interactions among calcium, calmodulin, and CaMKII, and I used an automatic parameter search algorithm

  10. Identification of Hematomas in Mild Traumatic Brain Injury Using an Index of Quantitative Brain Electrical Activity

    PubMed Central

    Naunheim, Rosanne; Bazarian, Jeffrey; Mould, W. Andrew; Hanley, Daniel

    2015-01-01

    Abstract Rapid identification of traumatic intracranial hematomas following closed head injury represents a significant health care need because of the potentially life-threatening risk they present. This study demonstrates the clinical utility of an index of brain electrical activity used to identify intracranial hematomas in traumatic brain injury (TBI) presenting to the emergency department (ED). Brain electrical activity was recorded from a limited montage located on the forehead of 394 closed head injured patients who were referred for CT scans as part of their standard ED assessment. A total of 116 of these patients were found to be CT positive (CT+), of which 46 patients with traumatic intracranial hematomas (CT+) were identified for study. A total of 278 patients were found to be CT negative (CT−) and were used as controls. CT scans were subjected to quanitative measurements of volume of blood and distance of bleed from recording electrodes by blinded independent experts, implementing a validated method for hematoma measurement. Using an algorithm based on brain electrical activity developed on a large independent cohort of TBI patients and controls (TBI-Index), patients were classified as either positive or negative for structural brain injury. Sensitivity to hematomas was found to be 95.7% (95% CI=85.2, 99.5), specificity was 43.9% (95% CI=38.0, 49.9). There was no significant relationship between the TBI-Index and distance of the bleed from recording sites (F=0.044, p=0.833), or volume of blood measured F=0.179, p=0.674). Results of this study are a validation and extension of previously published retrospective findings in an independent population, and provide evidence that a TBI-Index for structural brain injury is a highly sensitive measure for the detection of potentially life-threatening traumatic intracranial hematomas, and could contribute to the rapid, quantitative evaluation and treatment of such patients. PMID:25054838

  11. Cortical neuron activation induced by electromagnetic stimulation: a quantitative analysis via modelling and simulation.

    PubMed

    Wu, Tiecheng; Fan, Jie; Lee, Kim Seng; Li, Xiaoping

    2016-02-01

    Previous simulation works concerned with the mechanism of non-invasive neuromodulation has isolated many of the factors that can influence stimulation potency, but an inclusive account of the interplay between these factors on realistic neurons is still lacking. To give a comprehensive investigation on the stimulation-evoked neuronal activation, we developed a simulation scheme which incorporates highly detailed physiological and morphological properties of pyramidal cells. The model was implemented on a multitude of neurons; their thresholds and corresponding activation points with respect to various field directions and pulse waveforms were recorded. The results showed that the simulated thresholds had a minor anisotropy and reached minimum when the field direction was parallel to the dendritic-somatic axis; the layer 5 pyramidal cells always had lower thresholds but substantial variances were also observed within layers; reducing pulse length could magnify the threshold values as well as the variance; tortuosity and arborization of axonal segments could obstruct action potential initiation. The dependence of the initiation sites on both the orientation and the duration of the stimulus implies that the cellular excitability might represent the result of the competition between various firing-capable axonal components, each with a unique susceptibility determined by the local geometry. Moreover, the measurements obtained in simulation intimately resemble recordings in physiological and clinical studies, which seems to suggest that, with minimum simplification of the neuron model, the cable theory-based simulation approach can have sufficient verisimilitude to give quantitatively accurate evaluation of cell activities in response to the externally applied field. PMID:26719168

  12. Localized heuristic inverse quantitative structure activity relationship with bulk descriptors using numerical gradients.

    PubMed

    Stålring, Jonna; Almeida, Pedro R; Carlsson, Lars; Helgee Ahlberg, Ernst; Hasselgren, Catrin; Boyer, Scott

    2013-08-26

    State-of-the-art quantitative structure-activity relationship (QSAR) models are often based on nonlinear machine learning algorithms, which are difficult to interpret. From a pharmaceutical perspective, QSARs are used to enhance the chemical design process. Ultimately, they should not only provide a prediction but also contribute to a mechanistic understanding and guide modifications to the chemical structure, promoting compounds with desirable biological activity profiles. Global ranking of descriptor importance and inverse QSAR have been used for these purposes. This paper introduces localized heuristic inverse QSAR, which provides an assessment of the relative ability of the descriptors to influence the biological response in an area localized around the predicted compound. The method is based on numerical gradients with parameters optimized using data sets sampled from analytical functions. The heuristic character of the method reduces the computational requirements and makes it applicable not only to fragment based methods but also to QSARs based on bulk descriptors. The application of the method is illustrated on congeneric QSAR data sets, and it is shown that the predicted influential descriptors can be used to guide structural modifications that affect the biological response in the desired direction. The method is implemented into the AZOrange Open Source QSAR package. The current implementation of localized heuristic inverse QSAR is a step toward a generally applicable method for elucidating the structure activity relationship specifically for a congeneric region of chemical space when using QSARs based on bulk properties. Consequently, this method could contribute to accelerating the chemical design process in pharmaceutical projects, as well as provide information that could enhance the mechanistic understanding for individual scaffolds.

  13. Quantitative phosphokinome analysis of the Met pathway activated by the invasin internalin B from Listeria monocytogenes.

    PubMed

    Reinl, Tobias; Nimtz, Manfred; Hundertmark, Claudia; Johl, Thorsten; Kéri, György; Wehland, Jürgen; Daub, Henrik; Jänsch, Lothar

    2009-12-01

    Stimulated by its physiological ligand, hepatocyte growth factor, the transmembrane receptor tyrosine kinase Met activates a signaling machinery that leads to mitogenic, motogenic, and morphogenic responses. Remarkably, the food-borne human pathogen Listeria monocytogenes also promotes autophosphorylation of Met through its virulence factor internalin B (InlB) and subsequently exploits Met signaling to induce phagocytosis into a broad range of host cells. Although the interaction between InlB and Met has been studied in detail, the signaling specificity of components involved in InlB-triggered cellular responses remains poorly characterized. The analysis of regulated phosphorylation events on protein kinases is therefore of particular relevance, although this could not as yet be characterized systematically by proteomics. Here, we implemented a new pyridopyrimidine-based strategy that enabled the efficient capture of a considerable subset of the human kinome in a robust one-step affinity chromatographic procedure. Additionally, and to gain functional insights into the InlB/Met-induced bacterial invasion process, a quantitative survey of the phosphorylation pattern of these protein kinases was accomplished. In total, the experimental design of this study comprises affinity chromatographic procedures for the systematic enrichment of kinases, as well as phosphopeptides; the quantification of all peptides based on the iTRAQ reporter system; and a rational statistical strategy to evaluate the quality of phosphosite regulations. With this improved chemical proteomics strategy, we determined and relatively quantified 143 phosphorylation sites detected on 94 human protein kinases. Interestingly, InlB-mediated signaling shows striking similarities compared with the natural ligand hepatocyte growth factor that was intensively studied in the past. In addition, this systematic approach suggests a new subset of protein kinases including Nek9, which are differentially

  14. Quantitative trait locus (QTL) mapping using different testers and independent population samples in maize reveals low power of QTL detection and large bias in estimates of QTL effects.

    PubMed Central

    Melchinger, A E; Utz, H F; Schön, C C

    1998-01-01

    The efficiency of marker-assisted selection (MAS) depends on the power of quantitative trait locus (QTL) detection and unbiased estimation of QTL effects. Two independent samples N = 344 and 107 of F2 plants were genotyped for 89 RFLP markers. For each sample, testcross (TC) progenies of the corresponding F3 lines with two testers were evaluated in four environments. QTL for grain yield and other agronomically important traits were mapped in both samples. QTL effects were estimated from the same data as used for detection and mapping of QTL (calibration) and, based on QTL positions from calibration, from the second, independent sample (validation). For all traits and both testers we detected a total of 107 QTL with N = 344, and 39 QTL with N = 107, of which only 20 were in common. Consistency of QTL effects across testers was in agreement with corresponding genotypic correlations between the two TC series. Most QTL displayed no significant QTL x environment nor epistatic interactions. Estimates of the proportion of the phenotypic and genetic variance explained by QTL were considerably reduced when derived from the independent validation sample as opposed to estimates from the calibration sample. We conclude that, unless QTL effects are estimated from an independent sample, they can be inflated, resulting in an overly optimistic assessment of the efficiency of MAS. PMID:9584111

  15. Quantitative Estimates of the Social Benefits of Learning, 2: Health (Depression and Obesity). Wider Benefits of Learning Research Report.

    ERIC Educational Resources Information Center

    Feinstein, Leon

    This report used information from two United Kingdom national cohorts to estimate the magnitude of the effects of learning on depression and obesity. Members of the two cohorts were surveyed in 1999-00, when those in the 1970 cohort were age 33 years and those in the 1958 cohort were age 42 years. Overall, education was an important risk factor…

  16. A Concurrent Mixed Methods Approach to Examining the Quantitative and Qualitative Meaningfulness of Absolute Magnitude Estimation Scales in Survey Research

    ERIC Educational Resources Information Center

    Koskey, Kristin L. K.; Stewart, Victoria C.

    2014-01-01

    This small "n" observational study used a concurrent mixed methods approach to address a void in the literature with regard to the qualitative meaningfulness of the data yielded by absolute magnitude estimation scaling (MES) used to rate subjective stimuli. We investigated whether respondents' scales progressed from less to more and…

  17. Deep neural nets as a method for quantitative structure-activity relationships.

    PubMed

    Ma, Junshui; Sheridan, Robert P; Liaw, Andy; Dahl, George E; Svetnik, Vladimir

    2015-02-23

    Neural networks were widely used for quantitative structure-activity relationships (QSAR) in the 1990s. Because of various practical issues (e.g., slow on large problems, difficult to train, prone to overfitting, etc.), they were superseded by more robust methods like support vector machine (SVM) and random forest (RF), which arose in the early 2000s. The last 10 years has witnessed a revival of neural networks in the machine learning community thanks to new methods for preventing overfitting, more efficient training algorithms, and advancements in computer hardware. In particular, deep neural nets (DNNs), i.e. neural nets with more than one hidden layer, have found great successes in many applications, such as computer vision and natural language processing. Here we show that DNNs can routinely make better prospective predictions than RF on a set of large diverse QSAR data sets that are taken from Merck's drug discovery effort. The number of adjustable parameters needed for DNNs is fairly large, but our results show that it is not necessary to optimize them for individual data sets, and a single set of recommended parameters can achieve better performance than RF for most of the data sets we studied. The usefulness of the parameters is demonstrated on additional data sets not used in the calibration. Although training DNNs is still computationally intensive, using graphical processing units (GPUs) can make this issue manageable.

  18. Deep neural nets as a method for quantitative structure-activity relationships.

    PubMed

    Ma, Junshui; Sheridan, Robert P; Liaw, Andy; Dahl, George E; Svetnik, Vladimir

    2015-02-23

    Neural networks were widely used for quantitative structure-activity relationships (QSAR) in the 1990s. Because of various practical issues (e.g., slow on large problems, difficult to train, prone to overfitting, etc.), they were superseded by more robust methods like support vector machine (SVM) and random forest (RF), which arose in the early 2000s. The last 10 years has witnessed a revival of neural networks in the machine learning community thanks to new methods for preventing overfitting, more efficient training algorithms, and advancements in computer hardware. In particular, deep neural nets (DNNs), i.e. neural nets with more than one hidden layer, have found great successes in many applications, such as computer vision and natural language processing. Here we show that DNNs can routinely make better prospective predictions than RF on a set of large diverse QSAR data sets that are taken from Merck's drug discovery effort. The number of adjustable parameters needed for DNNs is fairly large, but our results show that it is not necessary to optimize them for individual data sets, and a single set of recommended parameters can achieve better performance than RF for most of the data sets we studied. The usefulness of the parameters is demonstrated on additional data sets not used in the calibration. Although training DNNs is still computationally intensive, using graphical processing units (GPUs) can make this issue manageable. PMID:25635324

  19. Quantitative structure-activity relationships and ecological risk assessment: an overview of predictive aquatic toxicology research.

    PubMed

    Bradbury, S P

    1995-09-01

    In the field of aquatic toxicology, quantitative structure-activity relationships (QSARs) have developed as scientifically credible tools for predicting the toxicity of chemicals when little or no empirical data are available. A fundamental understanding of toxicological principles has been considered an important component to the acceptance and application of QSAR approaches as biologically relevant in ecological risk assessments. As a consequence, there has been an evolution of QSAR development and application from that of a chemical-class perspective to one that is more consistent with assumptions regarding modes of toxic action. In this review, techniques to assess modes of toxic action from chemical structure are discussed, with consideration that toxicodynamic knowledge bases must be clearly defined with regard to exposure regimes, biological models/endpoints and compounds that adequately span the diversity of chemicals anticipated for future applications. With such knowledge bases, classification systems, including rule-based expert systems, have been established for use in predictive aquatic toxicology applications. The establishment of QSAR techniques that are based on an understanding of toxic mechanisms is needed to provide a link to physiologically based toxicokinetic and toxicodynamic models, which can provide the means to extrapolate adverse effects across species and exposure regimes. PMID:7570660

  20. Quantitative structure-activity relationships for chemical toxicity to environmental bacteria

    SciTech Connect

    Blum, D.J.; Speece, R.E. )

    1991-10-01

    Quantitative structure-activity relationships (QSARs) were developed for nonreactive chemical toxicity to each of four groups of bacteria of importance in environmental engineering: aerobic heterotrophs, methanogens, Nitrosomonas, and Microtox. The QSARs were based on chemicals covering a range of structures and including important environmental pollutants (i.e., chlorinated and other substituted benzenes, phenols, and aliphatic hydrocarbons). QSARs were developed for each chemical class and for combinations of chemical classes. Three QSAR methods (groups of chemical describing parameters) were evaluated for their accuracy and ease of use: log P, linear solvation energy relationships (LSER), and molecular connectivity. Successful QSARs were found for each group of bacteria and by each method, with correlation coefficients (adjusted r2) between 0.79 and 0.95. LSER QSARs incorporated the widest range of chemicals with the greatest accuracy. Log P and molecular connectivity QSARs are easier to use because their parameters are readily available. Outliers from the QSARs likely due to reactive toxicity included acryls, low pKa compounds, and aldehydes. Nitro compounds and chlorinated aliphatic hydrocarbons and alcohols showed enhanced toxicity to the methanogens only. Chemicals with low IC50 concentrations (log IC50 mumol/liter less than 1.5) were often outliers for Nitrosomonas. QSARs were validated statistically and with literature data. A suggested method is provided for use of the QSARs.

  1. Toxicity of ionic liquids: database and prediction via quantitative structure-activity relationship method.

    PubMed

    Zhao, Yongsheng; Zhao, Jihong; Huang, Ying; Zhou, Qing; Zhang, Xiangping; Zhang, Suojiang

    2014-08-15

    A comprehensive database on toxicity of ionic liquids (ILs) is established. The database includes over 4000 pieces of data. Based on the database, the relationship between IL's structure and its toxicity has been analyzed qualitatively. Furthermore, Quantitative Structure-Activity relationships (QSAR) model is conducted to predict the toxicities (EC50 values) of various ILs toward the Leukemia rat cell line IPC-81. Four parameters selected by the heuristic method (HM) are used to perform the studies of multiple linear regression (MLR) and support vector machine (SVM). The squared correlation coefficient (R(2)) and the root mean square error (RMSE) of training sets by two QSAR models are 0.918 and 0.959, 0.258 and 0.179, respectively. The prediction R(2) and RMSE of QSAR test sets by MLR model are 0.892 and 0.329, by SVM model are 0.958 and 0.234, respectively. The nonlinear model developed by SVM algorithm is much outperformed MLR, which indicates that SVM model is more reliable in the prediction of toxicity of ILs. This study shows that increasing the relative number of O atoms of molecules leads to decrease in the toxicity of ILs.

  2. Blood-brain barrier permeability mechanisms in view of quantitative structure-activity relationships (QSAR).

    PubMed

    Bujak, Renata; Struck-Lewicka, Wiktoria; Kaliszan, Michał; Kaliszan, Roman; Markuszewski, Michał J

    2015-04-10

    The goal of the present paper was to develop a quantitative structure-activity relationship (QSAR) method using a simple statistical approach, such as multiple linear regression (MLR) for predicting the blood-brain barrier (BBB) permeability of chemical compounds. The "best" MLR models, comprised logP and either molecular mass (M) or isolated atomic energy (E(isol)), tested on a structurally diverse set of 66 compounds, is characterized the by correlation coefficients (R) around 0.8. The obtained models were validated using leave-one-out (LOO) cross-validation technique and the correlation coefficient of leave-one-out- R(LOO)(2) (Q(2)) was at least 0.6. Analysis of a case from legal medicine demonstrated informative value of our QSAR model. To best authors' knowledge the present study is a first application of the developed QSAR models of BBB permeability to case from the legal medicine. Our data indicate that molecular energy-related descriptors, in combination with the well-known descriptors of lipophilicity may have a supportive value in predicting blood-brain distribution, which is of utmost importance in drug development and toxicological studies.

  3. Quantitative structure-activity relationships for weak acid respiratory uncouplers to Vibrio fisheri

    SciTech Connect

    Schultz, T.W.; Cronin, M.T.D.

    1997-02-01

    Acute toxicity values of 16 organic compounds thought to elicit their response via the weak acid respiratory uncoupling mechanism of toxic action were secured from the literature. Regression analysis of toxicities revealed that a measured 5-min V. fisheri potency value can be used as a surrogate for the 30-min value. Regression analysis of toxicity versus hydrophobicity, measured as the 1-octanol/water partition coefficient (log K{sub ow}), was used to formulate a quantitative structure-activity relationship (QSAR). The equation log pT{sub 30}{sup {minus}1} = 0.489(log K{sub ow}) + 0.126 was found to be a highly predictive model. This V. fisheri QSAR is statistically similar to QSARs generated from weak acid uncoupler potency data for Pimephales promelas survivability and Tetrahymena pyriformis population growth impairment. This work, therefore, suggests that the weak acid respiratory uncoupling mechanism of toxic action is present in V. fisheri, and as such is not restricted to mitochondria-containing organisms.

  4. A field instrument for quantitative determination of beryllium by activation analysis

    USGS Publications Warehouse

    Vaughn, William W.; Wilson, E.E.; Ohm, J.M.

    1960-01-01

    A low-cost instrument has been developed for quantitative determinations of beryllium in the field by activation analysis. The instrument makes use of the gamma-neutron reaction between gammas emitted by an artificially radioactive source (Sb124) and beryllium as it occurs in nature. The instrument and power source are mounted in a panel-type vehicle. Samples are prepared by hand-crushing the rock to approximately ?-inch mesh size and smaller. Sample volumes are kept constant by means of a standard measuring cup. Instrument calibration, made by using standards of known BeO content, indicates the analyses are reproducible and accurate to within ? 0.25 percent BeO in the range from 1 to 20 percent BeO with a sample counting time of 5 minutes. Sensitivity of the instrument maybe increased somewhat by increasing the source size, the sample size, or by enlarging the cross-sectional area of the neutron-sensitive phosphor normal to the neutron flux.

  5. Apparent Polyploidization after Gamma Irradiation: Pitfalls in the Use of Quantitative Polymerase Chain Reaction (qPCR) for the Estimation of Mitochondrial and Nuclear DNA Gene Copy Numbers

    PubMed Central

    Kam, Winnie W. Y.; Lake, Vanessa; Banos, Connie; Davies, Justin; Banati, Richard

    2013-01-01

    Quantitative polymerase chain reaction (qPCR) has been widely used to quantify changes in gene copy numbers after radiation exposure. Here, we show that gamma irradiation ranging from 10 to 100 Gy of cells and cell-free DNA samples significantly affects the measured qPCR yield, due to radiation-induced fragmentation of the DNA template and, therefore, introduces errors into the estimation of gene copy numbers. The radiation-induced DNA fragmentation and, thus, measured qPCR yield varies with temperature not only in living cells, but also in isolated DNA irradiated under cell-free conditions. In summary, the variability in measured qPCR yield from irradiated samples introduces a significant error into the estimation of both mitochondrial and nuclear gene copy numbers and may give spurious evidence for polyploidization. PMID:23722662

  6. On Using WWLLN Observations as Starting Information for the Quantitative Schumann Resonance Monitoring of Global Lightning Activity

    NASA Astrophysics Data System (ADS)

    Mushtak, V. C.; Guha, A.; Williams, E.

    2013-12-01

    , and exploring this variability, along with quantitative source strengths, is one of the major objectives of this study. The problem has been resolved by the exploitation of the WWLLN stroke location data for initial guesses of the spatial parameters of the source model, with electromagnetic observations (SR modal characteristics) used for estimating the initial relative contributions - and, hence, source strengths - of individual chimneys. Using data from nine SR stations scattered over the globe from the Arctic to Antarctica and from USA to India to Japan, the effectiveness of the technique has now been tested and confirmed. It has been shown that, with the relative hour-by-hour source strengths of the chimneys estimated from the whole net of the SR stations, the temporal variations of these activities as ';seen' from individual stations correlate with coefficients up to 0.8, thereby confirming the objectivity of the approach and the suitability of the initial guesses for further ';full-gear' SR inversion. As an additional benefit of this study, the quality of the absolute calibrations at individual stations has been assessed and compared.

  7. Quantitative estimation of climatic parameters from vegetation data in North America by the mutual climatic range technique

    USGS Publications Warehouse

    Anderson, Katherine H.; Bartlein, Patrick J.; Strickland, Laura E.; Pelltier, Richard T.; Thompson, Robert S.; Shafer, Sarah L.

    2012-01-01

    The mutual climatic range (MCR) technique is perhaps the most widely used method for estimating past climatic parameters from fossil assemblages, largely because it can be conducted on a simple list of the taxa present in an assemblage. When applied to plant macrofossil data, this unweighted approach (MCRun) will frequently identify a large range for a given climatic parameter where the species in an assemblage can theoretically live together. To narrow this range, we devised a new weighted approach (MCRwt) that employs information from the modern relations between climatic parameters and plant distributions to lessen the influence of the "tails" of the distributions of the climatic data associated with the taxa in an assemblage. To assess the performance of the MCR approaches, we applied them to a set of modern climatic data and plant distributions on a 25-km grid for North America, and compared observed and estimated climatic values for each grid point. In general, MCRwt was superior to MCRun in providing smaller anomalies, less bias, and better correlations between observed and estimated values. However, by the same measures, the results of Modern Analog Technique (MAT) approaches were superior to MCRwt. Although this might be reason to favor MAT approaches, they are based on assumptions that may not be valid for paleoclimatic reconstructions, including that: 1) the absence of a taxon from a fossil sample is meaningful, 2) plant associations were largely unaffected by past changes in either levels of atmospheric carbon dioxide or in the seasonal distributions of solar radiation, and 3) plant associations of the past are adequately represented on the modern landscape. To illustrate the application of these MCR and MAT approaches to paleoclimatic reconstructions, we applied them to a Pleistocene paleobotanical assemblage from the western United States. From our examinations of the estimates of modern and past climates from vegetation assemblages, we conclude that

  8. Quantitative estimation of granitoid composition from thermal infrared multispectral scanner (TIMS) data, Desolation Wilderness, northern Sierra Nevada, California

    NASA Technical Reports Server (NTRS)

    Sabine, Charles; Realmuto, Vincent J.; Taranik, James V.

    1994-01-01

    We have produced images that quantitatively depict modal and chemical parameters of granitoids using an image processing algorithm called MINMAP that fits Gaussian curves to normalized emittance spectra recovered from thermal infrared multispectral scanner (TIMS) radiance data. We applied the algorithm to TIMS data from the Desolation Wilderness, an extensively glaciated area near the northern end of the Sierra Nevada batholith that is underlain by Jurassic and Cretaceous plutons that range from diorite and anorthosite to leucogranite. The wavelength corresponding to the calculated emittance minimum lambda(sub min) varies linearly with quartz content, SiO2, and other modal and chemical parameters. Thematic maps of quartz and silica content derived from lambda(sub min) values distinguish bodies of diorite from surrounding granite, identify outcrops of anorthosite, and separate felsic, intermediate, and mafic rocks.

  9. Orange/Red Fluorescence of Active Caries by Retrospective Quantitative Light-Induced Fluorescence Image Analysis.

    PubMed

    Felix Gomez, Grace; Eckert, George J; Ferreira Zandona, Andrea

    2016-01-01

    This retrospective clinical study determined the association of caries activity and orange/red fluorescence on quantitative light-induced fluorescence (QLF) images of surfaces that progressed to cavitation, as determined by clinical visual examination. A random sample of QLF images from 565 children (5-13 years) previously enrolled in a longitudinal study was selected. Buccal, lingual and occlusal surface images obtained after professional brushing at baseline and every 4 months over a 4-year period were analyzed for red fluorescence. Surfaces that progressed (n = 224) to cavitation according to the International Caries Detection and Assessment System (ICDAS 0/1/2/3/4 to 5/6 or filling), and surfaces that did not progress (n = 486) were included. QA2 image analysis software outputs the percentage increase of the red/green components as x0394;R and area of x0394;R (areax0394;R) at different thresholds. Mixed-model ANOVA was used to compare progressive and nonprogressive surfaces to account for correlations of red fluorescence (x0394;R and areax0394;R) between surfaces within a subject. The first analysis used the first observation for each surface or the first available visit if the surface was unerupted (baseline), while the second analysis used the last observation prior to cavitation for surfaces that progressed and the last observation for surfaces that did not progress (final). There was a significant (p < 0.05) association between red fluorescence and progression to cavitation at thresholds x0394;R0, x0394;R10, x0394;R20, x0394;R60, x0394;R70, x0394;R80, x0394;R90 and x0394;Rmax at baseline and for x0394;R0 and x0394;R10 at the final observation. Quantification of orange/red fluorescence may help to identify lesions that progress to cavitation. Future studies identifying microbiological factors causing orange/ red fluorescence and its caries activity are indicated. PMID:27160323

  10. Polychlorinated biphenyls: correlation between in vivo and in vitro quantitative structure-activity relationships (QSARs)

    SciTech Connect

    Leece, B.; Denomme, M.A.; Towner, R.; Li, S.M.A.; Safe, S.

    1985-01-01

    The in vivo quantitative structure-activity relationships (QSARs) for several polychlorinated biphenyls (PCBs) were determined in the immature male Wistar rat. The ED25 and ED50 values for hepatic microsomal aryl hydrocarbon hydroxylase (AHH) and ethoxyresorufin O-deethylase (EROD) induction as well as for body weight loss and for thymic atrophy were determined for nine PCB congeners and 4'-bromo-2,3,4,5-tetrachlorobiphenyl. The most active compounds were the coplanar PCB congeners, 3,3',4,4',5-penta- and 3,3',4,4',5,5'-hexachlorobiphenyl; for example, their ED50 values for body weight loss were 3.25 and 15.1 ..mu..mol/kg, respectively. The in vivo toxicity of the coplanar PCB, 3,3',4,4'-tetrachlorobiphenyl, was significantly lower (ED50 for body weight loss = 730 ..mu..mol/kg) than the values observed for the more highly chlorinated homologs, and this was consistent with the more rapid metabolism of the lower chlorinated congener. The dose-response biologic and toxic effects of several mono-ortho-chloro-substituted analogs of the coplanar PCBs, including 2,3,4,4',5-, 2,3,3',4,4'-, 2',3,4,4',5- and 2,3',4,4',5-penta-, 2,3,3',4,4',5- and 2,3,3',4,4',5-hexachlorobiphenyl were also determined, and members of this group of compounds were all less toxic than 3,3',4,4',5-penta and 3,3',4,4',5,5'-hexachlorobiphenyl. There was a good rank order correlation between the in vivo QSAR data and the in vitro QSAR data and the in vitro QSARs for PCBs that were developed from their relative receptor binding affinities and potencies as inducers of AHH and EROD in rat hepatoma H-4-II E cells in culture.

  11. Quantitative estimation of the spin-wave features supported by a spin-torque-driven magnetic waveguide

    NASA Astrophysics Data System (ADS)

    Consolo, Giancarlo; Currò, Carmela; Valenti, Giovanna

    2014-12-01

    The main features of the spin-waves excited at the threshold via spin-polarized currents in a one-dimensional normally-to-plane magnetized waveguide are quantitatively determined both analytically and numerically. In particular, the dependence of the threshold current, frequency, wavenumber, and decay length is investigated as a function of the size of the nanocontact area through which the electric current is injected. From the analytical viewpoint, such a goal has required to solve the linearized Landau-Lifshitz-Gilbert-Slonczewski equation together with boundary and matching conditions associated with the waveguide geometry. Owing to the complexity of the resulting transcendent system, particular solutions have been obtained in the cases of elongated and contracted nanocontacts. These results have been successfully compared with those arising from numerical integration of the abovementioned transcendent system and with micromagnetic simulations. This quantitative agreement has been achieved thanks to the model here considered which takes explicitly into account the diagonal demagnetizing factors of a rectangular prism as well as the dependence of the relaxation rate on the wavenumber. Our analysis confirmed that the spin-wave features supported by such a waveguide geometry are significantly different from the ones observed in classical two-dimensional nanocontact devices. Moreover, it has been proved that the characteristic parameters depend strongly on the material properties and on the modulus of external field, but they could be independent of the nanocontact length. Finally, it is shown that spin-transfer oscillators based on contracted nanocontacts have a better capability to transmit spin-waves over large distances.

  12. Quantitative estimation of the spin-wave features supported by a spin-torque-driven magnetic waveguide

    SciTech Connect

    Consolo, Giancarlo Currò, Carmela; Valenti, Giovanna

    2014-12-07

    The main features of the spin-waves excited at the threshold via spin-polarized currents in a one-dimensional normally-to-plane magnetized waveguide are quantitatively determined both analytically and numerically. In particular, the dependence of the threshold current, frequency, wavenumber, and decay length is investigated as a function of the size of the nanocontact area through which the electric current is injected. From the analytical viewpoint, such a goal has required to solve the linearized Landau-Lifshitz-Gilbert-Slonczewski equation together with boundary and matching conditions associated with the waveguide geometry. Owing to the complexity of the resulting transcendent system, particular solutions have been obtained in the cases of elongated and contracted nanocontacts. These results have been successfully compared with those arising from numerical integration of the abovementioned transcendent system and with micromagnetic simulations. This quantitative agreement has been achieved thanks to the model here considered which takes explicitly into account the diagonal demagnetizing factors of a rectangular prism as well as the dependence of the relaxation rate on the wavenumber. Our analysis confirmed that the spin-wave features supported by such a waveguide geometry are significantly different from the ones observed in classical two-dimensional nanocontact devices. Moreover, it has been proved that the characteristic parameters depend strongly on the material properties and on the modulus of external field, but they could be independent of the nanocontact length. Finally, it is shown that spin-transfer oscillators based on contracted nanocontacts have a better capability to transmit spin-waves over large distances.

  13. A meta-analysis of neuroimaging studies on divergent thinking using activation likelihood estimation.

    PubMed

    Wu, Xin; Yang, Wenjing; Tong, Dandan; Sun, Jiangzhou; Chen, Qunlin; Wei, Dongtao; Zhang, Qinglin; Zhang, Meng; Qiu, Jiang

    2015-07-01

    In this study, an activation likelihood estimation (ALE) meta-analysis was used to conduct a quantitative investigation of neuroimaging studies on divergent thinking. Based on the ALE results, the functional magnetic resonance imaging (fMRI) studies showed that distributed brain regions were more active under divergent thinking tasks (DTTs) than those under control tasks, but a large portion of the brain regions were deactivated. The ALE results indicated that the brain networks of the creative idea generation in DTTs may be composed of the lateral prefrontal cortex, posterior parietal cortex [such as the inferior parietal lobule (BA 40) and precuneus (BA 7)], anterior cingulate cortex (ACC) (BA 32), and several regions in the temporal cortex [such as the left middle temporal gyrus (BA 39), and left fusiform gyrus (BA 37)]. The left dorsolateral prefrontal cortex (BA 46) was related to selecting the loosely and remotely associated concepts and organizing them into creative ideas, whereas the ACC (BA 32) was related to observing and forming distant semantic associations in performing DTTs. The posterior parietal cortex may be involved in the semantic information related to the retrieval and buffering of the formed creative ideas, and several regions in the temporal cortex may be related to the stored long-term memory. In addition, the ALE results of the structural studies showed that divergent thinking was related to the dopaminergic system (e.g., left caudate and claustrum). Based on the ALE results, both fMRI and structural MRI studies could uncover the neural basis of divergent thinking from different aspects (e.g., specific cognitive processing and stable individual difference of cognitive capability).

  14. Hawaii Clean Energy Initiative (HCEI) Scenario Analysis: Quantitative Estimates Used to Facilitate Working Group Discussions (2008-2010)

    SciTech Connect

    Braccio, R.; Finch, P.; Frazier, R.

    2012-03-01

    This report provides details on the Hawaii Clean Energy Initiative (HCEI) Scenario Analysis to identify potential policy options and evaluate their impact on reaching the 70% HECI goal, present possible pathways to attain the goal based on currently available technology, with an eye to initiatives under way in Hawaii, and provide an 'order-of-magnitude' cost estimate and a jump-start to action that would be adjusted with a better understanding of the technologies and market.

  15. A new computational scheme on quantitative inner pipe boundary identification based on the estimation of effective thermal conductivity

    NASA Astrophysics Data System (ADS)

    Fan, Chunli; Sun, Fengrui; Yang, Li

    2008-10-01

    In the paper, the irregular configuration of the inner pipe boundary is identified based on the estimation of the circumferential distribution of the effective thermal conductivity of pipe wall. In order to simulate the true temperature measurement in the numerical examples, the finite element method is used to calculate the temperature distribution at the outer pipe surface based on the irregular shaped inner pipe boundary to be determined. Then based on this simulated temperature distribution the inverse identification work is conducted by employing the modified one-dimensional correction method, along with the finite volume method, to estimate the circumferential distribution of the effective thermal conductivity of the pipe wall. Thereafter, the inner pipe boundary shape is calculated based on the conductivity estimation result. A series of numerical experiments with different temperature measurement errors and different thermal conductivities of pipe wall have certified the effectiveness of the method. It is proved that the method is a simple, fast and accurate one for this inverse heat conduction problem.

  16. Estimating Physical Activity in Youth Using a Wrist Accelerometer

    PubMed Central

    Crouter, Scott E.; Flynn, Jennifer I.; Bassett, David R.

    2014-01-01

    PURPOSE The purpose of this study was to develop and validate methods for analyzing wrist accelerometer data in youth. METHODS 181 youth (mean±SD; age, 12.0±1.5 yrs) completed 30-min of supine rest and 8-min each of 2 to 7 structured activities (selected from a list of 25). Receiver Operator Characteristic (ROC) curves and regression analyses were used to develop prediction equations for energy expenditure (child-METs; measured activity VO2 divided by measured resting VO2) and cut-points for computing time spent in sedentary behaviors (SB), light (LPA), moderate (MPA), and vigorous (VPA) physical activity. Both vertical axis (VA) and vector magnitude (VM) counts per 5 seconds were used for this purpose. The validation study included 42 youth (age, 12.6±0.8 yrs) who completed approximately 2-hrs of unstructured PA. During all measurements, activity data were collected using an ActiGraph GT3X or GT3X+, positioned on the dominant wrist. Oxygen consumption was measured using a Cosmed K4b2. Repeated measures ANOVAs were used to compare measured vs predicted child-METs (regression only), and time spent in SB, LPA, MPA, and VPA. RESULTS All ROC cut-points were similar for area under the curve (≥0.825), sensitivity (≥0.756), and specificity (≥0.634) and they significantly underestimated LPA and overestimated VPA (P<0.05). The VA and VM regression models were within ±0.21 child-METs of mean measured child-METs and ±2.5 minutes of measured time spent in SB, LPA, MPA, and VPA, respectively (P>0.05). CONCLUSION Compared to measured values, the VA and VM regression models developed on wrist accelerometer data had insignificant mean bias for child-METs and time spent in SB, LPA, MPA, and VPA; however they had large individual errors. PMID:25207928

  17. Quantitative estimation of farmland soil loss by wind-erosion using improved particle-size distribution comparison method (IPSDC)

    NASA Astrophysics Data System (ADS)

    Rende, Wang; Zhongling, Guo; Chunping, Chang; Dengpan, Xiao; Hongjun, Jiang

    2015-12-01

    The rapid and accurate estimation of soil loss by wind erosion still remains challenge. This study presents an improved scheme for estimating the soil loss by wind erosion of farmland. The method estimates the soil loss by wind erosion based on a comparison of the relative contents of erodible and non-erodible particles between the surface and sub-surface layers of the farmland ploughed layer after wind erosion. It is based on the features that the soil particle-size distribution of the sampling soil layer (approximately 2 cm) is relatively uniform, and that on the surface layer, wind erosion causes the relative numbers of erodible and non-erodible particles to decrease and increase, respectively. Estimations were performed using this method for the wind erosion periods (WEP) from Oct. of 2012 to May of 2013 and from Oct. of 2013 to April of 2014 and a large wind-erosion event (WEE) on May 3, 2014 in the Bashang area of Hebei Province. The results showed that the average soil loss of farmland by wind erosion from Oct. of 2012 to May of 2013 was 2852.14 g/m2 with an average depth of 0.21 cm, while soil loss by wind from Oct. of 2013 to April of 2014 was 1199.17 g/m2 with a mean depth of 0.08 cm. During the severe WEE on May 3, 2014, the average soil loss of farmland by wind erosion was 1299.19 g/m2 with an average depth of 0.10 cm. The soil loss by wind erosion of ploughed and raked fields (PRF) was approximately twice as large as that of oat-stubble fields (OSF). The improved method of particle-size distribution comparison (IPSDC) has several advantages. It can not only calculate the wind erosion amount, but also the wind deposition amount. Slight changes in the sampling thickness and in the particle diameter range of the non-erodible particles will not obviously influence the results. Furthermore, the method is convenient, rapid, simple to implement. It is suitable for estimating the soil loss or deposition by wind erosion of farmland with flat surfaces and high

  18. Development of response surface methodology for optimization of extraction parameters and quantitative estimation of embelin from Embelia ribes Burm by high performance liquid chromatography

    PubMed Central

    Alam, Md. Shamsir; Damanhouri, Zoheir A.; Ahmad, Aftab; Abidin, Lubna; Amir, Mohd; Aqil, Mohd; Khan, Shah Alam; Mujeeb, Mohd

    2015-01-01

    Background: Embelia ribes Burm is widely used medicinal plant for the treatment of different types of disorders in the Indian traditional systems of medicine. Objective: The present work was aimed to optimize the extraction parameters of embelin from E. ribes fruits and also to quantify embelin content in different extracts of the plant. Materials and Methods: Optimization of extraction parameters such as solvent: drug ratio, temperature and time were carried out by response surface methodology (RSM). Quantitative estimation of embelin in different extracts of E. ribes fruits was done through high performance liquid chromatography. Results: The optimal conditions determined for extraction of embelin through RSM were; extraction time (27.50 min), extraction temperature 45°C and solvent: drug ratio (8:1). Under the optimized conditions, the embelin yield (32.71%) was equitable to the expected yield (31.07%, P > 0.05). These results showed that the developed model is satisfactory and suitable for the extraction process of embelin. The analysis of variance showed a high goodness of model fit and the accomplishment of the RSM method for improving embelin extraction from the fruits of E. ribes. Conclusion: It is concluded that this may be a useful method for the extraction and quantitative estimation of embelin from the fruits of E. ribes. PMID:26109763

  19. A quantitative structure-activity relationship to predict efficacy of granular activated carbon adsorption to control emerging contaminants.

    PubMed

    Kennicutt, A R; Morkowchuk, L; Krein, M; Breneman, C M; Kilduff, J E

    2016-08-01

    A quantitative structure-activity relationship was developed to predict the efficacy of carbon adsorption as a control technology for endocrine-disrupting compounds, pharmaceuticals, and components of personal care products, as a tool for water quality professionals to protect public health. Here, we expand previous work to investigate a broad spectrum of molecular descriptors including subdivided surface areas, adjacency and distance matrix descriptors, electrostatic partial charges, potential energy descriptors, conformation-dependent charge descriptors, and Transferable Atom Equivalent (TAE) descriptors that characterize the regional electronic properties of molecules. We compare the efficacy of linear (Partial Least Squares) and non-linear (Support Vector Machine) machine learning methods to describe a broad chemical space and produce a user-friendly model. We employ cross-validation, y-scrambling, and external validation for quality control. The recommended Support Vector Machine model trained on 95 compounds having 23 descriptors offered a good balance between good performance statistics, low error, and low probability of over-fitting while describing a wide range of chemical features. The cross-validated model using a log-uptake (qe) response calculated at an aqueous equilibrium concentration (Ce) of 1 μM described the training dataset with an r(2) of 0.932, had a cross-validated r(2) of 0.833, and an average residual of 0.14 log units. PMID:27586364

  20. Quantitative structure-activity relationship modelling of oral acute toxicity and cytotoxic activity of fragrance materials in rodents.

    PubMed

    Papa, E; Luini, M; Gramatica, P

    2009-10-01

    Fragrance materials are used as ingredients in many consumer and personal care products. The wide and daily use of these substances, as well as their mainly uncontrolled discharge through domestic sewage, make fragrance materials both potential indoor and outdoor air pollutants which are also connected to possible toxic effects on humans (asthma, allergies, headaches). Unfortunately, little is known about the environmental fate and toxicity of these substances. However, the use of alternative, predictive approaches, such as quantitative structure-activity relationships (QSARs), can help in filling the data gap and in the characterization of the environmental and toxicological profile of these substances. In the proposed study, ordinary least squares regression-based QSAR models were developed for three toxicological endpoints: mouse oral LD(50), inhibition of NADH-oxidase (EC(50) NADH-Ox) and the effect on mitochondrial membrane potential (EC(50) DeltaPsim). Theoretical molecular descriptors were calculated by using DRAGON software, and the best QSAR models were developed according to the principles defined by the Organization for Economic Co-operation and Development.

  1. A quantitative structure-activity relationship to predict efficacy of granular activated carbon adsorption to control emerging contaminants.

    PubMed

    Kennicutt, A R; Morkowchuk, L; Krein, M; Breneman, C M; Kilduff, J E

    2016-08-01

    A quantitative structure-activity relationship was developed to predict the efficacy of carbon adsorption as a control technology for endocrine-disrupting compounds, pharmaceuticals, and components of personal care products, as a tool for water quality professionals to protect public health. Here, we expand previous work to investigate a broad spectrum of molecular descriptors including subdivided surface areas, adjacency and distance matrix descriptors, electrostatic partial charges, potential energy descriptors, conformation-dependent charge descriptors, and Transferable Atom Equivalent (TAE) descriptors that characterize the regional electronic properties of molecules. We compare the efficacy of linear (Partial Least Squares) and non-linear (Support Vector Machine) machine learning methods to describe a broad chemical space and produce a user-friendly model. We employ cross-validation, y-scrambling, and external validation for quality control. The recommended Support Vector Machine model trained on 95 compounds having 23 descriptors offered a good balance between good performance statistics, low error, and low probability of over-fitting while describing a wide range of chemical features. The cross-validated model using a log-uptake (qe) response calculated at an aqueous equilibrium concentration (Ce) of 1 μM described the training dataset with an r(2) of 0.932, had a cross-validated r(2) of 0.833, and an average residual of 0.14 log units.

  2. Three dimensional quantitative structure-activity relationships of sulfonamides binding monoclonal antibody by comparative molecular field analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The three-dimensional quantitative structure-activity relationship (3D-QSAR) model of sulfonamide analogs, binding a monoclonal antibody (MabSMR) produced against sulfamerazine was carried out by comparative molecular field analysis (CoMFA). The affinities of MabSMR, expressed as Log10IC50, for 17 ...

  3. A semianalytical algorithm for quantitatively estimating sediment and atmospheric deposition flux from MODIS-derived sea ice albedo in the Bohai Sea, China

    NASA Astrophysics Data System (ADS)

    Xu, Zhantang; Hu, Shuibo; Wang, Guifen; Zhao, Jun; Yang, Yuezhong; Cao, Wenxi; Lu, Peng

    2016-05-01

    Quantitative estimates of particulate matter [PM) concentration in sea ice using remote sensing data is helpful for studies of sediment transport and atmospheric dust deposition flux. In this study, the difference between the measured dirty and estimated clean albedo of sea ice was calculated and a relationship between the albedo difference and PM concentration was found using field and laboratory measurements. A semianalytical algorithm for estimating PM concentration in sea ice was established. The algorithm was then applied to MODIS data over the Bohai Sea, China. Comparisons between MODIS derived and in situ measured PM concentration showed good agreement, with a mean absolute percentage difference of 31.2%. From 2005 to 2010, the MODIS-derived annual average PM concentration was approximately 0.025 g/L at the beginning of January. After a month of atmospheric dust deposition, it increased to 0.038 g/L. Atmospheric dust deposition flux was estimated to be 2.50 t/km2/month, similar to 2.20 t/km2/month reported in a previous study. The result was compared with on-site measurements at a nearby ground station. The ground station was close to industrial and residential areas, where larger dust depositions occurred than in the sea, but although there were discrepancies between the absolute magnitudes of the two data sets, they demonstrated similar trends.

  4. Impedance rheoplethysmography. The role of estimation of vasodilatory activity.

    PubMed

    Demenge, P; Silice, C; Lebas, J F; Piquard, J F; Carraz, G

    1979-01-01

    The activity of a number of vasodilatory drugs was studied, with the help of impedance rheoplethysmography, on the vascular bed of the hind limb of anaesthetized rabbits. The vasodilators under study induce changes in rheoplethysmogram to a more or less important degree. The results were compared with those obtained with electromagnetic flowmetry. This method seems to be useful in the study of vasodilators because it allows to measure their effects and the duration thereof in a non-aggressive way. This method using flowmetry, allows to study in an analytical way those substances' effects on artery, vein and also capillary.

  5. Modeling number of bacteria per food unit in comparison to bacterial concentration in quantitative risk assessment: impact on risk estimates.

    PubMed

    Pouillot, Régis; Chen, Yuhuan; Hoelzer, Karin

    2015-02-01

    When developing quantitative risk assessment models, a fundamental consideration for risk assessors is to decide whether to evaluate changes in bacterial levels in terms of concentrations or in terms of bacterial numbers. Although modeling bacteria in terms of integer numbers may be regarded as a more intuitive and rigorous choice, modeling bacterial concentrations is more popular as it is generally less mathematically complex. We tested three different modeling approaches in a simulation study. The first approach considered bacterial concentrations; the second considered the number of bacteria in contaminated units, and the third considered the expected number of bacteria in contaminated units. Simulation results indicate that modeling concentrations tends to overestimate risk compared to modeling the number of bacteria. A sensitivity analysis using a regression tree suggests that processes which include drastic scenarios consisting of combinations of large bacterial inactivation followed by large bacterial growth frequently lead to a >10-fold overestimation of the average risk when modeling concentrations as opposed to bacterial numbers. Alternatively, the approach of modeling the expected number of bacteria in positive units generates results similar to the second method and is easier to use, thus potentially representing a promising compromise.

  6. Methodology for a bounding estimate of activation source-term.

    PubMed

    Culp, Todd

    2013-02-01

    Sandia National Laboratories' Z-Machine is the world's most powerful electrical device, and experiments have been conducted that make it the world's most powerful radiation source. Because Z-Machine is used for research, an assortment of materials can be placed into the machine; these materials can be subjected to a range of nuclear reactions, producing an assortment of activation products. A methodology was developed to provide a systematic approach to evaluate different materials to be introduced into the machine as wire arrays. This methodology is based on experiment specific characteristics, physical characteristics of specific radionuclides, and experience with Z-Machine. This provides a starting point for bounding calculations of radionuclide source-term that can be used for work planning, development of work controls, and evaluating materials for introduction into the machine.

  7. Toxicity of substituted anilines to Pseudokirchneriella subcapitata and quantitative structure-activity relationship analysis for polar narcotics.

    PubMed

    Chen, Chung-Yuan; Ko, Chia-Wen; Lee, Po-I

    2007-06-01

    This study evaluated the toxic effects of substituted anilines on Pseudokirchneriella subcapitata with the use of a closed algal toxicity testing technique with no headspace. Two response endpoints (i.e., dissolved oxygen production [DO] and algal growth rate) were used to evaluate the toxicity of anilines. Both DO and growth rate endpoints revealed similar sensitivity to the effects of anilines. However, trichloroanilines showed stronger inhibitory effects on microalgal photosynthetic reactions than that on algal growth. For various aquatic organisms, the relative sensitivity relationship for anilines is Daphnia magna > luminescent bacteria (Microtox) > or = Pocelia reticulata > or = Pseudokirchneriella subcapitata > or = fathead minnow > Tetrahymena pyriformis. The susceptibility of P. subcapitata to anilines is similar to fish, but P. subcapitata is apparently less sensitive than the water flea. The lack of correlation between the toxicity revealed by different aquatic organisms (microalgae, D. magna, luminescent bacteria, and P. reticulata) suggests that anilines might have different metabolic routes in these organisms. Both hydrogen bonding donor capacity (the lowest unoccupied molecular orbital energy, Elumo) and hydrophobicity (1-octanol:water partition coefficient, Kow) were found to provide satisfactory descriptions for the toxicity of polar narcotics (substituted anilines and chlorophenols). Quantitative structure-activity relationships (QSARs) based on Elumo, log Kow, or both values were established with r2 values varying from 0.75 to 0.92. The predictive power for the QSAR models were found to be satisfactory through leave-one-out cross-validation. Such relationships could provide useful information for the estimation of toxicity for other polar narcotic compounds.

  8. Augmented multivariate image analysis applied to quantitative structure-activity relationship modeling of the phytotoxicities of benzoxazinone herbicides and related compounds on problematic weeds.

    PubMed

    Freitas, Mirlaine R; Matias, Stella V B G; Macedo, Renato L G; Freitas, Matheus P; Venturin, Nelson

    2013-09-11

    Two of major weeds affecting cereal crops worldwide are Avena fatua L. (wild oat) and Lolium rigidum Gaud. (rigid ryegrass). Thus, development of new herbicides against these weeds is required; in line with this, benzoxazinones, their degradation products, and analogues have been shown to be important allelochemicals and natural herbicides. Despite earlier structure-activity studies demonstrating that hydrophobicity (log P) of aminophenoxazines correlates to phytotoxicity, our findings for a series of benzoxazinone derivatives do not show any relationship between phytotoxicity and log P nor with other two usual molecular descriptors. On the other hand, a quantitative structure-activity relationship (QSAR) analysis based on molecular graphs representing structural shape, atomic sizes, and colors to encode other atomic properties performed very accurately for the prediction of phytotoxicities of these compounds against wild oat and rigid ryegrass. Therefore, these QSAR models can be used to estimate the phytotoxicity of new congeners of benzoxazinone herbicides toward A. fatua L. and L. rigidum Gaud.

  9. [Ventricular activation sequence estimated by body surface isochrone map].

    PubMed

    Hayashi, H; Ishikawa, T; Takami, K; Kojima, H; Yabe, S; Ohsugi, S; Miyachi, K; Sotobata, I

    1985-06-01

    This study was performed to evaluate the usefulness of the body surface isochrone map (VAT map) for identifying the ventricular activation sequence, and it was correlated with the isopotential map. Subjects consisted of 42 normal healthy adults, 18 patients with artificial ventricular pacemakers, and 100 patients with ventricular premature beats (VPB). The sites of pacemaker implantations were the right ventricular endocardial apex (nine cases), right ventricular epicardial apex (five cases), right ventricular inflow tract (one case), left ventricular epicardial apex (one case), and posterior base of the left ventricle via the coronary sinus (two cases). An isopotential map was recorded by the mapper HPM-6500 (Chunichi-Denshi Co.) on the basis of an 87 unipolar lead ECG, and a VAT isochrone map was drawn by a minicomputer. The normal VAT map was classified by type according to alignment of isochrone lines, and their frequency was 57.1% for type A, 16.7% for type B, and 26.2% for type C. In the VAT map of ventricular pacing, the body surface area of initial isochrone lines represented well the sites of pacemaker stimuli. In the VAT map of VPB, the sites of origin of VPB agreed well with those as determined by the previous study using an isopotential map. The density of the isochrone lines suggested the mode of conduction via the specialized conduction system or ventricular muscle. The VAT map is a very useful diagnostic method to predict the ventricular activation sequence more directly in a single sheet of the map. PMID:2419457

  10. Estimation of age at death based on quantitation of the 4977-bp deletion of human mitochondrial DNA in skeletal muscle.

    PubMed

    Meissner, C; von Wurmb, N; Schimansky, B; Oehmichen, M

    1999-11-01

    The 4977-bp deletion in human mitochondrial DNA (mtDNA) is known to accumulate in various tissues with age. Since this deletion in mtDNA correlates closest with age in muscle tissue, iliopsoas muscle tissue was taken at autopsy from 50 persons aged 24-97 years to determine whether age at death can be estimated based on the amount of the 4977-bp deletion in skeletal muscle. Total DNA (nuclear and mtDNA) was extracted from 100 mg tissue and the 4977-bp deletion quantified using a kinetic polymerase chain reaction (PCR) followed by visualization of the products on silver stained polyacrylamide gels. The amount of the 4977-bp deletion of mtDNA ranged from 0.00049% to 0.14% depending on age, with a correlation coefficient of r = 0.83 (P = 0.0001). In forensic practice this method can aid in the estimation of age at death with a relatively wide confidence interval, thus enabling a discrimination between young and elderly persons in the identification of human remains based solely on skeletal muscle.

  11. Quantitative estimation of sodium, potassium and total protein in saliva of diabetic smokers and nonsmokers: A novel study

    PubMed Central

    Kallapur, Basavaraj; Ramalingam, Karthikeyan; Bastian; Mujib, Ahmed; Sarkar, Amitabha; Sethuraman, Sathya

    2013-01-01

    Aims: The aim of the study was to evaluate the difference in sodium, potassium, total protein in whole saliva in diabetic smokers, diabetic nonsmokers and healthy controls. Materials and Methods: Nonstimulated saliva samples were collected from a group of diabetic smokers, diabetic nonsmokers, and controls. Supernatant after centrifugation was used to determine the levels of sodium, potassium, and total protein by using semiautomatic analyzer. Results: There exists a statistical difference in the levels of potassium and total protein between diabetic smokers, nondiabetic smokers, and controls. Difference in the levels of sodium is only significant with nondiabetic smokers and controls. Conclusion: Diabetes mellitus is known to alter the composition of saliva. The purpose of this study was to estimate and compare the levels of salivary potassium, sodium, and total protein in smoker diabetic patients and nondiabetic smokers and controls, and to explore potential of salivary electrolytes [Na+, K+] and total proteins as markers. The estimated values of salivary constituents add to the data already recorded in Indian population. However, further studies using large samples are required to evaluate the findings in our study. PMID:24082729

  12. Identification of Thyroid Hormone Receptor Active Compounds Using a Quantitative High-Throughput Screening Platform

    PubMed Central

    Freitas, Jaime; Miller, Nicole; Mengeling, Brenda J.; Xia, Menghang; Huang, Ruili; Houck, Keith; Rietjens, Ivonne M.C.M.; Furlow, J. David; Murk, Albertinka J.

    2014-01-01

    To adapt the use of GH3.TRE-Luc reporter gene cell line for a quantitative high-throughput screening (qHTS) platform, we miniaturized the reporter gene assay to a 1536-well plate format. 1280 chemicals from the Library of Pharmacologically Active Compounds (LOPAC) and the National Toxicology Program (NTP) 1408 compound collection were analyzed to identify potential thyroid hormone receptor (TR) agonists and antagonists. Of the 2688 compounds tested, eight scored as potential TR agonists when the positive hit cut-off was defined at ≥10% efficacy, relative to maximal triiodothyronine (T3) induction, and with only one of those compounds reaching ≥20% efficacy. One common class of compounds positive in the agonist assays were retinoids such as all-trans retinoic acid, which are likely acting via the retinoid-X receptor, the heterodimer partner with the TR. Five potential TR antagonists were identified, including the antiallergy drug tranilast and the anxiolytic drug SB 205384 but also some cytotoxic compounds like 5-fluorouracil. None of the inactive compounds were structurally related to T3, nor had been reported elsewhere to be thyroid hormone disruptors, so false negatives were not detected. None of the low potency (>100µM) TR agonists resembled T3 or T4, thus these may not bind directly in the ligand-binding pocket of the receptor. For TR agonists, in the qHTS, a hit cut-off of ≥20% efficacy at 100 µM may avoid identification of positives with low or no physiological relevance. The miniaturized GH3.TRE-Luc assay offers a promising addition to the in vitro test battery for endocrine disruption, and given the low percentage of compounds testing positive, its high-throughput nature is an important advantage for future toxicological screening. PMID:24772387

  13. Peptide-level Robust Ridge Regression Improves Estimation, Sensitivity, and Specificity in Data-dependent Quantitative Label-free Shotgun Proteomics.

    PubMed

    Goeminne, Ludger J E; Gevaert, Kris; Clement, Lieven

    2016-02-01

    Peptide intensities from mass spectra are increasingly used for relative quantitation of proteins in complex samples. However, numerous issues inherent to the mass spectrometry workflow turn quantitative proteomic data analysis into a crucial challenge. We and others have shown that modeling at the peptide level outperforms classical summarization-based approaches, which typically also discard a lot of proteins at the data preprocessing step. Peptide-based linear regression models, however, still suffer from unbalanced datasets due to missing peptide intensities, outlying peptide intensities and overfitting. Here, we further improve upon peptide-based models by three modular extensions: ridge regression, improved variance estimation by borrowing information across proteins with empirical Bayes and M-estimation with Huber weights. We illustrate our method on the CPTAC spike-in study and on a study comparing wild-type and ArgP knock-out Francisella tularensis proteomes. We show that the fold change estimates of our robust approach are more precise and more accurate than those from state-of-the-art summarization-based methods and peptide-based regression models, which leads to an improved sensitivity and specificity. We also demonstrate that ionization competition effects come already into play at very low spike-in concentrations and confirm that analyses with peptide-based regression methods on peptide intensity values aggregated by charge state and modification status (e.g. MaxQuant's peptides.txt file) are slightly superior to analyses on raw peptide intensity values (e.g. MaxQuant's evidence.txt file).

  14. Forensic comparison and matching of fingerprints: using quantitative image measures for estimating error rates through understanding and predicting difficulty.

    PubMed

    Kellman, Philip J; Mnookin, Jennifer L; Erlikhman, Gennady; Garrigan, Patrick; Ghose, Tandra; Mettler, Everett; Charlton, David; Dror, Itiel E

    2014-01-01

    Latent fingerprint examination is a complex task that, despite advances in image processing, still fundamentally depends on the visual judgments of highly trained human examiners. Fingerprints collected from crime scenes typically contain less information than fingerprints collected under controlled conditions. Specifically, they are often noisy and distorted and may contain only a portion of the total fingerprint area. Expertise in fingerprint comparison, like other forms of perceptual expertise, such as face recognition or aircraft identification, depends on perceptual learning processes that lead to the discovery of features and relations that matter in comparing prints. Relatively little is known about the perceptual processes involved in making comparisons, and even less is known about what characteristics of fingerprint pairs make particular comparisons easy or difficult. We measured expert examiner performance and judgments of difficulty and confidence on a new fingerprint database. We developed a number of quantitative measures of image characteristics and used multiple regression techniques to discover objective predictors of error as well as perceived difficulty and confidence. A number of useful predictors emerged, and these included variables related to image quality metrics, such as intensity and contrast information, as well as measures of information quantity, such as the total fingerprint area. Also included were configural features that fingerprint experts have noted, such as the presence and clarity of global features and fingerprint ridges. Within the constraints of the overall low error rates of experts, a regression model incorporating the derived predictors demonstrated reasonable success in predicting objective difficulty for print pairs, as shown both in goodness of fit measures to the original data set and in a cross validation test. The results indicate the plausibility of using objective image metrics to predict expert performance and

  15. Forensic Comparison and Matching of Fingerprints: Using Quantitative Image Measures for Estimating Error Rates through Understanding and Predicting Difficulty

    PubMed Central

    Kellman, Philip J.; Mnookin, Jennifer L.; Erlikhman, Gennady; Garrigan, Patrick; Ghose, Tandra; Mettler, Everett; Charlton, David; Dror, Itiel E.

    2014-01-01

    Latent fingerprint examination is a complex task that, despite advances in image processing, still fundamentally depends on the visual judgments of highly trained human examiners. Fingerprints collected from crime scenes typically contain less information than fingerprints collected under controlled conditions. Specifically, they are often noisy and distorted and may contain only a portion of the total fingerprint area. Expertise in fingerprint comparison, like other forms of perceptual expertise, such as face recognition or aircraft identification, depends on perceptual learning processes that lead to the discovery of features and relations that matter in comparing prints. Relatively little is known about the perceptual processes involved in making comparisons, and even less is known about what characteristics of fingerprint pairs make particular comparisons easy or difficult. We measured expert examiner performance and judgments of difficulty and confidence on a new fingerprint database. We developed a number of quantitative measures of image characteristics and used multiple regression techniques to discover objective predictors of error as well as perceived difficulty and confidence. A number of useful predictors emerged, and these included variables related to image quality metrics, such as intensity and contrast information, as well as measures of information quantity, such as the total fingerprint area. Also included were configural features that fingerprint experts have noted, such as the presence and clarity of global features and fingerprint ridges. Within the constraints of the overall low error rates of experts, a regression model incorporating the derived predictors demonstrated reasonable success in predicting objective difficulty for print pairs, as shown both in goodness of fit measures to the original data set and in a cross validation test. The results indicate the plausibility of using objective image metrics to predict expert performance and

  16. A quantitative estimate of the function of soft-bottom sheltered coastal areas as essential flatfish nursery habitat

    NASA Astrophysics Data System (ADS)

    Trimoreau, E.; Archambault, B.; Brind'Amour, A.; Lepage, M.; Guitton, J.; Le Pape, O.

    2013-11-01

    Essential fish habitat suitability (EFHS) models and geographic information system (GIS) were combined to describe nursery habitats for three flatfish species (Solea solea, Pleuronectes platessa, Dicologlossa cuneata) in the Bay of Biscay (Western Europe), using physical parameters known or suspected to influence juvenile flatfish spatial distribution and density (i.e. bathymetry, sediment, estuarine influence and wave exposure). The effects of habitat features on juvenile distribution were first calculated from EFHS models, used to identify the habitats in which juvenile are concentrated. The EFHS model for S. solea confirmed previous findings regarding its preference for shallow soft bottom areas and provided new insights relating to the significant effect of wave exposure on nursery habitat suitability. The two other models extended these conclusions with some discrepancies among species related to their respective niches. Using a GIS, quantitative density maps were produced from EFHS models predictions. The respective areas of the different habitats were determined and their relative contributions (density × area) to the total amount of juveniles were calculated at the scale of stock management, in the Bay of Biscay. Shallow and muddy areas contributed to 70% of total juvenile relative abundance whereas only representing 16% of the coastal area, suggesting that they should be considered as essential habitats for these three flatfish species. For S. solea and P. platessa, wave exposure explained the propensity for sheltered areas, where concentration of juveniles was higher. Distribution maps of P. platessa and D. cuneata juveniles also revealed opposite spatial and temporal trends which were explained by the respective biogeographical distributions of these two species, close to their southern and northern limit respectively, and by their responses to hydroclimatic trends.

  17. Non-Exercise Estimation of VO[subscript 2]max Using the International Physical Activity Questionnaire

    ERIC Educational Resources Information Center

    Schembre, Susan M.; Riebe, Deborah A.

    2011-01-01

    Non-exercise equations developed from self-reported physical activity can estimate maximal oxygen uptake (VO[subscript 2]max) as well as sub-maximal exercise testing. The International Physical Activity Questionnaire is the most widely used and validated self-report measure of physical activity. This study aimed to develop and test a VO[subscript…

  18. Comparing Participants' Rating and Compendium Coding to Estimate Physical Activity Intensities

    ERIC Educational Resources Information Center

    Masse, Louise C.; Eason, Karen E.; Tortolero, Susan R.; Kelder, Steven H.

    2005-01-01

    This study assessed agreement between participants' rating (PMET) and compendium coding (CMET) of estimating physical activity intensity in a population of older minority women. As part of the Women on the Move study, 224 women completed a 7-day activity diary and wore an accelerometer for 7 days. All activities recorded were coded using PMET and…

  19. Isolation, Characterization of a Potential Degradation Product of Aspirin and an HPLC Method for Quantitative Estimation of Its Impurities.

    PubMed

    Acharya, Subasranjan; Daniel, Alex; Gyadangi, Bharath; Ramsamy, Sriramulu

    2015-10-01

    In this work, a new degradation product of Aspirin was isolated, characterized and analyzed along with other impurities. New unknown degradation product referred as UP was observed exceeding the limit of ICH Q3B identification thresholds in the stability study of Aspirin and Dipyridamole capsule. The UP isolated from the thermal degradation sample was further studied by IR, Mass and (1)H NMR spectrometry, revealing structural similarities with the parent molecule. Finally, UP was identified as a new compound generated from the interaction of Aspirin and Salicylic acid to form a dehydrated product. A specific HPLC method was developed and validated for the analysis of UP and other Aspirin impurities (A, B, C, E and other unknown degradation products). The proposed method was successfully employed for estimation of Aspirin impurities in a pharmaceutical preparation of Aspirin (Immediate Release) and Dipyridamole (Extended Release) Capsules.

  20. Estimating Toxicity Pathway Activating Doses for High Throughput Chemical Risk Assessments

    EPA Science Inventory

    Estimating a Toxicity Pathway Activating Dose (TPAD) from in vitro assays as an analog to a reference dose (RfD) derived from in vivo toxicity tests would facilitate high throughput risk assessments of thousands of data-poor environmental chemicals. Estimating a TPAD requires def...

  1. Structural similarity based kriging for quantitative structure activity and property relationship modeling.

    PubMed

    Teixeira, Ana L; Falcao, Andre O

    2014-07-28

    Structurally similar molecules tend to have similar properties, i.e. closer molecules in the molecular space are more likely to yield similar property values while distant molecules are more likely to yield different values. Based on this principle, we propose the use of a new method that takes into account the high dimensionality of the molecular space, predicting chemical, physical, or biological properties based on the most similar compounds with measured properties. This methodology uses ordinary kriging coupled with three different molecular similarity approaches (based on molecular descriptors, fingerprints, and atom matching) which creates an interpolation map over the molecular space that is capable of predicting properties/activities for diverse chemical data sets. The proposed method was tested in two data sets of diverse chemical compounds collected from the literature and preprocessed. One of the data sets contained dihydrofolate reductase inhibition activity data, and the second molecules for which aqueous solubility was known. The overall predictive results using kriging for both data sets comply with the results obtained in the literature using typical QSPR/QSAR approaches. However, the procedure did not involve any type of descriptor selection or even minimal information about each problem, suggesting that this approach is directly applicable to a large spectrum of problems in QSAR/QSPR. Furthermore, the predictive results improve significantly with the similarity threshold between the training and testing compounds, allowing the definition of a confidence threshold of similarity and error estimation for each case inferred. The use of kriging for interpolation over the molecular metric space is independent of the training data set size, and no reparametrizations are necessary when more compounds are added or removed from the set, and increasing the size of the database will consequentially improve the quality of the estimations. Finally it is shown

  2. Quantitative testing of the methodology for genome size estimation in plants using flow cytometry: a case study of the Primulina genus.

    PubMed

    Wang, Jing; Liu, Juan; Kang, Ming

    2015-01-01

    Flow cytometry (FCM) is a commonly used method for estimating genome size in many organisms. The use of FCM in plants is influenced by endogenous fluorescence inhibitors and may cause an inaccurate estimation of genome size; thus, falsifying the relationship between genome size and phenotypic traits/ecological performance. Quantitative optimization of FCM methodology minimizes such errors, yet there are few studies detailing this methodology. We selected the genus Primulina, one of the most representative and diverse genera of the Old World Gesneriaceae, to evaluate the methodology effect on determining genome size. Our results showed that buffer choice significantly affected genome size estimation in six out of the eight species examined and altered the 2C-value (DNA content) by as much as 21.4%. The staining duration and propidium iodide (PI) concentration slightly affected the 2C-value. Our experiments showed better histogram quality when the samples were stained for 40 min at a PI concentration of 100 μg ml(-1). The quality of the estimates was not improved by 1-day incubation in the dark at 4°C or by centrifugation. Thus, our study determined an optimum protocol for genome size measurement in Primulina: LB01 buffer supplemented with 100 μg ml(-1) PI and stained for 40 min. This protocol also demonstrated a high universality in other Gesneriaceae genera. We report the genome size of nine Gesneriaceae species for the first time. The results showed substantial genome size variation both within and among the species, with the 2C-value ranging between 1.62 and 2.71 pg. Our study highlights the necessity of optimizing the FCM methodology prior to obtaining reliable genome size estimates in a given taxon.

  3. Quantitative estimate of heat flow from a mid-ocean ridge axial valley, Raven field, Juan de Fuca Ridge: Observations and inferences

    NASA Astrophysics Data System (ADS)

    Salmi, Marie S.; Johnson, H. Paul; Tivey, Maurice A.; Hutnak, Michael

    2014-09-01

    A systematic heat flow survey using thermal blankets within the Endeavour segment of the Juan de Fuca Ridge axial valley provides quantitative estimates of the magnitude and distribution of conductive heat flow at a mid-ocean ridge, with the goal of testing current models of hydrothermal circulation present within newly formed oceanic crust. Thermal blankets were deployed covering an area of 700 by 450 m in the Raven Hydrothermal vent field area located 400 m north of the Main Endeavour hydrothermal field. A total of 176 successful blanket deployment sites measured heat flow values that ranged from 0 to 31 W m-2. Approximately 53% of the sites recorded values lower than 100 mW m-2, suggesting large areas of seawater recharge and advective extraction of lithospheric heat. High heat flow values were concentrated around relatively small "hot spots." Integration of heat flow values over the Raven survey area gives an estimate of conductive heat output of 0.3 MW, an average of 0.95 W m-2, over the survey area. Fluid circulation cell dimensions and scaling equations allow calculation of a Rayleigh number of approximately 700 in Layer 2A. The close proximity of high and low heat flow areas, coupled with previous estimates of surficial seafloor permeability, argues for the presence of small-scale hydrothermal fluid circulation cells within the high-porosity uppermost crustal layer of the axial seafloor.

  4. Comparison of optical microscopy and quantitative polymerase chain reaction for estimating parasitaemia in patients with kala-azar and modelling infectiousness to the vector Lutzomyia longipalpis

    PubMed Central

    Silva, Jailthon C; Zacarias, Danielle A; Silva, Vladimir C; Rolão, Nuno; Costa, Dorcas L; Costa, Carlos HN

    2016-01-01

    Currently, the only method for identifying infective hosts with Leishmania infantum to the vector Lutzomyia longipalpis is xenodiagnosis. More recently, quantitative polymerase chain reaction (qPCR) has been used to model human reservoir competence by assuming that detection of parasite DNA indicates the presence of viable parasites for infecting vectors. Since this assumption has not been proven, this study aimed to verify this hypothesis. The concentration of amastigotes in the peripheral blood of 30 patients with kala-azar was microscopically verified by leukoconcentration and was compared to qPCR estimates. Parasites were identified in 4.8 mL of peripheral blood from 67% of the patients, at a very low concentration (average 0.3 parasites/mL). However, qPCR showed 93% sensitivity and the estimated parasitaemia was over a thousand times greater, both in blood and plasma, with higher levels in plasma than in blood. Furthermore, the microscopic count of circulating parasites and the qPCR parasitaemia estimates were not mathematically compatible with the published proportions of infected sandflies in xenodiagnostic studies. These findings suggest that qPCR does not measure the concentration of circulating parasites, but rather measures DNA from other sites, and that blood might not be the main source of infection for vectors. PMID:27439033

  5. Comparison of optical microscopy and quantitative polymerase chain reaction for estimating parasitaemia in patients with kala-azar and modelling infectiousness to the vector Lutzomyia longipalpis.

    PubMed

    Silva, Jailthon C; Zacarias, Danielle A; Silva, Vladimir C; Rolão, Nuno; Costa, Dorcas L; Costa, Carlos Hn

    2016-07-18

    Currently, the only method for identifying infective hosts with Leishmania infantum to the vector Lutzomyia longipalpis is xenodiagnosis. More recently, quantitative polymerase chain reaction (qPCR) has been used to model human reservoir competence by assuming that detection of parasite DNA indicates the presence of viable parasites for infecting vectors. Since this assumption has not been proven, this study aimed to verify this hypothesis. The concentration of amastigotes in the peripheral blood of 30 patients with kala-azar was microscopically verified by leukoconcentration and was compared to qPCR estimates. Parasites were identified in 4.8 mL of peripheral blood from 67% of the patients, at a very low concentration (average 0.3 parasites/mL). However, qPCR showed 93% sensitivity and the estimated parasitaemia was over a thousand times greater, both in blood and plasma, with higher levels in plasma than in blood. Furthermore, the microscopic count of circulating parasites and the qPCR parasitaemia estimates were not mathematically compatible with the published proportions of infected sandflies in xenodiagnostic studies. These findings suggest that qPCR does not measure the concentration of circulating parasites, but rather measures DNA from other sites, and that blood might not be the main source of infection for vectors. PMID:27439033

  6. Quantitative Use of Fluorescent In Situ Hybridization To Examine Relationships between Mycolic Acid-Containing Actinomycetes and Foaming in Activated Sludge Plants

    PubMed Central

    Davenport, Russell J.; Curtis, Thomas P.; Goodfellow, Michael; Stainsby, Fiona M.; Bingley, Marc

    2000-01-01

    The formation of viscous foams on aeration basins and secondary clarifiers of activated sludge plants is a common and widespread problem. Foam formation is often attributed to the presence of mycolic acid-containing actinomycetes (mycolata). In order to examine the relationship between the number of mycolata and foam, we developed a group-specific probe targeting the 16S rRNA of the mycolata, a protocol to permeabilize mycolata, and a statistically robust quantification method. Statistical analyses showed that a lipase-based permeabilization method was quantitatively superior to previously described methods (P << 0.05). When mixed liquor and foam samples were examined, most of the mycolata present were rods or cocci, although filamentous mycolata were also observed. A nested analysis of variance showed that virtually all of the measured variance occurred between fields of view and not between samples. On this basis we determined that as few as five fields of view could be used to give a statistically meaningful sample. Quantitative fluorescent in situ hybridization (FISH) was used to examine the relationship between foaming and the concentration of mycolata in a 20-m3 completely mixed activated sludge plant. Foaming occurred when the number of mycolata exceeded a certain threshold value. Baffling of the plant affected foaming without affecting the number of mycolata. We tentatively estimated that the threshold foaming concentration of mycolata was about 2 × 106 cells ml−1 or 4 × 1012 cells m−2. We concluded that quantitative use of FISH is feasible and that quantification is a prerequisite for rational investigation of foaming in activated sludge. PMID:10698786

  7. Quantitative volcanic susceptibility analysis of Lanzarote and Chinijo Islands based on kernel density estimation via a linear diffusion process.

    PubMed

    Galindo, I; Romero, M C; Sánchez, N; Morales, J M

    2016-01-01

    Risk management stakeholders in high-populated volcanic islands should be provided with the latest high-quality volcanic information. We present here the first volcanic susceptibility map of Lanzarote and Chinijo Islands and their submarine flanks based on updated chronostratigraphical and volcano structural data, as well as on the geomorphological analysis of the bathymetric data of the submarine flanks. The role of the structural elements in the volcanic susceptibility analysis has been reviewed: vents have been considered since they indicate where previous eruptions took place; eruptive fissures provide information about the stress field as they are the superficial expression of the dyke conduit; eroded dykes have been discarded since they are single non-feeder dykes intruded in deep parts of Miocene-Pliocene volcanic edifices; main faults have been taken into account only in those cases where they could modified the superficial movement of magma. The application of kernel density estimation via a linear diffusion process for the volcanic susceptibility assessment has been applied successfully to Lanzarote and could be applied to other fissure volcanic fields worldwide since the results provide information about the probable area where an eruption could take place but also about the main direction of the probable volcanic fissures. PMID:27265878

  8. A New UPLC Approach for the Simultaneous Quantitative Estimation of Four Compounds in a Cough Syrup Formulation.

    PubMed

    Turak, Fatma; Güzel, Remziye; Dinç, Erdal

    2016-01-01

    A new ultra-performance liquid chromatographic (UPLC) method was developed for the simultaneous estimation of potassium guaiacolsulfonate (PGS), guaifenesin (GUA), diphenhydramine HCl (DIP) and carbepentane citrate (CAR) in a commercial cough syrup. The chromatographic separation of four compounds PGS, GUA, DIP and CAR was performed on a BEH phenyl column (100 × 2.1 mm, 1.7 µm i.d.) using a mobile phase consisting of acetonitrile and 0.1 M HCl (50 : 50, v/v). In addition, the optimized conditions of the chromatographic analysis were found with the flow rate of 0.38 mL/min, the column temperature of 30°C and the injection volume of 1.2 µL with the photodiode array detection of 220 nm. Calibration curves in the concentration ranges of 10-98 µg/mL for PGS, 5-80 µg/mL for GUA, 5-25 µg/mL for DIP and CAR were computed by the regression of the analyte concentration on the chromatographic peak area. The newly developed UPLC method was validated by analyzing the quaternary mixtures of the related compounds, intraday and interday experiment and standard addition samples. After method validation, the proposed UPLC approach was successfully applied for the analysis of the commercial syrup formulation containing PGS, GUA, DIP and CAR compounds. PMID:26202585

  9. Quantitative volcanic susceptibility analysis of Lanzarote and Chinijo Islands based on kernel density estimation via a linear diffusion process

    NASA Astrophysics Data System (ADS)

    Galindo, I.; Romero, M. C.; Sánchez, N.; Morales, J. M.

    2016-06-01

    Risk management stakeholders in high-populated volcanic islands should be provided with the latest high-quality volcanic information. We present here the first volcanic susceptibility map of Lanzarote and Chinijo Islands and their submarine flanks based on updated chronostratigraphical and volcano structural data, as well as on the geomorphological analysis of the bathymetric data of the submarine flanks. The role of the structural elements in the volcanic susceptibility analysis has been reviewed: vents have been considered since they indicate where previous eruptions took place; eruptive fissures provide information about the stress field as they are the superficial expression of the dyke conduit; eroded dykes have been discarded since they are single non-feeder dykes intruded in deep parts of Miocene-Pliocene volcanic edifices; main faults have been taken into account only in those cases where they could modified the superficial movement of magma. The application of kernel density estimation via a linear diffusion process for the volcanic susceptibility assessment has been applied successfully to Lanzarote and could be applied to other fissure volcanic fields worldwide since the results provide information about the probable area where an eruption could take place but also about the main direction of the probable volcanic fissures.

  10. Quantitative volcanic susceptibility analysis of Lanzarote and Chinijo Islands based on kernel density estimation via a linear diffusion process

    PubMed Central

    Galindo, I.; Romero, M. C.; Sánchez, N.; Morales, J. M.

    2016-01-01

    Risk management stakeholders in high-populated volcanic islands should be provided with the latest high-quality volcanic information. We present here the first volcanic susceptibility map of Lanzarote and Chinijo Islands and their submarine flanks based on updated chronostratigraphical and volcano structural data, as well as on the geomorphological analysis of the bathymetric data of the submarine flanks. The role of the structural elements in the volcanic susceptibility analysis has been reviewed: vents have been considered since they indicate where previous eruptions took place; eruptive fissures provide information about the stress field as they are the superficial expression of the dyke conduit; eroded dykes have been discarded since they are single non-feeder dykes intruded in deep parts of Miocene-Pliocene volcanic edifices; main faults have been taken into account only in those cases where they could modified the superficial movement of magma. The application of kernel density estimation via a linear diffusion process for the volcanic susceptibility assessment has been applied successfully to Lanzarote and could be applied to other fissure volcanic fields worldwide since the results provide information about the probable area where an eruption could take place but also about the main direction of the probable volcanic fissures. PMID:27265878

  11. High resolution fire danger modeling : integration of quantitative precipitation amount estimates derived from weather radars as an input of FWI

    NASA Astrophysics Data System (ADS)

    Cloppet, E.; Regimbeau, M.

    2009-09-01

    Fire meteo indices provide efficient guidance tools for the prevention, early warning and surveillance of forest fires. The indices are based on meteorological input data. The underlying approach is to exploit meteorological information as fully as possible to model the soil water content, biomass condition and fire danger. Fire meteorological danger is estimated by Météo-France at national level through the use of Fire Weather Index. The fire index services developed within the PREVIEW project (2005-2008) offer for the first time very high resolution mapping of forest fire risk. The high resolution FWI has been implemented in France complementary to the existing EFFIS operated by the Joint Research Center. A new method (ANTILOPE method) of combining precipitation data originating from different sources like rain gauges and weather radar measurements has been applied in the new service. Some of the advantages of this new service are: · Improved detection of local features of fire risk · More accurate analysis of meteorological input data used in forest fire index models providing added value for forest fire risk forecasts · Use of radar precipitation data "as is” utilizing the higher resolution, i.e. avoiding averaging operations The improved accuracy and spatial resolution of the indices provide a powerful early warning tool for national and regional civil protection and fire fighting authorities to alert and initiate forest fire fighting actions and measures.

  12. Quantitative volcanic susceptibility analysis of Lanzarote and Chinijo Islands based on kernel density estimation via a linear diffusion process.

    PubMed

    Galindo, I; Romero, M C; Sánchez, N; Morales, J M

    2016-06-06

    Risk management stakeholders in high-populated volcanic islands should be provided with the latest high-quality volcanic information. We present here the first volcanic susceptibility map of Lanzarote and Chinijo Islands and their submarine flanks based on updated chronostratigraphical and volcano structural data, as well as on the geomorphological analysis of the bathymetric data of the submarine flanks. The role of the structural elements in the volcanic susceptibility analysis has been reviewed: vents have been considered since they indicate where previous eruptions took place; eruptive fissures provide information about the stress field as they are the superficial expression of the dyke conduit; eroded dykes have been discarded since they are single non-feeder dykes intruded in deep parts of Miocene-Pliocene volcanic edifices; main faults have been taken into account only in those cases where they could modified the superficial movement of magma. The application of kernel density estimation via a linear diffusion process for the volcanic susceptibility assessment has been applied successfully to Lanzarote and could be applied to other fissure volcanic fields worldwide since the results provide information about the probable area where an eruption could take place but also about the main direction of the probable volcanic fissures.

  13. Comparison Of Quantitative Precipitation Estimates Derived From Rain Gauge And Radar Derived Algorithms For Operational Flash Flood Support.

    NASA Astrophysics Data System (ADS)

    Streubel, D. P.; Kodama, K.

    2014-12-01

    To provide continuous flash flood situational awareness and to better differentiate severity of ongoing individual precipitation events, the National Weather Service Research Distributed Hydrologic Model (RDHM) is being implemented over Hawaii and Alaska. In the implementation process of RDHM, three gridded precipitation analyses are used as forcing. The first analysis is a radar only precipitation estimate derived from WSR-88D digital hybrid reflectivity, a Z-R relationship and aggregated into an hourly ¼ HRAP grid. The second analysis is derived from a rain gauge network and interpolated into an hourly ¼ HRAP grid using PRISM climatology. The third analysis is derived from a rain gauge network where rain gauges are assigned static pre-determined weights to derive a uniform mean areal precipitation that is applied over a catchment on a ¼ HRAP grid. To assess the effect of different QPE analyses on the accuracy of RDHM simulations and to potentially identify a preferred analysis for operational use, each QPE was used to force RDHM to simulate stream flow for 20 USGS peak flow events. An evaluation of the RDHM simulations was focused on peak flow magnitude, peak flow timing, and event volume accuracy to be most relevant for operational use. Results showed RDHM simulations based on the observed rain gauge amounts were more accurate in simulating peak flow magnitude and event volume relative to the radar derived analysis. However this result was not consistent for all 20 events nor was it consistent for a few of the rainfall events where an annual peak flow was recorded at more than one USGS gage. Implications of this indicate that a more robust QPE forcing with the inclusion of uncertainty derived from the three analyses may provide a better input for simulating extreme peak flow events.

  14. Quantitative structure-activity relationship of the curcumin-related compounds using various regression methods

    NASA Astrophysics Data System (ADS)

    Khazaei, Ardeshir; Sarmasti, Negin; Seyf, Jaber Yousefi

    2016-03-01

    Quantitative structure activity relationship were used to study a series of curcumin-related compounds with inhibitory effect on prostate cancer PC-3 cells, pancreas cancer Panc-1 cells, and colon cancer HT-29 cells. Sphere exclusion method was used to split data set in two categories of train and test set. Multiple linear regression, principal component regression and partial least squares were used as the regression methods. In other hand, to investigate the effect of feature selection methods, stepwise, Genetic algorithm, and simulated annealing were used. In two cases (PC-3 cells and Panc-1 cells), the best models were generated by a combination of multiple linear regression and stepwise (PC-3 cells: r2 = 0.86, q2 = 0.82, pred_r2 = 0.93, and r2m (test) = 0.43, Panc-1 cells: r2 = 0.85, q2 = 0.80, pred_r2 = 0.71, and r2m (test) = 0.68). For the HT-29 cells, principal component regression with stepwise (r2 = 0.69, q2 = 0.62, pred_r2 = 0.54, and r2m (test) = 0.41) is the best method. The QSAR study reveals descriptors which have crucial role in the inhibitory property of curcumin-like compounds. 6ChainCount, T_C_C_1, and T_O_O_7 are the most important descriptors that have the greatest effect. With a specific end goal to design and optimization of novel efficient curcumin-related compounds it is useful to introduce heteroatoms such as nitrogen, oxygen, and sulfur atoms in the chemical structure (reduce the contribution of T_C_C_1 descriptor) and increase the contribution of 6ChainCount and T_O_O_7 descriptors. Models can be useful in the better design of some novel curcumin-related compounds that can be used in the treatment of prostate, pancreas, and colon cancers.

  15. Quantitative structure-activity relationship of the curcumin-related compounds using various regression methods

    NASA Astrophysics Data System (ADS)

    Khazaei, Ardeshir; Sarmasti, Negin; Seyf, Jaber Yousefi

    2016-03-01

    Quantitative structure activity relationship were used to study a series of curcumin-related compounds with inhibitory effect on prostate cancer PC-3 cells, pancreas cancer Panc-1 cells, and colon cancer HT-29 cells. Sphere exclusion method was used to split data set in two categories of train and test set. Multiple linear regression, principal component regression and partial least squares were used as the regression methods. In other hand, to investigate the effect of feature selection methods, stepwise, Genetic algorithm, and simulated annealing were used. In two cases (PC-3 cells and Panc-1 cells), the best models were generated by a combination of multiple linear regression and stepwise (PC-3 cells: r2 = 0.86, q2 = 0.82, pred_r2 = 0.93, and r2m (test) = 0.43, Panc-1 cells: r2 = 0.85, q2 = 0.80, pred_r2 = 0.71, and r2m (test) = 0.68). For the HT-29 cells, principal component regression with stepwise (r2 = 0.69, q2 = 0.62, pred_r2 = 0.54, and r2m (test) = 0.41) is the best method. The QSAR study reveals descriptors which have crucial role in the inhibitory property of curcumin-like compounds. 6ChainCount, T_C_C_1, and T_O_O_7 are the most important descriptors that have the greatest effect. With a specific end goal to design and optimization of novel efficient curcumin-related compounds it is useful to introduce heteroatoms such as nitrogen, oxygen, and sulfur atoms in the chemical structure (reduce the contribution of T_C_C_1 descriptor) and increase the contribution of 6ChainCount and T_O_O_7 descriptors. Models can be useful in the better design of some novel curcumin-related compounds that can be used in the treatment of prostate, pancreas, and colon cancers.

  16. Measuring slope to improve energy expenditure estimates during field-based activities

    PubMed Central

    Duncan, Glen E.; Lester, Jonathan; Migotsky, Sean; Higgins, Lisa; Borriello, Gaetano

    2013-01-01

    This technical note describes methods to improve activity energy expenditure estimates using a multi-sensor board (MSB) by measuring slope. Ten adults walked over a 2.5-mile course wearing an MSB and mobile calorimeter. Energy expenditure was estimated using accelerometry alone (base) and four methods to measure slope. The barometer and GPS methods improved accuracy 11% from the base (Ps < 0.05) to 86% overall. Measuring slope using the MSB improves energy expenditure estimates during field-based activities. PMID:23537030

  17. Estimation and Preparation of the Hypervariable Regions I/II Templates for Mitochondrial DNA Typing From Human Bones and Teeth Remains Using Singleplex Quantitative Polymerase Chain Reaction.

    PubMed

    Le, Thien Ngoc; Van Phan, Hieu; Dang, Anh Tuan Mai; Nguyen, Vy Thuy

    2016-09-01

    A method was designed for estimating and sequencing of mitochondrial DNA (mtDNA) that effectively and more quickly provides a complete mtDNA profile. In this context, we have developed this novel strategy for typing mtDNA from 10 bones and teeth remains (3 months to 44 years). The quantification of mtDNA was achieved by singleplex real-time polymerase chain reaction of the hypervariable region I fragment (445 bp) and hypervariable region II fragment (617 bp). Combined with the melting curve analysis, we have determined as little as 10 pg of mtDNA template that is suitable for sequence analysis. Furthermore, quantitative polymerase chain reaction products were directly used for following step of mtDNA typing by Sanger sequencing. This method allows the profile to be completely provided for faster human identification. PMID:27356010

  18. Quantitative structure-activity relationship study of P2X7 receptor inhibitors using combination of principal component analysis and artificial intelligence methods.

    PubMed

    Ahmadi, Mehdi; Shahlaei, Mohsen

    2015-01-01

    P2X7 antagonist activity for a set of 49 molecules of the P2X7 receptor antagonists, derivatives of purine, was modeled with the aid of chemometric and artificial intelligence techniques. The activity of these compounds was estimated by means of combination of principal component analysis (PCA), as a well-known data reduction method, genetic algorithm (GA), as a variable selection technique, and artificial neural network (ANN), as a non-linear modeling method. First, a linear regression, combined with PCA, (principal component regression) was operated to model the structure-activity relationships, and afterwards a combination of PCA and ANN algorithm was employed to accurately predict the biological activity of the P2X7 antagonist. PCA preserves as much of the information as possible contained in the original data set. Seven most important PC's to the studied activity were selected as the inputs of ANN box by an efficient variable selection method, GA. The best computational neural network model was a fully-connected, feed-forward model with 7-7-1 architecture. The developed ANN model was fully evaluated by different validation techniques, including internal and external validation, and chemical applicability domain. All validations showed that the constructed quantitative structure-activity relationship model suggested is robust and satisfactory. PMID:26600858

  19. Quantitative structure-activity relationship study of P2X7 receptor inhibitors using combination of principal component analysis and artificial intelligence methods.

    PubMed

    Ahmadi, Mehdi; Shahlaei, Mohsen

    2015-01-01

    P2X7 antagonist activity for a set of 49 molecules of the P2X7 receptor antagonists, derivatives of purine, was modeled with the aid of chemometric and artificial intelligence techniques. The activity of these compounds was estimated by means of combination of principal component analysis (PCA), as a well-known data reduction method, genetic algorithm (GA), as a variable selection technique, and artificial neural network (ANN), as a non-linear modeling method. First, a linear regression, combined with PCA, (principal component regression) was operated to model the structure-activity relationships, and afterwards a combination of PCA and ANN algorithm was employed to accurately predict the biological activity of the P2X7 antagonist. PCA preserves as much of the information as possible contained in the original data set. Seven most important PC's to the studied activity were selected as the inputs of ANN box by an efficient variable selection method, GA. The best computational neural network model was a fully-connected, feed-forward model with 7-7-1 architecture. The developed ANN model was fully evaluated by different validation techniques, including internal and external validation, and chemical applicability domain. All validations showed that the constructed quantitative structure-activity relationship model suggested is robust and satisfactory.

  20. Quantitative structure–activity relationship study of P2X7 receptor inhibitors using combination of principal component analysis and artificial intelligence methods

    PubMed Central

    Ahmadi, Mehdi; Shahlaei, Mohsen

    2015-01-01

    P2X7 antagonist activity for a set of 49 molecules of the P2X7 receptor antagonists, derivatives of purine, was modeled with the aid of chemometric and artificial intelligence techniques. The activity of these compounds was estimated by means of combination of principal component analysis (PCA), as a well-known data reduction method, genetic algorithm (GA), as a variable selection technique, and artificial neural network (ANN), as a non-linear modeling method. First, a linear regression, combined with PCA, (principal component regression) was operated to model the structure–activity relationships, and afterwards a combination of PCA and ANN algorithm was employed to accurately predict the biological activity of the P2X7 antagonist. PCA preserves as much of the information as possible contained in the original data set. Seven most important PC's to the studied activity were selected as the inputs of ANN box by an efficient variable selection method, GA. The best computational neural network model was a fully-connected, feed-forward model with 7−7−1 architecture. The developed ANN model was fully evaluated by different validation techniques, including internal and external validation, and chemical applicability domain. All validations showed that the constructed quantitative structure–activity relationship model suggested is robust and satisfactory. PMID:26600858

  1. A first calibration of nonmarine ostracod species for the quantitative estimation of Pleistocene climate change in southern Africa

    NASA Astrophysics Data System (ADS)

    Horne, D. J.; Martens, K.

    2009-04-01

    Although qualitative statements have been made about general climatic conditions in southern Africa during the Pleistocene, there are few quantifiable palaeoclimatic data based on field evidence, especially regarding whether the area was wetter or drier during the Last Glacial Maximum. Such information is critical in validating models of climate change, both in spatial and temporal dimensions. As an essential preliminary step towards palaeoclimate reconstructions using fossil ostracods from cored lake sediment sequences, we have calibrated a training set of living ostracod species' distributions against a modern climate dataset and other available environmental data. The modern ostracod dataset is based on the collections in the Royal Belgian Institute of Natural Sciences in Brussels, which constitutes the most diverse and comprehensive collection of southern African nonmarine ostracods available anywhere in the world. To date, c. 150 nominal species have been described from southern Africa (Martens, 2001) out of c. 450 species in the total Afrotropical area (Martens et al., 2008). Here we discuss the potential value and limitations of the training set for the estimation of past climatic parameters including air temperature (July and January means, maxima and minima, Mean Annual Air Temperature), precipitation, water conductivity and pH. The next step will be to apply the Mutual Ostracod Temperature Range method (Horne, 2007; Horne & Mezquita, 2008) to the palaeoclimatic analysis of fossil ostracod assemblages from sequences recording the Last Glacial Maximum in southern Africa. Ultimately this work will contribute to the development of a glacier-climate modelling project based on evidence of former niche glaciation of the Drakensberg Escarpment. Horne, D. J. 2007. A Mutual Temperature Range method for Quaternary palaeoclimatic analysis using European nonmarine Ostracoda. Quaternary Science Reviews, 26, 1398-1415. Horne, D. J. & Mezquita, F. 2008. Palaeoclimatic

  2. A fast method for the quantitative estimation of the distribution of hydrophobic and hydrophilic segments in alpha-helices of membrane proteins.

    PubMed

    Luzhkov, V B; Surkov, N F

    2000-01-01

    The work presents a fast quantitative approach for estimating the orientations of hydrophilic and hydrophobic regions in the helical wheels of membrane-spanning alpha-helices of transmembrane proteins. The common hydropathy analysis provides an estimate of the integral hydrophobicity in a moving window which scans an amino acid sequence. The new parameter, orientation hydrophobicity, is based on the estimate of hydrophobicity of the angular segment that scans the helical wheel of a given amino acid sequence. The corresponding procedure involves the treatment of transmembrane helices as cylinders with equal surface elements for each amino acid residue. The orientation hydrophobicity, P(phi), phi = 0-360 degrees, of a helical cylinder is given as a sum of hydrophobicities of individual amino acids which are taken as the S-shaped functions of the angle between the centre of amino acid surface element and the centre of the segment. Non-zero contribution to P(phi) comes only from the amino acids belonging to the angular segment for a given angle phi. The size of the angular segment is related to the size of the channel pore. The amplitudes of amino acid S-functions are calibrated in the way that their maximum values (reached when the amino acid is completely exposed into the pore) are equal to the corresponding hydropathy index in the selected scale (here taken as Goldman-Engelman-Steitz hydropathy scale). The given procedure is applied in the studies of three ionic channels with well characterized three-dimensional structures where the channel pore is formed by a bundle of alpha-helices: cholera toxin B, nicotinic acetylcholine homopentameric alpha7 receptor, and phospholamban. The estimated maximum of hydrophilic properties at the helical wheels are in a good agreement with the spatial orientations of alpha-helices in the corresponding channel pores.

  3. Neural networks involved in adolescent reward processing: An activation likelihood estimation meta-analysis of functional neuroimaging studies.

    PubMed

    Silverman, Merav H; Jedd, Kelly; Luciana, Monica

    2015-11-15

    Behavioral responses to, and the neural processing of, rewards change dramatically during adolescence and may contribute to observed increases in risk-taking during this developmental period. Functional MRI (fMRI) studies suggest differences between adolescents and adults in neural activation during reward processing, but findings are contradictory, and effects have been found in non-predicted directions. The current study uses an activation likelihood estimation (ALE) approach for quantitative meta-analysis of functional neuroimaging studies to: (1) confirm the network of brain regions involved in adolescents' reward processing, (2) identify regions involved in specific stages (anticipation, outcome) and valence (positive, negative) of reward processing, and (3) identify differences in activation likelihood between adolescent and adult reward-related brain activation. Results reveal a subcortical network of brain regions involved in adolescent reward processing similar to that found in adults with major hubs including the ventral and dorsal striatum, insula, and posterior cingulate cortex (PCC). Contrast analyses find that adolescents exhibit greater likelihood of activation in the insula while processing anticipation relative to outcome and greater likelihood of activation in the putamen and amygdala during outcome relative to anticipation. While processing positive compared to negative valence, adolescents show increased likelihood for activation in the posterior cingulate cortex (PCC) and ventral striatum. Contrasting adolescent reward processing with the existing ALE of adult reward processing reveals increased likelihood for activation in limbic, frontolimbic, and striatal regions in adolescents compared with adults. Unlike adolescents, adults also activate executive control regions of the frontal and parietal lobes. These findings support hypothesized elevations in motivated activity during adolescence. PMID:26254587

  4. Benzimidazole-Based Quinazolines: In Vitro Evaluation, Quantitative Structure-Activity Relationship, and Molecular Modeling as Aurora Kinase Inhibitors.

    PubMed

    Sharma, Alka; Luxami, Vijay; Saxena, Sanjai; Paul, Kamaldeep

    2016-03-01

    A series of benzimidazole-based quinazoline derivatives with different substitutions of primary and secondary amines at the C2 position (1-12) were evaluated for their Aurora kinase inhibitory activities. All compounds except for 3 and 6 showed good activity against Aurora kinase inhibitors, with IC50 values in the range of 0.035-0.532 μM. The ligand efficiency (LE) of the compounds with Aurora A kinase was also determined. The structure-activity relationship and the quantitative structure-activity relationship revealed that the Aurora inhibitory activities of these derivatives primarily depend on the different substitutions of the amine present at the C2 position of the quinazoline core. Molecular docking studies in the active binding site also provided theoretical support for the experimental biological data acquired. The current study identifies a novel class of Aurora kinase inhibitors, which can further be used for the treatment of cancer.

  5. The thermal tolerance of crayfish could be estimated from respiratory electron transport system activity.

    PubMed

    Simčič, Tatjana; Pajk, Franja; Jaklič, Martina; Brancelj, Anton; Vrezec, Al

    2014-04-01

    Whether electron transport system (ETS) activity could be used as an estimator of crayfish thermal tolerance has been investigated experimentally. Food consumption rate, respiration rates in the air and water, the difference between energy consumption and respiration costs at a given temperature ('potential growth scope', PGS), and ETS activity of Orconectes limosus and Pacifastacus leniusculus were determined over a temperature range of 5-30°C. All concerned parameters were found to be temperature dependent. The significant correlation between ETS activity and PGS indicates that they respond similarly to temperature change. The regression analysis of E